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eLife GAB 042014


Article-1 for Home Page News

Linking signaling pathways to transcriptional programs in breast cancer

The Leslie lab has developed a machine learning method that can predict transcription factor activity from a tumor’s protein expression profile and vice versa. The inferred protein signatures from mRNA profiles were also useful for predicting drug response and survival.

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.


Article-3 for Home Page News

Evolutionary trade-off between swimming ability and biofilm formation in bacteria

The Xavier lab coaxed P. aeruginosa to evolve into hyperswarmers at the cost of their ability to form biofilms associated with some diseases.

New York Times article
60-Second Science
Cell Reports


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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


Emergence of spatial structure in the tumor microenvironment due to the Warburg effect

Cancer cells undergo dramatic changes in metabolism that can reshape the tumor-stromal spatial structure, and ultimately potentiate tumor growth.

Carmona-Fontaine C, Bucci V, Akkari L, Deforet M, Joyce JA, Xavier JB. Proc Natl Acad Sci U S A 2013 Nov 11. more

Genomics Traces Carcinogen Fingerprints

Focus: Using genome-wide sequencing, investigators are identifying mutation patterns associated with specific carcinogen exposure.

Lee W, Ladanyi M. Sci Transl Med 2013 Aug 7, Vol 5(197):197fs31. 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.


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.


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.