In the News:
Article about GATE in Biomedical Computation Review: Animating Molecular Biology, Biomedical Computational Review
NIGMS Press release in "computing life" on a research article published in the April 20, 2010 issue of Science Signaling, NIGMS Press Release: 20 April 2010
A conversation about a Research Article published in the 20 April 2010 issue of Science Signaling, Science Signaling Podcast: 20 April 2010
News item in NCI web publication "Physical Sciences in Oncology" about Peskin and Rodriguez-Brenes publication in PNAS, March 2010, Telomere Model Predicts Cell Life Span
News and views item in Nature Biotechnology that describes the use of GATE in Stem Cell Biology, February 2010, Systematic tracking of cell fate changes
News item in NIGMS computing life about the GATE software, February 2010,
Computational Honeycombs Drip with Data
Blog post about GATE on Scientific American, December 2009, Molecular movies: New software animates gene expression data
Upcoming Events:
2010 Summer Undergraduate Research program Poster Session
August 6, 2010
Details to follow
OVERVIEW
Researchers and educators from Mount Sinai School of Medicine, Courant Institute of Mathematical Sciences NYU, Stony Brook University (SUNY), City College of New York (CUNY), National Centre for Biological Sciences (India), and the IBM T.J. Watson Research Center, form the Systems Biology Center, New York.
We want to understand how the effects of molecular interactions are propagated across scales of organization from cells to tissues and organs affecting physiology and pathophysiology. We posit that the dynamic organization of motifs (regulatory loops) within multi-scale networks provides the basis for propagation of effects across scales from molecules to cells to tissues. We study drug action at a genomic scale to understand and predict adverse events. Drugs have their effects by reorganizing network topology across these scales. We study selected processes in the heart and brain to test these hypotheses.
The goals of the Systems Biology Center New York are to develop and disseminate approaches that provide a mechanistic understanding of how molecular interactions within regulatory networks in cells lead to the physiological function of tissues and organs, and how therapeutic agents affect cellular regulatory networks to alter pathophysiological states i.e. "the therapeutic implications of the design logic of scalability in mammalian systems".
The Systems Biology Center New York will have five undergrad research fellowships for students to be introduced to and learn how to conduct Systems Biology research at the Center at Mount Sinai School of Medicine or in the laboratories of members of the Center. The fellowship will offer a stipend of $2500 for the ten week research period from May 31st to August 6th, 2010. We invite applications from students entering their junior or senior years. We are particularly interested in applicants who are planning to pursue PhD or MD/PhD degree programs after graduation and who are interested in incorporating computational approaches into the research that they pursue. Applications period for the 2010 program has ended. Applications for the 2011 program will be available in fall 2010. More»
Lachmann A, Ma'ayan A. Lists2Networks: integrated analysis of gene/protein lists. BMC Bioinformatics. 2010 Feb 12;11:87 
Macarthur BD, Lachmann A, Lemischka IR, Ma'ayan A. GATE: Software for the Analysis and Visualization of High-Dimensional Time-series Expression Data. Bioinformatics. 2010 Jan 1;26(1):143-4. Epub 2009 Nov 5
Lachmann A, Ma'ayan A. KEA: kinase enrichment analysis. Bioinformatics. 2009 Mar 1;25(5):684-6
Ray S, Bhalla US. PyMOOSE: Interoperable Scripting in Python for MOOSE. Front Neuroinformatics. 2008;2:6
Berger SI, Posner JM, Ma’ayan A. Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinformatics. 2007 Oct 4;8:372
Berger SI, Ma’ayan A, Iyengar R. Systems pharmacology of arrhythmias. Sci Signal. 2010 Apr 20;3(118):ra30
Rodriguez-Brenes IA, Peskin CS. Quantitative theory of telomere length regulation and cellular senescence. Proc Natl Acad Sci U S A. 2010 Mar 23;107(12):5387-92
Wang LJ, Sobie EA. Mathematical model of the neonatal mouse ventricular action potential. Am J Physiol Heart Circ Physiol. 2008 Jun;294(6):H2565-75
MacArthur BD, Sanchez-Garcia RJ, Ma'ayan, A. Microdynamics and criticality of adaptive regulatory networks. Phys. Rev. Lett. 2010; 104 (16) Abstract»