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Article-1 for Home Page News

Linking signaling pathways to transcriptional programs in breast cancer

The Leslie lab developed a machine learning method that predicts transcription factor activity from a tumor’s protein expression profile and vice versa. Inferred protein signatures from mRNA profiles were useful for predicting drug response and survival.
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Article-2 for Home Page News

T cells coordinate a collective response to a pathogen by scaling individual IL-2 production

The Altan-Bonnet lab showed that T cell populations scale their production of the cytokine IL-2 to antigen abundance over a large dynamic range, independent of population size.

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Article-3 for Home Page News

Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles

The Sander lab developed a computational method, Statius, to systematically predict metabolic vulnerabilities in tumor samples from genomic profiles.

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Computational Biology Center (cBio)

at MSKCC pursues computational and systems biology research and bioinformatics resource development in the following areas:

more about cBio

Publications

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

Using a workflow involving mouse models, clinical studies, metagenomic analyses and mathematical modeling, a probiotic candidate was identified that corrects a clinically relevant microbiome deficiency and may protect against C. difficile infection.

Buffie CG, Bucci V, Stein RR, et al. Nature 2015 Jan 8. more

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis.

Oqtans, an open-source workbench for quantitative transcriptome
analysis that is integrated in Galaxy.

Sreedharan VT, Schultheiss SJ, Jean G, et al. Bioinformatics 2014 May 1, Vol 30(9):1300-1. more

How much of a concern should the phenomenon of entropy-enthalpy compensation be in drug design?

Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design

Chodera JD, Mobley DL. Annu Rev Biophys. 2013;42:121-142.more

Cancer Genomics Sidebar

Data Portal

Explore cancer genomics data via the cBio Cancer Genomics Portal.

News

The CGDS R-package has been released.

NetBox version 1 has been released.

The Cancer Genome Atlas has announced the selection of six Genome Data Analysis Centers.

Publications

Mutual exclusivity analysis identifies oncogenic network modules. Genome Res. 2011 Sep 9. [Abstract] [PDF]

Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 29. [Abstract] [Full Text] [PDF]

Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res.. 2011 Jan (Database issue). [Abstract] [Full Text] [PDF]

Gene Ranker

Explore cancer genes with Gene Ranker.