genomics

Summary

Summary: The systematic study of the complete DNA sequences (GENOME) of organisms.

Top Publications

  1. 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
  2. pmc Fast and accurate short read alignment with Burrows-Wheeler transform
    Heng Li
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
    Bioinformatics 25:1754-60. 2009
  3. ncbi Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
    Ana Conesa
    Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
    Bioinformatics 21:3674-6. 2005
  4. pmc Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    Daniel R Zerbino
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 18:821-9. 2008
  5. pmc A map of human genome variation from population-scale sequencing
    Richard M Durbin
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
    Nature 467:1061-73. 2010
  6. pmc Circos: an information aesthetic for comparative genomics
    Martin Krzywinski
    Canada s Michael Smith Genome Sciences Center, Vancouver, British Columbia V5Z 4S6, Canada
    Genome Res 19:1639-45. 2009
  7. pmc Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
    Helga Thorvaldsdóttir
    Broad Institute, 7 Cambridge Center 301B 5057, Cambridge, MA 02142, USA
    Brief Bioinform 14:178-92. 2013
  8. pmc Ensembl 2011
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 39:D800-6. 2011
  9. pmc Integrative genomics viewer
    James T Robinson
    Nat Biotechnol 29:24-6. 2011
  10. ncbi 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

Detail Information

Publications341 found, 100 shown here

  1. 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...
  2. pmc Fast and accurate short read alignment with Burrows-Wheeler transform
    Heng Li
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
    Bioinformatics 25:1754-60. 2009
    ..The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals...
  3. ncbi Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
    Ana Conesa
    Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
    Bioinformatics 21:3674-6. 2005
    ..This tool offers a suitable platform for functional genomics research in non-model species...
  4. pmc Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    Daniel R Zerbino
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 18:821-9. 2008
    ..Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies...
  5. pmc A map of human genome variation from population-scale sequencing
    Richard M Durbin
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
    Nature 467:1061-73. 2010
    ..These methods and public data will support the next phase of human genetic research...
  6. pmc Circos: an information aesthetic for comparative genomics
    Martin Krzywinski
    Canada s Michael Smith Genome Sciences Center, Vancouver, British Columbia V5Z 4S6, Canada
    Genome Res 19:1639-45. 2009
    ....
  7. pmc Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
    Helga Thorvaldsdóttir
    Broad Institute, 7 Cambridge Center 301B 5057, Cambridge, MA 02142, USA
    Brief Bioinform 14:178-92. 2013
    ..The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing ..
  8. pmc Ensembl 2011
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 39:D800-6. 2011
    ..Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types...
  9. pmc Integrative genomics viewer
    James T Robinson
    Nat Biotechnol 29:24-6. 2011
  10. ncbi 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
    ..I also outline the broad range of applications for NGS technologies, in addition to providing guidelines for platform selection to address biological questions of interest...
  11. pmc NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
    Kim D Pruitt
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 40:D130-5. 2012
    ..More information about the resource is available online (see http://www.ncbi.nlm.nih.gov/RefSeq/)...
  12. pmc Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    Jeremy Goecks
    Department of Biology and Department of Mathematics and Computer Science, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
    Genome Biol 11:R86. 2010
    ..Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis...
  13. pmc The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data
    Ethan Cerami
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Cancer Discov 2:401-4. 2012
    The cBio Cancer Genomics Portal (http://cbioportal...
  14. pmc NCBI GEO: archive for functional genomics data sets--update
    Tanya Barrett
    National Center for Biotechnology Information, National Library of Medicine and Molecular Genetics Section, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Nucleic Acids Res 41:D991-5. 2013
    ..This article reports current status and recent database developments, including the release of GEO2R, an R-based web application that helps users analyse GEO data...
  15. pmc BEDTools: a flexible suite of utilities for comparing genomic features
    Aaron R Quinlan
    Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
    Bioinformatics 26:841-2. 2010
    Testing for correlations between different sets of genomic features is a fundamental task in genomics research...
  16. pmc Phytozome: a comparative platform for green plant genomics
    David M Goodstein
    US Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
    Nucleic Acids Res 40:D1178-86. 2012
    ..genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing...
  17. 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
    ..This allows other developers to contribute to the code base and freely redistribute the code. The MUMmer sources are available at http://www.tigr.org/software/mummer...
  18. ncbi Genome sequence of the palaeopolyploid soybean
    Jeremy Schmutz
    HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, Alabama 35806, USA
    Nature 463:178-83. 2010
    ..An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties...
  19. pmc Saccharomyces Genome Database: the genomics resource of budding yeast
    J Michael Cherry
    Department of Genetics, Stanford University, Stanford, CA 94305 5120, USA
    Nucleic Acids Res 40:D700-5. 2012
    ..Public access to these data is provided to researchers and educators via web pages designed for optimal ease of use...
  20. pmc Fast and accurate long-read alignment with Burrows-Wheeler transform
    Heng Li
    Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
    Bioinformatics 26:589-95. 2010
    ..For longer reads, hashing-based software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time...
  21. 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
    ....
  22. pmc Genome sequencing in microfabricated high-density picolitre reactors
    Marcel Margulies
    454 Life Sciences Corp, 20 Commercial Street, Branford, Connecticut 06405, USA
    Nature 437:376-80. 2005
    ..Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine...
  23. pmc The variant call format and VCFtools
    Petr Danecek
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
    Bioinformatics 27:2156-8. 2011
    ..VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API...
  24. pmc NCBI GEO: archive for functional genomics data sets--10 years on
    Tanya Barrett
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
    Nucleic Acids Res 39:D1005-10. 2011
    ..Today, GEO stores over 20,000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research ..
  25. 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...
  26. pmc FlyBase: enhancing Drosophila Gene Ontology annotations
    Susan Tweedie
    Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
    Nucleic Acids Res 37:D555-9. 2009
    ..Many of these changes stem from our participation in the GO Reference Genome Annotation Project--a multi-database collaboration producing comprehensive GO annotation sets for 12 diverse species...
  27. pmc RNAmmer: consistent and rapid annotation of ribosomal RNA genes
    Karin Lagesen
    Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, University of Oslo, NO 0027 Oslo, Norway
    Nucleic Acids Res 35:3100-8. 2007
    ..Novel, unannotated rRNAs are also predicted in many genomes. The software as well as the genome analysis results are available at the CBS web server...
  28. pmc High-throughput functional annotation and data mining with the Blast2GO suite
    Stefan Götz
    Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    Nucleic Acids Res 36:3420-35. 2008
    Functional genomics technologies have been widely adopted in the biological research of both model and non-model species...
  29. pmc FlyBase 101--the basics of navigating FlyBase
    Peter McQuilton
    Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
    Nucleic Acids Res 40:D706-14. 2012
    ..The final section concerns genomic data, including recent modENCODE (http://www.modencode.org) data, available through our Genome Browser, GBrowse...
  30. 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
    ..We have also introduced several usability features including track search and a context-sensitive menu of options available with a right-click anywhere on the Browser's image...
  31. ncbi MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
    Oliver Thimm
    Max Planck Institute for Molecular Plant Physiology, Golm, Germany
    Plant J 37:914-39. 2004
    ....
  32. 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
    ..More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine...
  33. pmc Ensembl's 10th year
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D557-62. 2010
    ....
  34. pmc The cancer genome
    Michael R Stratton
    Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Nature 458:719-24. 2009
    ..These studies will provide us with a detailed and comprehensive perspective on how individual cancers have developed...
  35. ncbi 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
    ..The utility of GREAT is not limited to ChIP-seq, as it could also be applied to open chromatin, localized epigenomic markers and similar functional data sets, as well as comparative genomics sets.
  36. pmc miRBase: tools for microRNA genomics
    Sam Griffiths-Jones
    Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, UK
    Nucleic Acids Res 36:D154-8. 2008
    ..miRBase provides a range of data to facilitate studies of miRNA genomics: all miRNAs are mapped to their genomic coordinates...
  37. pmc NCBI Reference Sequences: current status, policy and new initiatives
    Kim D Pruitt
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Rm 4As 47B, 45 Center Drive, Bethesda, MD, USA
    Nucleic Acids Res 37:D32-6. 2009
    ..In addition, we introduce RefSeqGene, a new initiative to support reporting variation data on a stable genomic coordinate system...
  38. 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...
  39. 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
    ....
  40. pmc ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments
    Helen Parkinson
    Functional Genomics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 39:D1002-4. 2011
    ..ebi.ac.uk/arrayexpress) is one of the three international public repositories of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies...
  41. pmc The landscape of somatic copy-number alteration across human cancers
    Rameen Beroukhim
    Cancer Program and Medical and Population Genetics Group, The Broad Institute of M I T and Harvard, 7 Cambridge Center
    Nature 463:899-905. 2010
    ..Finally, we demonstrate that a large majority of SCNAs identified in individual cancer types are present in several cancer types...
  42. pmc The UCSC Genome Browser database: update 2011
    Pauline A Fujita
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 39:D876-82. 2011
    ..New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. We also describe updates to existing tracks...
  43. pmc IMG: the Integrated Microbial Genomes database and comparative analysis system
    Victor M Markowitz
    Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA
    Nucleic Acids Res 40:D115-22. 2012
    ..jgi.doe.gov/er), teaching courses and training in microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu) and analysis of genomes related to the Human Microbiome Project (IMG/HMP: http://www.hmpdacc-resources.org/img_hmp)...
  44. ncbi Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
    Nathaniel D Heintzman
    Ludwig Institute for Cancer Research, University of California San Diego UCSD School of Medicine, 9500 Gilman Drive, La Jolla, California 92093 0653 USA
    Nat Genet 39:311-8. 2007
    ..Our results give insight into the connections between chromatin modifications and transcriptional regulatory activity and provide a new tool for the functional annotation of the human genome...
  45. pmc Accurate whole human genome sequencing using reversible terminator chemistry
    David R Bentley
    Illumina Cambridge Ltd Formerly Solexa Ltd, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex CB10 1XL, UK
    Nature 456:53-9. 2008
    ..Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications...
  46. pmc The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
    Ross Overbeek
    Fellowship for Interpretation of Genomes, 15W155 81st Street, Burr Ridge, IL 60527, USA
    Nucleic Acids Res 33:5691-702. 2005
    ..The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms...
  47. ncbi 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
    ....
  48. pmc Patterns of somatic mutation in human cancer genomes
    Christopher Greenman
    Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 446:153-8. 2007
    ..Systematic sequencing of cancer genomes therefore reveals the evolutionary diversity of cancers and implicates a larger repertoire of cancer genes than previously anticipated...
  49. pmc The Arabidopsis Information Resource (TAIR): gene structure and function annotation
    David Swarbreck
    Carnegie Institution, Department of Plant Biology, 260 Panama St, Stanford, CA 94305, USA
    Nucleic Acids Res 36:D1009-14. 2008
    ..A total of 681 new genes and 1002 new splice variants were added. Overall, 10,098 loci (one-third of all loci from the previous TAIR6 release) were updated for the TAIR7 release...
  50. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  51. pmc Entrez Gene: gene-centered information at NCBI
    Donna Maglott
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20852, USA
    Nucleic Acids Res 39:D52-7. 2011
    ....
  52. 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
    ....
  53. pmc Integration of biological networks and gene expression data using Cytoscape
    Melissa S Cline
    Institut Pasteur, 25 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
    Nat Protoc 2:2366-82. 2007
    ..protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest...
  54. pmc Predicting the functional impact of protein mutations: application to cancer genomics
    Boris Reva
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, NY 10065, USA
    Nucleic Acids Res 39:e118. 2011
    ..In addition, we estimate that at least 5% of cancer-relevant mutations involve switch of function, rather than simply loss or gain of function...
  55. ncbi An integrated semiconductor device enabling non-optical genome sequencing
    Jonathan M Rothberg
    Ion Torrent by Life Technologies, Suite 100, 246 Goose Lane, Guilford, Connecticut 06437, USA
    Nature 475:348-52. 2011
    ..We show the performance of the system by sequencing three bacterial genomes, its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome...
  56. pmc The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
    Peter Schattner
    Department of Biomolecular Engineering and the UCSC RNA Center, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 33:W686-9. 2005
    ..The tRNAscan-SE, snoscan and snoGPS servers are available at http://lowelab.ucsc.edu/tRNAscan-SE/, http://lowelab.ucsc.edu/snoscan/ and http://lowelab.ucsc.edu/snoGPS/, respectively...
  57. pmc Mapping copy number variation by population-scale genome sequencing
    Ryan E Mills
    Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, USA
    Nature 470:59-65. 2011
    ..Our analytical framework and SV map serves as a resource for sequencing-based association studies...
  58. pmc WebGestalt: an integrated system for exploring gene sets in various biological contexts
    Bing Zhang
    Graduate School in Genome Science and Technology, University of Tennessee Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Nucleic Acids Res 33:W741-8. 2005
    ..Exploration of all the 48 gene sets using WebGestalt is available for the public at http://genereg.ornl.gov/webgestalt/wg_enrich.php...
  59. pmc Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
    William McLaren
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Bioinformatics 26:2069-70. 2010
    ..In Ensembl, a web-based tool (the SNP Effect Predictor) and API interface can now functionally annotate variants in all Ensembl and Ensembl Genomes supported species...
  60. pmc Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes
    Geoffrey L Winsor
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
    Nucleic Acids Res 39:D596-600. 2011
    ..aids analysis of phenotypic variation between closely related isolates and strains, as well as wider population genomics and evolutionary studies...
  61. pmc The human microbiome project
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 449:804-10. 2007
    ..A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease...
  62. pmc ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression
    Helen Parkinson
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 37:D868-72. 2009
    ..ebi.ac.uk/arrayexpress consists of three components: the ArrayExpress Repository--a public archive of functional genomics experiments and supporting data, the ArrayExpress Warehouse--a database of gene expression profiles and other bio-..
  63. pmc Population genomics of domestic and wild yeasts
    Gianni Liti
    Institute of Genetics, Queen s Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
    Nature 458:337-41. 2009
    ....
  64. ncbi Principles and challenges of genomewide DNA methylation analysis
    Peter W Laird
    USC Epigenome Center, University of Southern California, Keck School of Medicine, Los Angeles, 90089 9601, USA
    Nat Rev Genet 11:191-203. 2010
    ..This Review discusses the different approaches and their relative merits and introduces considerations for data analysis...
  65. pmc BreakDancer: an algorithm for high-resolution mapping of genomic structural variation
    Ken Chen
    The Genome Center, Washington University School of Medicine, St Louis, Missouri, USA
    Nat Methods 6:677-81. 2009
    ..BreakDancer sensitively and accurately detected indels ranging from 10 base pairs to 1 megabase pair that are difficult to detect via a single conventional approach...
  66. 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
    ..Overall, despite a very high gene flow, genes co-exist in an organised genome...
  67. pmc The sequence and de novo assembly of the giant panda genome
    Ruiqiang Li
    BGI Shenzhen, Shenzhen 518083, China
    Nature 463:311-7. 2010
    ....
  68. ncbi Widespread changes in protein synthesis induced by microRNAs
    Matthias Selbach
    Max Delbruck Center for Molecular Medicine, Robert Rossle Str 10, D 13125 Berlin, Germany
    Nature 455:58-63. 2008
    ..Finally, our data suggest that a miRNA can, by direct or indirect effects, tune protein synthesis from thousands of genes...
  69. pmc Metagenomic analysis of the human distal gut microbiome
    Steven R Gill
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 312:1355-9. 2006
    ..Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes...
  70. pmc eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
    Sean Powell
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 40:D284-9. 2012
    ..Each group is amended by multiple sequence alignments and maximum-likelihood trees and broad functional descriptions are provided for 450,904 orthologous groups (62.5%)...
  71. pmc STRING 8--a global view on proteins and their functional interactions in 630 organisms
    Lars J Jensen
    European Molecular Biology Laboratory, Heidelberg, Germany
    Nucleic Acids Res 37:D412-6. 2009
    ..Version 8.0 of STRING covers about 2.5 million proteins from 630 organisms, providing the most comprehensive view on protein-protein interactions currently available. STRING can be reached at http://string-db.org/...
  72. pmc GAGE: A critical evaluation of genome assemblies and assembly algorithms
    Steven L Salzberg
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Genome Res 22:557-67. 2012
    ..To enable others to replicate our results, all of our data and methods are freely available, as are all assemblers used in this study...
  73. pmc GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics
    Daniel Tabas-Madrid
    Functional Bioinformatics Group, National Center for Biotechnology CNB CSIC, Madrid, Spain
    Nucleic Acids Res 40:W478-83. 2012
    ..in 2007, GeneCodis has become a valuable tool to functionally interpret results from experimental techniques in genomics. This web-based application integrates different sources of information to finding groups of genes with similar ..
  74. pmc NCBI GEO: archive for high-throughput functional genomic data
    Tanya Barrett
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
    Nucleic Acids Res 37:D885-90. 2009
    ..This article summarizes the GEO repository structure, content and operating procedures, as well as recently introduced data mining features. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/...
  75. pmc The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
    Ioanna Pagani
    Department of Energy Joint Genome Institute, Microbial Genomics and Metagenomics Program, 2800 Mitchell Drive, Walnut Creek, CA, USA
    Nucleic Acids Res 40:D571-9. 2012
    ....
  76. pmc Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium
    Li Jun Ma
    The Broad Institute, Cambridge, Massachusetts 02141, USA
    Nature 464:367-73. 2010
    ..oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective...
  77. pmc Diversity of human copy number variation and multicopy genes
    Peter H Sudmant
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
    Science 330:641-6. 2010
    ..Our approach makes ~1000 genes accessible to genetic studies of disease association...
  78. pmc Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx
    Eli Meyer
    University of Texas at Austin, 1 University Station C0930, Austin, TX 78712, USA
    BMC Genomics 10:219. 2009
    ..To facilitate genomics studies in corals and other non-model systems, we describe methods for transcriptome sequencing using 454, as ..
  79. ncbi Tumour evolution inferred by single-cell sequencing
    Nicholas Navin
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Nature 472:90-4. 2011
    ..In contrast to gradual models of tumour progression, our data indicate that tumours grow by punctuated clonal expansions with few persistent intermediates...
  80. pmc The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
    David Warde-Farley
    Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
    Nucleic Acids Res 38:W214-20. 2010
    ..Given a query list, GeneMANIA extends the list with functionally similar genes that it identifies using available genomics and proteomics data...
  81. pmc GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists
    Eran Eden
    Molecular Cell Biology Department, Weizmann Institute of Science, Rehovot, Israel
    BMC Bioinformatics 10:48. 2009
    ..A few tools also exist that support analyzing ranked lists. The latter typically rely on simulations or on union-bound correction for assigning statistical significance to the results...
  82. pmc Genome remodelling in a basal-like breast cancer metastasis and xenograft
    Li Ding
    The Genome Center at Washington University, St Louis, Missouri 63108, USA
    Nature 464:999-1005. 2010
    ..The differential mutation frequencies and structural variation patterns in metastasis and xenograft compared with the primary tumour indicate that secondary tumours may arise from a minority of cells within the primary tumour...
  83. 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...
  84. ncbi Advances in understanding cancer genomes through second-generation sequencing
    Matthew Meyerson
    Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
    Nat Rev Genet 11:685-96. 2010
    ..through whole-genome, whole-exome and whole-transcriptome approaches - is allowing substantial advances in cancer genomics. These methods are facilitating an increase in the efficiency and resolution of detection of each of the ..
  85. ncbi Next-generation DNA sequencing
    Jay Shendure
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195 5065, USA
    Nat Biotechnol 26:1135-45. 2008
    ....
  86. ncbi A new multipoint method for genome-wide association studies by imputation of genotypes
    Jonathan Marchini
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    Nat Genet 39:906-13. 2007
    ..A notable future use of our method will be to boost power by combining data from genome-wide scans that use different SNP sets...
  87. ncbi Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)
    S D Bentley
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 417:141-7. 2002
    ..The genome sequence will greatly increase our understanding of microbial life in the soil as well as aiding the generation of new drug candidates by genetic engineering...
  88. 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...
  89. ncbi Principal components analysis corrects for stratification in genome-wide association studies
    Alkes L Price
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 38:904-9. 2006
    ..Our simple, efficient approach can easily be applied to disease studies with hundreds of thousands of markers...
  90. pmc Limitations of next-generation genome sequence assembly
    Can Alkan
    Department of Genome Sciences, University of Washington School of Medicine and Howard Hughes Medical Institute, Seattle, Washington, USA
    Nat Methods 8:61-5. 2011
    ..We conclude that high-quality sequencing approaches must be considered in conjunction with high-throughput sequencing for comparative genomics analyses and studies of genome evolution.
  91. ncbi Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series
    Christine Desmedt
    Institut Jules Bordet, Universite Libre de Bruxelles, Brussels, Belgium
    Clin Cancer Res 13:3207-14. 2007
    ..The aims of this study conducted by TRANSBIG were to independently validate these results and to compare the outcome with clinical risk assessment...
  92. pmc EcoCyc: a comprehensive view of Escherichia coli biology
    Ingrid M Keseler
    SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
    Nucleic Acids Res 37:D464-70. 2009
    ..A new advanced query page guides users in interactively constructing complex database queries against EcoCyc. A Macintosh version of EcoCyc is now available. A series of Webinars is available to instruct users in the use of EcoCyc...
  93. pmc Integrative genomics identifies MCU as an essential component of the mitochondrial calcium uniporter
    Joshua M Baughman
    Department of Systems Biology, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
    Nature 476:341-5. 2011
    ..Our genomic, physiological, biochemical and pharmacological data firmly establish MCU as an essential component of the mitochondrial Ca(2+) uniporter...
  94. pmc Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism
    Simon W Baxter
    Department of Zoology, University of Cambridge, Cambridge, United Kingdom
    PLoS ONE 6:e19315. 2011
    ..mori chromosomes shows for the first time, genetic synteny appears common beyond the Macrolepidoptera. RAD sequencing is a powerful system capable of rapidly generating chromosome specific data for non-model organisms...
  95. pmc Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database
    Tim Carver
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Bioinformatics 24:2672-6. 2008
    ..Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences...
  96. ncbi Functional metagenomic profiling of nine biomes
    Elizabeth A Dinsdale
    Department of Biology, San Diego State University, San Diego, California 92182, USA
    Nature 452:629-32. 2008
    ....
  97. pmc PlasmoDB: a functional genomic database for malaria parasites
    Cristina Aurrecoechea
    Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
    Nucleic Acids Res 37:D539-43. 2009
    ..Various results can then be combined with each other on the query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis...
  98. pmc ENCODE whole-genome data in the UCSC Genome Browser
    Kate R Rosenbloom
    Center for Biomolecular Science and Engineering, School of Engineering, University of California, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 38:D620-5. 2010
    ..The UCSC Genome Browser Database: update 2010, in this issue). The ENCODE web portal at UCSC (http://encodeproject.org or http://genome.ucsc.edu/ENCODE) provides information about the ENCODE data and convenient links for access...
  99. pmc MEME-ChIP: motif analysis of large DNA datasets
    Philip Machanick
    Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
    Bioinformatics 27:1696-7. 2011
    ..While there are many existing tools for discovering TF binding site motifs in such datasets, most web-based tools cannot directly process such large datasets...

Research Grants77

  1. TRAINING PROGRAM IN GENETICS AND GENOMICS
    William Gelbart; Fiscal Year: 2006
    ..Museum of Comparative Zoology and Herbarium, and,within two years, a new facility housing the Center for Genomics Research. The application includes significant changes and enhancements to the program...
  2. Discovery metabolite profiling of the prolyl peptidases
    Alan Saghatelian; Fiscal Year: 2009
    ..Furthermore, the application of DMP to peptidases will demonstrate the generality of this approach for the future characterization of medically relevant enzymes and signaling pathways. ..
  3. Genetic variation and regulatory networks: Mechanisms and complexity
    DANA PE ER; Fiscal Year: 2009
    ..Our approach is based on the complementary duality between genetic sequence and functional genomics. A significant influence of genotype on phenotype is induced by fine tuned perturbations to the complex ..
  4. 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 ..
  5. Personalized Clinical Diagnostics and Beyond: Integrated Ring Resonator Arrays
    Ryan Bailey; Fiscal Year: 2009
    ABSTRACT Paradigm shifts in biology are often catalyzed by innovations in measurement technologies. Genomics and proteomics have revolutionized biology but would not have been possible without developments in capillary sequencing, cDNA ..
  6. Discovery of Small Molecule MBT Domain Antagonists
    STEPHEN VERNON FRYE; Fiscal Year: 2010
    ..Indeed, the Structural Genomics Consortium (SGC) has recently announced their intention to focus heavily on epigenetics and creation of chemical ..
  7. Immunomodulatory and regenerative effects of mesenchymal stem cells on allografts
    Norma S Kenyon; Fiscal Year: 2013
    ..monkey models of cellular (Project 1) and solid organ (Project 2) allotransplantation, in conjunction with genomics and proteomics to define MSC product release criteria and potential biomarkers (Core B), as well as sophisticated ..
  8. Genetics and Haloperidol Response
    Robert J Hitzemann; Fiscal Year: 2012
    ..of QTLs in heterogeneous stock [HS] animals, the integration of QTL analysis, sequence data and functional genomics, high throughput DNA sequencing, the use of short term selective breeding to confirm the role of Drd2 network ..
  9. Comparative Resistance Exercise Effects on Knee Osteoarthritis Pain, Functional I
    KEVIN ROBERT VINCENT; Fiscal Year: 2013
    ..study will also utilize the research cores (Recruitment, Clinical Research, Biostatistic and Data Management, and Genomics and Biomarkers) of the OAIC within the UF Institute on Aging, and the resources of the Clinical and translational ..
  10. Functional Genomics of the Mitochondrial Proteome
    Dennis R Winge; Fiscal Year: 2011
    ..The function of up to 30% of the mitochondrial proteome is unknown. This proposal will elucidate the function of these un-annotated mitochondrial proteins, providing new insights into the role of mitochondria in human disease. ..
  11. Mucosal Immunity, Vaccines and Microbiota Interplay in Humans and Animal
    Marcelo B Sztein; Fiscal Year: 2013
    ..molecular biology, mucosal biology and physiology, biochemistry, high-throughput technology, microbiology, genomics, protein chemistry and clinical gastroenterology and vaccinology (with extensive experience in performing ..
  12. Vitamin D Hormone Signaling in Bone Mineral Homeostasis
    Mark R Haussler; Fiscal Year: 2010
    ..Methodology will include genomics and chromatin immunoprecipitation (ChIP) assays to scan for candidate VDREs, plus DNA gel mobility shift, real ..
  13. AMERICAN SOCIETY OF HUMAN GENETICS PUBLIC HEALTH GENETICS FELLOWSHIP
    Joann A Boughman; Fiscal Year: 2011
    ..and Prevention (CDC)to train highly qualified genetics professional in the arena of public health genetics and genomics. ASHG and CDC will provide senior staff members to serve as co-directors and mentors for the program...
  14. Molecular Markers for Progression of Pulmonary Fibrosis in Systemic Sclerosis
    Shervin Assassi; Fiscal Year: 2013
    ..didactic curriculum complements the candidate's prior training in the Master's program with courses in genomics and proteomics, longitudinal and Bayesian data analysis, bioethics and advanced grant writing...
  15. Genomics of Antiviral Responses of Anopheles gambiae Against O'nyong-nyong Virus
    Young S Hong; Fiscal Year: 2010
    ..To this end, comparative genomics of orthologs of anti-ONNV genes of other arboviral mosquito vectors can be subsequently investigated as an ..
  16. Interdisciplinary Research Training in Reproduction for Indian Fellows
    John C Herr; Fiscal Year: 2010
    ..for scientific purposes to improve writing and communication skills, recombinant DMA technology, structural genomics, pharmacology, bioethics, and drug discovery, design, synthesis, and selection...
  17. Environmental Risk Factors for Copy Number Variation in Human Chromosomes
    THOMAS EDWARD WILSON; Fiscal Year: 2010
    This application addresses broad Challenge Area, (08) Genomics and Specific Challenge Topic, 08-ES-106: The role of environmental exposure in copy number variation (CNV): "Microscopic deletions and replications of the genome have ..
  18. VACCINE INDUCED IMMUNITY IN THE YOUNG AND AGED
    Rafi Ahmed; Fiscal Year: 2013
    ..A major emphasis of this proposal was to use genomics to define molecular signatures of a successful vaccine, and to use this knowledge to develop new vaccines against ..
  19. Endotoxin, the airway transcriptome, and obstructive lung disease
    PEGGY SUE LAI; Fiscal Year: 2013
    ..career objectives are to obtain further didactic training in environmental epidemiology, advanced biostatistics, genomics, and data mining, as well as practical skills in building a cohort, exposure assessment, obtaining biospecimens, ..
  20. Non-coding RNA engineers antibody diversity
    Uttiya Basu; Fiscal Year: 2011
    ..Here, we use a combination of modern computational biology, proteomics, high-throughput genomics and mouse genetics to identify and functionally characterize ncRNA generated in the Ig locus during affinity ..
  21. Effects of In Utero and Transgenerational Exposure of Avy Mice to Bisphenol A
    CHERYL SUSAN ROSENFELD; Fiscal Year: 2010
    This application addresses broad Challenge Area (08) Genomics and specific Challenge Topic, 08-ES-104, Identification of alterations in epigenetic marks related to environmental exposures...
  22. High throughput screen for selective inhibitors of cyclophilin B
    Richard J Bram; Fiscal Year: 2013
    ..with the high-throughput screening and medicinal chemistry expertise at the Conrad Prebys Center for Chemical Genomics (CPCCG) at the Sanford-Burnham Medical Research Institute (SBMRI), to identify and refine compounds that ..
  23. Epigenetic Analysis of iPS Cell Models of Aging and Alzheimer's Disease
    Bruce A Yankner; Fiscal Year: 2010
    ..project will bring together a multidisciplinary team with broad expertise in neurobiology, disease biology and genomics from Harvard Medical School, the Dana Farber Cancer Institute and the Broad Institute to characterize iPS cell ..
  24. Insights from Comparative Genomics for the Treatment of Pneumococcal Infections
    Natalia Luisa Hiller; Fiscal Year: 2011
    ..on bacterially- induced otitis media and the development of a suite of bioinformatic tools for comparative genomics to identify genotype-phenotype correlations...
  25. Analysis of epigenetic regulation in early mammalian embryos via RNA interference
    Charles R Long; Fiscal Year: 2010
    ..We will test our hypothesis by using RNA interference to study the functional genomics of epigenetic reprogramming in an established model of in vitro embryo development...
  26. Roles of RNA Polymerases IV and V in siRNA-mediated gene silencing
    CRAIG STUART PIKAARD; Fiscal Year: 2013
    ..subunits of Pol II, Pol IV and Pol V confer the unique functions of these novel polymerases? Using genetics and genomics as well as cell biological and biochemical approaches, our specific aims are designed to find answers to these ..
  27. Exploring persistent epigenetic changes after prenatal famine exposure in humans
    L H Lumey; Fiscal Year: 2010
    DESCRIPTION (provided by investigator): This application addresses the broad Challenge Area: 08: Genomics, and the specific Challenge Grant Topic: 08-AG-105**: Approaches to study the interactions among individual behaviors, social and ..
  28. Developing miRNA diagnostic methods and identifying tumor regulatory networks
    Thomas Tuschl; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): This application addresses Broad Challenge Area (08) Genomics and Specific Challenge Topic 08-CA-103: Micro-RNAs in Cancer...
  29. Insights from Comparative Genomics for the Treatment of Pneumococcal Infections
    Natalia Luisa Hiller; Fiscal Year: 2013
    ..on bacterially- induced otitis media and the development of a suite of bioinformatic tools for comparative genomics to identify genotype-phenotype correlations...
  30. A Rapid Point-of-care Diagnostic for C.trachomitis STDs
    RICHARD F contact SELDEN; Fiscal Year: 2010
    ..ulcer, vaginal and rectal samples;2) Expand our primer design to identify strain types based on comparative genomics of reference and clinical chlamydial STD strains (essential for directing therapy for invasive versus non-..
  31. Genome-wide measurement of bacterial transcriptional regulatory states
    Peter L Freddolino; Fiscal Year: 2013
    ..In the era of genomics, proteomics, and metabolomics, however, biologists are still bereft of a generally applicable method for rapid ..
  32. Functional roles of Nrf2 and NQO1 genetic variants in hyperoxic lung injury-ARDS
    Bhagavatula Moorthy; Fiscal Year: 2013
    ..Omics'approaches, including genomics (microarrays) and proteomics approaches will be used to determine the molecular mechanisms by which Nrf2 or NQO1 ..
  33. Anti- IL5 therapy for Churg-Strauss Syndrome: a double blind randomized, placebo-
    Michael E Wechsler; Fiscal Year: 2010
    ..g. biomarkers, genomics)...
  34. Transposons in Female Reproductive Health and Disease
    Zev Williams; Fiscal Year: 2013
    ..Over the course of this award period he will expand his proficiency in genomics, RNA biology, assay design and computational biology with the overarching goal of elucidating the effect of ..
  35. Integrative Pathway Analysis of Epigenomic/transcriptional Alteration in HNSCC
    Joseph A Califano; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): This application addresses broad Challenge Area (08) Genomics Topic: 08-DE-103: Epigenomics and Epigenetics of Oral Health and Disease The standard paradigm for characterization of genome wide ..
  36. Abdominal Symptom Phenotypes: Pathways to New Biomarkers
    Robert Shulman; Fiscal Year: 2010
    ..3) Advances in high throughput genomics and proteomics have increased the potential for new biomarkers including urine proteomics...
  37. Trophoblast MHC-I: Trigger for Immune-Mediated Rejection of Cloned Bovine Fetuses
    Kenneth L White; Fiscal Year: 2011
    ..This project will elucidate the functional genomics of the cross-talk between the placenta and uterine immune system in normal and abnormal pregnancies...
  38. Genomics of RNA Editing: Identification and Regulation
    Jin Billy Li; Fiscal Year: 2013
    ....
  39. Research Career Development in Child Health
    Michael W Konstan; Fiscal Year: 2012
    ..The technologies and methodologies to address these questions include genomics, proteomics, metabolomics, bioimaging, cell and molecular biology, bioinformatics, in vivo approaches including ..
  40. CSHL 2010 Conference on Molecular Genetics and Bacteria & Phages
    David J Stewart; Fiscal Year: 2010
    ..In recent years, efforts have been made to include emerging areas such as genomics and metagenomics, sociomicrobiology, molecular ecology, structural biology and systems analysis...
  41. ALS therapies and genomics for mutant TDP-43 and TLS/FUS
    Don W Cleveland; Fiscal Year: 2010
    ..therapy development) and 15-NS-103 (Demonstration of "proof-of-concept") and Broad Challenge area (08) Genomics, specific Challenge Topic 03-NS-101 (Cross-disease research to identify mechanisms common to Mendelian disorders ..
  42. OLFACTORY RECEPTOR COPY NUMBER ASSOCIATION WITH AGE AT ONSET OF ALZHEIMER DISEASE
    Kinga Szigeti; Fiscal Year: 2013
    ..These skills will provide an opportunity to become an independent scientist in the field of AD genomics, and to have the knowledge that is required to implement these discoveries into clinical practice irrespective of ..
  43. 2012 CSHL Bacteria &Phages Conference
    David J Stewart; Fiscal Year: 2012
    ..In recent years, efforts have been made to include emerging areas such as genomics and metagenomics, sociomicrobiology, molecular ecology, structural biology and systems analysis...
  44. Prevention and therapy of Staphylococcus aureus infections
    Olaf Schneewind; Fiscal Year: 2010
    ..The project also addresses Theme 1 (Applying Genomics and Other High Throughput Technologies) through the systematic analysis of human B cell responses as well as ..
  45. DNA methylation alterations in response to pesticides exposure
    Lifang Hou; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): This application addresses broad Challenge Area (08) Genomics and specific Challenge Topic, 08-ES-104: Identification of alterations in epigenetic marks related to environmental exposures...
  46. Haemophilus influenzae iron/heme regulon
    Terrence L Stull; Fiscal Year: 2012
    ..We propose a genomics analysis to define the genes whose expression is regulated by iron and heme levels (the FeHm regulon) and to ..
  47. Forward Genetics to Identify Complex Gene Interactions Involved in Glaucoma
    Elena V Semina; Fiscal Year: 2010
    This application is in response to (08) Genomics 09-EY-101: Genomics of complex eye diseases...
  48. Generation of Site-Specific Recombinase-Expressing Transgenic Rats using an Enhan
    Eric M Ostertag; Fiscal Year: 2011
    ..a method to identify new transcribed elements would accelerate a comprehensive understanding of mammalian genomics. Gene trap mutagenesis is a standard approach for identifying and exploiting new transcription units, but ..
  49. The Role of Long Non-coding RNAs in EMT and Cancer Stem Cells
    Jason I Herschkowitz; Fiscal Year: 2013
    ..Jason's graduate training has provided him with an expertise in cancer genomics and mouse models...
  50. Translating human PPARy binding regions to gene regulation and metabolic disease
    RAYMOND EDWARD SOCCIO; Fiscal Year: 2013
    ..The career development plan includes training in genomics, bioinformatics, and computational biology, since a thorough understanding of these burgeoning fields will be ..
  51. Ethnic/Racial Variation in Intracerebral Hemorrhage (ERICH)
    Daniel Woo; Fiscal Year: 2013
    ..will be developed for centralized DNA processing and sample handling at the Miami Institute for Human Genomics. And a data and statistical center will be developed at Wake Forest University...
  52. Identification of Disease-Causing Mutations in SCID Using Exome-Wide Sequencing
    Joseph L Roberts; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): This application addresses broad Challenge Area #8, Genomics, and specific Challenge Topic 08-HL-101, which seeks to identify causal genetic variants associated with heart, lung, and blood diseases by ..
  53. A Systems Biology Approach to the Model Apicomplexan Toxoplasma gondii
    William J Sullivan Jr; Fiscal Year: 2010
    ..It uses genomics and other high throughput technologies (thematic area 1) with a systems-level integration, analysis and mining of ..
  54. Translational Approaches to Reducing Health Disparities in Lung Disease
    Joe G N Garcia; Fiscal Year: 2012
    ..With the recent advances in genomics and DNA sequencing technologies, and targeted personalized medicine;tremendous progress has been made, however, ..
  55. Functional Genomics Approach to the Role of the JAK/STAT and MAPK Pathway in CBD
    Li Li; Fiscal Year: 2013
    ..There, she developed proficiency in genomics, and the immunopathogenic mechanisms of CBD. With Dr...
  56. Role of Central Neural NFkB and ER Stress in Obesity-induced Hypertension
    COLIN NEAL YOUNG; Fiscal Year: 2013
    ..In addition to advanced training in genomics, molecular biology and whole animal cardiovascular and autonomic physiology, the mentored guidance of Dr...
  57. The Effect of Gastric Bypass Surgery on Renal Function and Metabolism
    Benjamin K Canales; Fiscal Year: 2013
    ..injury and nephrolithiasis, with special focus on renal histology, transport physiology, tissue proteomics, and genomics. Our specific aims are: 1) To further characterize renal effects of RYGB surgery in a diet-induced obese rodent ..
  58. FASEB SRC on Hematopoietic Malignancies
    MICHELLE ALICE KELLIHER; Fiscal Year: 2011
    ..of the human genome project in investigations of hematological malignancies, with an emphasis on functional genomics;7) Application of systems biology approaches to hematopoietic malignancies and LSC biology;and 8) Recent ..
  59. Mutational Cloning in Familial Dementia and Alzheimers Disease
    Wendy H Raskind; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): This application addresses Broad Challenge Area (08) Genomics and Specific Challenge Topic 08-AG-106 Cross-disease research to identify commonly targeted pathways or mechanisms between low incidence, ..
  60. FASEB SRC on Yeast Chromosome Structure, Replication and Segregation
    Scott Keeney; Fiscal Year: 2012
    ..pombe, using a range of experimental approaches including genetics, cytology, biochemistry, molecular biology, genomics, and systems biology...
  61. Genome-Wide Analysis of RXR-alpha Binding In Mouse Liver Chromatin with ChIP-SEQ
    SAUL JOSEPH KARPEN; Fiscal Year: 2010
    ..in mouse liver chromatin with ChIP-SEQ Abstract: This proposal will address core items in Challenge Area 08 (Genomics), specifically targeting Challenge Topic 08-DK-107, Nuclear receptor mediated assembly of functional ..
  62. Molecular pathogenesis and genetic diversification of childhood falciparum malari
    STEVE MYER TAYLOR; Fiscal Year: 2013
    ..and 2) guidance from a Scientific Advisory Committee of more senior investigators in microbial pathogenesis and genomics from UNC, Duke University, and NIAID...
  63. The Thrifty Microbiome: The Role of the Gut Microbiota in Obesity in the Amish
    Alan R Shuldiner; Fiscal Year: 2010
    ..the relationship between gut microbiota and metabolic and cardiovascular disease traits, weight change, and host genomics in 1,000 Amish already characterized for these traits and in whom 500K Affymetrix SNP chips have already been ..
  64. Bioconductor: an open computing resource for genomics
    Martin Morgan; Fiscal Year: 2010
    ..While that type of "success measure" is hard to assess, more effort in this area in subsequent proposals would be helpful. ..
  65. Community Voices on Health Disparities and Translational Genomics Research
    Patricia A Marshall; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): Community Voices on Health Disparities and Translational Genomics Research Challenge Area and Specific Challenge Topic: The Challenge Area this research addresses is 02: Bioethics and the Specific ..
  66. CSHL Conference on Mouse Development, Genetics and Genomics
    David J Stewart; Fiscal Year: 2010
    ..The proposed meeting on "Mouse Development Genetics &Genomics" will assemble leaders in the field, junior faculty, postdoctoral fellows, and graduate students to discuss the ..
  67. 2009 NHP Models for AIDS Conference
    Amitinder Kaur; Fiscal Year: 2009
    ..The latest findings in primate pathogenesis, immunology, genomics, virology, vaccines and therapeutics will be presented...
  68. ELSI Issues: Colon Cancer and Cancer Genomics Research
    Patricia A Marshall; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): The promise of large-scale cancer genomics research and its translation to clinical settings can only be achieved with the support and involvement of the public...
  69. Developing Information Infrastructure Focused on Cancer Comparative Effectiveness
    DAVID ALAN FENSTERMACHER; Fiscal Year: 2010
    DESCRIPTION (Provided by the applicant): Progress in cancer genomics offers the possibility of ushering in a new era of personalized medicine. Specifically in cancer, different cancers can now be distinguished by their molecular profile...
  70. Novel estrogen receptor ligands from plant genomics
    John M Littleton; Fiscal Year: 2012
    ..The primary aim of this STTR is to transfer an "academic" plant genomics technology into drug discovery, targeting HNR ligands...
  71. GENOMICS, PROTEOMICS, BIOINFORMATICS & DEVELOPMENTAL TOX
    Philip Mirkes; Fiscal Year: 2000
    Recent developments in the fields of genomics, proteomics, and bioinformatics offer the potential to undertake global analyses of gene and protein expression...
  72. Evolutionary Genomics of Supersized Mitochondrial Genomes
    ANDREW ALVERSON; Fiscal Year: 2009
    ..One common and frustrating theme in plant mitochondrial genomics is that the overwhelming majority of size variation is due to large amounts of intergenic DNA with no ..
  73. MT INBRE BIOINFORMATICS CORE
    MICHAEL ROGER FRANKLIN; Fiscal Year: 2011
    ..and Jean Starkey and assisted by Informatics Coordinator Kate McInnerney, the MT INBRE Bioinformatics and Genomics Core provides investigators in the Research Core as well as faculty and students across the network and other ..
  74. MOLECULAR TARGETS OF BLOCKING MALARIA TRANSMISSION
    Joseph Vinetz; Fiscal Year: 2005
    ..Vinetz to have protected time to focus intensively on adapting advanced approaches in bioinformatics, genomics and cell biology to his ongoing, NIH-funded studies of malaria parasite biology...
  75. Functional Genomics Study and Database for Tuberculosis
    Li Fu; Fiscal Year: 2006
    The functional genomics of Mycobacterium tuberculosis will be studied and a database will be constructed for both scientific and clinical applications...
  76. Biochemical Genomics Linking Genes and Activities
    Eric Phizicky; Fiscal Year: 2004
    DESCRIPTION (Applicant's Abstract): A rapid, sensitive and widely applicable biochemical genomics approach has recently been developed to identify genes from the yeast Saccharomyces cerevisiae that specify biochemical activities...
  77. DUKE/NIDDK FUNCTIONAL GENOMICS CENTER
    Joseph Nevins; Fiscal Year: 2002
    DESCRIPTION (Abstract of the application) We propose-the development of an NIDDK Center for Functional Genomics at Duke University Medical Center to provide technology and resource support for the large scale analysis of gene expression...