Research Highlights

Dr. Marc Birtwitle
Dimerization-based Control of Cooperativity
Bouhaddou M, Birtwistle MR..
Mol Biosyst. 2014 Jun 3;10(7):1824-32.
Dr. Avi Ma'ayan
The Characteristic Direction: A Geometrical Approach to Identify Differentially Expressed Genes
Clark NR, Hu KS, Feldmann AS, Kou Y, Chen EY, Duan Q, Ma'ayan A.
BMC Bioinformatics 2014 Mar 21;15:79.
Dr. Ravi Iyengar
Interconnected Network Motifs Control Podocyte Morphology and Kidney Function
Azeloglu EU, Hardy SV, Eungdamrong NJ, Chen Y, Jayaraman G, Chuang PY, Fang W, Xiong H, Neves SR, Jain MR, Li H, Ma'ayan A, Gordon RE, He JC, Iyengar R.
Sci Signal. 2014 Feb 4;7(311).
Dr. Susana Neves
ERK Regulation of Phosphodiesterase 4 Enhances Dopamine-stimulated AMPA Receptor Membrane Insertion
Song RS, Massenburg B, Wenderski W, Jayaraman V, Thompson L, Neves SR.
Proc Natl Acad Sci U S A. 2013 Sep 17;110(38):15437-42.

Software for Gene Expression Data Analysis

Enrichr

Enrichr is an integrative web-based and mobile gene-list enrichment analysis tool developed by the Information Management Unit of SBCNY that includes over 30 gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library Data Driven Documents (D3). The software can also be embedded easily into any tools that perform gene list analysis. Enrichr is an easy to use, intuitive enrichment analysis web-based tool providing various types of visualization summaries of collective functions of gene lists. The software and source code are freely available at: http://amp.pharm.mssm.edu/Enrichr/ [PubMed]

Systems Biomedicine: Molecules, Cells and Networks

Network analysis of FDA approved drugs and their targets

This active-learning course will introduce core biochemical, cell biological and molecular mechanisms together with basic bioinformatic and systems biology concepts and applications in the context of human biomedical research. The emphasis is 'topdown', beginning with a pathophysiological condition studied from a clinical perspective and moving towards explication of the molecular and metabolic logic, regulatory circuits and cell and tissue specific properties that distinguish the disease and normal state. The goals of this course are to provide inquisitive, self-directed students with an appreciation of the complexity of biological systems across scales and to give insight into pathophysiology as a basis for scientific enquiry and development of new therapeutic strategies. Students will be guided to relevant textbook material and current reviews, and will also participate in analyses of primary journal articles to enhance their study of scientific method and to illustrate a variety of experimental and computational approaches to contemporary translational biomedicine.

Systems Biomedicine: Molecules, Cells and Networks