Curriculum Vitae

Animesh Ray, PhD (1985), is Professor, Systems Biology, at the Keck Graduate Institute of Applied Life Sciences in Claremont, California. Previously, he was Associate Professor of Biology at the University of Rochester, Rochester, New York, and Associate Professor Adjunct of Cell and Developmental Biology at the University of California San Diego. He is the lead principal investigator of an over $3.5M National Science Foundation-funded collaboration with several physicists, computer scientists and mathematicians on modeling complex gene regulatory networks. He had previously worked on mechanisms of homologous recombination with Professors Franklin W. Stahl (University of Oregon) and Ethan R. Signer (MIT).

Animesh's work on homologous recombination has centered on the role of DNA double strand breaks in repair and recombination of chromosomes in yeast and plants. Starting in 1991, Animesh began investigating gene regulatory mechanisms during development in plants. By 1994, his laboratory had discovered a new genetic pathway for specifying ovule development in flowering plants. Soon afterwards, his laboratory cloned and patented a gene now named DICER-LIKE1 (DCL1) that controls the production of micro RNA in flowering plants and thereby controls a large number of genes required for essential plant functions, including flowering and embryogenesis. This work helped extend the role of RNA silencing to plant development. He holds a patent on the DCL1 gene. Around this time his laboratory also showed that the plant embryo sac emits a long-distance signal that guides pollen tubes into the egg chamber for accomplishing fertilization.

In 1995, inspired by the pioneering work of Dr. Leonard Adleman of the University of Southern California, Animesh became interested in exploring the potential of biological systems for computing and information processing. In 1996, collaborating with a computer scientist colleague Mitsunori Ogihara, Animesh designed the first set of parallel logic gates with DNA, which was able to compute the solution to a Boolean Circuit-a logical framework important for many types of computation. This and their subsequent studies, along with those of several other scientists, helped launch a new field of research: molecular computing. His work in molecular computing was featured widely in the public media, including the New York Times, International Herald Tribune, by the British Broadcasting Corporation, and in the Times/Random House book "One Digital Day: How the microchip is changing our world". Ogihara and Ray were nominated for Discover Magazine 1997 Invention of the Year award. Since late 2001, Animesh's laboratory has begun to investigate modeling and mathematical analysis of complex gene regulatory pathways using data-integration methods and computational analysis.

Contact:
Dr. Animesh Ray, Professor
Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711.
Phone: (909) 607 9729
Fax: (909) 607 8598
Email: aray@kgi.edu  

Professional Activities

• Co-organizer with Dr. Maarten Chrispeels of San Diego Center for Molecular Agriculture Symposium on Proteomics, May 26, 2000
• Member, Physiological Detector Device Research Team, Center for Future Health, University of Rochester (Joint Directors: Dr. Philippe Fauchet and Alice Pentland, U. of Rochester, and Alex Pentland, MIT Media Lab)
• Consulting advisor (jointly with Dr. M. Ogihara) to the German Ministry for Science, Education, Research and Technology (through Fraunhofer Institut für Systemtechnik und Innovationsforschung, Karlsruhe), on future directions of information technology and biological research (September, 1998)
• Co-organizer (with Dr. Fred Sherman) of the University of Rochester DNA micro-array/genomics initiative, 1997-98
• Program Committee for the Fourth International Symposium on DNA Based Computing, University of Pennsylvania, June 16--19, 1998
• Invited panel member at the Ford Foundation/FAO workshop: "Apomixis", International Rice Research Institute, Manila, October 11-13, 1993.
• Reviewer for Proceedings of the National Academy of Sciences USA, Nature Biotechnology, Genes and Development, Genetics, Molecular and General Genetics, Plant Cell, Plant Physiology, Trends in Genetics, Trends in Plant Science, Development, and Plant Sexual Reproduction
• ad hoc reviewer for NSF, DOE and USDA since 1992; members of various NSF panels since 2001
• Panelist in DARP/NSF workshop on biosensors in defense application (August '02)
• Member of the Editorial Board, Current Proteomics
• Member, Scientific Advisory Board, Finistere Partners, LLC. (a technology consulting company).

Experience in Industry Research/Management

• July 1999-July 2000: AR was the first management level scientist recruited by Akkadix Corporation. AR identified strategic areas of plant biotechnology research; conceived of a research program on high throughput cis-regulatory element identification for tailor-made plant gene regulation through functional genomics approaches based on microarray-transcriptional profiling and RecA-mediated genome walking; hired two Senior Scientists and five research associates to implement the program and was responsible for five patent filings within this period.
• Aug 2000-Feb 2001: AR conceived of a second research program (involving 25% of total research effort) on developing gene targeting technology for higher plants; was instrumental in developing and successfully completing a large corporate partnership with PanGene Corporation that provided crucial intellectual property for the research area; hired a Senior Scientist and four research associates to begin implementing the project and filed for two patents in this area.
• Feb 2001-June 2001: AR took over senior research management as a Research Director (reporting to CEO/President), was instrumental in developing corporate relations with large pharma and European biotechnology companies.

External Funding

• NSF (September 1, 2002- August 31, 2005) PI: A.R. "A twin-framework to analyze, model and design robust, complex networks using biological and computational principles" EIA-0205061 (active) $3,042,549
• NSF (September 15, 2001-September 14, 2004) PI: A.R. "Causes of robustness and vulnerability in real-world networks: Lessons from molecular biology" EIA-0130059 (active) $501,105
• NSF (February 1, 2000-January 31, 2003) PI: A.R. "Molecular and genetic studies of SHORT INTEGUMETNS1 gene" IBN-9982414 $340,000
• NSF (June 1, 2000-June 1, 2003) Co-PI: A.R. "Integrated undergraduate computational biology program" DUE-9980943 $162,522
• NSF (1998-2002) PI: S. Houde-Walter, Co-PI: AR "MRI: Acquisition of SEM/EDX" (active) $260,000
• NSF (DARPA) (1997- 2001) Co-PIs: A.R. and M. Ogihara "Prototyping DNA Computer."
• NSF (1998- 2000) PI: A.R. "Genetic and molecular analysis of SHORT INTEGUMENTS1 "
• NSF (1996- 1998) PI: A.R. "Homologous recombination in Arabidopsis induced by the HO endonuclease."
• USDA (1992-1995) PI: A.R. "Genetics of female gametogenesis in Arabidopsis thaliana."
• NSF (1992-1994) PI: A.R. "In vivo cloning of defined chromosomal segments into YAC vectors."

Research Mentoring Experience:

1. Graduate students: Teresa Golden (Ph.D., 1999) is a postdoctoral fellow at the University of Alabama Medical School; Marybeth Langer (Ph.D., June, 2002) is a postdoctoral fellow at the Department of Biochemistry, University of Oklahoma. Stephen Schauer (Ph.D., 2002) is a NSF Foreign Fellow at the University of Zurich. Mark Salata, former graduate student, received M.S. in 1993.

2. Postdoctoral Associate, Dr. Jean Lang (Ph.D., U. of Chicago) 1991-1995.

3. AR recruited, supervised and mentored the following senior scientists in an industrial setting:

1999-2001 Dr. Ranjan Perera (PhD, Moscow State University, 1987); Postdoc in Belgium, 1988-90; Postdoc MIT, 1990-96; Research Assistant Professor, Georgia State University, 1996-97; Scientist, Genesys Corp., New Zealand, 1997-99; Senior Scientist, Akkadix Corp. 1999-00; Program Leader, 2000-01; Director of Genomics, Stowers Institute, 2001-02; currently Associate Director of Genomics, ISIS Pharmaceuticals, Carlsbad)

1999-2000 Dr. Min Ni (PhD, Purdue, 1994); Postdoc, UC Berkeley, 1994-99; Senior Scientist, Akkadix Corp., 1999-00; currently Assistant Professor, University of Minnesota.

1999-2001 Dr. Helge Zieler (PhD, Stanford, 1994); Postdoc, NIH, 1994-99; Senior Scientist, Akkadix Corporation, 2000-01; currently Senior Scientist, Chromatin Inc., Chicago.

1. Current postdoctoral researchers: Dr. Shubhada Godbole (from Dec, 2002); Dr. Debalina Ghosh (from Jan, 2003); Dr. Biranchi Patra (from July 2003)

2. Current visiting scientists: Dr. Kathrin Schrick (PhD, UW Seattle, 1995); Postdoc, U. Tübingen; Group leader, ZMBP, Tübingen; Dr. Ping Ao (Physicist, University of Washington, Seattle).

Patent:
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)

Media Reaction on Ray's Research in DNA Computation:

1. BBC channel 4 interview with Ray, Feb 8, 1997; BBC World Service interview with Ray, Feb 24, 1997.

2. Article by Wade in New Scientist, p. 14, February 8, 1997, on work by Ogihara and Ray; news reports in The Daily Telegraph of London, February 18, The International Herald Tribune of Paris, March 14, p.21a, in the New York Times Special CyberTimes Report of May 21, 1997, and in New York Times SCIENCE on August 11, 1998. Ray and Ogihara were "Top choice" for photo-coverage in "One Digital Day: How the microchip is changing our world" (Ed. R. Smolan) (Publisher: The Times Books/Random House, sponsored by Intel Corp.), the latest book of "A Day In The Life" series, April, 1998. Ogihara and Ray were nominated for Discover Magazine 1997 Invention of the Year award.