Gerstein Lab Publications

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This is part of a disjoint subdivision of all the papers into 4 types.
(1) review = all review papers published by Gerstein Lab & colaborators
(2) informatics-research-article = informatics research article lead by the Gerstein Lab
(3) expt-collab = research article driven by an experimental or informatics lab in collaboration with Gerstein Lab
(4) otherpub = not one of the above

Cross-Disciplinary Network Comparison: Matchmaking Between Hairballs.
KK Yan, D Wang, A Sethi, P Muir, R Kitchen, C Cheng, M Gerstein (2016). Cell Syst 2: 147-157.
 
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Who Owns Your DNA?
D Greenbaum, M Gerstein (2016). Cell 165:257-258.
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Illuminating the Genome's Dark Matter
D Greenbaum, M Gerstein (2015). Cell 163:1047-1048.
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The computer connection
D Greenbaum, M Gerstein (2015). Science 347: 956.
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Deep Inside Champions, Just Genes?
D Greenbaum, J Chen, M Gerstein (2013). Science 342: 560.
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Child development and structural variation in the human genome.
Y Zhang, R Haraksingh, F Grubert, A Abyzov, M Gerstein, S Weissman, AE Urban (2013). Child Dev 84: 34-48.
 
 
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Machine learning and genome annotation: a match meant to be?
KY Yip, C Cheng, M Gerstein (2013). Genome Biol 14: 205.
 
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ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
SG Landt, GK Marinov, A Kundaje, P Kheradpour, F Pauli, S Batzoglou, BE Bernstein, P Bickel, JB Brown, P Cayting, Y Chen, G DeSalvo, C Epstein, KI Fisher-Aylor, G Euskirchen, M Gerstein, J Gertz, AJ Hartemink, MM Hoffman, VR Iyer, YL Jung, S Karmakar, M Kellis, PV Kharchenko, Q Li, T Liu, XS Liu, L Ma, A Milosavljevic, RM Myers, PJ Park, MJ Pazin, MD Perry, D Raha, TE Reddy, J Rozowsky, N Shoresh, A Sidow, M Slattery, JA Stamatoyannopoulos, MY Tolstorukov, KP White, S Xi, PJ Farnham, JD Lieb, BJ Wold, M Snyder (2012). Genome Res 22: 1813-31.
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On sports and genes.
G Zilberman-Schapira, J Chen, M Gerstein (2012). Recent Pat DNA Gene Seq 6: 180-8.
 
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Performance comparison of whole-genome sequencing platforms.
HY Lam, MJ Clark, R Chen, R Chen, G Natsoulis, M O'Huallachain, FE Dewey, L Habegger, EA Ashley, MB Gerstein, AJ Butte, HP Ji, M Snyder (2011). Nat Biotechnol 30: 78-82.
 
 
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Genomics and Privacy: Implications of the New Reality of Closed Data for the Field
D Greenbaum, A Sboner, X J Mu, M Gerstein (2011). PLoS Comput Biol 7: e1002278
 
 
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The real cost of sequencing: higher than you think!
A Sboner, XJ Mu, D Greenbaum, RK Auerbach, MB Gerstein (2011). Genome Biol 12: 125.
 
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Annual Research Review: The promise of stem cell research for neuropsychiatric disorders.
FM Vaccarino, AE Urban, HE Stevens, A Szekely, A Abyzov, EL Grigorenko, M Gerstein, S Weissman (2011). J Child Psychol Psychiatry 52: 504-16.
 
 
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Annotating non-coding regions of the genome.
RP Alexander, G Fang, J Rozowsky, M Snyder, MB Gerstein (2010). Nat Rev Genet 11: 559-71.
 
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Getting started in gene orthology and functional analysis.
G Fang, N Bhardwaj, R Robilotto, MB Gerstein (2010). PLoS Comput Biol 6: e1000703.
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Personal genome sequencing: current approaches and challenges.
M Snyder, J Du, M Gerstein (2010). Genes Dev 24: 423-31.
 
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Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response.
M Zhong, W Niu, ZJ Lu, M Sarov, JI Murray, J Janette, D Raha, KL Sheaffer, HY Lam, E Preston, C Slightham, LW Hillier, T Brock, A Agarwal, R Auerbach, AA Hyman, M Gerstein, SE Mango, SK Kim, RH Waterston, V Reinke, M Snyder (2010). PLoS Genet 6: e1000848.
 
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Science and the Law: Grappling with the Gulf
D Greenbaum, MB Gerstein (2009). Science 323: 210.
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Computational analysis of membrane proteins: the largest class of drug targets.
Y Arinaminpathy, E Khurana, DM Engelman, MB Gerstein (2009). Drug Discov Today 14: 1130-5.
 
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Getting started in text mining: part two.
A Rzhetsky, M Seringhaus, MB Gerstein (2009). PLoS Comput Biol 5: e1000411.
 
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Personal phenotypes to go with personal genomes.
M Snyder, S Weissman, M Gerstein (2009). Mol Syst Biol 5: 273.
 
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RNA-Seq: a revolutionary tool for transcriptomics.
Z Wang, M Gerstein, M Snyder (2009). Nat Rev Genet 10: 57-63.
 
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Genomics Confounds Gene Classification
M Seringhaus, M Gerstein (2008). American Scientist 96:466-473 (Nov-Dec)
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Genomics: protein fossils live on as RNA.
R Sasidharan, M Gerstein (2008). Nature 453: 729-31.
 
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The current excitement about copy-number variation: how it relates to gene duplications and protein families.
JO Korbel, PM Kim, X Chen, AE Urban, S Weissman, M Snyder, MB Gerstein (2008). Curr Opin Struct Biol 18: 366-74.
 
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The minimum information required for reporting a molecular interaction experiment (MIMIx).
S Orchard, L Salwinski, S Kerrien, L Montecchi-Palazzi, M Oesterheld, V Stumpflen, A Ceol, A Chatr-aryamontri, J Armstrong, P Woollard, JJ Salama, S Moore, J Wojcik, GD Bader, M Vidal, ME Cusick, M Gerstein, AC Gavin, G Superti-Furga, J Greenblatt, J Bader, P Uetz, M Tyers, P Legrain, S Fields, N Mulder, M Gilson, M Niepmann, L Burgoon, J De Las Rivas, C Prieto, VM Perreau, C Hogue, HW Mewes, R Apweiler, I Xenarios, D Eisenberg, G Cesareni, H Hermjakob (2007). Nat Biotechnol 25: 894-8.
 
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What is a gene, post-ENCODE? History and updated definition.
MB Gerstein, C Bruce, JS Rozowsky, D Zheng, J Du, JO Korbel, O Emanuelsson, ZD Zhang, S Weissman, M Snyder (2007). Genome Res 17: 669-81.
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LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics.
AK Smith, KH Cheung, KY Yip, M Schultz, MK Gerstein (2007). BMC Bioinformatics 8 Suppl 3: S5.
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Getting connected: analysis and principles of biological networks.
X Zhu, M Gerstein, M Snyder (2007). Genes Dev 21: 1010-24.
 
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Publishing perishing? Towards tomorrow's information architecture.
MR Seringhaus, MB Gerstein (2007). BMC Bioinformatics 8: 17.
 
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An interdepartmental Ph.D. program in computational biology and bioinformatics: the Yale perspective.
M Gerstein, D Greenbaum, K Cheung, PL Miller (2007). J Biomed Inform 40: 73-9.
 
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Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies.
TE Royce, JS Rozowsky, NM Luscombe, O Emanuelsson, H Yu, X Zhu, M Snyder, MB Gerstein (2006). Methods Enzymol 411: 282-311.
 
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Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.
TE Royce, JS Rozowsky, P Bertone, M Samanta, V Stolc, S Weissman, M Snyder, M Gerstein (2005). Trends Genet 21: 466-75.
 
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Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery.
P Bertone, M Gerstein, M Snyder (2005). Chromosome Res 13: 259-74.
 
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Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions.
U Lehnert, Y Xia, TE Royce, CS Goh, Y Liu, A Senes, H Yu, ZL Zhang, DM Engelman, M Gerstein (2004). Q Rev Biophys 37: 121-46.
 
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Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction.
R Jansen, M Gerstein (2004). Curr Opin Microbiol 7: 535-45.
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Large-scale analysis of pseudogenes in the human genome.
Z Zhang, M Gerstein (2004). Curr Opin Genet Dev 14: 328-35.
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Structure and evolution of transcriptional regulatory networks.
MM Babu, NM Luscombe, L Aravind, M Gerstein, SA Teichmann (2004). Curr Opin Struct Biol 14: 283-91.
 
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Analyzing cellular biochemistry in terms of molecular networks.
Y Xia, H Yu, R Jansen, M Seringhaus, S Baxter, D Greenbaum, H Zhao, M Gerstein (2004). Annu Rev Biochem 73: 1051-87.
 
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Genomic analysis of essentiality within protein networks.
H Yu, D Greenbaum, H Xin Lu, X Zhu, M Gerstein (2004). Trends Genet 20: 227-31.
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Conformational changes associated with protein-protein interactions.
CS Goh, D Milburn, M Gerstein (2004). Curr Opin Struct Biol 14: 104-9.
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Exploring the range of protein flexibility, from a structural proteomics perspective.
M Gerstein, N Echols (2004). Curr Opin Chem Biol 8: 14-9.
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Comparative analysis of processed pseudogenes in the mouse and human genomes.
Z Zhang, N Carriero, M Gerstein (2004). Trends Genet 20: 62-7.
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Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements.
Z Zhang, M Gerstein (2003). J Biol 2: 11.
 
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Genomics. Defining genes in the genomics era.
M Snyder, M Gerstein (2003). Science 300: 258-60.
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Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level.
N Lan, GT Montelione, M Gerstein (2003). Curr Opin Chem Biol 7: 44-54.
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Studying genomes through the aeons: protein families, pseudogenes and proteome evolution.
PM Harrison, M Gerstein (2002). J Mol Biol 318: 1155-74.
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Proteomics. Integrating interactomes.
M Gerstein, N Lan, R Jansen (2002). Science 295: 284-7.
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Bridging structural biology and genomics: assessing protein interaction data with known complexes.
AM Edwards, B Kus, R Jansen, D Greenbaum, J Greenblatt, M Gerstein (2002). Trends Genet 18: 529-36.
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Structural genomics: a new era for pharmaceutical research.
Y Liu, NM Luscombe, V Alexandrov, P Bertone, P Harrison, Z Zhang, M Gerstein (2002). Genome Biol 3: REPORTS4004.
 
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What is bioinformatics? A proposed definition and overview of the field.
NM Luscombe, D Greenbaum, M Gerstein (2001). Methods Inf Med 40: 346-58.
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Global perspectives on proteins: comparing genomes in terms of folds, pathways and beyond.
R Das, J Junker, D Greenbaum, MB Gerstein (2001). Pharmacogenomics J 1: 115-25.
 
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Protein Geometry: Distances, Areas, and Volumes
M Gerstein, F M Richards (2001). International Tables for Crystallography (Volume F, Chapter 22.1.1, pages 531-539; M Rossmann & E Arnold, editors; Dordrecht: Kluwer)
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A Bauhaus for Biologists: An Introduction to Protein Architecture by A. M. Lesk
P Harrison, M Gerstein (2001). Trends Biochem Sci 26:204-205
 
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Integrative data mining: the new direction in bioinformatics.
P Bertone, M Gerstein (2001). IEEE Eng Med Biol Mag 20: 33-40.
 
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Integrative database analysis in structural genomics.
M Gerstein (2000). Nat Struct Biol 7 Suppl: 960-3.
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Structural proteomics: prospects for high throughput sample preparation.
D Christendat, A Yee, A Dharamsi, Y Kluger, M Gerstein, CH Arrowsmith, AM Edwards (2000). Prog Biophys Mol Biol 73: 339-45.
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The current excitement in bioinformatics-analysis of whole-genome expression data: how does it relate to protein structure and function?
M Gerstein, R Jansen (2000). Curr Opin Struct Biol 10: 574-84.
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Perspectives: signal transduction. Proteins in motion.
M Gerstein, C Chothia (1999). Science 285: 1682-3.
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Motions in a Database Framework: from Structure to Sequence
M Gerstein, R Jansen, T Johnson, J Tsai, W Krebs (1999). Rigidity Theory and Applications 401-442 (ed. M F Thorpe and P M Duxbury, Kluwer Academic/Plenum Publishers).
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E-publishing on the Web: promises, pitfalls, and payoffs for bioinformatics.
M Gerstein (1999). Bioinformatics 15: 429-31.
 
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Advances in structural genomics.
SA Teichmann, C Chothia, M Gerstein (1999). Curr Opin Struct Biol 9: 390-9.
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Comparing genomes in terms of protein structure: surveys of a finite parts list.
M Gerstein, H Hegyi (1998). FEMS Microbiol Rev 22: 277-304.
 
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Protein folding: the endgame.
M Levitt, M Gerstein, E Huang, S Subbiah, J Tsai (1997). Annu Rev Biochem 66: 549-79.
 
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DNA recognition code of transcription factors.
M Suzuki, SE Brenner, M Gerstein, N Yagi (1995). Protein Eng 8: 319-28.
 
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Structural mechanisms for domain movements in proteins.
M Gerstein, AM Lesk, C Chothia (1994). Biochemistry 33: 6739-49.
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