Research Highlights
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.
[PubMed] [PDF]
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.
[PubMed] [PDF]
Science Translational Medicine 2012 Mar 21;4(126):126ps7
New Resource
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 Biology of Disease and Therapeutics (SBDT)
Mount Sinai's Graduate School of Biological Sciences offers a PhD in Biomedical Sciences in several training areas, including Systems Biology of Disease and Therapeutics (SBDT). Systems Biology of Disease and Therapeutics trains graduate students in research that aims to understand the complex interactions underlying human disease, and how drugs can be used to treat these diseases. Knowledge of the healthy and diseased states of a cell, tissue, or organism, requires an understanding of networks of molecular interactions within and between cells. The Systems Biology of Disease and Therapeutics curriculum emphasizes the integration of concepts from multiple disciplines: genomics, molecular biology and biochemistry, physiology, and pharmacology. Important approaches for this integration are quantitative reasoning and computational biology. This program, set within a tightly knit medical school and hospital environment, provides unique opportunities to study systems from genomes and proteins to cells to animal models to humans at both the bench and the bedside