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Michael Snyder

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TOP 3
Michael James Clark; Rui Chen; Michael Snyder
Exome sequencing by targeted enrichment.
Hogune Im; Michael Snyder
Preparation of recombinant protein spotted arrays for proteome-wide identification of kinase targets.
Xiao A Huang; Debasish Raha; Michael Snyder; Sarah Sweeney; Hang Yin; Haifan Lin
A major epigenetic programming mechanism guided by piRNAs.

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All Publications

2013: Michael James Clark; Rui Chen; Michael Snyder
Exome sequencing by targeted enrichment.
Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.] 2013;Chapter 7():Unit7.12.
2013: Hogune Im; Michael Snyder
Preparation of recombinant protein spotted arrays for proteome-wide identification of kinase targets.
Current protocols in protein science / editorial board, John E. Coligan ... [et al.] 2013;Chapter 27():Unit 27.4.
2013: Xiao A Huang; Debasish Raha; Michael Snyder; Sarah Sweeney; Hang Yin; Haifan Lin
A major epigenetic programming mechanism guided by piRNAs.
Developmental cell 2013;24(5):502-16.
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: Karl Waern; Michael Snyder
Extensive transcript diversity and novel upstream open reading frame regulation in yeast.
G3 (Bethesda, Md.) 2013;3(2):343-52.
2013: Philippe Lefrançois; G Shirleen Roeder; Raymond K Auerbach; Christopher M Yellman; Michael Snyder
Centromere-like regions in the budding yeast genome.
PLoS genetics 2013;9(1):e1003209.
2013: Xiyan Li; Xin Wang; Michael Snyder
Systematic investigation of protein-small molecule interactions.
IUBMB life 2013;65(1):2-8.
2013: Rui Chen; Michael Snyder
Promise of personalized omics to precision medicine.
Wiley interdisciplinary reviews. Systems biology and medicine 2013;5(1):73-82.
2012: Rui Chen; Michael Snyder
Systems biology: personalized medicine for the future?
Current opinion in pharmacology 2012;12(5):623-8.
2012: Ghia Euskirchen; Raymond K Auerbach; Michael Snyder
SWI/SNF chromatin-remodeling factors: multiscale analyses and diverse functions.
The Journal of biological chemistry 2012;287(37):30897-905.
2012: Alan P Boyle; Yong Cheng; J Michael Cherry; Manoj Hariharan; Benjamin C Hitz; Eurie L Hong; Konrad Karczewski; Maya Kasowski; Julie Park; Marc A Schaub; Shuai Weng; Michael Snyder
Annotation of functional variation in personal genomes using RegulomeDB.
Genome research 2012;22(9):1790-7.
2012: Marc A Schaub; Serafim Batzoglou; Alan P Boyle; Anshul Kundaje; Michael Snyder
Linking disease associations with regulatory information in the human genome.
Genome research 2012;22(9):1748-59.
2012: Anshul Kundaje; Sofia Kyriazopoulou-Panagiotopoulou; Max Libbrecht; Debasish Raha; Serafim Batzoglou; Steven M Johnson; Cheryl L Smith; Michael Snyder; Elliott E Winters; Arend Sidow
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements.
Genome research 2012;22(9):1735-47.
2012: Alexandra E Charos; Debasish Raha; Brian D Reed; Anna M Szekely; Sherman M Weissman; Michael Snyder
A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells.
Genome research 2012;22(9):1668-79.
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: Grace Xiaolu Yang; Xiyan Li; Michael Snyder
Investigating metabolite-protein interactions: an overview of available techniques.
Methods (San Diego, Calif.) 2012;57(4):459-66.
2012: Hugo Y K Lam; Maeve O'Huallachain; Cuiping Pan; Carlos D Bustamante; Rui Chen; Michael J Clark; Mark B Gerstein; Rajini Haraksingh; Jeffrey M Kidd; Phil Lacroute; Michael Snyder
Detecting and annotating genetic variations using the HugeSeq pipeline.
Nature biotechnology 2012;30(3):226-9.
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: Michael Snyder
Q & A: the Snyderome.
Genome biology 2012;13(3):147.
2011: Janine Mok; Xiaowei Zhu; Michael Snyder
Dissecting phosphorylation networks: lessons learned from yeast.
Expert review of proteomics 2011;8(6):775-86.
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: Michael J Clark; Ghia Euskirchen; Konrad Karczewski; Hugo Y K Lam; Atul Butte; Rong Chen; Rui Chen; Michael Snyder
Performance comparison of exome DNA sequencing technologies.
Nature biotechnology 2011;29(10):908-14.
2011: Wei Zheng; Hongyu Zhao; Tara A Gianoulis; Konrad Karczewski; Michael Snyder
Regulatory variation within and between species.
Annual review of genomics and human genetics 2011;12():327-46.
2011: Konrad Karczewski; Stephen G Landt; Teri Slifer; Nicholas P Tatonetti; Xinqiong Yang; Russ B Altman; Michael Snyder
Cooperative transcription factor associations discovered using regulatory variation.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(32):13353-8.
2011: Xiyan Li; Michael Snyder
Metabolites as global regulators: a new view of protein regulation: systematic investigation of metabolite-protein interactions may help bridge the gap between genome-wide association studies and small molecule screening studies.
BioEssays : news and reviews in molecular, cellular and developmental biology 2011;33(7):485-9.
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: Sílvia Pérez-Lluch; Debasish Raha; Florenci Serras; Michael Snyder; Enrique Blanco; Albert Carbonell; Montserrat Corominas
Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing.
Nucleic acids research 2011;39(11):4628-39.
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: Ghia M Euskirchen; Raymond K Auerbach; Eugene Davidov; Tara A Gianoulis; Guoneng Zhong; Joel S Rozowsky; Nitin Bhardwaj; Mark B Gerstein; Michael Snyder
Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches.
PLoS genetics 2011;7(3):e1002008.
2011: Zhi John Lu; Kevin Yip; Guilin Wang; Chong Shou; LaDeana W Hillier; Ekta Khurana; Ashish Agarwal; Raymond Auerbach; Joel S Rozowsky; Chao Cheng; Masaomi Kato; David M Miller; Frank Slack; Michael Snyder; Robert H Waterston; Valerie Reinke; Mark B Gerstein
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.
Genome research 2011;21(2):276-85.
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: Karl Waern; Ugrappa Nagalakshmi; Michael Snyder
RNA sequencing.
Methods in molecular biology (Clifton, N.J.) 2011;759():125-32.
2011: Tara A Gianoulis; Michael Snyder; Ashish Agarwal; Mark B Gerstein
The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics.
Genome biology 2011;12(3):R32.
2011: Chong Shou; Nitin Bhardwaj; Hugo Y K Lam; Koon-Kiu Yan; Philip M Kim; Michael Snyder; Mark B Gerstein
Measuring the evolutionary rewiring of biological networks.
PLoS computational biology 2011;7(1):e1001050.
2011: Chen Zhao; Douglas Yasumura; Xiyan Li; Michael Matthes; Marcia Lloyd; Gregory Nielsen; Kelly Ahern; Michael Snyder; Dean Bok; Joshua L Dunaief; Matthew M LaVail; Douglas Vollrath
mTOR-mediated dedifferentiation of the retinal pigment epithelium initiates photoreceptor degeneration in mice.
The Journal of clinical investigation 2011;121(1):369-83.
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: Vincent Bruno; Zhong Wang; Sadie L Marjani; Ghia Euskirchen; Jeffrey Martin; Gavin Sherlock; Michael Snyder
Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq.
Genome research 2010;20(10):1451-8.
2010: Roger P Alexander; Gang Fang; Joel S Rozowsky; Michael Snyder; Mark B Gerstein
Annotating non-coding regions of the genome.
Nature reviews. Genetics 2010;11(8):559-71.
2010: Debasish Raha; Miyoung Hong; Michael Snyder
ChIP-Seq: a method for global identification of regulatory elements in the genome.
Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.] 2010;Chapter 21():Unit 21.19.1-14.
2010: Zarmik Moqtaderi; Jie Wang; Debasish Raha; Robert J White; Michael Snyder; Zhiping Weng; Kevin Struhl
Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells.
Nature structural & molecular biology 2010;17(5):635-40.
2010: Maya Kasowski; Fabian Grubert; Christopher Heffelfinger; Manoj Hariharan; Akwasi Asabere; Sebastian M Waszak; Lukas Habegger; Joel S Rozowsky; Minyi Shi; Alexander E Urban; Mi-Young Hong; Konrad Karczewski; Wolfgang Huber; Sherman M Weissman; Mark B Gerstein; Jan O Korbel; Michael Snyder
Variation in transcription factor binding among humans.
Science (New York, N.Y.) 2010;328(5975):232-5.
2010: Laura Camarena; Vincent Bruno; Ghia Euskirchen; Sebastian Poggio; Michael Snyder
Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing.
PLoS pathogens 2010;6(4):e1000834.
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: Yukio Yasukochi; Osamu Maruyama; Milind C Mahajan; Carolyn Padden; Ghia M Euskirchen; Vincent Schulz; Hideki Hirakawa; Satoru Kuhara; Xing-Hua Pan; Peter E Newburger; Michael Snyder; Sherman M Weissman
X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(8):3704-9.
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: Donald Sharon; Rui Chen; Michael Snyder
Systems biology approaches to disease marker discovery.
Disease markers 2010;28(4):209-24.
2010: Hugo Y K Lam; Philip M Kim; Janine Mok; Raffi Tonikian; Sachdev S Sidhu; Benjamin E Turk; Michael Snyder; Mark B Gerstein
MOTIPS: automated motif analysis for predicting targets of modular protein domains.
BMC bioinformatics 2010;11():243.
2010: Janine Mok; Philip M Kim; Hugo Y K Lam; Stacy Piccirillo; Xiuqiong Zhou; Grace R Jeschke; Douglas L Sheridan; Sirlester A Parker; Ved Desai; Miri Jwa; Elisabetta Cameroni; Hengyao Niu; Matthew Good; Attila Remenyi; Jia-Lin Nianhan Ma; YJ Sheu; Holly E Sassi; Richelle Sopko; Clarence S M Chan; Claudio de Virgilio; Nancy M Hollingsworth; Wendell A Lim; David F Stern; Bruce Stillman; Brenda J Andrews; Mark B Gerstein; Michael Snyder; Benjamin E Turk
Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs.
Science signaling 2010;3(109):ra12.
2010: Ugrappa Nagalakshmi; Karl Waern; Michael Snyder
RNA-Seq: a method for comprehensive transcriptome analysis.
Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.] 2010;Chapter 4():Unit 4.11.1-13.
2010: Hugo Y K Lam; Xinmeng Jasmine Mu; Adrian M Stütz; Andrea Tanzer; Philip D Cayting; Michael Snyder; Philip M Kim; Jan O Korbel; Mark B Gerstein
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.
Nature biotechnology 2010;28(1):47-55.
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: 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: Yong Zhang; Zarmik Moqtaderi; Barbara P Rattner; Ghia Euskirchen; Michael Snyder; James T Kadonaga; X Shirley Liu; Kevin Struhl
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.
Nature structural & molecular biology 2009;16(8):847-52.
2009: Du Jiang; Robert D Bjornson; Zhengdong D Zhang; Yong Kong; Michael Snyder; Mark B Gerstein
Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.
PLoS computational biology 2009;5(7):e1000432.
2009: Li Ni; Can Bruce; Christopher Hart; Justine Leigh-Bell; Daniel Gelperin; Lara Umansky; Mark B Gerstein; Michael Snyder
Dynamic and complex transcription factor binding during an inducible response in yeast.
Genes & development 2009;23(11):1351-63.
2009: Elias Theodorou; George Dalembert; Christopher Heffelfinger; Eric White; Sherman Weissman; Lynn Corcoran; Michael Snyder
A high throughput embryonic stem cell screen identifies Oct-2 as a bifunctional regulator of neuronal differentiation.
Genes & development 2009;23(5):575-88.
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: Janine Mok; Hogune Im; Michael Snyder
Global identification of protein kinase substrates by protein microarray analysis.
Nature protocols 2009;4(12):1820-7.
2009: Li A Kung; Sheng-Ce Tao; Jiang Qian; Michael G Smith; Michael Snyder; Heng Zhu
Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes.
Molecular systems biology 2009;5():308.
2009: Joseph Fasolo; Michael Snyder
Protein microarrays.
Methods in molecular biology (Clifton, N.J.) 2009;548():209-22.
2009: Michael Snyder; Sherman Weissman; Mark Gerstein
Personal phenotypes to go with personal genomes.
Molecular systems biology 2009;5():273.
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: Anjali K Nath; Michael Krauthammer; Puyao Li; Eugene Davidov; Lucas C Butler; Joshua Copel; Mikko Katajamaa; Matej Oresic; Irina A Buhimschi; Catalin S Buhimschi; Michael Snyder; Joseph A Madri
Proteomic-based detection of a protein cluster dysregulated during cardiovascular development identifies biomarkers of congenital heart defects.
PloS one 2009;4(1):e4221.
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: A Gordon Robertson; Mikhail Bilenky; Angela Tam; Yongjun Zhao; Thomas Zeng; Nina Thiessen; Timothee Cezard; Anthony P Fejes; Elizabeth D Wederell; Rebecca Cullum; Ghia Euskirchen; Martin Krzywinski; Inanc Birol; Michael Snyder; Pamela A Hoodless; Martin Hirst; Marco A Marra; Steven J M Jones
Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding.
Genome research 2008;18(12):1906-17.
2008: Xinghua Pan; Alexander Eckehart Urban; Dean Palejev; Vincent Schulz; Fabian Grubert; Yiping Hu; Michael Snyder; Sherman M Weissman
A procedure for highly specific, sensitive, and unbiased whole-genome amplification.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(40):15499-504.
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: 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: Anjali K Nath; Rachel M Brown; Michael Michaud; M Rocio Sierra-Honigmann; Michael Snyder; Joseph A Madri
Leptin affects endocardial cushion formation by modulating EMT and migration via Akt signaling cascades.
The Journal of cell biology 2008;181(2):367-80.
2008: Wakam Chang; Rania F Zaarour; Samara Reck-Peterson; John Rinn; Robert H Singer; Michael Snyder; Peter Novick; Mark S Mooseker
Myo2p, a class V myosin in budding yeast, associates with a large ribonucleic acid-protein complex that contains mRNAs and subunits of the RNA-processing body.
RNA (New York, N.Y.) 2008;14(3):491-502.
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: Brian D Reed; Alexandra E Charos; Anna M Szekely; Sherman M Weissman; Michael Snyder
Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes.
PLoS genetics 2008;4(7):e1000133.
2008: Jia Qian Wu; Michael Snyder
RNA polymerase II stalling: loading at the start prepares genes for a sprint.
Genome biology 2008;9(5):220.
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.
2007: Michael E Hudson; Irina Pozdnyakova; Kenneth Haines; Gil Mor; Michael Snyder
Identification of differentially expressed proteins in ovarian cancer using high-density protein microarrays.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(44):17494-9.
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: Sorina C Popescu; Michael Snyder; Sp Dinesh-Kumar
Arabidopsis protein microarrays for the high-throughput identification of protein-protein interactions.
Plant signaling & behavior 2007;2(5):416-20.
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: Gordon Robertson; Martin Hirst; Matthew N Bainbridge; Mikhail Bilenky; Yongjun Zhao; Thomas Zeng; Ghia Euskirchen; Bridget Bernier; Richard J Varhol; Allen D Delaney; Nina Thiessen; Obi L Griffith; Ann He; Marco Marra; Michael Snyder; Steven J M Jones
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.
Nature methods 2007;4(8):651-7.
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: Akshay A Bhinge; Jonghwan Kim; Ghia Euskirchen; Michael Snyder; Vishwanath R Iyer
Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE).
Genome research 2007;17(6):910-6.
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: Xiaowei Zhu; Mark Gerstein; Michael Snyder
Getting connected: analysis and principles of biological networks.
Genes & development 2007;21(9):1010-24.
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: 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: 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: David A Hall; Jason Ptacek; Michael Snyder
Protein microarray technology.
Mechanisms of ageing and development 2007;128(1):161-7.
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: Michael E Hudson; Michael Snyder
High-throughput methods of regulatory element discovery.
BioTechniques 2006;41(6):673, 675, 677 passim.
2006: Andrew Dewan; Mugen Liu; Stephen Hartman; Samuel Shao-Min Zhang; David T L Liu; Connie Zhao; Pancy O S Tam; Wai Man Chan; Dennis S C Lam; Michael Snyder; Colin J Barnstable; Chi Pui Pang; Josephine Hoh
HTRA1 promoter polymorphism in wet age-related macular degeneration.
Science (New York, N.Y.) 2006;314(5801):989-92.
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: Jason Ptacek; Michael Snyder
Charging it up: global analysis of protein phosphorylation.
Trends in genetics : TIG 2006;22(10):545-54.
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: Li A Kung; Michael Snyder
Proteome chips for whole-organism assays.
Nature reviews. Molecular cell biology 2006;7(8):617-22.
2006: Su-Wen Ho; Ghil Jona; Christina T L Chen; Mark Johnston; Michael Snyder
Linking DNA-binding proteins to their recognition sequences by using protein microarrays.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(26):9940-5.
2006: Jean Lu; Runhua Hou; Carmen J Booth; Shih-Hung Yang; Michael Snyder
Defined culture conditions of human embryonic stem cells.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(15):5688-93.
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: Heng Zhu; Shaohui Hu; Ghil Jona; Xiaowei Zhu; Nate Kreiswirth; Barbara M Willey; Tony Mazzulli; Guozhen Liu; Qifeng Song; Peng Chen; Mark Cameron; Andrea Tyler; Jian Wang; Jie Wen; Weijun Chen; Susan Compton; Michael Snyder
Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(11):4011-6.
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: Michael G Smith; Michael Snyder
Yeast as a model for human disease.
Current protocols in human genetics / editorial board, Jonathan L. Haines ... [et al.] 2006;Chapter 15():Unit 15.6.
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: 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: 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.
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: Daniel M Gelperin; Michael A White; Martha Wilkinson; Yoshiko Kon; Li A Kung; Kevin J Wise; Nelson Lopez-Hoyo; Lixia Jiang; Stacy Piccirillo; Haiyuan Yu; Mark Gerstein; Mark E Dumont; Eric M Phizicky; Michael Snyder; Elizabeth J Grayhack
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection.
Genes & development 2005;19(23):2816-26.
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: Paul Bertone; Michael Snyder
Advances in functional protein microarray technology.
The FEBS journal 2005;272(21):5400-11.
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: Paul Bertone; Michael Snyder
Prospects and challenges in proteomics.
Plant physiology 2005;138(2):560-2.
2005: John L Rinn; Michael Snyder
Sexual dimorphism in mammalian gene expression.
Trends in genetics : TIG 2005;21(5):298-305.
2005: Angie S Mah; Andrew E H Elia; Geeta Devgan; Jason Ptacek; Mike Schutkowski; Michael Snyder; Michael B Yaffe; Raymond J Deshaies
Substrate specificity analysis of protein kinase complex Dbf2-Mob1 by peptide library and proteome array screening.
BMC biochemistry 2005;6():22.
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: Michael G Smith; Ghil Jona; Jason Ptacek; Geeta Devgan; Heng Zhu; Xiaowei Zhu; Michael Snyder
Global analysis of protein function using protein microarrays.
Mechanisms of ageing and development 2005;126(1):171-5.
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: Sonali Mukherjee; Michael Berger; Ghil Jona; Xun S Wang; Dale Muzzey; Michael Snyder; Richard A Young; Martha L Bulyk
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.
Nature genetics 2004;36(12):1331-9.
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: 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: Michael G Smith; Shelley G Des Etages; Michael Snyder
Microbial synergy via an ethanol-triggered pathway.
Molecular and cellular biology 2004;24(9):3874-84.
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: Ghia Euskirchen; Michael Snyder
A plethora of sites.
Nature genetics 2004;36(4):325-6.
2004: Scott Bidlingmaier; Michael Snyder
Regulation of polarized growth initiation and termination cycles by the polarisome and Cdc42 regulators.
The Journal of cell biology 2004;164(2):207-18.
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.
2003: Gregory A Michaud; Michael Salcius; Fang Zhou; Rhonda Bangham; Jaclyn Bonin; Hong Guo; Michael Snyder; Paul Predki; Barry Schweitzer
Analyzing antibody specificity with whole proteome microarrays.
Nature biotechnology 2003;21(12):1509-12.
2003: Barry Schweitzer; Paul Predki; Michael Snyder
Microarrays to characterize protein interactions on a whole-proteome scale.
Proteomics 2003;3(11):2190-9.
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: Jessie Hanrahan; Michael Snyder
Cytoskeletal activation of a checkpoint kinase.
Molecular cell 2003;12(3):663-73.
2003: Beatriz Santos; Michael Snyder
Specific protein targeting during cell differentiation: polarized localization of Fus1p during mating depends on Chs5p in Saccharomyces cerevisiae.
Eukaryotic cell 2003;2(4):821-5.
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: Ghil Jona; Michael Snyder
Recent developments in analytical and functional protein microarrays.
Current opinion in molecular therapeutics 2003;5(3):271-7.
2003: Michael Snyder; Mark Gerstein
Genomics. Defining genes in the genomics era.
Science (New York, N.Y.) 2003;300(5617):258-60.
2003: Antonio Casamayor; Michael Snyder
Molecular dissection of a yeast septin: distinct domains are required for septin interaction, localization, and function.
Molecular and cellular biology 2003;23(8):2762-77.
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: Heng Zhu; Michael Snyder
Protein chip technology.
Current opinion in chemical biology 2003;7(1):55-63.
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: Heng Zhu; Metin Bilgin; Michael Snyder
Proteomics.
Annual review of biochemistry 2003;72():783-812.
2002: Gregory A Michaud; Michael Snyder
Proteomic approaches for the global analysis of proteins.
BioTechniques 2002;33(6):1308-16.
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: Laura G Vallier; Jeffrey E Segall; Michael Snyder
The alpha-factor receptor C-terminus is important for mating projection formation and orientation in Saccharomyces cerevisiae.
Cell motility and the cytoskeleton 2002;53(4):251-66.
2002: Paulo S R Coelho; Anthony C Bryan; Anuj Kumar; Gerald S Shadel; Michael Snyder
A novel mitochondrial protein, Tar1p, is encoded on the antisense strand of the nuclear 25S rDNA.
Genes & development 2002;16(21):2755-60.
2002: Kei-Hoi Cheung; Janet Hager; Kenneth Nelson; Kevin White; Yuli Li; Michael Snyder; Kenneth Williams; Perry Miller
A dynamic approach to mapping coordinates between microplates and microarrays.
Journal of biomedical informatics 2002;35(5-6):306-12.
2002: Christine E Horak; Michael Snyder
Global analysis of gene expression in yeast.
Functional & integrative genomics 2002;2(4-5):171-80.
2002: Scott Bidlingmaier; Michael Snyder
Carbohydrate analysis prepares to enter the "Omics" era.
Chemistry & biology 2002;9(4):400-1.
2002: Scott Bidlingmaier; Michael Snyder
Large-scale identification of genes important for apical growth in Saccharomyces cerevisiae by directed allele replacement technology (DART) screening.
Functional & integrative genomics 2002;1(6):345-56.
2002: Antonio Casamayor; Michael Snyder
Bud-site selection and cell polarity in budding yeast.
Current opinion in microbiology 2002;5(2):179-86.
2002: Heng Zhu; Michael Snyder
"Omic" approaches for unraveling signaling networks.
Current opinion in cell biology 2002;14(2):173-9.
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: 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: Christine E Horak; Michael Snyder
ChIP-chip: a genomic approach for identifying transcription factor binding sites.
Methods in enzymology 2002;350():469-83.
2002: Anuj Kumar; Susana Vidan; Michael Snyder
Insertional mutagenesis: transposon-insertion libraries as mutagens in yeast.
Methods in enzymology 2002;350():219-29.
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.
2002: Anuj Kumar; Kei-Hoi Cheung; Nick Tosches; Peter Masiar; Yang Liu; Perry Miller; Michael Snyder
The TRIPLES database: a community resource for yeast molecular biology.
Nucleic acids research 2002;30(1):73-5.
2001: S Erdman; Michael Snyder
A filamentous growth response mediated by the yeast mating pathway.
Genetics 2001;159(3):919-28.
2001: J Vogel; B Drapkin; J Oomen; D Beach; K Bloom; Michael Snyder
Phosphorylation of gamma-tubulin regulates microtubule organization in budding yeast.
Developmental cell 2001;1(5):621-31.
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: L Ni; Michael Snyder
A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae.
Molecular biology of the cell 2001;12(7):2147-70.
2001: Scott Bidlingmaier; Eric L. Weiss; C Seidel; David G Drubin; Michael Snyder
The Cbk1p pathway is important for polarized cell growth and cell separation in Saccharomyces cerevisiae.
Molecular and cellular biology 2001;21(7):2449-62.
2001: S Vidan; Michael Snyder
Large-scale mutagenesis: yeast genetics in the genome era.
Current opinion in biotechnology 2001;12(1):28-34.
2001: Heng Zhu; Michael Snyder
Protein arrays and microarrays.
Current opinion in chemical biology 2001;5(1):40-5.
2001: Kei-Hoi Cheung; Aniruddha M Deshpande; Nick Tosches; S Nath; A Agrawal; Perry Miller; Anuj Kumar; Michael Snyder
A metadata framework for interoperating heterogeneous genome data using XML.
Proceedings / AMIA ... Annual Symposium. AMIA Symposium 2001;():110-4.
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: J Vogel; Michael Snyder
The carboxy terminus of Tub4p is required for gamma-tubulin function in budding yeast.
Journal of cell science 2000;113 Pt 21():3871-82.
2000: J G Barrett; Brendan D Manning; Michael Snyder
The Kar3p kinesin-related protein forms a novel heterodimeric structure with its associated protein Cik1p.
Molecular biology of the cell 2000;11(7):2373-85.
2000: YJ Sheu; Y Barral; Michael Snyder
Polarized growth controls cell shape and bipolar bud site selection in Saccharomyces cerevisiae.
Molecular and cellular biology 2000;20(14):5235-47.
2000: Brendan D Manning; Michael Snyder
Drivers and passengers wanted! the role of kinesin-associated proteins.
Trends in cell biology 2000;10(7):281-9.
2000: P S Coelho; Anuj Kumar; Michael Snyder
Genome-wide mutant collections: toolboxes for functional genomics.
Current opinion in microbiology 2000;3(3):309-15.
2000: K H Cheung; Anuj Kumar; Michael Snyder; P Miller
An integrated web interface for large-scale characterization of sequence data.
Functional & integrative genomics 2000;1(1):70-5.
2000: Y Barral; Valerie Mermall; Mark S Mooseker; Michael Snyder
Compartmentalization of the cell cortex by septins is required for maintenance of cell polarity in yeast.
Molecular cell 2000;5(5):841-51.
2000: Beatriz Santos; Michael Snyder
Sbe2p and sbe22p, two homologous Golgi proteins involved in yeast cell wall formation.
Molecular biology of the cell 2000;11(2):435-52.
2000: Kei-Hoi Cheung; Perry Miller; A Sherman; S Weston; E Stratmann; Martin Schultz; Michael Snyder; Anuj Kumar
Graphically-enabled integration of bioinformatics tools allowing parallel execution.
Proceedings / AMIA ... Annual Symposium. AMIA Symposium 2000;():141-5.
2000: Anuj Kumar; Shelley Ann des Etages; P S Coelho; G Shirleen Roeder; Michael Snyder
High-throughput methods for the large-scale analysis of gene function by transposon tagging.
Methods in enzymology 2000;328():550-74.
2000: J Vogel; Michael Snyder
gamma-Tubulin of budding yeast.
Current topics in developmental biology 2000;49():75-104.
2000: Anuj Kumar; Kei-Hoi Cheung; PB Ross-Macdonald; P S Coelho; Perry Miller; Michael Snyder
TRIPLES: a database of gene function in Saccharomyces cerevisiae.
Nucleic acids research 2000;28(1):81-4.
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: Brendan D Manning; J G Barrett; J A Wallace; H Granok; Michael Snyder
Differential regulation of the Kar3p kinesin-related protein by two associated proteins, Cik1p and Vik1p.
The Journal of cell biology 1999;144(6):1219-33.
1999: Y Barral; M Parra; Scott Bidlingmaier; Michael Snyder
Nim1-related kinases coordinate cell cycle progression with the organization of the peripheral cytoskeleton in yeast.
Genes & development 1999;13(2):176-87.
1999: PB Ross-Macdonald; A Sheehan; C Friddle; G Shirleen Roeder; Michael Snyder
Transposon mutagenesis for the analysis of protein production, function, and localization.
Methods in enzymology 1999;303():512-32.
1998: YJ Sheu; B Santos; N Fortin; C Costigan; Michael Snyder
Spa2p interacts with cell polarity proteins and signaling components involved in yeast cell morphogenesis.
Molecular and cellular biology 1998;18(7):4053-69.
1998: S Erdman; L Lin; M Malczynski; Michael Snyder
Pheromone-regulated genes required for yeast mating differentiation.
The Journal of cell biology 1998;140(3):461-83.
1998: T Roemer; L Vallier; YJ Sheu; Michael Snyder
The Spa2-related protein, Sph1p, is important for polarized growth in yeast.
Journal of cell science 1998;111 ( Pt 4)():479-94.
1998: K Madden; Michael Snyder
Cell polarity and morphogenesis in budding yeast.
Annual review of microbiology 1998;52():687-744.
1997: Brendan D Manning; R Padmanabha; Michael Snyder
The Rho-GEF Rom2p localizes to sites of polarized cell growth and participates in cytoskeletal functions in Saccharomyces cerevisiae.
Molecular biology of the cell 1997;8(10):1829-44.
1997: K Madden; YJ Sheu; Kristin Baetz; Brenda Andrews; Michael Snyder
SBF cell cycle regulator as a target of the yeast PKC-MAP kinase pathway.
Science (New York, N.Y.) 1997;275(5307):1781-4.
1997: Beatriz Santos; Michael Snyder
Targeting of chitin synthase 3 to polarized growth sites in yeast requires Chs5p and Myo2p.
The Journal of cell biology 1997;136(1):95-110.
1997: PB Ross-Macdonald; A Sheehan; G Shirleen Roeder; Michael Snyder
A multipurpose transposon system for analyzing protein production, localization, and function in Saccharomyces cerevisiae.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(1):190-5.
1996: T Roemer; L G Vallier; Michael Snyder
Selection of polarized growth sites in yeast.
Trends in cell biology 1996;6(11):434-41.
1996: T Roemer; K Madden; J Chang; Michael Snyder
Selection of axial growth sites in yeast requires Axl2p, a novel plasma membrane glycoprotein.
Genes & development 1996;10(7):777-93.
1995: S G Sobel; Michael Snyder
A highly divergent gamma-tubulin gene is essential for cell growth and proper microtubule organization in Saccharomyces cerevisiae.
The Journal of cell biology 1995;131(6 Pt 2):1775-88.
1995: K Xie; Michael Snyder
Two short autoepitopes on the nuclear dot antigen are similar to epitopes encoded by the Epstein-Barr virus.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(5):1639-43.
1994: Michael Snyder
The spindle pole body of yeast.
Chromosoma 1994;103(6):369-80.
1994: C Costigan; Michael Snyder
SLK1, a yeast homolog of MAP kinase activators, has a RAS/cAMP-independent role in nutrient sensing.
Molecular & general genetics : MGG 1994;243(3):286-96.
1994: N Burns; B Grimwade; PB Ross-Macdonald; E Y Choi; Karin E Finberg; G Shirleen Roeder; Michael Snyder
Large-scale analysis of gene expression, protein localization, and gene disruption in Saccharomyces cerevisiae.
Genes & development 1994;8(9):1087-105.
1994: C Costigan; David Kolodrubetz; Michael Snyder
NHP6A and NHP6B, which encode HMG1-like proteins, are candidates for downstream components of the yeast SLT2 mitogen-activated protein kinase pathway.
Molecular and cellular biology 1994;14(4):2391-403.
1994: H Friedman; Michael Snyder
Mutations in PRG1, a yeast proteasome-related gene, cause defects in nuclear division and are suppressed by deletion of a mitotic cyclin gene.
Proceedings of the National Academy of Sciences of the United States of America 1994;91(6):2031-5.
1994: B D Page; L L Satterwhite; Mark D Rose; Michael Snyder
Localization of the Kar3 kinesin heavy chain-related protein requires the Cik1 interacting protein.
The Journal of cell biology 1994;124(4):507-19.
1993: K Xie; E J Lambie; Michael Snyder
Nuclear dot antigens may specify transcriptional domains in the nucleus.
Molecular and cellular biology 1993;13(10):6170-9.
1993: E G Flescher; K Madden; Michael Snyder
Components required for cytokinesis are important for bud site selection in yeast.
The Journal of cell biology 1993;122(2):373-86.
1993: D Granot; Michael Snyder
Carbon source induces growth of stationary phase yeast cells, independent of carbon source metabolism.
Yeast (Chichester, England) 1993;9(5):465-79.
1993: C S Copeland; Michael Snyder
Nuclear pore complex antigens delineate nuclear envelope dynamics in vegetative and conjugating Saccharomyces cerevisiae.
Yeast (Chichester, England) 1993;9(3):235-49.
1993: B D Page; Michael Snyder
Chromosome segregation in yeast.
Annual review of microbiology 1993;47():231-61.
1992: C H Yang; Michael Snyder
The nuclear-mitotic apparatus protein is important in the establishment and maintenance of the bipolar mitotic spindle apparatus.
Molecular biology of the cell 1992;3(11):1259-67.
1992: K Madden; Michael Snyder
Specification of sites for polarized growth in Saccharomyces cerevisiae and the influence of external factors on site selection.
Molecular biology of the cell 1992;3(9):1025-35.
1992: B D Page; Michael Snyder
CIK1: a developmentally regulated spindle pole body-associated protein important for microtubule functions in Saccharomyces cerevisiae.
Genes & development 1992;6(8):1414-29.
1992: C Costigan; S Gehrung; Michael Snyder
A synthetic lethal screen identifies SLK1, a novel protein kinase homolog implicated in yeast cell morphogenesis and cell growth.
Molecular and cellular biology 1992;12(3):1162-78.
1992: C Mirzayan; C S Copeland; Michael Snyder
The NUF1 gene encodes an essential coiled-coil related protein that is a potential component of the yeast nucleoskeleton.
The Journal of cell biology 1992;116(6):1319-32.
1992: C H Yang; E J Lambie; Michael Snyder
NuMA: an unusually long coiled-coil related protein in the mammalian nucleus.
The Journal of cell biology 1992;116(6):1303-17.
1992: D H Parma; Michael Snyder; S Sobolevski; M Nawroz; E Brody; L Gold
The Rex system of bacteriophage lambda: tolerance and altruistic cell death.
Genes & development 1992;6(3):497-510.
1992: K Madden; C Costigan; Michael Snyder
Cell polarity and morphogenesis in Saccharomyces cerevisiae.
Trends in cell biology 1992;2(1):22-9.
1991: R Padmanabha; S Gehrung; Michael Snyder
The KNS1 gene of Saccharomyces cerevisiae encodes a nonessential protein kinase homologue that is distantly related to members of the CDC28/cdc2 gene family.
Molecular & general genetics : MGG 1991;229(1):1-9.
1991: Michael Snyder; S Gehrung; B D Page
Studies concerning the temporal and genetic control of cell polarity in Saccharomyces cerevisiae.
The Journal of cell biology 1991;114(3):515-32.
1991: D Granot; Michael Snyder
Glucose induces cAMP-independent growth-related changes in stationary-phase cells of Saccharomyces cerevisiae.
Proceedings of the National Academy of Sciences of the United States of America 1991;88(13):5724-8.
1991: D Granot; Michael Snyder
Segregation of the nucleolus during mitosis in budding and fission yeast.
Cell motility and the cytoskeleton 1991;20(1):47-54.
1990: S Gehrung; Michael Snyder
The SPA2 gene of Saccharomyces cerevisiae is important for pheromone-induced morphogenesis and efficient mating.
The Journal of cell biology 1990;111(4):1451-64.
1989: C H Yang; E J Lambie; John Hardin; Joe Craft; Michael Snyder
Higher order structure is present in the yeast nucleus: autoantibody probes demonstrate that the nucleolus lies opposite the spindle pole body.
Chromosoma 1989;98(2):123-8.
1989: Michael Snyder
The SPA2 protein of yeast localizes to sites of cell growth.
The Journal of cell biology 1989;108(4):1419-29.
1988: Michael Snyder; R W Davis
SPA1: a gene important for chromosome segregation and other mitotic functions in S. cerevisiae.
Cell 1988;54(6):743-54.
1988: Michael Snyder; R J Sapolsky; R W Davis
Transcription interferes with elements important for chromosome maintenance in Saccharomyces cerevisiae.
Molecular and cellular biology 1988;8(5):2184-94.