Mark B. Gerstein - Publications

Affiliations: 
Molecular Biophysics and Biochemistry Yale University, New Haven, CT 
Area:
Computational Biology and Bioinformatics
Website:
https://sites.gersteinlab.org/research/

191 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.48
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  0.6
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  0.72
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  0.52
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  0.72
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  0.4
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  0.96
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  0.4
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  0.96
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/j.sbi.2015.11.003  0.96
2015 Abyzov A, Li S, Gerstein MB. Understanding genome structural variations. Oncotarget. PMID 26657727 DOI: 10.18632/oncotarget.6485  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.6
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
2014 Min MR, Ning X, Cheng C, Gerstein M. Interpretable sparse high-order Boltzmann machines Journal of Machine Learning Research. 33: 614-622.  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
2013 Greenbaum D, Chen J, Gerstein M. Deep inside champions, just genes? Science. 342: 560-561. DOI: 10.1126/science.1245795  0.96
2013 Gerstein M, Greenbaum D. Proceed with caution Scientist. 27.  0.96
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  0.96
2012 Gerstein M. Genomics: ENCODE leads the way on big data Nature. 489: 208. PMID 22972285 DOI: 10.1038/489208b  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
2012 Zilberman-Schapira G, Chen J, Gerstein M. On Sports and Genes Recent Patents On Dna and Gene Sequences. 6: 180-188. PMID 22762737  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.36
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  0.96
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  0.96
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  0.68
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.36
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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.  0.96
2011 Gerstein MB. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE Project (Science (2010) (1775)) Science. 331: 30.  0.96
2011 Greenbaum D, Gerstein M. The benefits of snooping Technology Review. 114: 6.  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.36
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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/j.sbi.2008.02.005  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
2001 Harrison PM, Echols N, Gerstein MB. Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome. Nucleic Acids Research. 29: 818-30. PMID 11160906  0.96
1995 Altman RB, Hughes C, Gerstein MB. Methods for displaying macromolecular structural uncertainty: application to the globins. Journal of Molecular Graphics. 13: 142-52, 109-2. PMID 7577841 DOI: 10.1016/0263-7855(95)00002-N  0.96
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