Michael Snyder

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Extensive transcript diversity and novel upstream open reading frame regulation in yeast
    Karl Waern
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    G3 (Bethesda) 3:343-52. 2013
  2. pmc Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches
    Ghia M Euskirchen
    Department of Genetics, Stanford University School of Medicine, California, United States of America
    PLoS Genet 7:e1002008. 2011
  3. pmc STAT3 targets suggest mechanisms of aggressive tumorigenesis in diffuse large B-cell lymphoma
    Jennifer Hardee
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305
    G3 (Bethesda) 3:2173-85. 2013
  4. pmc Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms
    Rajini R Haraksingh
    Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 6:e27859. 2011
  5. pmc Systems biology approaches to disease marker discovery
    Donald Sharon
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
    Dis Markers 28:209-24. 2010
  6. pmc Centromere-like regions in the budding yeast genome
    Philippe Lefrançois
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
    PLoS Genet 9:e1003209. 2013
  7. pmc Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing
    Laura Camarena
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
    PLoS Pathog 6:e1000834. 2010
  8. pmc High-throughput sequencing for biology and medicine
    Wendy Weijia Soon
    Department of Genetics, Stanford University School of Medicine, Alway Building, 300 Pasteur Drive, Stanford, CA 94305, USA
    Mol Syst Biol 9:640. 2013
  9. 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
  10. pmc Copy Number Variation detection from 1000 Genomes Project exon capture sequencing data
    Jiantao Wu
    Boston College, Boston, Chestnut Hill, MA, USA
    BMC Bioinformatics 13:305. 2012

Collaborators

Detail Information

Publications106 found, 100 shown here

  1. pmc Extensive transcript diversity and novel upstream open reading frame regulation in yeast
    Karl Waern
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    G3 (Bethesda) 3:343-52. 2013
    ..Moreover, transcript end diversity has important biological implications for the regulation of gene expression. In addition, our data also serve as a valuable resource for the scientific community...
  2. pmc Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches
    Ghia M Euskirchen
    Department of Genetics, Stanford University School of Medicine, California, United States of America
    PLoS Genet 7:e1002008. 2011
    ..Taken together the results from our ChIP and immunoprecipitation experiments suggest that SWI/SNF facilitates gene regulation and genome function more broadly and through a greater diversity of interactions than previously appreciated...
  3. pmc STAT3 targets suggest mechanisms of aggressive tumorigenesis in diffuse large B-cell lymphoma
    Jennifer Hardee
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305
    G3 (Bethesda) 3:2173-85. 2013
    ..Novel treatments aimed at these pathways may increase the survivability of activated B-cell-like diffuse large B-cell lymphoma. ..
  4. pmc Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms
    Rajini R Haraksingh
    Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 6:e27859. 2011
    ..Our results are important for cost effective CNV detection and validation for both basic and clinical applications...
  5. pmc Systems biology approaches to disease marker discovery
    Donald Sharon
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
    Dis Markers 28:209-24. 2010
    ..These new technologies have identified many potential disease markers. These markers are expected to be valuable to achieve the promise of truly personalized medicine...
  6. pmc Centromere-like regions in the budding yeast genome
    Philippe Lefrançois
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
    PLoS Genet 9:e1003209. 2013
    ..These studies provide general and important insights into the origin and evolution of centromeres...
  7. pmc Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing
    Laura Camarena
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
    PLoS Pathog 6:e1000834. 2010
    ..We suggest that the effect of ethanol on the virulence of A. baumannii is multifactorial and includes a general stress response and other specific components such as phospholipase C...
  8. pmc High-throughput sequencing for biology and medicine
    Wendy Weijia Soon
    Department of Genetics, Stanford University School of Medicine, Alway Building, 300 Pasteur Drive, Stanford, CA 94305, USA
    Mol Syst Biol 9:640. 2013
    ..Finally, we review recent developments in single-cell sequencing, and conclude with a discussion of possible future advances and obstacles for sequencing in biology and health...
  9. 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...
  10. pmc Copy Number Variation detection from 1000 Genomes Project exon capture sequencing data
    Jiantao Wu
    Boston College, Boston, Chestnut Hill, MA, USA
    BMC Bioinformatics 13:305. 2012
    ..However there has been little attention devoted to Copy Number Variation (CNV) detection from exome capture datasets despite the potentially high impact of CNVs in exonic regions on protein function...
  11. pmc Q & A: the Snyderome
    Michael Snyder
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Genome Biol 13:147. 2012
    b>Michael Snyder answers Genome Biology's questions on the human and professional stories underlying his Snyderome integrative omics project.
  12. pmc Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads
    Jeffrey Martin
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    BMC Genomics 11:663. 2010
    ....
  13. pmc Systems biology from a yeast omics perspective
    Michael Snyder
    Department of Genetics, Stanford University, Stanford, CA 94305, USA
    FEBS Lett 583:3895-9. 2009
    ..These studies have helped provide an understanding of cellular pathways and processes at a global and systems level...
  14. pmc Personal genome sequencing: current approaches and challenges
    Michael Snyder
    Department of Genetics, Stanford University School of Medicine, California 94305, USA
    Genes Dev 24:423-31. 2010
    ..Finally, we consider the possible individual and societal benefits of personal genome sequences...
  15. 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...
  16. pmc Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing
    Philippe Lefrançois
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
    BMC Genomics 10:37. 2009
    ....
  17. ncbi request reprint Architecture of the human regulatory network derived from ENCODE data
    Mark B Gerstein
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
    Nature 489:91-100. 2012
    ..The regulatory information obtained in this study will be crucial for interpreting personal genome sequences and understanding basic principles of human biology and disease...
  18. 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...
  19. 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...
  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. 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...
  22. 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...
  23. 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...
  24. 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
    ....
  25. 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
    ....
  26. 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...
  27. 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...
  28. 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...
  29. pmc Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans
    Wei Niu
    Department of Genetics, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 21:245-54. 2011
    ..Ultimately, the comprehensive mapping of transcription factor binding sites will identify features of transcriptional networks that regulate C. elegans developmental processes...
  30. 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...
  31. 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...
  32. ncbi request reprint Global analysis of protein phosphorylation in yeast
    Jason Ptacek
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
    Nature 438:679-84. 2005
    ..Because many yeast proteins and pathways are conserved, these results will provide insights into the mechanisms and roles of protein phosphorylation in many eukaryotes...
  33. 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...
  34. pmc Understanding transcriptional regulation by integrative analysis of transcription factor binding data
    Chao Cheng
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 22:1658-67. 2012
    ..The models imply that these features regulate transcription in a highly coordinated manner...
  35. 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...
  36. pmc Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes
    Joseph Fasolo
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Genes Dev 25:767-78. 2011
    ..Our results further demonstrate that protein microarrays uncover a diverse set of interactions not observed previously...
  37. 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...
  38. pmc A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells
    ALEXANDRA E CHAROS
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 22:1668-79. 2012
    ..Overall, our study provides an important framework for understanding the systems-level control of metabolic gene expression in humans...
  39. pmc Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data
    Chao Cheng
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
    PLoS Comput Biol 7:e1002190. 2011
    ..As more and more genome-wide ChIP-Seq and RNA-Seq data becomes available in the near future, our methods of data integration have various potential applications...
  40. 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...
  41. pmc Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
    Mark B Gerstein
    Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
    Science 330:1775-87. 2010
    ..Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome...
  42. 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...
  43. 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...
  44. 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...
  45. 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...
  46. pmc Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping
    Thomas E Royce
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Trends Genet 21:466-75. 2005
    ..We introduce the informatics challenges arising in the analysis of tiling microarray experiments as open problems to the scientific community and present initial approaches for the analysis of this nascent technology...
  47. pmc Extensive variation in chromatin states across humans
    Maya Kasowski
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Science 342:750-2. 2013
    ..Overall, our results provide insights into chromatin variation among humans. ..
  48. pmc Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data
    Zhi John Lu
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 21:276-85. 2011
    ..Overall, our study identifies many new potential ncRNAs in C. elegans and provides a method that can be adapted to other organisms...
  49. 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...
  50. 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...
  51. 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...
  52. pmc Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
    Kevin Y Yip
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Genome Biol 13:R48. 2012
    ..While this large amount of data creates a valuable resource, it is nonetheless overwhelmingly complex and simultaneously incomplete since it covers only a small fraction of all human transcription factors...
  53. pmc A major epigenetic programming mechanism guided by piRNAs
    Xiao A Huang
    Yale Stem Cell Center and Department of Cell Biology, Yale School of Medicine, New Haven, CT 06519, USA
    Dev Cell 24:502-16. 2013
    ..Piwi deficiency drastically changed the epigenetic landscape and polymerase II profile throughout the genome, revealing the Piwi-piRNA mechanism as a major epigenetic programming mechanism in Drosophila...
  54. pmc MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays
    Sorina C Popescu
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
    Genes Dev 23:80-92. 2009
    ..Our predicted MKK-MPK phosphorylation network constitutes a valuable resource to understand the function and specificity of MPK signaling systems...
  55. pmc Variation and genetic control of protein abundance in humans
    Linfeng Wu
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Nature 499:79-82. 2013
    ..This study demonstrates the feasibility of high-throughput human proteome quantification that, when integrated with DNA variation and transcriptome information, adds a new dimension to the characterization of gene expression regulation. ..
  56. pmc Accurate identification and analysis of human mRNA isoforms using deep long read sequencing
    Hagen Tilgner
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    G3 (Bethesda) 3:387-97. 2013
    ..Furthermore, we demonstrate that long read sequence can be assembled into full-length transcripts with considerable success. Our method is applicable to all long read sequencing technologies...
  57. pmc Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements
    Anshul Kundaje
    Department of Computer Science, Stanford University, Stanford, California 94305, USA
    Genome Res 22:1735-47. 2012
    ..Meta-analyses of the signal profiles revealed a common vocabulary of chromatin signals shared across multiple cell lines and binding proteins...
  58. pmc VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment
    Lukas Habegger
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Bioinformatics 28:2267-9. 2012
    ..Finally, in order to enable on-demand access and to minimize unnecessary transfers of large data files, VAT can be run as a virtual machine in a cloud-computing environment...
  59. 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...
  60. 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...
  61. 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...
  62. 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...
  63. 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...
  64. pmc Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae
    Michael Seringhaus
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Nucleic Acids Res 34:e57. 2006
    ..Thus, both transposons are effective tools for gene disruption, but Tn7 does so with less duplication and a more uniform distribution, better approximating the behavior of the ideal transposon...
  65. pmc AlleleSeq: analysis of allele-specific expression and binding in a network framework
    Joel Rozowsky
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Mol Syst Biol 7:522. 2011
    ..Furthermore, we investigate the coordination between ASE and ASB from multiple transcription factors events using a regulatory network framework. Correlation analyses and network motifs show mostly coordinated ASB and ASE...
  66. pmc Systematic functional regulatory assessment of disease-associated variants
    Konrad J Karczewski
    Biomedical Informatics Training Program, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 110:9607-12. 2013
    ..Thus, using this integrative approach, we provide a unique means to assign putative function to many disease-associated SNPs...
  67. pmc ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
    Stephen G Landt
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 22:1813-31. 2012
    ..All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE (http://encodeproject.org/ENCODE/) and modENCODE (http://www.modencode.org/) portals...
  68. pmc Linking disease associations with regulatory information in the human genome
    Marc A Schaub
    Department of Computer Science, Stanford University, Stanford, California 94305, USA
    Genome Res 22:1748-59. 2012
    ..Our results show that the experimental data sets generated by the ENCODE Consortium can be successfully used to suggest functional hypotheses for variants associated with diseases and other phenotypes...
  69. pmc Personal omics profiling reveals dynamic molecular and medical phenotypes
    Rui Chen
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Cell 148:1293-307. 2012
    ..This study demonstrates that longitudinal iPOP can be used to interpret healthy and diseased states by connecting genomic information with additional dynamic omics activity...
  70. pmc Performance comparison of whole-genome sequencing platforms
    Hugo Y K Lam
    Department of Genetics, Stanford University, Stanford, California, USA
    Nat Biotechnol 30:78-82. 2012
    ..Our results have important implications for understanding the accuracy and completeness of the genome sequencing platforms...
  71. pmc The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics
    Tara A Gianoulis
    Department of Genetics, 77 Ave of Louis Pasteur, Harvard Medical School, Boston, MA 02115, USA
    Genome Biol 12:R32. 2011
    ..Here we present an approach (CRIT) to find connections such as these and show how it can be applied in a variety of genomic contexts including chemogenomics data...
  72. doi request reprint iPOP goes the world: integrated personalized Omics profiling and the road toward improved health care
    Jennifer Li-Pook-Than
    Department of Genetics, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
    Chem Biol 20:660-6. 2013
    ....
  73. pmc Dynamic trans-acting factor colocalization in human cells
    Dan Xie
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Cell 155:713-24. 2013
    ..We show distinct functional annotations and properties of different TF cobinding patterns and provide insights into the complex regulatory landscape of the cell. ..
  74. pmc Annotation of functional variation in personal genomes using RegulomeDB
    Alan P Boyle
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Genome Res 22:1790-7. 2012
    ..Overall, we expect this approach and resource to be valuable for the annotation of human genome sequences...
  75. pmc Identification of genomic indels and structural variations using split reads
    Zhengdong D Zhang
    Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    BMC Genomics 12:375. 2011
    ..Here we present split-read identification, calibrated (SRiC), a sequence-based method for SV detection...
  76. pmc Cooperative transcription factor associations discovered using regulatory variation
    Konrad J Karczewski
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 108:13353-8. 2011
    ..We present a general approach for discovering combinatorial models of regulation and advance our understanding of the genetic basis of variation in transcription factor binding...
  77. pmc Whole-exome sequencing identifies tetratricopeptide repeat domain 7A (TTC7A) mutations for combined immunodeficiency with intestinal atresias
    Rui Chen
    Department of Genetics, Stanford University School of Medicine, CA, USA
    J Allergy Clin Immunol 132:656-664.e17. 2013
    ..Combined immunodeficiency with multiple intestinal atresias (CID-MIA) is a rare hereditary disease characterized by intestinal obstructions and profound immune defects...
  78. doi request reprint Preparation of recombinant protein spotted arrays for proteome-wide identification of kinase targets
    Hogune Im
    Department of Genetics, Stanford University, Stanford, California, USA
    Curr Protoc Protein Sci . 2013
    ..The same methodology can be readily applied to higher eukaryotic systems with careful consideration of overexpression strategy...
  79. pmc Systems biology: personalized medicine for the future?
    Rui Chen
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 5120, USA
    Curr Opin Pharmacol 12:623-8. 2012
    ..In this article, we review the efforts of systems biology in personalized medicine in the past 2 years, and discuss in detail achievements and concerns, as well as highlights and hurdles for future personalized health care...
  80. pmc SWI/SNF chromatin-remodeling factors: multiscale analyses and diverse functions
    Ghia Euskirchen
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 5120, USA
    J Biol Chem 287:30897-905. 2012
    ..These studies have greatly increased our understanding of complex nuclear processes...
  81. pmc Phosphorylation of yeast transcription factors correlates with the evolution of novel sequence and function
    Mark Kaganovich
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, United States
    J Proteome Res 11:261-8. 2012
    ..Overall, these studies have important implications for understanding divergence of gene function and regulation in eukaryotes...
  82. doi request reprint Performance comparison of exome DNA sequencing technologies
    Michael J Clark
    Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
    Nat Biotechnol 29:908-14. 2011
    ..We also compare exome sequencing and whole genome sequencing (WGS) of the same sample, demonstrating that exome sequencing can detect additional small variants missed by WGS...
  83. doi request reprint ChIP-Seq: a method for global identification of regulatory elements in the genome
    Debasish Raha
    Stanford University, Stanford, California, USA
    Curr Protoc Mol Biol . 2010
    ..ChIP DNA is purified, sequencing adapters are ligated, and 30- to 35-nucleotide (nt) sequence reads are generated. The sequence of the DNA fragments is mapped back to the reference genome for determination of the binding sites...
  84. pmc Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses
    Xiyan Li
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 5120, USA
    Cell 143:639-50. 2010
    ..Our study defines potential key regulatory steps in lipid biosynthetic pathways and suggests that small metabolites may play a more general role as regulators of protein activity and function than previously appreciated...
  85. pmc Coherent functional modules improve transcription factor target identification, cooperativity prediction, and disease association
    Konrad J Karczewski
    Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, California, United States of America Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Genet 10:e1004122. 2014
    ..These results show the power of combining expression data and ChIP-Seq data to remove noise and better extract the associations between TFs, functional modules, and disease. ..
  86. ncbi request reprint Clinical interpretation and implications of whole-genome sequencing
    Frederick E Dewey
    Stanford Center for Inherited Cardiovascular Disease, Stanford, California2Stanford Cardiovascular Institute, Stanford, California3Division of Cardiovascular Medicine, Stanford University, Stanford, California4Stanford Center for Genomics and Personalized
    JAMA 311:1035-45. 2014
    ..Whole-genome sequencing (WGS) is increasingly applied in clinical medicine and is expected to uncover clinically significant findings regardless of sequencing indication...
  87. pmc STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud
    Konrad J Karczewski
    Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, California, United States of America Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 9:e84860. 2014
    ..We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2. ..
  88. pmc Path-scan: a reporting tool for identifying clinically actionable variants
    Roxana Daneshjou
    Department of Genetics, Stanford University, Stanford, CA 94061, United States
    Pac Symp Biocomput 19:229-40. 2014
    ..Excluding the most commonly seen variant in 1000 Genomes, about 20% of all genomes analyzed had a ClinVar designated pathogenic variant that required further evaluation. ..
  89. pmc A single-molecule long-read survey of the human transcriptome
    Donald Sharon
    1 Department of Genetics, Stanford University, Stanford, California, USA 2 Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA 3
    Nat Biotechnol 31:1009-14. 2013
    ..As a group, transcripts mapping to unannotated regions have features of long, noncoding RNAs. Our results show the feasibility of deep sequencing full-length RNA from complex eukaryotic transcriptomes on a single-molecule level. ..
  90. doi request reprint Systematic investigation of protein-small molecule interactions
    Xiyan Li
    Department of Genetics, Stanford University, Stanford, CA, USA
    IUBMB Life 65:2-8. 2013
    ..In this review, we summarize recent advances of systematic investigation of protein-metabolite/small molecule interactions, and discuss the impact of such studies and their potential impact on both biological researches and medicine...
  91. doi request reprint Promise of personalized omics to precision medicine
    Rui Chen
    Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
    Wiley Interdiscip Rev Syst Biol Med 5:73-82. 2013
    ..We discuss here the advances and challenges in systems biology-powered personalized medicine at its current stage, as well as a prospective view of future personalized health care at the end of this review...
  92. ncbi request reprint Chromatin immunoprecipitation and multiplex sequencing (ChIP-Seq) to identify global transcription factor binding sites in the nematode Caenorhabditis elegans
    Cathleen M Brdlik
    Department of Genetics, Stanford University, Stanford, CA, USA
    Methods Enzymol 539:89-111. 2014
    ..2009) and thereby reduce the cost and amount of time needed for each result. The multiplex ChIP-Seq method described in this section has been developed for Caenorhabditis elegans, but is easily adaptable for other organisms. ..
  93. pmc Whole-genome haplotyping using long reads and statistical methods
    Volodymyr Kuleshov
    1 Department of Computer Science, Stanford University, Stanford, California, USA 2 Illumina Inc, San Diego, California, USA 3 Department of Genetics, Stanford University School of Medicine, Stanford, California, USA 4
    Nat Biotechnol 32:261-6. 2014
    ..SLRH should facilitate population-scale haplotyping of human genomes. ..
  94. pmc Investigating metabolite-protein interactions: an overview of available techniques
    Grace Xiaolu Yang
    Department of Genetics, Stanford University, Stanford, CA, USA
    Methods 57:459-66. 2012
    ..Information gained from the use of these approaches can be applied to the manipulation of cellular processes and therapeutic applications...
  95. pmc Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing
    Jia Qian Wu
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 107:5254-9. 2010
    ....
  96. 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...
  97. pmc Phased whole-genome genetic risk in a family quartet using a major allele reference sequence
    Frederick E Dewey
    Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
    PLoS Genet 7:e1002280. 2011
    ..These ethnicity-specific, family-based approaches to interpretation of genetic variation are emblematic of the next generation of genetic risk assessment using whole-genome sequencing...
  98. pmc Identification of STAT5A and STAT5B target genes in human T cells
    Takahiro Kanai
    Division of Immunology and Allergy, Department of Pediatrics, School of Medicine, Stanford University, Stanford, California, United States of America
    PLoS ONE 9:e86790. 2014
    ..The new identification of these genes regulated by STAT5A and/or STAT5B has major implications for understanding the pathophysiology of cancer progression, neural disorders, and immune abnormalities. ..
  99. ncbi request reprint Functional profiling of the Saccharomyces cerevisiae genome
    Guri Giaever
    Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
    Nature 418:387-91. 2002
    ..Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics...
  100. pmc Negative regulation of calcineurin signaling by Hrr25p, a yeast homolog of casein kinase I
    Kimberly A Kafadar
    Department of Biological Sciences Stanford University, Stanford, California, 94305 5020, USA
    Genes Dev 17:2698-708. 2003
    ..These findings represent the first identification of a negative regulator for Crz1p, and establish a novel physiological role for Hrr25p in antagonizing calcineurin signaling...
  101. pmc Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females
    G David Poznik
    Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, CA, USA
    Science 341:562-5. 2013
    ..Our findings suggest that, contrary to previous claims, male lineages do not coalesce significantly more recently than female lineages...