Abstract

The bioinformatics core will provide the resources and expertise necessary to integrate, analyze and share data generated by each of the three projects. Due to the inter-related nature of these projects and the large amount of data that will be generated in the genomics analyses of cancer stem cells, the core will be crucial to overall success of this proposal. It will provide a consistent and principled analysis framework for synthesizing high-dimensional data into biologically meaningful results. The bioinformatics core will be responsible for analyzing, sharing, and storing several forms of data, including genome sequence, genomewide expression measurements, and genome-wide DNA binding site information. The core's actions upon receiving these data will involve analysis using existing bioinformatics methods, development and application of novel methods, and data sharing and storage. The unique tools and resources of this core such as analytical programs developed by the Altman laboratory and access to the Clark Center supercomputer will be heavily used by all 3 projects in this proposal.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Program Projects (P01)
Project #
5P01CA139490-05
Application #
8465142
Study Section
Special Emphasis Panel (ZCA1-SRRB-C)
Project Start
Project End
Budget Start
2013-05-01
Budget End
2014-04-30
Support Year
5
Fiscal Year
2013
Total Cost
$115,033
Indirect Cost
$41,697

  Institution

Name
Stanford University
Department
Type
DUNS #
009214214
City
Stanford
State
CA
Country
United States
Zip Code
94305

  Publications

Lobo, Neethan Amit; Zabala, Maider; Qian, Dalong et al. (2018) Serially transplantable mammary epithelial cells express the Thy-1 antigen. Breast Cancer Res 20:121
Cai, Shang; Kalisky, Tomer; Sahoo, Debashis et al. (2017) A Quiescent Bcl11b High Stem Cell Population Is Required for Maintenance of the Mammary Gland. Cell Stem Cell 20:247-260.e5
Jeong, Youngtae; Hoang, Ngoc T; Lovejoy, Alexander et al. (2017) Role of KEAP1/NRF2 and TP53 Mutations in Lung Squamous Cell Carcinoma Development and Radiation Resistance. Cancer Discov 7:86-101
Betancur, Paola A; Abraham, Brian J; Yiu, Ying Y et al. (2017) A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer. Nat Commun 8:14802
Weiskopf, Kipp; Schnorr, Peter J; Pang, Wendy W et al. (2016) Myeloid Cell Origins, Differentiation, and Clinical Implications. Microbiol Spectr 4:
Weiskopf, Kipp; Jahchan, Nadine S; Schnorr, Peter J et al. (2016) CD47-blocking immunotherapies stimulate macrophage-mediated destruction of small-cell lung cancer. J Clin Invest 126:2610-20
Dalerba, Piero; Sahoo, Debashis; Paik, Soonmyung et al. (2016) CDX2 as a Prognostic Biomarker in Stage II and Stage III Colon Cancer. N Engl J Med 374:211-22
Jeong, Youngtae; Rhee, Horace; Martin, Shanique et al. (2016) Identification and genetic manipulation of human and mouse oesophageal stem cells. Gut 65:1077-86
Weiskopf, Kipp; Anderson, Katie L; Ito, Daisuke et al. (2016) Eradication of Canine Diffuse Large B-Cell Lymphoma in a Murine Xenograft Model with CD47 Blockade and Anti-CD20. Cancer Immunol Res 4:1072-1087
Krampitz, Geoffrey Wayne; George, Benson M; Willingham, Stephen B et al. (2016) Identification of tumorigenic cells and therapeutic targets in pancreatic neuroendocrine tumors. Proc Natl Acad Sci U S A 113:4464-9

Showing the most recent 10 out of 43 publications