Michael P Snyder

Summary

Affiliation: Yale University
Country: USA

Publications

  1. ncbi request reprint Proteomic approaches for the global analysis of proteins
    Gregory A Michaud
    Department of Molecular, Cellular, and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
    Biotechniques 33:1308-16. 2002
  2. pmc RNA polymerase II stalling: loading at the start prepares genes for a sprint
    Jia Qian Wu
    Molecular, Cellular and Developmental Biology Department, Yale University, PO Box 208103, New Haven, CT 06511, USA
    Genome Biol 9:220. 2008
  3. pmc Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes
    Li A Kung
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06620 8103, USA
    Mol Syst Biol 5:308. 2009
  4. pmc Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes
    Brian D Reed
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
    PLoS Genet 4:e1000133. 2008
  5. pmc Regulation of polarized growth initiation and termination cycles by the polarisome and Cdc42 regulators
    Scott Bidlingmaier
    Department of Molecular, Cellular, and Developmental Biology, Yale University, P O Box 208103, New Haven, CT 06520 8103, USA
    J Cell Biol 164:207-18. 2004
  6. pmc BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments
    Lu Yong Wang
    Integrated Data Systems Department, Siemens Corporate Research, 755 College Road East, Princeton, New Jersey 08540, USA
    Genome Biol 7:R102. 2006
  7. pmc Tilescope: online analysis pipeline for high-density tiling microarray data
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Genome Biol 8:R81. 2007
  8. pmc Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome
    Jia Qian Wu
    Molecular, Cellular and Developmental Biology Department, KBT918, Yale University, New Haven, Connecticut 06511, USA
    Genome Biol 9:R3. 2008
  9. pmc ProCAT: a data analysis approach for protein microarrays
    Xiaowei Zhu
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
    Genome Biol 7:R110. 2006
  10. pmc PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
    Jan O Korbel
    Gene Expression Unit, European Molecular Biology Laboratory EMBL, Meyerhofstr, Heidelberg, 69117, Germany
    Genome Biol 10:R23. 2009

Research Grants

Collaborators

Detail Information

Publications70

  1. ncbi request reprint Proteomic approaches for the global analysis of proteins
    Gregory A Michaud
    Department of Molecular, Cellular, and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
    Biotechniques 33:1308-16. 2002
    ..This wealth of information not only has facilitated our basic understanding of many biological processes but also has enormous potential for drug discovery and development...
  2. pmc RNA polymerase II stalling: loading at the start prepares genes for a sprint
    Jia Qian Wu
    Molecular, Cellular and Developmental Biology Department, Yale University, PO Box 208103, New Haven, CT 06511, USA
    Genome Biol 9:220. 2008
    ..Genome-wide surveys of the phenomenon suggest that it is likely to be a rate-limiting control on gene activation that poises developmental and stimulus-responsive genes for prompt expression when inducing signals are received...
  3. pmc Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes
    Li A Kung
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06620 8103, USA
    Mol Syst Biol 5:308. 2009
    ....
  4. pmc Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes
    Brian D Reed
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
    PLoS Genet 4:e1000133. 2008
    ..Our results provide insight into the regulatory circuitry in which SREBP1 and its network partners coordinate a complex transcriptional response in the liver with cues from the diet...
  5. pmc Regulation of polarized growth initiation and termination cycles by the polarisome and Cdc42 regulators
    Scott Bidlingmaier
    Department of Molecular, Cellular, and Developmental Biology, Yale University, P O Box 208103, New Haven, CT 06520 8103, USA
    J Cell Biol 164:207-18. 2004
    ..Our results define the first molecular regulators that control the timing of growth initiation and termination during eukaryotic cell differentiation...
  6. pmc BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments
    Lu Yong Wang
    Integrated Data Systems Department, Siemens Corporate Research, 755 College Road East, Princeton, New Jersey 08540, USA
    Genome Biol 7:R102. 2006
    ..We applied BoCaTFBS within the ENCODE project and showed that it outperforms many traditional binding site identification methods (for instance, profiles)...
  7. pmc Tilescope: online analysis pipeline for high-density tiling microarray data
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Genome Biol 8:R81. 2007
    ..The program is designed with a modular, three-tiered architecture, facilitating parallelism, and a graphic user-friendly interface, presenting results in an organized web page, downloadable for further analysis...
  8. pmc Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome
    Jia Qian Wu
    Molecular, Cellular and Developmental Biology Department, KBT918, Yale University, New Haven, Connecticut 06511, USA
    Genome Biol 9:R3. 2008
    ..However, there is still much uncertainty regarding precisely what portion of the genome is transcribed, the exact structures of these novel transcripts, and the levels of the transcripts produced...
  9. pmc ProCAT: a data analysis approach for protein microarrays
    Xiaowei Zhu
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
    Genome Biol 7:R110. 2006
    ..ProCAT provides a powerful and flexible new approach for analyzing many types of protein microarrays...
  10. pmc PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
    Jan O Korbel
    Gene Expression Unit, European Molecular Biology Laboratory EMBL, Meyerhofstr, Heidelberg, 69117, Germany
    Genome Biol 10:R23. 2009
    ..The simulations demonstrated high structural variant reconstruction efficiency for PEMer's coverage-adjusted multi-cutoff scoring-strategy and showed its relative insensitivity to base-calling errors...
  11. pmc Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays
    Michael Seringhaus
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    BMC Genomics 9:635. 2008
    ..Here, we present the results of two large-scale microarray experiments on S. cerevisiae and H. sapiens genomic DNA, to explore MM oligonucleotide behavior with real sample mixtures under tiling-array conditions...
  12. pmc Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing
    Philippe Lefran├žois
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
    BMC Genomics 10:37. 2009
    ....
  13. pmc Substrate specificity analysis of protein kinase complex Dbf2-Mob1 by peptide library and proteome array screening
    Angie S Mah
    Department of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    BMC Biochem 6:22. 2005
    ..The components of MEN that act upstream of Dbf2-Mob1 have been characterized, but physiological substrates for Dbf2-Mob1 have yet to be identified...
  14. pmc Genetic analysis of variation in transcription factor binding in yeast
    Wei Zheng
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
    Nature 464:1187-91. 2010
    ..Overall, these studies identified genetic regulators of molecular diversity among individuals and provide new insights into mechanisms of gene regulation...
  15. ncbi request reprint Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms
    Anthony R Borneman
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
    Funct Integr Genomics 7:335-45. 2007
    ..The HDO array platform provides a far more robust array system by all measures than PCR-based arrays, all of which is directly attributable to the large number of probes available...
  16. ncbi request reprint Regulation of gene expression by a metabolic enzyme
    David A Hall
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8005, USA
    Science 306:482-4. 2004
    ..Deletion of Arg5,6 causes altered transcript levels of both nuclear and mitochondrial target genes. These results indicate that metabolic enzymes can directly regulate eukaryotic gene expression...
  17. pmc 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
    Philip M Kim
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 18:1865-74. 2008
    ..In addition to a coarse-grained analysis, we performed targeted sequencing of 67 CNVs and then analyzed a combined set of 270 CNVs (540 breakpoints) to verify our conclusions...
  18. pmc Target hub proteins serve as master regulators of development in yeast
    Anthony R Borneman
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA
    Genes Dev 20:435-48. 2006
    ..Our results indicate that target hubs can serve as master regulators whose activity is sufficient for the induction of complex developmental responses and therefore represent important regulatory nodes in biological networks...
  19. pmc Modeling ChIP sequencing in silico with applications
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
    PLoS Comput Biol 4:e1000158. 2008
    ..This enables us to identify transcription-factor binding sites in ChIP-seq data in a statistically rigorous fashion...
  20. pmc The transcriptional landscape of the yeast genome defined by RNA sequencing
    Ugrappa Nagalakshmi
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Science 320:1344-9. 2008
    ..We also found unexpected 3'-end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated...
  21. ncbi request reprint Divergence of transcription factor binding sites across related yeast species
    Anthony R Borneman
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
    Science 317:815-9. 2007
    ..Transcription factor binding sites have therefore diverged substantially faster than ortholog content. Thus, gene regulation resulting from transcription factor binding is likely to be a major cause of divergence between related species...
  22. pmc Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants
    Jiang Du
    Department of Computer Science, Yale University, New Haven, Connecticut, USA
    PLoS Comput Biol 5:e1000432. 2009
    ..Our strategy should facilitate the sequencing of human genomes at maximum accuracy and low cost...
  23. pmc Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays
    Sorina C Popescu
    Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06520 8103, USA
    Proc Natl Acad Sci U S A 104:4730-5. 2007
    ..Our results suggest that calcium functions through distinct CaM/CML proteins to regulate a wide range of targets and cellular activities...
  24. pmc Close association of RNA polymerase II and many transcription factors with Pol III genes
    Debasish Raha
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 107:3639-44. 2010
    ..These results indicate that, contrary to previous expectations, polymerases can often work with one another to globally coordinate gene expression...
  25. pmc CREB binds to multiple loci on human chromosome 22
    Ghia Euskirchen
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520 8005, USA gt
    Mol Cell Biol 24:3804-14. 2004
    ..Our results provide novel molecular insights into how CREB mediates its functions in humans...
  26. ncbi request reprint A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge
    Jiang Du
    Department of Computer Science, Yale University, New Haven, CT 06520, USA
    Bioinformatics 22:3016-24. 2006
    ..Here we propose a supervised framework for doing this. It has the advantage of explicitly incorporating validated biological knowledge into the model and allowing for formal training and testing...
  27. pmc Variation in transcription factor binding among humans
    Maya Kasowski
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Science 328:232-5. 2010
    ..Our results indicate that many differences in individuals and species occur at the level of TF binding, and they provide insight into the genetic events responsible for these differences...
  28. ncbi request reprint A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution
    Paul Harrison
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    J Mol Biol 316:409-19. 2002
    ..See genecensus.org/pseudogene for further information.)..
  29. ncbi request reprint Global identification of human transcribed sequences with genome tiling arrays
    Paul Bertone
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 8103, USA
    Science 306:2242-6. 2004
    ..A large fraction of these are located in intergenic regions distal from previously annotated genes and exhibit significant homology to other mammalian proteins...
  30. ncbi request reprint Genomics. Defining genes in the genomics era
    Michael Snyder
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Science 300:258-60. 2003
  31. pmc MOTIPS: automated motif analysis for predicting targets of modular protein domains
    Hugo Y K Lam
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    BMC Bioinformatics 11:243. 2010
    ..However, predicting domain targets by motif sequence alone without considering other genomic and structural information has been shown to be lacking in accuracy...
  32. pmc GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis
    Christine E Horak
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 99:2924-9. 2002
    ..This approach will be of general utility for mapping transcription factor binding sites within the beta-globin locus and throughout the genome...
  33. ncbi request reprint An integrated approach for finding overlooked genes in yeast
    Anuj Kumar
    Department of Molecular, Cellular, and Developmental Biology, Yale University, P O Box 208103, New Haven, CT 06520 8103, USA
    Nat Biotechnol 20:58-63. 2002
    ..In total, the genes discovered using this approach constitute 2% of the yeast genome and represent a wealth of overlooked biology...
  34. pmc A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation
    Zheng Lian
    Department of Genetics, Yale University School of Medicine, New Haven, CT 06520 8005, USA
    Genome Res 18:1224-37. 2008
    ..The latter is often associated with polymerase pausing. Overall, our study reveals extensive sites of poly(A) addition and provides insights into the events that occur during 3' end formation...
  35. ncbi request reprint A Bayesian networks approach for predicting protein-protein interactions from genomic data
    Ronald Jansen
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, Post Office Box 208114, New Haven, CT 06520, USA
    Science 302:449-53. 2003
    ..We validate our predictions with TAP (tandem affinity purification) tagging experiments. Our analysis, which gives a comprehensive view of yeast interactions, is available at genecensus.org/intint...
  36. pmc Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae
    Christine E Horak
    Department of Molecular, Cellular, and Developmental Biology, Connecticut 06520 8103, USA
    Genes Dev 16:3017-33. 2002
    ....
  37. pmc The TRIPLES database: a community resource for yeast molecular biology
    Anuj Kumar
    Department of Molecular, Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, CT 06520 8103, USA
    Nucleic Acids Res 30:73-5. 2002
    ..TRIPLES may be accessed from the Yale Genome Analysis Center (YGAC) homepage at http://ygac.med.yale.edu...
  38. pmc Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response
    Mei Zhong
    Department of Molecular Cellular Developmental Biology, Yale University, New Haven, Connecticut, United States of America
    PLoS Genet 6:e1000848. 2010
    ..These results indicate distinct roles for this regulator in two different biological processes and demonstrate the versatility of transcription factors in mediating diverse biological roles...
  39. pmc Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
    Olof Emanuelsson
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
    Genome Res 17:886-97. 2007
    ..Finally, our experiments reveal a significant amount of novel transcription outside of known genes, and an appreciable sample of this was validated by independent experiments...
  40. doi request reprint Protein microarrays
    Joseph Fasolo
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Methods Mol Biol 548:209-22. 2009
    ..Protein microarrays are thus powerful tools for individual studies as well as systematic characterization of proteins and their biochemical activities and regulation...
  41. pmc Global changes in STAT target selection and transcription regulation upon interferon treatments
    Stephen E Hartman
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
    Genes Dev 19:2953-68. 2005
    ..Overall, our results reveal a wealth of new information regarding IFN/STAT-binding targets and also fundamental insights into mechanisms of regulation of gene expression in different cell states...
  42. pmc Mapping accessible chromatin regions using Sono-Seq
    Raymond K Auerbach
    Program in Computational Biology, Yale University, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 106:14926-31. 2009
    ..Furthermore, our results provide insights into the mapping of binding sites by using ChIP-Seq experiments and the value of reference samples that should be used in such experiments...
  43. pmc RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries
    Lukas Habegger
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
    Bioinformatics 27:281-3. 2011
    ..Moreover, the tools can readily be used to build customizable RNA-Seq workflows. In addition to the anonymization afforded by MRF, this format also facilitates the decoupling of the alignment of reads from downstream analyses...
  44. pmc PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
    Joel Rozowsky
    Molecular Biophysics and Biochemistry Dept, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
    Nat Biotechnol 27:66-75. 2009
    ..Our scoring procedure enables us to optimize experimental design by estimating the depth of sequencing required for a desired level of coverage and demonstrating that more than two replicates provides only a marginal gain in information...
  45. pmc Dynamic and complex transcription factor binding during an inducible response in yeast
    Li Ni
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
    Genes Dev 23:1351-63. 2009
    ....
  46. doi request reprint Annotating non-coding regions of the genome
    Roger P Alexander
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
    Nat Rev Genet 11:559-71. 2010
    ..Finally, one can relate functional genomics annotations to conserved units and measures of conservation derived from comparative sequence analysis...
  47. pmc A procedure for highly specific, sensitive, and unbiased whole-genome amplification
    Xinghua Pan
    Department of Genetics, Yale University School of Medicine, New Haven, CT 06520 8005, USA
    Proc Natl Acad Sci U S A 105:15499-504. 2008
    ..This procedure facilitates genomic analysis with single cells or other traces of DNA, and generates products suitable for analysis by massively parallel sequencing as well as microarray hybridization...
  48. pmc EBNA1 regulates cellular gene expression by binding cellular promoters
    Allon Canaan
    Department of Genetics, Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 106:22421-6. 2009
    ..We have correlated EBNA1 bound promoters with changes in gene expression. Sequence analysis of the 100 promoters most enriched revealed a DNA motif that differs from the EBNA1 binding site in the EBV genome...
  49. pmc Proteomic-based detection of a protein cluster dysregulated during cardiovascular development identifies biomarkers of congenital heart defects
    Anjali K Nath
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
    PLoS ONE 4:e4221. 2009
    ..However, the molecular pathways that underlie these structural defects in humans remain largely unknown hindering the development of molecular-based diagnostic tools and novel therapies...
  50. pmc Paired-end mapping reveals extensive structural variation in the human genome
    Jan O Korbel
    Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
    Science 318:420-6. 2007
    ..The breakpoint junction sequences of more than 200 SVs were determined with a novel pooling strategy and computational analysis. Our analysis provided insights into the mechanisms of SV formation in humans...
  51. ncbi request reprint Major molecular differences between mammalian sexes are involved in drug metabolism and renal function
    John L Rinn
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Dev Cell 6:791-800. 2004
    ..We conclude that there are persistent differences in gene expression between adult males and females. These molecular differences have important implications for the physiological differences between males and females...
  52. pmc Distribution of NF-kappaB-binding sites across human chromosome 22
    Rebecca Martone
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 8005, USA
    Proc Natl Acad Sci U S A 100:12247-52. 2003
    ....
  53. ncbi request reprint Proteomics
    Heng Zhu
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
    Annu Rev Biochem 72:783-812. 2003
    ..Also discussed are the approaches used for the integrated analysis of the voluminous sets of data generated by proteome analysis conducted on a global scale...
  54. ncbi request reprint A dynamic approach to mapping coordinates between microplates and microarrays
    Kei Hoi Cheung
    Department of Anesthesiology, Center for Medical Informatics, Yale University, New Haven, CT 06520, USA
    J Biomed Inform 35:306-12. 2002
    ..MAC and its source code can be accessed via the following Web address: http://ymd.med.yale.edu/kei-cgi/kc_mac_dev8.pl...
  55. pmc ExpressYourself: A modular platform for processing and visualizing microarray data
    Nicholas M Luscombe
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, PO Box 208114, New Haven CT 06520 8114, USA
    Nucleic Acids Res 31:3477-82. 2003
    ..The program is freely available for use at http://bioinfo.mbb.yale.edu/expressyourself...
  56. ncbi request reprint ChIP-chip: a genomic approach for identifying transcription factor binding sites
    Christine E Horak
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
    Methods Enzymol 350:469-83. 2002
  57. pmc Subcellular localization of the yeast proteome
    Anuj Kumar
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
    Genes Dev 16:707-19. 2002
    ..To facilitate access to these data, we provide a searchable database featuring 2900 fluorescent micrographs at http://ygac.med.yale.edu...
  58. ncbi request reprint "Omic" approaches for unraveling signaling networks
    Heng Zhu
    Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
    Curr Opin Cell Biol 14:173-9. 2002
    ....
  59. ncbi request reprint Genomic analysis of regulatory network dynamics reveals large topological changes
    Nicholas M Luscombe
    Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
    Nature 431:308-12. 2004
    ..We anticipate that many of the concepts presented here--particularly the large-scale topological changes and hub transience--will apply to other biological networks, including complex sub-systems in higher eukaryotes...
  60. ncbi request reprint Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery
    Paul Bertone
    Department of Molecular, Cellular, and Developmental Biology Yale University, New Haven, CT 06520 8103, USA
    Chromosome Res 13:259-74. 2005
    ....
  61. pmc Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies
    Ghia M Euskirchen
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520 8103, USA
    Genome Res 17:898-909. 2007
    ..Overall, this study provides information for robust identification, scoring, and validation of TF targets using ChIP-based technologies...
  62. pmc Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution
    Deyou Zheng
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 17:839-51. 2007
    ..These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues...
  63. pmc Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 17:787-97. 2007
    ..Data sets associated with histone modifications have particularly strong correlations. Finally, we show how the correlations between factors change when only regulatory elements far from the transcription start sites are considered...
  64. pmc The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci
    Joel S Rozowsky
    Molecular Biophysics and Biochemistry Department, Yale University, New Haven, Connecticut 06520 8114, USA
    Genome Res 17:732-45. 2007
    ..Overall, we find that 18 of the 46 connections tested validate by RT-PCR and four of five sequenced PCR products confirm connectivity unambiguously...
  65. ncbi request reprint What is a gene, post-ENCODE? History and updated definition
    Mark B Gerstein
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA
    Genome Res 17:669-81. 2007
    ..It also manifests how integral the concept of biological function is in defining genes...
  66. pmc Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome
    Jan O Korbel
    Departments of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 104:10110-5. 2007
    ..Further, it enabled us to demonstrate a clear Mendelian pattern of inheritance for one of the CNVs...
  67. ncbi request reprint Proteome chips for whole-organism assays
    Li A Kung
    Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06511, USA
    Nat Rev Mol Cell Biol 7:617-22. 2006
    ..Here, we explore some of the recent advances that have been made at the '-omic' level using protein microarrays...
  68. pmc High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays
    Alexander Eckehart Urban
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 103:4534-9. 2006
    ..Our results demonstrate that HR-CGH allows the detection of copy number changes in the human genome at an unprecedented level of resolution...
  69. pmc A question of size: the eukaryotic proteome and the problems in defining it
    Paul M Harrison
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, PO Box 208114, New Haven, CT 06520 8114, USA
    Nucleic Acids Res 30:1083-90. 2002
    ..Further information relating to yeast is available at http://genecensus.org/yeast/orfome)..
  70. pmc Microtubule capture by the cleavage apparatus is required for proper spindle positioning in yeast
    Justine Kusch
    Institute of Biochemistry, Federal Institute of Technology, CH 8092 Zurich, Switzerland
    Genes Dev 16:1627-39. 2002
    ..Together, our results indicate that septins and septin-dependent kinases may coordinate microtubule and actin functions in cell division...

Research Grants3

  1. TWO SIGNALING PATHWAYS INVOLVED IN YEAST MORPHOGENESIS
    Michael Snyder; Fiscal Year: 2007
    ..Since the Hsl1 signaling pathway is highly conserved with other eukaryotes these studies are expected to provide general insight into how this pathway coordinates diverse cellular processes. ..
  2. Global Analysis of Transcription Regulatory Networks
    Michael Snyder; Fiscal Year: 2009
    ..All of our results will be made available to the scientific community using a web accessible database. These studies are expected to help us understand how eukaryotic regulatory networks operate and evolve. ..
  3. Transcription and Regulatory Elements in ENCODE Regions
    Michael Snyder; Fiscal Year: 2006
    ..We expect these pilot studies of the ENCODE region to be scaleable to the analysis of the entire human genome. ..