Research Topics
Genomes and GenesSpecies | T R GingerasSummaryAffiliation: Affymetrix Inc Country: USA Publications
Research Grants
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Detail Information
Publications
Genome-wide analysis of estrogen receptor binding sitesJason 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...- Genome-wide transcription and the implications for genomic organizationPhilipp 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?.. 
Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experimentsSrinka 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...- Differential analysis for high density tiling microarray dataSrinka Ghosh
Affymetrix Inc, Santa Clara, CA 95051, USA
BMC Bioinformatics 8:359. 2007.... - Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arraysT R Gingeras
Affymetrix, Santa Clara, California 95051, USA
Genome Res 8:435-48. 1998.... - Origin of phenotypes: genes and transcriptsThomas 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... - Transcriptional maps of 10 human chromosomes at 5-nucleotide resolutionJill 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... - Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validationS 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... - Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAsSimon 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... - Large-scale transcriptional activity in chromosomes 21 and 22Philipp 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... - High density synthetic oligonucleotide arraysR 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... - Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arraysA 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... - Biological function of unannotated transcription during the early development of Drosophila melanogasterJ 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... - Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arraysPhilipp 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... - Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22Dione 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... - Analysis of drug pharmacology towards predicting drug behavior by expression profiling using high-density oligonucleotide arraysJ 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... - RNA maps reveal new RNA classes and a possible function for pervasive transcriptionPhilipp 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... - Beyond expression profiling: next generation uses of high density oligonucleotide arraysPhilipp 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... - TUF love for "junk" DNAAarron 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... - Prokaryotic RNA preparation methods useful for high density array analysis: comparison of two approachesC 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... - Transcriptional landscape of the human and fly genomes: nonlinear and multifunctional modular model of transcriptomesA 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... - Microarrays and genetic epidemiology: a multipurpose tool for a multifaceted fieldDennise 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... - Fifty years of molecular (DNA/RNA) diagnosticsThomas R Gingeras
Affymetrix, Inc, Santa Clara, CA, USA
Clin Chem 51:661-71. 2005 - Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regionsFrance 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.... - The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel lociJoel 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... - RNA reference materials for gene expression studies. Difficult first stepsThomas R Gingeras
Clin Chem 50:1289-90. 2004 - Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disordersAlvaro 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... - Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targetsDavid 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... - EGASP: the human ENCODE Genome Annotation Assessment ProjectRoderic 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... - Efficient targeted transcript discovery via array-based normalization of RACE librariesSarah 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.... - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function... - Mapping the strand-specific transcriptome of fission yeastThomas R Gingeras
Nat Genet 40:935-6. 2008 - Genomic maps and comparative analysis of histone modifications in human and mouseBradley 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... - Structured RNAs in the ENCODE selected regions of the human genomeStefan 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%)... - Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolutionDeyou 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... - Temporal profile of replication of human chromosomesYesu 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... - The multitasking genomeThomas R Gingeras
Nat Genet 38:608-9. 2006 - Characteristics of oligonucleotide tiling arrays measured by hybridizing full-length cDNA clones: causes of signal variation and false positive signalsDaisuke 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... - Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cellsAnnie 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... - Moving AHEAD with an international human epigenome projectPeter A Jones
Nature 454:711-5. 2008
Research Grants
- Mapping Sites of Transcription and RegulationThomas Gingeras; Fiscal Year: 2006..abstract_text> ..
- Comprehensive Characterization and Classification of the Human TranscriptomeThomas 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. ..