C Plant
Resume:
CURRICULUM VITAE: Michael Snyder
Present Address Dept of Genetics
Stanford University
Stanford, CA 94305
Office 203-***-****
Mobile 203-***-****
abqk3g@r.postjobfree.com
Education
****-**77 B.A. University of Rochester, Rochester, New York
Chemistry and Biology
1978-1982 Ph.D. California Institute of Technology, Pasadena, California
Department of Biology, Degree conferred 6/83
Professional Experience
1977-1978 Research Assistant, Department of Biology, University of
Rochester, Rochester, New York
1978-1982 Graduate Student with Dr. Norman Davidson, California Institute
of Technology, Pasadena, California
1982-1986 Postdoctoral Fellow with Dr. Ronald W. Davis, Department of
Biochemistry, Stanford University School of Medicine,
Stanford, California
1986-1990 Assistant Professor, Department of Biology, Yale University,
Connecticut
1990-1997 Associate Professor, Department of Biology, Yale University,
Connecticut (tenured 1994)
1997-present Professor, Dept. of Biology (now Mol. Cell. Devel. Biol.), Yale Univ., CT
1991-present Member Yale Comprehensive Cancer Center
1992-present Associate Professor/Professor (Joint Appointment), Department of
Molecular Biophysics and Biochemistry, Yale University
1998-2004 Chair, Dept. of Molecular, Cellular and Developmental Biology, Yale Univ.
(Dept. doubled in size and 3X in funds during my tenure).
2002-2009 Director, Yale Center for Genomics and Proteomics
2006-2009 Genetics Society of America Council Member (Elected)
2006- 2008 President, US HUPO (Elected)
2001-present PI, Yale Center of Excellence in the Genome Sciences
2004-present PI, NIH Training Grant in Genomics and Proteomics
2009- Chair, Department of Genetics, Stanford University School of Medicine
2009- Director, Center for Genomics and Personalized Medicine
Academic Honors/Fellowships
1978-1982 NIH Predoctoral Training Fellowship
1982-1985 Helen Hay Whitney Postdoctoral Fellowship
1986 United Scleroderma Foundation Award
1987-1991 Pew Scholar Award
1989 Yale Junior Faculty Fellowship
2000-2005 Burroughs Wellcome Scholar Award
2002 Genome Technology Finalist in Microarray Masters
2002-present Appointed Lewis B. Cullman Professor of MCDB
2007 Connecticut Medal of Science
2009 Pioneer Award, HUPO
Advisory Committees
1989,90, 94-98, Member NIH Study Section- Ad hoc Reviewer
2000-07
1993 Scientific Advisory Board Review Panel-American Cancer Society
1994-96 Howard Hughes Predoctoral Fellowship Review Committee
2002 Damon Runyan Walter Winchell Review Panel
1996-2002 March of Dimes Grant Review Panel
1997 ATCC Advisory Committee
1999 NSF Division Review Panel
2000, 2002 NIH Study Section Review Working Group
2000 Canadian Genome Center Review Panel
2001-present Northeast Structural Genomics Consortium Scientific Advisory Committee
2001-present Member, Institute of Genetics Advisory Council, CIHR Canada
2002-2007 Member, Ontario Genome Institute Scientific Advisory Board
2002-2006 Member, Chinese National Human Genome Institute Advisory Board
2007-present SAB, Integrated Genomics Project Univ. of Toronto
2008-present SAB, Duke Univ. Systems Biology Center
2003-2006 SAB, Blueprint Initiative
2003 NIH Special Road Map Advisory Committee
2003 External Reviewer, Dept. of Medical Genetics, Univ. of Toronto
2003-present Scientific Advisory Board, Gottenberg Univ. Genomics Meeting
2004-2007 Damon Runyan-Walter Winchell Review Panel
2007 NSF Plant Genomics Initiatives 5 Year Review
2008 External Review Committee, Gene Expression Unit, EMBL
2008 Proteomics Standards Initiative
2008 EDRN Review of Boston Group
2008 Review Committee for DOE Macromolecular Assemblies
2008 Proteomics Structure Committee Advisory Group
2008-present Member, MABS NIH Study Section
2006-present Genetic Society of America Members and Meetings Committee
2008-present Executive Committee of US HUPO
2008-present Executive Committee of HUPO
2009 Univ. of Pennsylvania, Genomics & Computational Graduate Program Review
2008-present Uppsala Univ. Advisory Broad on Bertolli Center for Neurobiology
2009-present Advisory Board Member, Yeast Proteomics Center, Univ. of Manchester
Meeting Organizer
1994 Coorganizer, Juan March Meeting on Signal Transduction & Morphogenesis
1996 Chair, FASEB Meeting: Yeast Chromosome Structure, Repl. & Segregation
2000 Yeast Genetics Meeting Program Committee
2004 CoOrganizer, ASBMB Genomics, Proteomics and Bioinformatics Meeting*
2004 CoOrganizer, GSA International Meeting on Yeast Molecular Genetics
2004 CoOrganizer, CSH Plant Genomes: From Sequence to Phenomes
2006 CoOrganizer, ASBMB Genomics, Proteomics and Bioinformatics Meeting
2006 Organizer, GSA International Meeting on Yeast Molecular Genetics*
2006 CoOrganizer, US HUPO
2007 CoOrganizer, CSH Plant Genomes: From Sequence to Phenomes
2007 CoOrganizer, Keystone Meeting on Functional Genomics
2008 CoOrganizer, Next is Now DNA Sequencing Symposium, Yale Univ.
Editorial Boards
1996-2000 Editorial Board, The Dynamic Cell
2001-2004 Editorial Board, Chemistry and Biology
2000-2006 Editorial Board, FEMS Yeast Research
2007-2008 Editorial Board, Gene
2000-present Editor-in-Chief (until 2002; now Editor) Functional and Integrative
Genomics
2001-present Editorial Board, Molecular and Cellular Proteomics
2002-present Editorial Board, Drug Discovery Today
2004- present Editorial Board, PloS Genetics
2005-present Editorial Board, Genes and Development
2005-present Editorial Board, Molecular Systems Biology
Named/Distinguished Lectureships (starting 2004)
2004 California Institute of Technology, Norman Davidson Lecture
2004 University of Chicago, Fredick Seitz Lecture
2004 Tulane University, Gerber Lecture
2004 University of Iowa, Raymond Fung Lecture
2006 Northeastern University, Hoehn Lecture
2007 EBI Distinguished Lecturer
2008 Northwestern University Distinguished Lectureship
2008 Fred Sherman Lecture, Univ. of Rochester
2008 MGH Distinguished Lecturer
2009 Univ of Pennsylvania, Bernard Cohen Lecture
Keynote/Featured Speaker
2000 University of Sherbrooke Graduate Symposium*
2001 CHI: Functional Genomics
2002 Yale University Pathology Retreat
2002 Georgia Bioinformatics Symposium
2003 University of Texas Medical Faculty Symposium
2003 Structural and Functional Genomics, Singapore
2004 International Meeting On Arabidopsis*
2004 Pennsylvania State Graduate Student Symposium
2005 Keystone Conference on Plant Signaling
2005 New York University: Genomics Symposium Genomes in Action
2005 Chip to Hits
2005 Systems Biology Meeting
2006 AGCT Genomics Meeting
2006 Genomes to Biology Meeting, Manchester, UK
2006 Keystone Conference on Plant Abiotic Stress
2006 CHI Genes to Targets
2006 AUHUPO*
2007 ABRF*
2007 Pan American and Brazilian Biochemistry and Molecular Biology Meeting*
2007 Uppsala Neuroscience Center Launch
2007 IBC Diagnostics 2 Discovery
2007 DREAM 2 Conference
2008 CHI Mining the Plasma Proteome
2008 Student Invited Speaker, Vanderbilt Genetics Retreat
2008 Genetics Day, Univ. of Rochester
2009 Lorne Genomics Meeting
2009 RECOMB2009
2009 Stanford Clinical Genomics Retreat
2009 Univ. of Toronto Genomic Symposium
2009 Biomedical Engineering Conference
2009 International Yeast Genetics and Molecular Biology Meeting
2009 International Conference of Systems Biology
*Meetings attended by over 900 people
Commercial Activity
Topogenetics/Exelexis 1990-1991 CoFounder
Genaissance 1999-2001 Scientific Advisory Board (SAB)
Mycota 1996-2000 SAB
Protometrix 2001-2004 (now subsidiary of Invitrogen) Founder and Chair of SAB
RxGen 2003-present SAB
Affomix 2006- Present Founder and Chair of SAB
Publications
1. Nagalakshmi U, Waern K, Snyder M. RNA-Seq: a method for comprehensive
transcriptome analysis. Curr Protoc Mol Biol. 2010 Jan; Chapter 4:Unit 4.11.1-13. PMID:
20069539
2. Lam HY, Mu XJ, St tz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO,
Gerstein MB. Nucleotide-resolution analysis of structural variants using BreakSeq and a
breakpoint library. Nat Biotechnol. 2010 Jan;28(1):47-55. Epub 2009 Dec 27. PMID:
20037582
3. Canaan A, Haviv I, Urban AE, Schulz VP, Hartman S, Zhang Z, Palejev D, Deisseroth AB,
Lacy J, Snyder M, Gerstein M, Weissman SM. EBNA1 regulates cellular gene expression
by binding cellular promoters. Proc Natl Acad Sci U S A. 2009 Dec 22; 106(52):22421-6.
PMID: 20080792
4. Mok J, Im H, Snyder M. Global identification of protein kinase substrates by protein
microarray analysis. Nat Protoc. 2009; 4(12):1820-7. PMID: 20010933
5. Snyder M, Gallagher JE. Systems biology from a yeast omics perspective. FEBS Lett.
2009 Dec 17; 583(24):3895-9. PMID: 19903479
6. Kung LA*, Tao S-C*, Qian J, Snyder M*, Zhu H*. Global analysis of the glycoproteome in
S. cerevisiae reveals new roles for protein glycosylation in eukaryotes. Mol. Systems Biol.
2009; 5:308. PMID: *Co corresponding authors.
7. Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefran ois P,
Struhl K, Gerstein M, Snyder M. Mapping accessible chromatin regions using Sono-Seq.
Proc Natl Acad Sci U S A. 2009 Aug 18. [Epub ahead of print] PMID: 19706456
8. Teytelman L, Ozaydin B, Zill O, Lefran ois P, Snyder M, Rine J, Eisen MB. Impact of
chromatin structures on DNA processing for genomic analyses. PLoS One. 2009 Aug
20;4(8):e6700. PMID: 19693276
9. Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl
K. Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions
in vivo. Nat Struct Mol Biol. 2009 Jul 20. PMID: 19620965.
10. Korbel JO*, Tirosh-Wagner T*, Urban AE*, Chen XN, Kasowski M, Dai L, Grubert F,
Erdman C, Gao MC, Lange K, Sobel EM, Barlow GM, Aylsworth AS, Carpenter NJ, Clark
RD, Cohen MY, Doran E, Falik-Zaccai T, Lewin SO, Lott IT, McGillivray BC, Moeschler
JB, Pettenati MJ, Pueschel SM, Rao KW, Shaffer LG, Shohat M, Van Riper AJ, Warburton
D, Weissman S, Gerstein MB, Snyder M*, Korenberg JR*. The genetic architecture of
Down syndrome phenotypes revealed by high-resolution analysis of human segmental
trisomies. Proc Natl Acad Sci USA. 2009 Jul 21;106(29):12031-6. Epub 2009 Jul 13. PMID:
19597142
11. Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB. Integrating sequencing
technologies in personal genomics: optimal low cost reconstruction of structural variants.
PLoS Comput Biol. 2009 Jul;5(7):e1000432. PMID: 19593373
12. Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai
EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP,
Waterston RH; modENCODE Consortium. Unlocking the secrets of the genome. Nature.
2009 Jun 18;459(7249):927-30. PMID: 19536255
13. Fasolo J, Snyder M. Protein microarrays. Methods Mol Biol. 2009;548:209-22. PMID:
19521827
14. Popescu SC, Popescu GV, Snyder M, Dinesh-Kumar SP. Integrated analysis of co-expressed
MAP kinase substrates in Arabidopsis thaliana. Plant Signal Behav. 2009 Jun;4(6):524-7.
Epub 2009 Jun 25. PMID: 19816141
15. Ni L, Bruce C, Hart C, Leigh-Bell J, Gelperin D, Umansky L, Gerstein MB, Snyder M.
Dynamic and complex transcription factor binding during an inducible response in yeast.
Genes Dev. 2009 Jun 1;23(11):1351-63. PMID: 19487574
16. Snyder M, Weissman S, Gerstein M. Mol Syst Biol. 2009 Personal phenotypes to go with
personal genomes. 5:273. Epub 2009 May 19. PMID: 19455137
17. Rodriguez H, Snyder M, Uhl n M, Andrews P, Beavis RC, Borchers CH, Chalkley R, Cho
SY, Cottingham K, Dunn M, Dylag T, Edgar R, Hare P, Heck AJ, Hirsch RF, Kennedy K,
Kolar P, Kraus HJ, Mallick P, Nesvizhskii A, Ping P, Ponten F, Yang L, Yates JR, Stein SE,
Hermjakob H, Kinsinger CR, Apweiler R. Recommendations from the 2008 International
Summit on Proteomics Data Release and Sharing Policy - A Summit Report. J Proteome Res.
2009 Apr 3. PMID: 19344107.
18. Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB.
PEMer: a computational framework with simulation-based error models for inferring
genomic structural variants from massive paired-end sequencing data. Genome Biol. 2009
Feb 23;10(2):R23. [Epub ahead of print] PMID: 19236709.
19. Theodorou E, Dalembert G, Heffelfinger C, Weissman, S, White E Corcoran L, Snyder M.
A High Throughput Embryonic Stem Cell Screen Identifies Oct-2 as a Bifunctional
Regulator of Neuronal Differentiation. Genes Dev. 2009 Mar 1;23(5):575-88. PMID:
19270158.
20. Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A,
Jensen LJ, Snyder M, Bork P, Gerstein MB. Quantifying environmental adaptation of
metabolic pathways in metagenomics. Proc Natl Acad Sci U S A. 2009 Jan 22. [Epub ahead
of print]. PMID: 19164758.
21. Lefrancois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein
M, Snyder M. Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC
Genomics. 2009 Jan 21;10(1):37. [Epub ahead of print]. PMID: 19159457.
22. Demichelis F, Setlur SR, Beroukhim R, Perner S, Korbel JO, Lafargue CJ, Pflueger D, Pina
C, Hofer MD, Sboner A, Svensson MA, Rickman DS, Urban A, Snyder M, Meyerson M,
Lee C, Gerstein MB, Kuefer R, Rubin MA. Distinct genomic aberrations associated with
ERG rearranged prostate cancer. Genes Chromosomes Cancer. 2009 Jan 20. [Epub ahead of
print]. PMID: 19156837.
23. Nath AK, Krauthammer M, Li P, Davidov E, Butler LC, Copel J, Katajamaa M, Oresic M,
Buhimschi I, Buhimschi C, Snyder M, Madri JA. Proteomic-based detection of a protein
cluster dysregulated during cardiovascular development identifies biomarkers of congenital
heart defects. PLoS ONE. 2009;4(1):e4221. Epub 2009 Jan 19. PMID: 19156209.
24. Zhang X, Lian Z, Padden C, Gerstein MB, Rozowsky J, Snyder M, Gingeras TR, Kapranov
P, Weissman SM, Newburger PE. A myelopoiesis-associated regulatory intergenic non-
coding RNA transcript within the human HOXA cluster. Blood. 2009 Jan 14. [Epub ahead of
print] PMID: 19144990.
25. Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N,
Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments
relative to controls. Nat Biotechnol. 2009 Jan;27(1):66-75. Epub 2009 Jan 4. PMID:
19122651.
26. Seringhaus M, Rozowsky J, Royce T, Nagalakshmi U, Jee J, Snyder M, Gerstein M.
Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling
microarrays. BMC Genomics. 2008 Dec 31;9(1):635. [Epub ahead of print] PMID:
19117516.
27. Popescu SC, Popescu GV, Bachan S, Zhang Z, Gerstein M, Snyder M*, Dinesh-Kumar SP*.
MAPK target networks in Arabidopsis thaliana revealed using functional protein
microarrays. Genes Dev. 2008 Dec 18. [Epub ahead of print] PMID: 19095804. *Co
corresponding authors.
28. Wang LY, Abyzov A, Korbel JO, Snyder M, Gerstein M. MSB: A mean-shift-based
approach for the analysis of structural variation in the genome. Genome Res. 2008 Nov 26.
[Epub ahead of print] PMID: 19037015.
29. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev
Genet. 2009 Jan;10(1):57-63. PMID: 19015660.
30. Hasin Y, Olender T, Khen M, Gonzaga-Jauregui C, Kim PM, Urban AE, Snyder M,
Gerstein MB, Lancet D, Korbel JO. High-resolution copy-number variation map reflects
human olfactory receptor diversity and evolution. PLoS Genet. 2008 Nov;4(11):e1000249.
Epub 2008 Nov 7. PMID: 18989455.
31. Kim PM, Lam HY, Urban AE, Korbel JO, Affourtit J, Grubert F, Chen X, Weissman S,
Snyder M, Gerstein MB. Analysis of copy number variants and segmental duplications in
the human genome: Evidence for a change in the process of formation in recent evolutionary
history. Genome Res. 2008 Dec;18(12):1865-74. Epub 2008 Oct 8. PMID: 18842824.
32. Pan X, Urban AE, Palejev D, Schulz V, Grubert F, Hu Y, Snyder M, Weissman SM. A
procedure for highly specific, sensitive, and unbiased whole-genome amplification. Proc
Natl Acad Sci U S A. 2008 Oct 7;105(40):15499-504. Epub 2008 Oct 1. PMID: 18832167.
33. Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, Cezard T, Fejes AP,
Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA,
Hirst M, Marra MA, Jones SJ. Genome-wide relationship between histone H3 lysine 4 mono-
and tri-methylation and transcription factor binding. Genome Res. 2008 Dec;18(12):1906-17.
Epub 2008 Sep 11. PMID: 18787082.
34. Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M. Modeling ChIP sequencing in
silico with applications. PLoS Comput Biol. 2008 Aug 22;4(8):e1000158. PMID: 18725927.
35. Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T,
Gebreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, Simon C,
Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME, Park J, Xin X,
Cusick ME, Moore T, Boone C, Snyder M, Roth FP, Barab si AL, Tavernier J, Hill DE,
Vidal M. High-quality binary protein interaction map of the yeast interactome network.
Science. 2008 Oct 3;322(5898):104-10. Epub 2008 Aug 21. PMID: 18719252.
36. Reed BD, Charos AE, Szekely AM, Weissman SM, Snyder M. Genome-wide occupancy of
SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial
regulation of distinct classes of genes. PLoS Genet. 2008 Jul 25;4(7):e1000133. PMID:
18654640.
37. Korbel JO, Kim PM, Chen X, Urban AE, Weissman S, Snyder M, Gerstein MB. The current
excitement about copy-number variation: how it relates to gene duplications and protein
families. Curr Opin Struct Biol. 2008 Jun;18(3):366-74. Epub 2008 May 27. PMID:
18511261.
38. Lian Z, Karpikov A, Lian J, Mahajan MC, Hartman S, Gerstein M, Snyder M, Weissman
SM. A Genomics Analysis of RNA polymerase II modification and chromatin architecture
related to 3' end RNA polyadenylation. Genome Res. 2008 May 16. [Epub ahead of print]
PMID: 18487515.
39. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The
Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing. Science. 2008
Jun 6;320(5881):1344-9. Epub 2008 May 1 PMID: 18451266
40. Wu JQ, Snyder M. RNA polymerase II stalling: loading at the start prepares genes for a
sprint. Genome Biol. 2008 May 2;9:220. PMID: 18466645
41. Wu JQ, Du J, Rozowsky J, Zhang Z, Urban AE, Euskirchen G, Weissman S, Gerstein M,
Snyder M. Systematic analysis of transcribed loci in ENCODE regions using RACE
sequencing reveals extensive transcription in the human genome. Genome Biol. 2008;9: R3.
42. Nath AK, Brown RM, Michaud M, Sierra-Honigmann MR, Snyder M, Madri JA. Leptin
affects endocardial cushion formation by modulating EMT and migration via Akt signaling
cascades. J. Cell Biol. 2008 181:367-80. Epub 2008 Apr 14. PMID: 18411306.
43. Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS,
Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix
DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green R, Song JS, McCuine SA, Anton E,
Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J,
Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z,
Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS. Systematic
evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome
Res. 2008. Mar;18(3):393-403. Epub 2008 Feb 7. PMID: 18258921.
44. Chang W, Zaarour RF, Reck-Peterson S, Rinn J, Singer RH, Snyder M, Novick P, Mooseker
MS. 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. 491-
502.
45. Hudson ME, Pozdnyakova I, Haines K, Mor G, Snyder M. Identification of differentially
expressed proteins in ovarian cancer using high-density protein microarrays. Proc Natl Acad
Sci USA. 2007;104: 17494-9.
46. ENCODE Project Consortium. Identification and analysis of functional elements in 1% of
the human genome by the ENCODE pilot project. Nature. 2007;447: 799-816.
47. Korbel JO,* Urban AE,* Affourtit J,* Godwin B, Grubert F, Simons JF, Kim PK, Palejev D,
Carriero N, Du L, Taillon B, Tanzer A, Chi J, Yang F, Carter N, Hurles ME, Weissman S,
Harkins T, Gerstein M, Egholm M, Snyder M. Paired-end mapping reveals extensive
structural variation in the human genome. Science. 2007;318: 420-6.
48. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B,
Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S.
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and
massively parallel sequencing. Nat Methods. 2007;4: 651-7.
49. Zhu X, Gerstein M, Snyder M. Getting connected: analysis and principles of biological
networks. Genes Dev. 2007;21: 1010-24.
50. Zhang ZD, Rozowsky J, Lam HY, Du J, Snyder M, Gerstein M. Tilescope: online analysis
pipeline for high-density tiling microarray data. Genome Biol. 2007;8: R81.
51. Korbel JO, Urban AE, Grubert F, Du J, Royce TE, Starr P, Zhong G, Emanuel BS,
Weissman SM, Snyder M, Gerstein MB. Systematic prediction and validation of breakpoints
associated with copy-number variants in the human genome. Proc Natl Acad Sci USA.
2007;104: 10110-5.
52. Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang
ZD, Weissman S, Snyder M. What is a gene, post-ENCODE? History and updated
definition. Genome Res. 2007;17: 669-81.
53. Trinklein ND, Karaoz U, Wu J, Halees A, Force Aldred S, Collins PJ, Zheng D, Zhang ZD,
Gerstein MB, Snyder M, Myers RM, Weng Z. Integrated analysis of experimental data sets
reveals many novel promoters in 1% of the human genome. Genome Res. 2007;17: 720-31.
54. Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang
J, Zheng D, Guigo R, Gingeras TR, Weissman S, Miller P, Snyder M, Gerstein MB. The
DART classification of unannotated transcription within the ENCODE regions: associating
transcription with known and novel loci. Genome Res. 2007;17: 732-45.
55. Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein MB.
Statistical analysis of the genomic distribution and correlation of regulatory elements in the
ENCODE regions. Genome Res. 2007;17: 787-97.
56. Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F,
Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigo R, Harrow J, Gerstein
MB. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription,
and evolution. Genome Res. 2007;17: 839-51.
57. Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermuller J, Hertel J,
Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde
J, Drenkow J, Kapranov P, Gingeras TR, Guigo R, Snyder M, Gerstein MB, Reymond A,
Hofacker IL, Stadler PF. Structured RNAs in the ENCODE selected regions of the human
genome. Genome Res. 2007;17: 852-64.
58. Bhinge AA, Kim J, Euskirchen GM, Snyder M, Iyer VR. Mapping the chromosomal targets
of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Res.
2007;17: 910-6.
59. Borneman AR, Zhang ZD, Rozowsky J, Seringhaus MR, Gerstein M, Snyder M.
Transcription factor binding site identification in yeast: a comparison of high-density
oligonucleotide and PCR-based microarray platforms. Funct Integr Genomics. 2007;7: 335-
45.
60. Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang LY,
Gerstein M, Snyder M. Divergence of transcription factor binding sites across related yeast
species. Science. 2007;317: 815-19.
61. Devgan G, Snyder M. Kinase substrate identification using yeast protein microarrays. In:
Functional Microarrays in Drug Discovery. P Predki, ed. 2007. CRC Press 351-360.
62. Popescu SC, Popescu GV, Bachan S, Zhang Z, Seay M, Gerstein M, Snyder M, Dinesh-
Kumar SP. Differential binding of calmoduin related proteins to their targets revealed using
high density Arabidopsis protein microarrays. Proc Natl Acad Sci USA. 2007;104: 4730-5.
63. Rozowsky J, Wu J, Lian Z, Nagalakshmi U, Korbel JO, Kapranov PD, Zheng D, Dyke S,
Newburger P, Miller P, Gingeras T, Weissman S, Gerstein M, Snyder M. Novel transcribed
regions in the human genome. Cold Spring Harb Symp Quant Biol. 2007;71: 111-116.
64. Euskirchen GM, Rozowsky J, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O,
Stolc V, Weissman S, Gerstein M, Ruan Y, Snyder M. Mapping of transcription factor
binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based
technologies. Genome Res. 2007;17: 898-909.
65. Smith MG, Gianoulis TA, Pukatzki S, Mekalanos J, Ornston LN, Gerstein M, Snyder M.
New insights into Acinetobacter baumannii pathogenesis revealed by high-density
pyrosequencing and transposon mutagenesis. Genes Dev. 2007;21: 601-14.
66. Hall DA, Ptacek J, Snyder M. Protein microarray technology. Mech Aging Dev. 2007;128:
161-7.
67. Emanuelsson O, Nagalakshmi U, Zheng D, Rozowsky JS, Urban AE, Du J, Lian Z, Stolc V,
Weissman S, Snyder M, Gerstein M. Assessing the performance of different high-density
tiling microarray strategies for mapping transcribed regions of the human genome. Genome
Res. 2007;17: 886-97.
68. Yu H, Nguyen K, Royce T, Qian J, Nelson K, Snyder M, Gerstein M. Positional artifacts in
microarrays: experimental verification and construction of COP, an automated detection tool.
Nucleic Acids Res. 2007;35.e8.
69. Snyder M. Yeast is still the beast. GSA Newsletter. Fall 2006.
70. Dewan A, Liu M, Hartman S, Zhang SS, Liu DT, Zhao C, Tam PO, Chan WM, Lam DS,
Snyder M, Barnstable C, Pang CP, Hoh J. HTRA1 promoter polymorphism in wet age-
related macular degeneration. Science. 2006;314: 989-92.
71. Wang LY, Snyder M, Gerstein M. BoCaTFBS: a boosted cascade learner to refine the
binding sites suggested by ChIP-chip experiments. Genome Biol. 2006;7:R102.
72. Zhu X, Gerstein M, Snyder M. ProCAT: a data analysis approach for protein microarrays.
Genome Biol. 2006;7: R110.
73. Hudson ME, Snyder M. High-throughput methods of regulatory element discovery.
Biotechniques. 2006;41: 673-677.
74. Du J, Rozowsky JS, Korbel JO, Zhang ZD, Royce TE, Schultz MH, Snyder M, Gerstein M.
A supervised hidden markov model framework for efficiently segmenting tiling array data in
transcriptional and ChIP-chip experiments: systematically incorporating validated biological
knowledge. Bioinformatics. 2006;22: 3016-24.
75. Seringhaus M, Paccanaro A, Borneman A, Snyder M, Gerstein M. Predicting essential genes
in fungal genomes. Genome Res. 2006;16: 1126-35.
76. Ptacek J, Snyder M. Charging it up: global analysis of protein phosphorylation. Trends
Genet. 2006;22: 545-54
77. Srikantha T, Borneman AR, Daniels KJ, Pujol C, Wu W, Seringhaus MR, Gerstein M, Yi S,
Snyder M, Soll DR. TOS9 regulates white-opaque switching in Candida albicans. Eukaryot
Cell. 2006;5: 1674-87.
78. Kastenmayer JP,* Ni L,* Chu A, Kitchen LE, Au WC, Yang H, Carter CD, Wheeler D,
Davis RW, Boeke JD, Snyder MA, Basrai MA. Functional genomics of genes with small
open reading frames (sORFs) in S. cerevisiae. Genome Res. 2006;16: 365-73.
79. Seringhaus M, Kumar A, Hartigan J, Snyder M, Gerstein M. Genomic analysis of insertion
behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces
cerevisiae. Nucleic Acids Res. 2006;34: e57.
80. Kung LA, Snyder M. Proteome chips for whole-organism assays. Nat Rev Mol Cell Biol.
2006;7: 617-22.
81. Sopko R, Huang D, Preston N, Chua G, Papp B, Kafadar K, Snyder M, Oliver SG, Cyert M,
Hughes TR, Boone C, Andrews B. Mapping pathways and phenotypes by systematic gene
overexpression. Mol Cell. 2006;21: 319-30.
82. Snyder M, Gelperin D. Community resources for Saccharomyces cerevisiae. 2006, Jan/Feb
9.
83. Lu J, Hou R, Booth CJ, Yang S-H, Snyder M. Defined culture of human embryonic stem
cells. Proc Natl Acad Sci USA. 2006;103: 5688-93.
84. Royce TE, Rozowsky JS, Luscombe NM, Emanuelsson O, Yu H, Zhu X, Snyder M,
Gerstein M. Extrapolating traditional DNA microarray statistics to the tiling and protein
microarray technologies. Meth Enzymol. 2006;411: 282-311.
85. Ho S, Jona G, Johnston M, Snyder M. Linking DNA-binding proteins to their recognition
sequences using protein microarrays. Proc Natl Acad Sci USA. 2006;103: 9940-45.
86. Smith MG, Snyder M. Yeast as a model for human disease. Current Protocols in Human
Genetics. 2006;15.6.1-15.6.8.
87. Urban AE, Korbel J, Selzer R, Popescu GV, Richmond T, Cubells JF, Green R, Emanuel BS,
Gerstein M, Weissman SM, Snyder M. High resolution mapping of DNA copy alterations
using high density tiling oligonucleotide arrays. Proc Natl Acad Sci USA. 2006;103: 4534-9.
88. Borneman R, Leigh-Bell J, Yu H, Bertone P, Gerstein M, Snyder M. Target hub proteins
serve as master regulators of the complex transcriptional network controlling yeast
pseudohyphal growth. Genes Devel. 2006;20: 435-448.
89. Zhu H, Hu S, Jona G, Zhu X, Kreiswirth N, Willey BM, Mazzulli T, Liu G, Song Q, Chen P,
Cameron M, Tyler A, Wang J, Wen J, Chen W, Compton S, Snyder M. SARS diagnostics
using a coronavirus protein chip. Proc Nat Acad Sci USA. 2006;103: 4011-16.
90. Bertone P, Trifonov V, Rozowsky JS, Schubert F, Emanuelsson O, Karro J, Kao M-Y,
Snyder M, Gerstein M. Design optimization methods for genomic DNA tiling arrays.
Genome Res. 2006;16: 271-81.
91. Stolc V, Li L, Wang X, Li X, Su N, Tongprasit W, Han B, Xue Y, Li J, Snyder M, Gerstein
M, Wang J, Deng XW. A pilot study of transcription unit analysis in rice using
oligonucleotide tiling-path microarray. Plant Mol Biol. 2005;59: 137-49.
92. Mah AS, Elia AE, Devgan G, Ptacek J, Schutkowski M, Snyder M, Yaffe MB, Deshaies RJ.
Substrate specificity analysis of protein kinase complex Dbf2-Mob1 by peptide library and
proteome array screening. BMC Biochem. 2005;6: 22.
93. Hartman SE, Bertone P, Nath A, Royce TE, Gerstein M, Weissman S, Snyder M. Global
changes in STAT target selection and transcription regulation upon interferon treatments.
Genes Devel. 2005;19: 2953-68.
94. Royce TE, Rozowsky JS, Bertone P, Samantac M, Stolc V, Weissman S, Snyder M,
Gerstein M. Issues in the analysis of oligonucleotide tiling microarrays for transcript
mapping. Trends Genet. 2005;21: 466-75.
95. Bertone P, Snyder M. Advances in functional protein microarrays. FEBS J. 2005;272:
5400-5411.
96. Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A,
Sopko R, Lee S, McCartney RR, Schmidt MC, Rachidi N, Stark MJR, Stern DF, Tyers M, de
Virgilio C, Andrews B, Gerstein M, Schweitzer B, Predki P, Snyder M. Global analysis of
protein phosphorylation in yeast. Nature. 2005;438: 679-84.
97. Gelperin DM, White MA, Wilkinson ML, Kon Y, Li A, Kung LA, Wise KJ, Lopez-Hoyo N,
Jiang L, Piccirillo S,Yu H, Gerstein M, Dumont ME, Phizicky EM, Snyder M,* Grayhack
EJ.* Biochemical and genetic analysis of the yeast proteome with a movable ORF collection.
Genes Devel. 2005;19: 2816-26. *Co-Senior Authors
98. Pot I, Knockleby J, Aneliunas V, Nguyen T, Ah-Kye S, Liszt G, Snyder M, Hieter P, Vogel
J. Spindle checkpoint maintenance requires Ame1 and Okp1. Cell Cycle. 2005;4: 1448-56.
99. Oh SW, Moon JD, Lim HJ, Park SY, Kim T, Park J, Han MH, Snyder M, Choi EY.
Calixarene derivative as a tool for highly sensitive detection and oriented immobilization of
proteins in a microarray format through noncovalent molecular interaction. FASEB J.
2005;19: 1335-7.
100. Bertone P, Snyder M. Prospects and challenges in proteomics. Plant Physiol. 2005;138:
560-2.
101. Bertone P, Gerstein M, Snyder M. Applications of DNA tiling arrays to experimental
genome annotation and regulatory pathway discovery. Chromosome Res. 2005;13: 259-74.
102. Martone R, Snyder M. Mapping transcription factor binding sites using chIP Chip - general
considerations. DNA Microarrays. 2005, in press.
103. Rinn JL, Snyder M. Sexual dimorphism in mammalian gene expression. Trends Genet.
2005;21: 298-305.
104. Smith MG, Jona G, Ptacek J, Devgan G, Zhu H, Zhu X, Snyder M. Global analysis of
protein function using protein microarrays. Mechanisms Ageing Devel. 2005;126: 171-175.
105. ENCODE Project Consortium. The ENCODE (EnCyclopedia Of DNA Elements) Project.
Science. 2004;306: 636-640.
106. Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W,
Samanta M, Weissman S, Gerstein M, Snyder M. Global identification of human transcribed
sequences with genome tiling arrays. Science. 2004;306: 2242-6.
107. Mukherjee S, Berger MF, Jona G, Wang XS, Muzzey D, Snyder M, Young RA, Bulyk ML.
Rapid analysis of the DNA-binding specificities of transcription factors with DNA
microarrays. Nat Genet. 2004;36: 1331-9.
108. White EJ, Emanuelsson O, Scalzo D, Royce T, Kosak S, Weissman S, Gerstein M, Groudine
M, Snyder M, Schubeler D. High resolution DNA replication analysis of human
chromosome 22 reveals cell type specific differences in DNA replication timing. Proc Natl
Acad Sci USA. 2004;101: 17771-6.
109. Kumar A, Seringhaus M, Biery MC, Sarnovsky RJ, Umansky L, Piccirillo S, Matson S,
Heidtman M, Cheung KH, Dobry CJ, Gerstein M, Craig NL, Snyder M. Large-scale
mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon. Genome Res.
2004;14: 1975-86.
110. Luscombe NM, Babu MM,Yu H, Snyder M, Teichmann SA, Gerstein M. Genome analysis
of regulatory network dynamics reveals large topological changes. Nature. 2004;431: 308-
12.
111. Hall DA, Zhu H, Royce T, Gerstein M, Snyder M. Regulation of gene expression by a
metabolic enzyme. Science. 2004;306: 482-484.
112. Berman P, Bertone P, DasGupta B, Gerstein M, Ming-Yang Kao M-Y, Snyder M. Fast
optimal genome tiling with applications to microarray design and homology search. J.
Computational Biol. 2004;11: 766-785.
113. Euskirchen G, Snyder M. A plethora of sites. Nat Genet. 2004;36: 325-326.
114. Rinn JL, Rozowsky JS, Laurenz IJ, Petersen PH, Zou K, Zhong W, Gerstein M, Snyder M.
Major molecular differences between mammalian sexes are involved in drug metabolism and
renal function. Dev Cell. 2004;6: 791-800.
115. Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe
NM, Miller P, Gerstein M, Weissman S, Snyder M. CREB binds to multiple loci on
chromosome 22. Mol Cell Biol. 2004;24: 3804-3814.
116. Smith M, des Etages S, Snyder M. Microbial synergy via an ethanol triggered pathway.
Mol Cell Biol. 2004;24: 3874-3884.
117. Bidlingmaier S, Snyder M. Regulation of polarized growth initiation and termination cycles
by the polarisome and Cdc42 regulators. J Cell Biol. 2004;164: 201-18. (Featured on cover).
118. Huang J, Zhu H, Haggarty SJ, Spring DR, Snyder M, Schreiber S. Finding new components
of the TOR signaling pathway using chemical genetics and proteome chips. Proc Natl Acad
Sci USA. 2004;101: 16594-9.
119. Lian Z, Euskirchen G, Rinn J, Martone R, Bertone P, Hartman S, Royce T, Nelson K,
Sayward F, Luscombe N, Yang J, Li JL, Miller P, Urban AE, Gerstein M, Weissman S,
Snyder M. Identification of novel functional elements in the human genome. Cold Spring
Harb Symp Quant Biol. 2003;68: 317-322.
120. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M,
Greenblatt JF, Gerstein M. A Bayesian networks approach for predicting protein-protein
interactions from genomic data. Science. 2003;302: 449-53.
121. Michaud GA, Salcius M, Zhou F, Bangham R, Bonin J, Guo H, Snyder M, Predki PF,
Schweitzer BI. Analyzing antibody specificity with whole proteome microarrays. Nat
Biotechnol. 2003;21: 1509-12.
122. Kafadar KA, Zhu H, Snyder M, Cyert M. Negative regulation of calcineurin signaling by
Hrr25p, a yeast homolog of casein kinase I. Genes Devel. 2003;17: 2698-708.
123. Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NL, Rinn JL, Nelson
FK, Miller P, Gerstein M, Weissman S, Snyder M. Distribution of NF- B binding sites
across human chromosome 22. Proc Natl Acad Sci USA. 2003;100: 122**-*****.
124. Schweitzer B, Predki P, Snyder M. Microarrays to characterize protein interactions on a
whole-proteome scale. Proteomics. 2003;3: 2190-9.
125. Ball J, Schweitzer B, Predki P, Snyder. Development and applications of functional protein
arrays. M Schena ed. Jones and Bartlett Publishers, Boston. Protein Microarrays. 2003. p421-
440.
126. Phizicky E, Bastiaens PI, Zhu H, Snyder M, Fields S. Protein analysis on a proteomic scale.
Nature. 2003;422: 208-15.
127. Hanrahan J, Snyder M. Cytoskeletal activation of a checkpoint kinase. Mol Cell. 2003;12:
663-73. (Featured on cover)
128. Jona G, Snyder M. Recent developments in analytical and functional protein microarrays.
Curr Opin Mol Ther. 2003;3: 271-7.
129. Santos B, Snyder M. Protein targeting during cell differentiation: polarized localization of
Fus1p during mating depends on Chs5p in Saccharomyces cerevisiae. Eucaryotic Cell.
2003;2: 821-825.
130. Reboul J, Vaglio P, Rual JF, Lamesch P, Martinez M, Armstrong CM, Li S, Jacotot L, Bertin
N, Janky R, Moore T, Hudson JR Jr, Hartley JL, Brasch MA, Vandenhaute J, Boulton S,
Endress GA, Jenna S, Chevet E, Papasotiropoulos V, Tolias PP, Ptacek J, Snyder M, Huang
R, Chance MR, Lee H, Doucette-Stamm L, Hill DE, Vidal M. C. elegans ORFeome version
1.1: experimental verification of the genome annotation and resource for proteome-scale
protein expression. Nat Genet. 2003;34: 35-41.
131. Luscombe NM Royce TE, Bertone P, Echols N, Horak CE, Chang JT, Snyder M, Gerstein
M. Express yourself: a modular platform for processing and visualizing microarray data.
Nucleic Acids Res. 2003;31: 3477-82.
132. Zhu H, Bilgin M, Snyder M. Proteomics. Ann Rev Biochem. 2003;72: 783-812.
133. Snyder M, Gerstein M. Defining genes in the genomics era. Science. 2003;300; 258-260.
134. Casamayor A, Snyder M. Molecular dissection of a yeast septin: distinct domains are
required for septin interaction, localization and function. Mol Cell Biol. 2003;23; 2762-2777.
135. Zhu H, Snyder M. Protein chip technology. Curr Opin Chem Biol. 2003;7: 55-63.
136. Rinn JR, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM,
Nelson FN, Miller P, Gerstein M, Weissman S, Snyder M. The transcriptional activity of
human chromosome 22. Genes Devel. 2003;17: 529-40.
137. Cheung KH, White K, Hager J, Gerstein M, Reinke V, Nelson K, Masiar P, Srivastava R, Li
Y, Li J, Zhao H, Li J, Allison DB, Snyder M, Miller P, Williams K. YMD: a microarray
database for large-scale gene expression analysis. Proc AMIA Symp. 2002: 140-4.
138. Michaud G, Snyder M. Proteomic approaches for global analysis of proteins. Biotechniques.
2002;33: 1308-18.
139. Horak CE, Luscombe NM, Qian J, Piccirrillo S, Gerstein M, Snyder M. Complex
transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev.
2002;16; 3017-33.
140. Coelho PSR, Bryan AC, Kumar A, Shadel GS, Snyder M. A novel mitochondrial protein,
Tar1p, is encoded on the antisense strand of the nuclear 25S rDNA. Genes Devel. 2002;16:
2755-2760.
141. Vallier L, Segall J, Snyder M. The alpha-factor receptor C-terminus is important for mating
projection formation and orientation in Saccharomyces cerevisiae. Cell Motil Cytoskeleton.
2002;53: 251-266.
142. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A,
Anderson K, Andre B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R,
Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury
F, Garfinkel DJ, Gerstein M, Gotte D, Guldener U, Hegemann JH, Hempel S, Herman Z,
Jaramillo DF, Kelly DE, Kelly SL, Kotter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H,
Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelt JL, Roberts CJ, Rose M, Ross-
Macdonald P, Scherensm B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S,
Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang CY, Ward TR, Wilhelmy J,
Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M,
Philippsen P, Davis RW, Johnston M. Functional profiling of the Saccharomyces cerevisiae
genome. Nature. 2002;418: 387-91.
143. Horak CE, Snyder M. Global analysis of gene expression in yeast. Funct Integr Genomics.
2002;2: 171-80.
144. Snyder M, Kumar A. Yeast genomics: past, present, and future promise. Funct Integr
Genomics. 2002;2: 135-137.
145. Bidlingmaier S, Snyder M. Carbohydrate analysis prepares to enter the "Omics" era. Chem
Biol. 2002;9: 400-1.
146. Horak CE, Mahajan MC, Luscombe NM, Gerstein M, Weissman SM, Snyder M. GATA-1
binding sites mapped in the -globin locus by using mammalian ChIp-chip analysis. Proc
Natl Acad Sci USA. 2002;99: 2924-29.
147. Kusch J, Meyer A, Snyder M, Barral Y. Proper positioning of the spindle and the cleavage
plane relative to each other involves microtubule capture by the cleavage apparatus in yeast.
Genes Dev. 2002;16: 1627-1639
148. Zhu H, Snyder M. OMIC approaches to unraveling cell signaling. Curr Opin Cell Biol.
2002;14: 173-179.
149. Casamayor A, Snyder M. Bud site selection and cell polarity in budding yeast. Curr Opin
Microbiol. 2002;5: 179-86.
150. Harrison PM, Kumar A, Snyder M, Gerstein MB. A question of size: the eukaryotic
proteome and the problems in defining it. Nucl Acids Res. 2002;30: 1083-90.
151. Kumar A, Cheung K-H, Marenco L, Tosches N, Masiar P, Liu Y, Miller P, Snyder M. The
TRIPLES database of yeast protein function. In: Analyzing Gene Expression (ed.,
Lorkowski, S. and Cullen, P., et al.) Wiley-VCH Verlag GmbH, Weinheim, Germany. 2002,
in press.
152. Harrison P, Kumar A, Lan N, Echols N, Snyder M, Gerstein MB. A small reservior of
disabled ORFs in the Saccharomyces cervisiae genome and its implication for the dynamics
of proteome evolution. J Mol Biol. 2002;316: 409-19.
153. Kumar A, Cheung K-H, Tosches N, Masiar P, Liu Y, Miller P, Snyder M. The TRIPLES
database: a community resource for yeast molecular biology. Nucl Acids Res. 2002;30: 73-
75.
154. Kumar A, Snyder M. Protein complexes take the bait. Nature. 2002;415: 123-124.
155. Kumar A, Agarwal S, Heyman JA, Matson S, Heidtman M, Piccirillo S, Umansky L, Drawid
A, Jansen R, Liu Y, Cheung K-H, Miller P, Gerstein MB, Roeder GS, Snyder M.
Subcellular localization of the yeast proteome. Genes Dev. 2002;16: 707-719.
156. Kumar A, Vidan S, Snyder M. Insertional mutagenesis: transposon-insertion libraries as
mutagens in yeast. Methods Enzymol. 2002;350: 219-229.
157. Horak C, Snyder M. ChIP chip: a genomic approach for identifying transcription factor
binding sites. Methods Enzymol. 2002;350: 469-484.
158. Bidlingmaier S, Snyder M. Large-scale identification of genes important for apical growth
in Saccharomyces cerevisiae by direct allele replacement technology (DART) screening.
Funct Integr Genomics. 2002;1: 345-356.
159. Kumar A, Harrison PS, Cheung K-H, Lan N, Echols N, Bertone P, Miller P, Gerstein MB,
Snyder M. An integrated approach for finding overlooked genes in yeast. Nat Biotech.
2002;20: 58-63. (Featured in Nat Biotech News and Views).
160. Cheung KH, Deshpande AM, Tosches N, Nath S, Agrawal A, Miller P, Kumar A, Snyder
M. A metadata framework for interoperating heterogeneous genome data using XML. Proc
AMIA Symp. 2001; 110-4.
161. Vidan S, Snyder M. Making drug addicts out of yeast. Nature Biotech. 2001;19: 1022-1023.
162. Vogel J, Drapkin B, Oomen J, Beach D, Bloom K, Snyder M. Phosphorylation of gamma-
tubulin regulates microtubule organization in budding yeast. Dev Cell. 2001;1: 621-631.
163. Zhu H, Snyder M. Biochemical assays in a chip format. Current Drug Discovery. 2001;31-
34.
164. Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R,
Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean DA, Gerstein M, Snyder M. Global
analysis of protein activities using proteome chips. Science. 2001;293: 2101-2105. (Featured
in many journals, websites and newspapers.)
165. Sheu Y-J, Snyder M. Control of cell polarity and shape in S. cerevisiae. Howard and N.
Gow eds. Springer, Heidelberg. Mycota Vol VIII: The Biology of the Fungal Cell. 2001 p.
19-53.
166. Cheung KH, Hager J, White K, Williams K, Nelson K, Snyder M, Li Y, Miller P. MAC: a
Web interface for convoluting data from plates to microarrays. 2001, in press.
167. Ni L, Snyder M. A genomic study of the bipolar bud site selection pattern in Saccharomyces
cerevisiae. Mol Biol Cell. 2001;12: 2147-70.
168. Kumar A, Snyder M. Emerging technologies in yeast genomics. Nature Rev Genet. 2001;2:
302-312.
169. Bidlingmaier S, Weiss EL, Siedel C, Drubin DG, Snyder M. The Cbk1 pathway is important
for polarized cell growth and cell separation in Saccharomyces cerevisiae. Mol Cell Biol.
2001;21: 2449-62.
170. Iyer VI,* Horak CA,* Scafe CS, Botstein D, Snyder M, Brown PO. Genomic binding
distribution of the yeast cell-cycle transcription factors SBF and MBF. Nature. 2001;409:
533-538.
171. Vidan S, Snyder M. Large-scale mutagenesis: yeast genetics in the genome era. Curr Opin
Biotech. 2001;12: 28-34.
172. Zhu H, Snyder M. Protein arrays and microarrays. Curr Opin Chem Biol. 2001;5: 40-45.
173. Erdman S, Snyder M. A filamentous growth response mediated by the yeast mating
pathway. Genetics. 2001;159: 919-928.
174. Cheung K, Miller P, Sherman A, Weston S, Stratmann E, Schultz M, Snyder M, Kumar A.
Graphically-enabled integration of bioinformatics tools allowing parallel execution. Proc.
AMIA Symp. 2000;20: 141-5.
175. Zhu H, Klemic JF, Chang S, Bertone P, Klemic KG, Smith D, Gerstein M, Reed MA,
Snyder M. Analysis of yeast protein kinases using protein chips. Nat Genet. 2000;26: 283-
289.
176. Bouquin N, Barral Y, Courbeyrette R, Blondel M, Snyder M, Mann C. Regulation of
cytokinesis by the Elm1 protein kinase in Saccharomyces cerevisiae. J Cell Sci. 2000;113:
1435-45.
177. Vogel J, Snyder M. The carboxy terminus of Tub4p is required for gamma-tubulin function
in budding yeast. J Cell Sci. 2000;113: 3871-82.
178. Coehlo PSR, Kumar A, Snyder M. Genome-wide mutant collections: toolboxes for
functional genomics. Curr Opin Microbiol. 2000;3: 309-315.
179. Deng Y, Lee JP, Tianasoa-Ramamonjy M, Snyder M, Des Etages SA, Kanada D, Snyder
MP, Turner CJ. New Antimicrobial flavanones from Physena madagascariensis. J Natural
Products. 2000;63: 1082-9.
180. Manning BD, Snyder M. Drivers and passengers wanted: kinesin associated proteins. Trends
Cell Biol. 2000;10: 281-289.
181. Barrett JG, Manning BD, Snyder M. The Kar3p kinesin-related protein forms a novel
heterodimer structure with its associated protein Cik1p. Mol Biol Cell. 2000;11: 2373-2385.
182. Barral Y, Mermall V, Mooseker MS, Snyder M. The septins form a barrier necessary for the
maintenance of cell polarity in yeast. Molecular Cell. 2000;5: 841-851.
183. Kumar A, Snyder M. Genome-wide transposon mutagenesis in yeast. In: Current Protocols
in Molecular Biology, 2000. (ed, Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.,
Seidman, J.G., Smith, J.A., and Struhl, K.) Wiley and Sons, N.Y., N.Y. Unit 13.3.
184. Sheu Y-J, Barral Y, Snyder M. Polarized growth controls cell shape and bud site selection in
Saccharomyces cerevisiae. Mol Cell Biol. 2000;14: 5235-5247.
185. Cheung KH, Kumar A, Snyder M, Miller P. An integrated web interface for large-scale
characterization of sequence data. Funct Integr Genomics. 2000;1: 70-75.
186. Zhan X, Lee M, Abenes G, Von Reis I, Kittinunvorakoon C, Ross-Macdonald P, Snyder M,
Liu F. Mutagenesis of murine cytomegalovirus using a Tn3-based transposon. Virology.
2000;266: 264-74.
187. Santos B, Snyder M. Sbe2p and Sbe22p, two homologous Golgi proteins involved in yeast
cell wall formation. Mol Biol Cell. 2000;11: 435-452.
188. Kumar A, des Etages SA, Coelho PSR, Roeder GS, Snyder M. High-throughput methods for
the large-scale analysis of gene function by transposon tagging. Methods Enzymol. 2000;328:
550-74.
189. Kumar A, Cheung K-H, Ross-Macdonald P, Coelho PSR, Miller P, Snyder M. TRIPLES: a
database of gene function in S. cerevisiae. Nuc Acids Res. 2000;28: 81-84.
190. Mattagajasingh SN, Huang SC, Hartenstein JS, Snyder M, Marchesi VT, Benz EJ. A
nonerythroid isoform of protein 4.1R interacts with the nuclear mitotic apparatus (NuMA)
protein. J Cell Biol. 1999;145: 29-43.
191. des Etages SA, Kumar A, Snyder M. Transposons as tools. In: Encyclopedia of Genetics,
1999. S Brenner and JH Miller, eds. Academic Press, San Diego. p. 2034-2040.
192. Vogel J, Snyder M. The centrosome in cell replication and development. Curr Topics Devel.
1999;49: 75-104.
193. Ross-Macdonald P, Coelho PSR, Roemer T, Agarwal S, Kumar A, Jansen R, Cheung K-H,
Sheehan A, Symoniatis D, Umansky L, Heitman M, Nelson FK, Iwasaki H, Hager K,
Gerstein M, Miller P, Roeder GS, Snyder M. Large-scale analysis of the yeast genome by
transposon tagging and gene disruption. Nature. 1999;402: 413-418. (Featured in News and
Views.)
194. Winzeler EA, Astromoff A, Liang H, Shoemaker DD, Anderson K, Bangham R, Boeke JD,
Bussey H, Connelly C, Davis K, Dietrich F, Foury F, Friend S, Gentalen E, Giaever G, Jones
T, Laub M, Liao H, Lockhart D, Lussier M, Ross-Macdonald P, Menard P, Mittmann M, Pai
C, Philippsen P, Rebischung C, Riles L, Rine J, Roberts C, Snyder M, Stroms RK,
Veronneau S, Ward T, Whelan S, Yen G, Yu K, Johnston M, Davis RW. Functional
characterization of the Saccharomyces cerevisiae genome by comprehensive and precise
gene deletion and massively parallel analysis. Science. 1999;285: 901-906.
195. Manning BD, Barrett J, Wallace J, Granok H, Snyder M. Differential regulation of the
Kar3p kinesin-related protein by two associated proteins, Vik1p and Cik1p. J Cell Biol.
1999;144: 1219-1233.
196. Hong SK, Han SB, Snyder M, Choi EY. SHC1, a high pH inducible gene required for
growth at alkaline pH in Saccharomyces cerevisiae. Biochem Biophys Res Comm. 1999;255:
116-122.
197. Barral Y, Parra M, Bidlingmaier S, Snyder M. Nim1-related kinases coordinate cell cycle
progression with organization of the peripheral cytoskeleton. Genes Dev. 1999;13: 176-187.
(Featured on Cover.)
198. Ross-MacDonald P, Sheehan A, Friddle C, Roeder GS, Snyder M. Transposon mutagenesis
for the analysis of protein production, function and localization. Methods Enzymol.
1999;303: 512-532.
199. Madden K, Snyder M. Cell polarity and morphogenesis in budding yeast. Ann Rev
Microbiol. 1998;52: 687-744.
200. Sheu Y-J, Santos B, Fortin N, Costigan C, Snyder M. Spa2p interacts with cell polarity
proteins and signaling components involved in yeast cell morphogenesis. Mol Cell Biol.
1998;18: 4053-4069.
201. Roemer T, Vallier L, Sheu Y-J, Snyder M. The yeast Sph1 protein is important for cell
morphogenesis in yeast. J Cell Science. 1998;111: 479-494.
202. Erdman S, Lin L, Malczynski M, Snyder M. Pheromone-regulated genes required for yeast
mating differentiation. J Cell Biol. 1998;140: 461-483.
203. Ross-MacDonald P, Sheehan A, Friddle C, Roeder GS, Snyder M. Transposon tagging: a
novel system for monitoring protein production, function and localization. In: Methods in
Microbiology: Yeast Gene Analysis, 1998. M.F. Tuite & A.J.P. Brown, eds, Academic
Press, London, Vol 26, 161-179.
204. Costigan C, Snyder M. Cell polarity in the budding yeast, Saccharomyces cerevisiae. Adv
Mol Cell Biol. 1998;26: 1-66.
205. Manning BD, Padmanabha R, Snyder M. The Rho-GEF Rom2p localizes to sites of
polarized cell growth and participates in cytoskeletal functions in Saccharomyces cerevisiae.
Mol Biol Cell. 1997;8: 1829-1844.
206. Semenov MV, Snyder M. Human dishevelled genes comprise a DHR-containing multigene
family. Genomics. 1997;42: 302-310.
207. Madden K, Sheu Y-J, Baetz K, Andrews B, Snyder M. SBF cell cycle regulator as a target
of yeast PKC-MAP kinase pathway. Science. 1997;275: 1781-1784.
208. Santos B, Snyder M. Targetting of chitin synthase 3 to polarized growth sites in yeast
requires Chs5p and Myo2p. J Cell Biol. 1997;136: 95-110.
209. Ross-MacDonald P, Sheehan A, Roeder GS, Snyder M. A multipurpose transposon system
for analyzing protein production, localization and function in Saccharomyces cerevisiae.
Proc Natl Acad Sci USA. 1997;94: 190-195.
210. Roemer T, Vallier L, Snyder M. Selection of polarized growth sites in yeast. Trends Cell
Biol. 1996;6: 434-441.
211. Roemer T, Madden K, Chang J, Snyder M. Selection of axial growth sites in yeast requires
Axl2p, a novel plasma membrane glycoprotein. Genes Devel. 1996;10: 777-793.
212. Chen CR, Malik M, Snyder M, Drlica K. DNA gyrase and topoisomerase IV on the bacterial
chromosome: quinolone-induced DNA cleavage. J Mol Biol. 1996;258: 627-637.
213. Burns N, Ross-Macdonald P, Roeder GS, Snyder M. Generation, screening and analysis of
lacZ fusions in yeast. In: Microbial Genome Methods, 1996. K. Adolph, ed. CRC Press, New
York p. 61-79.
214. Friedman-Einat M, Einat P, Snyder M, Ruddle F. Target gene identification: target specific
transcriptional activation by three murine homeodomain/VP16 hybrid proteins in
Saccharomyces cerevisiae. J Exp Zoology. 1996;274: 145-156.
215. Ross-Macdonald P, Burns N, Malczynski M, Sheehan A, Roeder GS, Snyder M. Methods
for large-scale analysis of gene expression, protein localization and disruption phenotypes in
Saccharomyces cerevisiae. Methods Mol Cell Biol. 1995;5: 298-308.
216. Heath CV, Copeland CS, Amberg DC, Del Priore V, Snyder M, Cole CN. Nuclear pore
complex clustering and nuclear accumulation of poly(A)+ RNA associated with mutation of
the Saccharomyces cerevisiae RAT2/NUP120 gene. J Cell Biol. 1995;131: 1677-1697.
217. Sobel S, Snyder M. A highly divergent -tubulin is essential for cell growth and proper
microtubule organization. J Cell Biol. 1995;131: 1775-1788.
218. Cid VJ, Duran A, del Rey F, Snyder M, Nombela C, Sanchez M. Molecular basis of cell
integrity and morphogenesis in Saccharomyces cerevisiae. Microbiol Rev. 1995;59: 345-386.
219. Li O, Heath CV, Amberg DC, Dockendorff TC, Copeland CS, Snyder M, Cole CN.
Mutation or deletion of the Saccharomyces cerevisiae RAT3/NUP133 gene causes
temperature-dependent nuclear accumulation of poly(A)+ RNA and constitutive clustering of
nuclear pore complexes. Mol Biol Cell. 1995;6: 401-417.
220. Xie K, Snyder M. Two short autoepitopes on the nuclear dot antigen are similar to eptiopes
encoded by Ebstein Barr Virus. Proc Natl Acad Sci USA. 1995;92: 1639-1643
221. Snyder M. The spindle pole body of yeast. Chromosoma. 1994;103: 369-380.
222. Costigan C, Snyder M. SLK1, a homolog of MAP kinase activators, mediates nutrient
sensing independently of the yeast cAMP-dependent protein kinase pathway. Mol Gen
Genet. 1994;243: 286-296.
223. Burns N, Grimwade B, Ross-Macdonald PB, Choi EY, Finberg K, Roeder GS, Snyder M.
Large-scale analysis of gene expression, protein localization and gene disruption in
Saccharomyces cerevisiae. Genes Devel. 1994;8: 1087-1105. (Featured in News and Views.)
224. Friedman H, Snyder M. Temperature-sensitive mutations in PRG1, a yeast proteasome-
related gene cause defects in nuclear division and are suppressed by deletion of a mitotic
cyclin gene. Proc Natl Acad Sci USA. 1994;91: 2031-2035.
225. Costigan C, Kolodrubetz D, Snyder M. NHP6A and NHP6B, which encode HMG1-like
proteins, are candidates for downstream components of the yeast SLT2 mitogen-activated
protein kinase pathway. Mol Cell Biol. 1994;14: 2391-2403.
226. Page BD, Satterwhite LL, Rose MD, Snyder M. Localization of the Kar3 kinesin heavy
chain-like protein requires the Cik1 interacting protein. J Cell Biol. 1994;124: 507-519.
227. Xie K, Lambie E, Snyder M. Nuclear dot antigens may specify transcriptional domains in
the nucleus. Mol Cell Biol. 1993;13: 6170-6179.
228. Page BD, Snyder M. Chromosome segregation in yeast. Ann Rev Microbiol. 1993;47: 231-
201.
229. Flescher EG, Madden K, Snyder M. Components required for cytokinesis are important for
bud site selection in yeast. J Cell Biol. 1993;122: 373-386.
230. Granot D, Snyder M. Carbon source induces growth in stationary phase cells of yeast,
independent of carbon source metabolism. Yeast. 1993;9: 465-479.
231. Copeland CS, Snyder M. Nuclear pore complex antigens delineate nuclear envelope
dynamics in vegetative and conjugating Saccharomyces cerevisiae. Yeast. 1993;9: 235-249.
232. Yang CH, Snyder M. The nuclear mitotic apparatus protein (NuMA) is important in the
establishment and maintenance of the bipolar mitotic spindle apparatus. Mol Biol Cell.
1992;3: 1259-1267.
233. Friedman H, Goebel M, Snyder M. A homolog of the MHC proteosome-related RING10
gene is essential for yeast cell growth. Gene. 1992;122: 203-206.
234. Madden K, Snyder M. Specification of sites for polarized growth in Saccharomyces
cerevisiae and the influence of external factors on site selection. Mol Biol Cell. 1992;3:
1025-1035.
235. Page BD, Snyder M. CIK1: a developmentally regulated spindle pole body-associated
protein important for microtubule functions in Saccharomyces cerevisiae. Genes Devel.
1992;6: 1414-1429.
236. Mirzayan C, Copeland C, Snyder M. The NUF1 gene encodes a coiled-coil related protein
that is a potential component of the yeast nucleoskeleton. J Cell Biol. 1992;116: 1319-1332.
237. Yang C, Lambie EJ, Snyder M. NuMA: an unusually large coiled-coil protein in the
mammalian nucleus. J Cell Biol. 1992;116: 1303-1317.
238. Costigan C, Gehrung S, Snyder M. A synthetic lethal screen identifies SLK1, a novel protein
kinase homologue important in yeas
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