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Author Gerstein [198 articles]

Recent papers posted to CiteULike by the author Gerstein.
  • The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci
    Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 732-745.
    by Joel S Rozowsky, Daniel Newburger, Fred Sayward, Jiaqian Wu, Greg Jordan, Jan O Korbel, Ugrappa Nagalakshmi, Jin Yang, Deyou Zheng, Roderic Guigo, Thomas R Gingeras, Sherman Weissman, Perry Miller, Michael Snyder, Mark B Gerstein
  • The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
    Science (1 May 2008), 1158441.
    by Ugrappa Nagalakshmi, Zhong Wang, Karl Waern, Chong Shou, Debasish Raha, Mark Gerstein, Michael Snyder
  • Interrelating different types of genomic data, from proteome to secretome: 'oming in on function.
    Genome research, Vol. 11, No. 9. (September 2001), pp. 1463-1468.
    posted to no-tag by tvdbulck on 2008-07-22 14:53:58 as **
  • Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
    Nature (22 March 2006)
    by Nevan J Krogan, Gerard Cagney, Haiyuan Yu, Gouqing Zhong, Xinghua Guo, Alexandr Ignatchenko, Joyce Li, Shuye Pu, Nira Datta, Aaron P Tikuisis, Thanuja Punna, Josã© M Peregrã­n-Alvarez, Michael Shales, Xin Zhang, Michael Davey, Mark D Robinson, Alberto Paccanaro, James E Bray, Anthony Sheung, Bryan Beattie, Dawn P Richards, Veronica Canadien, Atanas Lalev, Frank Mena, Peter Wong, Andrei Starostine, Myra M Canete, James Vlasblom, Samuel Wu, Chris Orsi, Sean R Collins, Shamanta Chandran, Robin Haw, Jennifer J Rilstone, Kiran Gandi, Natalie J Thompson, Gabe Musso, Peter St Onge, Shaun Ghanny, Mandy HY Lam, Gareth Butland, Amin M Altaf-Ul, Shigehiko Kanaya, Ali Shilatifard, Erin O'Shea, Jonathan S Weissman, James C Ingles, Timothy R Hughes, John Parkinson, Mark Gerstein, Shoshana J Wodak, Andrew Emili, Jack F Greenblatt
  • Seeking a New Biology through Text Mining
    Cell, Vol. 134, No. 1. (11 July 2008), pp. 9-13.
    by Andrey Rzhetsky, Michael Seringhaus, Mark Gerstein
    posted to 2d by icq242500260 on 2008-07-20 23:10:07 as ** along with 3 people jyuh bootsy pzoot
  • Design principles of molecular networks revealed by global comparisons and composite motifs
    Genome Biology, Vol. 7 (19 July 2006), R55.
    by Haiyuan Yu, Yu Xia, Valery Trifonov, Mark Gerstein
  • Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.
    Genome Res, Vol. 14, No. 6. (June 2004), pp. 1107-1118.
    by H Yu, NM Luscombe, HX Lu, X Zhu, Y Xia, JD Han, N Bertin, S Chung, M Vidal, M Gerstein
  • Global analysis of protein phosphorylation in yeast
    Nature, Vol. 438, No. 7068., pp. 679-684.
    by Jason Ptacek, Geeta Devgan, Gregory Michaud, Heng Zhu, Xiaowei Zhu, Joseph Fasolo, Hong Guo, Ghil Jona, Ashton Breitkreutz, Richelle Sopko, Rhonda R Mccartney, Martin C Schmidt, Najma Rachidi, Soo-Jung Lee, Angie S Mah, Lihao Meng, Michael JR Stark, David F Stern, Claudio De Virgilio, Mike Tyers, Brenda Andrews, Mark Gerstein, Barry Schweitzer, Paul F Predki, Michael Snyder
  • Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions
    Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 787-797.
    by Zhengdong D Zhang, Alberto Paccanaro, Yutao Fu, Sherman Weissman, Zhiping Weng, Joseph Chang, Michael Snyder, Mark B Gerstein
  • Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome
    Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 720-731.
    by Nathan D Trinklein, Ulas Karaoz, Jiaqian Wu, Anason Halees, Force, Patrick J Collins, Deyou Zheng, Zhengdong D Zhang, Mark B Gerstein, Michael Snyder, Richard M Myers, Zhiping Weng
    posted to encode by jasonflannick on 2008-07-11 17:16:38 as ** along with 5 people jyuh djkt olympos cjeans Garamonfok
  • Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.
    Genome Res (21 November 2006)
    by Olof Emanuelsson, Ugrappa Nagalakshmi, Deyou Zheng, Joel S S Rozowsky, Alexander E E Urban, Jiang Du, Zheng Lian, Viktor Stolc, Sherman Weissman, Michael Snyder, Mark Gerstein
    posted to encode by jasonflannick on 2008-07-11 17:16:15 as ** along with 1 person eckart_bindewald
  • Genomic analysis of gene expression relationships in transcriptional regulatory networks
    Trends in Genetics, Vol. 19, No. 8. (August 2003), pp. 422-427.
    by Haiyuan Yu, Nicholas M Luscombe, Jiang Qian, Mark Gerstein
    posted to regulatory-net by Takayuki on 2008-07-10 13:05:33 as ** along with 1 person tmmurali
  • Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae
    Genes Dev., Vol. 16, No. 23. (1 December 2002), pp. 3017-3033.
    by Christine E Horak, Nicholas M Luscombe, Jiang Qian, Paul Bertone, Stacy Piccirrillo, Mark Gerstein, Michael Snyder
    posted to regulatory-net by Takayuki on 2008-07-10 12:57:21 as **
  • Genomic analysis of essentiality within protein networks.
    Trends Genet, Vol. 20, No. 6. (June 2004), pp. 227-231.
    by H Yu, D Greenbaum, H Xin Lu, X Zhu, M Gerstein
  • The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics
    PLoS Computational Biology, Vol. preprint, No. 2007. (1 February 2007), e59.eor.
    by Haiyuan Yu, Philip M Kim, Emmett Sprecher, Valery Trifinov, Mark Gerstein
  • What is a gene, post-ENCODE? History and updated definition.
    Genome Research, Vol. 17, No. 6. (June 2007), pp. 669-681.
    by Mark B Gerstein, Can Bruce, Joel S Rozowsky, Deyou Zheng, Jiang Du, Jan O Korbel, Olof Emanuelsson, Zhengdong D Zhang, Sherman Weissman, Michael Snyder
  • Functional profiling of the Saccharomyces cerevisiae genome.
    Nature, Vol. 418, No. 6896. (25 July 2002), pp. 387-391.
  • A cognitive vulnerability-stress perspective on bipolar spectrum disorders in a normative adolescent brain, cognitive, and emotional development context.
    Development and psychopathology, Vol. 18, No. 4. (2006), pp. 1055-1103.
    by LB Alloy, LY Abramson, PD Walshaw, J Keyser, RK Gerstein
  • A map of the interactome network of the metazoan C. elegans.
    Science, Vol. 303, No. 5657. (23 January 2004), pp. 540-543.
    by S Li, CM Armstrong, N Bertin, H Ge, S Milstein, M Boxem, PO Vidalain, JD Han, A Chesneau, T Hao, DS Goldberg, N Li, M Martinez, JF Rual, P Lamesch, L Xu, M Tewari, SL Wong, LV Zhang, GF Berriz, L Jacotot, P Vaglio, J Reboul, T Hirozane-Kishikawa, Q Li, HW Gabel, A Elewa, B Baumgartner, DJ Rose, H Yu, S Bosak, R Sequerra, A Fraser, SE Mango, WM Saxton, S Strome, S Van Den Heuvel, F Piano, J Vandenhaute, C Sardet, M Gerstein, L Doucette-Stamm, KC Gunsalus, JW Harper, ME Cusick, FP Roth, DE Hill, M Vidal
  • HIV risk behaviors in African-American drug injector networks: implications of injection-partner mixing and partnership characteristics.
    Addiction (Abingdon, England), Vol. 97, No. 8. (August 2002), pp. 1011-1024.
    by RA Johnson, DR Gerstein, A Pach, FG Cerbone, J Brown
    posted to usa idu by rds on 2008-07-02 22:50:14 as **
  • Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies
    Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 898-909.
    by Ghia M Euskirchen, Joel S Rozowsky, Chia-Lin Wei, Wah H Lee, Zhengdong D Zhang, Stephen Hartman, Olof Emanuelsson, Viktor Stolc, Sherman Weissman, Mark B Gerstein, Yijun Ruan, Michael Snyder
  • The role of disorder in interaction networks: a structural analysis
    Mol Syst Biol, Vol. 4 (25 March 2008)
    by Philip M Kim, Andrea Sboner, Yu Xia, Mark Gerstein
  • Conformational changes associated with protein-protein interactions
    Current Opinion in Structural Biology, Vol. 14, No. 1. (February 2004), pp. 104-109.
    by Chern-Sing Goh, Duncan Milburn, Mark Gerstein
    posted to thesis conformational change by nigham on 2008-06-29 07:40:29 as ** along with 2 people apaydin bicko
  • Assessing the limits of genomic data integration for predicting protein networks.
    Genome Res, Vol. 15, No. 7. (July 2005), pp. 945-953.
    by LJ Lu, Y Xia, A Paccanaro, H Yu, M Gerstein
  • Relating whole-genome expression data with protein-protein interactions.
    Genome Res, Vol. 12, No. 1. (January 2002), pp. 37-46.
  • Protein folding: the endgame.
    Annual review of biochemistry, Vol. 66 (1997), pp. 549-579.
    by M Levitt, M Gerstein, E Huang, S Subbiah, J Tsai
    posted to structure scp review by carlk on 2008-06-26 16:21:29 as **
  • A Bayesian networks approach for predicting protein-protein interactions from genomic data.
    Science, Vol. 302, No. 5644. (17 October 2003), pp. 449-453.
    by R Jansen, H Yu, D Greenbaum, Y Kluger, NJ Krogan, S Chung, A Emili, M Snyder, JF Greenblatt, M Gerstein
  • Flirting with Disaster: Why Accidents Are Rarely Accidental
    (03 June 2008)
    by Marc S Gerstein, Michael Ellsberg
    posted to decisionmaking catastrophe by bellavita on 2008-06-24 14:03:39 as **
  • What is bioinformatics? A proposed definition and overview of the field.
    Methods Inf Med, Vol. 40, No. 4. (2001), pp. 346-358.
    posted to no-tag by adilson_mohr on 2008-06-23 16:26:13 as read along with 1 person minostro
  • Colloquium Papers: Genomic analysis of the hierarchical structure of regulatory networks
    PNAS, Vol. 103, No. 40. (3 October 2006), pp. 14724-14731.
    by Haiyuan Yu, Mark Gerstein
    posted to bioregulationoverview by dquest on 2008-06-20 01:25:03 as ** along with 2 people bootsy RobMills
  • Getting connected: analysis and principles of biological networks.
    Genes Dev, Vol. 21, No. 9. (1 May 2007), pp. 1010-1024.
    by X Zhu, M Gerstein, M Snyder
  • Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome.
    Science (27 September 2007)
    by Jan O O Korbel, Alexander Eckehart E Urban, Jason P P Affourtit, Brian Godwin, Fabian Grubert, Jan Fredrik F Simons, Philip M M Kim, Dean Palejev, Nicholas J J Carriero, Lei Du, Bruce E E Taillon, Zhoutao Chen, Andrea Tanzer, A C Eugenia C Saunders, Jianxiang Chi, Fengtang Yang, Nigel P P Carter, Matthew E E Hurles, Sherman M M Weissman, Timothy T T Harkins, Mark B B Gerstein, Michael Egholm, Michael Snyder
  • LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics.
    BMC Bioinformatics, Vol. 8 Suppl 3 (2007)
    by AK Smith, KH Cheung, KY Yip, M Schultz, MK Gerstein
  • Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics
    Bioinformatics, Vol. 23, No. 22. (15 November 2007), pp. 3073-3079.
    by Andrew Smith, Kei Cheung, Michael Krauthammer, Martin Schultz, Mark Gerstein
    posted to no-tag by dansullivanblk on 2008-06-12 19:58:49 as ***** along with 2 people jyuh dullhunk
  • Dynamics of neuronal firing correlation: modulation of "effective connectivity"
    J Neurophysiol, Vol. 61, No. 5. (1 May 1989), pp. 900-917.
    by AM Aertsen, GL Gerstein, MK Habib, G Palm
  • Targeting the human cancer pathway protein interaction network by structural genomics.
    Molecular & cellular proteomics : MCP (18 May 2008)
    by Yuanpeng Janet J Huang, Dehua Hang, Long Jason J Lu, Liang Tong, Mark B B Gerstein, Gaetano T T Montelione
    posted to pathways networks databases by carlk on 2008-06-10 16:45:25 as ** along with 1 person cabbagesofdoom
  • The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics
    PLoS Computational Biology, Vol. 3, No. 4. (1 April 2007), e59.
    by Haiyuan Yu, Philip M Kim, Emmett Sprecher, Valery Trifonov, Mark Gerstein
  • Relating three-dimensional structures to protein networks provides evolutionary insights.
    Science, Vol. 314, No. 5807. (22 December 2006), pp. 1938-1941.
    by PM Kim, LJ Lu, Y Xia, MB Gerstein
  • Genomics: Protein fossils live on as RNA
    Nature, Vol. 453, No. 7196. (5 June 2008), pp. 729-731.
    by Rajkumar Sasidharan, Mark Gerstein
    posted to rnai by tmmurali on 2008-06-04 19:06:26 as **
  • The current excitement about copy-number variation: how it relates to gene duplications and protein families.
    Current opinion in structural biology (27 May 2008)
    by Jan O O Korbel, Philip M M Kim, Xueying Chen, Alexander Eckehart E Urban, Sherman Weissman, Michael Snyder, Mark B B Gerstein
    posted to variation number copy by Neeperando on 2008-06-02 15:29:44 as ** along with 1 person cabbagesofdoom
  • Predicting essential genes in fungal genomes
    Genome Res., Vol. 16, No. 9. (1 September 2006), pp. 1126-1135.
    by Michael Seringhaus, Alberto Paccanaro, Anthony Borneman, Michael Snyder, Mark Gerstein
  • Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction.
    Curr Opin Microbiol, Vol. 7, No. 5. (October 2004), pp. 535-545.
  • An integrated system for studying residue coevolution in proteins
    Bioinformatics, Vol. 24, No. 2. (15 January 2008), pp. 290-292.
    by Kevin Y Yip, Prianka Patel, Philip M Kim, Donald M Engelman, Drew Mcdermott, Mark Gerstein
  • Target hub proteins serve as master regulators of development in yeast.
    Genes Dev, Vol. 20, No. 4. (15 February 2006), pp. 435-448.
  • Genomic analysis of regulatory network dynamics reveals large topological changes.
    Nature, Vol. 431, No. 7006. (16 September 2004), pp. 308-312.
    by NM Luscombe, MM Babu, H Yu, M Snyder, SA Teichmann, M Gerstein
  • A Genomics Analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation.
    Genome research (16 May 2008)
    by Zheng Lian, Alexander Karpikov, Jin Lian, Milind C C Mahajan, Stephen Hartman, Mark Gerstein, Michael Snyder, Sherman M M Weissman
    posted to polyadenylation intron human antisense alternative by rschulz on 2008-05-20 18:16:48 as **
  • Spectral biclustering of microarray data: coclustering genes and conditions.
    Genome Res, Vol. 13, No. 4. (April 2003), pp. 703-716.
    by Y Kluger, R Basri, JT Chang, M Gerstein
    posted to no-tag by tvdbulck on 2008-05-20 14:28:45 as ** along with 6 people rmj001 tuck yuval filippone shigepong dps
  • Signal-to-noise ratio improvement in multiple electrode recording.
    Journal of neuroscience methods, Vol. 115, No. 1. (30 March 2002), pp. 29-43.
    by PG Musial, SN Baker, GL Gerstein, EA King, JG Keating
    posted to spikesorting by bayesian on 2008-05-19 13:41:20 as **
  • YeastHub: a semantic web use case for integrating data in the life sciences domain.
    Bioinformatics, Vol. 21 Suppl 1 (1 June 2005)
    by KH Cheung, KY Yip, A Smith, R Deknikker, A Masiar, M Gerstein
  • Comparing protein abundance and mRNA expression levels on a genomic scale.
    Genome Biol, Vol. 4, No. 9. (2003)
    posted to isis2008 by ihpark on 2008-05-16 10:45:35 as ** along with 3 people and 1 group penka JeremyZucker roys Nie
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