Curriculum Vitae Resume

After receiving my BS in math from Caltech, I got an MS in computer science (advisor: Prof. Richard Fateman) and a PhD in math (advisor: Prof. Bernd Sturmfels) from UC Berkeley, specializing in game theory.

I lectured at UC Davis for a quarter, teaching two large calculus classes (two preps), before working as a software engineer for Google for 2½ years, in International Search Quality and Google Book Search. I then moved into computational biology, working as a postdoc first in the Berkeley Phylogenomics Group under Prof. Kimmen Sjölander and then in the Center for Evolution and Cancer under Prof. Carlo Maley.

In September 2014 I joined the Mathematical Biosciences Institute as a postdoctoral fellow.

I'm on LinkedIn, GitHub, Quora, Google+, FriendFeed, and Twitter.

Mathematics of community interactions

I study the dynamics of populations of interacting agents in communities, considering their shared and competing interests and their varying power, information, and resources.

I model the human organism as an evolving ecological community. In particular, in my current position at the Mathematical Biosciences Institute, I study the interaction between cancer and its microenvironment, especially the immune system. More generally, I study mutualistic networks.

My profile on Google Scholar

Select Publications

Modelling the evolution of genetic instability during tumour progression,
by Ruchira S. Datta, Alice Gutteridge, Charles Swanton, Carlo C. Maley, and Trevor A. Graham,
in Evolutionary Applications, Volume 6, Issue 1, pages 20–33, January 2013. doi:10.1111/eva.12024

Finding All Nash Equilbria of a Finite Game Using Polynomial Algebra,
by Ruchira S. Datta,
invited contribution to Economic Theory, published January 2010, Volume 42, issue 1, pp. 55–96.

Berkeley PHOG: PhyloFacts orthology group prediction web server,
by Ruchira S. Datta, Christopher Meacham, Bushra Samad, Christoph Neyer, and Kimmen Sjölander,
in Nucleic Acids Research 2009, doi: 10.1093/nar/gkp373.
Please try the Berkeley PHOG webserver!

Using Computer Algebra To Compute Nash Equilibria,
by Ruchira S. Datta,
in the (refereed) Proceedings of the 2003 International Symposium on Symbolic and Algebraic Computation.

Universality of Nash Equilibria,
by Ruchira S. Datta,
in Mathematics of Operations Research, Volume 28, Number 3, August 2003, 424--32. It is also on the arXiv. An expanded version appears as the second chapter of my Ph.D thesis. The thesis chapter differs from the journal version mostly by including examples, and (I hope) by being more self-contained, especially for those not familiar with game theory. Executive summary: "Every shape arises in game theory."

Ortholog identification in the presence of domain architecture rearrangement,
by Kimmen Sjölander, Ruchira S. Datta, Yaoqing Shen, and Grant Shoffner,
in Briefings in Bioinformatics 2011, September; 12(5): 413–422. doi:10.1093/bib/bbr036

Toward community standards in the quest for orthologs,
by Christophe Dessimoz, Toni Gabaldón, David S. Roos, Erik L. L. Sonnhammer, Javier Herrero, Adrian Altenhoff, Rolf Apweiler, Michael Ashburner, Judith Blake, Brigitte Boeckmann, Alan Bridge, Elspeth Bruford, Mike Cherry, Matthieu Conte, Dannie Durand, Ruchira Datta, Jean-Baka Domelevo Entfellner, Ingo Ebersberger, Michael Galperin, Jacob Joseph, Tina Koestler, Evgenia Kriventseva, Odile Lecompte, Jack Leunissen, Suzanna Lewis, Benjamin Linard, Michael S. Livstone, Hui-Chun Lu, Maria Martin, Raja Mazumder, David Messina, Vincent Miele, Matthieu Muffato, Guy Perrière, Macro Punta, Mathieu Rouard, Thomas Schmitt, Fabian Schreiber, Alan Silva, Kimmen Sjölander, Nives ┼ákunca, Eleanor Stanley, Radek Szklarczyk, Paul Thomas, Ikuo Uchiyama, Michiel Van Bel, Klaas Vandepoele, Albert J. Vilella, Andrew Yates, and Evgeny Zdobnov,
in Bioinformatics, Vol. 28, Issue 6, pp. 900–904. doi:10.1093/bioinformatics/bts050

ModBase, a database of annotated comparative protein structure models, and associated resources,
by Ursula Pieper, Benjamin M. Webb, David T. Barkan, Dina Schneidman-Duhovny, Avner Schlessinger, Hannes Braberg, Zheng Yang, Elaine C. Meng, Eric F. Pettersen, Conrad C. Huang, Ruchira S. Datta, Parthasarathy Sampathkumar, Mallur S. Madhusudan, Kimmen Sjölander, Thomas E. Ferrin, Stephen K. Burley, and Andrej Sali,
in Nucleic Acids Research 2011. doi: 10.1093/nar/gkq1091

SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction,
by Raffi Hagopian, John R. Davidson, Ruchira S. Datta, Bushra Samad, Glen R. Jarvis, and Kimmen Sjölander,
in Nucleic Acids Research 2010.
Please try the SATCHMO-JS webserver!

PLoS Computational Biology Conference Postcards from PSB 2010,
by Ruchira S. Datta, Matthew Lux, and Phil Bourne,
in PLoS Computational Biology.

Live Coverage of Scientific Conferences Using Web Technologies,
by Allyson Lister, Ruchira S. Datta, Oliver Hofmann, Roland Krause, Michael Kuhn, Bettina Roth, and Reinhard Schneider,
in PLoS Computational Biology.

Live Coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009,
by Allyson Lister, Ruchira S. Datta, Oliver Hofmann, Roland Krause, Michael Kuhn, Bettina Roth, and Reinhard Schneider,
in PLoS Computational Biology.

Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase,
by P. Gaudet, L. Lane, P. Fey, A. Bridge, S. Poux, A. Auchincloss, K. Axelsen, S. Braconi Quintaje, E. Boutet, P. Brown, E. Coudert, R.S. Datta, W.C. de Lima, T. de Oliveira Lima, S. Duvaud, N. Farriol-Mathis, S. Ferro Rojas, M. Feuermann, A. Gateau, U. Hinz, C. Hulo, J. James, S. Jimenez, F. Jungo, G. Keller, P. Lemercier, D. Lieberherr, M. Moinat, A. Nikolskaya, I. Pedruzzi, C. Rivoire, B. Roechert, M. Schneider, E. Stanley, M. Tognolli, Kimmen Sjölander, L. Bouguelert, R.L. Chisholm and A. Bairoch,
in Database 2009. doi:10.1093/database/bap016

Polynomial Graphs With Applications To Graphical Games, Extensive-Form Games, and Games With Emergent Node Tree Structures,
by Ruchira S. Datta,
on the arXiv 2006.

Comparison of Wireless Token Ring Protocol with IEEE 802.11,
by Mustafa Ergen, Duke Lee, Ruchira Datta, Jeff Ko, Anuj Puri, Raja Sengupta, and Pravin Varaiya,
in Journal of Internet Technology, Vol. 4, No. 4, October 2003. DOI:10.5297/ser.1201.002

Most of these are from before I became a postdoc. In the previous research groups where I've worked as a postdoc, we generally don't put our presentations on the web.

Applying High-Dimensional Clustering Methods for Phylogenetic Profiling,
slides for a talk I gave in the Student Algebraic Statistics Seminar at the University of California at Berkeley on May 7th, 2007. These slides have evolved from talks I gave to the Evolution Discussion Group Seminar at UC Davis on May 2nd, 2007, at Virginia Bioinformatics Institute on April 10th, 2007, to the Algorithms & Theory Group at IBM Almaden Research Center on March 15th, 2007, and in the Seminar Series in BioMathematical Methodology at Stanford University on March 6th, 2007.

Polynomial Graphs With Applications in Game Theory,
slides for a talk I gave at the Student Algebraic Statistics Seminar at the University of California at Berkeley on December 11th, 2006. These slides have evolved from talks I gave at the Algebra-Geometry-Combinatorics Seminar at San Francisco State University on December 2nd, 2005, at the Algorithmic, Combinatorial and Applicable Real Algebraic Geometry workshop at MSRI on April 14th, 2004 (video), to the Discrete Math & Representation Theory Seminar at the University of California at Davis on February 27th, 2004, and to the Microeconomic Theory Seminar at the University of California at Berkeley on February 23rd, 2004.

Universality of Nash Equilibria,
slides for a talk I gave at the Math Colloquium at Santa Clara University on April 19th, 2005. These slides are very similar to the slides for the talks I gave to the Algorithms & Theory Group at IBM Almaden Research Center on March 15th, 2007, at the Tulane Math Colloquium at Tulane University on February 3rd, 2004, to the Math Colloquium at the University of Arizona on January 22nd, 2004, to the Algebraic Geometry Seminar at Georgia Tech on November 14th, 2003, to the Theory Group at Microsoft Research on March 5th, 2003, at MSRI on March 3rd, 2003, to the Computational Algebra Seminar at the University of California at Berkeley on January 28th, 2003, to the Combinatorics Seminar at the University of Minnesota on September 20th, 2002, and at Symbolic Computational Algebra 2002 at University of Western Ontario on July 17th, 2002.

I assiduously liveblog talks and conferences, alone or in collaboration. I co-authored a paper on liveblogging.

2nd International Biennial Evolution and Cancer Conference 2013

Big Data in Biomedicine 2013

Dance As A Way of Knowing: Philosophy Talk Live with guest Alva Noë, January 27th, 2013

What Now? Health Reform in the Aftermath of the Supreme Court Decision, a panel discussion at UCSF on June 29th, 2012, the day after the Supreme Court upheld the Affordable Care Act

When Good Bugs Go Bad: Microbiome Dynamics and Disease, from the 2012 meeting of the American Society for Microbiology. (Note: I liveblogged this from the livestream; Thomas Sharpton and Erick Matsen liveblogged ASM 2012 itself.)

International Human Microbiome Congress 2012

Rita Colwell: Global Infectious Diseases - Climate, Oceans, and Cholera, March 17th, 2011

Rita Colwell: Genomic Sequencing as a Useful Tool for Identification of Pathogens, March 16th, 2011

International Human Microbiome Congress 2011

Human Microbiome Research Conference 2010

Lake Arrowhead Microbial Genomics 2010

Pacific Symposium for Bioinformatics 2010

Quest for Orthologs 2009

Intelligent Systems for Molecular Biology / European Conference on Computational Biology 2009

I tutor high school mathematics at Jewish Family and Children's Services in San Francisco.

I am one of the coordinators of the volunteer translation project which has translated Développement d'applications avec Objective Caml, the French OCaml book published by O'Reilly France, into Developing applications with Objective Caml, its English version. Both versions can be read on the Web.

I drew the Bengali glyphs in xmbdfed and contributed them to the GNU Unifont. You should be able to see them here starting in column 098.

I volunteer with Factory Farming Awareness Coalition. Read the UCSF Academic Senate Resolution calling for phasing out factory farmed meat. Cf. my liveblog of Lance Price's talk at Lake Arrowhead Microbial Genomics 2010.

I support through social media and donations. Bringing clean water and sanitation to everyone is one of the greatest leverage points for breaking the vicious cycle of disease and poverty.

The picture of the Tree of Life at the upper left has special meaning for me as a mathematical biologist. Mathematics is the study of pattern, and while life's knotty complexity is intricate, it does reveal pattern to the discerning eye—therein lies its fascination. I see the rising sun as signifying our growing knowledge.

Thanks to the artist Dawbun for licensing this image for noncommercial use.

I purchased EPS files of the lotus icons (closed Closed Lotus and open Open Lotus) by silverrose1 from CanStockPhoto.

Ruchira S. Datta
Research Specialist
Center for Evolution and Cancer
Helen Diller Family Comprehensive Cancer Center
Department of Surgery
University of California, San Francisco
2340 Sutter St. Box 1351
San Francisco, California 94143-1351