T R Gingeras

Summary

Affiliation: Affymetrix Inc
Country: USA

Publications

  1. ncbi request reprint Genome-wide analysis of estrogen receptor binding sites
    Jason S Carroll
    Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney St, Boston, Massachusetts 02115, USA
    Nat Genet 38:1289-97. 2006
  2. ncbi request reprint Genome-wide transcription and the implications for genomic organization
    Philipp Kapranov
    Affymetrix, Inc, 3420 Central Expressway, Santa Clara, California 95051, USA
    Nat Rev Genet 8:413-23. 2007
  3. pmc Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments
    Srinka Ghosh
    Affymetrix Inc, Santa Clara, CA 95051, USA
    BMC Bioinformatics 7:434. 2006
  4. pmc Differential analysis for high density tiling microarray data
    Srinka Ghosh
    Affymetrix Inc, Santa Clara, CA 95051, USA
    BMC Bioinformatics 8:359. 2007
  5. ncbi request reprint Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays
    T R Gingeras
    Affymetrix, Santa Clara, California 95051, USA
    Genome Res 8:435-48. 1998
  6. ncbi request reprint Origin of phenotypes: genes and transcripts
    Thomas R Gingeras
    Affymetrix, Inc, Santa Clara, California 95051, USA
    Genome Res 17:682-90. 2007
  7. ncbi request reprint Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
    Jill Cheng
    Affymetrix Inc, Santa Clara, CA 95051, USA
    Science 308:1149-54. 2005
  8. pmc Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation
    S Dong
    Affymetrix, Inc, Santa Clara, California 95051, USA
    Genome Res 11:1418-24. 2001
  9. ncbi request reprint Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
    Simon Cawley
    Affymetrix, 3380 Central Expressway, Santa Clara, CA 95051, USA
    Cell 116:499-509. 2004
  10. ncbi request reprint Large-scale transcriptional activity in chromosomes 21 and 22
    Philipp Kapranov
    Affymetrix, Santa Clara, CA 95051, USA, National Cancer Institute, Bethesda, MD 20892, USA
    Science 296:916-9. 2002

Research Grants

Detail Information

Publications40

  1. ncbi request reprint Genome-wide analysis of estrogen receptor binding sites
    Jason S Carroll
    Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney St, Boston, Massachusetts 02115, USA
    Nat Genet 38:1289-97. 2006
    ..Furthermore, this resource has allowed the identification of cis-regulatory sites in previously unexplored regions of the genome and the cooperating transcription factors underlying estrogen signaling in breast cancer...
  2. ncbi request reprint Genome-wide transcription and the implications for genomic organization
    Philipp Kapranov
    Affymetrix, Inc, 3420 Central Expressway, Santa Clara, California 95051, USA
    Nat Rev Genet 8:413-23. 2007
    ..What are the implications and consequences of such an interleaved genomic architecture in terms of increased information content, transcriptional complexity, evolution and disease states?..
  3. pmc Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments
    Srinka Ghosh
    Affymetrix Inc, Santa Clara, CA 95051, USA
    BMC Bioinformatics 7:434. 2006
    ..The detection and assessment of significance for interactions that emanate from non-canonical and/or un-annotated regions of the genome is especially challenging. This is the motivation behind the proposed algorithm...
  4. pmc Differential analysis for high density tiling microarray data
    Srinka Ghosh
    Affymetrix Inc, Santa Clara, CA 95051, USA
    BMC Bioinformatics 8:359. 2007
    ....
  5. ncbi request reprint Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays
    T R Gingeras
    Affymetrix, Santa Clara, California 95051, USA
    Genome Res 8:435-48. 1998
    ....
  6. ncbi request reprint Origin of phenotypes: genes and transcripts
    Thomas R Gingeras
    Affymetrix, Inc, Santa Clara, California 95051, USA
    Genome Res 17:682-90. 2007
    ..This complex transcriptional organization and other recently observed features of genomes argue for the reconsideration of the term "gene" and suggests that transcripts may be used to define the operational unit of a genome...
  7. ncbi request reprint Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
    Jill Cheng
    Affymetrix Inc, Santa Clara, CA 95051, USA
    Science 308:1149-54. 2005
    ..This organization has important implications for interpreting genotype-phenotype associations, regulation of gene expression, and the definition of a gene...
  8. pmc Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation
    S Dong
    Affymetrix, Inc, Santa Clara, California 95051, USA
    Genome Res 11:1418-24. 2001
    ..With flexible sample preparation, high-density oligonucleotide arrays can be tailored for even larger scale genome-wide SNP discovery as well as validation...
  9. ncbi request reprint Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
    Simon Cawley
    Affymetrix, 3380 Central Expressway, Santa Clara, CA 95051, USA
    Cell 116:499-509. 2004
    ..Thus, the human genome contains roughly comparable numbers of protein-coding and noncoding genes that are bound by common transcription factors and regulated by common environmental signals...
  10. ncbi request reprint Large-scale transcriptional activity in chromosomes 21 and 22
    Philipp Kapranov
    Affymetrix, Santa Clara, CA 95051, USA, National Cancer Institute, Bethesda, MD 20892, USA
    Science 296:916-9. 2002
    ..When compared with the sequence annotations available for these chromosomes, it is noted that as much as an order of magnitude more of the genomic sequence is transcribed than accounted for by the predicted and characterized exons...
  11. ncbi request reprint High density synthetic oligonucleotide arrays
    R J Lipshutz
    Affymetrix, Inc, Santa Clara, California 95051, USA
    Nat Genet 21:20-4. 1999
    ..Here, we describe the fabrication of the arrays, their design and some specific applications to high-throughput genetic and cellular analysis...
  12. pmc Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays
    A Troesch
    bioMerieux, 69280 Marcy l Etoile, France
    J Clin Microbiol 37:49-55. 1999
    ..This parallel testing format opens new perspectives in terms of patient management for bacterial diseases by allowing a number of genetic tests to be simultaneously run...
  13. ncbi request reprint Biological function of unannotated transcription during the early development of Drosophila melanogaster
    J Robert Manak
    Affymetrix, Inc, Santa Clara, California, 95051, USA
    Nat Genet 38:1151-8. 2006
    ..Collectively, these data indicate that at least 85% of the fly genome is transcribed and processed into mature transcripts representing at least 30% of the fly genome...
  14. pmc Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays
    Philipp Kapranov
    Affymetrix Inc, Santa Clara, California 95051, USA
    Genome Res 15:987-97. 2005
    ..These results have important implications concerning the correlation of genotypes to phenotypes, the regulation of complex interlaced transcriptional patterns, and the definition of a gene...
  15. pmc Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22
    Dione Kampa
    Affymetrix, Santa Clara, California 95051, USA
    Genome Res 14:331-42. 2004
    ..These observations strongly support the argument for a re-evaluation of the total number of human genes and an alternative term for "gene" to encompass these growing, novel classes of RNA transcripts in the human genome...
  16. ncbi request reprint Analysis of drug pharmacology towards predicting drug behavior by expression profiling using high-density oligonucleotide arrays
    J S Hu
    Affymetrix, Incorporated, Santa Clara, California 95051, USA
    Ann N Y Acad Sci 919:9-15. 2000
    ..We describe here a strategy that was used to identify a set of genes whose differential expression pattern correlates with activation mode and target specificity of a specific group of drug compounds...
  17. ncbi request reprint 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
    ..These data support a highly interleaved organization of the human transcriptome...
  18. ncbi request reprint Beyond expression profiling: next generation uses of high density oligonucleotide arrays
    Philipp Kapranov
    Affymetrix, Inc, Santa Clara, CA 95051, USA
    Brief Funct Genomic Proteomic 2:47-56. 2003
    ..Integrating all this information will provide novel global views of the locations of RNA transcription, DNA replication and the protein nucleic acid interactions that regulate these processes...
  19. ncbi request reprint TUF love for "junk" DNA
    Aarron T Willingham
    Affymetrix, Inc, Santa Clara, CA 95051, USA
    Cell 125:1215-20. 2006
    ..Study of ncRNAs is increasing our understanding of the organization and regulation of genomes...
  20. pmc Prokaryotic RNA preparation methods useful for high density array analysis: comparison of two approaches
    C Rosenow
    Affymetrix Inc, 3380 Central Expressway, Santa Clara, CA 95051, USA
    Nucleic Acids Res 29:E112. 2001
    ..However, both labeling methods can detect the same relative gene expression changes when RNA from IPTG-induced cells was labeled and compared to RNA from uninduced E.coli cells...
  21. ncbi request reprint Transcriptional landscape of the human and fly genomes: nonlinear and multifunctional modular model of transcriptomes
    A T Willingham
    Affymetrix, Inc, Santa Clara, California 95051, USA
    Cold Spring Harb Symp Quant Biol 71:101-10. 2006
    ..This model illustrates the underappreciated organizational complexity of the genome and one of the functional roles of transcription from unannotated portions of the genome...
  22. ncbi request reprint Microarrays and genetic epidemiology: a multipurpose tool for a multifaceted field
    Dennise D Dalma-Weiszhausz
    Affymetrix, Inc, Santa Clara, California 95051, USA
    Genet Epidemiol 23:4-20. 2002
    ..Although many challenges lie ahead, microarrays' multiple abilities appear uniquely poised to accelerate the advance of genetic epidemiology's multiple fronts...
  23. ncbi request reprint Fifty years of molecular (DNA/RNA) diagnostics
    Thomas R Gingeras
    Affymetrix, Inc, Santa Clara, CA, USA
    Clin Chem 51:661-71. 2005
  24. pmc Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions
    France Denoeud
    Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
    Genome Res 17:746-59. 2007
    ....
  25. pmc The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci
    Joel S Rozowsky
    Molecular Biophysics and Biochemistry Department, Yale University, New Haven, Connecticut 06520 8114, USA
    Genome Res 17:732-45. 2007
    ..Overall, we find that 18 of the 46 connections tested validate by RT-PCR and four of five sequenced PCR products confirm connectivity unambiguously...
  26. ncbi request reprint RNA reference materials for gene expression studies. Difficult first steps
    Thomas R Gingeras
    Clin Chem 50:1289-90. 2004
  27. pmc Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders
    Alvaro Rada-Iglesias
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    Genome Res 18:380-92. 2008
    ..This expands our understanding about the transcriptional control of metabolic processes and its alteration in metabolic disorders...
  28. pmc Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
    David S Johnson
    Department of Genetics, Stanford University Medical Center, Stanford, California 94305, USA
    Genome Res 18:393-403. 2008
    ..The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated...
  29. pmc EGASP: the human ENCODE Genome Annotation Assessment Project
    Roderic Guigo
    Centre de Regulacio Genomica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, E08003 Barcelona, Catalonia, Spain
    Genome Biol 7:S2.1-31. 2006
    ..These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment...
  30. pmc Efficient targeted transcript discovery via array-based normalization of RACE libraries
    Sarah Djebali
    Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
    Nat Methods 5:629-35. 2008
    ....
  31. 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...
  32. doi request reprint Mapping the strand-specific transcriptome of fission yeast
    Thomas R Gingeras
    Nat Genet 40:935-6. 2008
  33. ncbi request reprint Genomic maps and comparative analysis of histone modifications in human and mouse
    Bradley E Bernstein
    Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
    Cell 120:169-81. 2005
    ..This suggests that the DNA elements that direct the methylation represent only a small fraction of the region or lie at some distance from the site...
  34. pmc Structured RNAs in the ENCODE selected regions of the human genome
    Stefan Washietl
    Institute for Theoretical Chemistry, University of Vienna, A 1090 Wien, Austria
    Genome Res 17:852-64. 2007
    ..One hundred seventy-five selected candidates were tested by RT-PCR in six tissues, and expression could be verified in 43 cases (24.6%)...
  35. pmc Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution
    Deyou Zheng
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 17:839-51. 2007
    ..These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues...
  36. pmc Temporal profile of replication of human chromosomes
    Yesu Jeon
    Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
    Proc Natl Acad Sci U S A 102:6419-24. 2005
    ..Thus, at least for aneuploid cancer cells, a typical discrete time of replication in S phase is not seen for large segments of the chromosomes...
  37. ncbi request reprint The multitasking genome
    Thomas R Gingeras
    Nat Genet 38:608-9. 2006
  38. ncbi request reprint Characteristics of oligonucleotide tiling arrays measured by hybridizing full-length cDNA clones: causes of signal variation and false positive signals
    Daisuke Sasaki
    Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
    Genomics 89:541-51. 2007
    ..It was also demonstrated that hybridization of full-length cDNA clones is an excellent method to investigate the characteristics of oligonucleotide tiling arrays...
  39. ncbi request reprint Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells
    Annie Yang
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Mol Cell 24:593-602. 2006
    ..Many p63 binding regions are evolutionarily conserved and/or associated with sequence motifs for other transcription factors, suggesting that a substantial portion of p63 sites is biologically relevant...

Research Grants4

  1. Mapping Sites of Transcription and Regulation
    Thomas Gingeras; Fiscal Year: 2006
    ..abstract_text> ..
  2. Comprehensive Characterization and Classification of the Human Transcriptome
    Thomas Gingeras; Fiscal Year: 2007
    ..However, the utility of these and other genomic resources are dependent upon having a complete and high quality catalogue of transcribed regions. ..