Research Topics
Genomes and Genes | Thomas D WuSummaryAffiliation: Genentech Inc Country: USA Publications
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Publications
Fast and SNP-tolerant detection of complex variants and splicing in short readsThomas D Wu
Department of Bioinformatics, Genentech, Inc, 1 DNA Way, South San Francisco, CA, USA
Bioinformatics 26:873-81. 2010..Our program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite-treated DNA for the study of methylation state...
GMAP: a genomic mapping and alignment program for mRNA and EST sequencesThomas D Wu
Department of Bioinformatics Genentech, Inc, South San Francisco, CA 94080, USA
Bioinformatics 21:1859-75. 2005....- Large-scale analysis of gene expression profilesThomas D Wu
Department of Bioinformatics, Genetech Inc, South San Francisco, CA 94080, USA
Brief Bioinform 3:7-17. 2002..Hypothesis tests may be applied to expression profiles on a large scale to identify candidate genes of interest... - Analysing gene expression data from DNA microarrays to identify candidate genesT D Wu
Department of Bioinformatics, Genentech, Inc, South San Francisco, CA 94080, USA
J Pathol 195:53-65. 2001.... - Fast probabilistic analysis of sequence function using scoring matricesT D Wu
Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
Bioinformatics 16:233-44. 2000..The resulting increase in speed should allow scoring matrices to be used more widely in large-scale sequencing and annotation projects... - GEPIS--quantitative gene expression profiling in normal and cancer tissuesYan Zhang
Department of Bioinformatics, Genentech Inc, South San Francisco, CA 94080, USA
Bioinformatics 20:2390-8. 2004..com/share/gepis. An interactive version of GEPIS will soon be freely available at http://www.cgl.ucsf.edu/Research/genentech/gepis/. The source code, modules, data and gene lists can be downloaded at http://share.gene.com/share/gepis... 
Genetic alterations and oncogenic pathways associated with breast cancer subtypesXiaolan Hu
Department of Bioinformatics, Genentech, Inc, South San Francisco, CA, USA
Mol Cancer Res 7:511-22. 2009..The genome-wide and region-specific differences between subtypes suggest the differential activation of oncogenic pathways...- TMEFF2 is a PDGF-AA binding protein with methylation-associated gene silencing in multiple cancer types including gliomaKui Lin
Genentech, South San Francisco, California, United States of America
PLoS ONE 6:e18608. 2011..The biological function of TMEFF2 remains unclear with conflicting reports suggesting both a positive and a negative association between TMEFF2 expression and human cancers... - Proteolytic activation of pro-macrophage-stimulating protein by hepsinRajkumar Ganesan
Department of Early Discovery Biochemistry, Genentech, Inc, 1 DNA Way, MS 27, South San Francisco, CA 94080, USA
Mol Cancer Res 9:1175-86. 2011..These findings suggest that the MSP/RON signaling pathway may be regulated by hepsin in tissue homeostasis and in disease pathologies, such as in cancer and immune disorders... - Genome-wide identification of chromosomal regions of increased tumor expression by transcriptome analysisYan Zhou
Department of Bioinformatics, Genentech, Inc, South San Francisco, California 94080, USA
Cancer Res 63:5781-4. 2003..Our large-scale transcriptome analysis led to identification of many additional chromosomal regions with increased tumor expression, regions that represent potential tumor amplicons... - The serine protease marapsin is expressed in stratified squamous epithelia and is up-regulated in the hyperproliferative epidermis of psoriasis and regenerating woundsWei Li
Department of Protein Engineering, Genentech, Inc, South San Francisco, California 94080, USA
J Biol Chem 284:218-28. 2009..Marapsin's restricted expression, localization, and cytokine-inducible expression suggest a role in the terminal differentiation of keratinocytes in hyperproliferating squamous epithelia... - Recurrent R-spondin fusions in colon cancerSomasekar Seshagiri
Department of Molecular Biology, Genentech Inc, 1 DNA Way, South San Francisco, California 94080, USA
Nature 488:660-4. 2012..The R-spondin gene fusions and several other gene mutations identified in this study provide new potential opportunities for therapeutic intervention in colon cancer... - Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesisHeidi S Phillips
Department of Tumor Biology and Angiogenesis, Genentech, Inc, South San Francisco, California 94080, USA
Cancer Cell 9:157-73. 2006..A robust two-gene prognostic model utilizing PTEN and DLL3 expression suggests that Akt and Notch signaling are hallmarks of poor prognosis versus better prognosis gliomas, respectively... - High-resolution genomic and expression analyses of copy number alterations in breast tumorsPeter M Haverty
Department of Bioinformatics, Genentech, Inc, South San Francisco, CA 94080, USA
Genes Chromosomes Cancer 47:530-42. 2008..This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat... - Microarray analysis of RNA extracted from formalin-fixed, paraffin-embedded and matched fresh-frozen ovarian adenocarcinomasGrazyna Fedorowicz
Department of Molecular Biology, Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
BMC Med Genomics 2:23. 2009..We also demonstrated that profiling of not only FF but also of FFPE samples can be successfully used to identify differentially expressed genes characteristic of ovarian carcinoma... - Expression of vascular endothelial growth factor, hypoxia inducible factor 1alpha, and carbonic anhydrase IX in human tumoursA M Jubb
Department of Pathology, Genentech Inc, South San Francisco, CA94080, USA
J Clin Pathol 57:504-12. 2004.... - The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patientsZhaoshi Jiang
Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, California 94080, USA
Genome Res 22:593-601. 2012..Thus, we report the most comprehensive characterization of HBV integration in hepatocellular carcinoma patients. Such widespread random viral integration will likely increase carcinogenic opportunities in HBV-infected individuals... - Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samplesSerban Nacu
Department of Bioinformatics and Molecular Biology, Genentech, Inc, South San Francisco, California 94080, USA
BMC Med Genomics 4:11. 2011..Deep transcriptional sequencing (RNA-Seq) now makes it possible to study the occurrence and expression levels of TICs in individual samples across the genome... - Genomic DNA microarray comparison of gene expression patterns in Paracoccidioides brasiliensis mycelia and yeasts in vitroJomar Patricio Monteiro
California Institute for Medical Research, San Jose, CA, USA
Microbiology 155:2795-808. 2009..These findings expand our knowledge of the different morphological forms of P. brasiliensis during growth in culture... - Minimal-risk scoring matrices for sequence analysisT D Wu
Department of Biochemistry, Stanford University School of Medicine, California 94305 5307, USA
J Comput Biol 6:219-35. 1999..Our method is implemented in the package EMATRIX, which is available on the Internet at http://motif.stanford.edu/ematrix... - Disruption of PH-kinase domain interactions leads to oncogenic activation of AKT in human cancersChaitali Parikh
Department of Molecular Biology, Genentech Inc, South San Francisco, CA 94080, USA
Proc Natl Acad Sci U S A 109:19368-73. 2012..These results have important implications for therapeutic intervention in patients with AKT mutations at the PH-KD interface... - Identification of hepatocyte growth factor activator inhibitor-1B as a potential physiological inhibitor of prostasinBin Fan
Department of Protein Engineering, Genentech, Inc, South San Francisco, California 94080, USA
J Biol Chem 280:34513-20. 2005..The identification of HAI-1B as a potential physiological regulator of prostasin function, as described herein, may further the investigation of the role of prostasin in normal physiology and cancer... - Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatmentsThomas D Wu
Department of Biochemistry, Stanford University, Stanford, California 94305, USA
J Virol 77:4836-47. 2003..The presence of mutational clusters provides insight into the complex mutational patterns required for HIV-1 protease inhibitor resistance... - In silico data filtering to identify new angiogenesis targets from a large in vitro gene profiling data setMary E Gerritsen
Department of Cardiovascular Research, Genentech, South San Francisco, California 94080, USA
Physiol Genomics 10:13-20. 2002.... - Gene expression profile and angiogenic marker correlates with response to neoadjuvant bevacizumab followed by bevacizumab plus chemotherapy in breast cancerSherry X Yang
National Clinical Target Validation Laboratory, Division of Cancer Treatment and Diagnosis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
Clin Cancer Res 14:5893-9. 2008..To identify biomarkers and gene expression profile signatures to distinguish patients with partial response (PR) from those with stable disease (SD) and progressive disease (PD)...