genome

Summary

Summary: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.

Top Publications

  1. pmc KEGG: kyoto encyclopedia of genes and genomes
    M Kanehisa
    Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 28:27-30. 2000
  2. pmc Versatile and open software for comparing large genomes
    Stefan Kurtz
    Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
    Genome Biol 5:R12. 2004
  3. pmc Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
    Aravind Subramanian
    Broad Institute of Massachusetts Institute of Technology and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
    Proc Natl Acad Sci U S A 102:15545-50. 2005
  4. pmc The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
    Aaron McKenna
    Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Genome Res 20:1297-303. 2010
  5. pmc Multiplex genome engineering using CRISPR/Cas systems
    Le Cong
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Science 339:819-23. 2013
  6. pmc The Sequence Alignment/Map format and SAMtools
    Heng Li
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
    Bioinformatics 25:2078-9. 2009
  7. ncbi MicroRNAs: genomics, biogenesis, mechanism, and function
    David P Bartel
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Cell 116:281-97. 2004
  8. pmc tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    T M Lowe
    Department of Genetics, Washington University School of Medicine, 660 South Euclid, Box 8232, St Louis, MO 63110, USA
    Nucleic Acids Res 25:955-64. 1997
  9. pmc In vivo genome editing using a high-efficiency TALEN system
    Victoria M Bedell
    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
    Nature 491:114-8. 2012
  10. pmc The UCSC Genome Browser database: update 2010
    Brooke Rhead
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 38:D613-9. 2010

Detail Information

Publications337 found, 100 shown here

  1. pmc KEGG: kyoto encyclopedia of genes and genomes
    M Kanehisa
    Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 28:27-30. 2000
    ..KEGG provides Java graphics tools for browsing genome maps, comparing two genome maps and manipulating expression maps, as well as computational tools for sequence ..
  2. pmc Versatile and open software for comparing large genomes
    Stefan Kurtz
    Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
    Genome Biol 5:R12. 2004
    ..Two new graphical viewing tools provide alternative ways to analyze genome alignments. The new system is the first version of MUMmer to be released as open-source software...
  3. pmc Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
    Aravind Subramanian
    Broad Institute of Massachusetts Institute of Technology and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
    Proc Natl Acad Sci U S A 102:15545-50. 2005
    ..The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets...
  4. pmc The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
    Aaron McKenna
    Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Genome Res 20:1297-303. 2010
    ..However, the massive data sets generated by NGS--the 1000 Genome pilot alone includes nearly five terabases--make writing feature-rich, efficient, and robust analysis tools ..
  5. pmc Multiplex genome engineering using CRISPR/Cas systems
    Le Cong
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Science 339:819-23. 2013
    Functional elucidation of causal genetic variants and elements requires precise genome editing technologies...
  6. pmc The Sequence Alignment/Map format and SAMtools
    Heng Li
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
    Bioinformatics 25:2078-9. 2009
    ..SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments...
  7. ncbi MicroRNAs: genomics, biogenesis, mechanism, and function
    David P Bartel
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Cell 116:281-97. 2004
    ..Although they escaped notice until relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in multicellular organisms and likely influence the output of many protein-coding genes...
  8. pmc tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    T M Lowe
    Department of Genetics, Washington University School of Medicine, 660 South Euclid, Box 8232, St Louis, MO 63110, USA
    Nucleic Acids Res 25:955-64. 1997
    ..tRNAscan-SE searches at approximately 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes...
  9. pmc In vivo genome editing using a high-efficiency TALEN system
    Victoria M Bedell
    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
    Nature 491:114-8. 2012
    ..However, the inability to readily modify the genome in a targeted fashion has been a bottleneck in the field...
  10. pmc The UCSC Genome Browser database: update 2010
    Brooke Rhead
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 38:D613-9. 2010
    The University of California, Santa Cruz (UCSC) Genome Browser website (http://genome.ucsc...
  11. pmc OrthoMCL: identification of ortholog groups for eukaryotic genomes
    Li Li
    Department of Biology and Genetics, Center for Bioinformatics, and Genomics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Res 13:2178-89. 2003
    The identification of orthologous groups is useful for genome annotation, studies on gene/protein evolution, comparative genomics, and the identification of taxonomically restricted sequences...
  12. pmc Efficient genome editing in zebrafish using a CRISPR-Cas system
    Woong Y Hwang
    Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, Massachusetts, USA
    Nat Biotechnol 31:227-9. 2013
    ....
  13. pmc The UCSC Genome Browser database: extensions and updates 2011
    Timothy R Dreszer
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 40:D918-23. 2012
    The University of California Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms...
  14. pmc Genome-scale DNA methylation maps of pluripotent and differentiated cells
    Alexander Meissner
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 454:766-70. 2008
    ..Our knowledge about the genome-wide distribution of DNA methylation, how it changes during cellular differentiation and how it relates to histone ..
  15. pmc Statistical significance for genomewide studies
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 100:9440-5. 2003
    ..Our approach avoids a flood of false positive results, while offering a more liberal criterion than what has been used in genome scans for linkage.
  16. ncbi Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    A Krogh
    Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    J Mol Biol 305:567-80. 2001
    ..We discuss the possible relevance of this finding for our understanding of membrane protein assembly mechanisms. A TMHMM prediction service is available at http://www.cbs.dtu.dk/services/TMHMM/...
  17. pmc MEGAN analysis of metagenomic data
    Daniel H Huson
    Center for Bioinformatics, Tubingen University, Sand 14, 72076 Tubingen, Germany
    Genome Res 17:377-86. 2007
    ..Also, simulations that evaluate the performance of the approach for different read lengths are presented...
  18. pmc The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse
    Janan T Eppig
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 40:D881-6. 2012
    The Mouse Genome Database (MGD, http://www.informatics.jax.org) is the international community resource for integrated genetic, genomic and biological data about the laboratory mouse...
  19. pmc Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity
    F Ann Ran
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Cell 154:1380-9. 2013
    Targeted genome editing technologies have enabled a broad range of research and medical applications...
  20. pmc The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    Ron Caspi
    SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA, USA
    Nucleic Acids Res 40:D742-53. 2012
    ..BioCyc (http://biocyc.org/) is a collection of more than 1700 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism...
  21. pmc Human DNA methylomes at base resolution show widespread epigenomic differences
    Ryan Lister
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
    Nature 462:315-22. 2009
    ..cytosine methylation is a central epigenetic modification that has essential roles in cellular processes including genome regulation, development and disease...
  22. doi A draft sequence of the Neandertal genome
    Richard E Green
    Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D 04103 Leipzig, Germany
    Science 328:710-22. 2010
    ..We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals...
  23. ncbi GenePattern 2.0
    Michael Reich
    Nat Genet 38:500-1. 2006
  24. doi A TALE nuclease architecture for efficient genome editing
    Jeffrey C Miller
    Sangamo BioSciences, Inc, Richmond, California, USA
    Nat Biotechnol 29:143-8. 2011
    ..These studies demonstrate the effective application of designed TALE transcription factors and nucleases for the targeted regulation and modification of endogenous genes...
  25. pmc The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics
    Judith A Blake
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 39:D842-8. 2011
    The Mouse Genome Database (MGD) is the community model organism database for the laboratory mouse and the authoritative source for phenotype and functional annotations of mouse genes...
  26. ncbi Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals
    Rudolf Jaenisch
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Nat Genet 33:245-54. 2003
    ..The extent to which environmental effects can provoke epigenetic responses represents an exciting area of future research...
  27. pmc KAAS: an automatic genome annotation and pathway reconstruction server
    Yuki Moriya
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 35:W182-5. 2007
    ..Here, we have developed a web-based server called KAAS (KEGG Automatic Annotation Server: http://www.genome.jp/kegg/kaas/) i.e...
  28. pmc CTCF: master weaver of the genome
    Jennifer E Phillips
    Department of Biology, Emory University, Atlanta, GA 30322, USA
    Cell 137:1194-211. 2009
    ..Here we re-evaluate data supporting these roles in the context of mechanistic insights provided by recent genome-wide studies and highlight evidence for CTCF-mediated intra- and interchromosomal contacts at several ..
  29. doi Sequencing technologies - the next generation
    Michael L Metzker
    Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Nat Rev Genet 11:31-46. 2010
    Demand has never been greater for revolutionary technologies that deliver fast, inexpensive and accurate genome information. This challenge has catalysed the development of next-generation sequencing (NGS) technologies...
  30. pmc The UCSC Genome Browser database: 2014 update
    Donna Karolchik
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz UCSC, 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 42:D764-70. 2014
    The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc...
  31. pmc Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
    Marie Touchon
    Atelier de BioInformatique, Universite Pierre et Marie Curie Paris 6, Paris, France
    PLoS Genet 5:e1000344. 2009
    ..b>Genome flux in E...
  32. pmc The sequence and de novo assembly of the giant panda genome
    Ruiqiang Li
    BGI Shenzhen, Shenzhen 518083, China
    Nature 463:311-7. 2010
    ..sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2...
  33. pmc GREAT improves functional interpretation of cis-regulatory regions
    Cory Y McLean
    Department of Computer Science, Stanford University, Stanford, California, USA
    Nat Biotechnol 28:495-501. 2010
    ..significance of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate ..
  34. ncbi RNA maps reveal new RNA classes and a possible function for pervasive transcription
    Philipp Kapranov
    Affymetrix Laboratory, Affymetrix, Inc, 3420 Central Expressway, Santa Clara, CA, 95051, USA
    Science 316:1484-8. 2007
    ..RNAs longer than 200 nucleotides (nt) and whole-cell RNAs less than 200 nt were investigated in this genome-wide study...
  35. pmc The genome sequence of Atlantic cod reveals a unique immune system
    Bastiaan Star
    Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, PO Box 1066, Blindern, N 0316 Oslo, Norway
    Nature 477:207-10. 2011
    ..Here we present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an ..
  36. pmc Rapid SNP discovery and genetic mapping using sequenced RAD markers
    Nathan A Baird
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
    PLoS ONE 3:e3376. 2008
    ..Sequencing of RAD markers is an integrated platform for SNP discovery and genotyping. This approach should be widely applicable to genetic mapping in a variety of organisms...
  37. doi The oyster genome reveals stress adaptation and complexity of shell formation
    Guofan Zhang
    Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
    Nature 490:49-54. 2012
    ..Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and ..
  38. doi Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans
    Brian J Haas
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Nature 461:393-8. 2009
    ..Here we report the sequence of the P. infestans genome, which at approximately 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the ..
  39. doi Efficient methods to compute genomic predictions
    P M Vanraden
    Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 2350, USA
    J Dairy Sci 91:4414-23. 2008
    ..Actual gains may differ because the simulation did not account for linkage disequilibrium in the base population or selection in subsequent generations...
  40. doi DNA methylation landscapes: provocative insights from epigenomics
    Miho M Suzuki
    The Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Michael Swann Building, The King s Buildings, Edinburgh EH9 3JR, UK
    Nat Rev Genet 9:465-76. 2008
    ..To understand the biological significance of this epigenetic mark it is essential to know where in the genome it is located...
  41. pmc Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    Ron Edgar
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Lister Hill Center, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:207-10. 2002
    ..A series organizes samples into the meaningful data sets which make up an experiment. The GEO repository is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo...
  42. ncbi R/qtl: QTL mapping in experimental crosses
    Karl W Broman
    Department of Biostatistics, Johns Hopkins University, 615 N Wolfe St, Baltimore, MD 21205, USA
    Bioinformatics 19:889-90. 2003
    ..software, R, and includes functions for estimating genetic maps, identifying genotyping errors, and performing single-QTL and two-dimensional, two-QTL genome scans by multiple methods, with the possible inclusion of covariates.
  43. pmc Synonymous but not the same: the causes and consequences of codon bias
    Joshua B Plotkin
    Department of Biology and Program in Applied Mathematics and Computational Science, University of Pennsylvania, 433 South University Avenue, Philadelphia, Pennsylvania 19104, USA
    Nat Rev Genet 12:32-42. 2011
    ..Ongoing work to quantify the dynamics of initiation and elongation is as important for understanding natural synonymous variation as it is for designing transgenes in applied contexts...
  44. pmc The zebrafish reference genome sequence and its relationship to the human genome
    Kerstin Howe
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 496:498-503. 2013
    ..To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a ..
  45. pmc Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    D Allan Drummond
    FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
    Cell 134:341-52. 2008
    ....
  46. ncbi Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research...
  47. pmc Heritable genome editing in C. elegans via a CRISPR-Cas9 system
    Ari E Friedland
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Nat Methods 10:741-3. 2013
    ..Our results demonstrate that targeted, heritable genetic alterations can be achieved in C. elegans, providing a convenient and effective approach for generating loss-of-function mutants. ..
  48. pmc A conditional knockout resource for the genome-wide study of mouse gene function
    William C Skarnes
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 474:337-42. 2011
    Gene targeting in embryonic stem cells has become the principal technology for manipulation of the mouse genome, offering unrivalled accuracy in allele design and access to conditional mutagenesis...
  49. pmc Genome engineering using the CRISPR-Cas9 system
    F Ann Ran
    1 Broad Institute of Massachusetts Institute of Technology MIT and Harvard, Cambridge, Massachusetts, USA 2 McGovern Institute for Brain Research, Cambridge, Massachusetts, USA 3 Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, USA 4 Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA 5 Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA 6
    Nat Protoc 8:2281-308. 2013
    Targeted nucleases are powerful tools for mediating genome alteration with high precision...
  50. pmc Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system
    Li En Jao
    Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232 8240, USA
    Proc Natl Acad Sci U S A 110:13904-9. 2013
    ..short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) system has been adapted to serve as a targeted genome mutagenesis tool...
  51. pmc The KEGG resource for deciphering the genome
    Minoru Kanehisa
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 32:D277-80. 2004
    ..a knowledge-based approach for network prediction, which is to predict, given a complete set of genes in the genome, the protein interaction networks that are responsible for various cellular processes. KEGG at http://www.genome...
  52. ncbi MicroRNAs: small RNAs with a big role in gene regulation
    Lin He
    Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nat Rev Genet 5:522-31. 2004
  53. pmc Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
    Kai Ye
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Bioinformatics 25:2865-71. 2009
    ..Indel detection using next-gen data is difficult and identification of long structural variations is extremely challenging...
  54. pmc Insights into hominid evolution from the gorilla genome sequence
    Aylwyn Scally
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Nature 483:169-75. 2012
    ..Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera...
  55. pmc Applications of genome-scale metabolic reconstructions
    Matthew A Oberhardt
    Department of Biomedical Engineering, University of Virginia, Health System, Charlottesville, VA, USA
    Mol Syst Biol 5:320. 2009
    The availability and utility of genome-scale metabolic reconstructions have exploded since the first genome-scale reconstruction was published a decade ago...
  56. pmc The UCSC Table Browser data retrieval tool
    Donna Karolchik
    Center for Biomolecular Science and Engineering, University of California Santa Cruz UCSC, School of Engineering, 1156 High Street, Santa Cruz, CA 95064 1077, USA
    Nucleic Acids Res 32:D493-6. 2004
    The University of California Santa Cruz (UCSC) Table Browser (http://genome.ucsc.edu/cgi-bin/hgText) provides text-based access to a large collection of genome assemblies and annotation data stored in the Genome Browser Database...
  57. doi Genome-scale RNAi screen for host factors required for HIV replication
    Honglin Zhou
    Department of Virus and Cell Biology, Merck and Co, Inc, West Point, PA 19486, USA
    Cell Host Microbe 4:495-504. 2008
    ..To discover cellular factors associated with HIV-1 replication, we conducted a genome-scale siRNA screen, revealing more than 311 host factors, including 267 that were not previously linked to HIV...
  58. pmc The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells
    Stefanie Seisenberger
    Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
    Mol Cell 48:849-62. 2012
    b>Genome-wide DNA methylation reprogramming occurs in mouse primordial germ cells (PGCs) and preimplantation embryos, but the precise dynamics and biological outcomes are largely unknown...
  59. pmc Sequence-based characterization of structural variation in the mouse genome
    Binnaz Yalcin
    The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
    Nature 477:326-9. 2011
    ..We identified 24 SVs that disrupt coding exons, acting as rare variants of large effect on gene function. One-third of the genes so affected have immunological functions...
  60. pmc The Amphimedon queenslandica genome and the evolution of animal complexity
    Mansi Srivastava
    Center for Integrative Genomics and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Nature 466:720-6. 2010
    ..Here we present the draft genome sequence of Amphimedon queenslandica, a demosponge from the Great Barrier Reef, and show that it is remarkably ..
  61. pmc TALENs: a widely applicable technology for targeted genome editing
    J Keith Joung
    Massachusetts General Hospital, Molecular Pathology Unit, The Center for Computational and Integrative Biology, and the Center for Cancer Research, Harvard Medical School, Department of Pathology, 149 13th Street, 6th Floor, Charlestown, Massachusetts 02129, USA
    Nat Rev Mol Cell Biol 14:49-55. 2013
    ..The capability to quickly and efficiently alter genes using TALENs promises to have profound impacts on biological research and to yield potential therapeutic strategies for genetic diseases...
  62. ncbi Genome maintenance mechanisms for preventing cancer
    J H Hoeijmakers
    MGC Department of Cell Biology and Genetics, Centre for Biomedical Genetics, Erasmus University, PO Box 1738, 3000DR Rotterdam, The Netherlands
    Nature 411:366-74. 2001
    The early notion that cancer is caused by mutations in genes critical for the control of cell growth implied that genome stability is important for preventing oncogenesis...
  63. pmc Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags
    PAUL A HOHENLOHE
    Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon, United States of America
    PLoS Genet 6:e1000862. 2010
    Next-generation sequencing technology provides novel opportunities for gathering genome-scale sequence data in natural populations, laying the empirical foundation for the evolving field of population genomics...
  64. pmc HITS-CLIP yields genome-wide insights into brain alternative RNA processing
    Donny D Licatalosi
    Laboratory of Molecular Neuro Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nature 456:464-9. 2008
    ..Here we develop a genome-wide means of mapping protein-RNA binding sites in vivo, by high-throughput sequencing of RNA isolated by ..
  65. pmc Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency
    Christian Popp
    Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge, UK
    Nature 463:1101-5. 2010
    ..Here we profiled DNA methylation throughout the genome by unbiased bisulphite next generation sequencing in wild-type and AID-deficient mouse PGCs at embryonic day (E)13...
  66. ncbi GenABEL: an R library for genome-wide association analysis
    Yurii S Aulchenko
    Department of Epidemiology and Biostatistics, Erasmus MC Rotterdam, Postbus 2040, 3000 CA Rotterdam, The Netherlands
    Bioinformatics 23:1294-6. 2007
    Here we describe an R library for genome-wide association (GWA) analysis...
  67. pmc Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
    Dominic Schmidt
    Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Science 328:1036-40. 2010
    ..we used chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) to determine experimentally the genome-wide occupancy of two TFs, CCAAT/enhancer-binding protein alpha and hepatocyte nuclear factor 4 alpha, in the ..
  68. doi Horizontal gene transfer in eukaryotic evolution
    Patrick J Keeling
    Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z, Canada
    Nat Rev Genet 9:605-18. 2008
    Horizontal gene transfer (HGT; also known as lateral gene transfer) has had an important role in eukaryotic genome evolution, but its importance is often overshadowed by the greater prevalence and our more advanced understanding of gene ..
  69. pmc A map of the cis-regulatory sequences in the mouse genome
    Yin Shen
    Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093 0653, USA
    Nature 488:116-20. 2012
    ..The 2.6 × 10(9) bases of the mouse genome possess a high degree of conservation with the human genome, so a thorough annotation of the mouse genome will be ..
  70. doi Genome editing with engineered zinc finger nucleases
    Fyodor D Urnov
    Sangamo Biosciences Inc, Richmond, California 94804, USA
    Nat Rev Genet 11:636-46. 2010
    ..genetics in model organisms such as Drosophila melanogaster, Arabidopsis thaliana, zebrafish and rats, efficient genome engineering in human embryonic stem and induced pluripotent stem cells, targeted integration in crop plants, and ..
  71. pmc Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication
    Angel Amores
    Institute of Neuroscience University of Oregon, Eugene, Oregon 97403, USA
    Genetics 188:799-808. 2011
    ..evolutionary, agricultural, economic, and medical importance are unavailable due to the expense of well-assembled genome sequences and difficulties with multigenerational studies...
  72. pmc The dynamic genome of Hydra
    Jarrod A Chapman
    US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 464:592-6. 2010
    ..Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis and other animals...
  73. pmc Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages
    Dominic Schmidt
    Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Cell 148:335-48. 2012
    ..To gain insight into how these DNA elements are conserved and spread through the genome, we defined the full spectrum of CTCF-binding sites, including a 33/34-mer motif, and identified over five ..
  74. pmc Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
    William A Pastor
    Harvard Medical School, Immune Disease Institute and Program in Cellular and Molecular Medicine, Children s Hospital Boston, Boston, Massachusetts 02115, USA
    Nature 473:394-7. 2011
    ..5hmC and TET proteins have been implicated in stem cell biology and cancer, but information on the genome-wide distribution of 5hmC is limited...
  75. pmc Comparative and demographic analysis of orang-utan genomes
    Devin P Locke
    The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA
    Nature 469:529-33. 2011
    ..Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes...
  76. 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
    ..using high-throughput next-generation instrumentation is fast, replacing chromatin immunoprecipitation followed by genome tiling array analysis (ChIP-chip) as the preferred approach for mapping of sites of transcription-factor binding ..
  77. pmc Efficient control of population structure in model organism association mapping
    Hyun Min Kang
    Department of Computer Science, University of California, Los Angeles, California 90095 1596, USA
    Genetics 178:1709-23. 2008
    ..We applied EMMA to in silico whole-genome association mapping of inbred mouse strains involving hundreds of thousands of SNPs, in addition to Arabidopsis ..
  78. pmc Genome-wide identification of polycomb-associated RNAs by RIP-seq
    Jing Zhao
    Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
    Mol Cell 40:939-53. 2010
    ..Here we develop a RIP-seq method to capture the PRC2 transcriptome and identify a genome-wide pool of >9000 PRC2-interacting RNAs in embryonic stem cells...
  79. pmc Galaxy: a platform for interactive large-scale genome analysis
    Belinda Giardine
    Center for Comparative Genomics and Bioinformatics, Huck Institutes for Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA
    Genome Res 15:1451-5. 2005
    ..Here we describe an interactive system, Galaxy, that combines the power of existing genome annotation databases with a simple Web portal to enable users to search remote resources, combine data from ..
  80. pmc Development and applications of CRISPR-Cas9 for genome engineering
    Patrick D Hsu
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02141, USA McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Cell 157:1262-78. 2014
    Recent advances in genome engineering technologies based on the CRISPR-associated RNA-guided endonuclease Cas9 are enabling the systematic interrogation of mammalian genome function...
  81. pmc ENCODE whole-genome data in the UCSC Genome Browser: update 2012
    Kate R Rosenbloom
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 40:D912-7. 2012
    ..DNA Elements (ENCODE) Consortium is entering its 5th year of production-level effort generating high-quality whole-genome functional annotations of the human genome...
  82. doi Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
    Xi Chen
    Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672
    Cell 133:1106-17. 2008
    ..Collectively, the comprehensive mapping of TF-binding sites identifies important features of the transcriptional regulatory networks that define ES-cell identity...
  83. doi Scaffolding pre-assembled contigs using SSPACE
    Marten Boetzer
    BaseClear B V, Einsteinweg 5, 2333 CC Leiden, Leiden, The Netherlands
    Bioinformatics 27:578-9. 2011
    ..SSPACE shows promising results on both prokaryote and eukaryote genomic testsets where the amount of initial contigs was reduced by at least 75%...
  84. pmc Transposable elements and the evolution of regulatory networks
    CEDRIC FESCHOTTE
    Department of Biology, Life Science Building, Box 19498, University of Texas, Arlington, Texas 76019, USA
    Nat Rev Genet 9:397-405. 2008
    ..Here I revisit and expand earlier models and propose that genomic repeats, and in particular transposable elements, have been a rich source of material for the assembly and tinkering of eukaryotic gene regulatory systems...
  85. pmc High-quality draft assemblies of mammalian genomes from massively parallel sequence data
    Sante Gnerre
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 108:1513-8. 2011
    ..for a wide range of biomedical applications, it has proven difficult to use them to generate high-quality de novo genome assemblies of large, repeat-rich vertebrate genomes...
  86. pmc Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
    Peter D Karp
    Artificial Intelligence Center, SRI International, 333 Ravenswood Ave, AE206, Menlo Park, CA 94025, USA
    Brief Bioinform 11:40-79. 2010
    ..Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB)...
  87. pmc An integrated software system for analyzing ChIP-chip and ChIP-seq data
    Hongkai Ji
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA
    Nat Biotechnol 26:1293-300. 2008
    We present CisGenome, a software system for analyzing genome-wide chromatin immunoprecipitation (ChIP) data...
  88. doi Genome-wide genetic marker discovery and genotyping using next-generation sequencing
    John W Davey
    Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, King s Buildings, West Mains Road, Edinburgh, EH9 3JT, UK
    Nat Rev Genet 12:499-510. 2011
    ..Here we review and discuss best practices for several NGS methods for genome-wide genetic marker development and genotyping that use restriction enzyme digestion of target genomes to reduce ..
  89. pmc Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
    Tarjei S Mikkelsen
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Nature 448:553-60. 2007
    ..By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts...
  90. doi Invited review: Genomic selection in dairy cattle: progress and challenges
    B J Hayes
    Department of Primary Industries Victoria, Biosciences Research Division, Bundoora, Australia
    J Dairy Sci 92:433-43. 2009
    ..calculated as the sum of the effects of dense genetic markers, or haplotypes of these markers, across the entire genome, thereby potentially capturing all the quantitative trait loci (QTL) that contribute to variation in a trait...
  91. ncbi HEGESMA: genome search meta-analysis and heterogeneity testing
    Elias Zintzaras
    Department of Biomathematics, University of Thessaly School of Medicine, Larissa 41222, Greece
    Bioinformatics 21:3672-3. 2005
    Heterogeneity and genome search meta-analysis (HEGESMA) is a comprehensive software for performing genome scan meta-analysis, a quantitative method to identify genetic regions (bins) with consistently increased linkage score across ..
  92. ncbi De novo identification of repeat families in large genomes
    Alkes L Price
    Department of Computer Science and Engineering, University of California San Diego La Jolla, CA 92093 0114, USA
    Bioinformatics 21:i351-8. 2005
    ..As the number of genome sequencing projects increases, there is a pressing need to identify the repeat families present in large, newly ..
  93. doi Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle
    Songlin Chen
    1 Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences CAFS, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China 2 3
    Nat Genet 46:253-60. 2014
    ..Pertinent to the current debate about heterogametic sex-chromosome decay, we find that massive gene loss occurred in the wake of sex-chromosome 'birth'. ..
  94. ncbi Genome-wide atlas of gene expression in the adult mouse brain
    Ed S Lein
    Allen Institute for Brain Science, Seattle, Washington 98103, USA
    Nature 445:168-76. 2007
    ..Newly developed image-based informatics tools allow global genome-scale structural analysis and cross-correlation, as well as identification of regionally enriched genes...
  95. doi Genome-wide evolutionary analysis of eukaryotic DNA methylation
    Assaf Zemach
    Department of Plant and Microbial Biology, 211 Koshland Hall, University of California, Berkeley, CA 94720, USA
    Science 328:916-9. 2010
    ..Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes...
  96. pmc Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    Adam Siepel
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 15:1034-50. 2005
    We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu rubripes)...
  97. ncbi The evolutionary fate and consequences of duplicate genes
    M Lynch
    Department of Biology, University of Oregon, Eugene, OR 97403, USA
    Science 290:1151-5. 2000
    ..Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species...
  98. pmc The Cancer Genome Atlas Pan-Cancer analysis project
    John N Weinstein
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
    Nat Genet 45:1113-20. 2013
    The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels...
  99. pmc Genome editing with RNA-guided Cas9 nuclease in zebrafish embryos
    Nannan Chang
    Institute of Molecular Medicine, Peking University, Beijing 100871, China
    Cell Res 23:465-72. 2013
    ..type II clustered regularly interspaced short palindromic repeats (CRISPR) system promise an improved approach to genome editing...
  100. pmc The ecoresponsive genome of Daphnia pulex
    John K Colbourne
    Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
    Science 331:555-61. 2011
    We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes...
  101. pmc The complete genome sequence of a Neanderthal from the Altai Mountains
    Kay Prüfer
    Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
    Nature 505:43-9. 2014
    We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors...

Research Grants73

  1. Genetic variation and regulatory networks: Mechanisms and complexity
    DANA PE ER; Fiscal Year: 2009
    ..These tools will be made publicly available, including a friendly graphical user interface and visualization. ..
  2. Variation in M. tuberculosis in response to host selection
    Sarah Fortune; Fiscal Year: 2009
    ..We will use new genomics technologies[unreadable]low cost genome sequencing and expression profiling[unreadable]to systematically assess genetic and epigenetic variation in ..
  3. Personalized Clinical Diagnostics and Beyond: Integrated Ring Resonator Arrays
    Ryan Bailey; Fiscal Year: 2009
    ..This technology promises to broadly impact the landscape of the biomedical sciences, both meeting the clinical diagnostic challenges of today and pioneering the paradigm-shifting discoveries of tomorrow. ..
  4. NIH Director's Pioneer Award
    Junying Yuan; Fiscal Year: 2009
    ..No Abstract provided ..
  5. High Throughput Genotyping and DNA Sequencing for Studying the Genetic Contributi
    Sonia Dua; Fiscal Year: 2013
    ..Of these samples, 60,000 may be for whole genome association studies requiring between 250,000 and 5,000,000 SNP genotypes per sample in the first two years and up ..
  6. Optimization of DNA Repair by Abh8
    Lauren Endres; Fiscal Year: 2013
    ..To ensure fidelity during DNA replication, the repair of single and double strand breaks is critical for genome maintenance and chromosome stability. If left unrepaired, these DNA lesions can result in cell death or mutations...
  7. Regulation of HSV-1 Gene Expression and Replication by Nuclear Hormone Receptors
    SHAOCHUNG VICTOR HSIA; Fiscal Year: 2013
    ..In searching for hormone responsive elements in HSV-1 genome, we identified thyroid hormone receptor responsive elements (TREs) in the regulatory regions of HSV-1 thymidine ..
  8. Vaccine Development for Falciparum Malaria in Pregnant Women and Their Offspring
    Ian C Michelow; Fiscal Year: 2013
    ..and genetically manipulate malaria parasites, perform cell-based infection assays, interrogate the malaria genome/proteome databases, use sophisticated cell imaging technologies, model complex data using advanced statistical ..
  9. Role of the Y-Located TSPY Gene in Human Oncogenesis
    Yun Fai Chris Lau; Fiscal Year: 2013
    ..is tandemly repeated up to 64 times, constituting the largest tandem array of functional sequences in the human genome. The TSPY repeats are hot spots for both genomic instability and epigenetic dysregulation on the Y chromosome...
  10. The Primate Corpus Luteum: Functional Regression and Cardiovascular Impacts
    Randy L Bogan; Fiscal Year: 2012
    ..LXR1 and LXR2 in inducing the RCT system during regression of the primate CL, and in vitro studies will identify genome-wide changes in gene expression of the primate CL induced by activation of both or individual LXR isoforms...
  11. Identification of Genetic and Epigenetic Alterations in Spondyloarthritis
    Tibor T Glant; Fiscal Year: 2013
    ..Using genome-wide screening, we identified Pgis2 (on chromosome [Chr] 2, syntenic with human Chr9:SPA locus) as one of the most ..
  12. Genome-wide recombination as a risk factor for nondisjunction
    NATASHA D HOLLIS; Fiscal Year: 2010
    ..The goal of the work presented in this proposal is to look at recombination patterns in the rest of the genome to determine if the altered patterns observed on chromosome 21 are due to cis-acting or trans-acting factors...
  13. Comprehensive biomarker study to capitalize on existing GWAS in 10K South Asians
    Danish Saleheen; Fiscal Year: 2010
    ..Comprehensive biomarker study to capitalize on existing GWAS in 10K South Asians The NHLBI portfolio of genome-wide association studies (GWAS) is large but does not currently include South Asians, even though the burden of ..
  14. Discovery of Small Molecule MBT Domain Antagonists
    STEPHEN VERNON FRYE; Fiscal Year: 2010
    ..Epigenetics refers to these heritable changes in how the genome is accessed in different cell-types and during development and differentiation...
  15. Induction and maintenance of regulatory T cells
    Mitchell Kronenberg; Fiscal Year: 2013
    ..ligase regulates Foxp3 gene transcription via modulating Foxo3a-directed gene transcription and to perform genome-wide gene profiling of Tregs to understand the molecular regulation of epigenetic control in Tregs;2) to examine ..
  16. Role of IKK in NSCLC: Modulation of SMRT and NF-kappaB
    Marty W Mayo; Fiscal Year: 2012
    ..1 will identify NF-?B regulated genes that coordinate epigenetic reprogramming in cancer progenitor cells using genome-wide analysis...
  17. Remodeling Neuronal Chromatin in Mouse Models for Depression
    Schahram Akbarian; Fiscal Year: 2013
    ..manipulation of other histone modifications and histone modifying enzymes, particularly those defined by a genome-wide enrichment pattern that is highly divergent as compared to acetylation...
  18. VitC to Decrease Effects of Smoking in Pregnancy on Infant Lung Function-CCC-Lead
    CYNTHIA T MCEVOY; Fiscal Year: 2013
    ..Smoking is a unique morbidity in that it is addictive, heavily advertised and recent genome studies show there are genotypes that significantly increase the likelihood of being unable to quit...
  19. Epigenetics of Sex Differences in Brain and Behavior
    BRIDGET NUGENT; Fiscal Year: 2012
    ..We will use a genome-wide microarray analysis of mRNA from male and female animals treated with DNMT inhibitors or vehicle to ..
  20. Cellular &Molecular Defects in Human B Cell Development
    Charlotte Cunningham-Rundles; Fiscal Year: 2013
    ..genetic factors that promote anti-bacterial immunity in humans are largely unknown, thus we have also undertaken a genome-wide approach, investigating patients with no known genetic defect who have experienced severe pneumococcal ..
  21. Transgenesis and Xenotransplantation
    Jorge A Piedrahita; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): The ability to efficiently modify the swine genome to generate genetically modified animals has the potential to provide a novel source of cells/tissues for clinical applications...
  22. BIOCHEMISTRY OF PRE-MRNA SPLICING
    Adrian R Krainer; Fiscal Year: 2010
    ..proteins together with molecular and reverse-genetic approaches in cell culture, bioinformatics analysis of the genome, and methods to modulate gene expression...
  23. Genomics of Antiviral Responses of Anopheles gambiae Against O'nyong-nyong Virus
    Young S Hong; Fiscal Year: 2010
    ..Because of its medical importance, the whole genome sequence of An. gambiae is fully determined. With this genome sequence available, An...
  24. Molecular Mechanisms of Parvovirus Gene Expression and Replication
    Jianming Qiu; Fiscal Year: 2013
    ..B19V does not use the host replication machinery to replicate its ssDNA genome;rather, it appears to induce a DDR and subsequently co-opts the host DNA repair mechanism to facilitate its own ..
  25. The Relationship Between STK39, Salt Sensitivity, and HCTZ-induced BP Response
    YEN PEI CHRISTY CHANG; Fiscal Year: 2010
    ..Recently, our laboratory identified a novel HTN gene, STK39, from a genome-wide association of baseline blood pressure (BP) in the Old Order Amish, a genetically homogeneous founder ..
  26. Osteocalcin and Metabolic Risk Factors. The Framingham Study
    Yi Hsiang Hsu; Fiscal Year: 2011
    ..In this application we are proposing a genome-wide association (GWA) approach in the Framingham Heart Study to identify (1) novel genetic variants for serum OC ..
  27. Regulation of Type 1 Interferon Production by Autoimmunity-Associated PTPN22
    Yaya Wang; Fiscal Year: 2013
    ..b>Genome-wide association studies have identified a number of genetic polymorphisms that convey an increased risk for ..
  28. Mechanisms of Sex Determination in Zebrafish
    JOHN HARVEY POSTLETHWAIT; Fiscal Year: 2013
    ..Aim 1 is to identify genetic factors linked to sex phenotype in F2 mapping crosses. Aim 2 is to conduct a genome-wide search for genes expressed sex specifically by comparing transcriptomes of all-male populations of zebrafish ..
  29. Chronic Stress and Abdominal Pain: Novel Mechanisms
    John W Wiley; Fiscal Year: 2013
    ..The field of epigenetics has emerged rapidly in the past decade based on seminal studies demonstrating genome-wide distribution of methylation and acetylation sites in primary cells and human cell lines...
  30. Regulation of the Vibrio cholerae intestinal exit plan
    ANISIA J SILVA BENITEZ; Fiscal Year: 2010
    ..cholerae genome. This data will be used to putatively identify intermediate regulators linking RpoS with the regulation of ..
  31. Unbiased genome-wide screen to identify genes regulating mucous cell hyperplasia
    Jeffrey A Whitsett; Fiscal Year: 2010
    ..of Lung Disease Summary/Abstract Project Synopsis: This Challenge Research project will undertake 1) a mouse genome-wide shRNA library screen to identify genes and associated gene networks inducing or inhibiting goblet cell ..
  32. Epigenomic Events in Development of the Locus Coeruleus Noradrenergic Neurons
    Jan Krzysztof Blusztajn; Fiscal Year: 2012
    ..several state-of-the-art experimental approaches, we will generate the first comprehensive characterization of the genome-wide developmental pattern of the LCNN transcriptome [for both messenger RNA (mRNA) and microRNA (miRNA)], the DNA ..
  33. Environmental Risk Factors for Copy Number Variation in Human Chromosomes
    THOMAS EDWARD WILSON; Fiscal Year: 2010
    ..The role of environmental exposure in copy number variation (CNV): "Microscopic deletions and replications of the genome have attracted increasing attention for their potential role in many complex human diseases...
  34. Lipid Droplet Metabolism
    Fredric B Kraemer; Fiscal Year: 2013
    ..of LD metabolism have been made through a variety of approaches, including microscopy, proteomics, and genome-wide screens. LDs are most prominently associated with adipose cells, where triacylglycerol (TAG) is stored...
  35. Roles for microRNA-122 in hepatitis C virus RNA amplification
    Peter Sarnow; Fiscal Year: 2013
    ..two molecules of a liver-specific microRNA, miR-122, resulting in a novel, unprecedented upregulation of the viral genome. Sequestration of miR-122 in HCV-infected cultured cells or in livers of infected chimpanzees leads to a dramatic ..
  36. Cell signaling as a leukemia biomarker
    JAMES WILLIAM JACOBBERGER; Fiscal Year: 2013
    ..involves phosphorylation/de-phosphorylation cycles on pathway proteins, essentially from membrane surfaces to the genome, and between pathways (networks)...
  37. Bioassay for Breast Cancer Prevention
    JoEllen Welsh; Fiscal Year: 2010
    ..sites in multiple tissues, and it is the error-prone repair of these breaks that cause mutations throughout the genome. The initial damage to the DNA is no longer identifiable once cancer eventually develops...
  38. Exome re-sequencing candidate loci for familial essential tremor
    Barry E Kosofsky; Fiscal Year: 2012
    ..Advances in genome bioinformatics and the availability of validated normative population databases (e.g...
  39. MECHANISMS OF RADIORESISTANCE AND CELL CYCLE PROGRESSION
    Howard B Lieberman; Fiscal Year: 2013
    ..However, mechanisms are available to repair the damage, stabilize the genome and neutralize harmful effects...
  40. MAPPING OF ARTHRITIS SUSCEPTIBILITY GENES
    Tibor T Glant; Fiscal Year: 2013
    ..Although large-scale genome-wide association (GVA) studies repeatedly showed linkage between certain chromosome regions and RA, not a single ..
  41. CPG METHYLATION AND MUTATION
    Gerd P Pfeifer; Fiscal Year: 2013
    ..As a key technology to accomplish these goals, we have recently developed a method that enables the precise genome-wide analysis of DNA cytosine methylation patterns in mammalian DNA...
  42. Targeting AP-1 proteins in COPD
    SEKHAR M POTHIREDDY; Fiscal Year: 2010
    ..The human genome encodes ~ 56 b-ZIP proteins that play key roles in regulating various cellular processes, including the ..
  43. Identification of Proteins Important for Male Osteoporosis
    Hong Wen Deng; Fiscal Year: 2013
    ..In combination with our ongoing projects for identifying risk genes of osteoporosis through genome-wide DNA association scan and genome-wide mRNA expression study of osteogenic cells, this study will powerfully ..
  44. Interplay Between Tissue Architecture and Nuclear Organization in the DNA Damage
    Pierre Alexandre Vidi; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Double-strand DNA breaks (DSBs) constitute a constant threat for genome integrity. In absence of accurate repair, they lead to mutations and chromosomal translocations promoting cancer progression...
  45. Novel genomic effects of Y-linked polymorphisms
    Daniel L Hartl; Fiscal Year: 2012
    ..chromosome are likely to be quite general among organisms with genomes rich in heterochromatin including the human genome. Hence we predict that important phenotypic variation affecting human health and disease will ultimately be traced ..
  46. Transgenerational effects of endocrine disruptors: epigenetics and physiology
    Rebecca A Simmons; Fiscal Year: 2013
    ..In addition to testing the expression and DNA methylation of imprinted genes, we will assay genome-wide DNA methylation changes and key histone modifications in F1-F3 offspring...
  47. Genetics of the Neuromuscular Junction: Mechanisms and Disease Models
    Robert W Burgess; Fiscal Year: 2013
    ..1. We will also determine if the same region of the human genome contributes to variable severity in CMT2D patients in collaboration with Dr. Albena Jordanova...
  48. Complex I: Role of L Subunit in Proton Translocation
    Steven B Vik; Fiscal Year: 2011
    ..Mitochondria contain a small subset of the human genome, and several of these genes code for proteins that are components of an extremely important enzyme called Complex ..
  49. Characterization of new toxins (YmgD and YdfD) from E.coli, targeting cell wall
    Hisako Masuda; Fiscal Year: 2012
    ..considered to be a single cellular, free living organism, yet they carry toxin or suicidal genes on their genome. These toxins are usually coexpressed with their cognate antitoxins...
  50. Non-invasive zoonotic pathogen exposure and outcome biomarkers with follow-up in
    Christopher D Heaney; Fiscal Year: 2013
    ..Microbiomics and Human Health at TGen, North, to continue training in multi-locus sequence typing (MLST) and whole genome SNP analysis (WGSA) of multidrug-resistant Staphylococcus aureus (MDRSA) isolated from nasal swabs of livestock ..
  51. Regulation of NFkappaB activity by the Estrogen Receptor
    Kendall W Nettles; Fiscal Year: 2012
    ..We also propose a genome scale siRNA screen for genes required for ER cross-talk with NF-B, providing an unbiased approach to define ..
  52. Mechanisms of Stem Cell Self-Renewal and Aging
    PAUL CHRISTIAN SCHILLER; Fiscal Year: 2013
    ..will decrease their osteoblastic capacity in vitro;and alter the binding of osterix to its target sites in the genome. We also expect that farnesyl-transferase inhibitors will attenuate these effects...
  53. Screening Complete TB Proteome for Protective Antigens
    Alan Greener; Fiscal Year: 2010
    ..the identification and immunogenicity analyses of all proteins encoded by the Mycobacterium tuberculosis (Mtb) genome, yielding a pool of protective antigens that will immediately enter development as subunit vaccines for ..
  54. Interaction between RNA interference and RNA editing pathways
    Kazuko Nishikura; Fiscal Year: 2013
    ..When A I RNA editing occurs within a coding sequence, synthesis of proteins not directly encoded by the genome can result, as demonstrated with transcripts of glutamate receptor (GluR) ion channels and 5-HT2C serotonin ..
  55. MECHANISMS OF EUKARYOTIC TRANSCRIPTIONAL REGULATION
    Michael R Green; Fiscal Year: 2013
    ..During the past funding period, we have performed a genome-wide shRNA screen to identify 28 factors required for epigenetic silencing of Fas, and a select group of other ..
  56. Mouse models of genomic instability and birth defects
    CATHERINE ELIZABETH KEEGAN; Fiscal Year: 2013
    ..anomalies) association in humans, and the Acd gene encodes a protein that has a role in telomere protection and genome stability...
  57. Molecular Biology of Human Erythrocyte Alpha Spectrin
    Patrick G Gallagher; Fiscal Year: 2013
    ..be utilized include chromatin immunoprecipitation experiments followed by array hybridization (ChIP-chip) or whole genome sequencing (ChIP-seq), high throughput DNase I hypersensitive site mapping, and functional studies of gene ..
  58. Pax8-PPARgamma regulation of transcription and metabolism in thyroid cancer
    RONALD JAY KOENIG; Fiscal Year: 2013
    ..Aim, chromatin immunoprecipitation - deep sequencing (ChIP-Seq) will be used to identify PPFP binding sites on a genome wide level...
  59. The Role of MYST Histone Acetyltransferase in Genome Stability
    M Mitchell Smith; Fiscal Year: 2013
    ..Failures in the function of MYST genes are associated with genome instability and many diseases including human cancers...
  60. Folate Status, Genomic Uracil, and the Balance of Base Excision Repair Activity
    Michael D Wyatt; Fiscal Year: 2011
    ..A significant mechanism by which folate deficiency is thought to be procarcinogenic is by increasing genome instability...
  61. BMP signaling in vertebrate development
    Ken W Y Cho; Fiscal Year: 2013
    ..lack of knowledge is that we have not, until recently, had methods to examine how BMPs directly impact genes on a genome-wide level...
  62. Arsenic Exposure, Genetic Determinants and Diabetes Risk in a Family Study
    Ana Navas-Acien; Fiscal Year: 2013
    ..52. In a small linkage study, we detected potential quantitative trait loci associated with %MMA in areas of the genome close to methyltransferase genes...
  63. Genetic &Functional Analyses of Hypertension Susceptibility Genes
    YEN PEI CHRISTY CHANG; Fiscal Year: 2013
    ..Variants that play a role in determining blood pressure (BP) and HTN susceptibility have been uncovered by recent genome-wide association studies (GWAS), but the biological underpinning of such signals is often unclear...
  64. Integrative Pathway Analysis of Epigenomic/transcriptional Alteration in HNSCC
    Joseph A Califano; Fiscal Year: 2010
    ..08-DE-103: Epigenomics and Epigenetics of Oral Health and Disease The standard paradigm for characterization of genome wide epigenetic alteration in human cancers has been focused on discovery of specific promoter hypermethylated ..
  65. Protein composition and interactions of telemeric chromatin
    Michael P Killoran; Fiscal Year: 2010
    ..date, a focus on individual genes has dominated the landscape of studies examining the link between telomeres and genome instability...
  66. Development of a novel whole genome amplification method that mimics nature
    Huimin Kong; Fiscal Year: 2009
    DESCRIPTION (provided by applicant): BioHelix is the exclusive licensee for a novel, primase-based Whole Genome Amplification (pWGA) technology invented by Drs. Stanley Tabor and Charles Richardson at Harvard Medical School...
  67. Targeted Manipulation of the Zebrafish Genome through Homologous Recombination
    Brian Ciruna; Fiscal Year: 2010
    ..recombination technologies for targeting specific (and clinically relevant) mutations into the zebrafish genome (for use in these studies)...
  68. ANALYSIS OF THE TRYPANOSOMA BRUCEI GENOME USING TILING ARRAYS
    Christian Tschudi; Fiscal Year: 2009
    ..The next challenge will be to gain a complete understanding of the genome's information, which will dramatically improve our understanding of various biological processes...
  69. Methylation Landscape of the Human Genome
    Timothy Bestor; Fiscal Year: 2003
    The information content of the human genome is expanded by the covalent methylation of cytosine residues, which introduces approximately 3 X 10(7) residues of 5-methylcytosine per haploid genome...
  70. Simian Virus 40 (SV40) uncoating and penetration
    Daniel Hebert; Fiscal Year: 2009
    ..this, viruses have evolved mechanisms to penetrate or permeabilize the endocytic membrane, or to transport their genome across membranes. Some viruses, including SV40 are transported to the endoplasmic reticulum (ER)...
  71. TRYPANASOMA CRUZI GENOME-SBRI
    Kenneth Stuart; Fiscal Year: 2004
    We propose to sequence the genome of Trypanosoma cruzi, a human pathogen of global importance, as part of an interactive research project...
  72. Genome Wide Analysis of DNA Methylation
    Joseph Ecker; Fiscal Year: 2006
    ..by applicant): This proposal aims to identify functional, non-coding elements in eukaryotic genomes by surveying genome-wide DNA methylation...
  73. Development of a novel whole genome amplification method that mimics nature
    Huimin Kong; Fiscal Year: 2007
    ..by applicant): BioHelix is the exclusive licensee for the commercialization of a novel, primase- based Whole Genome Amplification (pWGA) technology invented by Drs. Stanley Tabor and Charles Richardson at Harvard Medical School...