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Mark B. Gerstein - Publications

Molecular Biophysics and Biochemistry Yale University, New Haven, CT 
Computational Biology and Bioinformatics

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Year Citation  Score
2021 Zhao X, Collins RL, Lee WP, Weber AM, Jun Y, Zhu Q, Weisburd B, Huang Y, Audano PA, Wang H, Walker M, Lowther C, Fu J, Gerstein MB, et al. Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies. American Journal of Human Genetics. PMID 33789087 DOI: 10.1016/j.ajhg.2021.03.014  0.76
2021 Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, ... ... Gerstein MB, et al. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science (New York, N.Y.). PMID 33632895 DOI: 10.1126/science.abf7117  0.84
2021 Emani PS, Warrell J, Anticevic A, Bekiranov S, Gandal M, McConnell MJ, Sapiro G, Aspuru-Guzik A, Baker JT, Bastiani M, Murray JD, Sotiropoulos SN, Taylor J, Senthil G, Lehner T, ... Gerstein MB, et al. Quantum computing at the frontiers of biological sciences. Nature Methods. PMID 33398186 DOI: 10.1038/s41592-020-01004-3  0.52
2020 Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S, Saksena G, Ellrott K, Wendl MC, ... ... Gerstein MB, et al. Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications. 11: 6232. PMID 33257764 DOI: 10.1038/s41467-020-20128-w  0.68
2020 Li B, Yang YT, Capra JA, Gerstein MB. Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks. Plos Computational Biology. 16: e1008291. PMID 33253214 DOI: 10.1371/journal.pcbi.1008291  0.8
2020 Kumar S, Harmanci A, Vytheeswaran J, Gerstein MB. SVFX: a machine learning framework to quantify the pathogenicity of structural variants. Genome Biology. 21: 274. PMID 33168059 DOI: 10.1186/s13059-020-02178-x  0.64
2020 Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Kelso S, Saksena G, Ellrott K, Wendl MC, Wheeler DA, ... ... Gerstein MB, et al. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications. 11: 4748. PMID 32958763 DOI: 10.1038/s41467-020-18151-y  0.68
2020 Galeano D, Li S, Gerstein M, Paccanaro A. Predicting the frequencies of drug side effects. Nature Communications. 11: 4575. PMID 32917868 DOI: 10.1038/s41467-020-18305-y  0.88
2020 Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, ... ... Gerstein MB, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 583: 699-710. PMID 32728249 DOI: 10.1038/s41586-020-2493-4  0.88
2020 Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, et al. Perspectives on ENCODE. Nature. 583: 693-698. PMID 32728248 DOI: 10.1038/s41586-020-2449-8  0.64
2020 Sisu C, Muir P, Frankish A, Fiddes I, Diekhans M, Thybert D, Odom DT, Flicek P, Keane TM, Hubbard T, Harrow J, Gerstein M. Transcriptional activity and strain-specific history of mouse pseudogenes. Nature Communications. 11: 3695. PMID 32728065 DOI: 10.1038/s41467-020-17157-w  0.64
2020 Zhang J, Lee D, Dhiman V, Jiang P, Xu J, McGillivray P, Yang H, Liu J, Meyerson W, Clarke D, Gu M, Li S, Lou S, Xu J, Lochovsky L, ... ... Gerstein M, et al. An integrative ENCODE resource for cancer genomics. Nature Communications. 11: 3696. PMID 32728046 DOI: 10.1038/s41467-020-14743-w  0.88
2020 Zhang J, Liu J, Lee D, Feng JJ, Lochovsky L, Lou S, Rutenberg-Schoenberg M, Gerstein M. RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins. Genome Biology. 21: 151. PMID 32727537 DOI: 10.1186/s13059-020-01979-4  0.88
2020 Gürsoy G, Brannon CM, Navarro FCP, Gerstein M. FANCY: Fast Estimation of Privacy Risk in Functional Genomics Data. Bioinformatics (Oxford, England). PMID 32726397 DOI: 10.1093/bioinformatics/btaa661  0.8
2020 Gürsoy G, Bjornson R, Green ME, Gerstein M. Using blockchain to log genome dataset access: efficient storage and query. Bmc Medical Genomics. 13: 78. PMID 32693796 DOI: 10.1186/s12920-020-0716-z  0.8
2020 Li S, Crawford FW, Gerstein MB. Using sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood. Nature Communications. 11: 3575. PMID 32681003 DOI: 10.1038/s41467-020-17388-x  0.68
2020 Lou S, Li T, Kong X, Zhang J, Liu J, Lee D, Gerstein M. TopicNet: a framework for measuring transcriptional regulatory network change. Bioinformatics (Oxford, England). 36: i474-i481. PMID 32657410 DOI: 10.1093/bioinformatics/btaa403  0.88
2020 Zhang J, Liu J, Lee D, Lou S, Chen Z, Gürsoy G, Gerstein M. DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring. Bmc Bioinformatics. 21: 281. PMID 32615918 DOI: 10.1186/s12859-020-03605-3  0.88
2020 Lee D, Zhang J, Liu J, Gerstein M. Epigenome-based splicing prediction using a recurrent neural network. Plos Computational Biology. 16: e1008006. PMID 32584815 DOI: 10.1371/journal.pcbi.1008006  0.88
2020 Spakowicz D, Lou S, Barron B, Gomez JL, Li T, Liu Q, Grant N, Yan X, Hoyd R, Weinstock G, Chupp GL, Gerstein M. Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients. Genome Biology. 21: 150. PMID 32571363 DOI: 10.1186/s13059-020-02033-z  0.88
2020 Meyerson W, Leisman J, Navarro FCP, Gerstein M. Origins and characterization of variants shared between databases of somatic and germline human mutations. Bmc Bioinformatics. 21: 227. PMID 32498674 DOI: 10.1186/s12859-020-3508-8  0.6
2020 Gürsoy G, Brannon CM, Gerstein M. Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts. Bmc Medical Genomics. 13: 74. PMID 32487214 DOI: 10.1186/s12920-020-00732-x  0.8
2020 Ye C, Paccanaro A, Gerstein M, Yan KK. The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data. Bmc Bioinformatics. 21: 222. PMID 32471347 DOI: 10.1186/s12859-020-03545-y  0.88
2020 Qing T, Mohsen H, Marczyk M, Ye Y, O'Meara T, Zhao H, Townsend JP, Gerstein M, Hatzis C, Kluger Y, Pusztai L. Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden. Nature Communications. 11: 2438. PMID 32415133 DOI: 10.1038/s41467-020-16293-7  0.84
2020 Shuch B, Li S, Risch H, Bindra RS, McGillivray PD, Gerstein M. Estimation of the carrier frequency of fumarate hydratase alterations and implications for kidney cancer risk in hereditary leiomyomatosis and renal cancer. Cancer. PMID 32413184 DOI: 10.1002/cncr.32914  0.68
2020 Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, Park PJ. Publisher Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nature Genetics. PMID 32404988 DOI: 10.1038/s41588-020-0634-1  0.32
2020 Shook BA, Wasko RR, Mano O, Rutenberg-Schoenberg M, Rudolph MC, Zirak B, Rivera-Gonzalez GC, López-Giráldez F, Zarini S, Rezza A, Clark DA, Rendl M, Rosenblum MD, Gerstein MB, Horsley V. Dermal Adipocyte Lipolysis and Myofibroblast Conversion Are Required for Efficient Skin Repair. Cell Stem Cell. PMID 32302523 DOI: 10.1016/j.stem.2020.03.013  0.76
2020 Yan KK, Wang D, Xiong K, Gerstein M. Comparing Technological Development and Biological Evolution from a Network Perspective. Cell Systems. 10: 219-222. PMID 32213348 DOI: 10.1016/j.cels.2020.02.004  0.72
2020 Kumar S, Warrell J, Li S, McGillivray PD, Meyerson W, Salichos L, Harmanci A, Martinez-Fundichely A, Chan CWY, Nielsen MM, Lochovsky L, Zhang Y, Li X, Lou S, Pedersen JS, ... ... Gerstein MB, et al. Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences. Cell. PMID 32084333 DOI: 10.1016/j.cell.2020.01.032  0.88
2020 Lu L, Chen T, Chen Y, Yuan M, Gerstein M, Li T, Liang H, Froehlich T. Towards developing a practical artificial intelligence tool for diagnosing and evaluating autism spectrum disorder: A study using multicenter ABIDE II datasets. Jmir Medical Informatics. PMID 32041690 DOI: 10.2196/15767  0.88
2020 Ash GI, Stults-Kolehmainen M, Busa MA, Gregory R, Garber CE, Liu J, Gerstein M, Casajus JA, Gonzalez-Aguero A, Constantinou D, Geistlinger M, Guppy FM, Pigozzi F, Pitsiladis YP. 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. Current Sports Medicine Reports. 19: 45-49. PMID 32028347 DOI: 10.1249/JSR.0000000000000680  0.88
2020 Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, ... ... Gerstein M, et al. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 578: 102-111. PMID 32025015 DOI: 10.1038/s41586-020-1965-x  0.88
2020 Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M, Weischenfeldt J, Beroukhim R, Campbell PJ, et al. Patterns of somatic structural variation in human cancer genomes. Nature. 578: 112-121. PMID 32025012 DOI: 10.1038/s41586-019-1913-9  0.44
2020 Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, Park PJ. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nature Genetics. PMID 32025003 DOI: 10.1038/s41588-019-0576-7  0.44
2020 Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, ... ... Gerstein M, et al. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nature Genetics. PMID 32024998 DOI: 10.1038/s41588-019-0562-0  0.76
2020 Salichos L, Meyerson W, Warrell J, Gerstein M. Estimating growth patterns and driver effects in tumor evolution from individual samples. Nature Communications. 11: 732. PMID 32024824 DOI: 10.1038/s41467-020-14407-9  0.6
2020 Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, Creighton CJ. High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nature Communications. 11: 736. PMID 32024823 DOI: 10.1038/s41467-019-13885-w  0.68
2020 Shanta O, Noor A, Sebat J. The effects of common structural variants on 3D chromatin structure. Bmc Genomics. 21: 95. PMID 32000688 DOI: 10.1186/s12864-020-6516-1  0.36
2019 Johnson JS, Spakowicz DJ, Hong BY, Petersen LM, Demkowicz P, Chen L, Leopold SR, Hanson BM, Agresta HO, Gerstein M, Sodergren E, Weinstock GM. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nature Communications. 10: 5029. PMID 31695033 DOI: 10.1038/s41467-019-13036-1  0.64
2019 Koupenova M, Mick E, Corkrey HA, Singh A, Tanriverdi SE, Vitseva O, Levy D, Keeler AM, Ezzaty Mirhashemi M, ElMallah MK, Gerstein M, Rozowsky J, Tanriverdi K, Freedman JE. Pollen-derived RNAs Are Found in the Human Circulation. Iscience. 19: 916-926. PMID 31518900 DOI: 10.1016/j.isci.2019.08.035  0.72
2019 Lou S, Cotter KA, Li T, Liang J, Mohsen H, Liu J, Zhang J, Cohen S, Xu J, Yu H, Rubin MA, Gerstein M. GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner. Plos Genetics. 15: e1007860. PMID 31469829 DOI: 10.1371/journal.pgen.1007860  0.96
2019 Kumar S, Clarke D, Gerstein MB. Leveraging protein dynamics to identify cancer mutational hotspots using 3D structures. Proceedings of the National Academy of Sciences of the United States of America. PMID 31462496 DOI: 10.1073/pnas.1901156116  0.4
2019 Navarro FC, Hoops J, Bellfy L, Cerveira E, Zhu Q, Zhang C, Lee C, Gerstein MB. TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements. Plos Computational Biology. 15: e1007293. PMID 31425522 DOI: 10.1371/journal.pcbi.1007293  0.72
2019 Polioudakis D, de la Torre-Ubieta L, Langerman J, Elkins AG, Shi X, Stein JL, Vuong CK, Nichterwitz S, Gevorgian M, Opland CK, Lu D, Connell W, Ruzzo EK, Lowe JK, Hadzic T, ... ... Gerstein MB, et al. A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation. Neuron. PMID 31303374 DOI: 10.1016/j.neuron.2019.06.011  0.56
2019 Wang B, Yan C, Lou S, Emani P, Li B, Xu M, Kong X, Meyerson W, Yang YT, Lee D, Gerstein M. Building a Hybrid Physical-Statistical Classifier for Predicting the Effect of Variants Related to Protein-Drug Interactions. Structure (London, England : 1993). PMID 31279629 DOI: 10.1016/j.str.2019.06.001  0.88
2019 Navarro FCP, Mohsen H, Yan C, Li S, Gu M, Meyerson W, Gerstein M. Genomics and data science: an application within an umbrella. Genome Biology. 20: 109. PMID 31142351 DOI: 10.1186/s13059-019-1724-1  0.8
2019 Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, ... ... Gerstein MB, et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nature Communications. 10: 1784. PMID 30992455 DOI: 10.1038/s41467-018-08148-z  0.88
2019 Rozowsky J, Kitchen RR, Park JJ, Galeev TR, Diao J, Warrell J, Thistlethwaite W, Subramanian SL, Milosavljevic A, Gerstein M. exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling. Cell Systems. PMID 30956140 DOI: 10.1016/j.cels.2019.03.004  0.72
2019 Murillo OD, Thistlethwaite W, Rozowsky J, Subramanian SL, Lucero R, Shah N, Jackson AR, Srinivasan S, Chung A, Laurent CD, Kitchen RR, Galeev T, Warrell J, Diao JA, Welsh JA, ... ... Gerstein MB, et al. exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids. Cell. 177: 463-477.e15. PMID 30951672 DOI: 10.1016/j.cell.2019.02.018  0.72
2019 Das S, Ansel KM, Bitzer M, Breakefield XO, Charest A, Galas DJ, Gerstein MB, Gupta M, Milosavljevic A, McManus MT, Patel T, Raffai RL, Rozowsky J, Roth ME, et al. The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research. Cell. 177: 231-242. PMID 30951667 DOI: 10.1016/j.cell.2019.03.023  0.72
2019 Ho EY, Cao Q, Gu M, Chan RW, Wu Q, Gerstein M, Yip KY. Shaping the nebulous enhancer in the era of high-throughput assays and genome editing. Briefings in Bioinformatics. PMID 30895290 DOI: 10.1093/bib/bbz030  0.76
2019 Yardımcı GG, Ozadam H, Sauria MEG, Ursu O, Yan KK, Yang T, Chakraborty A, Kaul A, Lajoie BR, Song F, Zhan Y, Ay F, Gerstein M, Kundaje A, Li Q, et al. Measuring the reproducibility and quality of Hi-C data. Genome Biology. 20: 57. PMID 30890172 DOI: 10.1186/s13059-019-1658-7  0.72
2019 Moro A, Driscoll TP, Boraas LC, Armero W, Kasper DM, Baeyens N, Jouy C, Mallikarjun V, Swift J, Ahn SJ, Lee D, Zhang J, Gu M, Gerstein M, Schwartz M, et al. MicroRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis. Nature Cell Biology. PMID 30742093 DOI: 10.1038/s41556-019-0272-y  0.88
2019 Posey JE, O'Donnell-Luria AH, Chong JX, Harel T, Jhangiani SN, Coban Akdemir ZH, Buyske S, Pehlivan D, Carvalho CMB, Baxter S, Sobreira N, Liu P, Wu N, Rosenfeld JA, Kumar S, ... ... Gerstein M, et al. Insights into genetics, human biology and disease gleaned from family based genomic studies. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 30655598 DOI: 10.1038/s41436-018-0408-7  0.84
2019 Li S, Gerstein MB. Next-Generation Sequencing to Diagnose Suspected Genetic Disorders. The New England Journal of Medicine. 380: 200. PMID 30628427 DOI: 10.1056/NEJMc1814955#SA1  0.68
2018 Gerstein MB, Navarro FCP. Gene names can confound most-searched listings. Nature. 553: 405. PMID 32094824 DOI: 10.1038/d41586-018-01077-3  0.48
2018 Wang D, Liu S, Warrell J, Won H, Shi X, Navarro FCP, Clarke D, Gu M, Emani P, Yang YT, Xu M, Gandal MJ, Lou S, Zhang J, Park JJ, ... ... Gerstein MB, et al. Comprehensive functional genomic resource and integrative model for the human brain. Science (New York, N.Y.). 362. PMID 30545857 DOI: 10.1126/science.aat8464  0.88
2018 Gandal MJ, Zhang P, Hadjimichael E, Walker RL, Chen C, Liu S, Won H, van Bakel H, Varghese M, Wang Y, Shieh AW, Haney J, Parhami S, Belmont J, Kim M, ... ... Gerstein M, et al. Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder. Science (New York, N.Y.). 362. PMID 30545856 DOI: 10.1126/science.aat8127  1
2018 Li M, Santpere G, Imamura Kawasawa Y, Evgrafov OV, Gulden FO, Pochareddy S, Sunkin SM, Li Z, Shin Y, Zhu Y, Sousa AMM, Werling DM, Kitchen RR, Kang HJ, Pletikos M, ... ... Gerstein MB, et al. Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science (New York, N.Y.). 362. PMID 30545854 DOI: 10.1126/science.aat7615  0.72
2018 Amiri A, Coppola G, Scuderi S, Wu F, Roychowdhury T, Liu F, Pochareddy S, Shin Y, Safi A, Song L, Zhu Y, Sousa AMM, Gerstein M, Crawford GE, et al. Transcriptome and epigenome landscape of human cortical development modeled in organoids. Science (New York, N.Y.). 362. PMID 30545853 DOI: 10.1126/science.aat6720  0.84
2018 Shi W, Ng CKY, Lim RS, Jiang T, Kumar S, Li X, Wali VB, Piscuoglio S, Gerstein MB, Chagpar AB, Weigelt B, Pusztai L, Reis-Filho JS, Hatzis C. Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity. Cell Reports. 25: 1446-1457. PMID 30404001 DOI: 10.1016/j.celrep.2018.10.046  0.68
2018 Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, ... ... Gerstein M, et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Research. PMID 30357393 DOI: 10.1093/nar/gky955  0.68
2018 Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, ... ... Gerstein M, et al. Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. Nature Genetics. PMID 30275530 DOI: 10.1038/s41588-018-0223-8  0.64
2018 Onuchic V, Lurie E, Carrero I, Pawliczek P, Patel RY, Rozowsky J, Galeev T, Huang Z, Altshuler RC, Zhang Z, Harris RA, Coarfa C, Ashmore L, Bertol JW, Fakhouri WD, ... ... Gerstein M, et al. Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. Science (New York, N.Y.). PMID 30139913 DOI: 10.1126/science.aar3146  0.92
2018 Carlyle BC, Kitchen RR, Zhang J, Wilson R, Lam TT, Rozowsky JS, Williams KR, Sestan N, Gerstein M, Nairn AC. Isoform level interpretation of high-throughput proteomic data enabled by deep integration with RNA-seq. Journal of Proteome Research. PMID 30125121 DOI: 10.1021/acs.jproteome.8b00310  0.88
2018 Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, ... ... Gerstein M, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 36: 566-569. PMID 29979655 DOI: 10.1038/nbt.4163  0.72
2018 Barber KW, Muir P, Szeligowski RV, Rogulina S, Gerstein M, Sampson JR, Isaacs FJ, Rinehart J. Encoding human serine phosphopeptides in bacteria for proteome-wide identification of phosphorylation-dependent interactions. Nature Biotechnology. PMID 29889213 DOI: 10.1038/nbt.4150  0.44
2018 Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, ... ... Gerstein M, et al. Repeat associated mechanisms of genome evolution and function revealed by theandgenomes. Genome Research. PMID 29563166 DOI: 10.1101/gr.234096.117  0.6
2018 McGillivray P, Ault R, Pawashe M, Kitchen R, Balasubramanian S, Gerstein M. A comprehensive catalog of predicted functional upstream open reading frames in humans. Nucleic Acids Research. PMID 29562350 DOI: 10.1093/nar/gky188  0.68
2018 Becker T, Lee WP, Leone J, Zhu Q, Zhang C, Liu S, Sargent J, Shanker K, Mil-Homens A, Cerveira E, Ryan M, Cha J, Navarro FCP, Galeev T, Gerstein M, et al. FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods. Genome Biology. 19: 38. PMID 29559002 DOI: 10.1186/s13059-018-1404-6  0.72
2018 Gerstein MB, Navarro FCP. Gene names can confound most-searched listings. Nature. 553: 405. PMID 29368714 DOI: 10.1038/d41586-018-01077-3  0.48
2018 Piening BD, Zhou W, Contrepois K, Röst H, Gu Urban GJ, Mishra T, Hanson BM, Bautista EJ, Leopold S, Yeh CY, Spakowicz D, Banerjee I, Chen C, Kukurba K, Perelman D, ... ... Gerstein M, et al. Integrative Personal Omics Profiles during Periods of Weight Gain and Loss. Cell Systems. PMID 29361466 DOI: 10.1016/j.cels.2017.12.013  0.72
2017 Kudron MM, Victorsen A, Gevirtzman L, Hillier LW, Fisher WW, Vafeados D, Kirkey M, Hammonds AS, Gersch J, Ammouri H, Wall ML, Moran J, Steffen D, Szynkarek M, Seabrook-Sturgis S, ... ... Gerstein M, et al. The modERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors. Genetics. PMID 29284660 DOI: 10.1534/genetics.117.300657  0.72
2017 Carlyle BC, Kitchen RR, Kanyo JE, Voss EZ, Pletikos M, Sousa AMM, Lam TT, Gerstein MB, Sestan N, Nairn AC. A multiregional proteomic survey of the postnatal human brain. Nature Neuroscience. 20: 1787-1795. PMID 29184206 DOI: 10.1038/s41593-017-0011-2  0.52
2017 Sousa AMM, Zhu Y, Raghanti MA, Kitchen RR, Onorati M, Tebbenkamp ATN, Stutz B, Meyer KA, Li M, Kawasawa YI, Liu F, Perez RG, Mele M, Carvalho T, Skarica M, ... ... Gerstein MB, et al. Molecular and cellular reorganization of neural circuits in the human lineage. Science (New York, N.Y.). 358: 1027-1032. PMID 29170230 DOI: 10.1126/science.aan3456  0.52
2017 Lochovsky L, Zhang J, Gerstein M. MOAT: Efficient Detection of Highly Mutated Regions with the Mutations Overburdening Annotations Tool. Bioinformatics (Oxford, England). PMID 29121169 DOI: 10.1093/bioinformatics/btx700  0.88
2017 Kaczor-Urbanowicz KE, Kim Y, Li F, Galeev T, Kitchen RR, Koyano K, Jeong SH, Wang X, Elashoff D, Kang SY, Kim SM, Kim K, Kim S, Chia D, Xiao X, et al. Novel approaches for bioinformatic analysis of salivary RNA Sequencing data in the biomarker development process. Bioinformatics (Oxford, England). PMID 28961734 DOI: 10.1093/bioinformatics/btx504  0.52
2017 Cao Q, Anyansi C, Hu X, Xu L, Xiong L, Tang W, Mok MTS, Cheng C, Fan X, Gerstein M, Cheng ASL, Yip KY. Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines. Nature Genetics. PMID 28869592 DOI: 10.1038/ng.3950  0.76
2017 Balasubramanian S, Fu Y, Pawashe M, McGillivray P, Jin M, Liu J, Karczewski KJ, MacArthur DG, Gerstein M. Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes. Nature Communications. 8: 382. PMID 28851873 DOI: 10.1038/s41467-017-00443-5  0.88
2017 Yan KK, Lou S, Gerstein M. MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions. Plos Computational Biology. 13: e1005647. PMID 28742097 DOI: 10.1371/journal.pcbi.1005647  0.88
2017 Sahraeian SME, Mohiyuddin M, Sebra R, Tilgner H, Afshar PT, Au KF, Bani Asadi N, Gerstein MB, Wong WH, Snyder MP, Schadt E, Lam HYK. Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis. Nature Communications. 8: 59. PMID 28680106 DOI: 10.1038/s41467-017-00050-4  0.84
2017 Zhang Y, Li S, Abyzov A, Gerstein MB. Landscape and variation of novel retroduplications in 26 human populations. Plos Computational Biology. 13: e1005567. PMID 28662076 DOI: 10.1371/journal.pcbi.1005567  0.84
2017 Kumar S, Gerstein M. Cancer genomics: Less is more in the hunt for driver mutations. Nature. PMID 28658210 DOI: 10.1038/nature23085  0.36
2017 Dhingra P, Fu Y, Gerstein M, Khurana E. Using FunSeq2 for Coding and Non-Coding Variant Annotation and Prioritization. Current Protocols in Bioinformatics. 57: 15.11.1-15.11.17. PMID 28463398 DOI: 10.1002/cpbi.23  0.84
2017 Alves P, Liu S, Wang D, Gerstein M. Multiple-Swarm Ensembles: Improving the Predictive Power and Robustness of Predictive Models and Its Use in Computational Biology. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 28391206 DOI: 10.1109/TCBB.2017.2691329  0.72
2017 Despic V, Dejung M, Gu M, Krishnan J, Zhang J, Herzel L, Straube K, Gerstein MB, Butter F, Neugebauer KM. Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition. Genome Research. PMID 28381614 DOI: 10.1101/gr.215954.116  0.88
2017 Greenbaum D, Rozowsky J, Stodden V, Gerstein M. Structuring supplemental materials in support of reproducibility. Genome Biology. 18: 64. PMID 28381262 DOI: 10.1186/s13059-017-1205-3  0.96
2017 Yan KK, Gürkan Yardimci G, Yan C, Noble WS, Gerstein M. HiC-Spector: A matrix library for spectral and reproducibility analysis of Hi-C contact maps. Bioinformatics (Oxford, England). PMID 28369339 DOI: 10.1093/bioinformatics/btx152  0.72
2017 Li S, Shuch BM, Gerstein MB. Whole-genome analysis of papillary kidney cancer finds significant noncoding alterations. Plos Genetics. 13: e1006685. PMID 28358873 DOI: 10.1371/journal.pgen.1006685  0.68
2017 Kasper DM, Moro A, Ristori E, Narayanan A, Hill-Teran G, Fleming E, Moreno-Mateos M, Vejnar CE, Zhang J, Lee D, Gu M, Gerstein M, Giraldez A, Nicoli S. MicroRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos. Developmental Cell. 40: 552-565.e5. PMID 28350988 DOI: 10.1016/j.devcel.2017.02.021  0.88
2017 Abyzov A, Tomasini L, Zhou B, Vasmatzis N, Coppola G, Amenduni M, Pattni R, Wilson M, Gerstein M, Weissman S, Urban AE, Vaccarino FM. One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin. Genome Research. PMID 28235832 DOI: 10.1101/gr.215517.116  0.84
2016 Chen J, Wang B, Regan L, Gerstein M. Intensification: A resource for amplifying population-genetic signals with protein repeats. Journal of Molecular Biology. PMID 27939289 DOI: 10.1016/j.jmb.2016.12.003  0.84
2016 Kumar S, Clarke D, Gerstein M. Localized structural frustration for evaluating the impact of sequence variants. Nucleic Acids Research. 44: 10062-10073. PMID 27915290 DOI: 10.1093/nar/gkw927  0.4
2016 Cheung KH, Keerthikumar S, Roncaglia P, Subramanian SL, Roth ME, Samuel M, Anand S, Gangoda L, Gould S, Alexander R, Galas D, Gerstein MB, Hill AF, Kitchen RR, Lötvall J, et al. Extending gene ontology in the context of extracellular RNA and vesicle communication. Journal of Biomedical Semantics. 7: 19. PMID 27765065 DOI: 10.1186/s13326-016-0061-5  0.72
2016 Wang D, He F, Maslov S, Gerstein M. DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks. Plos Computational Biology. 12: e1005146. PMID 27760135 DOI: 10.1371/journal.pcbi.1005146  0.72
2016 Yang CC, Andrews EH, Chen MH, Wang WY, Chen JJ, Gerstein M, Liu CC, Cheng C. iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data. Bmc Genomics. 17: 632. PMID 27519564 DOI: 10.1186/s12864-016-2963-0  1
2016 Choo SW, Rayko M, Tan TK, Hari R, Komissarov A, Wee WY, Yurchenko A, Kliver S, Tamazian G, Antunes A, Wilson RK, Warren WC, Koepfli KP, Minx P, Krasheninnikova K, ... ... Gerstein MB, et al. Pangolin genomes and the evolution of mammalian scales and immunity. Genome Research. PMID 27510566 DOI: 10.1101/gr.203521.115  1
2016 Freedman JE, Gerstein M, Mick E, Rozowsky J, Levy D, Kitchen R, Das S, Shah R, Danielson K, Beaulieu L, Navarro FC, Wang Y, Galeev TR, Holman A, Kwong RY, et al. Corrigendum: Diverse human extracellular RNAs are widely detected in human plasma. Nature Communications. 7: 11902. PMID 27255613 DOI: 10.1038/ncomms11902  0.72
2016 Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J, Gerstein M. Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation. Genome Biology. 17: 78. PMID 27125642 DOI: 10.1186/s13059-016-0961-9  0.88
2016 Shah R, Tanriverdi K, Levy D, Larson M, Gerstein M, Mick E, Rozowsky J, Kitchen R, Murthy V, Mikalev E, Freedman JE. Discordant Expression of Circulating microRNA from Cellular and Extracellular Sources. Plos One. 11: e0153691. PMID 27123852 DOI: 10.1371/journal.pone.0153691  1
2016 Freedman JE, Gerstein M, Mick E, Rozowsky J, Levy D, Kitchen R, Das S, Shah R, Danielson K, Beaulieu L, Navarro FC, Wang Y, Galeev TR, Holman A, Kwong RY, et al. Diverse human extracellular RNAs are widely detected in human plasma. Nature Communications. 7: 11106. PMID 27112789 DOI: 10.1038/ncomms11106  1
2016 Chen J, Rozowsky J, Galeev TR, Harmanci A, Kitchen R, Bedford J, Abyzov A, Kong Y, Regan L, Gerstein M. A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals. Nature Communications. 7: 11101. PMID 27089393 DOI: 10.1038/ncomms11101  1
2016 Cheung KH, Keerthikumar S, Roncaglia P, Subramanian SL, Roth ME, Samuel M, Anand S, Gangoda L, Gould S, Alexander R, Galas D, Gerstein MB, Hill AF, Kitchen RR, Lötvall J, et al. Extending gene ontology in the context of extracellular RNA and vesicle communication. Journal of Biomedical Semantics. 7: 19. PMID 27076901 DOI: 10.1186/s13326-016-0061-5  0.72
2016 Clarke D, Sethi A, Li S, Kumar S, Chang RW, Chen J, Gerstein M. Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation. Structure (London, England : 1993). PMID 27066750 DOI: 10.1016/j.str.2016.03.008  1
2016 Yan KK, Wang D, Sethi A, Muir P, Kitchen R, Cheng C, Gerstein M. Cross-Disciplinary Network Comparison: Matchmaking Between Hairballs. Cell Systems. 2: 147-157. PMID 27047991 DOI: 10.1016/j.cels.2016.02.014  1
2016 He F, Yoo S, Wang D, Kumari S, Gerstein M, Ware D, Maslov S. Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis. The Plant Journal : For Cell and Molecular Biology. PMID 27015116 DOI: 10.1111/tpj.13175  1
2016 Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J, Gerstein M. The real cost of sequencing: scaling computation to keep pace with data generation. Genome Biology. 17: 53. PMID 27009100 DOI: 10.1186/s13059-016-0917-0  1
2016 Wang D, Yan KK, Rozowsky J, Pan E, Gerstein M. Temporal Dynamics of Collaborative Networks in Large Scientific Consortia. Trends in Genetics : Tig. PMID 27005445 DOI: 10.1016/j.tig.2016.02.006  1
2016 Harmanci A, Gerstein M. Quantification of private information leakage from phenotype-genotype data: linking attacks. Nature Methods. 13: 251-6. PMID 26828419 DOI: 10.1038/nmeth.3746  1
2016 Khurana E, Fu Y, Chakravarty D, Demichelis F, Rubin MA, Gerstein M. Role of non-coding sequence variants in cancer. Nature Reviews. Genetics. 17: 93-108. PMID 26781813 DOI: 10.1038/nrg.2015.17  1
2015 Sethi A, Clarke D, Chen J, Kumar S, Galeev TR, Regan L, Gerstein M. Reads meet rotamers: structural biology in the age of deep sequencing. Current Opinion in Structural Biology. 35: 125-134. PMID 26658741 DOI: 10.1016/  1
2015 Abyzov A, Li S, Gerstein MB. Understanding genome structural variations. Oncotarget. PMID 26657727 DOI: 10.18632/oncotarget.6485  1
2015 Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, ... ... Gerstein MB, et al. The PsychENCODE project. Nature Neuroscience. 18: 1707-1712. PMID 26605881 DOI: 10.1038/nn.4156  1
2015 Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, ... ... Gerstein MB, et al. An integrated map of structural variation in 2,504 human genomes. Nature. 526: 75-81. PMID 26432246 DOI: 10.1038/nature15394  1
2015 Mu JC, Tootoonchi Afshar P, Mohiyuddin M, Chen X, Li J, Bani Asadi N, Gerstein MB, Wong WH, Lam HY. Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods. Scientific Reports. 5: 14493. PMID 26412485 DOI: 10.1038/srep14493  1
2015 Fang LT, Afshar PT, Chhibber A, Mohiyuddin M, Fan Y, Mu JC, Gibeling G, Barr S, Asadi NB, Gerstein MB, Koboldt DC, Wang W, Wong WH, Lam HY. An ensemble approach to accurately detect somatic mutations using SomaticSeq. Genome Biology. 16: 197. PMID 26381235 DOI: 10.1186/s13059-015-0758-2  1
2015 Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB. Erratum: Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. Nature Communications. 6: 8389. PMID 26346554 DOI: 10.1038/ncomms9389  0.84
2015 Duffy EE, Rutenberg-Schoenberg M, Stark CD, Kitchen RR, Gerstein MB, Simon MD. Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry. Molecular Cell. 59: 858-66. PMID 26340425 DOI: 10.1016/j.molcel.2015.07.023  1
2015 Subramanian SL, Kitchen RR, Alexander R, Carter BS, Cheung KH, Laurent LC, Pico A, Roberts LR, Roth ME, Rozowsky JS, Su AI, Gerstein MB, Milosavljevic A. Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. Journal of Extracellular Vesicles. 4: 27497. PMID 26320941 DOI: 10.3402/jev.v4.27497  0.76
2015 Lochovsky L, Zhang J, Fu Y, Khurana E, Gerstein M. LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations. Nucleic Acids Research. PMID 26304545 DOI: 10.1093/nar/gkv803  1
2015 Mariani J, Coppola G, Zhang P, Abyzov A, Provini L, Tomasini L, Amenduni M, Szekely A, Palejev D, Wilson M, Gerstein M, Grigorenko EL, Chawarska K, Pelphrey KA, Howe JR, et al. FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders. Cell. 162: 375-90. PMID 26186191 DOI: 10.1016/j.cell.2015.06.034  1
2015 Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB. Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. Nature Communications. 6: 7256. PMID 26028266 DOI: 10.1038/ncomms8256  1
2015 Wang D, Yan KK, Sisu C, Cheng C, Rozowsky J, Meyerson W, Gerstein MB. Loregic: a method to characterize the cooperative logic of regulatory factors. Plos Computational Biology. 11: e1004132. PMID 25884877 DOI: 10.1371/journal.pcbi.1004132  1
2015 Cheng C, Andrews E, Yan KK, Ung M, Wang D, Gerstein M. An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome. Genome Biology. 16: 63. PMID 25880651 DOI: 10.1186/s13059-015-0624-2  1
2015 Mohiyuddin M, Mu JC, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY. MetaSV: an accurate and integrative structural-variant caller for next generation sequencing. Bioinformatics (Oxford, England). PMID 25861968 DOI: 10.1093/bioinformatics/btv204  1
2015 Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin A, Tanzer A, Lagarde J, Zaleski C, See LH, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, ... ... Gerstein M, et al. Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression. Nature Communications. 6: 5903. PMID 25582907 DOI: 10.1038/ncomms6903  1
2015 Mu JC, Mohiyuddin M, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY. VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. Bioinformatics (Oxford, England). 31: 1469-71. PMID 25524895 DOI: 10.1093/bioinformatics/btu828  1
2015 Kuksa PP, Min MR, Dugar R, Gerstein M. High-order neural networks and kernel methods for peptide-MHC binding prediction Bioinformatics. 31: 3600-3607. DOI: 10.1093/bioinformatics/btv371  1
2015 Abeshouse A, Ahn J, Akbani R, Ally A, Amin S, Andry CD, Annala M, Aprikian A, Armenia J, Arora A, Auman JT, Balasundaram M, Balu S, Barbieri CE, Bauer T, ... ... Gerstein MB, et al. The Molecular Taxonomy of Primary Prostate Cancer Cell. 163: 1011-1025. DOI: 10.1016/j.cell.2015.10.025  1
2014 Kitchen RR, Rozowsky JS, Gerstein MB, Nairn AC. Decoding neuroproteomics: integrating the genome, translatome and functional anatomy. Nature Neuroscience. 17: 1491-9. PMID 25349915 DOI: 10.1038/nn.3829  1
2014 Harmanci A, Rozowsky J, Gerstein M. MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework. Genome Biology. 15: 474. PMID 25292436 DOI: 10.1186/s13059-014-0474-3  1
2014 Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, et al. Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proceedings of the National Academy of Sciences of the United States of America. 111: E3366. PMID 25275169 DOI: 10.1073/pnas.1410434111  1
2014 Fu Y, Liu Z, Lou S, Bedford J, Mu XJ, Yip KY, Khurana E, Gerstein M. FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer. Genome Biology. 15: 480. PMID 25273974 DOI: 10.1186/s13059-014-0480-5  1
2014 Di C, Yuan J, Wu Y, Li J, Lin H, Hu L, Zhang T, Qi Y, Gerstein MB, Guo Y, Lu ZJ. Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features. The Plant Journal : For Cell and Molecular Biology. 80: 848-61. PMID 25256571 DOI: 10.1111/tpj.12679  1
2014 Yan KK, Wang D, Rozowsky J, Zheng H, Cheng C, Gerstein M. OrthoClust: an orthology-based network framework for clustering data across multiple species. Genome Biology. 15: R100. PMID 25249401 DOI: 10.1186/gb-2014-15-8-r100  1
2014 Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, ... ... Gerstein M, et al. Comparative analysis of regulatory information and circuits across distant species. Nature. 512: 453-6. PMID 25164757 DOI: 10.1038/nature13668  1
2014 Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, et al. Comparative analysis of the transcriptome across distant species. Nature. 512: 445-8. PMID 25164755 DOI: 10.1038/nature13424  1
2014 Sisu C, Pei B, Leng J, Frankish A, Zhang Y, Balasubramanian S, Harte R, Wang D, Rutenberg-Schoenberg M, Clark W, Diekhans M, Rozowsky J, Hubbard T, Harrow J, Gerstein MB. Comparative analysis of pseudogenes across three phyla. Proceedings of the National Academy of Sciences of the United States of America. 111: 13361-6. PMID 25157146 DOI: 10.1073/pnas.1407293111  1
2014 Talbert-Slagle K, Atkins KE, Yan KK, Khurana E, Gerstein M, Bradley EH, Berg D, Galvani AP, Townsend JP. Cellular superspreaders: an epidemiological perspective on HIV infection inside the body. Plos Pathogens. 10: e1004092. PMID 24811311 DOI: 10.1371/journal.ppat.1004092  1
2014 MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, ... ... Gerstein MB, et al. Guidelines for investigating causality of sequence variants in human disease. Nature. 508: 469-76. PMID 24759409 DOI: 10.1038/nature13127  1
2014 Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, et al. Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 111: 6131-8. PMID 24753594 DOI: 10.1073/pnas.1318948111  1
2014 Miller JA, Ding SL, Sunkin SM, Smith KA, Ng L, Szafer A, Ebbert A, Riley ZL, Royall JJ, Aiona K, Arnold JM, Bennet C, Bertagnolli D, Brouner K, Butler S, ... ... Gerstein MB, et al. Transcriptional landscape of the prenatal human brain. Nature. 508: 199-206. PMID 24695229 DOI: 10.1038/nature13185  1
2014 Chen C, Ha BH, Thévenin AF, Lou HJ, Zhang R, Yip KY, Peterson JR, Gerstein M, Kim PM, Filippakopoulos P, Knapp S, Boggon TJ, Turk BE. Identification of a major determinant for serine-threonine kinase phosphoacceptor specificity. Molecular Cell. 53: 140-7. PMID 24374310 DOI: 10.1016/j.molcel.2013.11.013  1
2014 Greenbaum D, Harmanci A, Gerstein M. Proposed social and technological solutions to issues of data privacy in personal genomics 2014 Ieee International Symposium On Ethics in Science, Technology and Engineering, Ethics 2014. DOI: 10.1109/ETHICS.2014.6893418  1
2014 Min MR, Ning X, Cheng C, Gerstein M. Interpretable sparse high-order Boltzmann machines Journal of Machine Learning Research. 33: 614-622.  1
2013 Steijger T, Abril JF, Engström PG, Kokocinski F, Hubbard TJ, Guigó R, Harrow J, Bertone P. Assessment of transcript reconstruction methods for RNA-seq. Nature Methods. 10: 1177-84. PMID 24185837 DOI: 10.1038/nmeth.2714  1
2013 Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, ... ... Gerstein M, et al. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science (New York, N.Y.). 342: 1235587. PMID 24092746 DOI: 10.1126/science.1235587  1
2013 Abyzov A, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L, Lee C, Gerstein M. Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division. Genome Research. 23: 2042-52. PMID 24026178 DOI: 10.1101/gr.154625.113  1
2013 Cheng C, Fu Y, Shen L, Gerstein M. Identification of yeast cell cycle regulated genes based on genomic features. Bmc Systems Biology. 7: 70. PMID 23895232 DOI: 10.1186/1752-0509-7-70  1
2013 Qian F, Chung L, Zheng W, Bruno V, Alexander RP, Wang Z, Wang X, Kurscheid S, Zhao H, Fikrig E, Gerstein M, Snyder M, Montgomery RR. Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis. Viruses. 5: 1664-81. PMID 23881275 DOI: 10.3390/v5071664  1
2013 Fang G, Passalacqua KD, Hocking J, Llopis PM, Gerstein M, Bergman NH, Jacobs-Wagner C. Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution Bmc Genomics. 14. PMID 23829427 DOI: 10.1186/1471-2164-14-450  1
2013 Yip KY, Cheng C, Gerstein MB. Machine learning and genome annotation: A match meant to be? Genome Biology. 205. PMID 23731483 DOI: 10.1186/gb-2013-14-5-205  1
2013 Doolittle WF, Fraser P, Gerstein MB, Graveley BR, Henikoff S, Huttenhower C, Oshlack A, Ponting CP, Rinn JL, Schatz MC, Ule J, Weigel D, Weinstock GM. Sixty years of genome biology. Genome Biology. 14: 113. PMID 23651518 DOI: 10.1186/gb-2013-14-4-113  1
2013 Khurana E, Fu Y, Chen J, Gerstein M. Interpretation of Genomic Variants Using a Unified Biological Network Approach Plos Computational Biology. 9. PMID 23505346 DOI: 10.1371/journal.pcbi.1002886  1
2013 Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J, MacArthur DG, ... ... Gerstein M, et al. The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Research. 23: 749-61. PMID 23478400 DOI: 10.1101/gr.148718.112  1
2013 Tilgner H, Raha D, Habegger L, Mohiuddin M, Gerstein M, Snyder M. Accurate identification and analysis of human mRNA isoforms using deep long read sequencing. G3 (Bethesda, Md.). 3: 387-97. PMID 23450794 DOI: 10.1534/g3.112.004812  1
2013 Kittler R, Zhou J, Hua S, Ma L, Liu Y, Pendleton E, Cheng C, Gerstein M, White KP. A comprehensive nuclear receptor network for breast cancer cells. Cell Reports. 3: 538-51. PMID 23375374 DOI: 10.1016/j.celrep.2013.01.004  1
2013 Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V. Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biology. 14: R5. PMID 23347407 DOI: 10.1186/gb-2013-14-1-r5  0.8
2013 Zhang Y, Haraksingh R, Grubert F, Abyzov A, Gerstein M, Weissman S, Urban AE. Child development and structural variation in the human genome. Child Development. 84: 34-48. PMID 23311762 DOI: 10.1111/cdev.12051  1
2013 Lin PC, Chiu YL, Banerjee S, Park K, Mosquera JM, Giannopoulou E, Alves P, Tewari AK, Gerstein MB, Beltran H, Melnick AM, Elemento O, Demichelis F, Rubin MA. Epigenetic repression of miR-31 disrupts androgen receptor homeostasis and contributes to prostate cancer progression. Cancer Research. 73: 1232-44. PMID 23233736 DOI: 10.1158/0008-5472.CAN-12-2968  1
2013 Wang D, Pan E, Fang G, Kumari S, He F, Ware D, Maslov S, Gerstein M. Comparative network analysis of gene co-expression networks reveals the conserved and species-specific functions of cell-wall related genes between arabidopsis and poplar 2013 Acm Conference On Bioinformatics, Computational Biology and Biomedical Informatics, Acm-Bcb 2013. 689-690. DOI: 10.1145/2506583.2506690  1
2013 Greenbaum D, Chen J, Gerstein M. Deep inside champions, just genes? Science. 342: 560-561. DOI: 10.1126/science.1245795  1
2013 Gerstein M, Greenbaum D. Proceed with caution Scientist. 27.  1
2012 Abyzov A, Mariani J, Palejev D, Zhang Y, Haney MS, Tomasini L, Ferrandino AF, Rosenberg Belmaker LA, Szekely A, Wilson M, Kocabas A, Calixto NE, Grigorenko EL, Huttner A, Chawarska K, ... ... Gerstein M, et al. Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. Nature. 492: 438-42. PMID 23160490 DOI: 10.1038/nature11629  1
2012 Gerstein M. Genomics: ENCODE leads the way on big data Nature. 489: 208. PMID 22972285 DOI: 10.1038/489208b  1
2012 Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, ... Gerstein M, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 22: 1813-31. PMID 22955991 DOI: 10.1101/gr.136184.111  1
2012 Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, ... ... Gerstein M, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Research. 22: 1760-74. PMID 22955987 DOI: 10.1101/gr.135350.111  1
2012 Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, ... ... Gerstein M, et al. Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Research. 22: 1658-67. PMID 22955978 DOI: 10.1101/gr.136838.111  1
2012 Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, ... ... Gerstein M, et al. Landscape of transcription in human cells. Nature. 489: 101-8. PMID 22955620 DOI: 10.1038/nature11233  1
2012 Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 489: 91-100. PMID 22955619 DOI: 10.1038/nature11245  1
2012 . An integrated encyclopedia of DNA elements in the human genome. Nature. 489: 57-74. PMID 22955616 DOI: 10.1038/nature11247  0.96
2012 Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, Reymond A, Hubbard TJ, Harrow J, Gerstein MB. The GENCODE pseudogene resource. Genome Biology. 13: R51. PMID 22951037 DOI: 10.1186/gb-2012-13-9-r51  1
2012 Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, Gerstein M. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biology. 13: R48. PMID 22950945 DOI: 10.1186/gb-2012-13-9-r48  1
2012 Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E, Weng Z. Modeling gene expression using chromatin features in various cellular contexts. Genome Biology. 13: R53. PMID 22950368 DOI: 10.1186/gb-2012-13-9-r53  1
2012 Iskow RC, Gokcumen O, Abyzov A, Malukiewicz J, Zhu Q, Sukumar AT, Pai AA, Mills RE, Habegger L, Cusanovich DA, Rubel MA, Perry GH, Gerstein M, Stone AC, Gilad Y, et al. Regulatory element copy number differences shape primate expression profiles. Proceedings of the National Academy of Sciences of the United States of America. 109: 12656-61. PMID 22797897 DOI: 10.1073/pnas.1205199109  1
2012 Zilberman-Schapira G, Chen J, Gerstein M. On Sports and Genes Recent Patents On Dna and Gene Sequences. 6: 180-188. PMID 22762737  1
2012 Habegger L, Balasubramanian S, Chen DZ, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M. VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinformatics (Oxford, England). 28: 2267-9. PMID 22743228 DOI: 10.1093/bioinformatics/bts368  1
2012 Bamshad MJ, Shendure JA, Valle D, Hamosh A, Lupski JR, Gibbs RA, Boerwinkle E, Lifton RP, Gerstein M, Gunel M, Mane S, Nickerson DA. The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions. American Journal of Medical Genetics. Part A. 158: 1523-5. PMID 22628075 DOI: 10.1002/ajmg.a.35470  1
2012 Vidal M, Chan DW, Gerstein M, Mann M, Omenn GS, Tagle D, Sechi S. The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare. Clinical Proteomics. 9: 6. PMID 22583803 DOI: 10.1186/1559-0275-9-6  1
2012 Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Chen R, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Cheng Y, Clark MJ, Im H, Habegger L, Balasubramanian S, ... ... Gerstein M, et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 148: 1293-307. PMID 22424236 DOI: 10.1016/j.cell.2012.02.009  1
2012 Cotney J, Leng J, Oh S, DeMare LE, Reilly SK, Gerstein MB, Noonan JP. Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb. Genome Research. 22: 1069-80. PMID 22421546 DOI: 10.1101/gr.129817.111  0.4
2012 Wu JQ, Seay M, Schulz VP, Hariharan M, Tuck D, Lian J, Du J, Shi M, Ye Z, Gerstein M, Snyder MP, Weissman S. Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line. Plos Genetics. 8: e1002565. PMID 22412390 DOI: 10.1371/journal.pgen.1002565  1
2012 Lam HY, Pan C, Clark MJ, Lacroute P, Chen R, Haraksingh R, O'Huallachain M, Gerstein MB, Kidd JM, Bustamante CD, Snyder M. Detecting and annotating genetic variations using the HugeSeq pipeline. Nature Biotechnology. 30: 226-9. PMID 22398614 DOI: 10.1038/nbt.2134  1
2012 Gianoulis TA, Griffin MA, Spakowicz DJ, Dunican BF, Alpha CJ, Sboner A, Sismour AM, Kodira C, Egholm M, Church GM, Gerstein MB, Strobel SA. Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides. Plos Genetics. 8: e1002558. PMID 22396667 DOI: 10.1371/journal.pgen.1002558  0.84
2012 MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, ... ... Gerstein MB, et al. A systematic survey of loss-of-function variants in human protein-coding genes. Science (New York, N.Y.). 335: 823-8. PMID 22344438 DOI: 10.1126/science.1215040  1
2012 Clarke D, Bhardwaj N, Gerstein MB. Novel insights through the integration of structural and functional genomics data with protein networks. Journal of Structural Biology. 179: 320-6. PMID 22343087 DOI: 10.1016/j.jsb.2012.02.001  1
2012 Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, ... ... Gerstein M, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 148: 84-98. PMID 22265404 DOI: 10.1016/j.cell.2011.12.014  1
2012 Du J, Leng J, Habegger L, Sboner A, McDermott D, Gerstein M. IQSeq: integrated isoform quantification analysis based on next-generation sequencing. Plos One. 7: e29175. PMID 22238592 DOI: 10.1371/journal.pone.0029175  1
2012 Lam HY, Clark MJ, Chen R, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M. Performance comparison of whole-genome sequencing platforms. Nature Biotechnology. 30: 78-82. PMID 22178993 DOI: 10.1038/nbt.2065  1
2012 Cheng C, Gerstein M. Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells Nucleic Acids Research. 40: 553-568. PMID 21926158 DOI: 10.1093/nar/gkr752  1
2011 Beltran H, Rickman D, Park K, Sboner A, Macdonald T, Tagawa ST, Gerstein MB, Demichelis F, Nanus DM, Rubin MA. Molecular characterization of neuroendocrine prostate cancer (NEPC) and identification of new drug targets. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 29: 4536. PMID 28023415 DOI: 10.1200/jco.2011.29.15_suppl.4536  0.84
2011 Beltran H, Rickman D, Park K, Sboner A, Macdonald T, Tagawa ST, Gerstein MB, Demichelis F, Nanus DM, Rubin MA. Molecular characterization of neuroendocrine prostate cancer (NEPC) and identification of new drug targets. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 29: 19. PMID 27968392 DOI: 10.1200/jco.2011.29.7_suppl.19  0.84
2011 Beltran H, Rickman DS, Park K, Chae SS, Sboner A, MacDonald TY, Wang Y, Sheikh KL, Terry S, Tagawa ST, Dhir R, Nelson JB, de la Taille A, Allory Y, Gerstein MB, et al. Molecular characterization of neuroendocrine prostate cancer and identification of new drug targets. Cancer Discovery. 1: 487-95. PMID 22389870 DOI: 10.1158/2159-8290.CD-11-0130  0.4
2011 Bhardwaj N, Clarke D, Gerstein M. Systematic control of protein interactions for systems biology. Proceedings of the National Academy of Sciences of the United States of America. 108: 20279-80. PMID 22160691 DOI: 10.1073/pnas.1118084109  1
2011 Greenbaum D, Sboner A, Mu XJ, Gerstein M. Genomics and privacy: implications of the new reality of closed data for the field. Plos Computational Biology. 7: e1002278. PMID 22144881 DOI: 10.1371/journal.pcbi.1002278  1
2011 Haraksingh RR, Abyzov A, Gerstein M, Urban AE, Snyder M. Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms. Plos One. 6: e27859. PMID 22140474 DOI: 10.1371/journal.pone.0027859  1
2011 Cheng C, Yan KK, Hwang W, Qian J, Bhardwaj N, Rozowsky J, Lu ZJ, Niu W, Alves P, Kato M, Snyder M, Gerstein M. Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. Plos Computational Biology. 7: e1002190. PMID 22125477 DOI: 10.1371/journal.pcbi.1002190  1
2011 Cheng C, Shou C, Yip KY, Gerstein MB. Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors. Genome Biology. 12: R111. PMID 22060676 DOI: 10.1186/gb-2011-12-11-r111  1
2011 Greenbaum D, Gerstein M. The role of cloud computing in managing the deluge of potentially private genetic data. The American Journal of Bioethics : Ajob. 11: 39-41. PMID 22047125 DOI: 10.1080/15265161.2011.608242  1
2011 Cheng C, Min R, Gerstein M. TIP: a probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles. Bioinformatics (Oxford, England). 27: 3221-7. PMID 22039215 DOI: 10.1093/bioinformatics/btr552  1
2011 Flores SC, Gerstein MB. Predicting protein ligand binding motions with the conformation explorer. Bmc Bioinformatics. 12: 417. PMID 22032721 DOI: 10.1186/1471-2105-12-417  1
2011 Tanas MR, Sboner A, Oliveira AM, Erickson-Johnson MR, Hespelt J, Hanwright PJ, Flanagan J, Luo Y, Fenwick K, Natrajan R, Mitsopoulos C, Zvelebil M, Hoch BL, Weiss SW, Debiec-Rychter M, ... ... Gerstein MB, et al. Identification of a disease-defining gene fusion in epithelioid hemangioendothelioma. Science Translational Medicine. 3: 98ra82. PMID 21885404 DOI: 10.1126/scitranslmed.3002409  1
2011 Sboner A, Mu XJ, Greenbaum D, Auerbach RK, Gerstein MB. The real cost of sequencing: higher than you think! Genome Biology. 12: 125. PMID 21867570 DOI: 10.1186/gb-2011-12-8-125  1
2011 Yip KY, Utz L, Sitwell S, Hu X, Sidhu SS, Turk BE, Gerstein M, Kim PM. Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps. Bmc Biology. 9: 53. PMID 21835011 DOI: 10.1186/1741-7007-9-53  1
2011 Bhardwaj N, Abyzov A, Clarke D, Shou C, Gerstein MB. Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions. Protein Science : a Publication of the Protein Society. 20: 1745-54. PMID 21826754 DOI: 10.1002/pro.710  1
2011 Rozowsky J, Abyzov A, Wang J, Alves P, Raha D, Harmanci A, Leng J, Bjornson R, Kong Y, Kitabayashi N, Bhardwaj N, Rubin M, Snyder M, Gerstein M. AlleleSeq: analysis of allele-specific expression and binding in a network framework. Molecular Systems Biology. 7: 522. PMID 21811232 DOI: 10.1038/msb.2011.54  1
2011 Zhang ZD, Du J, Lam H, Abyzov A, Urban AE, Snyder M, Gerstein M. Identification of genomic indels and structural variations using split reads. Bmc Genomics. 12: 375. PMID 21787423 DOI: 10.1186/1471-2164-12-375  1
2011 Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A, Rozowsky JS, Gerstein MB, Wahlestedt C, Hayashizaki Y, Carninci P, et al. The reality of pervasive transcription. Plos Biology. 9: e1000625; discussion. PMID 21765801 DOI: 10.1371/journal.pbio.1000625  1
2011 Yan KK, Gerstein M. The spread of scientific information: Insights from the web usage statistics in PLoS article-level metrics Plos One. 6. PMID 21603617 DOI: 10.1371/journal.pone.0019917  1
2011 Mu XJ, Lu ZJ, Kong Y, Lam HY, Gerstein MB. Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. Nucleic Acids Research. 39: 7058-76. PMID 21596777 DOI: 10.1093/nar/gkr342  1
2011 Greenbaum D, Gerstein M. Social considerations in research: consider them but don't use them. The American Journal of Bioethics : Ajob. 11: 31-2. PMID 21534147 DOI: 10.1080/15265161.2011.562598  1
2011 . A user's guide to the encyclopedia of DNA elements (ENCODE). Plos Biology. 9: e1001046. PMID 21526222 DOI: 10.1371/journal.pbio.1001046  0.32
2011 Fasolo J, Sboner A, Sun MG, Yu H, Chen R, Sharon D, Kim PM, Gerstein M, Snyder M. Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes. Genes & Development. 25: 767-78. PMID 21460040 DOI: 10.1101/gad.1998811  1
2011 Gianoulis TA, Agarwal A, Snyder M, Gerstein MB. The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics. Genome Biology. 12: R32. PMID 21453526 DOI: 10.1186/gb-2011-12-3-r32  1
2011 Nègre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, Li Z, Ishii H, Spokony RF, Chen J, Hwang L, ... ... Gerstein M, et al. A cis-regulatory map of the Drosophila genome. Nature. 471: 527-31. PMID 21430782 DOI: 10.1038/nature09990  1
2011 Lipman D, Flicek P, Salzberg S, Gerstein M, Knight R. Closure of the NCBI SRA and implications for the long-term future of genomics data storage. Genome Biology. 12: 402. PMID 21418618 DOI: 10.1186/gb-2011-12-3-402  1
2011 Euskirchen GM, Auerbach RK, Davidov E, Gianoulis TA, Zhong G, Rozowsky J, Bhardwaj N, Gerstein MB, Snyder M. Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. Plos Genetics. 7: e1002008. PMID 21408204 DOI: 10.1371/journal.pgen.1002008  1
2011 Jee J, Rozowsky J, Yip KY, Lochovsky L, Bjornson R, Zhong G, Zhang Z, Fu Y, Wang J, Weng Z, Gerstein M. ACT: aggregation and correlation toolbox for analyses of genome tracks. Bioinformatics (Oxford, England). 27: 1152-4. PMID 21349863 DOI: 10.1093/bioinformatics/btr092  1
2011 Karpikov A, Rozowsky J, Gerstein M. Tiling array data analysis: A multiscale approach using wavelets Bmc Bioinformatics. 12. PMID 21338513 DOI: 10.1186/1471-2105-12-57  1
2011 Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Research. 21: 974-84. PMID 21324876 DOI: 10.1101/gr.114876.110  1
2011 Cheng C, Yan KK, Yip KY, Rozowsky J, Alexander R, Shou C, Gerstein M. A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets. Genome Biology. 12: R15. PMID 21324173 DOI: 10.1186/gb-2011-12-2-r15  1
2011 Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, Sougnez C, Onofrio R, Carter SL, Park K, Habegger L, Ambrogio L, ... ... Gerstein MB, et al. The genomic complexity of primary human prostate cancer. Nature. 470: 214-20. PMID 21307934 DOI: 10.1038/nature09744  1
2011 Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, ... ... Gerstein MB, et al. Mapping copy number variation by population-scale genome sequencing. Nature. 470: 59-65. PMID 21293372 DOI: 10.1038/nature09708  1
2011 Shou C, Bhardwaj N, Lam HY, Yan KK, Kim PM, Snyder M, Gerstein MB. Measuring the evolutionary rewiring of biological networks. Plos Computational Biology. 7: e1001050. PMID 21253555 DOI: 10.1371/journal.pcbi.1001050  1
2011 Abyzov A, Gerstein M. AGE: Defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision Bioinformatics. 27: 595-603. PMID 21233167 DOI: 10.1093/bioinformatics/btq713  1
2011 Balasubramanian S, Habegger L, Frankish A, MacArthur DG, Harte R, Tyler-Smith C, Harrow J, Gerstein M. Gene inactivation and its implications for annotation in the era of personal genomics. Genes & Development. 25: 1-10. PMID 21205862 DOI: 10.1101/gad.1968411  1
2011 Vaccarino FM, Urban AE, Stevens HE, Szekely A, Abyzov A, Grigorenko EL, Gerstein M, Weissman S. Annual Research Review: The promise of stem cell research for neuropsychiatric disorders. Journal of Child Psychology and Psychiatry, and Allied Disciplines. 52: 504-16. PMID 21204834 DOI: 10.1111/j.1469-7610.2010.02348.x  1
2011 Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, ... ... Gerstein MB, et al. Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome Research. 21: 276-85. PMID 21177971 DOI: 10.1101/gr.110189.110  1
2011 Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E, Slightham C, Jiang L, Hyman AA, Kim SK, Waterston RH, ... Gerstein M, et al. Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Research. 21: 245-54. PMID 21177963 DOI: 10.1101/gr.114587.110  1
2011 Habegger L, Sboner A, Gianoulis TA, Rozowsky J, Agarwal A, Snyder M, Gerstein M. RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinformatics (Oxford, England). 27: 281-3. PMID 21134889 DOI: 10.1093/bioinformatics/btq643  1
2011 Pflueger D, Terry S, Sboner A, Habegger L, Esgueva R, Lin PC, Svensson MA, Kitabayashi N, Moss BJ, MacDonald TY, Cao X, Barrette T, Tewari AK, Chee MS, Chinnaiyan AM, ... ... Gerstein MB, et al. Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing. Genome Research. 21: 56-67. PMID 21036922 DOI: 10.1101/gr.110684.110  1
2011 Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, ... ... Gerstein MB, et al. Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data (Genome Research (2011) 21, (276-285)) Genome Research. 21: 811.  1
2011 Gerstein MB. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE Project (Science (2010) (1775)) Science. 331: 30.  1
2011 Greenbaum D, Gerstein M. The benefits of snooping Technology Review. 114: 6.  1
2010 Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (New York, N.Y.). 330: 1775-87. PMID 21177976 DOI: 10.1126/science.1196914  1
2010 Bhardwaj N, Kim PM, Gerstein MB. Rewiring of transcriptional regulatory networks: hierarchy, rather than connectivity, better reflects the importance of regulators. Science Signaling. 3: ra79. PMID 21045205 DOI: 10.1126/scisignal.2001014  1
2010 Li X, Gianoulis TA, Yip KY, Gerstein M, Snyder M. Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses. Cell. 143: 639-50. PMID 21035178 DOI: 10.1016/j.cell.2010.09.048  1
2010 Zhang ZD, Gerstein MB. Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model. Bmc Bioinformatics. 11: 539. PMID 21034510 DOI: 10.1186/1471-2105-11-539  1
2010 Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, Demichelis F, Rubin MA, Gerstein MB. FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biology. 11: R104. PMID 20964841 DOI: 10.1186/gb-2010-11-10-r104  1
2010 Cheung KH, Samwald M, Auerbach RK, Gerstein MB. Structured digital tables on the Semantic Web: toward a structured digital literature. Molecular Systems Biology. 6: 403. PMID 20739925 DOI: 10.1038/msb.2010.45  1
2010 Alexander RP, Fang G, Rozowsky J, Snyder M, Gerstein MB. Annotating non-coding regions of the genome. Nature Reviews. Genetics. 11: 559-71. PMID 20628352 DOI: 10.1038/nrg2814  1
2010 Khurana E, Lam HY, Cheng C, Carriero N, Cayting P, Gerstein MB. Segmental duplications in the human genome reveal details of pseudogene formation. Nucleic Acids Research. 38: 6997-7007. PMID 20615899 DOI: 10.1093/nar/gkq587  1
2010 Agarwal A, Koppstein D, Rozowsky J, Sboner A, Habegger L, Hillier LW, Sasidharan R, Reinke V, Waterston RH, Gerstein M. Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays Bmc Genomics. 11. PMID 20565764 DOI: 10.1186/1471-2164-11-383  1
2010 Holford ME, Khurana E, Cheung KH, Gerstein M. Using semantic web rules to reason on an ontology of pseudogenes Bioinformatics. 26. PMID 20529940 DOI: 10.1093/bioinformatics/btq173  1
2010 Bhardwaj N, Carson MB, Abyzov A, Yan KK, Lu H, Gerstein MB. Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets. Plos Computational Biology. 6: e1000755. PMID 20523742 DOI: 10.1371/journal.pcbi.1000755  1
2010 Voss NR, Gerstein M. 3V: cavity, channel and cleft volume calculator and extractor. Nucleic Acids Research. 38: W555-62. PMID 20478824 DOI: 10.1093/nar/gkq395  1
2010 Lam HY, Kim PM, Mok J, Tonikian R, Sidhu SS, Turk BE, Snyder M, Gerstein MB. MOTIPS: automated motif analysis for predicting targets of modular protein domains. Bmc Bioinformatics. 11: 243. PMID 20459839 DOI: 10.1186/1471-2105-11-243  1
2010 Yan KK, Fang G, Bhardwaj N, Alexander RP, Gerstein M. Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks. Proceedings of the National Academy of Sciences of the United States of America. 107: 9186-91. PMID 20439753 DOI: 10.1073/pnas.0914771107  1
2010 Patel PV, Gianoulis TA, Bjornson RD, Yip KY, Engelman DM, Gerstein MB. Analysis of membrane proteins in metagenomics: networks of correlated environmental features and protein families. Genome Research. 20: 960-71. PMID 20430783 DOI: 10.1101/gr.102814.109  1
2010 Lee Y, Yang X, Huang Y, Fan H, Zhang Q, Wu Y, Li J, Hasina R, Cheng C, Lingen MW, Gerstein MB, Weichselbaum RR, Xing HR, Lussier YA. Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis. Plos Computational Biology. 6: e1000730. PMID 20369013 DOI: 10.1371/journal.pcbi.1000730  1
2010 Fang G, Bhardwaj N, Robilotto R, Gerstein MB. Getting started in gene orthology and functional analysis. Plos Computational Biology. 6: e1000703. PMID 20361041 DOI: 10.1371/journal.pcbi.1000703  1
2010 Bhardwaj N, Yan KK, Gerstein MB. Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels. Proceedings of the National Academy of Sciences of the United States of America. 107: 6841-6. PMID 20351254 DOI: 10.1073/pnas.0910867107  1
2010 Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong MY, Karczewski KJ, Huber W, Weissman SM, Gerstein MB, et al. Variation in transcription factor binding among humans. Science (New York, N.Y.). 328: 232-5. PMID 20299548 DOI: 10.1126/science.1183621  1
2010 Sboner A, Demichelis F, Calza S, Pawitan Y, Setlur SR, Hoshida Y, Perner S, Adami HO, Fall K, Mucci LA, Kantoff PW, Stampfer M, Andersson SO, Varenhorst E, Johansson JE, ... Gerstein MB, et al. Molecular sampling of prostate cancer: a dilemma for predicting disease progression. Bmc Medical Genomics. 3: 8. PMID 20233430 DOI: 10.1186/1755-8794-3-8  1
2010 Zhang ZD, Frankish A, Hunt T, Harrow J, Gerstein M. Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. Genome Biology. 11: R26. PMID 20210993 DOI: 10.1186/gb-2010-11-3-r26  1
2010 Wu JQ, Habegger L, Noisa P, Szekely A, Qiu C, Hutchison S, Raha D, Egholm M, Lin H, Weissman S, Cui W, Gerstein M, Snyder M. Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proceedings of the National Academy of Sciences of the United States of America. 107: 5254-9. PMID 20194744 DOI: 10.1073/pnas.0914114107  1
2010 Snyder M, Du J, Gerstein M. Personal genome sequencing: Current approaches and challenges Genes and Development. 24: 423-431. PMID 20194435 DOI: 10.1101/gad.1864110  1
2010 Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HY, Preston E, Slightham C, Hillier LW, Brock T, Agarwal A, Auerbach R, ... ... Gerstein M, et al. Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. Plos Genetics. 6: e1000848. PMID 20174564 DOI: 10.1371/journal.pgen.1000848  1
2010 Mok J, Kim PM, Lam HY, Piccirillo S, Zhou X, Jeschke GR, Sheridan DL, Parker SA, Desai V, Jwa M, Cameroni E, Niu H, Good M, Remenyi A, Ma JL, ... ... Gerstein MB, et al. Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Science Signaling. 3: ra12. PMID 20159853 DOI: 10.1126/scisignal.2000482  1
2010 Raha D, Wang Z, Moqtaderi Z, Wu L, Zhong G, Gerstein M, Struhl K, Snyder M. Close association of RNA polymerase II and many transcription factors with Pol III genes. Proceedings of the National Academy of Sciences of the United States of America. 107: 3639-44. PMID 20139302 DOI: 10.1073/pnas.0911315106  1
2010 Yip KY, Alexander RP, Yan KK, Gerstein M. Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data. Plos One. 5: e8121. PMID 20126643 DOI: 10.1371/journal.pone.0008121  1
2010 Bhardwaj N, Gerstein M, Lu H. Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique. Bmc Bioinformatics. 11: S6. PMID 20122235 DOI: 10.1186/1471-2105-11-S1-S6  1
2010 Lam HY, Mu XJ, Stütz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB. Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nature Biotechnology. 28: 47-55. PMID 20037582 DOI: 10.1038/nbt.1600  1
2010 Abyzov A, Bjornson R, Felipe M, Gerstein M. RigidFinder: A fast and sensitive method to detect rigid blocks in large macromolecular compleses Proteins: Structure, Function and Bioinformatics. 78: 309-324. PMID 19705487 DOI: 10.1002/prot.22544  1
2010 Sboner A, Karpikov A, Chen G, Smith M, Mattoon D, Freeman-Cook L, Schweitzer B, Gerstein MB. Robust-linear-model normalization to reduce technical variability in functional protein microarrays (Journal Proteome Research (2009) 8, (5451-5464)) Journal of Proteome Research. 9: 636. DOI: 10.1021/pr901104y  0.4
2009 Canaan A, Haviv I, Urban AE, Schulz VP, Hartman S, Zhang Z, Palejev D, Deisseroth AB, Lacy J, Snyder M, Gerstein M, Weissman SM. EBNA1 regulates cellular gene expression by binding cellular promoters. Proceedings of the National Academy of Sciences of the United States of America. 106: 22421-6. PMID 20080792 DOI: 10.1073/pnas.0911676106  1
2009 Greenbaum D, Gerstein M. Social networking and personal genomics: suggestions for optimizing the interaction. The American Journal of Bioethics : Ajob. 9: 15-9. PMID 19998104 DOI: 10.1080/15265160902894039  1
2009 Tonikian R, Xin X, Toret CP, Gfeller D, Landgraf C, Panni S, Paoluzi S, Castagnoli L, Currell B, Seshagiri S, Yu H, Winsor B, Vidal M, Gerstein MB, Bader GD, et al. Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. Plos Biology. 7: e1000218. PMID 19841731 DOI: 10.1371/journal.pbio.1000218  1
2009 Liu YJ, Zheng D, Balasubramanian S, Carriero N, Khurana E, Robilotto R, Gerstein MB. 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. Bmc Genomics. 10: 480. PMID 19835609 DOI: 10.1186/1471-2164-10-480  1
2009 Sboner A, Karpikov A, Chen G, Smith M, Mattoon D, Dawn M, Freeman-Cook L, Schweitzer B, Gerstein MB. Robust-linear-model normalization to reduce technical variability in functional protein microarrays. Journal of Proteome Research. 8: 5451-64. PMID 19817483 DOI: 10.1021/pr900412k  1
2009 Cheng C, Bhardwaj N, Gerstein M. The relationship between the evolution of microRNA targets and the length of their UTRs. Bmc Genomics. 10: 431. PMID 19751524 DOI: 10.1186/1471-2164-10-431  0.76
2009 Arinaminpathy Y, Khurana E, Engelman DM, Gerstein MB. Computational analysis of membrane proteins: the largest class of drug targets. Drug Discovery Today. 14: 1130-5. PMID 19733256 DOI: 10.1016/j.drudis.2009.08.006  1
2009 Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefrançois P, Struhl K, Gerstein M, Snyder M. Mapping accessible chromatin regions using Sono-Seq. Proceedings of the National Academy of Sciences of the United States of America. 106: 14926-31. PMID 19706456 DOI: 10.1073/pnas.0905443106  1
2009 Yip KY, Kim PM, McDermott D, Gerstein M. Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels. Bmc Bioinformatics. 10: 241. PMID 19656385 DOI: 10.1186/1471-2105-10-241  1
2009 Rzhetsky A, Seringhaus M, Gerstein MB. Getting started in text mining: part two. Plos Computational Biology. 5: e1000411. PMID 19649304 DOI: 10.1371/journal.pcbi.1000411  1
2009 Pflueger D, Rickman DS, Sboner A, Perner S, LaFargue CJ, Svensson MA, Moss BJ, Kitabayashi N, Pan Y, de la Taille A, Kuefer R, Tewari AK, Demichelis F, Chee MS, Gerstein MB, et al. N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer. Neoplasia (New York, N.Y.). 11: 804-11. PMID 19649210 DOI: 10.1593/neo.09572  1
2009 Guo X, Zhang Z, Gerstein MB, Zheng D. Small RNAs originated from pseudogenes: cis- or trans-acting? Plos Computational Biology. 5: e1000449. PMID 19649160 DOI: 10.1371/journal.pcbi.1000449  1
2009 Alexander RP, Kim PM, Emonet T, Gerstein MB. Understanding modularity in molecular networks requires dynamics. Science Signaling. 2: pe44. PMID 19638611 DOI: 10.1126/scisignal.281pe44  1
2009 Sasidharan R, Agarwal A, Rozowsky J, Gerstein M. An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping. Bmc Research Notes. 2: 150. PMID 19630981 DOI: 10.1186/1756-0500-2-150  1
2009 Korbel JO, Tirosh-Wagner T, Urban AE, Chen XN, Kasowski M, Dai L, Grubert F, Erdman C, Gao MC, Lange K, Sobel EM, Barlow GM, Aylsworth AS, Carpenter NJ, Clark RD, ... ... Gerstein MB, et al. The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies. Proceedings of the National Academy of Sciences of the United States of America. 106: 12031-6. PMID 19597142 DOI: 10.1073/pnas.0813248106  1
2009 Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB. Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants. Plos Computational Biology. 5: e1000432. PMID 19593373 DOI: 10.1371/journal.pcbi.1000432  1
2009 Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, et al. Unlocking the secrets of the genome. Nature. 459: 927-30. PMID 19536255 DOI: 10.1038/459927a  1
2009 Xia Y, Franzosa EA, Gerstein MB. Integrated assessment of genomic correlates of protein evolutionary rate. Plos Computational Biology. 5: e1000413. PMID 19521505 DOI: 10.1371/journal.pcbi.1000413  1
2009 Ni L, Bruce C, Hart C, Leigh-Bell J, Gelperin D, Umansky L, Gerstein MB, Snyder M. Dynamic and complex transcription factor binding during an inducible response in yeast. Genes & Development. 23: 1351-63. PMID 19487574 DOI: 10.1101/gad.1781909  1
2009 Snyder M, Weissman S, Gerstein M. Personal phenotypes to go with personal genomes. Molecular Systems Biology. 5: 273. PMID 19455137 DOI: 10.1038/msb.2009.32  0.76
2009 Cheng C, Li LM, Alves P, Gerstein M. Systematic identification of transcription factors associated with patient survival in cancers. Bmc Genomics. 10: 225. PMID 19442316 DOI: 10.1186/1471-2164-10-225  0.36
2009 Mishima Y, Abreu-Goodger C, Staton AA, Stahlhut C, Shou C, Cheng C, Gerstein M, Enright AJ, Giraldez AJ. Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Genes & Development. 23: 619-32. PMID 19240126 DOI: 10.1101/gad.1760209  1
2009 Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB. PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biology. 10: R23. PMID 19236709 DOI: 10.1186/gb-2009-10-2-r23  1
2009 Keating KS, Flores SC, Gerstein MB, Kuhn LA. StoneHinge: hinge prediction by network analysis of individual protein structures. Protein Science : a Publication of the Protein Society. 18: 359-71. PMID 19180449 DOI: 10.1002/pro.38  1
2009 Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB. Quantifying environmental adaptation of metabolic pathways in metagenomics. Proceedings of the National Academy of Sciences of the United States of America. 106: 1374-9. PMID 19164758 DOI: 10.1073/pnas.0808022106  1
2009 Lefrançois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M. Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. Bmc Genomics. 10: 37. PMID 19159457 DOI: 10.1186/1471-2164-10-37  1
2009 Demichelis F, Setlur SR, Beroukhim R, Perner S, Korbel JO, Lafargue CJ, Pflueger D, Pina C, Hofer MD, Sboner A, Svensson MA, Rickman DS, Urban A, Snyder M, Meyerson M, ... ... Gerstein MB, et al. Distinct genomic aberrations associated with ERG rearranged prostate cancer. Genes, Chromosomes & Cancer. 48: 366-80. PMID 19156837 DOI: 10.1002/gcc.20647  1
2009 Zhang X, Lian Z, Padden C, Gerstein MB, Rozowsky J, Snyder M, Gingeras TR, Kapranov P, Weissman SM, Newburger PE. A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood. 113: 2526-34. PMID 19144990 DOI: 10.1182/blood-2008-06-162164  1
2009 Balasubramanian S, Zheng D, Liu YJ, Fang G, Frankish A, Carriero N, Robilotto R, Cayting P, Gerstein M. Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes. Genome Biology. 10: R2. PMID 19123937 DOI: 10.1186/gb-2009-10-1-r2  0.88
2009 Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nature Biotechnology. 27: 66-75. PMID 19122651 DOI: 10.1038/nbt.1518  1
2009 Popescu SC, Popescu GV, Bachan S, Zhang Z, Gerstein M, Snyder M, Dinesh-Kumar SP. MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Genes & Development. 23: 80-92. PMID 19095804 DOI: 10.1101/gad.1740009  1
2009 Wang LY, Abyzov A, Korbel JO, Snyder M, Gerstein M. MSB: a mean-shift-based approach for the analysis of structural variation in the genome. Genome Research. 19: 106-17. PMID 19037015 DOI: 10.1101/gr.080069.108  1
2009 Yip KY, Gerstein M. Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions. Bioinformatics (Oxford, England). 25: 243-50. PMID 19015141 DOI: 10.1093/bioinformatics/btn602  1
2009 Lam HY, Khurana E, Fang G, Cayting P, Carriero N, Cheung KH, Gerstein MB. Pseudofam: the pseudogene families database. Nucleic Acids Research. 37: D738-43. PMID 18957444 DOI: 10.1093/nar/gkn758  1
2009 Brown T, Murphy ER, Gerstein M, Greenbaum D. When scientific data become legal evidence Science. 324: 335-336. DOI: 10.1126/science.324.5925.335  1
2009 Greenbaum D, Gerstein M. Can't run from DNA New Scientist. 203: 28-29. DOI: 10.1016/S0262-4079(09)62555-0  1
2008 Seringhaus M, Rozowsky J, Royce T, Nagalakshmi U, Jee J, Snyder M, Gerstein M. Mismatch oligonucleotides in human and yeast: Guidelines for probe design on tiling microarrays Bmc Genomics. 9. PMID 19117516 DOI: 10.1186/1471-2164-9-635  1
2008 Yam AY, Xia Y, Lin HT, Burlingame A, Gerstein M, Frydman J. Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies. Nature Structural & Molecular Biology. 15: 1255-62. PMID 19011634 DOI: 10.1038/nsmb.1515  1
2008 Greenbaum D, Du J, Gerstein M. Genomic anonymity: have we already lost it? The American Journal of Bioethics : Ajob. 8: 71-4. PMID 19003717 DOI: 10.1080/15265160802478560  1
2008 Hasin Y, Olender T, Khen M, Gonzaga-Jauregui C, Kim PM, Urban AE, Snyder M, Gerstein MB, Lancet D, Korbel JO. High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution. Plos Genetics. 4: e1000249. PMID 18989455 DOI: 10.1371/journal.pgen.1000249  1
2008 Kim PM, Lam HY, Urban AE, Korbel JO, Affourtit J, Grubert F, Chen X, Weissman S, Snyder M, Gerstein MB. 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. Genome Research. 18: 1865-74. PMID 18842824 DOI: 10.1101/gr.081422.108  1
2008 Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M. Modeling ChIP sequencing in silico with applications. Plos Computational Biology. 4: e1000158. PMID 18725927 DOI: 10.1371/journal.pcbi.1000158  0.36
2008 Rzhetsky A, Seringhaus M, Gerstein M. Seeking a New Biology through Text Mining Cell. 134: 9-13. PMID 18614002 DOI: 10.1016/j.cell.2008.06.029  1
2008 Korbel JO, Kim PM, Chen X, Urban AE, Weissman S, Snyder M, Gerstein MB. The current excitement about copy-number variation: how it relates to gene duplications and protein families. Current Opinion in Structural Biology. 18: 366-74. PMID 18511261 DOI: 10.1016/  1
2008 Huang YJ, Hang D, Lu LJ, Tong L, Gerstein MB, Montelione GT. Targeting the human cancer pathway protein interaction network by structural genomics. Molecular & Cellular Proteomics : McP. 7: 2048-60. PMID 18487680 DOI: 10.1074/mcp.M700550-MCP200  1
2008 Lian Z, Karpikov A, Lian J, Mahajan MC, Hartman S, Gerstein M, Snyder M, Weissman SM. A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation. Genome Research. 18: 1224-37. PMID 18487515 DOI: 10.1101/gr.075804.107  1
2008 Mertz KD, Demichelis F, Sboner A, Hirsch MS, Dal Cin P, Struckmann K, Storz M, Scherrer S, Schmid DM, Strebel RT, Probst-Hensch NM, Gerstein M, Moch H, Rubin MA. Association of cytokeratin 7 and 19 expression with genomic stability and favorable prognosis in clear cell renal cell cancer. International Journal of Cancer. Journal International Du Cancer. 123: 569-76. PMID 18478571 DOI: 10.1002/ijc.23565  0.84
2008 Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (New York, N.Y.). 320: 1344-9. PMID 18451266 DOI: 10.1126/science.1158441  1
2008 Flores SC, Keating KS, Painter J, Morcos F, Nguyen K, Merritt EA, Kuhn LA, Gerstein MB. HingeMaster: normal mode hinge prediction approach and integration of complementary predictors. Proteins. 73: 299-319. PMID 18433058 DOI: 10.1002/prot.22060  1
2008 Bourne PE, Fink JL, Gerstein M. Open access: taking full advantage of the content. Plos Computational Biology. 4: e1000037. PMID 18369428 DOI: 10.1371/journal.pcbi.1000037  1
2008 Kim PM, Sboner A, Xia Y, Gerstein M. The role of disorder in interaction networks: a structural analysis. Molecular Systems Biology. 4: 179. PMID 18364713 DOI: 10.1038/msb.2008.16  1
2008 Seringhaus M, Gerstein M. Manually structured digital abstracts: A scaffold for automatic text mining Febs Letters. 582: 1170. PMID 18328823 DOI: 10.1016/j.febslet.2008.02.073  1
2008 Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, ... ... Gerstein M, et al. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Research. 18: 393-403. PMID 18258921 DOI: 10.1101/gr.7080508  1
2008 Seringhaus MR, Cayting PD, Gerstein MB. Uncovering trends in gene naming. Genome Biology. 9: 401. PMID 18254929 DOI: 10.1186/gb-2008-9-1-401  1
2008 Wu JQ, Du J, Rozowsky J, Zhang Z, Urban AE, Euskirchen G, Weissman S, Gerstein M, Snyder M. Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biology. 9: R3. PMID 18173853 DOI: 10.1186/gb-2008-9-1-r3  0.92
2008 Yip KY, Patel P, Kim PM, Engelman DM, McDermott D, Gerstein M. An integrated system for studying residue coevolution in proteins. Bioinformatics (Oxford, England). 24: 290-2. PMID 18056067 DOI: 10.1093/bioinformatics/btm584  1
2008 Seringhaus M, Gerstein M. Genomics confounds gene classification American Scientist. 96: 466-473. DOI: 10.1511/2008.75.466  1
2007 Kim PM, Korbel JO, Gerstein MB. Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context. Proceedings of the National Academy of Sciences of the United States of America. 104: 20274-9. PMID 18077332 DOI: 10.1073/pnas.0710183104  1
2007 Zhang ZD, Cayting P, Weinstock G, Gerstein M. Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories. Molecular Biology and Evolution. 25: 131-43. PMID 18065488 DOI: 10.1093/MOLBEV/MSM251  0.44
2007 Setlur SR, Royce TE, Sboner A, Mosquera JM, Demichelis F, Hofer MD, Mertz KD, Gerstein M, Rubin MA. Integrative microarray analysis of pathways dysregulated in metastatic prostate cancer. Cancer Research. 67: 10296-303. PMID 17974971 DOI: 10.1158/0008-5472.CAN-07-2173  0.4
2007 McClellan AJ, Xia Y, Deutschbauer AM, Davis RW, Gerstein M, Frydman J. Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches. Cell. 131: 121-35. PMID 17923092 DOI: 10.1016/j.cell.2007.07.036  1
2007 Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders AC, Chi J, ... ... Gerstein MB, et al. Paired-end mapping reveals extensive structural variation in the human genome. Science (New York, N.Y.). 318: 420-6. PMID 17901297 DOI: 10.1126/science.1149504  1
2007 Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang LY, Gerstein M, Snyder M. Divergence of transcription factor binding sites across related yeast species. Science (New York, N.Y.). 317: 815-9. PMID 17690298 DOI: 10.1126/science.1140748  1
2007 Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, ... ... Gerstein M, et al. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nature Biotechnology. 25: 894-8. PMID 17687370 DOI: 10.1038/nbt1324  1
2007 Royce TE, Rozowsky JS, Gerstein MB. Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification. Nucleic Acids Research. 35: e99. PMID 17686789 DOI: 10.1093/nar/gkm549  1
2007 Borneman AR, Zhang ZD, Rozowsky J, Seringhaus MR, Gerstein M, Snyder M. Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. Functional & Integrative Genomics. 7: 335-45. PMID 17638031 DOI: 10.1007/s10142-007-0054-7  1
2007 Flores SC, Gerstein MB. FlexOracle: predicting flexible hinges by identification of stable domains. Bmc Bioinformatics. 8: 215. PMID 17587456 DOI: 10.1186/1471-2105-8-215  1
2007 Lu LJ, Sboner A, Huang YJ, Lu HX, Gianoulis TA, Yip KY, Kim PM, Montelione GT, Gerstein MB. Comparing classical pathways and modern networks: towards the development of an edge ontology. Trends in Biochemical Sciences. 32: 320-31. PMID 17583513 DOI: 10.1016/j.tibs.2007.06.003  1
2007 Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB, Ruan Y, Snyder M. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Research. 17: 898-909. PMID 17568005 DOI: 10.1101/gr.5583007  1
2007 Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, ... ... Gerstein MB, et al. Structured RNAs in the ENCODE selected regions of the human genome. Genome Research. 17: 852-64. PMID 17568003 DOI: 10.1101/gr.5650707  1
2007 Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigó R, Harrow J, ... Gerstein MB, et al. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Research. 17: 839-51. PMID 17568002 DOI: 10.1101/gr.5586307  1
2007 Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein MB. Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Research. 17: 787-97. PMID 17567997 DOI: 10.1101/gr.5573107  1
2007 Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R, Gingeras TR, Weissman S, Miller P, Snyder M, Gerstein MB. The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Research. 17: 732-45. PMID 17567993 DOI: 10.1101/gr.5696007  1
2007 Trinklein ND, Karaöz U, Wu J, Halees A, Force Aldred S, Collins PJ, Zheng D, Zhang ZD, Gerstein MB, Snyder M, Myers RM, Weng Z. Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Research. 17: 720-31. PMID 17567992 DOI: 10.1101/gr.5716607  1
2007 Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M. What is a gene, post-ENCODE? History and updated definition. Genome Research. 17: 669-81. PMID 17567988 DOI: 10.1101/gr.6339607  1
2007 Royce TE, Carriero NJ, Gerstein MB. An efficient pseudomedian filter for tiling microrrays. Bmc Bioinformatics. 8: 186. PMID 17555595 DOI: 10.1186/1471-2105-8-186  1
2007 Korbel JO, Urban AE, Grubert F, Du J, Royce TE, Starr P, Zhong G, Emanuel BS, Weissman SM, Snyder M, Gerstein MB. Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 104: 10110-5. PMID 17551006 DOI: 10.1073/pnas.0703834104  1
2007 Yu H, Jansen R, Stolovitzky G, Gerstein M. Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications. Bioinformatics (Oxford, England). 23: 2163-73. PMID 17540677 DOI: 10.1093/bioinformatics/btm291  1
2007 Flores SC, Lu LJ, Yang J, Carriero N, Gerstein MB. Hinge Atlas: relating protein sequence to sites of structural flexibility. Bmc Bioinformatics. 8: 167. PMID 17519025 DOI: 10.1186/1471-2105-8-167  1
2007 Zhang ZD, Rozowsky J, Lam HY, Du J, Snyder M, Gerstein M. Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biology. 8: R81. PMID 17501994 DOI: 10.1186/gb-2007-8-5-r81  0.96
2007 Gerstein M, Seringhaus M, Fields S. Structured digital abstract makes text mining easy [1] Nature. 447: 142. PMID 17495904 DOI: 10.1038/447142a  1
2007 Smith AK, Cheung KH, Yip KY, Schultz M, Gerstein MK. LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics. Bmc Bioinformatics. 8: S5. PMID 17493288 DOI: 10.1186/1471-2105-8-S3-S5  1
2007 Zhu X, Gerstein M, Snyder M. Getting connected: analysis and principles of biological networks. Genes & Development. 21: 1010-24. PMID 17473168 DOI: 10.1101/gad.1528707  1
2007 Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. Plos Computational Biology. 3: e59. PMID 17447836 DOI: 10.1371/journal.pcbi.0030059  1
2007 Royce TE, Rozowsky JS, Gerstein MB. Assessing the need for sequence-based normalization in tiling microarray experiments. Bioinformatics (Oxford, England). 23: 988-97. PMID 17387113 DOI: 10.1093/bioinformatics/btm052  1
2007 Zheng D, Gerstein MB. The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they? Trends in Genetics : Tig. 23: 219-24. PMID 17382428 DOI: 10.1016/j.tig.2007.03.003  1
2007 Li L, Wang X, Sasidharan R, Stolc V, Deng W, He H, Korbel J, Chen X, Tongprasit W, Ronald P, Chen R, Gerstein M, Deng XW. Global identification and characterization of transcriptionally active regions in the rice genome Plos One. 2. PMID 17372628 DOI: 10.1371/journal.pone.0000294  1
2007 Popescu SC, Popescu GV, Bachan S, Zhang Z, Seay M, Gerstein M, Snyder M, Dinesh-Kumar SP. Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays. Proceedings of the National Academy of Sciences of the United States of America. 104: 4730-5. PMID 17360592 DOI: 10.1073/pnas.0611615104  1
2007 Zhang Z, Pang AW, Gerstein M. Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human. Bmc Evolutionary Biology. 7: S14. PMID 17288572 DOI: 10.1186/1471-2148-7-S1-S14  0.92
2007 Seringhaus MR, Gerstein MB. Publishing perishing? Towards tomorrow's information architecture. Bmc Bioinformatics. 8: 17. PMID 17239245 DOI: 10.1186/1471-2105-8-17  1
2007 Seringhaus M, Gerstein M. Chemistry nobel rich in structure [5] Science. 315: 40-41. PMID 17204626 DOI: 10.1126/science.315.5808.40  1
2007 Yu H, Nguyen K, Royce T, Qian J, Nelson K, Snyder M, Gerstein M. Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool. Nucleic Acids Research. 35: e8. PMID 17158151 DOI: 10.1093/nar/gkl871  1
2007 Emanuelsson O, Nagalakshmi U, Zheng D, Rozowsky JS, Urban AE, Du J, Lian Z, Stolc V, Weissman S, Snyder M, Gerstein MB. Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. Genome Research. 17: 886-97. PMID 17119069 DOI: 10.1101/gr.5014606  1
2007 Karro JE, Yan Y, Zheng D, Zhang Z, Carriero N, Cayting P, Harrrison P, Gerstein M. a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Research. 35: D55-60. PMID 17099229 DOI: 10.1093/nar/gkl851  1
2007 Gerstein M, Greenbaum D, Cheung K, Miller PL. An interdepartmental Ph.D. program in computational biology and bioinformatics: the Yale perspective. Journal of Biomedical Informatics. 40: 73-9. PMID 16650809 DOI: 10.1016/j.jbi.2006.02.008  1
2007 Sayward FG, Yang J, Nelson FK, Euskirchen G, Urban AE, Bertone P, Rinn J, Weissman S, Gerstein M, Snyder M, Miller PL. Design issues in implementing a portable Sample Tracking and Analysis Research Support (STARS) system for PCR based microarray research 2006 Ieee Conference On Information Sciences and Systems, Ciss 2006 - Proceedings. 1578-1598. DOI: 10.1109/CISS.2006.286390  1
2007 Cheung KH, Smith AK, Yip KYL, Baker CJO, Gerstein MB. Semantic web approach to database integration in the life sciences Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences. 11-30. DOI: 10.1007/978-0-387-48438-9_2  1
2007 Greenbaum D, Gerstein M. Semantic web standards: Legal and social issues and implications Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences. 413-433. DOI: 10.1007/978-0-387-48438-9_19  1
2006 Rozowsky J, Wu J, Lian Z, Nagalakshmi U, Korbel JO, Kapranov P, Zheng D, Dyke S, Newburger P, Miller P, Gingeras TR, Weissman S, Gerstein M, Snyder M. Novel transcribed regions in the human genome. Cold Spring Harbor Symposia On Quantitative Biology. 71: 111-6. PMID 17381286 DOI: 10.1101/sqb.2006.71.054  1
2006 Kim PM, Lu LJ, Xia Y, Gerstein MB. Relating three-dimensional structures to protein networks provides evolutionary insights. Science (New York, N.Y.). 314: 1938-41. PMID 17185604 DOI: 10.1126/science.1136174  1
2006 Liu Y, Li J, Sam L, Goh CS, Gerstein M, Lussier YA. An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits. Plos Computational Biology. 2: e159. PMID 17112314 DOI: 10.1371/journal.pcbi.0020159  1
2006 Zhu X, Gerstein M, Snyder M. ProCAT: a data analysis approach for protein microarrays. Genome Biology. 7: R110. PMID 17109749 DOI: 10.1186/gb-2006-7-11-r110  1
2006 Wang LY, Snyder M, Gerstein M. BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments. Genome Biology. 7: R102. PMID 17078876 DOI: 10.1186/gb-2006-7-11-r102  0.76
2006 Burba AE, Lehnert U, Yu EZ, Gerstein M. Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins. Bioinformatics (Oxford, England). 22: 2735-8. PMID 17060355 DOI: 10.1093/bioinformatics/btl274  0.32
2006 Du J, Rozowsky JS, Korbel JO, Zhang ZD, Royce TE, Schultz MH, Snyder M, Gerstein M. A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge. Bioinformatics (Oxford, England). 22: 3016-24. PMID 17038339 DOI: 10.1093/bioinformatics/btl515  1
2006 Goh CS, Gianoulis TA, Liu Y, Li J, Paccanaro A, Lussier YA, Gerstein M. Integration of curated databases to identify genotype-phenotype associations. Bmc Genomics. 7: 257. PMID 17038185 DOI: 10.1186/1471-2164-7-257  1
2006 Yip KY, Yu H, Kim PM, Schultz M, Gerstein M. The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. Bioinformatics (Oxford, England). 22: 2968-70. PMID 17021160 DOI: 10.1093/bioinformatics/btl488  1
2006 Yu H, Gerstein M. Genomic analysis of the hierarchical structure of regulatory networks. Proceedings of the National Academy of Sciences of the United States of America. 103: 14724-31. PMID 17003135 DOI: 10.1073/pnas.0508637103  1
2006 Srikantha T, Borneman AR, Daniels KJ, Pujol C, Wu W, Seringhaus MR, Gerstein M, Yi S, Snyder M, Soll DR. TOS9 regulates white-opaque switching in Candida albicans. Eukaryotic Cell. 5: 1674-87. PMID 16950924 DOI: 10.1128/EC.00252-06  1
2006 Royce TE, Rozowsky JS, Luscombe NM, Emanuelsson O, Yu H, Zhu X, Snyder M, Gerstein MB. Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies. Methods in Enzymology. 411: 282-311. PMID 16939796 DOI: 10.1016/S0076-6879(06)11015-0  1
2006 Pinard R, de Winter A, Sarkis GJ, Gerstein MB, Tartaro KR, Plant RN, Egholm M, Rothberg JM, Leamon JH. Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. Bmc Genomics. 7: 216. PMID 16928277 DOI: 10.1186/1471-2164-7-216  1
2006 Zheng D, Gerstein MB. A computational approach for identifying pseudogenes in the ENCODE regions. Genome Biology. 7: S13.1-10. PMID 16925835 DOI: 10.1186/gb-2006-7-s1-s13  1
2006 Seringhaus M, Paccanaro A, Borneman A, Snyder M, Gerstein M. Predicting essential genes in fungal genomes. Genome Research. 16: 1126-35. PMID 16899653 DOI: 10.1101/gr.5144106  1
2006 Gerstein M, Zheng D. The real life of pseudogenes. Scientific American. 295: 48-55. PMID 16866288 DOI: 10.1038/SCIENTIFICAMERICAN0806-48  1
2006 Yu H, Xia Y, Trifonov V, Gerstein M. Design principles of molecular networks revealed by global comparisons and composite motifs. Genome Biology. 7: R55. PMID 16859507 DOI: 10.1186/gb-2006-7-7-r55  1
2006 Seringhaus M, Kumar A, Hartigan J, Snyder M, Gerstein M. Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae. Nucleic Acids Research. 34: e57. PMID 16648358 DOI: 10.1093/nar/gkl184  1
2006 Zhang Z, Carriero N, Zheng D, Karro J, Harrison PM, Gerstein M. PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics (Oxford, England). 22: 1437-9. PMID 16574694 DOI: 10.1093/bioinformatics/btl116  0.92
2006 Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, ... ... Gerstein M, et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 440: 637-43. PMID 16554755 DOI: 10.1038/nature04670  1
2006 Urban AE, Korbel JO, Selzer R, Richmond T, Hacker A, Popescu GV, Cubells JF, Green R, Emanuel BS, Gerstein MB, Weissman SM, Snyder M. High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proceedings of the National Academy of Sciences of the United States of America. 103: 4534-9. PMID 16537408 DOI: 10.1073/pnas.0511340103  1
2006 Yu H, Paccanaro A, Trifonov V, Gerstein M. Predicting interactions in protein networks by completing defective cliques. Bioinformatics (Oxford, England). 22: 823-9. PMID 16455753 DOI: 10.1093/bioinformatics/btl014  1
2006 Borneman AR, Leigh-Bell JA, Yu H, Bertone P, Gerstein M, Snyder M. Target hub proteins serve as master regulators of development in yeast. Genes & Development. 20: 435-48. PMID 16449570 DOI: 10.1101/gad.1389306  1
2006 Xia Y, Lu LJ, Gerstein M. Integrated prediction of the helical membrane protein interactome in yeast. Journal of Molecular Biology. 357: 339-49. PMID 16413578 DOI: 10.1016/J.JMB.2005.12.067  0.56
2006 Flores S, Echols N, Milburn D, Hespenheide B, Keating K, Lu J, Wells S, Yu EZ, Thorpe M, Gerstein M. The Database of Macromolecular Motions: new features added at the decade mark. Nucleic Acids Research. 34: D296-301. PMID 16381870 DOI: 10.1093/nar/gkj046  1
2006 Bertone P, Trifonov V, Rozowsky JS, Schubert F, Emanuelsson O, Karro J, Kao MY, Snyder M, Gerstein M. Design optimization methods for genomic DNA tiling arrays. Genome Research. 16: 271-81. PMID 16365382 DOI: 10.1101/gr.4452906  1
2005 Gelperin DM, White MA, Wilkinson ML, Kon Y, Kung LA, Wise KJ, Lopez-Hoyo N, Jiang L, Piccirillo S, Yu H, Gerstein M, Dumont ME, Phizicky EM, Snyder M, Grayhack EJ. Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes & Development. 19: 2816-26. PMID 16322557 DOI: 10.1101/gad.1362105  1
2005 Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney RR, Schmidt MC, Rachidi N, Lee SJ, Mah AS, ... ... Gerstein M, et al. Global analysis of protein phosphorylation in yeast. Nature. 438: 679-84. PMID 16319894 DOI: 10.1038/nature04187  1
2005 Hartman SE, Bertone P, Nath AK, Royce TE, Gerstein M, Weissman S, Snyder M. Global changes in STAT target selection and transcription regulation upon interferon treatments. Genes & Development. 19: 2953-68. PMID 16319195 DOI: 10.1101/gad.1371305  1
2005 Stolc V, Li L, Wang X, Li X, Su N, Tongprasit W, Han B, Xue Y, Li J, Snyder M, Gerstein M, Wang J, Deng XW. A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray. Plant Molecular Biology. 59: 137-49. PMID 16217608 DOI: 10.1007/s11103-005-6164-5  0.84
2005 Smith A, Greenbaum D, Douglas SM, Long M, Gerstein M. Network security and data integrity in academia: an assessment and a proposal for large-scale archiving. Genome Biology. 6: 119. PMID 16168090 DOI: 10.1186/gb-2005-6-9-119  1
2005 Douglas SM, Montelione GT, Gerstein M. PubNet: a flexible system for visualizing literature derived networks. Genome Biology. 6: R80. PMID 16168087 DOI: 10.1186/gb-2005-6-9-r80  1
2005 Gerstein M, Huleihel M, Mane R, Stilman M, Kashtuzki I, Hallak M, Golan H. Remodeling of hippocampal GABAergic system in adult offspring after maternal hypoxia and magnesium sulfate load: immunohistochemical study. Experimental Neurology. 196: 18-29. PMID 16081066 DOI: 10.1016/j.expneurol.2005.06.019  1
2005 Lu LJ, Xia Y, Paccanaro A, Yu H, Gerstein M. Assessing the limits of genomic data integration for predicting protein networks. Genome Research. 15: 945-53. PMID 15998909 DOI: 10.1101/gr.3610305  1
2005 Royce TE, Rozowsky JS, Bertone P, Samanta M, Stolc V, Weissman S, Snyder M, Gerstein M. Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends in Genetics : Tig. 21: 466-75. PMID 15979196 DOI: 10.1016/j.tig.2005.06.007  1
2005 Cheung KH, Yip KY, Smith A, Deknikker R, Masiar A, Gerstein M. YeastHub: a semantic web use case for integrating data in the life sciences domain. Bioinformatics (Oxford, England). 21: i85-96. PMID 15961502 DOI: 10.1093/bioinformatics/bti1026  1
2005 Zheng D, Zhang Z, Harrison PM, Karro J, Carriero N, Gerstein M. Integrated pseudogene annotation for human chromosome 22: evidence for transcription. Journal of Molecular Biology. 349: 27-45. PMID 15876366 DOI: 10.1016/j.jmb.2005.02.072  0.92
2005 Bertone P, Gerstein M, Snyder M. Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery. Chromosome Research : An International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology. 13: 259-74. PMID 15868420 DOI: 10.1007/s10577-005-2165-0  1
2005 Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP. Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Research. 15: 674-80. PMID 15867429 DOI: 10.1101/gr.3335705  0.72
2005 Harrison PM, Zheng D, Zhang Z, Carriero N, Gerstein M. Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Research. 33: 2374-83. PMID 15860774 DOI: 10.1093/nar/gki531  0.92
2005 Huber D, Boyd D, Xia Y, Olma MH, Gerstein M, Beckwith J. Use of thioredoxin as a reporter to identify a subset of Escherichia coli signal sequences that promote signal recognition particle-dependent translocation Journal of Bacteriology. 187: 2983-2991. PMID 15838024 DOI: 10.1128/JB.187.9.2983-2991.2005  1
2005 Acton TB, Gunsalus KC, Xiao R, Ma LC, Aramini J, Baran MC, Chiang YW, Climent T, Cooper B, Denissova NG, Douglas SM, Everett JK, Ho CK, Macapagal D, Rajan PK, ... ... Gerstein M, et al. Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium. Methods in Enzymology. 394: 210-43. PMID 15808222 DOI: 10.1016/S0076-6879(05)94008-1  1
2005 Balasubramanian S, Xia Y, Freinkman E, Gerstein M. Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms. Nucleic Acids Research. 33: 1710-21. PMID 15784611 DOI: 10.1093/nar/gki311  1
2005 Grosshans H, Johnson T, Reinert KL, Gerstein M, Slack FJ. The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans. Developmental Cell. 8: 321-30. PMID 15737928 DOI: 10.1016/j.devcel.2004.12.019  1
2005 Greenbaum D, Smith A, Gerstein M. Impediments to database interoperation: legal issues and security concerns. Nucleic Acids Research. 33: D3-4. PMID 15608202 DOI: 10.1093/nar/gki134  1
2005 Carriero N, Osier MV, Cheung KH, Miller PL, Gerstein M, Zhao H, Wu B, Rifkin S, Chang J, Zhang H, White K, Williams K, Schultz M. A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies. Journal of the American Medical Informatics Association : Jamia. 12: 90-8. PMID 15492032 DOI: 10.1197/jamia.M1571  1
2005 Paccanarot A, Trifonov V, Yu H, Gerstein M. Inferring protein-protein interactions using interaction network topologies Proceedings of the International Joint Conference On Neural Networks. 1: 161-166. DOI: 10.1109/IJCNN.2005.1555823  1
2005 Lu LJ, Xia Y, Yu H, Rives A, Lu H, Schubert F, Gerstein M. Protein Interaction Prediction by Integrating Genomic Features and Protein Interaction Network Analysis Data Analysis and Visualization in Genomics and Proteomics. 61-81. DOI: 10.1002/0470094419.ch5  1
2005 Rozowsky J, Bertone P, Royce T, Weissman S, Snyder M, Gerstein M. Analysis of genomic tiling microarrays for transcript mapping and the identification of transcription factor binding sites Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). 3594: 28-29.  1
2004 White EJ, Emanuelsson O, Scalzo D, Royce T, Kosak S, Oakeley EJ, Weissman S, Gerstein M, Groudine M, Snyder M, Schübeler D. DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proceedings of the National Academy of Sciences of the United States of America. 101: 17771-6. PMID 15591350 DOI: 10.1073/pnas.0408170101  1
2004 Berman P, Bertone P, Dasgupta B, Gerstein M, Kao MY, Snyder M. Fast optimal genome tiling with applications to microarray design and homology search. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 766-85. PMID 15579244 DOI: 10.1089/cmb.2004.11.766  1
2004 Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M. Global identification of human transcribed sequences with genome tiling arrays. Science (New York, N.Y.). 306: 2242-6. PMID 15539566 DOI: 10.1126/science.1103388  1
2004 Lin N, Wu B, Jansen R, Gerstein M, Zhao H. Information assessment on predicting protein-protein interactions. Bmc Bioinformatics. 5: 154. PMID 15491499 DOI: 10.1186/1471-2105-5-154  1
2004 Hall DA, Zhu H, Zhu X, Royce T, Gerstein M, Snyder M. Regulation of gene expression by a metabolic enzyme. Science (New York, N.Y.). 306: 482-4. PMID 15486299 DOI: 10.1126/science.1096773  1
2004 Kumar A, Seringhaus M, Biery MC, Sarnovsky RJ, Umansky L, Piccirillo S, Heidtman M, Cheung KH, Dobry CJ, Gerstein MB, Craig NL, Snyder M. Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon. Genome Research. 14: 1975-86. PMID 15466296 DOI: 10.1101/gr.2875304  1
2004 Jansen R, Gerstein M. Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction. Current Opinion in Microbiology. 7: 535-45. PMID 15451510 DOI: 10.1016/j.mib.2004.08.012  1
2004 Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature. 431: 308-12. PMID 15372033 DOI: 10.1038/nature02782  1
2004 Liu Y, Harrison PM, Kunin V, Gerstein M. Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes. Genome Biology. 5: R64. PMID 15345048 DOI: 10.1186/gb-2004-5-9-r64  0.8
2004 Zhang Z, Gerstein M. Large-scale analysis of pseudogenes in the human genome. Current Opinion in Genetics & Development. 14: 328-35. PMID 15261647 DOI: 10.1016/j.gde.2004.06.003  0.92
2004 Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA. Structure and evolution of transcriptional regulatory networks. Current Opinion in Structural Biology. 14: 283-91. PMID 15193307 DOI: 10.1016/  1
2004 Xia Y, Yu H, Jansen R, Seringhaus M, Baxter S, Greenbaum D, Zhao H, Gerstein M. Analyzing cellular biochemistry in terms of molecular networks. Annual Review of Biochemistry. 73: 1051-87. PMID 15189167 DOI: 10.1146/annurev.biochem.73.011303.073950  1
2004 Rinn JL, Rozowsky JS, Laurenzi IJ, Petersen PH, Zou K, Zhong W, Gerstein M, Snyder M. Major molecular differences between mammalian sexes are involved in drug metabolism and renal function. Developmental Cell. 6: 791-800. PMID 15177028 DOI: 10.1016/j.devcel.2004.05.005  1
2004 Greenbaum D, Douglas SM, Smith A, Lim J, Fischer M, Schultz M, Gerstein M. Computer security in academia-a potential roadblock to distributed annotation of the human genome. Nature Biotechnology. 22: 771-2. PMID 15175700 DOI: 10.1038/nbt0604-771  1
2004 Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M. Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Research. 14: 1107-18. PMID 15173116 DOI: 10.1101/gr.1774904  1
2004 Yu H, Greenbaum D, Xin Lu H, Zhu X, Gerstein M. Genomic analysis of essentiality within protein networks. Trends in Genetics : Tig. 20: 227-31. PMID 15145574 DOI: 10.1016/j.tig.2004.04.008  1
2004 Goh CS, Milburn D, Gerstein M. Conformational changes associated with protein-protein interactions. Current Opinion in Structural Biology. 14: 104-9. PMID 15102456 DOI: 10.1016/  1
2004 Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S, Snyder M. CREB binds to multiple loci on human chromosome 22. Molecular and Cellular Biology. 24: 3804-14. PMID 15082775 DOI: 10.1128/MCB.24.9.3804-3814.2004  1
2004 Das R, Gerstein M. 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. Proteins. 55: 455-63. PMID 15048835 DOI: 10.1002/prot.10639  0.8
2004 Gerstein M, Echols N. Exploring the range of protein flexibility, from a structural proteomics perspective. Current Opinion in Chemical Biology. 8: 14-9. PMID 15036151 DOI: 10.1016/j.cbpa.2003.12.006  1
2004 Zhang Z, Carriero N, Gerstein M. Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends in Genetics : Tig. 20: 62-7. PMID 14746985 DOI: 10.1016/j.tig.2003.12.005  0.92
2004 Goh CS, Lan N, Douglas SM, Wu B, Echols N, Smith A, Milburn D, Montelione GT, Zhao H, Gerstein M. Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis. Journal of Molecular Biology. 336: 115-30. PMID 14741208 DOI: 10.1016/j.jmb.2003.11.053  1
2004 Yu H, Zhu X, Greenbaum D, Karro J, Gerstein M. TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics. Nucleic Acids Research. 32: 328-37. PMID 14724320 DOI: 10.1093/nar/gkh164  1
2004 Alexandrov V, Gerstein M. Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures. Bmc Bioinformatics. 5: 2. PMID 14715091 DOI: 10.1186/1471-2105-5-2  1
2004 Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual JF, Lamesch P, ... ... Gerstein M, et al. A map of the interactome network of the metazoan C. elegans. Science (New York, N.Y.). 303: 540-3. PMID 14704431 DOI: 10.1126/science.1091403  1
2003 Lian Z, Euskirchen G, Rinn J, Martone R, Bertone P, Hartman S, Royce T, Nelson K, Sayward F, Luscombe N, Yang J, Li JL, Miller P, Urban AE, Gerstein M, et al. Identification of novel functional elements in the human genome. Cold Spring Harbor Symposia On Quantitative Biology. 68: 317-22. PMID 15338632  1
2003 Krebs WG, Tsai J, Alexandrov V, Junker J, Jansen R, Gerstein M. Tools and databases to analyze protein flexibility; approaches to mapping implied features onto sequences. Methods in Enzymology. 374: 544-84. PMID 14696388 DOI: 10.1016/S0076-6879(03)74023-3  1
2003 Kluger Y, Yu H, Qian J, Gerstein M. Relationship between gene co-expression and probe localization on microarray slides. Bmc Genomics. 4: 49. PMID 14667251 DOI: 10.1186/1471-2164-4-49  1
2003 Zhang Z, Harrison PM, Liu Y, Gerstein M. Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Research. 13: 2541-58. PMID 14656962 DOI: 10.1101/gr.1429003  0.92
2003 Jiao Y, Yang H, Ma L, Sun N, Yu H, Liu T, Gao Y, Gu H, Chen Z, Wada M, Gerstein M, Zhao H, Qu LJ, Deng XW. A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development. Plant Physiology. 133: 1480-93. PMID 14605227 DOI: 10.1104/pp.103.029439  1
2003 Zhang Z, Gerstein M. Reconstructing genetic networks in yeast. Nature Biotechnology. 21: 1295-7. PMID 14595359 DOI: 10.1038/nbt1103-1295  0.92
2003 Harrison PM, Carriero N, Liu Y, Gerstein M. A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs. Journal of Molecular Biology. 333: 885-92. PMID 14583187 DOI: 10.1016/J.JMB.2003.09.016  0.88
2003 Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (New York, N.Y.). 302: 449-53. PMID 14564010 DOI: 10.1126/science.1087361  1
2003 Qian J, Lin J, Luscombe NM, Yu H, Gerstein M. Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinformatics (Oxford, England). 19: 1917-26. PMID 14555624 DOI: 10.1093/bioinformatics/btg347  1
2003 Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. Distribution of NF-kappaB-binding sites across human chromosome 22. Proceedings of the National Academy of Sciences of the United States of America. 100: 12247-52. PMID 14527995 DOI: 10.1073/pnas.2135255100  1
2003 Zhang Z, Gerstein M. Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Research. 31: 5338-48. PMID 12954770  0.92
2003 Greenbaum D, Colangelo C, Williams K, Gerstein M. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biology. 4: 117. PMID 12952525 DOI: 10.1186/gb-2003-4-9-117  1
2003 Greenbaum D, Gerstein M. A universal legal framework as a prerequisite for database interoperability. Nature Biotechnology. 21: 979-82. PMID 12949555 DOI: 10.1038/nbt0903-979  1
2003 Zhang Z, Gerstein M. The human genome has 49 cytochrome c pseudogenes, including a relic of a primordial gene that still functions in mouse. Gene. 312: 61-72. PMID 12909341  0.92
2003 Yu H, Luscombe NM, Qian J, Gerstein M. Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends in Genetics : Tig. 19: 422-7. PMID 12902159 DOI: 10.1016/S0168-9525(03)00175-6  1
2003 Qian J, Kluger Y, Yu H, Gerstein M. Identification and correction of spurious spatial correlations in microarray data. Biotechniques. 35: 42-4, 46, 48. PMID 12866403  1
2003 Gerstein M, Thornton JM. Sequences and topology. Current Opinion in Structural Biology. 13: 341-3. PMID 12831885 DOI: 10.1016/s0959-440x(03)00080-0  0.4
2003 Luscombe NM, Royce TE, Bertone P, Echols N, Horak CE, Chang JT, Snyder M, Gerstein M. ExpressYourself: A modular platform for processing and visualizing microarray data. Nucleic Acids Research. 31: 3477-82. PMID 12824348 DOI: 10.1093/nar/gkg628  1
2003 Zhang Z, Gerstein M. Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements. Journal of Biology. 2: 11. PMID 12814519 DOI: 10.1186/1475-4924-2-11  0.92
2003 Harrison PM, Gerstein M. A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes. Genome Biology. 4: R40. PMID 12801414 DOI: 10.1186/gb-2003-4-6-r40  0.68
2003 Kimber MS, Vallee F, Houston S, Necakov A, Skarina T, Evdokimova E, Beasley S, Christendat D, Savchenko A, Arrowsmith CH, Vedadi M, Gerstein M, Edwards AM. Data mining crystallization databases: knowledge-based approaches to optimize protein crystal screens. Proteins. 51: 562-8. PMID 12784215 DOI: 10.1002/prot.10340  1
2003 Goh CS, Lan N, Echols N, Douglas SM, Milburn D, Bertone P, Xiao R, Ma LC, Zheng D, Wunderlich Z, Acton T, Montelione GT, Gerstein M. SPINE 2: a system for collaborative structural proteomics within a federated database framework. Nucleic Acids Research. 31: 2833-8. PMID 12771210 DOI: 10.1093/nar/gkg397  1
2003 Zhang Z, Gerstein M. Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome. Genomics. 81: 468-80. PMID 12706105  0.92
2003 Jansen R, Bussemaker HJ, Gerstein M. 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. Nucleic Acids Research. 31: 2242-51. PMID 12682375 DOI: 10.1093/nar/gkg306  1
2003 Kluger Y, Basri R, Chang JT, Gerstein M. Spectral biclustering of microarray data: coclustering genes and conditions. Genome Research. 13: 703-16. PMID 12671006 DOI: 10.1101/gr.648603  1
2003 Gerstein M, Edwards A, Arrowsmith CH, Montelione GT. Structural genomics: Current progress [3] Science. 299: 1663. PMID 12637721 DOI: 10.1126/science.299.5613.1663a  1
2003 Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. The transcriptional activity of human Chromosome 22. Genes & Development. 17: 529-40. PMID 12600945 DOI: 10.1101/gad.1055203  1
2003 Harrison PM, Milburn D, Zhang Z, Bertone P, Gerstein M. Identification of pseudogenes in the Drosophila melanogaster genome. Nucleic Acids Research. 31: 1033-7. PMID 12560500 DOI: 10.1093/nar/gkg169  1
2003 Savchenko A, Yee A, Khachatryan A, Skarina T, Evdokimova E, Pavlova M, Semesi A, Northey J, Beasley S, Lan N, Das R, Gerstein M, Arrowmith CH, Edwards AM. Strategies for structural proteomics of prokaryotes: Quantifying the advantages of studying orthologous proteins and of using both NMR and X-ray crystallography approaches. Proteins. 50: 392-9. PMID 12557182 DOI: 10.1002/prot.10282  0.8
2003 Lan N, Montelione GT, Gerstein M. Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level. Current Opinion in Chemical Biology. 7: 44-54. PMID 12547426 DOI: 10.1016/S1367-5931(02)00020-0  1
2003 Echols N, Milburn D, Gerstein M. MolMovDB: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Research. 31: 478-82. PMID 12520056 DOI: 10.1093/nar/gkg104  1
2003 Greenbaum D, Lim J, Gerstein M. An analysis of the present system of scientific publishing: What's wrong and where to go from here Interdisciplinary Science Reviews. 28: 293-302. DOI: 10.1179/030801803225005238  1
2002 Jansen R, Lan N, Qian J, Gerstein M. Integration of genomic datasets to predict protein complexes in yeast. Journal of Structural and Functional Genomics. 2: 71-81. PMID 12836664 DOI: 10.1023/A:1020495201615  1
2002 Horak CE, Luscombe NM, Qian J, Bertone P, Piccirrillo S, Gerstein M, Snyder M. Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes & Development. 16: 3017-33. PMID 12464632 DOI: 10.1101/gad.1039602  1
2002 Mateos A, Dopazo J, Jansen R, Tu Y, Gerstein M, Stolovitzky G. Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons. Genome Research. 12: 1703-15. PMID 12421757 DOI: 10.1101/gr.192502  1
2002 Zhang ZL, Harrison PM, Gerstein M. Digging deep for ancient relics: a survey of protein motifs in the intergenic sequences of four eukaryotic genomes. Journal of Molecular Biology. 323: 811-22. PMID 12417195 DOI: 10.1016/S0022-2836(02)01035-5  0.68
2002 Lin J, Qian J, Greenbaum D, Bertone P, Das R, Echols N, Senes A, Stenger B, Gerstein M. GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing. Nucleic Acids Research. 30: 4574-82. PMID 12384605  1
2002 Lian Z, Kluger Y, Greenbaum DS, Tuck D, Gerstein M, Berliner N, Weissman SM, Newburger PE. Genomic and proteomic analysis of the myeloid differentiation program: global analysis of gene expression during induced differentiation in the MPRO cell line. Blood. 100: 3209-20. PMID 12384419 DOI: 10.1182/blood-2002-03-0850  1
2002 Liu Y, Engelman DM, Gerstein M. Genomic analysis of membrane protein families: abundance and conserved motifs. Genome Biology. 3: research0054. PMID 12372142  1
2002 Zhang Z, Harrison P, Gerstein M. Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Research. 12: 1466-82. PMID 12368239 DOI: 10.1101/gr.331902  0.92
2002 Edwards AM, Kus B, Jansen R, Greenbaum D, Greenblatt J, Gerstein M. Bridging structural biology and genomics: assessing protein interaction data with known complexes. Trends in Genetics : Tig. 18: 529-36. PMID 12350343 DOI: 10.1016/S0168-9525(02)02763-4  1
2002 Krebs WG, Alexandrov V, Wilson CA, Echols N, Yu H, Gerstein M. Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins. 48: 682-95. PMID 12211036 DOI: 10.1002/prot.10168  1
2002 Luscombe NM, Qian J, Zhang Z, Johnson T, Gerstein M. The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties. Genome Biology. 3: RESEARCH0040. PMID 12186647  1
2002 Giaever G, Chu AM, Ni L, Connelly C, Riles L, Véronneau S, Dow S, Lucau-Danila A, Anderson K, André B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, ... ... Gerstein M, et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature. 418: 387-91. PMID 12140549 DOI: 10.1038/nature00935  1
2002 Tsai J, Gerstein M. Calculations of protein volumes: sensitivity analysis and parameter database. Bioinformatics (Oxford, England). 18: 985-95. PMID 12117797 DOI: 10.1093/bioinformatics/18.7.985  1
2002 Harrison PM, Gerstein M. Studying genomes through the aeons: protein families, pseudogenes and proteome evolution. Journal of Molecular Biology. 318: 1155-74. PMID 12083509 DOI: 10.1016/S0022-2836(02)00109-2  0.68
2002 Balasubramanian S, Harrison P, Hegyi H, Bertone P, Luscombe N, Echols N, McGarvey P, Zhang Z, Gerstein M. SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes. Pharmacogenomics. 3: 393-402. PMID 12052146 DOI: 10.1517/14622416.3.3.393  1
2002 Echols N, Harrison P, Balasubramanian S, Luscombe NM, Bertone P, Zhang Z, Gerstein M. Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes. Nucleic Acids Research. 30: 2515-23. PMID 12034841  1
2002 Greenbaum D, Jansen R, Gerstein M. 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. Bioinformatics (Oxford, England). 18: 585-96. PMID 12016056  1
2002 Hegyi H, Lin J, Greenbaum D, Gerstein M. Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds. Proteins. 47: 126-41. PMID 11933060 DOI: 10.1002/prot.10078  1
2002 Kumar A, Agarwal S, Heyman JA, Matson S, Heidtman M, Piccirillo S, Umansky L, Drawid A, Jansen R, Liu Y, Cheung KH, Miller P, Gerstein M, Roeder GS, Snyder M. Subcellular localization of the yeast proteome. Genes & Development. 16: 707-19. PMID 11914276 DOI: 10.1101/gad.970902  1
2002 Horak CE, Mahajan MC, Luscombe NM, Gerstein M, Weissman SM, Snyder M. GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis. Proceedings of the National Academy of Sciences of the United States of America. 99: 2924-9. PMID 11867748 DOI: 10.1073/pnas.052706999  1
2002 Harrison P, Kumar A, Lan N, Echols N, Snyder M, Gerstein M. A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution. Journal of Molecular Biology. 316: 409-19. PMID 11866506 DOI: 10.1006/jmbi.2001.5343  1
2002 Liu Y, Luscombe NM, Alexandrov V, Bertone P, Harrison P, Zhang Z, Gerstein M. Structural genomics: a new era for pharmaceutical research. Genome Biology. 3: REPORTS4004. PMID 11864367  1
2002 Harrison PM, Kumar A, Lang N, Snyder M, Gerstein M. A question of size: the eukaryotic proteome and the problems in defining it. Nucleic Acids Research. 30: 1083-90. PMID 11861898 DOI: 10.1093/NAR/30.5.1083  0.76
2002 Harrison PM, Hegyi H, Balasubramanian S, Luscombe NM, Bertone P, Echols N, Johnson T, Gerstein M. Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Research. 12: 272-80. PMID 11827946 DOI: 10.1101/gr.207102  1
2002 Das R, Gerstein M. The stability of thermophilic proteins: a study based on comprehensive genome comparison. Functional & Integrative Genomics. 1: 76-88. PMID 11793224 DOI: 10.1007/s101420000003  0.44
2002 Gerstein M, Lan N, Jansen R. Proteomics. Integrating interactomes. Science (New York, N.Y.). 295: 284-7. PMID 11786630 DOI: 10.1126/science.1068664  1
2002 Jansen R, Greenbaum D, Gerstein M. Relating whole-genome expression data with protein-protein interactions. Genome Research. 12: 37-46. PMID 11779829 DOI: 10.1101/gr.205602  1
2002 Kumar A, Harrison PM, Cheung KH, Lan N, Echols N, Bertone P, Miller P, Gerstein MB, Snyder M. An integrated approach for finding overlooked genes in yeast. Nature Biotechnology. 20: 58-63. PMID 11753363 DOI: 10.1038/nbt0102-58  1
2002 Lan N, Jansen R, Gerstein M. Toward a systematic definition of protein function that scales to the genome level: Defining function in terms of interactions Proceedings of the Ieee. 90: 1848-1858. DOI: 10.1109/JPROC.2002.805302  1
2001 Das R, Junker J, Greenbaum D, Gerstein MB. Global perspectives on proteins: comparing genomes in terms of folds, pathways and beyond. The Pharmacogenomics Journal. 1: 115-25. PMID 11911438  1
2001 Qian J, Dolled-Filhart M, Lin J, Yu H, Gerstein M. Beyond synexpression relationships: Local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions Journal of Molecular Biology. 314: 1053-1066. PMID 11743722 DOI: 10.1006/jmbi.2000.5219  1
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