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Mark Gerstein

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Oligonucleotide Array Sequence Analysis

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Chemicals & Drugs

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Genes & Molecular Sequences

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Saccharomyces cerevisiae

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TOP 3
Ekta Khurana; Jieming Chen; Yao Fu; Mark Gerstein
Interpretation of genomic variants using a unified biological network approach.
Hagen Tilgner; Mark Gerstein; Lukas Habegger; Mohammed Mohiuddin; Debasish Raha; Michael Snyder
Accurate identification and analysis of human mRNA isoforms using deep long read sequencing.
Ralf Kittler; Yuwen Liu; Lijia Ma; Elisha Pendleton; Chao Cheng; Mark Gerstein; Sujun Hua; Jie Zhou; Kevin P White
A comprehensive nuclear receptor network for breast cancer cells.

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All Publications

2013: Ekta Khurana; Jieming Chen; Yao Fu; Mark Gerstein
Interpretation of genomic variants using a unified biological network approach.
PLoS computational biology 2013;9(3):e1002886.
2013: Hagen Tilgner; Mark Gerstein; Lukas Habegger; Mohammed Mohiuddin; Debasish Raha; Michael Snyder
Accurate identification and analysis of human mRNA isoforms using deep long read sequencing.
G3 (Bethesda, Md.) 2013;3(3):387-97.
2013: Ralf Kittler; Yuwen Liu; Lijia Ma; Elisha Pendleton; Chao Cheng; Mark Gerstein; Sujun Hua; Jie Zhou; Kevin P White
A comprehensive nuclear receptor network for breast cancer cells.
Cell reports 2013;3(2):538-51.
2013: Ying Zhang; Sherman Weissman; Alexej Abyzov; Mark Gerstein; Fabian Grubert; Rajini Haraksingh; Alexander E Urban
Child development and structural variation in the human genome.
Child development 2013;84(1):34-48.
2012: Alexej Abyzov; Nathaniel E Calixto; Katarzyna Chawarska; Anthony F Ferrandino; Mark Gerstein; Elena L Grigorenko; Michael Seamus Haney; Anita Huttner; Arif Kocabas; Jessica Mariani; Dean Palejev; Lior A Rosenberg Belmaker; Anna Szekely; Livia Tomasini; Alexander Eckehart Urban; Sherman Weissman; Michael Wilson; Ying Zhang; Flora M Vaccarino
Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells.
Nature 2012;492(7429):438-42.
2012: Gili Zilberman-Schapira; Jieming Chen; Mark Gerstein
On sports and genes.
Recent patents on DNA & gene sequences 2012;6(3):180-8.
2012: Chao Cheng; Carrie A Davis; Sarah Djebali; Xianjun Dong; Roger Alexander; Ewan Birney; piero carninci; Thomas R Gingeras; Roderic Guigó; Timo Lassman; Jing Leng; Renqiang Min; Joel S Rozowsky; Yijun Ruan; Michael Snyder; Zhiping Weng; Koon-Kiu Yan; Kevin Yip; Mark Gerstein
Understanding transcriptional regulation by integrative analysis of transcription factor binding data.
Genome research 2012;22(9):1658-67.
2012: Rebecca C Iskow; Alexej Abyzov; Darren A Cusanovich; Mark Gerstein; Yoav Gilad; Omer Gokcumen; Lukas Habegger; Joanna Malukiewicz; Ryan E Mills; Athma A Pai; George H Perry; Meagan A Rubel; Anne C Stone; Ann T Sukumar; Qihui Zhu; Charles Lee
Regulatory element copy number differences shape primate expression profiles.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(31):12656-61.
2012: Kevin Yip; Nitin Bhardwaj; Peter Bickel; Ewan Birney; James B Brown; Chao Cheng; Anshul Kundaje; Jing Leng; Joel S Rozowsky; Michael Snyder; Mark Gerstein
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors.
Genome biology 2012;13(9):R48.
2012: Jia Qian Wu; Zhijia Ye; Jiang Du; Mark Gerstein; Manoj Hariharan; Jin Lian; Vincent P Schulz; Montrell Seay; Minyi Shi; Michael P Snyder; David Tuck; Sherman Weissman
Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line.
PLoS genetics 2012;8(3):e1002565.
2012: Chao Cheng; Mark Gerstein
Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells.
Nucleic acids research 2012;40(2):553-68.
2011: Dov Greenbaum; Xinmeng Jasmine Mu; Andrea Sboner; Mark Gerstein
Genomics and privacy: implications of the new reality of closed data for the field.
PLoS computational biology 2011;7(12):e1002278.
2011: Chao Cheng; Renqiang Min; Mark Gerstein
TIP: a probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles.
Bioinformatics (Oxford, England) 2011;27(23):3221-7.
2011: Chao Cheng; Pedro Alves; Nitin Bhardwaj; Woochang Hwang; Masaomi Kato; Zhi John Lu; Wei Niu; Jiang Qian; Joel S Rozowsky; Michael Snyder; Koon-Kiu Yan; Mark Gerstein
Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data.
PLoS computational biology 2011;7(11):e1002190.
2011: Alexej Abyzov; Alexander E Urban; Michael Snyder; Mark Gerstein
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
Genome research 2011;21(6):974-84.
2011: Dov Greenbaum; Mark Gerstein
Social considerations in research: consider them but don't use them.
The American journal of bioethics : AJOB 2011;11(5):31-2.
2011: Justin Jee; Joel S Rozowsky; Kevin Yip; Lucas Lochovsky; Robert Bjornson; Guoneng Zhong; Zhengdong Zhang; Yutao Fu; Jie Wang; Zhiping Weng; Mark Gerstein
ACT: aggregation and correlation toolbox for analyses of genome tracks.
Bioinformatics (Oxford, England) 2011;27(8):1152-4.
2011: Joseph Fasolo; Andrea Sboner; Mark G F Sun; Haiyuan Yu; Rui Chen; Donald Sharon; Philip M Kim; Mark Gerstein; Michael Snyder
Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes.
Genes & development 2011;25(7):767-78.
2011: Flora M Vaccarino; Alexander Eckehart Urban; Hanna E Stevens; Anna Szekely; Alexej Abyzov; Elena L Grigorenko; Mark Gerstein; Sherman Weissman
Annual Research Review: The promise of stem cell research for neuropsychiatric disorders.
Journal of child psychology and psychiatry, and allied disciplines 2011;52(4):504-16.
2011: Wei Niu; Zhi John Lu; Mei Zhong; Mihail Sarov; John I Murray; Cathleen M Brdlik; Judith Janette; Chao Chen; Pedro Alves; Elicia Preston; Cindie Slightham; Lixia Jiang; Anthony A Hyman; Stuart K Kim; Robert H Waterston; Mark Gerstein; Michael Snyder; Valerie Reinke
Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans.
Genome research 2011;21(2):245-54.
2011: Lukas Habegger; Andrea Sboner; Tara A Gianoulis; Joel S Rozowsky; Ashish Agarwal; Michael Snyder; Mark Gerstein
RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.
Bioinformatics (Oxford, England) 2011;27(2):281-3.
2011: Rajini R Haraksingh; Alexej Abyzov; Mark Gerstein; Alexander E Urban; Michael Snyder
Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms.
PloS one 2011;6(11):e27859.
2011: Kevin Y Yip; Mark Gerstein; Xihao Hu; Sachdev S Sidhu; Simon Sitwell; Benjamin E Turk; Lukas Utz; Philip M Kim
Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps.
BMC biology 2011;9():53.
2011: Koon-Kiu Yan; Mark Gerstein
The spread of scientific information: insights from the web usage statistics in PLoS article-level metrics.
PloS one 2011;6(5):e19917.
2011: Alexander Karpikov; Joel S Rozowsky; Mark Gerstein
Tiling array data analysis: a multiscale approach using wavelets.
BMC bioinformatics 2011;12():57.
2011: Chao Cheng; Roger Alexander; Joel S Rozowsky; Chong Shou; Koon-Kiu Yan; Kevin Yip; Mark Gerstein
A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets.
Genome biology 2011;12(2):R15.
2011: Suganthi Balasubramanian; Lukas Habegger; Adam Frankish; Daniel G MacArthur; Rachel Harte; Chris Tyler-Smith; Jennifer Harrow; Mark Gerstein
Gene inactivation and its implications for annotation in the era of personal genomics.
Genes & development 2011;25(1):1-10.
2010: Xiyan Li; Tara A Gianoulis; Kevin Yip; Mark Gerstein; Michael Snyder
Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses.
Cell 2010;143(4):639-50.
2010: Matthew E Holford; Ekta Khurana; Kei-Hoi Cheung; Mark Gerstein
Using semantic web rules to reason on an ontology of pseudogenes.
Bioinformatics (Oxford, England) 2010;26(12):i71-8.
2010: Koon-Kiu Yan; Gang Fang; Nitin Bhardwaj; Roger P Alexander; Mark Gerstein
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 2010;107(20):9186-91.
2010: Jia Qian Wu; Lukas Habegger; Parinya Noisa; Anna Szekely; Caihong Qiu; Stephen Hutchison; Debasish Raha; Michael Egholm; Haifan Lin; Sherman Weissman; Wei Cui; Mark Gerstein; Michael Snyder
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 2010;107(11):5254-9.
2010: Debasish Raha; Zhong Wang; Zarmik Moqtaderi; Linfeng Wu; Guoneng Zhong; Mark Gerstein; Kevin Struhl; Michael Snyder
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 2010;107(8):3639-44.
2010: Mei Zhong; Wei Niu; Zhi John Lu; Mihail Sarov; John I Murray; Judith Janette; Debasish Raha; Karyn L Sheaffer; Hugo Y K Lam; Elicia Preston; Cindie Slightham; LaDeana W Hillier; Trisha Brock; Ashish Agarwal; Raymond Auerbach; Anthony A Hyman; Mark Gerstein; Susan E Mango; Stuart K Kim; Robert H Waterston; Valerie Reinke; Michael Snyder
Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response.
PLoS genetics 2010;6(2):e1000848.
2010: Alexej Abyzov; Robert Bjornson; Mihali Felipe; Mark Gerstein
RigidFinder: a fast and sensitive method to detect rigid blocks in large macromolecular complexes.
Proteins 2010;78(2):309-24.
2010: Ashish Agarwal; David Koppstein; Joel S Rozowsky; Andrea Sboner; Lukas Habegger; LaDeana W Hillier; Rajkumar Sasidharan; Valerie Reinke; Robert H Waterston; Mark Gerstein
Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays.
BMC genomics 2010;11():383.
2010: Zhengdong D Zhang; Adam Frankish; Toby Hunt; Jennifer Harrow; Mark Gerstein
Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates.
Genome biology 2010;11(3):R26.
2010: Kevin Yip; Roger P Alexander; Koon-Kiu Yan; Mark Gerstein
Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data.
PloS one 2010;5(1):e8121.
2009: Allon Canaan; Izhak Haviv; Alexander E Urban; Vincent P Schulz; Steve Hartman; Zhengdong Zhang; Dean Palejev; Albert B Deisseroth; Jill Lacy; Michael Snyder; Mark Gerstein; Sherman M Weissman
EBNA1 regulates cellular gene expression by binding cellular promoters.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(52):22421-6.
2009: Kristina Talbert-Slagle; Sara Marlatt; Francisco Barrera; Ekta Khurana; Joanne Oates; Mark Gerstein; Donald M Engelman; Ann M Dixon; Daniel DiMaio
Artificial transmembrane oncoproteins smaller than the bovine papillomavirus E5 protein redefine sequence requirements for activation of the platelet-derived growth factor beta receptor.
Journal of virology 2009;83(19):9773-85.
2009: Raymond K Auerbach; Ghia Euskirchen; Joel Rozowsky; Nathan Lamarre-Vincent; Zarmik Moqtaderi; Philippe Lefrançois; Kevin Struhl; Mark Gerstein; Michael Snyder
Mapping accessible chromatin regions using Sono-Seq.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(35):14926-31.
2009: Nitin Bhardwaj; Mark Gerstein
Relating protein conformational changes to packing efficiency and disorder.
Protein science : a publication of the Protein Society 2009;18(6):1230-40.
2009: Yuichiro Mishima; Cei Abreu-Goodger; Alison A Staton; Carlos Stahlhut; Chong Shou; Chao Cheng; Mark Gerstein; Anton J Enright; Antonio J Giraldez
Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization.
Genes & development 2009;23(5):619-32.
2009: Tara A Gianoulis; Jeroen Raes; Prianka V Patel; Robert Bjornson; Jan O Korbel; Ivica Letunic; Takuji Yamada; Alberto Paccanaro; Lars Jensen; Michael Snyder; Peer Bork; Mark Gerstein
Quantifying environmental adaptation of metabolic pathways in metagenomics.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(5):1374-9.
2009: Kevin S Keating; Samuel C Flores; Mark Gerstein; Leslie A Kuhn
StoneHinge: hinge prediction by network analysis of individual protein structures.
Protein science : a publication of the Protein Society 2009;18(2):359-71.
2009: Kevin Yip; Mark Gerstein
Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions.
Bioinformatics (Oxford, England) 2009;25(2):243-50.
2009: Chao Cheng; Nitin Bhardwaj; Mark Gerstein
The relationship between the evolution of microRNA targets and the length of their UTRs.
BMC genomics 2009;10():431.
2009: Chao Cheng; Xuping Fu; Pedro Alves; Mark Gerstein
mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer.
Genome biology 2009;10(9):R90.
2009: Kevin Yip; Philip M Kim; Drew McDermott; Mark Gerstein
Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels.
BMC bioinformatics 2009;10():241.
2009: Rajkumar Sasidharan; Ashish Agarwal; Joel Rozowsky; Mark Gerstein
An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping.
BMC research notes 2009;2():150.
2009: Michael Snyder; Sherman Weissman; Mark Gerstein
Personal phenotypes to go with personal genomes.
Molecular systems biology 2009;5():273.
2009: Chao Cheng; Lei M Li; Pedro Alves; Mark Gerstein
Systematic identification of transcription factors associated with patient survival in cancers.
BMC genomics 2009;10():225.
2009: Philippe Lefrançois; Ghia M Euskirchen; Raymond K Auerbach; Joel S Rozowsky; Theodore Gibson; Christopher M Yellman; Mark Gerstein; Michael Snyder
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.
BMC genomics 2009;10():37.
2009: Suganthi Balasubramanian; Deyou Zheng; Yuen-Jong Liu; Gang Fang; Adam Frankish; Nicholas Carriero; Rebecca Robilotto; Philip Cayting; Mark Gerstein
Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes.
Genome biology 2009;10(1):R2.
2009: Joel S Rozowsky; Ghia Euskirchen; Raymond K Auerbach; Zhengdong D Zhang; Theodore Gibson; Robert Bjornson; Nicholas Carriero; Michael Snyder; Mark Gerstein
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.
Nature biotechnology 2009;27(1):66-75.
2009: Sorina C Popescu; George V Popescu; Shawn Bachan; Zimei Zhang; Mark Gerstein; Michael Snyder; Savithramma P Dinesh-Kumar
MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays.
Genes & development 2009;23(1):80-92.
2009: Lu-Yong Wang; Alexej Abyzov; Jan O Korbel; Michael Snyder; Mark Gerstein
MSB: a mean-shift-based approach for the analysis of structural variation in the genome.
Genome research 2009;19(1):106-17.
2008: Philip M Kim; Hugo Y K Lam; Alexander Eckehart Urban; Jan O Korbel; Jason Affourtit; Fabian Grubert; Xueying Chen; Sherman Weissman; Michael Snyder; Mark Gerstein
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 2008;18(12):1865-74.
2008: Samuel C Flores; Kevin S Keating; Jay Painter; Faruck Morcos; Khang Nguyen; Ethan A Merritt; Leslie A Kuhn; Mark Gerstein
HingeMaster: normal mode hinge prediction approach and integration of complementary predictors.
Proteins 2008;73(2):299-319.
2008: Zheng Lian; Alexander Karpikov; Jin Lian; Milind C Mahajan; Stephen Hartman; Mark Gerstein; Michael Snyder; Sherman M Weissman
A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation.
Genome research 2008;18(8):1224-37.
2008: Kirsten D Mertz; Francesca Demichelis; Andrea Sboner; Michelle S Hirsch; Paola Dal Cin; Kirsten Struckmann; Martina Storz; Simone Scherrer; Daniel M Schmid; Räto T Strebel; Nicole M Probst-Hensch; Mark Gerstein; Holger Moch; Mark A Rubin
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 2008;123(3):569-76.
2008: Andrey Rzhetsky; Michael Seringhaus; Mark Gerstein
Seeking a new biology through text mining.
Cell 2008;134(1):9-13.
2008: Ugrappa Nagalakshmi; Zhong Wang; Karl Waern; Chong Shou; Debasish Raha; Mark Gerstein; Michael Snyder
The transcriptional landscape of the yeast genome defined by RNA sequencing.
Science (New York, N.Y.) 2008;320(5881):1344-9.
2008: Jan O Korbel; Philip M Kim; Xueying Chen; Alexander Eckehart Urban; Sherman Weissman; Michael Snyder; Mark Gerstein
The current excitement about copy-number variation: how it relates to gene duplications and protein families.
Current opinion in structural biology 2008;18(3):366-74.
2008: Zhengdong D Zhang; George Weinstock; Mark Gerstein
Rapid evolution by positive Darwinian selection in T-cell antigen CD4 in primates.
Journal of molecular evolution 2008;66(5):446-56.
2008: Michael Seringhaus; Mark Gerstein
Manually structured digital abstracts: a scaffold for automatic text mining.
FEBS letters 2008;582(8):1170.
2008: Kevin Yip; Prianka Patel; Philip M Kim; Donald M Engelman; Drew McDermott; Mark Gerstein
An integrated system for studying residue coevolution in proteins.
Bioinformatics (Oxford, England) 2008;24(2):290-2.
2008: Michael Seringhaus; Joel S Rozowsky; Thomas E Royce; Ugrappa Nagalakshmi; Justin Jee; Michael Snyder; Mark Gerstein
Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays.
BMC genomics 2008;9():635.
2008: Zhengdong D Zhang; Joel Rozowsky; Michael Snyder; Joseph Chang; Mark Gerstein
Modeling ChIP sequencing in silico with applications.
PLoS computational biology 2008;4(8):e1000158.
2008: Rajkumar Sasidharan; Andrew Smith; Mark Gerstein
Transmembrane protein oxygen content and compartmentalization of cells.
PloS one 2008;3(7):e2726.
2008: Philip M Kim; Andrea Sboner; Yu Xia; Mark Gerstein
The role of disorder in interaction networks: a structural analysis.
Molecular systems biology 2008;4():179.
2008: Jia Qian Wu; Jiang Du; Joel S Rozowsky; Zhengdong Zhang; Alexander E Urban; Ghia Euskirchen; Sherman Weissman; Mark Gerstein; Michael Snyder
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome.
Genome biology 2008;9(1):R3.
2008: Zhengdong D Zhang; Philip Cayting; George Weinstock; Mark Gerstein
Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories.
Molecular biology and evolution 2008;25(1):131-43.
2007: Philip M Kim; Jan O Korbel; Mark Gerstein
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 2007;104(51):20274-9.
2007: Andrew Smith; Kei Cheung; Michael Krauthammer; Martin Schultz; Mark Gerstein
Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics.
Bioinformatics (Oxford, England) 2007;23(22):3073-9.
2007: Sunita R Setlur; Thomas E Royce; Andrea Sboner; Juan-Miguel Mosquera; Francesca Demichelis; Matthias D Hofer; Kirsten D Mertz; Mark Gerstein; Mark A Rubin
Integrative microarray analysis of pathways dysregulated in metastatic prostate cancer.
Cancer research 2007;67(21):10296-303.
2007: Jan O Korbel; Alexander Eckehart Urban; Jason P Affourtit; Brian Godwin; Fabian Grubert; Jan Fredrik Simons; Philip M Kim; Dean Palejev; Nicholas Carriero; Lei Du; bruce taillon; Zhoutao Chen; Andrea Tanzer; A C Eugenia Saunders; jianxiang chi; Fengtang Yang; Nigel P Carter; Matthew E Hurles; Sherman M Weissman; Timothy T Harkins; Mark Gerstein; Michael Egholm; Michael Snyder
Paired-end mapping reveals extensive structural variation in the human genome.
Science (New York, N.Y.) 2007;318(5849):420-6.
2007: Anthony R Borneman; Zhengdong D Zhang; Joel S Rozowsky; Michael Seringhaus; Mark Gerstein; Michael Snyder
Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.
Functional & integrative genomics 2007;7(4):335-45.
2007: Haiyuan Yu; Ronald Jansen; Gustavo Stolovitzky; Mark Gerstein
Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications.
Bioinformatics (Oxford, England) 2007;23(16):2163-73.
2007: Anthony R Borneman; Tara A Gianoulis; Zhengdong D Zhang; Haiyuan Yu; Joel S Rozowsky; Michael Seringhaus; Lu Yong Wang; Mark Gerstein; Michael Snyder
Divergence of transcription factor binding sites across related yeast species.
Science (New York, N.Y.) 2007;317(5839):815-9.
2007: Linfeng Wu; Sun-Il Hwang; Karim Rezaul; Long J Lu; Viveka Mayya; Mark Gerstein; Jimmy K Eng; Deborah H Lundgren; David K Han
Global survey of human T leukemic cells by integrating proteomics and transcriptomics profiling.
Molecular & cellular proteomics : MCP 2007;6(8):1343-53.
2007: Long J Lu; Andrea Sboner; Yuanpeng J Huang; Hao Xin Lu; Tara A Gianoulis; Kevin Yip; Philip M Kim; Gaetano T Montelione; Mark Gerstein
Comparing classical pathways and modern networks: towards the development of an edge ontology.
Trends in biochemical sciences 2007;32(7):320-31.
2007: Jan O Korbel; Alexander Eckehart Urban; Fabian Grubert; Du Jiang; Thomas E Royce; Peter Starr; Guoneng Zhong; Beverly S Emanuel; Sherman M Weissman; Michael Snyder; Mark Gerstein
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 2007;104(24):10110-5.
2007: Ghia Euskirchen; Joel S Rozowsky; Chia-Lin Wei; Wah Heng Lee; Zhengdong D Zhang; Stephen Hartman; Olof Emanuelsson; Viktor Stolc; Sherman Weissman; Mark Gerstein; Yijun Ruan; Michael Snyder
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies.
Genome research 2007;17(6):898-909.
2007: Stefan Washietl; Jakob S Pedersen; Jan O Korbel; Claudia Stocsits; Andreas R Gruber; Jorg Hackermuller; Jana Hertel; Manja Lindemeyer; Kristin Reiche; Andrea Tanzer; Catherine Ucla; Carine Wyss; Stylianos E Antonarakis; France Denoeud; Julien Lagarde; Jorg Drenkow; Philipp Kapranov; Thomas Gingeras; Roderic Guigó; Michael Snyder; Mark Gerstein; Alexandre Reymond; Ivo L Hofacker; Peter F Stadler
Structured RNAs in the ENCODE selected regions of the human genome.
Genome research 2007;17(6):852-64.
2007: Deyou Zheng; Adam Frankish; Robert Baertsch; Philipp Kapranov; Alexandre Reymond; Siew Woh Choo; Yontao Lu; France Denoeud; Stylianos E Antonarakis; Michael Snyder; Yijun Ruan; Chia-Lin Wei; Thomas Gingeras; Roderic Guigó; Jennifer Harrow; Mark Gerstein
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.
Genome research 2007;17(6):839-51.
2007: Zhengdong D Zhang; Alberto Paccanaro; Yutao Fu; Sherman Weissman; Zhiping Weng; Joseph Chang; Michael Snyder; Mark Gerstein
Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions.
Genome research 2007;17(6):787-97.
2007: Joel S Rozowsky; Daniel Newburger; Fred Sayward; Jiaqian Wu; Greg Jordan; Jan O Korbel; Ugrappa Nagalakshmi; Jin Yang; Deyou Zheng; Roderic Guigó; Thomas Gingeras; Sherman Weissman; Perry Miller; Michael Snyder; Mark Gerstein
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.
Genome research 2007;17(6):732-45.
2007: Mark Gerstein; Can Bruce; Joel S Rozowsky; Deyou Zheng; Du Jiang; Jan O Korbel; Olof Emanuelsson; Zhengdong D Zhang; Sherman Weissman; Michael Snyder
What is a gene, post-ENCODE? History and updated definition.
Genome research 2007;17(6):669-81.
2007: Olof Emanuelsson; Ugrappa Nagalakshmi; Deyou Zheng; Joel S Rozowsky; Alexander Eckehart Urban; Du Jiang; Zheng Lian; Viktor Stolc; Sherman Weissman; Michael Snyder; Mark Gerstein
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.
Genome research 2007;17(6):886-97.
2007: Mark Gerstein; Michael Seringhaus; Stanley Fields
Structured digital abstract makes text mining easy.
Nature 2007;447(7141):142.
2007: Xiaowei Zhu; Mark Gerstein; Michael Snyder
Getting connected: analysis and principles of biological networks.
Genes & development 2007;21(9):1010-24.
2007: Deyou Zheng; Mark Gerstein
The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?
Trends in genetics : TIG 2007;23(5):219-24.
2007: Haiyuan Yu; Philip M Kim; Emmett Sprecher; Valery Trifonov; Mark Gerstein
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics.
PLoS computational biology 2007;3(4):e59.
2007: Thomas E Royce; Joel S Rozowsky; Mark Gerstein
Assessing the need for sequence-based normalization in tiling microarray experiments.
Bioinformatics (Oxford, England) 2007;23(8):988-97.
2007: Sorina C Popescu; George V Popescu; Shawn Bachan; Zimei Zhang; Montrell D Seay; Mark Gerstein; Michael Snyder; Savithramma P Dinesh-Kumar
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 2007;104(11):4730-5.
2007: Michael G Smith; Tara A Gianoulis; Stefan Pukatzki; John J Mekalanos; L Nicholas Ornston; Mark Gerstein; Michael Snyder
New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis.
Genes & development 2007;21(5):601-14.
2007: Mark Gerstein; Dov Greenbaum; Kei Cheung; Perry L Miller
An interdepartmental Ph.D. program in computational biology and bioinformatics: the Yale perspective.
Journal of biomedical informatics 2007;40(1):73-9.
2007: Michael Seringhaus; Mark Gerstein
Chemistry Nobel rich in structure.
Science (New York, N.Y.) 2007;315(5808):40-1.
2007: Eric Z Yu; Anne Counterman Burba; Mark Gerstein
PARE: a tool for comparing protein abundance and mRNA expression data.
BMC bioinformatics 2007;8():309.
2007: Thomas E Royce; Joel S Rozowsky; Mark Gerstein
Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification.
Nucleic acids research 2007;35(15):e99.
2007: Samuel C Flores; Mark Gerstein
FlexOracle: predicting flexible hinges by identification of stable domains.
BMC bioinformatics 2007;8():215.
2007: Thomas E Royce; Nicholas Carriero; Mark Gerstein
An efficient pseudomedian filter for tiling microrrays.
BMC bioinformatics 2007;8():186.
2007: Samuel C Flores; Long J Lu; Julie Yang; Nicholas Carriero; Mark Gerstein
Hinge Atlas: relating protein sequence to sites of structural flexibility.
BMC bioinformatics 2007;8():167.
2007: Zhengdong D Zhang; Joel S Rozowsky; Hugo Y K Lam; Du Jiang; Michael Snyder; Mark Gerstein
Tilescope: online analysis pipeline for high-density tiling microarray data.
Genome biology 2007;8(5):R81.
2007: Lei Li; xiangfeng wang; Rajkumar Sasidharan; Viktor Stolc; Wei Deng; Hang He; Jan Korbel; Xuewei Chen; Waraporn Tongprasit; Pamela Ronald; Runsheng Chen; Mark Gerstein; Xing Wang Deng
Global identification and characterization of transcriptionally active regions in the rice genome.
PloS one 2007;2(3):e294.
2007: Zhaolei Zhang; Andy Wing Chun Pang; Mark Gerstein
Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.
BMC evolutionary biology 2007;7 Suppl 1():S14.
2007: Michael Seringhaus; Mark Gerstein
Publishing perishing? Towards tomorrow's information architecture.
BMC bioinformatics 2007;8():17.
2007: Haiyuan Yu; Katherine Nguyen; Thomas E Royce; Jiang Qian; Kenneth Nelson; Michael Snyder; Mark Gerstein
Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool.
Nucleic acids research 2007;35(2):e8.
2007: John Karro; Yangpan Yan; Deyou Zheng; Zhaolei Zhang; Nicholas Carriero; Philip Cayting; Paul Harrrison; Mark Gerstein
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.
Nucleic acids research 2007;35(Database issue):D55-60.
2006: Philip M Kim; Long J Lu; Yu Xia; Mark Gerstein
Relating three-dimensional structures to protein networks provides evolutionary insights.
Science (New York, N.Y.) 2006;314(5807):1938-41.
2006: Du Jiang; Joel S Rozowsky; Jan O Korbel; Zhengdong D Zhang; Thomas E Royce; Martin H Schultz; Michael Snyder; Mark Gerstein
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) 2006;22(24):3016-24.
2006: Kevin Yip; Haiyuan Yu; Philip M Kim; Martin Schultz; Mark Gerstein
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks.
Bioinformatics (Oxford, England) 2006;22(23):2968-70.
2006: Yang Liu; Jianrong Li; Lee Sam; Chern-Sing Goh; Mark Gerstein; Yves lussier
An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits.
PLoS computational biology 2006;2(11):e159.
2006: Anne Counterman Burba; Ursula Lehnert; Eric Z Yu; Mark Gerstein
Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins.
Bioinformatics (Oxford, England) 2006;22(22):2735-8.
2006: Haiyuan Yu; Mark Gerstein
Genomic analysis of the hierarchical structure of regulatory networks.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(40):14724-31.
2006: Thyagarajan Srikantha; Anthony R Borneman; Karla J Daniels; Claude Pujol; Wei Wu; Michael Seringhaus; Mark Gerstein; Song Yi; Michael Snyder; David Soll
TOS9 regulates white-opaque switching in Candida albicans.
Eukaryotic cell 2006;5(10):1674-87.
2006: Michael Seringhaus; Alberto Paccanaro; Anthony R Borneman; Michael Snyder; Mark Gerstein
Predicting essential genes in fungal genomes.
Genome research 2006;16(9):1126-35.
2006: N R Voss; Mark Gerstein; Thomas A Steitz; Peter B Moore
The geometry of the ribosomal polypeptide exit tunnel.
Journal of molecular biology 2006;360(4):893-906.
2006: Zhaolei Zhang; Nicholas Carriero; Deyou Zheng; John Karro; Paul M Harrison; Mark Gerstein
PseudoPipe: an automated pseudogene identification pipeline.
Bioinformatics (Oxford, England) 2006;22(12):1437-9.
2006: Haiyuan Yu; Alberto Paccanaro; Valery Trifonov; Mark Gerstein
Predicting interactions in protein networks by completing defective cliques.
Bioinformatics (Oxford, England) 2006;22(7):823-9.
2006: Alexander Eckehart Urban; Jan O Korbel; Rebecca Selzer; Richmond Todd; April Hacker; George V Popescu; Joseph F Cubells; Roland Green; Beverly S Emanuel; Mark Gerstein; Sherman M Weissman; Michael Snyder
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 2006;103(12):4534-9.
2006: Yu Xia; Long J Lu; Mark Gerstein
Integrated prediction of the helical membrane protein interactome in yeast.
Journal of molecular biology 2006;357(1):339-49.
2006: Anthony R Borneman; Justine A Leigh-Bell; Haiyuan Yu; Paul Bertone; Mark Gerstein; Michael Snyder
Target hub proteins serve as master regulators of development in yeast.
Genes & development 2006;20(4):435-48.
2006: Paul Bertone; Valery Trifonov; Joel S Rozowsky; Falk Schubert; Olof Emanuelsson; John Karro; Ming-Yang Kao; Michael Snyder; Mark Gerstein
Design optimization methods for genomic DNA tiling arrays.
Genome research 2006;16(2):271-81.
2006: Joel S Rozowsky; J Wu; Zheng Lian; Ugrappa Nagalakshmi; Jan O Korbel; Philipp Kapranov; Deyou Zheng; S Dyke; Peter E Newburger; Perry Miller; Thomas Gingeras; Sherman Weissman; Mark Gerstein; Michael Snyder
Novel transcribed regions in the human genome.
Cold Spring Harbor symposia on quantitative biology 2006;71():111-6.
2006: Xiaowei Zhu; Mark Gerstein; Michael Snyder
ProCAT: a data analysis approach for protein microarrays.
Genome biology 2006;7(11):R110.
2006: Chern-Sing Goh; Tara A Gianoulis; Yang Liu; Jianrong Li; Alberto Paccanaro; Yves lussier; Mark Gerstein
Integration of curated databases to identify genotype-phenotype associations.
BMC genomics 2006;7():257.
2006: Thomas E Royce; Joel S Rozowsky; Nicholas M Luscombe; Olof Emanuelsson; Haiyuan Yu; Xiaowei Zhu; Michael Snyder; Mark Gerstein
Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies.
Methods in enzymology 2006;411():282-311.
2006: Robert Pinard; Alex de Winter; Gary J Sarkis; Mark Gerstein; Karrie R Tartaro; Ramona N Plant; Michael Egholm; Jonathan M Rothberg; John Leamon
Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing.
BMC genomics 2006;7():216.
2006: Deyou Zheng; Mark Gerstein
A computational approach for identifying pseudogenes in the ENCODE regions.
Genome biology 2006;7 Suppl 1():S13.1-10.
2006: Haiyuan Yu; Yu Xia; Valery Trifonov; Mark Gerstein
Design principles of molecular networks revealed by global comparisons and composite motifs.
Genome biology 2006;7(7):R55.
2006: Michael Seringhaus; Anuj Kumar; John Hartigan; Michael Snyder; Mark Gerstein
Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae.
Nucleic acids research 2006;34(8):e57.
2006: Samuel Flores; Nathaniel Echols; Duncan Milburn; Brandon M Hespenheide; Kevin Keating; Jason Lu; Stephen Wells; Eric Z Yu; Michael F Thorpe; Mark Gerstein
The Database of Macromolecular Motions: new features added at the decade mark.
Nucleic acids research 2006;34(Database issue):D296-301.
2005: Stephen Hartman; Paul Bertone; Anjali K Nath; Thomas E Royce; Mark Gerstein; Sherman Weissman; Michael Snyder
Global changes in STAT target selection and transcription regulation upon interferon treatments.
Genes & development 2005;19(24):2953-68.
2005: Jason Ptacek; Geeta Devgan; Gregory A 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 J R Stark; David F Stern; Claudio de Virgilio; Mike Tyers; Brenda Andrews; Mark Gerstein; Barry Schweitzer; Paul Predki; Michael Snyder
Global analysis of protein phosphorylation in yeast.
Nature 2005;438(7068):679-84.
2005: Tatjana Coric; Deyou Zheng; Mark Gerstein; Cecilia M Canessa
Proton sensitivity of ASIC1 appeared with the rise of fishes by changes of residues in the region that follows TM1 in the ectodomain of the channel.
The Journal of physiology 2005;568(Pt 3):725-35.
2005: Viktor Stolc; Lei Li; xiangfeng wang; Xueyong Li; Ning Su; Waraporn Tongprasit; Bin Han; Yongbiao Xue; Jiayang Li; Michael Snyder; Mark Gerstein; Jun Wang; Xing Wang Deng
A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.
Plant molecular biology 2005;59(1):137-49.
2005: Thomas E Royce; Joel S Rozowsky; Paul Bertone; Manoj Pratim Samanta; Viktor Stolc; Sherman Weissman; Michael Snyder; Mark Gerstein
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.
Trends in genetics : TIG 2005;21(8):466-75.
2005: Long J Lu; Yu Xia; Alberto Paccanaro; Haiyuan Yu; Mark Gerstein
Assessing the limits of genomic data integration for predicting protein networks.
Genome research 2005;15(7):945-53.
2005: Kei-Hoi Cheung; Kevin Yip; Andrew Smith; Remko Deknikker; Andy Masiar; Mark Gerstein
YeastHub: a semantic web use case for integrating data in the life sciences domain.
Bioinformatics (Oxford, England) 2005;21 Suppl 1():i85-96.
2005: Deyou Zheng; Zhaolei Zhang; Paul M Harrison; John Karro; Nicholas Carriero; Mark Gerstein
Integrated pseudogene annotation for human chromosome 22: evidence for transcription.
Journal of molecular biology 2005;349(1):27-45.
2005: Yoav Gilad; Scott A Rifkin; Paul Bertone; Mark Gerstein; Kevin P White
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles.
Genome research 2005;15(5):674-80.
2005: Helge Grosshans; Ted Johnson; Kristy L Reinert; Mark Gerstein; Frank J Slack
The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans.
Developmental cell 2005;8(3):321-30.
2005: Vadim Alexandrov; Ursula Lehnert; Nathaniel Echols; Duncan Milburn; Donald M Engelman; Mark Gerstein
Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool.
Protein science : a publication of the Protein Society 2005;14(3):633-43.
2005: N R Voss; Mark Gerstein
Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly.
Journal of molecular biology 2005;346(2):477-92.
2005: Andrew Smith; Dov Greenbaum; Shawn Douglas; Morrow Long; Mark Gerstein
Network security and data integrity in academia: an assessment and a proposal for large-scale archiving.
Genome biology 2005;6(9):119.
2005: Shawn Douglas; Gaetano T Montelione; Mark Gerstein
PubNet: a flexible system for visualizing literature derived networks.
Genome biology 2005;6(9):R80.
2005: Paul Bertone; Mark Gerstein; Michael Snyder
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 2005;13(3):259-74.
2005: Paul M Harrison; Deyou Zheng; Zhaolei Zhang; Nicholas Carriero; Mark Gerstein
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.
Nucleic acids research 2005;33(8):2374-83.
2005: Thomas B Acton; Kristin C Gunsalus; Rong Xiao; Li Chung Ma; James M Aramini; Michael C Baran; Yi-Wen Chiang; Teresa Climent; Bonnie Cooper; Natalia G Denissova; Shawn Douglas; John K Everett; Chi Kent Ho; Daphne Macapagal; Paranji K Rajan; Ritu Shastry; Liang-Yu Shih; G V T Swapna; Michael Wilson; Margaret Wu; Mark Gerstein; Masayori Inouye; John F Hunt; Gaetano T Montelione
Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium.
Methods in enzymology 2005;394():210-43.
2005: Suganthi Balasubramanian; Yu Xia; Elizaveta Freinkman; Mark Gerstein
Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms.
Nucleic acids research 2005;33(5):1710-21.
2005: Nicholas Carriero; Michael V Osier; Kei-Hoi Cheung; Perry L Miller; Mark Gerstein; Hongyu Zhao; Baolin Wu; Scott Rifkin; Joseph Chang; Heping Zhang; Kevin White; Kenneth Williams; Martin Schultz
A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies.
Journal of the American Medical Informatics Association : JAMIA 2005;12(1):90-8.
2004: Paul Bertone; Viktor Stolc; Thomas E Royce; Joel S Rozowsky; Alexander Eckehart Urban; Xiaowei Zhu; John L Rinn; Waraporn Tongprasit; Manoj Pratim Samanta; Sherman Weissman; Mark Gerstein; Michael Snyder
Global identification of human transcribed sequences with genome tiling arrays.
Science (New York, N.Y.) 2004;306(5705):2242-6.
2004: Eric J White; Olof Emanuelsson; d scalzo; Thomas E Royce; Steven Kosak; Edward J Oakeley; Sherman Weissman; Mark Gerstein; Mark Groudine; Michael Snyder; Dirk Schübeler
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 2004;101(51):17771-6.
2004: David A Hall; Heng Zhu; Xiaowei Zhu; Thomas E Royce; Mark Gerstein; Michael Snyder
Regulation of gene expression by a metabolic enzyme.
Science (New York, N.Y.) 2004;306(5695):482-4.
2004: Anuj Kumar; Michael Seringhaus; Matthew C Biery; Robert J Sarnovsky; Lara Umansky; Stacy Piccirillo; Matthew Heidtman; Kei-Hoi Cheung; Craig J Dobry; Mark Gerstein; Nancy Craig; Michael Snyder
Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon.
Genome research 2004;14(10A):1975-86.
2004: Nicholas M Luscombe; M Madan Babu; Haiyuan Yu; Michael Snyder; Sarah A Teichmann; Mark Gerstein
Genomic analysis of regulatory network dynamics reveals large topological changes.
Nature 2004;431(7006):308-12.
2004: Zhaolei Zhang; Mark Gerstein
Large-scale analysis of pseudogenes in the human genome.
Current opinion in genetics & development 2004;14(4):328-35.
2004: Zeba Wunderlich; Thomas B Acton; Jinfeng Liu; Gregory Kornhaber; John Everett; Phil Carter; Ning Lan; Nathaniel Echols; Mark Gerstein; Burkhard Rost; Gaetano T Montelione
The protein target list of the Northeast Structural Genomics Consortium.
Proteins 2004;56(2):181-7.
2004: John L Rinn; Joel S Rozowsky; Ian J Laurenzi; Petur H Petersen; Kaiyong Zou; Weimin Zhong; Mark Gerstein; Michael Snyder
Major molecular differences between mammalian sexes are involved in drug metabolism and renal function.
Developmental cell 2004;6(6):791-800.
2004: Dov Greenbaum; Shawn Douglas; Andrew Smith; Joanna Lim; Michael Fischer; Martin Schultz; Mark Gerstein
Computer security in academia-a potential roadblock to distributed annotation of the human genome.
Nature biotechnology 2004;22(6):771-2.
2004: Haiyuan Yu; Nicholas M Luscombe; Hao Xin Lu; Xiaowei Zhu; Yu Xia; Jing-Dong J Han; Nicolas Bertin; Sambath Chung; Marc Vidal; Mark Gerstein
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.
Genome research 2004;14(6):1107-18.
2004: Haiyuan Yu; Dov Greenbaum; Hao Xin Lu; Xiaowei Zhu; Mark Gerstein
Genomic analysis of essentiality within protein networks.
Trends in genetics : TIG 2004;20(6):227-31.
2004: Lisa L Freeman-Cook; Ann M Dixon; Jennifer B Frank; Yu Xia; Lara Ely; Mark Gerstein; Donald M Engelman; Daniel DiMaio
Selection and characterization of small random transmembrane proteins that bind and activate the platelet-derived growth factor beta receptor.
Journal of molecular biology 2004;338(5):907-20.
2004: Ursula Lehnert; Yu Xia; Thomas E Royce; Chern-Sing Goh; Yang Liu; Alessandro Senes; Haiyuan Yu; Zhao Lei Zhang; Donald M Engelman; Mark Gerstein
Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions.
Quarterly reviews of biophysics 2004;37(2):121-46.
2004: Ghia Euskirchen; Thomas E Royce; Paul Bertone; Rebecca Martone; John L Rinn; F Kenneth Nelson; Fred Sayward; Nicholas M Luscombe; Perry Miller; Mark Gerstein; Sherman Weissman; Michael Snyder
CREB binds to multiple loci on human chromosome 22.
Molecular and cellular biology 2004;24(9):3804-14.
2004: Rajdeep Das; Mark Gerstein
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 2004;55(2):455-63.
2004: Yang Liu; Mark Gerstein; Donald M Engelman
Transmembrane protein domains rarely use covalent domain recombination as an evolutionary mechanism.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(10):3495-7.
2004: Chern-Sing Goh; Ning Lan; Shawn Douglas; Baolin Wu; Nathaniel Echols; Andrew Smith; Duncan Milburn; Gaetano T Montelione; Hongyu Zhao; Mark Gerstein
Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis.
Journal of molecular biology 2004;336(1):115-30.
2004: Chern-Sing Goh; Duncan Milburn; Mark Gerstein
Conformational changes associated with protein-protein interactions.
Current opinion in structural biology 2004;14(1):104-9.
2004: Mark Gerstein; Nathaniel Echols
Exploring the range of protein flexibility, from a structural proteomics perspective.
Current opinion in chemical biology 2004;8(1):14-9.
2004: Zhaolei Zhang; Nicholas Carriero; Mark Gerstein
Comparative analysis of processed pseudogenes in the mouse and human genomes.
Trends in genetics : TIG 2004;20(2):62-7.
2004: Aled M Edwards; Dov Greenbaum; Jack Greenblatt; Ronald Jansen; Bart Kus; Mark Gerstein
Bridging structural biology and genomics: assessing protein interaction data with known complexes.
Drug discovery today 2004;9(2 Suppl):S32-40.
2004: Vadim Alexandrov; Mark Gerstein
Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures.
BMC bioinformatics 2004;5():2.
2004: Piotr Berman; Paul Bertone; Bhaskar Dasgupta; Mark Gerstein; Ming-Yang Kao; Michael Snyder
Fast optimal genome tiling with applications to microarray design and homology search.
Journal of computational biology : a journal of computational molecular cell biology 2004;11(4):766-85.
2004: Yang Liu; Paul M Harrison; Victor Kunin; Mark Gerstein
Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes.
Genome biology 2004;5(9):R64.
2004: Yu Xia; Haiyuan Yu; Ronald Jansen; Michael Seringhaus; Sarah Baxter; Dov Greenbaum; Hongyu Zhao; Mark Gerstein
Analyzing cellular biochemistry in terms of molecular networks.
Annual review of biochemistry 2004;73():1051-87.
2004: Haiyuan Yu; Xiaowei Zhu; Dov Greenbaum; John Karro; Mark Gerstein
TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics.
Nucleic acids research 2004;32(1):328-37.
2003: Yuval Kluger; Haiyuan Yu; Jiang Qian; Mark Gerstein
Relationship between gene co-expression and probe localization on microarray slides.
BMC genomics 2003;4(1):49.
2003: Zhaolei Zhang; Paul M Harrison; Yin Liu; Mark Gerstein
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome.
Genome research 2003;13(12):2541-58.
2003: Paul M Harrison; Nicholas Carriero; Yang Liu; Mark Gerstein
A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs.
Journal of molecular biology 2003;333(5):885-92.
2003: Ronald Jansen; Haiyuan Yu; Dov Greenbaum; Yuval Kluger; Nevan J Krogan; Sambath Chung; Andrew Emili; Michael Snyder; Jack F Greenblatt; Mark Gerstein
A Bayesian networks approach for predicting protein-protein interactions from genomic data.
Science (New York, N.Y.) 2003;302(5644):449-53.
2003: Rebecca Martone; Ghia Euskirchen; Paul Bertone; Stephen Hartman; Thomas E Royce; Nicholas M Luscombe; John L Rinn; F Kenneth Nelson; Perry Miller; Mark Gerstein; Sherman Weissman; Michael Snyder
Distribution of NF-kappaB-binding sites across human chromosome 22.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(21):12247-52.
2003: Zhaolei Zhang; Mark Gerstein
Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes.
Nucleic acids research 2003;31(18):5338-48.
2003: Dov Greenbaum; Mark Gerstein
A universal legal framework as a prerequisite for database interoperability.
Nature biotechnology 2003;21(9):979-82.
2003: Haiyuan Yu; Nicholas M Luscombe; Jiang Qian; Mark Gerstein
Genomic analysis of gene expression relationships in transcriptional regulatory networks.
Trends in genetics : TIG 2003;19(8):422-7.
2003: Zhaolei Zhang; Mark Gerstein
The human genome has 49 cytochrome c pseudogenes, including a relic of a primordial gene that still functions in mouse.
Gene 2003;312():61-72.
2003: Jiang Qian; Yuval Kluger; Haiyuan Yu; Mark Gerstein
Identification and correction of spurious spatial correlations in microarray data.
BioTechniques 2003;35(1):42-4, 46, 48.
2003: Nicholas M Luscombe; Thomas E Royce; Paul Bertone; Nathaniel Echols; Christine E Horak; Joseph T Chang; Michael Snyder; Mark Gerstein
ExpressYourself: A modular platform for processing and visualizing microarray data.
Nucleic acids research 2003;31(13):3477-82.
2003: Chern-Sing Goh; Ning Lan; Nathaniel Echols; Shawn Douglas; Duncan Milburn; Paul Bertone; Rong Xiao; Li-Chung Ma; Deyou Zheng; Zeba Wunderlich; Thomas B Acton; Gaetano T Montelione; Mark Gerstein
SPINE 2: a system for collaborative structural proteomics within a federated database framework.
Nucleic acids research 2003;31(11):2833-8.
2003: Zhaolei Zhang; Mark Gerstein
Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome.
Genomics 2003;81(5):468-80.
2003: Ronald Jansen; Harmen J Bussemaker; Mark Gerstein
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 2003;31(8):2242-51.
2003: Michael Snyder; Mark Gerstein
Genomics. Defining genes in the genomics era.
Science (New York, N.Y.) 2003;300(5617):258-60.
2003: Yuval Kluger; Ronen Basri; Joseph T Chang; Mark Gerstein
Spectral biclustering of microarray data: coclustering genes and conditions.
Genome research 2003;13(4):703-16.
2003: John L Rinn; Ghia Euskirchen; Paul Bertone; Rebecca Martone; Nicholas M Luscombe; Stephen Hartman; Paul M Harrison; F Kenneth Nelson; Perry Miller; Mark Gerstein; Sherman Weissman; Michael Snyder
The transcriptional activity of human Chromosome 22.
Genes & development 2003;17(4):529-40.
2003: Paul M Harrison; Duncan Milburn; Zhaolei Zhang; Paul Bertone; Mark Gerstein
Identification of pseudogenes in the Drosophila melanogaster genome.
Nucleic acids research 2003;31(3):1033-7.
2003: Zheng Lian; Ghia Euskirchen; John L Rinn; Rebecca Martone; Paul Bertone; Stephen Hartman; Thomas E Royce; K Nelson; Fred Sayward; Nicholas M Luscombe; J Yang; J L Li; Perry Miller; Alexander Eckehart Urban; Mark Gerstein; Sherman Weissman; Michael Snyder
Identification of novel functional elements in the human genome.
Cold Spring Harbor symposia on quantitative biology 2003;68():317-22.
2003: WG Krebs; J Tsai; Vadim Alexandrov; Jochen Junker; Ronald Jansen; Mark Gerstein
Tools and databases to analyze protein flexibility; approaches to mapping implied features onto sequences.
Methods in enzymology 2003;374():544-84.
2003: Dov Greenbaum; Christopher Colangelo; Kenneth Williams; Mark Gerstein
Comparing protein abundance and mRNA expression levels on a genomic scale.
Genome biology 2003;4(9):117.
2003: Zhaolei Zhang; Mark Gerstein
Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements.
Journal of biology 2003;2(2):11.
2003: Paul M Harrison; Mark Gerstein
A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes.
Genome biology 2003;4(6):R40.
2003: Nathaniel Echols; Duncan Milburn; Mark Gerstein
MolMovDB: analysis and visualization of conformational change and structural flexibility.
Nucleic acids research 2003;31(1):478-82.
2002: Dirk Schneider; Yang Liu; Mark Gerstein; Donald M Engelman
Thermostability of membrane protein helix-helix interaction elucidated by statistical analysis.
FEBS letters 2002;532(1-2):231-6.
2002: Christine E Horak; Nicholas M Luscombe; Jiang Qian; Paul Bertone; Stacy Piccirrillo; Mark Gerstein; Michael Snyder
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae.
Genes & development 2002;16(23):3017-33.
2002: Zhao Lei Zhang; Paul M Harrison; Mark Gerstein
Digging deep for ancient relics: a survey of protein motifs in the intergenic sequences of four eukaryotic genomes.
Journal of molecular biology 2002;323(5):811-22.
2002: Zheng Lian; Yuval Kluger; Dov S Greenbaum; David Tuck; Mark Gerstein; Nancy Berliner; Sherman M Weissman; Peter E Newburger
Genomic and proteomic analysis of the myeloid differentiation program: global analysis of gene expression during induced differentiation in the MPRO cell line.
Blood 2002;100(9):3209-20.
2002: Jimmy Lin; Jiang Qian; Dov Greenbaum; Paul Bertone; R Das; Nathaniel Echols; Alessandro Senes; B Stenger; Mark Gerstein
GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing.
Nucleic acids research 2002;30(20):4574-82.
2002: Zhaolei Zhang; Paul Harrison; Mark Gerstein
Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome.
Genome research 2002;12(10):1466-82.
2002: Aled M Edwards; Bart Kus; Ronald Jansen; Dov Greenbaum; Jack Greenblatt; Mark Gerstein
Bridging structural biology and genomics: assessing protein interaction data with known complexes.
Trends in genetics : TIG 2002;18(10):529-36.
2002: Yang Liu; Donald M Engelman; Mark Gerstein
Genomic analysis of membrane protein families: abundance and conserved motifs.
Genome biology 2002;3(10):research0054.
2002: WG Krebs; Vadim Alexandrov; Cyrus A Wilson; Nathaniel Echols; Haiyuan Yu; Mark Gerstein
Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic.
Proteins 2002;48(4):682-95.
2002: Nicholas M Luscombe; Jiang Qian; Zhaolei Zhang; Ted Johnson; Mark Gerstein
The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties.
Genome biology 2002;3(8):RESEARCH0040.
2002: Nathaniel Echols; Paul Harrison; Suganthi Balasubramanian; Nicholas M Luscombe; Paul Bertone; Zhaolei Zhang; Mark Gerstein
Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes.
Nucleic acids research 2002;30(11):2515-23.
2002: Paul M Harrison; Mark Gerstein
Studying genomes through the aeons: protein families, pseudogenes and proteome evolution.
Journal of molecular biology 2002;318(5):1155-74.
2002: Suganthi Balasubramanian; Paul Harrison; Hedi Hegyi; Paul Bertone; Nicholas M Luscombe; Nathaniel Echols; Patrick McGarvey; Zhaolei Zhang; Mark Gerstein
SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes.
Pharmacogenomics 2002;3(3):393-402.
2002: Hedi Hegyi; Jimmy Lin; Dov Greenbaum; Mark Gerstein
Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds.
Proteins 2002;47(2):126-41.
2002: Dov Greenbaum; Ronald Jansen; Mark Gerstein
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) 2002;18(4):585-96.
2002: Anuj Kumar; Seema Agarwal; John A Heyman; Sandra Matson; Matthew Heidtman; Stacy Piccirillo; Lara Umansky; Amar Drawid; Ronald Jansen; Yang Liu; Kei-Hoi Cheung; Perry Miller; Mark Gerstein; G Shirleen Roeder; Michael Snyder
Subcellular localization of the yeast proteome.
Genes & development 2002;16(6):707-19.
2002: Christine E Horak; Milind C Mahajan; Nicholas M Luscombe; Mark Gerstein; Sherman M Weissman; Michael Snyder
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 2002;99(5):2924-9.
2002: Paul M Harrison; Anuj Kumar; Ning Lang; Michael Snyder; Mark Gerstein
A question of size: the eukaryotic proteome and the problems in defining it.
Nucleic acids research 2002;30(5):1083-90.
2002: Paul Harrison; Anuj Kumar; Ning Lan; Nathaniel Echols; Michael Snyder; Mark Gerstein
A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution.
Journal of molecular biology 2002;316(3):409-19.
2002: Paul M Harrison; Hedi Hegyi; Suganthi Balasubramanian; Nicholas M Luscombe; Paul Bertone; Nathaniel Echols; Ted Johnson; Mark Gerstein
Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22.
Genome research 2002;12(2):272-80.
2002: Mark Gerstein; Ning Lan; Ronald Jansen
Proteomics. Integrating interactomes.
Science (New York, N.Y.) 2002;295(5553):284-7.
2002: Ronald Jansen; Ning Lan; Jiang Qian; Mark Gerstein
Integration of genomic datasets to predict protein complexes in yeast.
Journal of structural and functional genomics 2002;2(2):71-81.
2002: Kei-Hoi Cheung; Kevin White; Janet Hager; Mark Gerstein; Valerie Reinke; Kenneth Nelson; Peter Masiar; Ranjana Srivastava; Yuli Li; Jinming Li; Hongyu Zhao; Jinming Li; David Allison; Michael Snyder; Perry Miller; Kenneth Williams
YMD: a microarray database for large-scale gene expression analysis.
Proceedings / AMIA ... Annual Symposium. AMIA Symposium 2002;():140-4.
2002: Yang Liu; Nicholas M Luscombe; Vadim Alexandrov; Paul Bertone; Paul Harrison; Zhaolei Zhang; Mark Gerstein
Structural genomics: a new era for pharmaceutical research.
Genome biology 2002;3(2):REPORTS4004.
2002: Ronald Jansen; Dov Greenbaum; Mark Gerstein
Relating whole-genome expression data with protein-protein interactions.
Genome research 2002;12(1):37-46.
2002: Anuj Kumar; Paul M Harrison; Kei-Hoi Cheung; Ning Lan; Nathaniel Echols; Paul Bertone; Perry Miller; Mark Gerstein; Michael Snyder
An integrated approach for finding overlooked genes in yeast.
Nature biotechnology 2002;20(1):58-63.
2001: Jiang Qian; Marisa Dolled-Filhart; J Lin; H Yu; Mark Gerstein
Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions.
Journal of molecular biology 2001;314(5):1053-66.
2001: Jiang Qian; Nicholas M Luscombe; Mark Gerstein
Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model.
Journal of molecular biology 2001;313(4):673-81.
2001: Hedi Hegyi; Mark Gerstein
Annotation transfer for genomics: measuring functional divergence in multi-domain proteins.
Genome research 2001;11(10):1632-40.
2001: Heng Zhu; Metin Bilgin; Rhonda Bangham; D Hall; Antonio Casamayor; Paul Bertone; Ning Lan; Ronald Jansen; Scott Bidlingmaier; Thomas D Houfek; T Mitchell; P Miller; R A Dean; Mark Gerstein; Michael Snyder
Global analysis of protein activities using proteome chips.
Science (New York, N.Y.) 2001;293(5537):2101-5.
2001: Dov Greenbaum; Nicholas M Luscombe; Ronald Jansen; Jiang Qian; Mark Gerstein
Interrelating different types of genomic data, from proteome to secretome: 'oming in on function.
Genome research 2001;11(9):1463-8.
2001: Zheng Lian; Lin Wang; Shigeru Yamaga; W Bonds; Y Beazer-Barclay; Yuval Kluger; Mark Gerstein; Peter E Newburger; Nancy Berliner; Sherman M Weissman
Genomic and proteomic analysis of the myeloid differentiation program.
Blood 2001;98(3):513-24.
2001: Paul Bertone; Y Kluger; Ning Lan; Deyou Zheng; Dinesh Christendat; Adelinda Yee; A M Edwards; C H Arrowsmith; Gaetano T Montelione; Mark Gerstein
SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics.
Nucleic acids research 2001;29(13):2884-98.
2001: Jiang Qian; B Stenger; C A Wilson; Jimmy Lin; Ronald Jansen; Sarah A Teichmann; J Park; WG Krebs; Haiyuan Yu; Vadim Alexandrov; Nathaniel Echols; Mark Gerstein
PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information.
Nucleic acids research 2001;29(8):1750-64.
2001: YV Subrahmanyam; Shigeru Yamaga; Y Prashar; H H Lee; N P Hoe; Yuval Kluger; Mark Gerstein; J D Goguen; Peter E Newburger; Sherman M Weissman
RNA expression patterns change dramatically in human neutrophils exposed to bacteria.
Blood 2001;97(8):2457-68.
2001: Paul M Harrison; Nathaniel Echols; Mark Gerstein
Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome.
Nucleic acids research 2001;29(3):818-30.
2001: Nicholas M Luscombe; Dov Greenbaum; Mark Gerstein
What is bioinformatics? A proposed definition and overview of the field.
Methods of information in medicine 2001;40(4):346-58.
2000: Mark Gerstein
Integrative database analysis in structural genomics.
Nature structural biology 2000;7 Suppl():960-3.
2000: Heng Zhu; James F Klemic; S Chang; Paul Bertone; Antonio Casamayor; Kathryn G Klemic; D Smith; Mark Gerstein; Mark A Reed; Michael Snyder
Analysis of yeast protein kinases using protein chips.
Nature genetics 2000;26(3):283-9.
2000: R Das; Hedi Hegyi; Mark Gerstein
Genome analyses of spirochetes: a study of the protein structures, functions and metabolic pathways in Treponema pallidum and Borrelia burgdorferi.
Journal of molecular microbiology and biotechnology 2000;2(4):387-92.
2000: Amar Drawid; Ronald Jansen; Mark Gerstein
Genome-wide analysis relating expression level with protein subcellular localization.
Trends in genetics : TIG 2000;16(10):426-30.
2000: Mark Gerstein; R Jansen
The current excitement in bioinformatics-analysis of whole-genome expression data: how does it relate to protein structure and function?
Current opinion in structural biology 2000;10(5):574-84.
2000: Dinesh Christendat; Adelinda Yee; Akil Dharamsi; Y Kluger; Alexei Savchenko; John R Cort; V Booth; Cameron Mackereth; Vivian Saridakis; Irena Ekiel; Guennadi Kozlov; Karen L Maxwell; Ning Wu; Lawrence P McIntosh; Kalle Gehring; Michael A Kennedy; Alan R Davidson; Emil F Pai; Mark Gerstein; Aled M Edwards; Cheryl H Arrowsmith
Structural proteomics of an archaeon.
Nature structural biology 2000;7(10):903-9.
2000: Amar Drawid; Mark Gerstein
A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome.
Journal of molecular biology 2000;301(4):1059-75.
2000: Suganthi Balasubramanian; T Schneider; Mark Gerstein; L Regan
Proteomics of Mycoplasma genitalium: identification and characterization of unannotated and atypical proteins in a small model genome.
Nucleic acids research 2000;28(16):3075-82.
2000: J Lin; Mark Gerstein
Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels.
Genome research 2000;10(6):808-18.
2000: R Das; Mark Gerstein
The stability of thermophilic proteins: a study based on comprehensive genome comparison.
Functional & integrative genomics 2000;1(1):76-88.
2000: WG Krebs; Mark Gerstein
The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework.
Nucleic acids research 2000;28(8):1665-75.
2000: C A Wilson; J Kreychman; Mark Gerstein
Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.
Journal of molecular biology 2000;297(1):233-49.
2000: Ronald Jansen; Mark Gerstein
Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins.
Nucleic acids research 2000;28(6):1481-8.
2000: Alessandro Senes; Mark Gerstein; Donald M Engelman
Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions.
Journal of molecular biology 2000;296(3):921-36.
2000: Dinesh Christendat; Adelinda Yee; Akil Dharamsi; Y Kluger; Mark Gerstein; Cheryl H Arrowsmith; Aled M Edwards
Structural proteomics: prospects for high throughput sample preparation.
Progress in biophysics and molecular biology 2000;73(5):339-45.
2000: Mark Gerstein; Jimmy Lin; Hedi Hegyi
Protein folds in the worm genome.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2000;():30-41.
1999: PB Ross-Macdonald; P S Coelho; T Roemer; Seema Agarwal; Anuj Kumar; Ronald Jansen; Kei-Hoi Cheung; A Sheehan; D Symoniatis; Lara Umansky; Matthew Heidtman; F K Nelson; H Iwasaki; Karl Hager; Mark Gerstein; Perry Miller; G Shirleen Roeder; Michael Snyder
Large-scale analysis of the yeast genome by transposon tagging and gene disruption.
Nature 1999;402(6760):413-8.
1999: Mark Gerstein; C Chothia
Perspectives: signal transduction. Proteins in motion.
Science (New York, N.Y.) 1999;285(5434):1682-3.
1999: Hedi Hegyi; Mark Gerstein
The relationship between protein structure and function: a comprehensive survey with application to the yeast genome.
Journal of molecular biology 1999;288(1):147-64.
1998: Mark Gerstein
Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census.
Proteins 1998;33(4):518-34.
1998: Mark Gerstein; Hedi Hegyi
Comparing genomes in terms of protein structure: surveys of a finite parts list.
FEMS microbiology reviews 1998;22(4):277-304.
1998: Mark Gerstein; WG Krebs
A database of macromolecular motions.
Nucleic acids research 1998;26(18):4280-90.
1998: Mark Gerstein; M Levitt
Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins.
Protein science : a publication of the Protein Society 1998;7(2):445-56.
1998: Mark Gerstein
How representative are the known structures of the proteins in a complete genome? A comprehensive structural census.
Folding & design 1998;3(6):497-512.
1998: Mark Gerstein
Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence.
Bioinformatics (Oxford, England) 1998;14(8):707-14.
1997: Mark Gerstein
A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure.
Journal of molecular biology 1997;274(4):562-76.
1997: Mark Gerstein; M Levitt
A structural census of the current population of protein sequences.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(22):11911-6.