Curriculum Vitae Resume
`datta.53@mbi.osu.edu`

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.

### 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 Škunca, 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

**Algebraic Methods in Game Theory**

my Ph.D dissertation in mathematics;

also in **PostScript**

**Using Computer Algebra To Compute
Nash Equilibria**

my computer science master's project report;

also in **PostScript**

Two posts on the Official Google Blog, Introduction to Search Quality and Technologies behind Google Ranking, explain a bit about the problems I worked on as a software engineer in International Search Quality at Google, working on synonyms.

Example queries: [gudrun thorsdottir] and Serbian [srpski]

Query
language determination using query terms and interface language,

US Patent 8,762,358. Inventors: Datta, Ruchira S; Lopiano, Fabio.

Augmenting queries with synonyms from synonyms map,

US Patent 8,255,376. Inventors: Datta, Ruchira S.

Simplifying query terms with transliteration,

US Patent 7,835,903. Inventors: Datta, Ruchira S.

Augmenting
queries with synonyms selected using language statistics,

U.S. Patent 7,475,063. Inventors: Datta, Ruchira S; Lopiano, Fabio.

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.

**Modeling
Mimicry in the Microenvironment**,

video of a talk I gave in the Workshop on the Ecology
and Evolution of Cancer on September 16th, 2014.

**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.

**The
Mathematics of Web Information Retrieval (video)**,

a talk I gave at the Industrial
Problems Seminar at IMA
on February 3rd, 2006,
and to math and computer science undergraduates at SFSU
on December 2nd, 2006.

**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.

**PHIL: The Probabilistic Hierarchical Inferential
Learner**,

slides for a talk I gave on April 9th, 2005 at the
Tenth Bay Area
Discrete Math Day
held at San Jose State
University.

**Using Computer Algebra To Compute
Nash Equilibria**,

slides for a talk I gave on August 5, 2003 at the
International Symposium
on Symbolic and Algebraic Computation 2003
held at Drexel University
in Philadelphia,
and at the NSF/DARPA CARGO Review Meeting,
Santa Rosa, California on May 12, 2003.

**Stochastic Stability In
Evolutionary Game Theory**,

slides introducing discussion
of The
Evolution of Conventions and Stochastic
Evolutionary Game Dynamics on July 29th, 2003 at the
systems biology journal club held at Arkin Laboratory for
Dynamical Genomics at LBL.

**Leveraging Algebra and Logic To
Model Biological Systems**,

a paper for CS 294, Section 8:
Computational Biology for Computer Scientists.

**Computing Handelman
Representations**,

slides for a talk I gave at Mathematical Theory of
Networks and Systems 2002 on August 14th, 2002.

**Computing With Polynomials: A
Personal Odyssey**,

a paper for CS 282:
Algebraic Algorithms.

**Discussion** of Refactoring:
Improving the Design of Existing Code

by Martin Fowler for CS 294, Section 1:
Software Development.
I should point out that I actually think
refactoring is a very valuable activity,
which may not be evident from the presentation above.
My task
was to lead a discussion for an hour-and-a-half,
which I couldn't very well do by saying
Hey, everybody! Isn't refactoring great?

**Finding Representations for
Nonnegative Polynomials on Semialgebraic Sets**,

the talk
I gave for my qualifying examination and at the Informal
Optimization Seminar at UC Davis.

**Implementing the Wireless Token Ring Protocol on
QNX**,

about my work for the Communication
Systems subproject
of the Automated
Vehicle Control and Safety Systems project
of California PATH (Partners for Advanced
Transit and Highways).

**Programs, Proofs, and Service
Networks**,

a presentation for
the MICA project, of which I
was a member.

**Survey**
of A Type System for
Higher-Order Modules,

by Karl
Crary, Robert Harper, and Derek Dreyer,
for CS 263: Design and Analysis
of Programming Languages.

**Using Semidefinite Programming for
Minimizing Polynomials**,

a paper for EE227A: Convex
optimization and applications
and Math 170:
Introduction to Optimization,
with utility
code in OCaml.

**Modular Network
Architecture: Link Module Interface**,

which I presented at the
Illinois/Berkeley
Workshop on Wireless Networks and Convergence
hosted by Prof. P. R.
Kumar and his group in the
Department of Electrical and
Computer Engineering,
University of
Illinois, Urbana-Champaign.

**Implementing the Wireless
Token Ring Protocol
As a Linux Kernel Module**,

which I did for the Wireless Token Ring
Protocol Project
of the Berkeley
Web Over Wireless Group, of which I was a member.

**Survey** of Using Bayesian Networks to Analyze
Expression Data

by Nir
Friedman, Michal
Linial, Iftach
Nachman, and Dana Pe'er,
for Math 290: Research Seminar
in Computational Biology.

I was on the organizing committe for Bay Area Discrete Math Day (BAD Math Day) from 2006 to 2009. I was the local organizer for the Twelfth BAD Math Day, which took place at Google on April 15th, 2006. You can watch all the talks on video. I was also local coorganizer for the Sixteenth BAD Math Day which took place at MSRI, Berkeley on April 5th, 2008.

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

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

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 water.org 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.

My Blogs: Mind Without Borders and Datta Analysis.

My Erdős number is 4.

What Do These People Have In Common?

Caltech Chamber Music, where I played piano as an accompanist for four years.

Pendemonium will custom grind italic nibs onto fountain pens for you.

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 and open ) 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

Ruchira.Datta@ucsfmedctr.org