Animesh Ray, PhDProfessor
Areas of Expertise
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, during which periods he developed methods for precise in vivo chromosome engineering in yeast and in an experimental plant. He was an Assistant Professor from 1991 to 1995 and Associate Professor from 1996 to 2001 of Biology at the University of Rochester, New York, and an adjunct associate professor at the University of California, San Diego from 2001 to 2004. He was a visiting professor at the University of Rochester from 2001 to 2004, at Institute for Systems Biology in Seattle in 2009, University of Hyderabad in 2009, and is currently a visiting faculty in California Institute of Technology, Pasadena. 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 biogenesis. His PhD student 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.
His current research work involve systems biology of Huntington's disease, chromosome instability, non-coding RNAs in cancers, and cancer drug resistance mechanisms.
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 was KGI's faculty chair (2010-2016) and director of KGI's PhD programs (2006-2016).
ALS 300: Molecular Biotechnology
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.ALS 407: Pharmacogenomics and Precision Medicine
We will focus on the opportunities presented by the growing contribution of human evolutionary and population genetics, and of human genomic information and technologies to interdisciplinary approaches in the study of variable responses of humans to drugs and toxic agents, and how research may benefit the individual. The course will provide an in depth analysis of salient examples where genetic thinking has impacted pharmacological sciences, including issues on genetic variability in biochemistry and physiology of drug action, drug uptake and metabolism; the opportunities for discovery and design of new therapeutic agents. While a small section of the course will cover issues in personalizing medicine, understanding and managing adverse drug reactions, ethical, legal, regulatory and social consequences of genetics applied to medicines, the major part of the course will consist of in-depth studies of the primary literature on pharmacogenetics and genomics. The course will aim to make students aware of the interdisciplinary research effort in human genetics and pharmacogenetics, which are poised to revolutionize drug development and therapeutic management.
- Selected Publications
See complete list of publications at: https://www.researchgate.net/profile/Animesh_Ray/publications/
Frumkin J.P., Patra B.N., Sevold A., Ganguly K., Patel C., Yoon S., Schmid M.B., and Ray A. The interplay between chromosome stability and cell cycle control explored through gene–gene interaction and computational simulation. Nucleic Acids Research doi: 10.1093/nar/gkw715 August 22 (2016)
Mazar J, Qi F, Lee B, Marchia J, Govindarajan S, Shelley J, Li JL, Ray A, Perera RJ. miR-211 functions as a metabolic switch in human melanoma cells. Mol. Cell. Biol., 36:1090 doi: 10.1128/MCB.00762-15 (2016)
An MC, O'Brien RN, Zhang N, Patra BN, De La Cruz M, Ray A, Ellerby LM. Polyglutamine disease modeling: epitope based screen for homologous recombination using CRISPR/Cas9 System. PloS Curr. doi: 10.1371/currents.hd.0242d2e7ad72225efa72f6964589369a. (2014)
Bhan, A. and Ray, A. A signature of power law network dynamics. BioRxiv doi: http://dx.doi.org/10.1101/004028 (2014)
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, Ray A, 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)
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, Ray A 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
Dr. Ray's laboratory is interested in exploring robustness of the genome. A variety of model systems and questions suitable for these model systems are being pursued. For example, work with yeast led to the discovery of a network of approximately 600 genes that can rewire cellular physiology to enable survival when one or more of approximately 50 genes essential for viability are mutated. This work has led to the paradigm that eukaryotic genome has previously unrecognized extent of robustness to lethal assaults, which has led to a novel approach to the discovery of genes that could impart drug resistance to lung cancer cells. 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. Non-coding RNAs as agents of gene regulation in cancer is another aspect that is being pursued by Dr. Ray's research, in collaboration with investigators in Sanford-Burnham Institute. Recent collaborative research in Dr. Ray's laboratory has also developed computational methods for predicting protein-protein interaction pairs, a method for analyzing complex interaction networks, and in collaboration with researchers at San Diego Supercomputer Center designed 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
Computational analysis of Huntington's disease interactome (PhD student Sonali Talele Lokhande)
Discovery of genes imparting resistance to targeted anti-cancer drugs in Non-Small Cell Lung Cancer (NSCLC) cells (PhD student Michael De La Cruz, MBS/MS students Stephanie Leguizamon and Payam Amiri) (in collaboration with John Yim of City of Hope Medical Center, and Kumkum Ganguly of Los Alamos National Laboratory) (Funded by the DoD)
Analysis of the neural basis of rational choice behavior in Caenorhabditis elegans (in collaboration with Paul Sternberg, Wen Chen and David Angeles of Caltech)
Non-coding RNA molecules in melanoma (in collaboration with Ranjan Perera of Sanford Burnham Institute)
1. Animesh Ray and Teresa Golden, “The gene encoding SHORT INTEGUMENTS1 of Arabidopsis thaliana and uses thereof” (Issued US Patent no. US6737561; May 18, 2004)
2. Ranjan Perera, Min Lu, and Animesh Ray, “Polynucleotide sequences from rice” (Issued US Patent no. US6544783; April 8, 2003)
3. Ranjan Perera, Min Lu, and Animesh Ray, “Polynucleotide sequences from rice” (Issued US Patent no. US7232940; June 19, 2007)
|Animesh Ray, PhD|
|Location:||Building 535, Room 156E|