Ruchira S. Datta's Homepage

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

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.