Main Scientific Publications

Total papers: 642

(Last updated Sat Sep 25 02:01:25 2021)

-- Preprint (12) --

PLIGHT: A tool to assess privacy risk by inferring identifying characteristics from sparse, noisy genotypes
PS Emani, G Gursoy, AD Miranker, M Gerstein (2021). bioRxiv.

Discovering a less-is-more effect to select transcription factor binding sites informative for motif inference
Jinrui Xu, Jiahao Gao, Mark Gerstein (2021). bioRxiv.

Network Propagation-based Prioritization of Long Tail Genes in 17 Cancer Types
H Mohsen, V Gunasekharan, T Qing, M Seay, Y Surovtseva, S Negahban, Z Szallasi, L Pusztai, M Gerstein (2021). bioRxiv.

Genetic determination of regional connectivity in modelling the spread of COVID-19 outbreak for improved mitigation strategies
L Salichos, J Warrell, H Cevasco, A Chung, M Gerstein (2021). bioRxiv.

DECODE: A Deep-learning Framework for Condensing Enhancers and Refining Boundaries with Large-scale Functional Assays
Z Chen, J Zhang, J Liu, Y Dai, D Lee, MR Min, M Xu, M Gerstein (2021). bioRxiv.

Non-adaptive factors determine which equally effective regulatory motif evolves to generate pulses
K Xiong, M Gerstein, J Masel (2020). bioRxiv.

Recovering genomes and phenotypes using allele-specific gene expression
G Gursoy, N Lu, S Wagner, M Gerstein (2020). bioRxiv.

Privacy-preserving genotype imputation with fully homomorphic encryption
G Gursoy, E Chielle, C Brannon, M Maniatakos, M Gerstein (2020). bioRxiv.

Storing and analyzing a genome on a blockchain
G Gursoy, C Brannon, S Wagner, M Gerstein (2020). bioRxiv.

LESSeq: Local event-based analysis of alternative splicing using RNA-Seq data
J Leng, CJF Cameron, S Oh, E Khurana, JP Noonan, MB Gerstein (2019). bioRxiv.

Compression-based Network Interpretability Schemes
J Warrell, H Mohsen, M Gerstein (2020). bioRxiv.

Latent Evolutionary Signatures: A General Framework for Analyzing Music and Cultural Evolution
J Warrell, L Salichos, M Gerstein (2020). bioRxiv.

-- 2021 (7) --

Establishing a Global Standard for Wearable Devices in Sport and Exercise Medicine: Perspectives from Academic and Industry Stakeholders.
GI Ash, M Stults-Kolehmainen, MA Busa, AE Gaffey, K Angeloudis, B Muniz-Pardos, R Gregory, RA Huggins, NS Redeker, SA Weinzimer, LA Grieco, K Lyden, E Megally, I Vogiatzis, L Scher, X Zhu, JS Baker, C Brandt, MS Businelle, LM Fucito, S Griggs, R Jarrin, BJ Mortazavi, T Prioleau, W Roberts, EK Spanakis, LM Nally, A Debruyne, N Bachl, F Pigozzi, F Halabchi, DA Ramagole, DC Janse van Rensburg, B Wolfarth, C Fossati, S Rozenstoka, K Tanisawa, M Borjesson, JA Casajus, A Gonzalez-Aguero, I Zelenkova, J Swart, G Gursoy, W Meyerson, J Liu, D Greenbaum, YP Pitsiladis, MB Gerstein (2021). Sports Med.

Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions.
J Liu, DJ Spakowicz, GI Ash, R Hoyd, R Ahluwalia, A Zhang, S Lou, D Lee, J Zhang, C Presley, A Greene, M Stults-Kolehmainen, LM Nally, JS Baker, LM Fucito, SA Weinzimer, AV Papachristos, M Gerstein (2021). PLoS Comput Biol 17: e1009303.

Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers.
X Li, S Kumar, A Harmanci, S Li, RR Kitchen, Y Zhang, VB Wali, SM Reddy, WA Woodward, JM Reuben, J Rozowsky, C Hatzis, NT Ueno, S Krishnamurthy, L Pusztai, M Gerstein (2021). Genome Med 13: 70.

Gene Tracer: A smart, interactive, voice-controlled Alexa skill for gene information retrieval and browsing, mutation annotation, and network visualization.
S Lou, T Li, J Liu, M Gerstein (2021). Bioinformatics.

SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments.
Z Chen, J Zhang, J Liu, Z Zhang, J Zhu, D Lee, M Xu, M Gerstein (2021). Bioinformatics.

Molecular medicine tumor board: whole-genome sequencing to inform on personalized medicine for a man with advanced prostate cancer.
AJ Armstrong, X Li, M Tucker, S Li, XJ Mu, KW Eng, A Sboner, M Rubin, M Gerstein (2021). Prostate Cancer Prostatic Dis 24: 786-793.

Quantum computing at the frontiers of biological sciences.
PS Emani, J Warrell, A Anticevic, S Bekiranov, M Gandal, MJ McConnell, G Sapiro, A Aspuru-Guzik, JT Baker, M Bastiani, JD Murray, SN Sotiropoulos, J Taylor, G Senthil, T Lehner, MB Gerstein, AW Harrow (2021). Nat Methods 18: 701-709.

-- 2020 (41) --

Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden.
T Qing, H Mohsen, M Marczyk, Y Ye, T O'Meara, H Zhao, JP Townsend, M Gerstein, C Hatzis, Y Kluger, L Pusztai (2020). Nat Commun 11: 2438.

To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq.
J Xu, MM Kudron, A Victorsen, J Gao, HN Ammouri, FCP Navarro, L Gevirtzman, RH Waterston, KP White, V Reinke, M Gerstein (2020). Nucleic Acids Res 49: e17.

Weight-based Neural Network Interpretability using Activation Tuning and Personalized Products
H Mohsen, J Warrell, MR Min, S Negahban, M Gerstein (2020). The 15th Machine Learning in Computational Biology Workshop.

STARRPeaker: uniform processing and accurate identification of STARR-seq active regions.
D Lee, M Shi, J Moran, M Wall, J Zhang, J Liu, D Fitzgerald, Y Kyono, L Ma, KP White, M Gerstein (2020). Genome Biol 21: 298.

A Frankish, M Diekhans, I Jungreis, J Lagarde, JE Loveland, JM Mudge, C Sisu, JC Wright, J Armstrong, I Barnes, A Berry, A Bignell, C Boix, S Carbonell Sala, F Cunningham, T Di Domenico, S Donaldson, IT Fiddes, C Garcia Giron, JM Gonzalez, T Grego, M Hardy, T Hourlier, KL Howe, T Hunt, OG Izuogu, R Johnson, FJ Martin, L Martinez, S Mohanan, P Muir, FCP Navarro, A Parker, B Pei, F Pozo, FC Riera, M Ruffier, BM Schmitt, E Stapleton, MM Suner, I Sycheva, B Uszczynska-Ratajczak, MY Wolf, J Xu, YT Yang, A Yates, D Zerbino, Y Zhang, JS Choudhary, M Gerstein, R Guigo, TJP Hubbard, M Kellis, B Paten, ML Tress, P Flicek (2020). Nucleic Acids Res 49: D916-D923.

Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks.
B Li, YT Yang, JA Capra, MB Gerstein (2020). PLoS Comput Biol 16: e1008291.

Data Sanitization to Reduce Private Information Leakage from Functional Genomics.
G Gursoy, P Emani, CM Brannon, OA Jolanki, A Harmanci, JS Strattan, JM Cherry, AD Miranker, M Gerstein (2020). Cell 183: 905-917e16.

SVFX: a machine learning framework to quantify the pathogenicity of structural variants.
S Kumar, A Harmanci, J Vytheeswaran, MB Gerstein (2020). Genome Biol 21: 274.

NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis.
J Zhang, J Liu, P McGillivray, C Yi, L Lochovsky, D Lee, M Gerstein (2020). BMC Bioinformatics 21: 474.

Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients.
S Lou, T Li, D Spakowicz, X Yan, GL Chupp, M Gerstein (2020). BMC Bioinformatics 21: 457.

Moving beyond buzzwords
D Greenbaum, M Gerstein (2020). Science. 370 (6513):178.

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
MH Bailey, WU Meyerson, LJ Dursi, LB Wang, G Dong, WW Liang, A Weerasinghe, S Li, Y Li, S Kelso, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, G Saksena, K Ellrott, MC Wendl, DA Wheeler, G Getz, JT Simpson, MB Gerstein, L Ding, PCAWG Consortium (2020). Nat Commun 11: 4748.

Predicting the frequencies of drug side effects.
D Galeano, S Li, M Gerstein, A Paccanaro (2020). Nat Commun 11: 4575.

Sex differences in oncogenic mutational processes.
CH Li, SD Prokopec, RX Sun, F Yousif, N Schmitz, PCAWG Tumour Subtypes and Clinical Translation, PC Boutros, PCAWG Consortium (2020). Nat Commun 11: 4330.

Cyclic and Multilevel Causation in Evolutionary Processes
J Warrell, M Gerstein (2020). Biology & Philosophy, 35(5), pp.1-36.

Expanded encyclopaedias of DNA elements in the human and mouse genomes.
ENCODE Project Consortium, JE Moore, MJ Purcaro, HE Pratt, CB Epstein, N Shoresh, J Adrian, T Kawli, CA Davis, A Dobin, R Kaul, J Halow, EL Van Nostrand, P Freese, DU Gorkin, Y Shen, Y He, M Mackiewicz, F Pauli-Behn, BA Williams, A Mortazavi, CA Keller, XO Zhang, SI Elhajjajy, J Huey, DE Dickel, V Snetkova, X Wei, X Wang, JC Rivera-Mulia, J Rozowsky, J Zhang, SB Chhetri, J Zhang, A Victorsen, KP White, A Visel, GW Yeo, CB Burge, E Lecuyer, DM Gilbert, J Dekker, J Rinn, EM Mendenhall, JR Ecker, M Kellis, RJ Klein, WS Noble, A Kundaje, R Guigo, PJ Farnham, JM Cherry, RM Myers, B Ren, BR Graveley, MB Gerstein, LA Pennacchio, MP Snyder, BE Bernstein, B Wold, RC Hardison, TR Gingeras, JA Stamatoyannopoulos, Z Weng (2020). Nature 583: 699-710.

Perspectives on ENCODE.
ENCODE Project Consortium, MP Snyder, TR Gingeras, JE Moore, Z Weng, MB Gerstein, B Ren, RC Hardison, JA Stamatoyannopoulos, BR Graveley, EA Feingold, MJ Pazin, M Pagan, DA Gilchrist, BC Hitz, JM Cherry, BE Bernstein, EM Mendenhall, DR Zerbino, A Frankish, P Flicek, RM Myers (2020). Nature 583: 693-698.

An integrative ENCODE resource for cancer genomics.
J Zhang, D Lee, V Dhiman, P Jiang, J Xu, P McGillivray, H Yang, J Liu, W Meyerson, D Clarke, M Gu, S Li, S Lou, J Xu, L Lochovsky, M Ung, L Ma, S Yu, Q Cao, A Harmanci, KK Yan, A Sethi, G Gursoy, MR Schoenberg, J Rozowsky, J Warrell, P Emani, YT Yang, T Galeev, X Kong, S Liu, X Li, J Krishnan, Y Feng, JC Rivera-Mulia, J Adrian, JR Broach, M Bolt, J Moran, D Fitzgerald, V Dileep, T Liu, S Mei, T Sasaki, C Trevilla-Garcia, S Wang, Y Wang, C Zang, D Wang, RJ Klein, M Snyder, DM Gilbert, K Yip, C Cheng, F Yue, XS Liu, KP White, M Gerstein (2020). Nat Commun 11: 3696.

Transcriptional activity and strain-specific history of mouse pseudogenes.
C Sisu, P Muir, A Frankish, I Fiddes, M Diekhans, D Thybert, DT Odom, P Flicek, TM Keane, T Hubbard, J Harrow, M Gerstein (2020). Nat Commun 11: 3695.

RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins.
J Zhang, J Liu, D Lee, JJ Feng, L Lochovsky, S Lou, M Rutenberg-Schoenberg, M Gerstein (2020). Genome Biol 21: 151.

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation.
A Sethi, M Gu, E Gumusgoz, L Chan, KK Yan, J Rozowsky, I Barozzi, V Afzal, JA Akiyama, I Plajzer-Frick, C Yan, CS Novak, M Kato, TH Garvin, Q Pham, A Harrington, BJ Mannion, EA Lee, Y Fukuda-Yuzawa, A Visel, DE Dickel, KY Yip, R Sutton, LA Pennacchio, M Gerstein (2020). Nat Methods 17: 807-814.

FANCY: fast estimation of privacy risk in functional genomics data.
G Gursoy, CM Brannon, FCP Navarro, M Gerstein (2020). Bioinformatics 36: 5145-5150.

Using blockchain to log genome dataset access: efficient storage and query.
G Gursoy, R Bjornson, ME Green, M Gerstein (2020). BMC Med Genomics 13: 78.

Using sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood.
S Li, FW Crawford, MB Gerstein (2020). Nat Commun 11: 3575.

DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring.
J Zhang, J Liu, D Lee, S Lou, Z Chen, G Gursoy, M Gerstein (2020). BMC Bioinformatics 21: 281.

Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients.
D Spakowicz, S Lou, B Barron, JL Gomez, T Li, Q Liu, N Grant, X Yan, R Hoyd, G Weinstock, GL Chupp, M Gerstein (2020). Genome Biol 21: 150.

TopicNet: a framework for measuring transcriptional regulatory network change.
S Lou, T Li, X Kong, J Zhang, J Liu, D Lee, M Gerstein (2020). Bioinformatics 36: i474-i481.

Epigenome-based splicing prediction using a recurrent neural network.
D Lee, J Zhang, J Liu, M Gerstein (2020). PLoS Comput Biol 16: e1008006.

Origins and characterization of variants shared between databases of somatic and germline human mutations.
W Meyerson, J Leisman, FCP Navarro, M Gerstein (2020). BMC Bioinformatics 21: 227.

Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts.
G Gursoy, CM Brannon, M Gerstein (2020). BMC Med Genomics 13: 74.

The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data.
C Ye, A Paccanaro, M Gerstein, KK Yan (2020). BMC Bioinformatics 21: 222.

Dermal Adipocyte Lipolysis and Myofibroblast Conversion Are Required for Efficient Skin Repair.
BA Shook, RR Wasko, O Mano, M Rutenberg-Schoenberg, MC Rudolph, B Zirak, GC Rivera-Gonzalez, F Lopez-Giraldez, S Zarini, A Rezza, DA Clark, M Rendl, MD Rosenblum, MB Gerstein, V Horsley (2020). Cell Stem Cell 26: 880-895e6.

Estimation of the carrier frequency of fumarate hydratase alterations and implications for kidney cancer risk in hereditary leiomyomatosis and renal cancer.
B Shuch, S Li, H Risch, RS Bindra, PD McGillivray, M Gerstein (2020). Cancer 126: 3657-3666.

Comparing Technological Development and Biological Evolution from a Network Perspective.
KK Yan, D Wang, K Xiong, M Gerstein (2020). Cell Syst 10: 219-222.

Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences.
S Kumar, J Warrell, S Li, PD McGillivray, W Meyerson, L Salichos, A Harmanci, A Martinez-Fundichely, CWY Chan, MM Nielsen, L Lochovsky, Y Zhang, X Li, S Lou, JS Pedersen, C Herrmann, G Getz, E Khurana, MB Gerstein (2020). Cell 180: 915-927e16.

The Development of a Practical Artificial Intelligence Tool for Diagnosing and Evaluating Autism Spectrum Disorder: Multicenter Study.
T Chen, Y Chen, M Yuan, M Gerstein, T Li, H Liang, T Froehlich, L Lu (2020). JMIR Med Inform 8: e15767.

Establishing a Global Standard for Wearable Devices in Sport and Fitness: Perspectives from the New England Chapter of the American College of Sports Medicine Members.
GI Ash, M Stults-Kolehmainen, MA Busa, R Gregory, CE Garber, J Liu, M Gerstein, JA Casajus, A Gonzalez-Aguero, D Constantinou, M Geistlinger, FM Guppy, F Pigozzi, YP Pitsiladis (2020). Curr Sports Med Rep 19: 45-49.

Pan-cancer analysis of whole genomes.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020). Nature 578: 82-93.

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.
E Rheinbay, MM Nielsen, F Abascal, JA Wala, O Shapira, G Tiao, H Hornshj, JM Hess, RI Juul, Z Lin, L Feuerbach, R Sabarinathan, T Madsen, J Kim, L Mularoni, S Shuai, A Lanzos, C Herrmann, YE Maruvka, C Shen, SB Amin, P Bandopadhayay, J Bertl, KA Boroevich, J Busanovich, J Carlevaro-Fita, D Chakravarty, CWY Chan, D Craft, P Dhingra, K Diamanti, NA Fonseca, A Gonzalez-Perez, Q Guo, MP Hamilton, NJ Haradhvala, C Hong, K Isaev, TA Johnson, M Juul, A Kahles, A Kahraman, Y Kim, J Komorowski, K Kumar, S Kumar, D Lee, KV Lehmann, Y Li, EM Liu, L Lochovsky, K Park, O Pich, ND Roberts, G Saksena, SE Schumacher, N Sidiropoulos, L Sieverling, N Sinnott-Armstrong, C Stewart, D Tamborero, JMC Tubio, HM Umer, L Uuskula-Reimand, C Wadelius, L Wadi, X Yao, CZ Zhang, J Zhang, JE Haber, A Hobolth, M Imielinski, M Kellis, MS Lawrence, C von Mering, H Nakagawa, BJ Raphael, MA Rubin, C Sander, LD Stein, JM Stuart, T Tsunoda, DA Wheeler, R Johnson, J Reimand, M Gerstein, E Khurana, PJ Campbell, N Lopez-Bigas, PCAWG Drivers and Functional Interpretation Working Group, PCAWG Structural Variation Working Group, J Weischenfeldt, R Beroukhim, I Martincorena, JS Pedersen, G Getz, PCAWG Consortium (2020). Nature 578: 102-111.

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.
B Rodriguez-Martin, EG Alvarez, A Baez-Ortega, J Zamora, F Supek, J Demeulemeester, M Santamarina, YS Ju, J Temes, D Garcia-Souto, H Detering, Y Li, J Rodriguez-Castro, A Dueso-Barroso, AL Bruzos, SC Dentro, MG Blanco, G Contino, D Ardeljan, M Tojo, ND Roberts, S Zumalave, PAW Edwards, J Weischenfeldt, M Puiggros, Z Chong, K Chen, EA Lee, JA Wala, K Raine, A Butler, SM Waszak, FCP Navarro, SE Schumacher, J Monlong, F Maura, N Bolli, G Bourque, M Gerstein, PJ Park, DC Wedge, R Beroukhim, D Torrents, JO Korbel, I Martincorena, RC Fitzgerald, P Van Loo, HH Kazazian, KH Burns, PCAWG Structural Variation Working Group, PJ Campbell, JMC Tubio, PCAWG Consortium (2020). Nat Genet 52: 306-319.

Estimating growth patterns and driver effects in tumor evolution from individual samples.
L Salichos, W Meyerson, J Warrell, M Gerstein (2020). Nat Commun 11: 732.

-- 2019 (19) --

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis.
JS Johnson, DJ Spakowicz, BY Hong, LM Petersen, P Demkowicz, L Chen, SR Leopold, BM Hanson, HO Agresta, M Gerstein, E Sodergren, GM Weinstock (2019). Nat Commun 10: 5029.

Hierarchical PAC-Bayes Bounds via Deep Probabilistic Programming
J Warrell, MB Gerstein (2019). Bayesian Deep Learning Workshop at NeurIPS.

Pollen-derived RNAs Are Found in the Human Circulation.
M Koupenova, E Mick, HA Corkrey, A Singh, SE Tanriverdi, O Vitseva, D Levy, AM Keeler, M Ezzaty Mirhashemi, MK ElMallah, M Gerstein, J Rozowsky, K Tanriverdi, JE Freedman (2019). iScience 19: 916-926.

GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner.
S Lou, KA Cotter, T Li, J Liang, H Mohsen, J Liu, J Zhang, S Cohen, J Xu, H Yu, MA Rubin, M Gerstein (2019). PLoS Genet 15: e1007860.

Leveraging protein dynamics to identify cancer mutational hotspots using 3D structures.
S Kumar, D Clarke, MB Gerstein (2019). Proc Natl Acad Sci U S A 116: 18962-18970.

Sharing data
D Greenbaum, M Gerstein (2019). Science 365 (6455):764.

TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements.
FC Navarro, J Hoops, L Bellfy, E Cerveira, Q Zhu, C Zhang, C Lee, MB Gerstein (2019). PLoS Comput Biol 15: e1007293.

A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation.
D Polioudakis, L de la Torre-Ubieta, J Langerman, AG Elkins, X Shi, JL Stein, CK Vuong, S Nichterwitz, M Gevorgian, CK Opland, D Lu, W Connell, EK Ruzzo, JK Lowe, T Hadzic, FI Hinz, S Sabri, WE Lowry, MB Gerstein, K Plath, DH Geschwind (2019). Neuron 103: 785-801e8.

Building a Hybrid Physical-Statistical Classifier for Predicting the Effect of Variants Related to Protein-Drug Interactions.
B Wang, C Yan, S Lou, P Emani, B Li, M Xu, X Kong, W Meyerson, YT Yang, D Lee, M Gerstein (2019). Structure 27: 1469-1481e3.

Genomics and data science: an application within an umbrella.
FCP Navarro, H Mohsen, C Yan, S Li, M Gu, W Meyerson, M Gerstein (2019). Genome Biol 20: 109.

Multi-platform discovery of haplotype-resolved structural variation in human genomes.
MJP Chaisson, AD Sanders, X Zhao, A Malhotra, D Porubsky, T Rausch, EJ Gardner, OL Rodriguez, L Guo, RL Collins, X Fan, J Wen, RE Handsaker, S Fairley, ZN Kronenberg, X Kong, F Hormozdiari, D Lee, AM Wenger, AR Hastie, D Antaki, T Anantharaman, PA Audano, H Brand, S Cantsilieris, H Cao, E Cerveira, C Chen, X Chen, CS Chin, Z Chong, NT Chuang, CC Lambert, DM Church, L Clarke, A Farrell, J Flores, T Galeev, DU Gorkin, M Gujral, V Guryev, WH Heaton, J Korlach, S Kumar, JY Kwon, ET Lam, JE Lee, J Lee, WP Lee, SP Lee, S Li, P Marks, K Viaud-Martinez, S Meiers, KM Munson, FCP Navarro, BJ Nelson, C Nodzak, A Noor, S Kyriazopoulou-Panagiotopoulou, AWC Pang, Y Qiu, G Rosanio, M Ryan, A Stutz, DCJ Spierings, A Ward, AE Welch, M Xiao, W Xu, C Zhang, Q Zhu, X Zheng-Bradley, E Lowy, S Yakneen, S McCarroll, G Jun, L Ding, CL Koh, B Ren, P Flicek, K Chen, MB Gerstein, PY Kwok, PM Lansdorp, GT Marth, J Sebat, X Shi, A Bashir, K Ye, SE Devine, ME Talkowski, RE Mills, T Marschall, JO Korbel, EE Eichler, C Lee (2019). Nat Commun 10: 1784.

exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling.
J Rozowsky, RR Kitchen, JJ Park, TR Galeev, J Diao, J Warrell, W Thistlethwaite, SL Subramanian, A Milosavljevic, M Gerstein (2019). Cell Syst 8: 352-357e3.

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.
OD Murillo, W Thistlethwaite, J Rozowsky, SL Subramanian, R Lucero, N Shah, AR Jackson, S Srinivasan, A Chung, CD Laurent, RR Kitchen, T Galeev, J Warrell, JA Diao, JA Welsh, K Hanspers, A Riutta, S Burgstaller-Muehlbacher, RV Shah, A Yeri, LM Jenkins, ME Ahsen, C Cordon-Cardo, N Dogra, SM Gifford, JT Smith, G Stolovitzky, AK Tewari, BH Wunsch, KK Yadav, KM Danielson, J Filant, C Moeller, P Nejad, A Paul, B Simonson, DK Wong, X Zhang, L Balaj, R Gandhi, AK Sood, RP Alexander, L Wang, C Wu, DTW Wong, DJ Galas, K Van Keuren-Jensen, T Patel, JC Jones, S Das, KH Cheung, AR Pico, AI Su, RL Raffai, LC Laurent, ME Roth, MB Gerstein, A Milosavljevic (2019). Cell 177: 463-477e15.

The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research.
S Das, Extracellular RNA Communication Consortium, KM Ansel, M Bitzer, XO Breakefield, A Charest, DJ Galas, MB Gerstein, M Gupta, A Milosavljevic, MT McManus, T Patel, RL Raffai, J Rozowsky, ME Roth, JA Saugstad, K Van Keuren-Jensen, AM Weaver, LC Laurent (2019). Cell 177: 231-242.

Shaping the nebulous enhancer in the era of high-throughput assays and genome editing.
EY Ho, Q Cao, M Gu, RW Chan, Q Wu, M Gerstein, KY Yip (2019). Brief Bioinform 21: 836-850.

Measuring the reproducibility and quality of Hi-C data.
GG Yardmc, H Ozadam, MEG Sauria, O Ursu, KK Yan, T Yang, A Chakraborty, A Kaul, BR Lajoie, F Song, Y Zhan, F Ay, M Gerstein, A Kundaje, Q Li, J Taylor, F Yue, J Dekker, WS Noble (2019). Genome Biol 20: 57.

MicroRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis.
A Moro, TP Driscoll, LC Boraas, W Armero, DM Kasper, N Baeyens, C Jouy, V Mallikarjun, J Swift, SJ Ahn, D Lee, J Zhang, M Gu, M Gerstein, M Schwartz, S Nicoli (2019). Nat Cell Biol 21: 348-358.

Insights into genetics, human biology and disease gleaned from family based genomic studies.
JE Posey, AH O'Donnell-Luria, JX Chong, T Harel, SN Jhangiani, ZH Coban Akdemir, S Buyske, D Pehlivan, CMB Carvalho, S Baxter, N Sobreira, P Liu, N Wu, JA Rosenfeld, S Kumar, D Avramopoulos, JJ White, KF Doheny, PD Witmer, C Boehm, VR Sutton, DM Muzny, E Boerwinkle, M Gunel, DA Nickerson, S Mane, DG MacArthur, RA Gibbs, A Hamosh, RP Lifton, TC Matise, HL Rehm, M Gerstein, MJ Bamshad, D Valle, JR Lupski, Centers for Mendelian Genomics (2019). Genet Med 21: 798-812.

Next-Generation Sequencing to Diagnose Suspected Genetic Disorders.
S Li, MB Gerstein (2019). N Engl J Med 380: 200.

-- 2018 (25) --

Dependent Type Networks: A Probabilistic Logic via the Curry-Howard Correspondence in a System of Probabilistic Dependent Types
J Warrell, MB Gerstein (2018). Uncertainty in Artificial Intelligence Workshop on Uncertainty in Deep Learning.

Rank Projection Trees for Multilevel Neural Network Interpretation
J Warrell, H Mohsen, MB Gerstein (2018). NeurIPS Workshop on Machine Learning for Health.

Revealing the brain's molecular architecture.
PsychENCODE Consortium (2018). Science 362: 1262-1263.

Comprehensive functional genomic resource and integrative model for the human brain.
D Wang, S Liu, J Warrell, H Won, X Shi, FCP Navarro, D Clarke, M Gu, P Emani, YT Yang, M Xu, MJ Gandal, S Lou, J Zhang, JJ Park, C Yan, SK Rhie, K Manakongtreecheep, H Zhou, A Nathan, M Peters, E Mattei, D Fitzgerald, T Brunetti, J Moore, Y Jiang, K Girdhar, GE Hoffman, S Kalayci, ZH Gumus, GE Crawford, PsychENCODE Consortium, P Roussos, S Akbarian, AE Jaffe, KP White, Z Weng, N Sestan, DH Geschwind, JA Knowles, MB Gerstein (2018). Science 362.

Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder.
MJ Gandal, P Zhang, E Hadjimichael, RL Walker, C Chen, S Liu, H Won, H van Bakel, M Varghese, Y Wang, AW Shieh, J Haney, S Parhami, J Belmont, M Kim, P Moran Losada, Z Khan, J Mleczko, Y Xia, R Dai, D Wang, YT Yang, M Xu, K Fish, PR Hof, J Warrell, D Fitzgerald, K White, AE Jaffe, PsychENCODE Consortium, MA Peters, M Gerstein, C Liu, LM Iakoucheva, D Pinto, DH Geschwind (2018). Science 362.

Integrative functional genomic analysis of human brain development and neuropsychiatric risks.
M Li, G Santpere, Y Imamura Kawasawa, OV Evgrafov, FO Gulden, S Pochareddy, SM Sunkin, Z Li, Y Shin, Y Zhu, AMM Sousa, DM Werling, RR Kitchen, HJ Kang, M Pletikos, J Choi, S Muchnik, X Xu, D Wang, B Lorente-Galdos, S Liu, P Giusti-Rodriguez, H Won, CA de Leeuw, AF Pardinas, BrainSpan Consortium, PsychENCODE Consortium, PsychENCODE Developmental Subgroup, M Hu, F Jin, Y Li, MJ Owen, MC O'Donovan, JTR Walters, D Posthuma, MA Reimers, P Levitt, DR Weinberger, TM Hyde, JE Kleinman, DH Geschwind, MJ Hawrylycz, MW State, SJ Sanders, PF Sullivan, MB Gerstein, ES Lein, JA Knowles, N Sestan (2018). Science 362.

Transcriptome and epigenome landscape of human cortical development modeled in organoids.
A Amiri, G Coppola, S Scuderi, F Wu, T Roychowdhury, F Liu, S Pochareddy, Y Shin, A Safi, L Song, Y Zhu, AMM Sousa, PsychENCODE Consortium, M Gerstein, GE Crawford, N Sestan, A Abyzov, FM Vaccarino (2018). Science 362.

Text mining systems biology: Turning the microscope back on the observer
X Kong, M Gerstein (2018). Current Opinion in Systems Biology 11:117-122.

Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity.
W Shi, CKY Ng, RS Lim, T Jiang, S Kumar, X Li, VB Wali, S Piscuoglio, MB Gerstein, AB Chagpar, B Weigelt, L Pusztai, JS Reis-Filho, C Hatzis (2018). Cell Rep 25: 1446-1457.

GENCODE reference annotation for the human and mouse genomes.
A Frankish, M Diekhans, AM Ferreira, R Johnson, I Jungreis, J Loveland, JM Mudge, C Sisu, J Wright, J Armstrong, I Barnes, A Berry, A Bignell, S Carbonell Sala, J Chrast, F Cunningham, T Di Domenico, S Donaldson, IT Fiddes, C Garcia Giron, JM Gonzalez, T Grego, M Hardy, T Hourlier, T Hunt, OG Izuogu, J Lagarde, FJ Martin, L Martinez, S Mohanan, P Muir, FCP Navarro, A Parker, B Pei, F Pozo, M Ruffier, BM Schmitt, E Stapleton, MM Suner, I Sycheva, B Uszczynska-Ratajczak, J Xu, A Yates, D Zerbino, Y Zhang, B Aken, JS Choudhary, M Gerstein, R Guigo, TJP Hubbard, M Kellis, B Paten, A Reymond, ML Tress, P Flicek (2018). Nucleic Acids Res 47: D766-D773.

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.
J Lilue, AG Doran, IT Fiddes, M Abrudan, J Armstrong, R Bennett, W Chow, J Collins, S Collins, A Czechanski, P Danecek, M Diekhans, DD Dolle, M Dunn, R Durbin, D Earl, A Ferguson-Smith, P Flicek, J Flint, A Frankish, B Fu, M Gerstein, J Gilbert, L Goodstadt, J Harrow, K Howe, X Ibarra-Soria, M Kolmogorov, CJ Lelliott, DW Logan, J Loveland, CE Mathews, R Mott, P Muir, S Nachtweide, FCP Navarro, DT Odom, N Park, S Pelan, SK Pham, M Quail, L Reinholdt, L Romoth, L Shirley, C Sisu, M Sjoberg-Herrera, M Stanke, C Steward, M Thomas, G Threadgold, D Thybert, J Torrance, K Wong, J Wood, B Yalcin, F Yang, DJ Adams, B Paten, TM Keane (2018). Nat Genet 50: 1574-1583.

What’s next for humanity?
D Greenbaum, M Gerstein (2018). Science 362 (6415):648.

Human History, Human Genomes
D Greenbaum, M Gerstein (2018). Cell 174:1043-1044.

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci.
V Onuchic, E Lurie, I Carrero, P Pawliczek, RY Patel, J Rozowsky, T Galeev, Z Huang, RC Altshuler, Z Zhang, RA Harris, C Coarfa, L Ashmore, JW Bertol, WD Fakhouri, F Yu, M Kellis, M Gerstein, A Milosavljevic (2018). Science 361.

Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq.
BC Carlyle, RR Kitchen, J Zhang, RS Wilson, TT Lam, JS Rozowsky, KR Williams, N Sestan, MB Gerstein, AC Nairn (2018). J Proteome Res 17: 3431-3444.

KBase: The United States Department of Energy Systems Biology Knowledgebase.
AP Arkin, RW Cottingham, CS Henry, NL Harris, RL Stevens, S Maslov, P Dehal, D Ware, F Perez, S Canon, MW Sneddon, ML Henderson, WJ Riehl, D Murphy-Olson, SY Chan, RT Kamimura, S Kumari, MM Drake, TS Brettin, EM Glass, D Chivian, D Gunter, DJ Weston, BH Allen, J Baumohl, AA Best, B Bowen, SE Brenner, CC Bun, JM Chandonia, JM Chia, R Colasanti, N Conrad, JJ Davis, BH Davison, M DeJongh, S Devoid, E Dietrich, I Dubchak, JN Edirisinghe, G Fang, JP Faria, PM Frybarger, W Gerlach, M Gerstein, A Greiner, J Gurtowski, HL Haun, F He, R Jain, MP Joachimiak, KP Keegan, S Kondo, V Kumar, ML Land, F Meyer, M Mills, PS Novichkov, T Oh, GJ Olsen, R Olson, B Parrello, S Pasternak, E Pearson, SS Poon, GA Price, S Ramakrishnan, P Ranjan, PC Ronald, MC Schatz, SMD Seaver, M Shukla, RA Sutormin, MH Syed, J Thomason, NL Tintle, D Wang, F Xia, H Yoo, S Yoo, D Yu (2018). Nat Biotechnol 36: 566-569.

Analysis of sensitive information leakage in functional genomics signal profiles through genomic deletions.
A Harmanci, M Gerstein (2018). Nat Commun 9: 2453.

Encoding human serine phosphopeptides in bacteria for proteome-wide identification of phosphorylation-dependent interactions.
KW Barber, P Muir, RV Szeligowski, S Rogulina, M Gerstein, JR Sampson, FJ Isaacs, J Rinehart (2018). Nat Biotechnol 36: 638-644.

Network Analysis as a Grand Unifier in Biomedical Data Science
P McGillivray, D Clarke, W Meyerson, J Zhang, D Lee, M Gu, S Kumar, H Zhou, MB Gerstein (2018). Annual Review of Biomedical Data Science Vol. 1.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli
D Thybert, M Roller, FCP Navarro, I Fiddes, I Streeter, C Feig, D Martin-Galvez, M Kolmogorov, V Janousek, W Akanni, B Aken, S Aldridge, V Chakrapani, W Chow, L Clarke, C Cummins, A Doran, M Dunn, L Goodstadt, K Howe, M Howell, AA Josselin, RC Karn, CM Laukaitis, L Jingtao, F Martin, M Muffato, S Nachtweide, MA Quail, C Sisu, M Stanke, K Stefflova, C Van Oosterhout, F Veyrunes, B Ward, F Yang, G Yazdanifar, A Zadissa, DJ Adams, A Brazma, M Gerstein, B Paten, S Pham, TM Keane, DT Odom, P Flicek (2018). Genome Res 28: 448-459.

A comprehensive catalog of predicted functional upstream open reading frames in humans.
P McGillivray, R Ault, M Pawashe, R Kitchen, S Balasubramanian, M Gerstein (2018). Nucleic Acids Res 46: 3326-3338.

FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods.
T Becker, WP Lee, J Leone, Q Zhu, C Zhang, S Liu, J Sargent, K Shanker, A Mil-Homens, E Cerveira, M Ryan, J Cha, FCP Navarro, T Galeev, M Gerstein, RE Mills, DG Shin, C Lee, A Malhotra (2018). Genome Biol 19: 38.

Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap.
MJ Gandal, JR Haney, NN Parikshak, V Leppa, G Ramaswami, C Hartl, AJ Schork, V Appadurai, A Buil, TM Werge, C Liu, KP White, CommonMind Consortium, PsychENCODE Consortium, iPSYCH-BROAD Working Group, S Horvath, DH Geschwind (2018). Science 359: 693-697.

Gene names can confound most-searched listings.
MB Gerstein, FCP Navarro (2018). Nature 553: 405.

Integrative Personal Omics Profiles during Periods of Weight Gain and Loss.
BD Piening, W Zhou, K Contrepois, H Rost, GJ Gu Urban, T Mishra, BM Hanson, EJ Bautista, S Leopold, CY Yeh, D Spakowicz, I Banerjee, C Chen, K Kukurba, D Perelman, C Craig, E Colbert, D Salins, S Rego, S Lee, C Zhang, J Wheeler, MR Sailani, L Liang, C Abbott, M Gerstein, A Mardinoglu, U Smith, DL Rubin, S Pitteri, E Sodergren, TL McLaughlin, GM Weinstock, MP Snyder (2018). Cell Syst 6: 157-170e8.

-- 2017 (20) --

Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.
KE Kaczor-Urbanowicz, Y Kim, F Li, T Galeev, RR Kitchen, M Gerstein, K Koyano, SH Jeong, X Wang, D Elashoff, SY Kang, SM Kim, K Kim, S Kim, D Chia, X Xiao, J Rozowsky, DTW Wong (2017). Bioinformatics 34: 1-8.

The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila
MM Kudron, A Victorsen, L Gevirtzman, LW Hillier, WW Fisher, D Vafeados, M Kirkey, AS Hammonds, J Gersch, H Ammouri, ML Wall, J Moran, D Steffen, M Szynkarek, S Seabrook-Sturgis, N Jameel, M Kadaba, J Patton, R Terrell, M Corson, TJ Durham, S Park, S Samanta, M Han, J Xu, KK Yan, SE Celniker, KP White, L Ma, M Gerstein, V Reinke, RH Waterston (2017). Genetics 208: 937-949.

A multiregional proteomic survey of the postnatal human brain.
BC Carlyle, RR Kitchen, JE Kanyo, EZ Voss, M Pletikos, AMM Sousa, TT Lam, MB Gerstein, N Sestan, AC Nairn (2017). Nat Neurosci 20: 1787-1795.

Molecular and cellular reorganization of neural circuits in the human lineage.
AMM Sousa, Y Zhu, MA Raghanti, RR Kitchen, M Onorati, ATN Tebbenkamp, B Stutz, KA Meyer, M Li, YI Kawasawa, F Liu, RG Perez, M Mele, T Carvalho, M Skarica, FO Gulden, M Pletikos, A Shibata, AR Stephenson, MK Edler, JJ Ely, JD Elsworth, TL Horvath, PR Hof, TM Hyde, JE Kleinman, DR Weinberger, M Reimers, RP Lifton, SM Mane, JP Noonan, MW State, ES Lein, JA Knowles, T Marques-Bonet, CC Sherwood, MB Gerstein, N Sestan (2017). Science 358: 1027-1032.

MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool.
L Lochovsky, J Zhang, M Gerstein (2017). Bioinformatics 34: 1031-1033.

Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines.
Q Cao, C Anyansi, X Hu, L Xu, L Xiong, W Tang, MTS Mok, C Cheng, X Fan, M Gerstein, ASL Cheng, KY Yip (2017). Nat Genet 49: 1428-1436.

Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes.
S Balasubramanian, Y Fu, M Pawashe, P McGillivray, M Jin, J Liu, KJ Karczewski, DG MacArthur, M Gerstein (2017). Nat Commun 8: 382.

MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions.
KK Yan, S Lou, M Gerstein (2017). PLoS Comput Biol 13: e1005647.

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis.
SME Sahraeian, M Mohiyuddin, R Sebra, H Tilgner, PT Afshar, KF Au, N Bani Asadi, MB Gerstein, WH Wong, MP Snyder, E Schadt, HYK Lam (2017). Nat Commun 8: 59.

Landscape and variation of novel retroduplications in 26 human populations.
Y Zhang, S Li, A Abyzov, MB Gerstein (2017). PLoS Comput Biol 13: e1005567.

Cancer genomics: Less is more in the hunt for driver mutations.
S Kumar, M Gerstein (2017). Nature 547: 40-41.

Using FunSeq2 for Coding and Non-Coding Variant Annotation and Prioritization.
P Dhingra, Y Fu, M Gerstein, E Khurana (2017). Curr Protoc Bioinformatics 57: 15111-151117.

Multiple-Swarm Ensembles: Improving the Predictive Power and Robustness of Predictive Models and Its Use in Computational Biology.
P Alves, S Liu, D Wang, M Gerstein (2017). IEEE/ACM Trans Comput Biol Bioinform 15: 926-933.

Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition.
V Despic, M Dejung, M Gu, J Krishnan, J Zhang, L Herzel, K Straube, MB Gerstein, F Butter, KM Neugebauer (2017). Genome Res 27: 1184-1194.

Structuring supplemental materials in support of reproducibility.
D Greenbaum, J Rozowsky, V Stodden, M Gerstein (2017). Genome Biol 18: 64.

HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps.
KK Yan, GG Yardimci, C Yan, WS Noble, M Gerstein (2017). Bioinformatics 33: 2199-2201.

Whole-genome analysis of papillary kidney cancer finds significant noncoding alterations.
S Li, BM Shuch, MB Gerstein (2017). PLoS Genet 13: e1006685.

MicroRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos.
DM Kasper, A Moro, E Ristori, A Narayanan, G Hill-Teran, E Fleming, M Moreno-Mateos, CE Vejnar, J Zhang, D Lee, M Gu, M Gerstein, A Giraldez, S Nicoli (2017). Dev Cell 40: 552-565e5.

Stroke and Circulating Extracellular RNAs.
E Mick, R Shah, K Tanriverdi, V Murthy, M Gerstein, J Rozowsky, R Kitchen, MG Larson, D Levy, JE Freedman (2017). Stroke 48: 828-834.

One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin.
A Abyzov, L Tomasini, B Zhou, N Vasmatzis, G Coppola, M Amenduni, R Pattni, M Wilson, M Gerstein, S Weissman, AE Urban, FM Vaccarino (2017). Genome Res 27: 512-523.

-- 2016 (19) --

Intensification: A Resource for Amplifying Population-Genetic Signals with Protein Repeats.
J Chen, B Wang, L Regan, M Gerstein (2016). J Mol Biol 429: 435-445.

Localized structural frustration for evaluating the impact of sequence variants.
S Kumar, D Clarke, M Gerstein (2016). Nucleic Acids Res 44: 10062-10073.

DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks.
D Wang, F He, S Maslov, M Gerstein (2016). PLoS Comput Biol 12: e1005146.

Opinion: GMOs Are Not “Frankenfoods”
D Greenbaum, M Gerstein (2016). The Scientist (30 Aug).

iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.
CC Yang, EH Andrews, MH Chen, WY Wang, JJ Chen, M Gerstein, CC Liu, C Cheng (2016). BMC Genomics 17: 632.

Pangolin genomes and the evolution of mammalian scales and immunity.
SW Choo, M Rayko, TK Tan, R Hari, A Komissarov, WY Wee, AA Yurchenko, S Kliver, G Tamazian, A Antunes, RK Wilson, WC Warren, KP Koepfli, P Minx, K Krasheninnikova, A Kotze, DL Dalton, E Vermaak, IC Paterson, P Dobrynin, FT Sitam, JJ Rovie-Ryan, WE Johnson, AM Yusoff, SJ Luo, KV Karuppannan, G Fang, D Zheng, MB Gerstein, L Lipovich, SJ O'Brien, GJ Wong (2016). Genome Res 26: 1312-1322.

Discordant Expression of Circulating microRNA from Cellular and Extracellular Sources.
R Shah, K Tanriverdi, D Levy, M Larson, M Gerstein, E Mick, J Rozowsky, R Kitchen, V Murthy, E Mikalev, JE Freedman (2016). PLoS One 11: e0153691.

Diverse human extracellular RNAs are widely detected in human plasma.
JE Freedman, M Gerstein, E Mick, J Rozowsky, D Levy, R Kitchen, S Das, R Shah, K Danielson, L Beaulieu, FC Navarro, Y Wang, TR Galeev, A Holman, RY Kwong, V Murthy, SE Tanriverdi, M Koupenova-Zamor, E Mikhalev, K Tanriverdi (2016). Nat Commun 7: 11106.

Extending gene ontology in the context of extracellular RNA and vesicle communication.
KH Cheung, S Keerthikumar, P Roncaglia, SL Subramanian, ME Roth, M Samuel, S Anand, L Gangoda, S Gould, R Alexander, D Galas, MB Gerstein, AF Hill, RR Kitchen, J Lotvall, T Patel, DC Procaccini, P Quesenberry, J Rozowsky, RL Raffai, A Shypitsyna, AI Su, C Thery, K Vickers, MH Wauben, S Mathivanan, A Milosavljevic, LC Laurent (2016). J Biomed Semantics 7: 19.

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals.
J Chen, J Rozowsky, TR Galeev, A Harmanci, R Kitchen, J Bedford, A Abyzov, Y Kong, L Regan, M Gerstein (2016). Nat Commun 7: 11101.

Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation.
D Clarke, A Sethi, S Li, S Kumar, RWF Chang, J Chen, M Gerstein (2016). Structure 24: 826-837.

Cross-Disciplinary Network Comparison: Matchmaking Between Hairballs.
KK Yan, D Wang, A Sethi, P Muir, R Kitchen, C Cheng, M Gerstein (2016). Cell Syst 2: 147-157.

Who Owns Your DNA?
D Greenbaum, M Gerstein (2016). Cell 165:257-258.

Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis.
F He, S Yoo, D Wang, S Kumari, M Gerstein, D Ware, S Maslov (2016). Plant J 86: 472-80.

The real cost of sequencing: scaling computation to keep pace with data generation.
P Muir, S Li, S Lou, D Wang, DJ Spakowicz, L Salichos, J Zhang, GM Weinstock, F Isaacs, J Rozowsky, M Gerstein (2016). Genome Biol 17: 53.

Temporal Dynamics of Collaborative Networks in Large Scientific Consortia.
D Wang, KK Yan, J Rozowsky, E Pan, M Gerstein (2016). Trends Genet 32: 251-253.

Quantification of private information leakage from phenotype-genotype data: linking attacks.
A Harmanci, M Gerstein (2016). Nat Methods 13: 251-6.

Role of non-coding sequence variants in cancer.
E Khurana, Y Fu, D Chakravarty, F Demichelis, MA Rubin, M Gerstein (2016). Nat Rev Genet 17: 93-108.

Understanding genome structural variations.
A Abyzov, S Li, MB Gerstein (2016). Oncotarget 7: 7370-1.

-- 2015 (19) --

Knowledge Based Factorized High Order Sparse Learning Models
S Purushotham, MR Min, CJ Kuo, M Gerstein (2015). NIPS Workshop on Machine Learning in Computational Biology.

The Molecular Taxonomy of Primary Prostate Cancer.
Cancer Genome Atlas Research Network (2015). Cell 163: 1011-25.

Reads meet rotamers: structural biology in the age of deep sequencing.
A Sethi, D Clarke, J Chen, S Kumar, TR Galeev, L Regan, M Gerstein (2015). Curr Opin Struct Biol 35: 125-34.

The PsychENCODE project.
PsychENCODE Consortium, S Akbarian, C Liu, JA Knowles, FM Vaccarino, PJ Farnham, GE Crawford, AE Jaffe, D Pinto, S Dracheva, DH Geschwind, J Mill, AC Nairn, A Abyzov, S Pochareddy, S Prabhakar, S Weissman, PF Sullivan, MW State, Z Weng, MA Peters, KP White, MB Gerstein, A Amiri, C Armoskus, AE Ashley-Koch, T Bae, A Beckel-Mitchener, BP Berman, GA Coetzee, G Coppola, N Francoeur, M Fromer, R Gao, K Grennan, J Herstein, DH Kavanagh, NA Ivanov, Y Jiang, RR Kitchen, A Kozlenkov, M Kundakovic, M Li, Z Li, S Liu, LM Mangravite, E Mattei, E Markenscoff-Papadimitriou, FC Navarro, N North, L Omberg, D Panchision, N Parikshak, J Poschmann, AJ Price, M Purcaro, TE Reddy, P Roussos, S Schreiner, S Scuderi, R Sebra, M Shibata, AW Shieh, M Skarica, W Sun, V Swarup, A Thomas, J Tsuji, H van Bakel, D Wang, Y Wang, K Wang, DM Werling, AJ Willsey, H Witt, H Won, CC Wong, GA Wray, EY Wu, X Xu, L Yao, G Senthil, T Lehner, P Sklar, N Sestan (2015). Nat Neurosci 18: 1707-12.

Illuminating the Genome's Dark Matter
D Greenbaum, M Gerstein (2015). Cell 163:1047-1048.

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.
Cancer Genome Atlas Research Network, WM Linehan, PT Spellman, CJ Ricketts, CJ Creighton, SS Fei, C Davis, DA Wheeler, BA Murray, L Schmidt, CD Vocke, M Peto, AA Al Mamun, E Shinbrot, A Sethi, S Brooks, WK Rathmell, AN Brooks, KA Hoadley, AG Robertson, D Brooks, R Bowlby, S Sadeghi, H Shen, DJ Weisenberger, M Bootwalla, SB Baylin, PW Laird, AD Cherniack, G Saksena, S Haake, J Li, H Liang, Y Lu, GB Mills, R Akbani, MD Leiserson, BJ Raphael, P Anur, D Bottaro, L Albiges, N Barnabas, TK Choueiri, B Czerniak, AK Godwin, AA Hakimi, TH Ho, J Hsieh, M Ittmann, WY Kim, B Krishnan, MJ Merino, KR Mills Shaw, VE Reuter, E Reznik, CS Shelley, B Shuch, S Signoretti, R Srinivasan, P Tamboli, G Thomas, S Tickoo, K Burnett, D Crain, J Gardner, K Lau, D Mallery, S Morris, JD Paulauskis, RJ Penny, C Shelton, WT Shelton, M Sherman, E Thompson, P Yena, MT Avedon, J Bowen, JM Gastier-Foster, M Gerken, KM Leraas, TM Lichtenberg, NC Ramirez, T Santos, L Wise, E Zmuda, JA Demchok, I Felau, CM Hutter, M Sheth, HJ Sofia, R Tarnuzzer, Z Wang, L Yang, JC Zenklusen, J Zhang, B Ayala, J Baboud, S Chudamani, J Liu, L Lolla, R Naresh, T Pihl, Q Sun, Y Wan, Y Wu, A Ally, M Balasundaram, S Balu, R Beroukhim, T Bodenheimer, C Buhay, YS Butterfield, R Carlsen, SL Carter, H Chao, E Chuah, A Clarke, KR Covington, M Dahdouli, N Dewal, N Dhalla, HV Doddapaneni, JA Drummond, SB Gabriel, RA Gibbs, R Guin, W Hale, A Hawes, DN Hayes, RA Holt, AP Hoyle, SR Jefferys, SJ Jones, CD Jones, D Kalra, C Kovar, L Lewis, J Li, Y Ma, MA Marra, M Mayo, S Meng, M Meyerson, PA Mieczkowski, RA Moore, D Morton, LE Mose, AJ Mungall, D Muzny, JS Parker, CM Perou, J Roach, JE Schein, SE Schumacher, Y Shi, JV Simons, P Sipahimalani, T Skelly, MG Soloway, C Sougnez, A Tam, D Tan, N Thiessen, U Veluvolu, M Wang, MD Wilkerson, T Wong, J Wu, L Xi, J Zhou, J Bedford, F Chen, Y Fu, M Gerstein, D Haussler, K Kasaian, P Lai, S Ling, A Radenbaugh, D Van Den Berg, JN Weinstein, J Zhu, M Albert, I Alexopoulou, JJ Andersen, JT Auman, J Bartlett, S Bastacky, J Bergsten, ML Blute, L Boice, RJ Bollag, J Boyd, E Castle, YB Chen, JC Cheville, E Curley, B Davies, A DeVolk, R Dhir, L Dike, J Eckman, J Engel, J Harr, R Hrebinko, M Huang, L Huelsenbeck-Dill, M Iacocca, B Jacobs, M Lobis, JK Maranchie, S McMeekin, J Myers, J Nelson, J Parfitt, A Parwani, N Petrelli, B Rabeno, S Roy, AL Salner, J Slaton, M Stanton, RH Thompson, L Thorne, K Tucker, PM Weinberger, C Winemiller, LA Zach, R Zuna (2015). N Engl J Med 374: 135-45.

A global reference for human genetic variation.
1000 Genomes Project Consortium, A Auton, LD Brooks, RM Durbin, EP Garrison, HM Kang, JO Korbel, JL Marchini, S McCarthy, GA McVean, GR Abecasis (2015). Nature 526: 68-74.

An integrated map of structural variation in 2,504 human genomes.
PH Sudmant, T Rausch, EJ Gardner, RE Handsaker, A Abyzov, J Huddleston, Y Zhang, K Ye, G Jun, MH Fritz, MK Konkel, A Malhotra, AM Stutz, X Shi, FP Casale, J Chen, F Hormozdiari, G Dayama, K Chen, M Malig, MJP Chaisson, K Walter, S Meiers, S Kashin, E Garrison, A Auton, HYK Lam, XJ Mu, C Alkan, D Antaki, T Bae, E Cerveira, P Chines, Z Chong, L Clarke, E Dal, L Ding, S Emery, X Fan, M Gujral, F Kahveci, JM Kidd, Y Kong, EW Lameijer, S McCarthy, P Flicek, RA Gibbs, G Marth, CE Mason, A Menelaou, DM Muzny, BJ Nelson, A Noor, NF Parrish, M Pendleton, A Quitadamo, B Raeder, EE Schadt, M Romanovitch, A Schlattl, R Sebra, AA Shabalin, A Untergasser, JA Walker, M Wang, F Yu, C Zhang, J Zhang, X Zheng-Bradley, W Zhou, T Zichner, J Sebat, MA Batzer, SA McCarroll, 1000 Genomes Project Consortium, RE Mills, MB Gerstein, A Bashir, O Stegle, SE Devine, C Lee, EE Eichler, JO Korbel (2015). Nature 526: 75-81.

Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods.
JC Mu, P Tootoonchi Afshar, M Mohiyuddin, X Chen, J Li, N Bani Asadi, MB Gerstein, WH Wong, HY Lam (2015). Sci Rep 5: 14493.

An ensemble approach to accurately detect somatic mutations using SomaticSeq.
LT Fang, PT Afshar, A Chhibber, M Mohiyuddin, Y Fan, JC Mu, G Gibeling, S Barr, NB Asadi, MB Gerstein, DC Koboldt, W Wang, WH Wong, HY Lam (2015). Genome Biol 16: 197.

Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry.
EE Duffy, M Rutenberg-Schoenberg, CD Stark, RR Kitchen, MB Gerstein, MD Simon (2015). Mol Cell 59: 858-66.

LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations.
L Lochovsky, J Zhang, Y Fu, E Khurana, M Gerstein (2015). Nucleic Acids Res 43: 8123-34.

High-order neural networks and kernel methods for peptide-MHC binding prediction.
PP Kuksa, MR Min, R Dugar, M Gerstein (2015). Bioinformatics 31: 3600-7.

FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders.
J Mariani, G Coppola, P Zhang, A Abyzov, L Provini, L Tomasini, M Amenduni, A Szekely, D Palejev, M Wilson, M Gerstein, EL Grigorenko, K Chawarska, KA Pelphrey, JR Howe, FM Vaccarino (2015). Cell 162: 375-390.

Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.
A Abyzov, S Li, DR Kim, M Mohiyuddin, AM Stutz, NF Parrish, XJ Mu, W Clark, K Chen, M Hurles, JO Korbel, HY Lam, C Lee, MB Gerstein (2015). Nat Commun 6: 7256.

The computer connection
D Greenbaum, M Gerstein (2015). Science 347: 956.

MetaSV: an accurate and integrative structural-variant caller for next generation sequencing.
M Mohiyuddin, JC Mu, J Li, N Bani Asadi, MB Gerstein, A Abyzov, WH Wong, HY Lam (2015). Bioinformatics 31: 2741-4.

Loregic: a method to characterize the cooperative logic of regulatory factors.
D Wang, KK Yan, C Sisu, C Cheng, J Rozowsky, W Meyerson, MB Gerstein (2015). PLoS Comput Biol 11: e1004132.

An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome.
C Cheng, E Andrews, KK Yan, M Ung, D Wang, M Gerstein (2015). Genome Biol 16: 63.

-- 2014 (15) --

Proposed social and technological solutions to issues of data privacy in personal genomics
D Greenbaum, A Harmanci, M Gerstein (2014). IEEE IEEE International Symposium on Ethics in Science, Technology and Engineering.

Ensemble Learning Based Sparse High-Order Boltzmann Machine for Unsupervised Feature Interaction Identification
MR Min, X Ning, Y Qi, C Cheng, A Bonner, M Gerstein (2014). NIPS Workshop on Machine Learning in Computational Biology.

Interpretable Sparse High-Order Boltzmann Machines
MR Min, X Ning, C Cheng, M Gerstein (2014). JMLR W&CP 33:614-622 (AISTATS 2014).

VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.
JC Mu, M Mohiyuddin, J Li, N Bani Asadi, MB Gerstein, A Abyzov, WH Wong, HY Lam (2014). Bioinformatics 31: 1469-71.

Decoding neuroproteomics: integrating the genome, translatome and functional anatomy.
RR Kitchen, JS Rozowsky, MB Gerstein, AC Nairn (2014). Nat Neurosci 17: 1491-9.

MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework.
A Harmanci, J Rozowsky, M Gerstein (2014). Genome Biol 15: 474.

FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.
Y Fu, Z Liu, S Lou, J Bedford, XJ Mu, KY Yip, E Khurana, M Gerstein (2014). Genome Biol 15: 480.

Comparative analysis of regulatory information and circuits across distant species.
AP Boyle, CL Araya, C Brdlik, P Cayting, C Cheng, Y Cheng, K Gardner, LW Hillier, J Janette, L Jiang, D Kasper, T Kawli, P Kheradpour, A Kundaje, JJ Li, L Ma, W Niu, EJ Rehm, J Rozowsky, M Slattery, R Spokony, R Terrell, D Vafeados, D Wang, P Weisdepp, YC Wu, D Xie, KK Yan, EA Feingold, PJ Good, MJ Pazin, H Huang, PJ Bickel, SE Brenner, V Reinke, RH Waterston, M Gerstein, KP White, M Kellis, M Snyder (2014). Nature 512: 453-6.

Comparative analysis of the transcriptome across distant species.
MB Gerstein, J Rozowsky, KK Yan, D Wang, C Cheng, JB Brown, CA Davis, L Hillier, C Sisu, JJ Li, B Pei, AO Harmanci, MO Duff, S Djebali, RP Alexander, BH Alver, R Auerbach, K Bell, PJ Bickel, ME Boeck, NP Boley, BW Booth, L Cherbas, P Cherbas, C Di, A Dobin, J Drenkow, B Ewing, G Fang, M Fastuca, EA Feingold, A Frankish, G Gao, PJ Good, R Guigo, A Hammonds, J Harrow, RA Hoskins, C Howald, L Hu, H Huang, TJ Hubbard, C Huynh, S Jha, D Kasper, M Kato, TC Kaufman, RR Kitchen, E Ladewig, J Lagarde, E Lai, J Leng, Z Lu, M MacCoss, G May, R McWhirter, G Merrihew, DM Miller, A Mortazavi, R Murad, B Oliver, S Olson, PJ Park, MJ Pazin, N Perrimon, D Pervouchine, V Reinke, A Reymond, G Robinson, A Samsonova, GI Saunders, F Schlesinger, A Sethi, FJ Slack, WC Spencer, MH Stoiber, P Strasbourger, A Tanzer, OA Thompson, KH Wan, G Wang, H Wang, KL Watkins, J Wen, K Wen, C Xue, L Yang, K Yip, C Zaleski, Y Zhang, H Zheng, SE Brenner, BR Graveley, SE Celniker, TR Gingeras, R Waterston (2014). Nature 512: 445-8.

Comparative analysis of pseudogenes across three phyla.
C Sisu, B Pei, J Leng, A Frankish, Y Zhang, S Balasubramanian, R Harte, D Wang, M Rutenberg-Schoenberg, W Clark, M Diekhans, J Rozowsky, T Hubbard, J Harrow, MB Gerstein (2014). Proc Natl Acad Sci U S A 111: 13361-6.

OrthoClust: an orthology-based network framework for clustering data across multiple species.
KK Yan, D Wang, J Rozowsky, H Zheng, C Cheng, M Gerstein (2014). Genome Biol 15: R100.

Guidelines for investigating causality of sequence variants in human disease.
DG MacArthur, TA Manolio, DP Dimmock, HL Rehm, J Shendure, GR Abecasis, DR Adams, RB Altman, SE Antonarakis, EA Ashley, JC Barrett, LG Biesecker, DF Conrad, GM Cooper, NJ Cox, MJ Daly, MB Gerstein, DB Goldstein, JN Hirschhorn, SM Leal, LA Pennacchio, JA Stamatoyannopoulos, SR Sunyaev, D Valle, BF Voight, W Winckler, C Gunter (2014). Nature 508: 469-76.

Defining functional DNA elements in the human genome.
M Kellis, B Wold, MP Snyder, BE Bernstein, A Kundaje, GK Marinov, LD Ward, E Birney, GE Crawford, J Dekker, I Dunham, LL Elnitski, PJ Farnham, EA Feingold, M Gerstein, MC Giddings, DM Gilbert, TR Gingeras, ED Green, R Guigo, T Hubbard, J Kent, JD Lieb, RM Myers, MJ Pazin, B Ren, JA Stamatoyannopoulos, Z Weng, KP White, RC Hardison (2014). Proc Natl Acad Sci U S A 111: 6131-8.

Transcriptional landscape of the prenatal human brain.
JA Miller, SL Ding, SM Sunkin, KA Smith, L Ng, A Szafer, A Ebbert, ZL Riley, JJ Royall, K Aiona, JM Arnold, C Bennet, D Bertagnolli, K Brouner, S Butler, S Caldejon, A Carey, C Cuhaciyan, RA Dalley, N Dee, TA Dolbeare, BA Facer, D Feng, TP Fliss, G Gee, J Goldy, L Gourley, BW Gregor, G Gu, RE Howard, JM Jochim, CL Kuan, C Lau, CK Lee, F Lee, TA Lemon, P Lesnar, B McMurray, N Mastan, N Mosqueda, T Naluai-Cecchini, NK Ngo, J Nyhus, A Oldre, E Olson, J Parente, PD Parker, SE Parry, A Stevens, M Pletikos, M Reding, K Roll, D Sandman, M Sarreal, S Shapouri, NV Shapovalova, EH Shen, N Sjoquist, CR Slaughterbeck, M Smith, AJ Sodt, D Williams, L Zollei, B Fischl, MB Gerstein, DH Geschwind, IA Glass, MJ Hawrylycz, RF Hevner, H Huang, AR Jones, JA Knowles, P Levitt, JW Phillips, N Sestan, P Wohnoutka, C Dang, A Bernard, JG Hohmann, ES Lein (2014). Nature 508: 199-206.

Identification of a major determinant for serine-threonine kinase phosphoacceptor specificity.
C Chen, BH Ha, AF Thevenin, HJ Lou, R Zhang, KY Yip, JR Peterson, M Gerstein, PM Kim, P Filippakopoulos, S Knapp, TJ Boggon, BE Turk (2014). Mol Cell 53: 140-7.

-- 2013 (14) --

Interpretable Sparse High-Order Boltzmann Machines for Transcription Factor Interaction Identification
MR Min, X Ning, C Cheng, M Gerstein (2013). NIPS Workshop on Machine Learning in Computational Biology.

Assessment of transcript reconstruction methods for RNA-seq.
T Steijger, JF Abril, PG Engstrom, F Kokocinski, RGASP Consortium, TJ Hubbard, R Guigo, J Harrow, P Bertone (2013). Nat Methods 10: 1177-84.

Deep Inside Champions, Just Genes?
D Greenbaum, J Chen, M Gerstein (2013). Science 342: 560.

Integrative annotation of variants from 1092 humans: application to cancer genomics.
E Khurana, Y Fu, V Colonna, XJ Mu, HM Kang, T Lappalainen, A Sboner, L Lochovsky, J Chen, A Harmanci, J Das, A Abyzov, S Balasubramanian, K Beal, D Chakravarty, D Challis, Y Chen, D Clarke, L Clarke, F Cunningham, US Evani, P Flicek, R Fragoza, E Garrison, R Gibbs, ZH Gumus, J Herrero, N Kitabayashi, Y Kong, K Lage, V Liluashvili, SM Lipkin, DG MacArthur, G Marth, D Muzny, TH Pers, GRS Ritchie, JA Rosenfeld, C Sisu, X Wei, M Wilson, Y Xue, F Yu, 1000 Genomes Project Consortium, ET Dermitzakis, H Yu, MA Rubin, C Tyler-Smith, M Gerstein (2013). Science 342: 1235587.

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division.
A Abyzov, R Iskow, O Gokcumen, DW Radke, S Balasubramanian, B Pei, L Habegger, 1000 Genomes Project Consortium, C Lee, M Gerstein (2013). Genome Res 23: 2042-52.

Proceed with Caution
D Greenbaum, M Gerstein (2013). The Scientist 27:26 (1 Oct.)

Identification of yeast cell cycle regulated genes based on genomic features.
C Cheng, Y Fu, L Shen, M Gerstein (2013). BMC Syst Biol 7: 70.

Child development and structural variation in the human genome.
Y Zhang, R Haraksingh, F Grubert, A Abyzov, M Gerstein, S Weissman, AE Urban (2013). Child Dev 84: 34-48.

A comprehensive nuclear receptor network for breast cancer cells.
R Kittler, J Zhou, S Hua, L Ma, Y Liu, E Pendleton, C Cheng, M Gerstein, KP White (2013). Cell Rep 3: 538-51.

Accurate identification and analysis of human mRNA isoforms using deep long read sequencing.
H Tilgner, D Raha, L Habegger, M Mohiuddin, M Gerstein, M Snyder (2013). G3 (Bethesda) 3: 387-97.

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.
SB Montgomery, DL Goode, E Kvikstad, CA Albers, ZD Zhang, XJ Mu, G Ananda, B Howie, KJ Karczewski, KS Smith, V Anaya, R Richardson, J Davis, 1000 Genomes Project Consortium, DG MacArthur, A Sidow, L Duret, M Gerstein, KD Makova, J Marchini, G McVean, G Lunter (2013). Genome Res 23: 749-61.

Sixty years of genome biology.
WF Doolittle, P Fraser, MB Gerstein, BR Graveley, S Henikoff, C Huttenhower, A Oshlack, CP Ponting, JL Rinn, MC Schatz, J Ule, D Weigel, GM Weinstock (2013). Genome Biol 14: 113.

Machine learning and genome annotation: a match meant to be?
KY Yip, C Cheng, M Gerstein (2013). Genome Biol 14: 205.

Interpretation of genomic variants using a unified biological network approach.
E Khurana, Y Fu, J Chen, M Gerstein (2013). PLoS Comput Biol 9: e1002886.

-- 2012 (26) --

Epigenetic repression of miR-31 disrupts androgen receptor homeostasis and contributes to prostate cancer progression.
PC Lin, YL Chiu, S Banerjee, K Park, JM Mosquera, E Giannopoulou, P Alves, AK Tewari, MB Gerstein, H Beltran, AM Melnick, O Elemento, F Demichelis, MA Rubin (2012). Cancer Res 73: 1232-44.

Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells.
A Abyzov, J Mariani, D Palejev, Y Zhang, MS Haney, L Tomasini, AF Ferrandino, LA Rosenberg Belmaker, A Szekely, M Wilson, A Kocabas, NE Calixto, EL Grigorenko, A Huttner, K Chawarska, S Weissman, AE Urban, M Gerstein, FM Vaccarino (2012). Nature 492: 438-42.

An integrated map of genetic variation from 1,092 human genomes.
1000 Genomes Project Consortium, GR Abecasis, A Auton, LD Brooks, MA DePristo, RM Durbin, RE Handsaker, HM Kang, GT Marth, GA McVean (2012). Nature 491: 56-65.

Genomics: ENCODE leads the way on big data.
M Gerstein (2012). Nature 489: 208.

An integrated encyclopedia of DNA elements in the human genome.
ENCODE Project Consortium (2012). Nature 489: 57-74.

Architecture of the human regulatory network derived from ENCODE data.
MB Gerstein, A Kundaje, M Hariharan, SG Landt, KK Yan, C Cheng, XJ Mu, E Khurana, J Rozowsky, R Alexander, R Min, P Alves, A Abyzov, N Addleman, N Bhardwaj, AP Boyle, P Cayting, A Charos, DZ Chen, Y Cheng, D Clarke, C Eastman, G Euskirchen, S Frietze, Y Fu, J Gertz, F Grubert, A Harmanci, P Jain, M Kasowski, P Lacroute, JJ Leng, J Lian, H Monahan, H O'Geen, Z Ouyang, EC Partridge, D Patacsil, F Pauli, D Raha, L Ramirez, TE Reddy, B Reed, M Shi, T Slifer, J Wang, L Wu, X Yang, KY Yip, G Zilberman-Schapira, S Batzoglou, A Sidow, PJ Farnham, RM Myers, SM Weissman, M Snyder (2012). Nature 489: 91-100.

Landscape of transcription in human cells.
S Djebali, CA Davis, A Merkel, A Dobin, T Lassmann, A Mortazavi, A Tanzer, J Lagarde, W Lin, F Schlesinger, C Xue, GK Marinov, J Khatun, BA Williams, C Zaleski, J Rozowsky, M Roder, F Kokocinski, RF Abdelhamid, T Alioto, I Antoshechkin, MT Baer, NS Bar, P Batut, K Bell, I Bell, S Chakrabortty, X Chen, J Chrast, J Curado, T Derrien, J Drenkow, E Dumais, J Dumais, R Duttagupta, E Falconnet, M Fastuca, K Fejes-Toth, P Ferreira, S Foissac, MJ Fullwood, H Gao, D Gonzalez, A Gordon, H Gunawardena, C Howald, S Jha, R Johnson, P Kapranov, B King, C Kingswood, OJ Luo, E Park, K Persaud, JB Preall, P Ribeca, B Risk, D Robyr, M Sammeth, L Schaffer, LH See, A Shahab, J Skancke, AM Suzuki, H Takahashi, H Tilgner, D Trout, N Walters, H Wang, J Wrobel, Y Yu, X Ruan, Y Hayashizaki, J Harrow, M Gerstein, T Hubbard, A Reymond, SE Antonarakis, G Hannon, MC Giddings, Y Ruan, B Wold, P Carninci, R Guigo, TR Gingeras (2012). Nature 489: 101-8.

GENCODE: the reference human genome annotation for The ENCODE Project.
J Harrow, A Frankish, JM Gonzalez, E Tapanari, M Diekhans, F Kokocinski, BL Aken, D Barrell, A Zadissa, S Searle, I Barnes, A Bignell, V Boychenko, T Hunt, M Kay, G Mukherjee, J Rajan, G Despacio-Reyes, G Saunders, C Steward, R Harte, M Lin, C Howald, A Tanzer, T Derrien, J Chrast, N Walters, S Balasubramanian, B Pei, M Tress, JM Rodriguez, I Ezkurdia, J van Baren, M Brent, D Haussler, M Kellis, A Valencia, A Reymond, M Gerstein, R Guigo, TJ Hubbard (2012). Genome Res 22: 1760-74.

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors.
KY Yip, C Cheng, N Bhardwaj, JB Brown, J Leng, A Kundaje, J Rozowsky, E Birney, P Bickel, M Snyder, M Gerstein (2012). Genome Biol 13: R48.

Understanding transcriptional regulation by integrative analysis of transcription factor binding data.
C Cheng, R Alexander, R Min, J Leng, KY Yip, J Rozowsky, KK Yan, X Dong, S Djebali, Y Ruan, CA Davis, P Carninci, T Lassman, TR Gingeras, R Guigo, E Birney, Z Weng, M Snyder, M Gerstein (2012). Genome Res 22: 1658-67.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
SG Landt, GK Marinov, A Kundaje, P Kheradpour, F Pauli, S Batzoglou, BE Bernstein, P Bickel, JB Brown, P Cayting, Y Chen, G DeSalvo, C Epstein, KI Fisher-Aylor, G Euskirchen, M Gerstein, J Gertz, AJ Hartemink, MM Hoffman, VR Iyer, YL Jung, S Karmakar, M Kellis, PV Kharchenko, Q Li, T Liu, XS Liu, L Ma, A Milosavljevic, RM Myers, PJ Park, MJ Pazin, MD Perry, D Raha, TE Reddy, J Rozowsky, N Shoresh, A Sidow, M Slattery, JA Stamatoyannopoulos, MY Tolstorukov, KP White, S Xi, PJ Farnham, JD Lieb, BJ Wold, M Snyder (2012). Genome Res 22: 1813-31.

The GENCODE pseudogene resource.
B Pei, C Sisu, A Frankish, C Howald, L Habegger, XJ Mu, R Harte, S Balasubramanian, A Tanzer, M Diekhans, A Reymond, TJ Hubbard, J Harrow, MB Gerstein (2012). Genome Biol 13: R51.

Modeling gene expression using chromatin features in various cellular contexts.
X Dong, MC Greven, A Kundaje, S Djebali, JB Brown, C Cheng, TR Gingeras, M Gerstein, R Guigo, E Birney, Z Weng (2012). Genome Biol 13: R53.

Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line.
JQ Wu, M Seay, VP Schulz, M Hariharan, D Tuck, J Lian, J Du, M Shi, Z Ye, M Gerstein, MP Snyder, S Weissman (2012). PLoS Genet 8: e1002565.

Detecting and annotating genetic variations using the HugeSeq pipeline.
HY Lam, C Pan, MJ Clark, P Lacroute, R Chen, R Haraksingh, M O'Huallachain, MB Gerstein, JM Kidd, CD Bustamante, M Snyder (2012). Nat Biotechnol 30: 226-9.

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb.
J Cotney, J Leng, S Oh, LE DeMare, SK Reilly, MB Gerstein, JP Noonan (2012). Genome Res 22: 1069-80.

The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare.
M Vidal, DW Chan, M Gerstein, M Mann, GS Omenn, D Tagle, S Sechi, Workshop Participants (2012). Clin Proteomics 9: 6.

The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions.
MJ Bamshad, JA Shendure, D Valle, A Hamosh, JR Lupski, RA Gibbs, E Boerwinkle, RP Lifton, M Gerstein, M Gunel, S Mane, DA Nickerson, Centers for Mendelian Genomics (2012). Am J Med Genet A 158A: 1523-5.

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.
L Habegger, S Balasubramanian, DZ Chen, E Khurana, A Sboner, A Harmanci, J Rozowsky, D Clarke, M Snyder, M Gerstein (2012). Bioinformatics 28: 2267-9.

On sports and genes.
G Zilberman-Schapira, J Chen, M Gerstein (2012). Recent Pat DNA Gene Seq 6: 180-8.

Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides.
TA Gianoulis, MA Griffin, DJ Spakowicz, BF Dunican, CJ Alpha, A Sboner, AM Sismour, C Kodira, M Egholm, GM Church, MB Gerstein, SA Strobel (2012). PLoS Genet 8: e1002558.

Personal omics profiling reveals dynamic molecular and medical phenotypes.
R Chen, GI Mias, J Li-Pook-Than, L Jiang, HY Lam, R Chen, E Miriami, KJ Karczewski, M Hariharan, FE Dewey, Y Cheng, MJ Clark, H Im, L Habegger, S Balasubramanian, M O'Huallachain, JT Dudley, S Hillenmeyer, R Haraksingh, D Sharon, G Euskirchen, P Lacroute, K Bettinger, AP Boyle, M Kasowski, F Grubert, S Seki, M Garcia, M Whirl-Carrillo, M Gallardo, MA Blasco, PL Greenberg, P Snyder, TE Klein, RB Altman, AJ Butte, EA Ashley, M Gerstein, KC Nadeau, H Tang, M Snyder (2012). Cell 148: 1293-307.

A systematic survey of loss-of-function variants in human protein-coding genes.
DG MacArthur, S Balasubramanian, A Frankish, N Huang, J Morris, K Walter, L Jostins, L Habegger, JK Pickrell, SB Montgomery, CA Albers, ZD Zhang, DF Conrad, G Lunter, H Zheng, Q Ayub, MA DePristo, E Banks, M Hu, RE Handsaker, JA Rosenfeld, M Fromer, M Jin, XJ Mu, E Khurana, K Ye, M Kay, GI Saunders, MM Suner, T Hunt, IH Barnes, C Amid, DR Carvalho-Silva, AH Bignell, C Snow, B Yngvadottir, S Bumpstead, DN Cooper, Y Xue, IG Romero, 1000 Genomes Project Consortium, J Wang, Y Li, RA Gibbs, SA McCarroll, ET Dermitzakis, JK Pritchard, JC Barrett, J Harrow, ME Hurles, MB Gerstein, C Tyler-Smith (2012). Science 335: 823-8.

Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.
G Li, X Ruan, RK Auerbach, KS Sandhu, M Zheng, P Wang, HM Poh, Y Goh, J Lim, J Zhang, HS Sim, SQ Peh, FH Mulawadi, CT Ong, YL Orlov, S Hong, Z Zhang, S Landt, D Raha, G Euskirchen, CL Wei, W Ge, H Wang, C Davis, KI Fisher-Aylor, A Mortazavi, M Gerstein, T Gingeras, B Wold, Y Sun, MJ Fullwood, E Cheung, E Liu, WK Sung, M Snyder, Y Ruan (2012). Cell 148: 84-98.

Novel insights through the integration of structural and functional genomics data with protein networks.
D Clarke, N Bhardwaj, MB Gerstein (2012). J Struct Biol 179: 320-6.

IQSeq: integrated isoform quantification analysis based on next-generation sequencing.
J Du, J Leng, L Habegger, A Sboner, D McDermott, M Gerstein (2012). PLoS One 7: e29175.

-- 2011 (40) --

Performance comparison of whole-genome sequencing platforms.
HY Lam, MJ Clark, R Chen, R Chen, G Natsoulis, M O'Huallachain, FE Dewey, L Habegger, EA Ashley, MB Gerstein, AJ Butte, HP Ji, M Snyder (2011). Nat Biotechnol 30: 78-82.

Systematic control of protein interactions for systems biology.
N Bhardwaj, D Clarke, M Gerstein (2011). Proc Natl Acad Sci U S A 108: 20279-80.

Genomics and Privacy: Implications of the New Reality of Closed Data for the Field
D Greenbaum, A Sboner, XJ Mu, M Gerstein (2011). PLoS Comput Biol 7: e1002278.

Closure of the NCBI SRA and implications for the long-term future of genomics data storage.
D Lipman, P Flicek, S Salzberg, M Gerstein, R Knight (2011). Genome Biol 12: 402.

Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms.
RR Haraksingh, A Abyzov, M Gerstein, AE Urban, M Snyder (2011). PLoS One 6: e27859.

Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data.
C Cheng, KK Yan, W Hwang, J Qian, N Bhardwaj, J Rozowsky, ZJ Lu, W Niu, P Alves, M Kato, M Snyder, M Gerstein (2011). PLoS Comput Biol 7: e1002190.

Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors.
C Cheng, C Shou, KY Yip, MB Gerstein (2011). Genome Biol 12: R111.

The role of cloud computing in managing the deluge of potentially private genetic data.
D Greenbaum, M Gerstein (2011). Am J Bioeth 11: 39-41.

TIP: a probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles.
C Cheng, R Min, M Gerstein (2011). Bioinformatics 27: 3221-7.

Predicting protein ligand binding motions with the conformation explorer.
SC Flores, MB Gerstein (2011). BMC Bioinformatics 12: 417.

Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps.
KY Yip, L Utz, S Sitwell, X Hu, SS Sidhu, BE Turk, M Gerstein, PM Kim (2011). BMC Biol 9: 53.

Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells.
C Cheng, M Gerstein (2011). Nucleic Acids Res 40: 553-68.

Identification of a disease-defining gene fusion in epithelioid hemangioendothelioma.
MR Tanas, A Sboner, AM Oliveira, MR Erickson-Johnson, J Hespelt, PJ Hanwright, J Flanagan, Y Luo, K Fenwick, R Natrajan, C Mitsopoulos, M Zvelebil, BL Hoch, SW Weiss, M Debiec-Rychter, R Sciot, RB West, AJ Lazar, A Ashworth, JS Reis-Filho, CJ Lord, MB Gerstein, MA Rubin, BP Rubin (2011). Sci Transl Med 3: 98ra82.

Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions.
N Bhardwaj, A Abyzov, D Clarke, C Shou, MB Gerstein (2011). Protein Sci 20: 1745-54.

The real cost of sequencing: higher than you think!
A Sboner, XJ Mu, D Greenbaum, RK Auerbach, MB Gerstein (2011). Genome Biol 12: 125.

AlleleSeq: analysis of allele-specific expression and binding in a network framework.
J Rozowsky, A Abyzov, J Wang, P Alves, D Raha, A Harmanci, J Leng, R Bjornson, Y Kong, N Kitabayashi, N Bhardwaj, M Rubin, M Snyder, M Gerstein (2011). Mol Syst Biol 7: 522.

Identification of genomic indels and structural variations using split reads.
ZD Zhang, J Du, H Lam, A Abyzov, AE Urban, M Snyder, M Gerstein (2011). BMC Genomics 12: 375.

The reality of pervasive transcription.
MB Clark, PP Amaral, FJ Schlesinger, ME Dinger, RJ Taft, JL Rinn, CP Ponting, PF Stadler, KV Morris, A Morillon, JS Rozowsky, MB Gerstein, C Wahlestedt, Y Hayashizaki, P Carninci, TR Gingeras, JS Mattick (2011). PLoS Biol 9: e1000625; discussion e1001102.

The spread of scientific information: insights from the web usage statistics in PLoS article-level metrics.
KK Yan, M Gerstein (2011). PLoS One 6: e19917.

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project.
XJ Mu, ZJ Lu, Y Kong, HY Lam, MB Gerstein (2011). Nucleic Acids Res 39: 7058-76.

Social considerations in research: consider them but don't use them.
D Greenbaum, M Gerstein (2011). Am J Bioeth 11: 31-2.

A user's guide to the encyclopedia of DNA elements (ENCODE).
ENCODE Project Consortium (2011). PLoS Biol 9: e1001046.

Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes.
J Fasolo, A Sboner, MG Sun, H Yu, R Chen, D Sharon, PM Kim, M Gerstein, M Snyder (2011). Genes Dev 25: 767-78.

The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics.
TA Gianoulis, A Agarwal, M Snyder, MB Gerstein (2011). Genome Biol 12: R32.

A cis-regulatory map of the Drosophila genome.
N Negre, CD Brown, L Ma, CA Bristow, SW Miller, U Wagner, P Kheradpour, ML Eaton, P Loriaux, R Sealfon, Z Li, H Ishii, RF Spokony, J Chen, L Hwang, C Cheng, RP Auburn, MB Davis, M Domanus, PK Shah, CA Morrison, J Zieba, S Suchy, L Senderowicz, A Victorsen, NA Bild, AJ Grundstad, D Hanley, DM MacAlpine, M Mannervik, K Venken, H Bellen, R White, M Gerstein, S Russell, RL Grossman, B Ren, JW Posakony, M Kellis, KP White (2011). Nature 471: 527-31.

Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches.
GM Euskirchen, RK Auerbach, E Davidov, TA Gianoulis, G Zhong, J Rozowsky, N Bhardwaj, MB Gerstein, M Snyder (2011). PLoS Genet 7: e1002008.

ACT: aggregation and correlation toolbox for analyses of genome tracks.
J Jee, J Rozowsky, KY Yip, L Lochovsky, R Bjornson, G Zhong, Z Zhang, Y Fu, J Wang, Z Weng, M Gerstein (2011). Bioinformatics 27: 1152-4.

Tiling array data analysis: a multiscale approach using wavelets.
A Karpikov, J Rozowsky, M Gerstein (2011). BMC Bioinformatics 12: 57.

CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
A Abyzov, AE Urban, M Snyder, M Gerstein (2011). Genome Res 21: 974-84.

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets.
C Cheng, KK Yan, KY Yip, J Rozowsky, R Alexander, C Shou, M Gerstein (2011). Genome Biol 12: R15.

The genomic complexity of primary human prostate cancer.
MF Berger, MS Lawrence, F Demichelis, Y Drier, K Cibulskis, AY Sivachenko, A Sboner, R Esgueva, D Pflueger, C Sougnez, R Onofrio, SL Carter, K Park, L Habegger, L Ambrogio, T Fennell, M Parkin, G Saksena, D Voet, AH Ramos, TJ Pugh, J Wilkinson, S Fisher, W Winckler, S Mahan, K Ardlie, J Baldwin, JW Simons, N Kitabayashi, TY MacDonald, PW Kantoff, L Chin, SB Gabriel, MB Gerstein, TR Golub, M Meyerson, A Tewari, ES Lander, G Getz, MA Rubin, LA Garraway (2011). Nature 470: 214-20.

Mapping copy number variation by population-scale genome sequencing.
RE Mills, K Walter, C Stewart, RE Handsaker, K Chen, C Alkan, A Abyzov, SC Yoon, K Ye, RK Cheetham, A Chinwalla, DF Conrad, Y Fu, F Grubert, I Hajirasouliha, F Hormozdiari, LM Iakoucheva, Z Iqbal, S Kang, JM Kidd, MK Konkel, J Korn, E Khurana, D Kural, HY Lam, J Leng, R Li, Y Li, CY Lin, R Luo, XJ Mu, J Nemesh, HE Peckham, T Rausch, A Scally, X Shi, MP Stromberg, AM Stutz, AE Urban, JA Walker, J Wu, Y Zhang, ZD Zhang, MA Batzer, L Ding, GT Marth, G McVean, J Sebat, M Snyder, J Wang, K Ye, EE Eichler, MB Gerstein, ME Hurles, C Lee, SA McCarroll, JO Korbel, 1000 Genomes Project (2011). Nature 470: 59-65.

Measuring the evolutionary rewiring of biological networks.
C Shou, N Bhardwaj, HY Lam, KK Yan, PM Kim, M Snyder, MB Gerstein (2011). PLoS Comput Biol 7: e1001050.

AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision.
A Abyzov, M Gerstein (2011). Bioinformatics 27: 595-603.

Gene inactivation and its implications for annotation in the era of personal genomics.
S Balasubramanian, L Habegger, A Frankish, DG MacArthur, R Harte, C Tyler-Smith, J Harrow, M Gerstein (2011). Genes Dev 25: 1-10.

Annual Research Review: The promise of stem cell research for neuropsychiatric disorders.
FM Vaccarino, AE Urban, HE Stevens, A Szekely, A Abyzov, EL Grigorenko, M Gerstein, S Weissman (2011). J Child Psychol Psychiatry 52: 504-16.

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.
ZJ Lu, KY Yip, G Wang, C Shou, LW Hillier, E Khurana, A Agarwal, R Auerbach, J Rozowsky, C Cheng, M Kato, DM Miller, F Slack, M Snyder, RH Waterston, V Reinke, MB Gerstein (2011). Genome Res 21: 276-85.

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans.
W Niu, ZJ Lu, M Zhong, M Sarov, JI Murray, CM Brdlik, J Janette, C Chen, P Alves, E Preston, C Slightham, L Jiang, AA Hyman, SK Kim, RH Waterston, M Gerstein, M Snyder, V Reinke (2011). Genome Res 21: 245-54.

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.
L Habegger, A Sboner, TA Gianoulis, J Rozowsky, A Agarwal, M Snyder, M Gerstein (2011). Bioinformatics 27: 281-3.

Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing.
D Pflueger, S Terry, A Sboner, L Habegger, R Esgueva, PC Lin, MA Svensson, N Kitabayashi, BJ Moss, TY MacDonald, X Cao, T Barrette, AK Tewari, MS Chee, AM Chinnaiyan, DS Rickman, F Demichelis, MB Gerstein, MA Rubin (2011). Genome Res 21: 56-67.

-- 2010 (32) --

Reproducible Research: Addressing the need for data and code sharing in computational science
Yale Law School Roundtable on Data and Code Sharing (2010). Computing in Science & Engineering 12(5): 8-13 (Sept/Oct).

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.
MB Gerstein, ZJ Lu, EL Van Nostrand, C Cheng, BI Arshinoff, T Liu, KY Yip, R Robilotto, A Rechtsteiner, K Ikegami, P Alves, A Chateigner, M Perry, M Morris, RK Auerbach, X Feng, J Leng, A Vielle, W Niu, K Rhrissorrakrai, A Agarwal, RP Alexander, G Barber, CM Brdlik, J Brennan, JJ Brouillet, A Carr, MS Cheung, H Clawson, S Contrino, LO Dannenberg, AF Dernburg, A Desai, L Dick, AC Dose, J Du, T Egelhofer, S Ercan, G Euskirchen, B Ewing, EA Feingold, R Gassmann, PJ Good, P Green, F Gullier, M Gutwein, MS Guyer, L Habegger, T Han, JG Henikoff, SR Henz, A Hinrichs, H Holster, T Hyman, AL Iniguez, J Janette, M Jensen, M Kato, WJ Kent, E Kephart, V Khivansara, E Khurana, JK Kim, P Kolasinska-Zwierz, EC Lai, I Latorre, A Leahey, S Lewis, P Lloyd, L Lochovsky, RF Lowdon, Y Lubling, R Lyne, M MacCoss, SD Mackowiak, M Mangone, S McKay, D Mecenas, G Merrihew, DM Miller, A Muroyama, JI Murray, SL Ooi, H Pham, T Phippen, EA Preston, N Rajewsky, G Ratsch, H Rosenbaum, J Rozowsky, K Rutherford, P Ruzanov, M Sarov, R Sasidharan, A Sboner, P Scheid, E Segal, H Shin, C Shou, FJ Slack, C Slightam, R Smith, WC Spencer, EO Stinson, S Taing, T Takasaki, D Vafeados, K Voronina, G Wang, NL Washington, CM Whittle, B Wu, KK Yan, G Zeller, Z Zha, M Zhong, X Zhou, modENCODE Consortium, J Ahringer, S Strome, KC Gunsalus, G Micklem, XS Liu, V Reinke, SK Kim, LW Hillier, S Henikoff, F Piano, M Snyder, L Stein, JD Lieb, RH Waterston (2010). Science 330: 1775-87.

Rewiring of transcriptional regulatory networks: hierarchy, rather than connectivity, better reflects the importance of regulators.
N Bhardwaj, PM Kim, MB Gerstein (2010). Sci Signal 3: ra79.

Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses.
X Li, TA Gianoulis, KY Yip, M Gerstein, M Snyder (2010). Cell 143: 639-50.

Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model.
ZD Zhang, MB Gerstein (2010). BMC Bioinformatics 11: 539.

A map of human genome variation from population-scale sequencing
1000 Genomes Project Consortium, GR Abecasis, D Altshuler, A Auton, LD Brooks, RM Durbin, RA Gibbs, ME Hurles, GA McVean (2010). Nature 467: 1061-73.

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data.
A Sboner, L Habegger, D Pflueger, S Terry, DZ Chen, JS Rozowsky, AK Tewari, N Kitabayashi, BJ Moss, MS Chee, F Demichelis, MA Rubin, MB Gerstein (2010). Genome Biol 11: R104.

Structured digital tables on the Semantic Web: toward a structured digital literature.
KH Cheung, M Samwald, RK Auerbach, MB Gerstein (2010). Mol Syst Biol 6: 403.

Annotating non-coding regions of the genome.
RP Alexander, G Fang, J Rozowsky, M Snyder, MB Gerstein (2010). Nat Rev Genet 11: 559-71.

Segmental duplications in the human genome reveal details of pseudogene formation.
E Khurana, HY Lam, C Cheng, N Carriero, P Cayting, MB Gerstein (2010). Nucleic Acids Res 38: 6997-7007.

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays.
A Agarwal, D Koppstein, J Rozowsky, A Sboner, L Habegger, LW Hillier, R Sasidharan, V Reinke, RH Waterston, M Gerstein (2010). BMC Genomics 11: 383.

Using semantic web rules to reason on an ontology of pseudogenes.
ME Holford, E Khurana, KH Cheung, M Gerstein (2010). Bioinformatics 26: i71-8.

Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets.
N Bhardwaj, MB Carson, A Abyzov, KK Yan, H Lu, MB Gerstein (2010). PLoS Comput Biol 6: e1000755.

3V: cavity, channel and cleft volume calculator and extractor.
NR Voss, M Gerstein (2010). Nucleic Acids Res 38: W555-62.

MOTIPS: automated motif analysis for predicting targets of modular protein domains.
HY Lam, PM Kim, J Mok, R Tonikian, SS Sidhu, BE Turk, M Snyder, MB Gerstein (2010). BMC Bioinformatics 11: 243.

Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks.
KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl Acad Sci U S A 107: 9186-91.

Analysis of membrane proteins in metagenomics: networks of correlated environmental features and protein families.
PV Patel, TA Gianoulis, RD Bjornson, KY Yip, DM Engelman, MB Gerstein (2010). Genome Res 20: 960-71.

Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis.
Y Lee, X Yang, Y Huang, H Fan, Q Zhang, Y Wu, J Li, R Hasina, C Cheng, MW Lingen, MB Gerstein, RR Weichselbaum, HR Xing, YA Lussier (2010). PLoS Comput Biol 6: e1000730.

Getting started in gene orthology and functional analysis.
G Fang, N Bhardwaj, R Robilotto, MB Gerstein (2010). PLoS Comput Biol 6: e1000703.

Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels.
N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107: 6841-6.

Variation in transcription factor binding among humans.
M Kasowski, F Grubert, C Heffelfinger, M Hariharan, A Asabere, SM Waszak, L Habegger, J Rozowsky, M Shi, AE Urban, MY Hong, KJ Karczewski, W Huber, SM Weissman, MB Gerstein, JO Korbel, M Snyder (2010). Science 328: 232-5.

Molecular sampling of prostate cancer: a dilemma for predicting disease progression.
A Sboner, F Demichelis, S Calza, Y Pawitan, SR Setlur, Y Hoshida, S Perner, HO Adami, K Fall, LA Mucci, PW Kantoff, M Stampfer, SO Andersson, E Varenhorst, JE Johansson, MB Gerstein, TR Golub, MA Rubin, O Andren (2010). BMC Med Genomics 3: 8.

Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates.
ZD Zhang, A Frankish, T Hunt, J Harrow, M Gerstein (2010). Genome Biol 11: R26.

Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique.
N Bhardwaj, M Gerstein, H Lu (2010). BMC Bioinformatics 11 Suppl 1: S6.

Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing.
JQ Wu, L Habegger, P Noisa, A Szekely, C Qiu, S Hutchison, D Raha, M Egholm, H Lin, S Weissman, W Cui, M Gerstein, M Snyder (2010). Proc Natl Acad Sci U S A 107: 5254-9.

Personal genome sequencing: current approaches and challenges.
M Snyder, J Du, M Gerstein (2010). Genes Dev 24: 423-31.

Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response.
M Zhong, W Niu, ZJ Lu, M Sarov, JI Murray, J Janette, D Raha, KL Sheaffer, HY Lam, E Preston, C Slightham, LW Hillier, T Brock, A Agarwal, R Auerbach, AA Hyman, M Gerstein, SE Mango, SK Kim, RH Waterston, V Reinke, M Snyder (2010). PLoS Genet 6: e1000848.

Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs.
J Mok, PM Kim, HY Lam, S Piccirillo, X Zhou, GR Jeschke, DL Sheridan, SA Parker, V Desai, M Jwa, E Cameroni, H Niu, M Good, A Remenyi, JL Ma, YJ Sheu, HE Sassi, R Sopko, CS Chan, C De Virgilio, NM Hollingsworth, WA Lim, DF Stern, B Stillman, BJ Andrews, MB Gerstein, M Snyder, BE Turk (2010). Sci Signal 3: ra12.

Close association of RNA polymerase II and many transcription factors with Pol III genes.
D Raha, Z Wang, Z Moqtaderi, L Wu, G Zhong, M Gerstein, K Struhl, M Snyder (2010). Proc Natl Acad Sci U S A 107: 3639-44.

Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data.
KY Yip, RP Alexander, KK Yan, M Gerstein (2010). PLoS One 5: e8121.

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.
HY Lam, XJ Mu, AM Stutz, A Tanzer, PD Cayting, M Snyder, PM Kim, JO Korbel, MB Gerstein (2010). Nat Biotechnol 28: 47-55.

RigidFinder: a fast and sensitive method to detect rigid blocks in large macromolecular complexes.
A Abyzov, R Bjornson, M Felipe, M Gerstein (2010). Proteins 78: 309-24.

-- 2009 (39) --

Science and the Law: Grappling with the Gulf
D Greenbaum, MB Gerstein (2009). Science 323: 210.

EBNA1 regulates cellular gene expression by binding cellular promoters.
A Canaan, I Haviv, AE Urban, VP Schulz, S Hartman, Z Zhang, D Palejev, AB Deisseroth, J Lacy, M Snyder, M Gerstein, SM Weissman (2009). Proc Natl Acad Sci U S A 106: 22421-6.

Social networking and personal genomics: suggestions for optimizing the interaction.
D Greenbaum, M Gerstein (2009). Am J Bioeth 9: 15-9.

Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins.
R Tonikian, X Xin, CP Toret, D Gfeller, C Landgraf, S Panni, S Paoluzi, L Castagnoli, B Currell, S Seshagiri, H Yu, B Winsor, M Vidal, MB Gerstein, GD Bader, R Volkmer, G Cesareni, DG Drubin, PM Kim, SS Sidhu, C Boone (2009). PLoS Biol 7: e1000218.

Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity.
YJ Liu, D Zheng, S Balasubramanian, N Carriero, E Khurana, R Robilotto, MB Gerstein (2009). BMC Genomics 10: 480.

Robust-linear-model normalization to reduce technical variability in functional protein microarrays.
A Sboner, A Karpikov, G Chen, M Smith, D Mattoon, M Dawn, L Freeman-Cook, B Schweitzer, MB Gerstein (2009). J Proteome Res 8: 5451-64.

The relationship between the evolution of microRNA targets and the length of their UTRs.
C Cheng, N Bhardwaj, M Gerstein (2009). BMC Genomics 10: 431.

Computational analysis of membrane proteins: the largest class of drug targets.
Y Arinaminpathy, E Khurana, DM Engelman, MB Gerstein (2009). Drug Discov Today 14: 1130-5.

mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer.
C Cheng, X Fu, P Alves, M Gerstein (2009). Genome Biol 10: R90.

Mapping accessible chromatin regions using Sono-Seq.
RK Auerbach, G Euskirchen, J Rozowsky, N Lamarre-Vincent, Z Moqtaderi, P Lefrancois, K Struhl, M Gerstein, M Snyder (2009). Proc Natl Acad Sci U S A 106: 14926-31.

Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels.
KY Yip, PM Kim, D McDermott, M Gerstein (2009). BMC Bioinformatics 10: 241.

Getting started in text mining: part two.
A Rzhetsky, M Seringhaus, MB Gerstein (2009). PLoS Comput Biol 5: e1000411.

N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer.
D Pflueger, DS Rickman, A Sboner, S Perner, CJ LaFargue, MA Svensson, BJ Moss, N Kitabayashi, Y Pan, A de la Taille, R Kuefer, AK Tewari, F Demichelis, MS Chee, MB Gerstein, MA Rubin (2009). Neoplasia 11: 804-11.

Small RNAs originated from pseudogenes: cis- or trans-acting?
X Guo, Z Zhang, MB Gerstein, D Zheng (2009). PLoS Comput Biol 5: e1000449.

Understanding modularity in molecular networks requires dynamics.
RP Alexander, PM Kim, T Emonet, MB Gerstein (2009). Sci Signal 2: pe44.

An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping.
R Sasidharan, A Agarwal, J Rozowsky, M Gerstein (2009). BMC Res Notes 2: 150.

Artificial transmembrane oncoproteins smaller than the bovine papillomavirus E5 protein redefine sequence requirements for activation of the platelet-derived growth factor beta receptor.
K Talbert-Slagle, S Marlatt, FN Barrera, E Khurana, J Oates, M Gerstein, DM Engelman, AM Dixon, D Dimaio (2009). J Virol 83: 9773-85.

The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies.
JO Korbel, T Tirosh-Wagner, AE Urban, XN Chen, M Kasowski, L Dai, F Grubert, C Erdman, MC Gao, K Lange, EM Sobel, GM Barlow, AS Aylsworth, NJ Carpenter, RD Clark, MY Cohen, E Doran, T Falik-Zaccai, SO Lewin, IT Lott, BC McGillivray, JB Moeschler, MJ Pettenati, SM Pueschel, KW Rao, LG Shaffer, M Shohat, AJ Van Riper, D Warburton, S Weissman, MB Gerstein, M Snyder, JR Korenberg (2009). Proc Natl Acad Sci U S A 106: 12031-6.

Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.
J Du, RD Bjornson, ZD Zhang, Y Kong, M Snyder, MB Gerstein (2009). PLoS Comput Biol 5: e1000432.

Unlocking the secrets of the genome.
SE Celniker, LA Dillon, MB Gerstein, KC Gunsalus, S Henikoff, GH Karpen, M Kellis, EC Lai, JD Lieb, DM MacAlpine, G Micklem, F Piano, M Snyder, L Stein, KP White, RH Waterston, modENCODE Consortium (2009). Nature 459: 927-30.

Integrated assessment of genomic correlates of protein evolutionary rate.
Y Xia, EA Franzosa, MB Gerstein (2009). PLoS Comput Biol 5: e1000413.

Dynamic and complex transcription factor binding during an inducible response in yeast.
L Ni, C Bruce, C Hart, J Leigh-Bell, D Gelperin, L Umansky, MB Gerstein, M Snyder (2009). Genes Dev 23: 1351-63.

Relating protein conformational changes to packing efficiency and disorder.
N Bhardwaj, M Gerstein (2009). Protein Sci 18: 1230-40.

Personal phenotypes to go with personal genomes.
M Snyder, S Weissman, M Gerstein (2009). Mol Syst Biol 5: 273.

Systematic identification of transcription factors associated with patient survival in cancers.
C Cheng, LM Li, P Alves, M Gerstein (2009). BMC Genomics 10: 225.

Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization.
Y Mishima, C Abreu-Goodger, AA Staton, C Stahlhut, C Shou, C Cheng, M Gerstein, AJ Enright, AJ Giraldez (2009). Genes Dev 23: 619-32.

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.
JO Korbel, A Abyzov, XJ Mu, N Carriero, P Cayting, Z Zhang, M Snyder, MB Gerstein (2009). Genome Biol 10: R23.

StoneHinge: hinge prediction by network analysis of individual protein structures.
KS Keating, SC Flores, MB Gerstein, LA Kuhn (2009). Protein Sci 18: 359-71.

Quantifying environmental adaptation of metabolic pathways in metagenomics.
TA Gianoulis, J Raes, PV Patel, R Bjornson, JO Korbel, I Letunic, T Yamada, A Paccanaro, LJ Jensen, M Snyder, P Bork, MB Gerstein (2009). Proc Natl Acad Sci U S A 106: 1374-9.

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.
P Lefrancois, GM Euskirchen, RK Auerbach, J Rozowsky, T Gibson, CM Yellman, M Gerstein, M Snyder (2009). BMC Genomics 10: 37.

Distinct genomic aberrations associated with ERG rearranged prostate cancer.
F Demichelis, SR Setlur, R Beroukhim, S Perner, JO Korbel, CJ Lafargue, D Pflueger, C Pina, MD Hofer, A Sboner, MA Svensson, DS Rickman, A Urban, M Snyder, M Meyerson, C Lee, MB Gerstein, R Kuefer, MA Rubin (2009). Genes Chromosomes Cancer 48: 366-80.

A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster.
X Zhang, Z Lian, C Padden, MB Gerstein, J Rozowsky, M Snyder, TR Gingeras, P Kapranov, SM Weissman, PE Newburger (2009). Blood 113: 2526-34.

Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes.
S Balasubramanian, D Zheng, YJ Liu, G Fang, A Frankish, N Carriero, R Robilotto, P Cayting, M Gerstein (2009). Genome Biol 10: R2.

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.
J Rozowsky, G Euskirchen, RK Auerbach, ZD Zhang, T Gibson, R Bjornson, N Carriero, M Snyder, MB Gerstein (2009). Nat Biotechnol 27: 66-75.

MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays.
SC Popescu, GV Popescu, S Bachan, Z Zhang, M Gerstein, M Snyder, SP Dinesh-Kumar (2009). Genes Dev 23: 80-92.

MSB: a mean-shift-based approach for the analysis of structural variation in the genome.
LY Wang, A Abyzov, JO Korbel, M Snyder, M Gerstein (2009). Genome Res 19: 106-17.

RNA-Seq: a revolutionary tool for transcriptomics.
Z Wang, M Gerstein, M Snyder (2009). Nat Rev Genet 10: 57-63.

Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions.
KY Yip, M Gerstein (2009). Bioinformatics 25: 243-50.

Pseudofam: the pseudogene families database.
HY Lam, E Khurana, G Fang, P Cayting, N Carriero, KH Cheung, MB Gerstein (2009). Nucleic Acids Res 37: D738-43.

-- 2008 (25) --

Genomics Confounds Gene Classification
M Seringhaus, M Gerstein (2008). American Scientist 96:466-473 (Nov-Dec)

Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays.
M Seringhaus, J Rozowsky, T Royce, U Nagalakshmi, J Jee, M Snyder, M Gerstein (2008). BMC Genomics 9: 635.

Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies.
AY Yam, Y Xia, HT Lin, A Burlingame, M Gerstein, J Frydman (2008). Nat Struct Mol Biol 15: 1255-62.

Genomic anonymity: have we already lost it?
D Greenbaum, J Du, M Gerstein (2008). Am J Bioeth 8: 71-4.

High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution.
Y Hasin, T Olender, M Khen, C Gonzaga-Jauregui, PM Kim, AE Urban, M Snyder, MB Gerstein, D Lancet, JO Korbel (2008). PLoS Genet 4: e1000249.

Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history.
PM Kim, HY Lam, AE Urban, JO Korbel, J Affourtit, F Grubert, X Chen, S Weissman, M Snyder, MB Gerstein (2008). Genome Res 18: 1865-74.

Modeling ChIP sequencing in silico with applications.
ZD Zhang, J Rozowsky, M Snyder, J Chang, M Gerstein (2008). PLoS Comput Biol 4: e1000158.

Transmembrane protein oxygen content and compartmentalization of cells.
R Sasidharan, A Smith, M Gerstein (2008). PLoS One 3: e2726.

Seeking a new biology through text mining.
A Rzhetsky, M Seringhaus, M Gerstein (2008). Cell 134: 9-13.

Genomics: protein fossils live on as RNA.
R Sasidharan, M Gerstein (2008). Nature 453: 729-31.

The current excitement about copy-number variation: how it relates to gene duplications and protein families.
JO Korbel, PM Kim, X Chen, AE Urban, S Weissman, M Snyder, MB Gerstein (2008). Curr Opin Struct Biol 18: 366-74.

Targeting the human cancer pathway protein interaction network by structural genomics.
YJ Huang, D Hang, LJ Lu, L Tong, MB Gerstein, GT Montelione (2008). Mol Cell Proteomics 7: 2048-60.

A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation.
Z Lian, A Karpikov, J Lian, MC Mahajan, S Hartman, M Gerstein, M Snyder, SM Weissman (2008). Genome Res 18: 1224-37.

Association of cytokeratin 7 and 19 expression with genomic stability and favorable prognosis in clear cell renal cell cancer.
KD Mertz, F Demichelis, A Sboner, MS Hirsch, P Dal Cin, K Struckmann, M Storz, S Scherrer, DM Schmid, RT Strebel, NM Probst-Hensch, M Gerstein, H Moch, MA Rubin (2008). Int J Cancer 123: 569-76.

The transcriptional landscape of the yeast genome defined by RNA sequencing.
U Nagalakshmi, Z Wang, K Waern, C Shou, D Raha, M Gerstein, M Snyder (2008). Science 320: 1344-9.

HingeMaster: normal mode hinge prediction approach and integration of complementary predictors.
SC Flores, KS Keating, J Painter, F Morcos, K Nguyen, EA Merritt, LA Kuhn, MB Gerstein (2008). Proteins 73: 299-319.

Rapid evolution by positive Darwinian selection in T-cell antigen CD4 in primates.
ZD Zhang, G Weinstock, M Gerstein (2008). J Mol Evol 66: 446-56.

Open access: taking full advantage of the content.
PE Bourne, JL Fink, M Gerstein (2008). PLoS Comput Biol 4: e1000037.

The role of disorder in interaction networks: a structural analysis.
PM Kim, A Sboner, Y Xia, M Gerstein (2008). Mol Syst Biol 4: 179.

Manually structured digital abstracts: a scaffold for automatic text mining.
M Seringhaus, M Gerstein (2008). FEBS Lett 582: 1170.

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
DS Johnson, W Li, DB Gordon, A Bhattacharjee, B Curry, J Ghosh, L Brizuela, JS Carroll, M Brown, P Flicek, CM Koch, I Dunham, M Bieda, X Xu, PJ Farnham, P Kapranov, DA Nix, TR Gingeras, X Zhang, H Holster, N Jiang, RD Green, JS Song, SA McCuine, E Anton, L Nguyen, ND Trinklein, Z Ye, K Ching, D Hawkins, B Ren, PC Scacheri, J Rozowsky, A Karpikov, G Euskirchen, S Weissman, M Gerstein, M Snyder, A Yang, Z Moqtaderi, H Hirsch, HP Shulha, Y Fu, Z Weng, K Struhl, RM Myers, JD Lieb, XS Liu (2008). Genome Res 18: 393-403.

Uncovering trends in gene naming.
MR Seringhaus, PD Cayting, MB Gerstein (2008). Genome Biol 9: 401.

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome.
JQ Wu, J Du, J Rozowsky, Z Zhang, AE Urban, G Euskirchen, S Weissman, M Gerstein, M Snyder (2008). Genome Biol 9: R3.

Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories.
ZD Zhang, P Cayting, G Weinstock, M Gerstein (2008). Mol Biol Evol 25: 131-43.

An integrated system for studying residue coevolution in proteins.
KY Yip, P Patel, PM Kim, DM Engelman, D McDermott, M Gerstein (2008). Bioinformatics 24: 290-2.

-- 2007 (45) --

Semantic Web Approach to Database Integration in the Life Sciences
KH Cheung, AK Smith, KYL Yip, CJO Baker, MB Gerstein (2007). in Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences (eds. C Baker and K Cheung, Springer, NY), pp. 11-30

Semantic Web Standards: Legal and Social Issues and Implications
D Greenbaum, M Gerstein (2007). in Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences (eds. C Baker and K Cheung, Springer, NY), pp. 413-433

Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context.
PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104: 20274-9.

Integrative microarray analysis of pathways dysregulated in metastatic prostate cancer.
SR Setlur, TE Royce, A Sboner, JM Mosquera, F Demichelis, MD Hofer, KD Mertz, M Gerstein, MA Rubin (2007). Cancer Res 67: 10296-303.

Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics.
A Smith, K Cheung, M Krauthammer, M Schultz, M Gerstein (2007). Bioinformatics 23: 3073-9.

Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches.
AJ McClellan, Y Xia, AM Deutschbauer, RW Davis, M Gerstein, J Frydman (2007). Cell 131: 121-35.

Paired-end mapping reveals extensive structural variation in the human genome.
JO Korbel, AE Urban, JP Affourtit, B Godwin, F Grubert, JF Simons, PM Kim, D Palejev, NJ Carriero, L Du, BE Taillon, Z Chen, A Tanzer, AC Saunders, J Chi, F Yang, NP Carter, ME Hurles, SM Weissman, TT Harkins, MB Gerstein, M Egholm, M Snyder (2007). Science 318: 420-6.

PARE: a tool for comparing protein abundance and mRNA expression data.
EZ Yu, AE Burba, M Gerstein (2007). BMC Bioinformatics 8: 309.

Divergence of transcription factor binding sites across related yeast species.
AR Borneman, TA Gianoulis, ZD Zhang, H Yu, J Rozowsky, MR Seringhaus, LY Wang, M Gerstein, M Snyder (2007). Science 317: 815-9.

The minimum information required for reporting a molecular interaction experiment (MIMIx).
S Orchard, L Salwinski, S Kerrien, L Montecchi-Palazzi, M Oesterheld, V Stumpflen, A Ceol, A Chatr-aryamontri, J Armstrong, P Woollard, JJ Salama, S Moore, J Wojcik, GD Bader, M Vidal, ME Cusick, M Gerstein, AC Gavin, G Superti-Furga, J Greenblatt, J Bader, P Uetz, M Tyers, P Legrain, S Fields, N Mulder, M Gilson, M Niepmann, L Burgoon, J De Las Rivas, C Prieto, VM Perreau, C Hogue, HW Mewes, R Apweiler, I Xenarios, D Eisenberg, G Cesareni, H Hermjakob (2007). Nat Biotechnol 25: 894-8.

Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification.
TE Royce, JS Rozowsky, MB Gerstein (2007). Nucleic Acids Res 35: e99.

Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.
AR Borneman, ZD Zhang, J Rozowsky, MR Seringhaus, M Gerstein, M Snyder (2007). Funct Integr Genomics 7: 335-45.

FlexOracle: predicting flexible hinges by identification of stable domains.
SC Flores, MB Gerstein (2007). BMC Bioinformatics 8: 215.

Comparing classical pathways and modern networks: towards the development of an edge ontology.
LJ Lu, A Sboner, YJ Huang, HX Lu, TA Gianoulis, KY Yip, PM Kim, GT Montelione, MB Gerstein (2007). Trends Biochem Sci 32: 320-31.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
ENCODE Project Consortium, E Birney, JA Stamatoyannopoulos, A Dutta, R Guigo, TR Gingeras, EH Margulies, Z Weng, M Snyder, ET Dermitzakis, RE Thurman, MS Kuehn, CM Taylor, S Neph, CM Koch, S Asthana, A Malhotra, I Adzhubei, JA Greenbaum, RM Andrews, P Flicek, PJ Boyle, H Cao, NP Carter, GK Clelland, S Davis, N Day, P Dhami, SC Dillon, MO Dorschner, H Fiegler, PG Giresi, J Goldy, M Hawrylycz, A Haydock, R Humbert, KD James, BE Johnson, EM Johnson, TT Frum, ER Rosenzweig, N Karnani, K Lee, GC Lefebvre, PA Navas, F Neri, SC Parker, PJ Sabo, R Sandstrom, A Shafer, D Vetrie, M Weaver, S Wilcox, M Yu, FS Collins, J Dekker, JD Lieb, TD Tullius, GE Crawford, S Sunyaev, WS Noble, I Dunham, F Denoeud, A Reymond, P Kapranov, J Rozowsky, D Zheng, R Castelo, A Frankish, J Harrow, S Ghosh, A Sandelin, IL Hofacker, R Baertsch, D Keefe, S Dike, J Cheng, HA Hirsch, EA Sekinger, J Lagarde, JF Abril, A Shahab, C Flamm, C Fried, J Hackermuller, J Hertel, M Lindemeyer, K Missal, A Tanzer, S Washietl, J Korbel, O Emanuelsson, JS Pedersen, N Holroyd, R Taylor, D Swarbreck, N Matthews, MC Dickson, DJ Thomas, MT Weirauch, J Gilbert, J Drenkow, I Bell, X Zhao, KG Srinivasan, WK Sung, HS Ooi, KP Chiu, S Foissac, T Alioto, M Brent, L Pachter, ML Tress, A Valencia, SW Choo, CY Choo, C Ucla, C Manzano, C Wyss, E Cheung, TG Clark, JB Brown, M Ganesh, S Patel, H Tammana, J Chrast, CN Henrichsen, C Kai, J Kawai, U Nagalakshmi, J Wu, Z Lian, J Lian, P Newburger, X Zhang, P Bickel, JS Mattick, P Carninci, Y Hayashizaki, S Weissman, T Hubbard, RM Myers, J Rogers, PF Stadler, TM Lowe, CL Wei, Y Ruan, K Struhl, M Gerstein, SE Antonarakis, Y Fu, ED Green, U Karaoz, A Siepel, J Taylor, LA Liefer, KA Wetterstrand, PJ Good, EA Feingold, MS Guyer, GM Cooper, G Asimenos, CN Dewey, M Hou, S Nikolaev, JI Montoya-Burgos, A Loytynoja, S Whelan, F Pardi, T Massingham, H Huang, NR Zhang, I Holmes, JC Mullikin, A Ureta-Vidal, B Paten, M Seringhaus, D Church, K Rosenbloom, WJ Kent, EA Stone, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, S Batzoglou, N Goldman, RC Hardison, D Haussler, W Miller, A Sidow, ND Trinklein, ZD Zhang, L Barrera, R Stuart, DC King, A Ameur, S Enroth, MC Bieda, J Kim, AA Bhinge, N Jiang, J Liu, F Yao, VB Vega, CW Lee, P Ng, A Shahab, A Yang, Z Moqtaderi, Z Zhu, X Xu, S Squazzo, MJ Oberley, D Inman, MA Singer, TA Richmond, KJ Munn, A Rada-Iglesias, O Wallerman, J Komorowski, JC Fowler, P Couttet, AW Bruce, OM Dovey, PD Ellis, CF Langford, DA Nix, G Euskirchen, S Hartman, AE Urban, P Kraus, S Van Calcar, N Heintzman, TH Kim, K Wang, C Qu, G Hon, R Luna, CK Glass, MG Rosenfeld, SF Aldred, SJ Cooper, A Halees, JM Lin, HP Shulha, X Zhang, M Xu, JN Haidar, Y Yu, Y Ruan, VR Iyer, RD Green, C Wadelius, PJ Farnham, B Ren, RA Harte, AS Hinrichs, H Trumbower, H Clawson, J Hillman-Jackson, AS Zweig, K Smith, A Thakkapallayil, G Barber, RM Kuhn, D Karolchik, L Armengol, CP Bird, PI de Bakker, AD Kern, N Lopez-Bigas, JD Martin, BE Stranger, A Woodroffe, E Davydov, A Dimas, E Eyras, IB Hallgrimsdottir, J Huppert, MC Zody, GR Abecasis, X Estivill, GG Bouffard, X Guan, NF Hansen, JR Idol, VV Maduro, B Maskeri, JC McDowell, M Park, PJ Thomas, AC Young, RW Blakesley, DM Muzny, E Sodergren, DA Wheeler, KC Worley, H Jiang, GM Weinstock, RA Gibbs, T Graves, R Fulton, ER Mardis, RK Wilson, M Clamp, J Cuff, S Gnerre, DB Jaffe, JL Chang, K Lindblad-Toh, ES Lander, M Koriabine, M Nefedov, K Osoegawa, Y Yoshinaga, B Zhu, PJ de Jong (2007). Nature 447: 799-816.

Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies.
GM Euskirchen, JS Rozowsky, CL Wei, WH Lee, ZD Zhang, S Hartman, O Emanuelsson, V Stolc, S Weissman, MB Gerstein, Y Ruan, M Snyder (2007). Genome Res 17: 898-909.

Structured RNAs in the ENCODE selected regions of the human genome.
S Washietl, JS Pedersen, JO Korbel, C Stocsits, AR Gruber, J Hackermuller, J Hertel, M Lindemeyer, K Reiche, A Tanzer, C Ucla, C Wyss, SE Antonarakis, F Denoeud, J Lagarde, J Drenkow, P Kapranov, TR Gingeras, R Guigo, M Snyder, MB Gerstein, A Reymond, IL Hofacker, PF Stadler (2007). Genome Res 17: 852-64.

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.
D Zheng, A Frankish, R Baertsch, P Kapranov, A Reymond, SW Choo, Y Lu, F Denoeud, SE Antonarakis, M Snyder, Y Ruan, CL Wei, TR Gingeras, R Guigo, J Harrow, MB Gerstein (2007). Genome Res 17: 839-51.

Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions.
ZD Zhang, A Paccanaro, Y Fu, S Weissman, Z Weng, J Chang, M Snyder, MB Gerstein (2007). Genome Res 17: 787-97.

The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.
JS Rozowsky, D Newburger, F Sayward, J Wu, G Jordan, JO Korbel, U Nagalakshmi, J Yang, D Zheng, R Guigo, TR Gingeras, S Weissman, P Miller, M Snyder, MB Gerstein (2007). Genome Res 17: 732-45.

Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome.
ND Trinklein, U Karaoz, J Wu, A Halees, S Force Aldred, PJ Collins, D Zheng, ZD Zhang, MB Gerstein, M Snyder, RM Myers, Z Weng (2007). Genome Res 17: 720-31.

What is a gene, post-ENCODE? History and updated definition.
MB Gerstein, C Bruce, JS Rozowsky, D Zheng, J Du, JO Korbel, O Emanuelsson, ZD Zhang, S Weissman, M Snyder (2007). Genome Res 17: 669-81.

An efficient pseudomedian filter for tiling microrrays.
TE Royce, NJ Carriero, MB Gerstein (2007). BMC Bioinformatics 8: 186.

Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome.
JO Korbel, AE Urban, F Grubert, J Du, TE Royce, P Starr, G Zhong, BS Emanuel, SM Weissman, M Snyder, MB Gerstein (2007). Proc Natl Acad Sci U S A 104: 10110-5.

Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications.
H Yu, R Jansen, G Stolovitzky, M Gerstein (2007). Bioinformatics 23: 2163-73.

Global survey of human T leukemic cells by integrating proteomics and transcriptomics profiling.
L Wu, SI Hwang, K Rezaul, LJ Lu, V Mayya, M Gerstein, JK Eng, DH Lundgren, DK Han (2007). Mol Cell Proteomics 6: 1343-53.

Hinge Atlas: relating protein sequence to sites of structural flexibility.
SC Flores, LJ Lu, J Yang, N Carriero, MB Gerstein (2007). BMC Bioinformatics 8: 167.

Tilescope: online analysis pipeline for high-density tiling microarray data.
ZD Zhang, J Rozowsky, HY Lam, J Du, M Snyder, M Gerstein (2007). Genome Biol 8: R81.

Structured digital abstract makes text mining easy.
M Gerstein, M Seringhaus, S Fields (2007). Nature 447: 142.

LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics.
AK Smith, KH Cheung, KY Yip, M Schultz, MK Gerstein (2007). BMC Bioinformatics 8 Suppl 3: S5.

Getting connected: analysis and principles of biological networks.
X Zhu, M Gerstein, M Snyder (2007). Genes Dev 21: 1010-24.

RNAi development.
M Gerstein, SM Douglas (2007). PLoS Comput Biol 3: e80.

The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics.
H Yu, PM Kim, E Sprecher, V Trifonov, M Gerstein (2007). PLoS Comput Biol 3: e59.

Assessing the need for sequence-based normalization in tiling microarray experiments.
TE Royce, JS Rozowsky, MB Gerstein (2007). Bioinformatics 23: 988-97.

The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?
D Zheng, MB Gerstein (2007). Trends Genet 23: 219-24.

Global identification and characterization of transcriptionally active regions in the rice genome.
L Li, X Wang, R Sasidharan, V Stolc, W Deng, H He, J Korbel, X Chen, W Tongprasit, P Ronald, R Chen, M Gerstein, XW Deng (2007). PLoS One 2: e294.

Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays.
SC Popescu, GV Popescu, S Bachan, Z Zhang, M Seay, M Gerstein, M Snyder, SP Dinesh-Kumar (2007). Proc Natl Acad Sci U S A 104: 4730-5.

New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis.
MG Smith, TA Gianoulis, S Pukatzki, JJ Mekalanos, LN Ornston, M Gerstein, M Snyder (2007). Genes Dev 21: 601-14.

Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.
Z Zhang, AW Pang, M Gerstein (2007). BMC Evol Biol 7 Suppl 1: S14.

Publishing perishing? Towards tomorrow's information architecture.
MR Seringhaus, MB Gerstein (2007). BMC Bioinformatics 8: 17.

Chemistry Nobel rich in structure.
M Seringhaus, M Gerstein (2007). Science 315: 40-1.

Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool.
H Yu, K Nguyen, T Royce, J Qian, K Nelson, M Snyder, M Gerstein (2007). Nucleic Acids Res 35: e8.

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.
O Emanuelsson, U Nagalakshmi, D Zheng, JS Rozowsky, AE Urban, J Du, Z Lian, V Stolc, S Weissman, M Snyder, MB Gerstein (2007). Genome Res 17: 886-97. a comprehensive database and comparison platform for pseudogene annotation.
JE Karro, Y Yan, D Zheng, Z Zhang, N Carriero, P Cayting, P Harrrison, M Gerstein (2007). Nucleic Acids Res 35: D55-60.

An interdepartmental Ph.D. program in computational biology and bioinformatics: the Yale perspective.
M Gerstein, D Greenbaum, K Cheung, PL Miller (2007). J Biomed Inform 40: 73-9.

-- 2006 (31) --

The Death of the Scientific Paper
Seringhaus M, Gerstein M (2006). The Scientist. 20(9): 25

Analytical Evolutionary Model for Protein Fold Occurrence in Genomes, Accounting for the Effects of Gene Duplication, Deletion, Acquisition and Selective Pressure
M Kamal, N Luscombe, J Qian, M Gerstein (2006). in Power Laws, Scale-Free Networks and Genome Biology (edited by EV Koonin, YI Wolf, GP Karev; Springer, New York), pages 165-193

Novel transcribed regions in the human genome.
J Rozowsky, J Wu, Z Lian, U Nagalakshmi, JO Korbel, P Kapranov, D Zheng, S Dyke, P Newburger, P Miller, TR Gingeras, S Weissman, M Gerstein, M Snyder (2006). Cold Spring Harb Symp Quant Biol 71: 111-6.

Relating three-dimensional structures to protein networks provides evolutionary insights.
PM Kim, LJ Lu, Y Xia, MB Gerstein (2006). Science 314: 1938-41.

Data mining on the web.
A Smith, M Gerstein (2006). Science 314: 1682; author reply 1682.

An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits.
Y Liu, J Li, L Sam, CS Goh, M Gerstein, YA Lussier (2006). PLoS Comput Biol 2: e159.

ProCAT: a data analysis approach for protein microarrays.
X Zhu, M Gerstein, M Snyder (2006). Genome Biol 7: R110.

BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments.
LY Wang, M Snyder, M Gerstein (2006). Genome Biol 7: R102.

Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins.
AE Burba, U Lehnert, EZ Yu, M Gerstein (2006). Bioinformatics 22: 2735-8.

A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge.
J Du, JS Rozowsky, JO Korbel, ZD Zhang, TE Royce, MH Schultz, M Snyder, M Gerstein (2006). Bioinformatics 22: 3016-24.

Integration of curated databases to identify genotype-phenotype associations.
CS Goh, TA Gianoulis, Y Liu, J Li, A Paccanaro, YA Lussier, M Gerstein (2006). BMC Genomics 7: 257.

The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks.
KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22: 2968-70.

Genomic analysis of the hierarchical structure of regulatory networks.
H Yu, M Gerstein (2006). Proc Natl Acad Sci U S A 103: 14724-31.

TOS9 regulates white-opaque switching in Candida albicans.
T Srikantha, AR Borneman, KJ Daniels, C Pujol, W Wu, MR Seringhaus, M Gerstein, S Yi, M Snyder, DR Soll (2006). Eukaryot Cell 5: 1674-87.

Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies.
TE Royce, JS Rozowsky, NM Luscombe, O Emanuelsson, H Yu, X Zhu, M Snyder, MB Gerstein (2006). Methods Enzymol 411: 282-311.

Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing.
R Pinard, A de Winter, GJ Sarkis, MB Gerstein, KR Tartaro, RN Plant, M Egholm, JM Rothberg, JH Leamon (2006). BMC Genomics 7: 216.

A computational approach for identifying pseudogenes in the ENCODE regions.
D Zheng, MB Gerstein (2006). Genome Biol 7 Suppl 1: S131-10.

Predicting essential genes in fungal genomes.
M Seringhaus, A Paccanaro, A Borneman, M Snyder, M Gerstein (2006). Genome Res 16: 1126-35.

The real life of pseudogenes.
M Gerstein, D Zheng (2006). Sci Am 295: 48-55.

Design principles of molecular networks revealed by global comparisons and composite motifs.
H Yu, Y Xia, V Trifonov, M Gerstein (2006). Genome Biol 7: R55.

The geometry of the ribosomal polypeptide exit tunnel.
NR Voss, M Gerstein, TA Steitz, PB Moore (2006). J Mol Biol 360: 893-906.

Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae.
M Seringhaus, A Kumar, J Hartigan, M Snyder, M Gerstein (2006). Nucleic Acids Res 34: e57.

Tools needed to navigate landscape of the genome.
M Gerstein (2006). Nature 440: 740.

PseudoPipe: an automated pseudogene identification pipeline.
Z Zhang, N Carriero, D Zheng, J Karro, PM Harrison, M Gerstein (2006). Bioinformatics 22: 1437-9.

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
NJ Krogan, G Cagney, H Yu, G Zhong, X Guo, A Ignatchenko, J Li, S Pu, N Datta, AP Tikuisis, T Punna, JM Peregrin-Alvarez, M Shales, X Zhang, M Davey, MD Robinson, A Paccanaro, JE Bray, A Sheung, B Beattie, DP Richards, V Canadien, A Lalev, F Mena, P Wong, A Starostine, MM Canete, J Vlasblom, S Wu, C Orsi, SR Collins, S Chandran, R Haw, JJ Rilstone, K Gandi, NJ Thompson, G Musso, P St Onge, S Ghanny, MH Lam, G Butland, AM Altaf-Ul, S Kanaya, A Shilatifard, E O'Shea, JS Weissman, CJ Ingles, TR Hughes, J Parkinson, M Gerstein, SJ Wodak, A Emili, JF Greenblatt (2006). Nature 440: 637-43.

High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays.
AE Urban, JO Korbel, R Selzer, T Richmond, A Hacker, GV Popescu, JF Cubells, R Green, BS Emanuel, MB Gerstein, SM Weissman, M Snyder (2006). Proc Natl Acad Sci U S A 103: 4534-9.

Predicting interactions in protein networks by completing defective cliques.
H Yu, A Paccanaro, V Trifonov, M Gerstein (2006). Bioinformatics 22: 823-9.

Target hub proteins serve as master regulators of development in yeast.
AR Borneman, JA Leigh-Bell, H Yu, P Bertone, M Gerstein, M Snyder (2006). Genes Dev 20: 435-48.

Integrated prediction of the helical membrane protein interactome in yeast.
Y Xia, LJ Lu, M Gerstein (2006). J Mol Biol 357: 339-49.

The Database of Macromolecular Motions: new features added at the decade mark.
S Flores, N Echols, D Milburn, B Hespenheide, K Keating, J Lu, S Wells, EZ Yu, M Thorpe, M Gerstein (2006). Nucleic Acids Res 34: D296-301.

Design optimization methods for genomic DNA tiling arrays.
P Bertone, V Trifonov, JS Rozowsky, F Schubert, O Emanuelsson, J Karro, MY Kao, M Snyder, M Gerstein (2006). Genome Res 16: 271-81.

-- 2005 (24) --

Inferring Protein-Protein Interactions Using Interaction Network Topologies
A Paccanaro, V Trifonov, H Yu, M Gerstein (2005). International Joint Conference on Neural Networks (IJCNN, Jul. 31-Aug. 4, Montreal, Canada), pages 161 - 166, vol. 1

Protein Interaction Prediction by Integrating Genomic Features and Protein Interaction Network Analysis
LJ Lu, Y Xia, H Yu, A Rives, H Lu, F Schubert, M Gerstein (2005). Data Analysis and Visualization in Genomics and Proteomics (Wiley, NY)

Biochemical and genetic analysis of the yeast proteome with a movable ORF collection.
DM Gelperin, MA White, ML Wilkinson, Y Kon, LA Kung, KJ Wise, N Lopez-Hoyo, L Jiang, S Piccirillo, H Yu, M Gerstein, ME Dumont, EM Phizicky, M Snyder, EJ Grayhack (2005). Genes Dev 19: 2816-26.

Global analysis of protein phosphorylation in yeast.
J Ptacek, G Devgan, G Michaud, H Zhu, X Zhu, J Fasolo, H Guo, G Jona, A Breitkreutz, R Sopko, RR McCartney, MC Schmidt, N Rachidi, SJ Lee, AS Mah, L Meng, MJ Stark, DF Stern, C De Virgilio, M Tyers, B Andrews, M Gerstein, B Schweitzer, PF Predki, M Snyder (2005). Nature 438: 679-84.

Global changes in STAT target selection and transcription regulation upon interferon treatments.
SE Hartman, P Bertone, AK Nath, TE Royce, M Gerstein, S Weissman, M Snyder (2005). Genes Dev 19: 2953-68.

A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.
V Stolc, L Li, X Wang, X Li, N Su, W Tongprasit, B Han, Y Xue, J Li, M Snyder, M Gerstein, J Wang, XW Deng (2005). Plant Mol Biol 59: 137-49.

Network security and data integrity in academia: an assessment and a proposal for large-scale archiving.
A Smith, D Greenbaum, SM Douglas, M Long, M Gerstein (2005). Genome Biol 6: 119.

PubNet: a flexible system for visualizing literature derived networks.
SM Douglas, GT Montelione, M Gerstein (2005). Genome Biol 6: R80.

Proton sensitivity of ASIC1 appeared with the rise of fishes by changes of residues in the region that follows TM1 in the ectodomain of the channel.
T Coric, D Zheng, M Gerstein, CM Canessa (2005). J Physiol 568: 725-35.

Assessing the limits of genomic data integration for predicting protein networks.
LJ Lu, Y Xia, A Paccanaro, H Yu, M Gerstein (2005). Genome Res 15: 945-53.

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.
TE Royce, JS Rozowsky, P Bertone, M Samanta, V Stolc, S Weissman, M Snyder, M Gerstein (2005). Trends Genet 21: 466-75.

YeastHub: a semantic web use case for integrating data in the life sciences domain.
KH Cheung, KY Yip, A Smith, R Deknikker, A Masiar, M Gerstein (2005). Bioinformatics 21 Suppl 1: i85-96.

Integrated pseudogene annotation for human chromosome 22: evidence for transcription.
D Zheng, Z Zhang, PM Harrison, J Karro, N Carriero, M Gerstein (2005). J Mol Biol 349: 27-45.

Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery.
P Bertone, M Gerstein, M Snyder (2005). Chromosome Res 13: 259-74.

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles.
Y Gilad, SA Rifkin, P Bertone, M Gerstein, KP White (2005). Genome Res 15: 674-80.

Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.
PM Harrison, D Zheng, Z Zhang, N Carriero, M Gerstein (2005). Nucleic Acids Res 33: 2374-83.

Use of thioredoxin as a reporter to identify a subset of Escherichia coli signal sequences that promote signal recognition particle-dependent translocation.
D Huber, D Boyd, Y Xia, MH Olma, M Gerstein, J Beckwith (2005). J Bacteriol 187: 2983-91.

Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium.
TB Acton, KC Gunsalus, R Xiao, LC Ma, J Aramini, MC Baran, YW Chiang, T Climent, B Cooper, NG Denissova, SM Douglas, JK Everett, CK Ho, D Macapagal, PK Rajan, R Shastry, LY Shih, GV Swapna, M Wilson, M Wu, M Gerstein, M Inouye, JF Hunt, GT Montelione (2005). Methods Enzymol 394: 210-43.

Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms.
S Balasubramanian, Y Xia, E Freinkman, M Gerstein (2005). Nucleic Acids Res 33: 1710-21.

The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans.
H Grosshans, T Johnson, KL Reinert, M Gerstein, FJ Slack (2005). Dev Cell 8: 321-30.

Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool.
V Alexandrov, U Lehnert, N Echols, D Milburn, D Engelman, M Gerstein (2005). Protein Sci 14: 633-43.

Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly.
NR Voss, M Gerstein (2005). J Mol Biol 346: 477-92.

Impediments to database interoperation: legal issues and security concerns.
D Greenbaum, A Smith, M Gerstein (2005). Nucleic Acids Res 33: D3-4.

A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies.
N Carriero, MV Osier, KH Cheung, PL Miller, M Gerstein, H Zhao, B Wu, S Rifkin, J Chang, H Zhang, K White, K Williams, M Schultz (2005). J Am Med Inform Assoc 12: 90-8.

-- 2004 (31) --

An XML-Based Approach to Integrating Heterogeneous Yeast Genome Data
KH Cheung, D Pan, A Smith, M Seringhaus, SM Douglas, M Gerstein (2004). International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS); pp 236-242

Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions.
U Lehnert, Y Xia, TE Royce, CS Goh, Y Liu, A Senes, H Yu, ZL Zhang, DM Engelman, M Gerstein (2004). Q Rev Biophys 37: 121-46.

DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states.
EJ White, O Emanuelsson, D Scalzo, T Royce, S Kosak, EJ Oakeley, S Weissman, M Gerstein, M Groudine, M Snyder, D Schubeler (2004). Proc Natl Acad Sci U S A 101: 17771-6.

Fast optimal genome tiling with applications to microarray design and homology search.
P Berman, P Bertone, B Dasgupta, M Gerstein, MY Kao, M Snyder (2004). J Comput Biol 11: 766-85.

Global identification of human transcribed sequences with genome tiling arrays.
P Bertone, V Stolc, TE Royce, JS Rozowsky, AE Urban, X Zhu, JL Rinn, W Tongprasit, M Samanta, S Weissman, M Gerstein, M Snyder (2004). Science 306: 2242-6.

The ENCODE (ENCyclopedia Of DNA Elements) Project.
ENCODE Project Consortium (2004). Science 306: 636-40.

Information assessment on predicting protein-protein interactions.
N Lin, B Wu, R Jansen, M Gerstein, H Zhao (2004). BMC Bioinformatics 5: 154.

Regulation of gene expression by a metabolic enzyme.
DA Hall, H Zhu, X Zhu, T Royce, M Gerstein, M Snyder (2004). Science 306: 482-4.

Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon.
A Kumar, M Seringhaus, MC Biery, RJ Sarnovsky, L Umansky, S Piccirillo, M Heidtman, KH Cheung, CJ Dobry, MB Gerstein, NL Craig, M Snyder (2004). Genome Res 14: 1975-86.

Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction.
R Jansen, M Gerstein (2004). Curr Opin Microbiol 7: 535-45.

Genomic analysis of regulatory network dynamics reveals large topological changes.
NM Luscombe, MM Babu, H Yu, M Snyder, SA Teichmann, M Gerstein (2004). Nature 431: 308-12.

Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes.
Y Liu, PM Harrison, V Kunin, M Gerstein (2004). Genome Biol 5: R64.

Large-scale analysis of pseudogenes in the human genome.
Z Zhang, M Gerstein (2004). Curr Opin Genet Dev 14: 328-35.

The protein target list of the Northeast Structural Genomics Consortium.
Z Wunderlich, TB Acton, J Liu, G Kornhaber, J Everett, P Carter, N Lan, N Echols, M Gerstein, B Rost, GT Montelione (2004). Proteins 56: 181-7.

Structure and evolution of transcriptional regulatory networks.
MM Babu, NM Luscombe, L Aravind, M Gerstein, SA Teichmann (2004). Curr Opin Struct Biol 14: 283-91.

Analyzing cellular biochemistry in terms of molecular networks.
Y Xia, H Yu, R Jansen, M Seringhaus, S Baxter, D Greenbaum, H Zhao, M Gerstein (2004). Annu Rev Biochem 73: 1051-87.

Major molecular differences between mammalian sexes are involved in drug metabolism and renal function.
JL Rinn, JS Rozowsky, IJ Laurenzi, PH Petersen, K Zou, W Zhong, M Gerstein, M Snyder (2004). Dev Cell 6: 791-800.

Computer security in academia-a potential roadblock to distributed annotation of the human genome.
D Greenbaum, SM Douglas, A Smith, J Lim, M Fischer, M Schultz, M Gerstein (2004). Nat Biotechnol 22: 771-2.

Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.
H Yu, NM Luscombe, HX Lu, X Zhu, Y Xia, JD Han, N Bertin, S Chung, M Vidal, M Gerstein (2004). Genome Res 14: 1107-18.

Genomic analysis of essentiality within protein networks.
H Yu, D Greenbaum, H Xin Lu, X Zhu, M Gerstein (2004). Trends Genet 20: 227-31.

Selection and characterization of small random transmembrane proteins that bind and activate the platelet-derived growth factor beta receptor.
LL Freeman-Cook, AM Dixon, JB Frank, Y Xia, L Ely, M Gerstein, DM Engelman, D DiMaio (2004). J Mol Biol 338: 907-20.

Conformational changes associated with protein-protein interactions.
CS Goh, D Milburn, M Gerstein (2004). Curr Opin Struct Biol 14: 104-9.

CREB binds to multiple loci on human chromosome 22.
G Euskirchen, TE Royce, P Bertone, R Martone, JL Rinn, FK Nelson, F Sayward, NM Luscombe, P Miller, M Gerstein, S Weissman, M Snyder (2004). Mol Cell Biol 24: 3804-14.

A method using active-site sequence conservation to find functional shifts in protein families: application to the enzymes of central metabolism, leading to the identification of an anomalous isocitrate dehydrogenase in pathogens.
R Das, M Gerstein (2004). Proteins 55: 455-63.

Exploring the range of protein flexibility, from a structural proteomics perspective.
M Gerstein, N Echols (2004). Curr Opin Chem Biol 8: 14-9.

Transmembrane protein domains rarely use covalent domain recombination as an evolutionary mechanism.
Y Liu, M Gerstein, DM Engelman (2004). Proc Natl Acad Sci U S A 101: 3495-7.

Comparative analysis of processed pseudogenes in the mouse and human genomes.
Z Zhang, N Carriero, M Gerstein (2004). Trends Genet 20: 62-7.

Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis.
CS Goh, N Lan, SM Douglas, B Wu, N Echols, A Smith, D Milburn, GT Montelione, H Zhao, M Gerstein (2004). J Mol Biol 336: 115-30.

TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics.
H Yu, X Zhu, D Greenbaum, J Karro, M Gerstein (2004). Nucleic Acids Res 32: 328-37.

Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures.
V Alexandrov, M Gerstein (2004). BMC Bioinformatics 5: 2.

A map of the interactome network of the metazoan C. elegans.
S Li, CM Armstrong, N Bertin, H Ge, S Milstein, M Boxem, PO Vidalain, JD Han, A Chesneau, T Hao, DS Goldberg, N Li, M Martinez, JF Rual, P Lamesch, L Xu, M Tewari, SL Wong, LV Zhang, GF Berriz, L Jacotot, P Vaglio, J Reboul, T Hirozane-Kishikawa, Q Li, HW Gabel, A Elewa, B Baumgartner, DJ Rose, H Yu, S Bosak, R Sequerra, A Fraser, SE Mango, WM Saxton, S Strome, S Van Den Heuvel, F Piano, J Vandenhaute, C Sardet, M Gerstein, L Doucette-Stamm, KC Gunsalus, JW Harper, ME Cusick, FP Roth, DE Hill, M Vidal (2004). Science 303: 540-3.

-- 2003 (33) --

Tools and databases to analyze protein flexibility; approaches to mapping implied features onto sequences.
WG Krebs, J Tsai, V Alexandrov, J Junker, R Jansen, M Gerstein (2003). Methods Enzymol 374: 544-84.

An analysis of the present system of scientific publishing: what's wrong and where to go from here
D Greenbaum, J Lim, M Gerstein (2003). Interdiscip Sci Rev 28:293-302

Identification of novel functional elements in the human genome.
Z Lian, G Euskirchen, J Rinn, R Martone, P Bertone, S Hartman, T Royce, K Nelson, F Sayward, N Luscombe, J Yang, JL Li, P Miller, AE Urban, M Gerstein, S Weissman, M Snyder (2003). Cold Spring Harb Symp Quant Biol 68: 317-22.

Relationship between gene co-expression and probe localization on microarray slides.
Y Kluger, H Yu, J Qian, M Gerstein (2003). BMC Genomics 4: 49.

Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome.
Z Zhang, PM Harrison, Y Liu, M Gerstein (2003). Genome Res 13: 2541-58.

A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development.
Y Jiao, H Yang, L Ma, N Sun, H Yu, T Liu, Y Gao, H Gu, Z Chen, M Wada, M Gerstein, H Zhao, LJ Qu, XW Deng (2003). Plant Physiol 133: 1480-93.

Reconstructing genetic networks in yeast.
Z Zhang, M Gerstein (2003). Nat Biotechnol 21: 1295-7.

A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs.
PM Harrison, N Carriero, Y Liu, M Gerstein (2003). J Mol Biol 333: 885-92.

A Bayesian networks approach for predicting protein-protein interactions from genomic data.
R Jansen, H Yu, D Greenbaum, Y Kluger, NJ Krogan, S Chung, A Emili, M Snyder, JF Greenblatt, M Gerstein (2003). Science 302: 449-53.

Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data.
J Qian, J Lin, NM Luscombe, H Yu, M Gerstein (2003). Bioinformatics 19: 1917-26.

Distribution of NF-kappaB-binding sites across human chromosome 22.
R Martone, G Euskirchen, P Bertone, S Hartman, TE Royce, NM Luscombe, JL Rinn, FK Nelson, P Miller, M Gerstein, S Weissman, M Snyder (2003). Proc Natl Acad Sci U S A 100: 12247-52.

Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes.
Z Zhang, M Gerstein (2003). Nucleic Acids Res 31: 5338-48.

Comparing protein abundance and mRNA expression levels on a genomic scale.
D Greenbaum, C Colangelo, K Williams, M Gerstein (2003). Genome Biol 4: 117.

A universal legal framework as a prerequisite for database interoperability.
D Greenbaum, M Gerstein (2003). Nat Biotechnol 21: 979-82.

The human genome has 49 cytochrome c pseudogenes, including a relic of a primordial gene that still functions in mouse.
Z Zhang, M Gerstein (2003). Gene 312: 61-72.

Genomic analysis of gene expression relationships in transcriptional regulatory networks.
H Yu, NM Luscombe, J Qian, M Gerstein (2003). Trends Genet 19: 422-7.

Identification and correction of spurious spatial correlations in microarray data.
J Qian, Y Kluger, H Yu, M Gerstein (2003). Biotechniques 35: 42-4, 46, 48.

Sequences and topology.
M Gerstein, JM Thornton (2003). Curr Opin Struct Biol 13: 341-3.

ExpressYourself: A modular platform for processing and visualizing microarray data.
NM Luscombe, TE Royce, P Bertone, N Echols, CE Horak, JT Chang, M Snyder, M Gerstein (2003). Nucleic Acids Res 31: 3477-82.

Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements.
Z Zhang, M Gerstein (2003). J Biol 2: 11.

A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes.
PM Harrison, M Gerstein (2003). Genome Biol 4: R40.

Data mining crystallization databases: knowledge-based approaches to optimize protein crystal screens.
MS Kimber, F Vallee, S Houston, A Necakov, T Skarina, E Evdokimova, S Beasley, D Christendat, A Savchenko, CH Arrowsmith, M Vedadi, M Gerstein, AM Edwards (2003). Proteins 51: 562-8.

SPINE 2: a system for collaborative structural proteomics within a federated database framework.
CS Goh, N Lan, N Echols, SM Douglas, D Milburn, P Bertone, R Xiao, LC Ma, D Zheng, Z Wunderlich, T Acton, GT Montelione, M Gerstein (2003). Nucleic Acids Res 31: 2833-8.

Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome.
Z Zhang, M Gerstein (2003). Genomics 81: 468-80.

Genomics. Defining genes in the genomics era.
M Snyder, M Gerstein (2003). Science 300: 258-60.

Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models.
R Jansen, HJ Bussemaker, M Gerstein (2003). Nucleic Acids Res 31: 2242-51.

Spectral biclustering of microarray data: coclustering genes and conditions.
Y Kluger, R Basri, JT Chang, M Gerstein (2003). Genome Res 13: 703-16.

Structural genomics: current progress.
M Gerstein, A Edwards, CH Arrowsmith, GT Montelione (2003). Science 299: 1663.

The transcriptional activity of human Chromosome 22.
JL Rinn, G Euskirchen, P Bertone, R Martone, NM Luscombe, S Hartman, PM Harrison, FK Nelson, P Miller, M Gerstein, S Weissman, M Snyder (2003). Genes Dev 17: 529-40.

Identification of pseudogenes in the Drosophila melanogaster genome.
PM Harrison, D Milburn, Z Zhang, P Bertone, M Gerstein (2003). Nucleic Acids Res 31: 1033-7.

Strategies for structural proteomics of prokaryotes: Quantifying the advantages of studying orthologous proteins and of using both NMR and X-ray crystallography approaches.
A Savchenko, A Yee, A Khachatryan, T Skarina, E Evdokimova, M Pavlova, A Semesi, J Northey, S Beasley, N Lan, R Das, M Gerstein, CH Arrowmith, AM Edwards (2003). Proteins 50: 392-9.

Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level.
N Lan, GT Montelione, M Gerstein (2003). Curr Opin Chem Biol 7: 44-54.

MolMovDB: analysis and visualization of conformational change and structural flexibility.
N Echols, D Milburn, M Gerstein (2003). Nucleic Acids Res 31: 478-82.

-- 2002 (32) --

Calculations of protein volumes: sensitivity analysis and parameter database.
J Tsai, M Gerstein (2002). Bioinformatics 18: 985-95.

Subcellular localization of the yeast proteome.
A Kumar, S Agarwal, JA Heyman, S Matson, M Heidtman, S Piccirillo, L Umansky, A Drawid, R Jansen, Y Liu, KH Cheung, P Miller, M Gerstein, GS Roeder, M Snyder (2002). Genes Dev 16: 707-19.

Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts.
D Greenbaum, R Jansen, M Gerstein (2002). Bioinformatics 18: 585-96.

Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds.
H Hegyi, J Lin, D Greenbaum, M Gerstein (2002). Proteins 47: 126-41.

A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution.
P Harrison, A Kumar, N Lan, N Echols, M Snyder, M Gerstein (2002). J Mol Biol 316: 409-19.

Studying genomes through the aeons: protein families, pseudogenes and proteome evolution.
PM Harrison, M Gerstein (2002). J Mol Biol 318: 1155-74.

A question of size: the eukaryotic proteome and the problems in defining it.
PM Harrison, A Kumar, N Lang, M Snyder, M Gerstein (2002). Nucleic Acids Res 30: 1083-90.

Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22.
PM Harrison, H Hegyi, S Balasubramanian, NM Luscombe, P Bertone, N Echols, T Johnson, M Gerstein (2002). Genome Res 12: 272-80.

Relating whole-genome expression data with protein-protein interactions.
R Jansen, D Greenbaum, M Gerstein (2002). Genome Res 12: 37-46.

Proteomics. Integrating interactomes.
M Gerstein, N Lan, R Jansen (2002). Science 295: 284-7.

Towards a systematic definition of protein function that scales to the genome level: Defining function in terms of interactions.
N Lan, R Jansen, M Gerstein (2002). Proceedings of the IEEE 90:1848-1858

Blurring the boundaries between scientific 'papers' and biological databases
M Gerstein, J Junker (2002). Nature Yearbook of Science and Technology 210-212 (ed. D Butler, Palgrave Macmillan Publishers)

Fast optimal genome tiling with applications to microarray design and homology search.
P Berman, P Bertone, B DasGupta, M Gerstein, M-Y Kao, M Snyder (2002). Proceedings of the 2nd International Workshop on Algorithms in Bioinformatics. Springer-Verlag LNCS 2452: 419-433

Integration of genomic datasets to predict protein complexes in yeast.
R Jansen, N Lan, J Qian, M Gerstein (2002). J Struct Funct Genomics 2: 71-81.

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae.
CE Horak, NM Luscombe, J Qian, P Bertone, S Piccirrillo, M Gerstein, M Snyder (2002). Genes Dev 16: 3017-33.

YMD: a microarray database for large-scale gene expression analysis.
KH Cheung, K White, J Hager, M Gerstein, V Reinke, K Nelson, P Masiar, R Srivastava, Y Li, J Li, H Zhao, J Li, DB Allison, M Snyder, P Miller, K Williams (2002). Proc AMIA Symp : 140-4.

Thermostability of membrane protein helix-helix interaction elucidated by statistical analysis.
D Schneider, Y Liu, M Gerstein, DM Engelman (2002). FEBS Lett 532: 231-6.

Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons.
A Mateos, J Dopazo, R Jansen, Y Tu, M Gerstein, G Stolovitzky (2002). Genome Res 12: 1703-15.

Digging deep for ancient relics: a survey of protein motifs in the intergenic sequences of four eukaryotic genomes.
ZL Zhang, PM Harrison, M Gerstein (2002). J Mol Biol 323: 811-22.

GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing.
J Lin, J Qian, D Greenbaum, P Bertone, R Das, N Echols, A Senes, B Stenger, M Gerstein (2002). Nucleic Acids Res 30: 4574-82.

Genomic and proteomic analysis of the myeloid differentiation program: global analysis of gene expression during induced differentiation in the MPRO cell line.
Z Lian, Y Kluger, DS Greenbaum, D Tuck, M Gerstein, N Berliner, SM Weissman, PE Newburger (2002). Blood 100: 3209-20.

Genomic analysis of membrane protein families: abundance and conserved motifs.
Y Liu, DM Engelman, M Gerstein (2002). Genome Biol 3: research0054.

Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome.
Z Zhang, P Harrison, M Gerstein (2002). Genome Res 12: 1466-82.

Bridging structural biology and genomics: assessing protein interaction data with known complexes.
AM Edwards, B Kus, R Jansen, D Greenbaum, J Greenblatt, M Gerstein (2002). Trends Genet 18: 529-36.

Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic.
WG Krebs, V Alexandrov, CA Wilson, N Echols, H Yu, M Gerstein (2002). Proteins 48: 682-95.

The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties.
NM Luscombe, J Qian, Z Zhang, T Johnson, M Gerstein (2002). Genome Biol 3: RESEARCH0040.

Functional profiling of the Saccharomyces cerevisiae genome.
G Giaever, AM Chu, L Ni, C Connelly, L Riles, S Veronneau, S Dow, A Lucau-Danila, K Anderson, B Andre, AP Arkin, A Astromoff, M El-Bakkoury, R Bangham, R Benito, S Brachat, S Campanaro, M Curtiss, K Davis, A Deutschbauer, KD Entian, P Flaherty, F Foury, DJ Garfinkel, M Gerstein, D Gotte, U Guldener, JH Hegemann, S Hempel, Z Herman, DF Jaramillo, DE Kelly, SL Kelly, P Kotter, D LaBonte, DC Lamb, N Lan, H Liang, H Liao, L Liu, C Luo, M Lussier, R Mao, P Menard, SL Ooi, JL Revuelta, CJ Roberts, M Rose, P Ross-Macdonald, B Scherens, G Schimmack, B Shafer, DD Shoemaker, S Sookhai-Mahadeo, RK Storms, JN Strathern, G Valle, M Voet, G Volckaert, CY Wang, TR Ward, J Wilhelmy, EA Winzeler, Y Yang, G Yen, E Youngman, K Yu, H Bussey, JD Boeke, M Snyder, P Philippsen, RW Davis, M Johnston (2002). Nature 418: 387-91.

SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes.
S Balasubramanian, P Harrison, H Hegyi, P Bertone, N Luscombe, N Echols, P McGarvey, Z Zhang, M Gerstein (2002). Pharmacogenomics 3: 393-402.

Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes.
N Echols, P Harrison, S Balasubramanian, NM Luscombe, P Bertone, Z Zhang, M Gerstein (2002). Nucleic Acids Res 30: 2515-23.

GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis.
CE Horak, MC Mahajan, NM Luscombe, M Gerstein, SM Weissman, M Snyder (2002). Proc Natl Acad Sci U S A 99: 2924-9.

Structural genomics: a new era for pharmaceutical research.
Y Liu, NM Luscombe, V Alexandrov, P Bertone, P Harrison, Z Zhang, M Gerstein (2002). Genome Biol 3: REPORTS4004.

An integrated approach for finding overlooked genes in yeast.
A Kumar, PM Harrison, KH Cheung, N Lan, N Echols, P Bertone, P Miller, MB Gerstein, M Snyder (2002). Nat Biotechnol 20: 58-63.

-- 2001 (21) --

Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model.
J Qian, NM Luscombe, M Gerstein (2001). J Mol Biol 313: 673-81.

Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions.
J Qian, M Dolled-Filhart, J Lin, H Yu, M Gerstein (2001). J Mol Biol 314: 1053-66.

Annotation transfer for genomics: measuring functional divergence in multi-domain proteins.
H Hegyi, M Gerstein (2001). Genome Res 11: 1632-40.

What is bioinformatics? A proposed definition and overview of the field.
NM Luscombe, D Greenbaum, M Gerstein (2001). Methods Inf Med 40: 346-58.

Global perspectives on proteins: comparing genomes in terms of folds, pathways and beyond.
R Das, J Junker, D Greenbaum, MB Gerstein (2001). Pharmacogenomics J 1: 115-25.

Global analysis of protein activities using proteome chips.
H Zhu, M Bilgin, R Bangham, D Hall, A Casamayor, P Bertone, N Lan, R Jansen, S Bidlingmaier, T Houfek, T Mitchell, P Miller, RA Dean, M Gerstein, M Snyder (2001). Science 293: 2101-5.

Calculating populations of subcellular compartments using density matrix formalism
V Alexandrov, M Gerstein (2001). International Journal of Quantum Chemistry 85:693-696

A standard reference frame for the description of nucleic acid base-pair geometry.
WK Olson, M Bansal, SK Burley, RE Dickerson, M Gerstein, SC Harvey, U Heinemann, XJ Lu, S Neidle, Z Shakked, H Sklenar, M Suzuki, CS Tung, E Westhof, C Wolberger, HM Berman (2001). J Mol Biol 313: 229-37.

Determining the minimum number of types necessary to represent the sizes of protein atoms.
J Tsai, N Voss, M Gerstein (2001). Bioinformatics 17: 949-56.

Interrelating different types of genomic data, from proteome to secretome: 'oming in on function.
D Greenbaum, NM Luscombe, R Jansen, J Qian, M Gerstein (2001). Genome Res 11: 1463-8.

Protein Geometry: Distances, Areas, and Volumes
M Gerstein, F M Richards (2001). International Tables for Crystallography (Volume F, Chapter 22.1.1, pages 531-539; M Rossmann & E Arnold, editors; Dordrecht: Kluwer)

A Bauhaus for Biologists: An Introduction to Protein Architecture by A. M. Lesk
P Harrison, M Gerstein (2001). Trends Biochem Sci 26:204-205

Integrative data mining: the new direction in bioinformatics.
P Bertone, M Gerstein (2001). IEEE Eng Med Biol Mag 20: 33-40.

Genomic and proteomic analysis of the myeloid differentiation program.
Z Lian, L Wang, S Yamaga, W Bonds, Y Beazer-Barclay, Y Kluger, M Gerstein, PE Newburger, N Berliner, SM Weissman (2001). Blood 98: 513-24.

RNA expression patterns change dramatically in human neutrophils exposed to bacteria.
YV Subrahmanyam, S Yamaga, Y Prashar, HH Lee, NP Hoe, Y Kluger, M Gerstein, JD Goguen, PE Newburger, SM Weissman (2001). Blood 97: 2457-68.

SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics.
P Bertone, Y Kluger, N Lan, D Zheng, D Christendat, A Yee, AM Edwards, CH Arrowsmith, GT Montelione, M Gerstein (2001). Nucleic Acids Res 29: 2884-98.

Sequences and Topology
M Gerstein, B Honig (2001). Current Opinion in Structural Biology 11: 327-329.

What is Bioinformatics? A Proposed Definition and Overview of the Field
N Luscombe, D Greenbaum, M Gerstein (2001). Intl. Medical Informatics Association (Yearbook, Pages 83-99)

Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome.
PM Harrison, N Echols, MB Gerstein (2001). Nucleic Acids Res 29: 818-30.

PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information.
J Qian, B Stenger, CA Wilson, J Lin, R Jansen, SA Teichmann, J Park, WG Krebs, H Yu, V Alexandrov, N Echols, M Gerstein (2001). Nucleic Acids Res 29: 1750-64.

An XML Application for Genomic Data Interoperation
Cheung KH, Liu Y, Kumar K, Snyder M, Gerstein M, Miller P (2001). IEEE International Symposium on Bio-Informatics and Biomedical Engineering (BIBE) pp. 97-103

-- 2000 (18) --

Integrative database analysis in structural genomics.
M Gerstein (2000). Nat Struct Biol 7 Suppl: 960-3.

Genome analyses of spirochetes: a study of the protein structures, functions and metabolic pathways in Treponema pallidum and Borrelia burgdorferi.
R Das, H Hegyi, M Gerstein (2000). J Mol Microbiol Biotechnol 2: 387-92.

Structural proteomics: prospects for high throughput sample preparation.
D Christendat, A Yee, A Dharamsi, Y Kluger, M Gerstein, CH Arrowsmith, AM Edwards (2000). Prog Biophys Mol Biol 73: 339-45.

Analysis of yeast protein kinases using protein chips.
H Zhu, JF Klemic, S Chang, P Bertone, A Casamayor, KG Klemic, D Smith, M Gerstein, MA Reed, M Snyder (2000). Nat Genet 26: 283-9.

Genome-wide analysis relating expression level with protein subcellular localization.
A Drawid, R Jansen, M Gerstein (2000). Trends Genet 16: 426-30.

The current excitement in bioinformatics-analysis of whole-genome expression data: how does it relate to protein structure and function?
M Gerstein, R Jansen (2000). Curr Opin Struct Biol 10: 574-84.

The stability of thermophilic proteins: a study based on comprehensive genome comparison.
R Das, M Gerstein (2000). Funct Integr Genomics 1: 76-88.

Measuring shifts in function and evolutionary opportunity using variability profiles: a case study of the globins.
GJ Naylor, M Gerstein (2000). J Mol Evol 51: 223-33.

Structural proteomics of an archaeon.
D Christendat, A Yee, A Dharamsi, Y Kluger, A Savchenko, JR Cort, V Booth, CD Mackereth, V Saridakis, I Ekiel, G Kozlov, KL Maxwell, N Wu, LP McIntosh, K Gehring, MA Kennedy, AR Davidson, EF Pai, M Gerstein, AM Edwards, CH Arrowsmith (2000). Nat Struct Biol 7: 903-9.

A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome.
A Drawid, M Gerstein (2000). J Mol Biol 301: 1059-75.

Proteomics of Mycoplasma genitalium: identification and characterization of unannotated and atypical proteins in a small model genome.
S Balasubramanian, T Schneider, M Gerstein, L Regan (2000). Nucleic Acids Res 28: 3075-82.

Protein folds in the worm genome.
M Gerstein, J Lin, H Hegyi (2000). Pac Symp Biocomput : 30-41.

Annotation of the human genome.
M Gerstein (2000). Science 288: 1590.

Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels.
J Lin, M Gerstein (2000). Genome Res 10: 808-18.

The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework.
WG Krebs, M Gerstein (2000). Nucleic Acids Res 28: 1665-75.

Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions.
A Senes, M Gerstein, DM Engelman (2000). J Mol Biol 296: 921-36.

Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.
CA Wilson, J Kreychman, M Gerstein (2000). J Mol Biol 297: 233-49.

Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins.
R Jansen, M Gerstein (2000). Nucleic Acids Res 28: 1481-8.

-- 1999 (10) --

Large-scale analysis of the yeast genome by transposon tagging and gene disruption.
P Ross-Macdonald, PS Coelho, T Roemer, S Agarwal, A Kumar, R Jansen, KH Cheung, A Sheehan, D Symoniatis, L Umansky, M Heidtman, FK Nelson, H Iwasaki, K Hager, M Gerstein, P Miller, GS Roeder, M Snyder (1999). Nature 402: 413-8.

Perspectives: signal transduction. Proteins in motion.
M Gerstein, C Chothia (1999). Science 285: 1682-3.

Motions in a Database Framework: from Structure to Sequence
M Gerstein, R Jansen, T Johnson, J Tsai, W Krebs (1999). Rigidity Theory and Applications 401-442 (ed. M F Thorpe and P M Duxbury, Kluwer Academic/Plenum Publishers).

E-publishing on the Web: promises, pitfalls, and payoffs for bioinformatics.
M Gerstein (1999). Bioinformatics 15: 429-31.

E-biomed and clinical research.
ES Brodkin, M Gerstein (1999). N Engl J Med 341: 1080; author reply 1081.

The packing density in proteins: standard radii and volumes.
J Tsai, R Taylor, C Chothia, M Gerstein (1999). J Mol Biol 290: 253-66.

Advances in structural genomics.
SA Teichmann, C Chothia, M Gerstein (1999). Curr Opin Struct Biol 9: 390-9.

Building the future of biocomputing.
M Gerstein (1999). Nature 399: 101.

The relationship between protein structure and function: a comprehensive survey with application to the yeast genome.
H Hegyi, M Gerstein (1999). J Mol Biol 288: 147-64.

Forging links in an electronic paper chain.
M Gerstein (1999). Nature 398: 20.

-- 1998 (9) --

Comparing genomes in terms of protein structure: surveys of a finite parts list.
M Gerstein, H Hegyi (1998). FEMS Microbiol Rev 22: 277-304.

How representative are the known structures of the proteins in a complete genome? A comprehensive structural census.
M Gerstein (1998). Fold Des 3: 497-512.

Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census.
M Gerstein (1998). Proteins 33: 518-34.

Simulating water and the molecules of life.
M Gerstein, M Levitt (1998). Sci Am 279: 100-5.

Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence.
M Gerstein (1998). Bioinformatics 14: 707-14.

A database of macromolecular motions.
M Gerstein, W Krebs (1998). Nucleic Acids Res 26: 4280-90.

Repeated tertiary fold of RNA polymerase II and implications for DNA binding.
J Fu, M Gerstein, PR David, AL Gnatt, DA Bushnell, AM Edwards, RD Kornberg (1998). J Mol Biol 280: 317-22.

A unified statistical framework for sequence comparison and structure comparison.
M Levitt, M Gerstein (1998). Proc Natl Acad Sci U S A 95: 5913-20.

Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins.
M Gerstein, M Levitt (1998). Protein Sci 7: 445-56.

-- 1997 (6) --

A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure.
M Gerstein (1997). J Mol Biol 274: 562-76.

Simulating the minimum core for hydrophobic collapse in globular proteins.
J Tsai, M Gerstein, M Levitt (1997). Protein Sci 6: 2606-16.

A structural census of the current population of protein sequences.
M Gerstein, M Levitt (1997). Proc Natl Acad Sci U S A 94: 11911-6.

Protein evolution. How far can sequences diverge?
C Chothia, M Gerstein (1997). Nature 385: 579, 581.

Protein folding: the endgame.
M Levitt, M Gerstein, E Huang, S Subbiah, J Tsai (1997). Annu Rev Biochem 66: 549-79.

LPFC: an Internet library of protein family core structures.
R Schmidt, M Gerstein, RB Altman (1997). Protein Sci 6: 246-8.

-- 1996 (4) --

Practicing Cyberlaw in the Year 2000.
R Becker, M Gerstein (1996). New Jersey Lawyer Magazine 179: 12-27 (September).

Keeping the Shape but Changing the Charges: A Simulation Study of Urea and its Isosteric Analogues
J Tsai, M Gerstein, M Levitt (1996). Journal of Chemical Physics 104: 9417-9430

Packing at the protein-water interface.
M Gerstein, C Chothia (1996). Proc Natl Acad Sci U S A 93: 10167-72.

Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures.
M Gerstein, M Levitt (1996). Proc Int Conf Intell Syst Mol Biol 4: 59-67.

-- 1995 (7) --

Using a measure of structural variation to define a core for the globins.
M Gerstein, RB Altman (1995). Comput Appl Biosci 11: 633-44.

Binding geometry of alpha-helices that recognize DNA.
M Suzuki, M Gerstein (1995). Proteins 23: 525-35.

Average core structures and variability measures for protein families: application to the immunoglobulins.
M Gerstein, RB Altman (1995). J Mol Biol 251: 161-75.

The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra.
M Gerstein, J Tsai, M Levitt (1995). J Mol Biol 249: 955-66.

Methods for displaying macromolecular structural uncertainty: application to the globins.
RB Altman, C Hughes, MB Gerstein (1995). J Mol Graph 13: 142-52, 109-2.

DNA recognition and superstructure formation by helix-turn-helix proteins.
M Suzuki, N Yagi, M Gerstein (1995). Protein Eng 8: 329-38.

DNA recognition code of transcription factors.
M Suzuki, SE Brenner, M Gerstein, N Yagi (1995). Protein Eng 8: 319-28.

-- 1994 (7) --

Purcell's early work on NMR: Contingency versus Inevitability
M Gerstein (1994). American Journal of Physics 62: 596-601

Stereochemical basis of DNA recognition by Zn fingers.
M Suzuki, M Gerstein, N Yagi (1994). Nucleic Acids Res 22: 3397-405.

Volume changes on protein folding.
Y Harpaz, M Gerstein, C Chothia (1994). Structure 2: 641-9.

Structural mechanisms for domain movements in proteins.
M Gerstein, AM Lesk, C Chothia (1994). Biochemistry 33: 6739-49.

Solution structure of the DNA binding octapeptide repeat of the K10 gene product.
M Suzuki, D Neuhaus, M Gerstein, S Aimoto (1994). Protein Eng 7: 461-70.

Volume changes in protein evolution.
M Gerstein, EL Sonnhammer, C Chothia (1994). J Mol Biol 236: 1067-78.

Finding an average core structure: application to the globins.
RB Altman, M Gerstein (1994). Proc Int Conf Intell Syst Mol Biol 2: 19-27.

-- 1993 (7) --

Simulation of Water around a Model Protein Helix. 1. Two-dimensional Projections of Solvent Structure.
M Gerstein, R Lynden-Bell (1993). Journal of Physical Chemistry 97: 2982-2991.

Simulation of Water around a Model Protein Helix. 2. The Relative Contributions of Packing, Hydrophobicity, and Hydrogen Bonding.
M Gerstein, R Lynden-Bell (1993). Journal of Physical Chemistry 97: 2991-2999.

Domain closure in lactoferrin. Two hinges produce a see-saw motion between alternative close-packed interfaces.
M Gerstein, BF Anderson, GE Norris, EN Baker, AM Lesk, C Chothia (1993). J Mol Biol 234: 357-72.

An NMR study on the DNA-binding SPKK motif and a model for its interaction with DNA.
M Suzuki, M Gerstein, T Johnson (1993). Protein Eng 6: 565-74.

What is the natural boundary of a protein in solution?
M Gerstein, RM Lynden-Bell (1993). J Mol Biol 230: 641-50.

Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers.
M Gerstein, G Schulz, C Chothia (1993). J Mol Biol 229: 494-501.

Electron diffraction analysis of structural changes in the photocycle of bacteriorhodopsin.
S Subramaniam, M Gerstein, D Oesterhelt, R Henderson (1993). EMBO J 12: 1-8.

-- 1992 (2) --

A Resolution-Sensitive Procedure for Comparing Protein Surfaces and its Application to the Comparison of Antigen-Combining Sites.
M Gerstein (1992). Acta Crystallographica A48: 271-276.

Polar zipper sequence in the high-affinity hemoglobin of Ascaris suum: amino acid sequence and structural interpretation.
I De Baere, L Liu, L Moens, J Van Beeumen, C Gielens, J Richelle, C Trotman, J Finch, M Gerstein, M Perutz (1992). Proc Natl Acad Sci U S A 89: 4638-42.

-- 1991 (1) --

Analysis of protein loop closure. Two types of hinges produce one motion in lactate dehydrogenase.
M Gerstein, C Chothia (1991). J Mol Biol 220: 133-49.

-- 1987 (1) --

Inverse Problem for Synchrotron Radiation in the Presence of Noise
N Fisch, A Kritz, M Gerstein (1987). Proceedings of the Sixth Joint Workshop on Electron Cyclotron Emission and Electron Cyclotron Resonance Heating. (eds. A Riviere, A Costley), 23-30 (Oxford, 16-17 September).