Animesh Ray, PhDProfessor, Faculty Chair, Director of the PhD Program, Director of the Center for Network Studies
Gene Function, Gene Regulatory Networks, Genomics, Homologous Recombination, Gene Targeting, MicroRNA, Systems Biology, Epigenetic Regulation, Plant Molecular Biology, Plant Development, Melanoma Biology, Synthetic Biology, Molecular Computing
Professor Ray earned his PhD in microbial genetics from Monash University in Melbourne, Australia. His PhD research led to the identification of a gene for efficient plasmid maintenance in Escherichia coli and a method for generating a multi-copy infectious plasmid that is packageable inside a virus coat-an early example of synthetic biology. He subsequently conducted research at the Institute of Molecular Biology, University of Oregon, and the Department of Biology, Massachusetts Institute of Technology, in which he developed methods for precise in vivo chromosome engineering in yeast and in an experimental plant. He was an Assistant Professor from 1991 to1995 and Associate Professor from 1996 to2001 of Biology at the University of Rochester, New York, and an adjunct faculty member at the University of California, San Diego from2001 to 2004. He was a visiting professor at the University of Rochester from 2001to 2004, Institute for Systems Biology in Seattle in 2009, and University of Hyderabad in2009. Research in his laboratory led to the discovery of the first known maternal effect embryo pattern formation gene in plants. His student, Teresa Golden, cloned a plant gene (DCL1) that later became known as the first member of the Dicer group of genes required for microRNA biosynthesis. Another of his students, Stephen Schauer, identified the remaining known plant Dicer genes (DCL2-4). From 1999 to 2001, while on extended leave of absence from the University of Rochester, Dr. Ray directed research programs on regulation of gene expression and gene targeting at a plant biotechnology start-up company in San Diego.
In the late 1990s, Dr. Ray, along with a computer scientist colleague Dr. Mitsunori Ogihara, published a series of papers on experimental and theoretical investigations on designing massively parallel computing devices using solution phase DNA chemistry. Accounts of this research were featured in several news media including the New York Times and the International Herald Tribune and he and Dr. Ogihara were featured in the book One Digital Day: How the Microchip is Changing Our World.
He currently teaches courses on molecular systems biology that includes molecular mechanisms of human diseases and pharmacogenomics. He is the director of KGI's PhD program and also of the Center for Network Studies.
Students will be exposed to the conceptual foundations of biotechnology and the role played by discoveries and applications of molecular biology principles in advancing biotechnology horizons. This is a case-based course in which students will read landmark original papers and patents that shaped biotechnology, and discuss these in the class.
This course examines the role of genes, proteins and RNA in causing or combating diseases, and emphasizes the current conceptual and analytical tools that are brought to bear, and their limitations, on our understanding.
Patra, B.N., Kon, Y., Yadav, G., Sevold, A., Frumkin, J.P., Vallabhajosyula, R.R., Hintze, A., Østman, B., Schosseau, J., Bhan, A., Marzolf, B., Tamashiro, J.K., Kaur, A., Baliga, N.S., Grayhack, E.J., Galas, D.J., Raval, A., Adami, C., Phizicky, E.M. & Ray, A. A genome wide dosage suppressor network reveals genetic robustness and a novel mechanism for Huntington's disease. BioRxiv
doi: 10.1101/000265 (November 12, 2013)
J-L Li, J Mazar, C Zhong, GJ Faulkner, SS Subramaniam, S Govindarajan, Z Zhang, ME Dinger, G Meredith, C Adams, S Zhang, JS Mattick, A Ray, and RJ Perera. Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network. Nature Sci. Report 3: 2962 (doi:10.1038/srep02962) (2013)
Chatterjee, R.S., Lui, G., Chaum, M, Patra, B.N. Ribosomal gene overexpression suppresses poly-Glutamine induced toxicity of N-terminal human Huntington's disease protein in yeast. Journal of Life Sci Tech (in press) (2013)
Perera, R. and Animesh Ray. Epigenetic Regulation of microRNA Genes and Their Role in Human Melanomas. Epigenomics 12: 81-90 (2012)
J Mazar, D Khaitan, D DeBlasio, SS Govindarajan, S Kopanathi, C Zhong, S Zhang, A Ray and RJ Perera The epigenetic regulation of microRNA genes and the role of miR-34b in cell invasion and motility in human melanomas. PloS ONE 6: e24922 (2011)
Kozhenkov S, Sedova M, Dubinina Y, Gupta A, Ray A, Ponomarenko J, Baitaluk M. "BiologicalNetworks - tools enabling the integration of multi-scale data for the host-pathogen studies". Bmc Systems Biology 2011 Jan 14;5:7 doi:10.1186/1752-0509-5-7
Mazar J, DeYoung K, Khaitan D, Meister E, Almodovar A, Goydos J, Ray A, Perera RJ. "The Regulation of miRNA-211 Expression and Its Role in Melanoma Cell Invasiveness". Plos One 2010;5(11):e13779
Vallabhajosyula RR, Chakravarti D, Lutfeali S, Ray A, Raval A. "Identifying Hubs in Protein Interaction Networks". Plos One 2009;4(4):e5344
Paladugu SR, Zhao S, Ray A, Raval A. "Mining protein networks for synthetic genetic interactions". Bmc Bioinformatics 2008;9(1):426
Langer M, Sniderhan LF, Grossniklaus U, Ray A. "Transposon Excision from an Atypical Site: A Mechanism of Evolution of Novel Transposable Elements". Plos One 2007;2(10):e965
Chickarmane V, Ray A, Sauro HM, Nadim A. "A model for p53 dynamics triggered by DNA damage". Siam Journal on Applied Dynamical Systems 2007;6(1):61-78
Baitaluk M, Sedova M, Ray A, Gupta A. "BiologicalNetworks: visualization and analysis tool for systems biology". Nucleic Acids Res. 2006 Jul 1;34(supp_2):W466-W471
Ray A. "Plant genetics - RNA cache genome trash?" Nature 2005 Sep 1;437(7055):E1-E2
Mlotshwa S, Schauer SE, Smith TH, Mallory AC, Herr JM, Roth B, Merchant DS, Ray A, Bowman LH, Vance VB. "Ectopic DICER-LIKE1 expression in P1/HC-Pro Arabidopsis rescues phenotypic anomalies but not defects in microRNA and silencing pathways". Plant Cell 2005 Nov;17(11):2873-2885
Book: Introduction to Biological Networks
Alpan raval and Animesh ray
04/2013; Publisher: Chapman & Hall/CRC Mathematical & Computational Biology, ISBN: 978-1584884637
Current research in Dr. Ray's laboratory uses yeast as a model system to address the basis of evolutionary robustness of the genome. I n collaboration with colleagues at the University of Rochester, University of Toronto, and the Institute for Systems Biology in Seattle, Dr. Ray's laboratory has discovered a network of over 700 genes that can bypass the lethal effects of mutations in some forty other genes. These results have revealed a previously unappreciated view of the complex organization of a genome, which allows the cells to potentially bypass the deleterious effects of mutations by reshuffling and reorganizing their genomes. Dr. Ray's laboratory has also identified genes that cause chromosome instability. Chromosome instability is a hallmark of cancer and identifying such genes in a model organism would allow for better assessment of human cancer cell functions. Recent collaborative research in Dr. Ray's laboratory has also led to the discovery of a mechanism of chromosome break repair in plants, a human microRNA associated with melanoma, the development of a computational method for predicting protein-protein interaction pairs, the design of a systems biology computational platform (BiologicalNetworks.org), and a mathematical model that simulates the dynamics of gene expression in certain cancer cells in response to DNA damage.
Current Research Projects
Genome-wide Bypass Network of Essential Gene Mutation (Dr. Biranchi Patra, postdoctoral researcher in Dr. Ray's laboratory and in collaboration with the University of Rochester Medical School and the University of Toronto): Mutation studies of each essential gene of Saccharomyces cerevisiae and selection for all possible genes in the genome which, if over-expressed, could potentially suppress the lethal effects of the original mutation. These collaborative studies have the potential to reduce the deleterious effects of drugs on normal cells while maximizing the lethal effects of the same drugs on diseased cells.
Genes That Induce Chromosome Instability by Gain-of-function: PhD student Jesse Frumkin is conducting a medium throughput screen for genes that cause high frequency chromosome instability when these genes are over-expressed. At least 24 such genes have been confirmed. The Ray lab anticipates that by using this information, it would be possible to identify human homologues, some of which might cause chromosome instability in cancer cells.
Evolutionary Games and Genome Evolution: The Ray lab is addressing whether evolutionary robustness through genetic bypass systems can be understood through the abstract model of evolutionary game theory using a hybrid experimental and theoretical approach.
Future Research Interests
Dr. Ray and the Center for Network Studies are looking for collaborators to extend their work on mutational bypass systems in yeast into chemotherapy bypass mechanisms in cancer cells under targeted chemotherapy. They would also like to collaborate to identify genes that cause chromosome instability in human systems.
1. Animesh Ray and Teresa Golden, “The gene encoding SHORT INTEGUMENTS1 of Arabidopsis thaliana and uses thereof” (Issued US Patent no. US6737561)
2. Ranjan Perera, Min Lu, and Animesh Ray, “Polynucleotide sequences from rice” (Issued US Patent no. US6544783)
|Animesh Ray, PhD|
|Location:||Building 535, Room 156C|