Faculty & Staff

Animesh Ray, PhD

Professor Ray, who joined KGI in July 2001, 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.

Dr. Ray 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 program (2006-2016).

In his leisure, Ray is an avid amateur photographer, who has been profiled at a number of sites including in the Street Photography Magazine June 2018 issue.

See complete list of 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

  1. Alpan Raval & Animesh Ray, Introduction to Biological Networks, Chapman & Hall/CRC (April 29, 2013; eEdition published in 2016). Link
  2. Yuan, M., Mahmud, I., Katsushima, K., Joshi, K., Saulnier, O., Pokhrel, R., Lee, B., Liyanage, W., Kunhiraman, H., Stapleton, S., Gonzalez-Gomez, I., Kannan, R.M., Eisemann, T., Kolanthai, E., Seal, S., Garrett, T.J., Abbasi, S., Bockley, K., Hanes, J., Chapagain, P., Jallo, G., Wechsler-Reya, R.J., Taylor, M.D., Eberhart, C.G., Ray, A. & Perera, R.J. miRNA-211 maintains metabolic homeostasis in medulloblastoma through its target gene long-chain acyl-CoA synthetase 4. Acta Neuropathol Commun 11: 203 (2023). DOI
  3. Ray, A., Kunhiraman, H., and Perera, R. The paradoxical behavior of microRNA211 in melanomas and other human cancers. Front Oncol 10:628367 (2021). DOI
  4. Lee, B., Sahoo, A., Marchica, J., Holzhauser, E., Chen, X., Li, J.-L., Seki, T., Govindarajan, S., Markey, F.B., Batish, M., Lokhande, S.J., Zhang, S., Ray, A. & Perera, R.J. The long noncoding RNA SPRIGHTLY acts as an intra-nuclear organizing hub for pre-mRNA molecules. Science Adv 3: e1602505 (May 3, 2017). DOI
  5. 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 genomic robustness. Nucleic Acids Res 45 (1): 255–270 (2017). DOI
  6. Frumkin, J.P., Patra, B.N., Sevold, A., Ganguly, K., Patel, C., Yoon, S., Schmid, M.B. & Ray, A. The interplay between chromosome stability and cell cycle control explored through gene–gene interaction and computational simulation. Nucleic Acids Res 44 (17): 8073–8085 (2016). DOI
  7. M. Ogihara and A. Ray, “Simulating Boolean circuits on a DNA Computer.” Algorithmica 25: 239–250 (1999).
  8. M. Ogihara and A. Ray, “DNA Computing on a Chip.” Nature 403: 143–145 (2000).
  9. S. Ray, S.-S. Park, and A. Ray. Pollen tube guidance by the female gametophyte. Development 124: 2489–2498 (1997).
  10. Ray, A., Siddiqi, I., Kolodkin, A., and Stahl, F. W. Intra-chromosomal Gene Conversion Induced by a DNA Double Strand Break in Saccharomyces cerevisiae. J. Mol. Biol. 201: 247–260 (1988).

Research Interests

Research in Dr. Ray’s 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).

In the late 1990s, Dr. Ray, along with computer scientist Dr. Mitsunori Ogihara, were pioneers in the field of massively parallel computing with DNA. Accounts of this work 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.

His current research work concerns understanding the molecular basis of non-coding RNA regulation in cancer, engaging machine learning (especially, Large Language Models) to decipher the biophysical basis of antigen-antibody interaction, systems biology of fungi, biological response to ionizing radiation, and chromosome instability.

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)