Thomas D Wu

Summary

Affiliation: Genentech Inc
Country: USA

Publications

  1. ncbi request reprint Fast probabilistic analysis of sequence function using scoring matrices
    T D Wu
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
    Bioinformatics 16:233-44. 2000
  2. ncbi request reprint Analysing gene expression data from DNA microarrays to identify candidate genes
    T D Wu
    Department of Bioinformatics, Genentech, Inc, South San Francisco, CA 94080, USA
    J Pathol 195:53-65. 2001
  3. ncbi request reprint Large-scale analysis of gene expression profiles
    Thomas D Wu
    Department of Bioinformatics, Genetech Inc, South San Francisco, CA 94080, USA
    Brief Bioinform 3:7-17. 2002
  4. pmc Fast and SNP-tolerant detection of complex variants and splicing in short reads
    Thomas D Wu
    Department of Bioinformatics, Genentech, Inc, 1 DNA Way, South San Francisco, CA, USA
    Bioinformatics 26:873-81. 2010
  5. ncbi request reprint GMAP: a genomic mapping and alignment program for mRNA and EST sequences
    Thomas D Wu
    Department of Bioinformatics Genentech, Inc, South San Francisco, CA 94080, USA
    Bioinformatics 21:1859-75. 2005
  6. ncbi request reprint GEPIS--quantitative gene expression profiling in normal and cancer tissues
    Yan Zhang
    Department of Bioinformatics, Genentech Inc, South San Francisco, CA 94080, USA
    Bioinformatics 20:2390-8. 2004
  7. doi request reprint Genetic alterations and oncogenic pathways associated with breast cancer subtypes
    Xiaolan Hu
    Department of Bioinformatics, Genentech, Inc, South San Francisco, CA, USA
    Mol Cancer Res 7:511-22. 2009
  8. pmc TMEFF2 is a PDGF-AA binding protein with methylation-associated gene silencing in multiple cancer types including glioma
    Kui Lin
    Genentech, South San Francisco, California, United States of America
    PLoS ONE 6:e18608. 2011
  9. pmc Disruption of PH-kinase domain interactions leads to oncogenic activation of AKT in human cancers
    Chaitali Parikh
    Department of Molecular Biology, Genentech Inc, South San Francisco, CA 94080, USA
    Proc Natl Acad Sci U S A 109:19368-73. 2012
  10. doi request reprint Proteolytic activation of pro-macrophage-stimulating protein by hepsin
    Rajkumar 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

Collaborators

Detail Information

Publications26

  1. ncbi request reprint Fast probabilistic analysis of sequence function using scoring matrices
    T 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...
  2. ncbi request reprint Analysing gene expression data from DNA microarrays to identify candidate genes
    T D Wu
    Department of Bioinformatics, Genentech, Inc, South San Francisco, CA 94080, USA
    J Pathol 195:53-65. 2001
    ....
  3. ncbi request reprint Large-scale analysis of gene expression profiles
    Thomas 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...
  4. pmc Fast and SNP-tolerant detection of complex variants and splicing in short reads
    Thomas 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...
  5. ncbi request reprint GMAP: a genomic mapping and alignment program for mRNA and EST sequences
    Thomas D Wu
    Department of Bioinformatics Genentech, Inc, South San Francisco, CA 94080, USA
    Bioinformatics 21:1859-75. 2005
    ....
  6. ncbi request reprint GEPIS--quantitative gene expression profiling in normal and cancer tissues
    Yan Zhang
    Department of Bioinformatics, Genentech Inc, South San Francisco, CA 94080, USA
    Bioinformatics 20:2390-8. 2004
    ..The vast collection of expressed sequence tags (ESTs) and the associated tissue source information provides an attractive opportunity for studying gene expression...
  7. doi request reprint Genetic alterations and oncogenic pathways associated with breast cancer subtypes
    Xiaolan 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...
  8. pmc TMEFF2 is a PDGF-AA binding protein with methylation-associated gene silencing in multiple cancer types including glioma
    Kui 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...
  9. pmc Disruption of PH-kinase domain interactions leads to oncogenic activation of AKT in human cancers
    Chaitali 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...
  10. doi request reprint Proteolytic activation of pro-macrophage-stimulating protein by hepsin
    Rajkumar 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...
  11. doi request reprint The serine protease marapsin is expressed in stratified squamous epithelia and is up-regulated in the hyperproliferative epidermis of psoriasis and regenerating wounds
    Wei 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...
  12. ncbi request reprint Genome-wide identification of chromosomal regions of increased tumor expression by transcriptome analysis
    Yan 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...
  13. pmc Integrated exome and transcriptome sequencing reveals ZAK isoform usage in gastric cancer
    Jinfeng Liu
    Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, California 94080, USA
    Nat Commun 5:3830. 2014
    ..These results reveal the spectrum of genomic and transcriptomic alterations in gastric cancer, and identify isoform-specific oncogenic properties of ZAK. ..
  14. pmc Recurrent R-spondin fusions in colon cancer
    Somasekar 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...
  15. doi request reprint High-resolution genomic and expression analyses of copy number alterations in breast tumors
    Peter 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...
  16. ncbi request reprint Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis
    Heidi 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...
  17. pmc Microarray analysis of RNA extracted from formalin-fixed, paraffin-embedded and matched fresh-frozen ovarian adenocarcinomas
    Grazyna 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...
  18. pmc Expression of vascular endothelial growth factor, hypoxia inducible factor 1alpha, and carbonic anhydrase IX in human tumours
    A M Jubb
    Department of Pathology, Genentech Inc, South San Francisco, CA94080, USA
    J Clin Pathol 57:504-12. 2004
    ....
  19. pmc The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients
    Zhaoshi 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...
  20. pmc Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples
    Serban 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...
  21. pmc Genomic DNA microarray comparison of gene expression patterns in Paracoccidioides brasiliensis mycelia and yeasts in vitro
    Jomar 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...
  22. ncbi request reprint Minimal-risk scoring matrices for sequence analysis
    T 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...
  23. ncbi request reprint Identification of hepatocyte growth factor activator inhibitor-1B as a potential physiological inhibitor of prostasin
    Bin 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...
  24. pmc Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments
    Thomas 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...
  25. ncbi request reprint In silico data filtering to identify new angiogenesis targets from a large in vitro gene profiling data set
    Mary E Gerritsen
    Department of Cardiovascular Research, Genentech, South San Francisco, California 94080, USA
    Physiol Genomics 10:13-20. 2002
    ....
  26. pmc Gene expression profile and angiogenic marker correlates with response to neoadjuvant bevacizumab followed by bevacizumab plus chemotherapy in breast cancer
    Sherry 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)...