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Article-1 for Home Page News
The Leslie lab sheds light on how transcriptional programs during cell differentiation are regulated
The team discovered that regulatory complexity and early enhancer establishment during hematopoietic differentiation shape transcriptional programs, and quantitatively modeled gene expression changes during cell state transitions.
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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.
Article-3 for Home Page News
Nomination of combination therapies for drug-resistant melanoma using perturbation biology
Based on computer simulations of comprehensive signaling models, the Sander lab discovered that co-targeting BRAF, a key upstream genomic aberration, and the downstream c-Myc pathway inhibits growth of drug-resistant melanoma cells in culture.
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Computational Biology Center (cBio)
at MSKCC pursues computational and systems biology research and bioinformatics resource development in the following areas:
- Cancer genomics and proteomics
- Molecular pathways and networks
- Gene regulation
- Tumor-stromal cell interactions
- Cell-to-cell communication
- Self/non-self discrimination in immunology & cancer biology
- Sequence-structure analysis
- Diagnostic and prognostic markers
- Design of combinatorial cancer therapy
- Social interaction in microbes
- Human microbiome
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.