Srinath SridharB. S. Computer Science, University of Texas at Austin, 2003.
Ph. D. Computer Science, Carnegie Mellon University, 2007.
srinath at cs cmu edu
I received my PhD in 2007 and my dissertation can be found here: Algorithms for Analyzing Intraspecific Sequence Variation. Facebook probably knows where I am currently.
Our work (Egan et al.) was listed as one of the contributing papers for Science magazine's breakthrough of the year 2007.
The paper was also listed (at some point) as one of the top 10 most read papers of recent time in nature genetics.
The Parameterized Complexity Newsletter contains an article about our work. It seems like we have a fast algorithm for `people search'. Or at least to find Prof. Buneman. A slashdot reference to our work. A Carnegie Mellon Today article.
We are developing these online tools using methods from the papers below. Note: The tools hosted by CMU are temporarily offline due to security concerns.
Reconstructing maximum parsimony phylogenetic trees from Haplotypes Reconstructing maximum parsimony phylogeny from Genotypes Detecting Population substructure
Publications: Generalizing the Splits Equivalence Theorem and Four Gamete Condition: Perfect Phylogeny on Three State Characters. To appear in SIAM Journal of Discrete Mathematics 2010. Preliminary version of the paper appeared in proc WABI 2009.
A Human Genome-Wide Library of Local Phylogeny Predictions for Whole Genome Inference Problems. In BMC Genomics 2008.
Estimating Local Ancestry in Admixed Populations. In American Journal of Human Genetics 2008.
Direct Maximum Parsimony Phylogeny Reconstruction from Genotype Data. BMC Bioinformatics 2007.
Recurrent DNA copy number variation in the laboratory mouse. Nature Genetics 2007.
Mixed Integer Linear Programming for Maximum Parsimony Phylogeny Inference.
ACM/IEEE Transactions on Computational Biology and Bioinformatics (TCBB).
Journal version: ISBRA 2007 + webserver + max parsimony phylogenies around ever SNP loci (~4 million phylogenies) of the HapMap CEU, YRI populations accessible online + alternate LP formulations.
Efficiently Finding the Most Parsimonious Phylogenetic Tree via Linear ProgrammingIn proc International Symposium on Bioinformatics Research and Applications (ISBRA) 2007.
Won Best Paper Award
An Efficient and Accurate Graph-Based Method to Detect Population Substructure.In proc Research in Computational Molecular Biology (RECOMB) 2007.
Optimal Imperfect Phylogeny Reconstruction and Haplotyping.In Proc Computational Systems Bioinformatics (CSB) 2006.
Algorithms for Efficient Near-Perfect Phylogenetic Tree Reconstruction in Theory and Practice.In ACM/IEEE Transactions on Computational Biology and Bioinformatics(TCBB).
Journal version: IWBRA 2006 + ICALP 2006 + improved analysis + experiments.
Fixed Parameter Tractability of Binary Near-Perfect Phylogenetic Tree Reconstruction.In Proc International Colloquium on Automata, Languages and Programming (ICALP) 2006.
Simple Reconstruction of Binary Near-Perfect Phylogenetic Trees.In Proc International Workshop on Bioinformatics Research and Applications (IWBRA) 2006.
Relaxing Haplotype Block Models for Association Testing.In Proc Pacific Symposium on Biocomputing (PSB) 2006.
Experimental Evaluation of a New Shortest Paths Algorithm.In Proc Algorithm Engineering and Experiments (ALENEX) 2002.
A Heap-Based Inversions-Sensitive Sorting Algorithm.University of Texas, Austin, Computer Science Tech Report.
Evaluation of the Haplotype Motif Model using the Principle of Minimum Description.Carnegie Mellon University, Computer Science Tech Report.
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