The research team led by John Cijiang He MD, PhD and Avi Ma'ayan PhD used a systems biology approach in a mouse model of HIV infection to identify the key factors involved in this process, thus identifying the kinase HIPK2 as one such factor. They also show that HIPK2 genetic deletion prevented renal fibrosis in two other mouse models, suggesting this kinase has a general role in the fibrotic process.
Nature Medicine 2012 Mar 11;18(4):580-8.
The authors propose a new approach to building pharmacodynamic models for drug efficacy. Such models are termed enhanced pharmacodynamics (ePD) models. The authors describe a process using systems biology approaches to explicitly incorporate genomic and epigenomic characteristics into ordinary differential equation based models of drug efficacy. Such models can aid the personalization of therapy within the context of precision medicine.
Science Translational Medicine 2012 Mar 21;4(126):126ps7
Software for Gene Expression Data Analysis
Expression2Kinases (X2K) is new software developed by the Information Management Unit of SBCNY to identify upstream pathways likely responsible for observed changes in genome-wide gene expression. The software uses ChIP-seq/chip and position-weight-matrices (PWMs) data to identify enriched transcription factors upstream of differentially expressed genes; then protein-protein interactions to build subnetworks centered on the identified transcription factors; and then kinase-substrate phosphorylation reaction databases to infer upstream kinases regulating the proteins within the subnetwork. The software and source code are freely available at: http://www.maayanlab.net/X2K [PubMed]
Systems Biomedicine: Molecules, Cells and Networks
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.