Funding

My work is currently supported by NSF grants DMS-1149312 (CAREER), DMS-1614242 and CCF-1740707 (TRIPODS). Past funding includes NSF grant DMS-1248176 and an Alfred P. Sloan Research Fellowship.


External Profiles

arXiv, Google Scholar, dblp, PubMed


Preprints

Generalized least squares can overcome the critical threshold in respondent-driven sampling
Preprint, 2017. With Karl Rohe.
Critical threshold for ancestral reconstruction by maximum parsimony on general phylogenies
Preprint, 2017. With Jason Wang.
Coalescent-based species tree estimation: a stochastic Farris transform
Preprint, 2017. With Gautam Dasarathy, Elchanan Mossel, Robert Nowak.
Efficient and consistent inference of ancestral sequences in an evolutionary model with insertions and deletions under dense taxon sampling
Preprint, 2017. With L. Fan.
Necessary and sufficient conditions for consistent root reconstruction in Markov models on trees
Preprint, 2017. With L. Fan.
Circular Networks from Distorted Metrics
Preprint, 2017. With J. Wang.
Species tree estimation using ASTRAL: how many genes are enough?
Preprint, 2017. With S. Shekhar and S. Mirarab.
Conference abstract in Proceedings of RECOMB 2017, 393-395.
Species trees are recoverable from unrooted gene tree topologies under a constant rate of horizontal gene transfer
Preprint, 2017. With C. Daskalakis.
Conference abstract in ACM-SIAM SODA 2016, 1621-1630.
Phase transition in the sample complexity of likelihood-based phylogeny inference
To appear in Probability Theory and Related Fields, 2017. With A. Sly.
Distance-based species tree estimation under the coalescent: information-theoretic trade-off between number of loci and sequence length
To appear in The Annals of Applied Probability, 2017. With E. Mossel.
Conference abstract in Proceedings of RANDOM 2015, 931-942.

Journal Papers

Phase transition on the convergence rate of parameter estimation under an Ornstein-Uhlenbeck diffusion on a tree
Journal of Mathematical Biology, 74(1):355--385, 2017. With C. Ane and L. Ho.
On the robustness to gene tree estimation error (or lack thereof) of coalescent-based species tree methods
Systematic Biology, 64(4):663--676, 2015. With T. Warnow.
Data requirement for phylogenetic inference from multiple loci: A new distance method
IEEE/ACM Trans. Comput. Biology Bioinform., 12(2):422-432, 2015. With Gautam Dasarathy and Robert Nowak.
Conference abstract in Proceedings of ISIT 2014, 2037-2041.
Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
Theoretical Population Biology, 100:56-62, 2015. With M. Steel.
Recovering the tree-like trend of evolution despite extensive lateral genetic transfer: A probabilistic analysis
Journal of Computational Biology, 20(2):93-112, 2013. With S. Snir.
Conference abstract in Proceedings of RECOMB 2012, 224-238.
Identifiability and inference of non-parametric rates-across-sites models on large-scale phylogenies
Journal of Mathematical Biology, 67(4):767-797, 2013. With E. Mossel.
Robust Estimation of Latent Tree Graphical Models: Inferring Hidden States with Inexact Parameters
IEEE Transactions on Information Theory, 59(7):4357-4373, 2013. With E. Mossel and A. Sly.
Alignment-Free Phylogenetic Reconstruction: Sample Complexity via a Branching Process Analysis
Annals of Applied Probability, 23(2):693-721, 2013. With C. Daskalakis.
Conference abstract in Proceedings of RECOMB 2010, 123-137.
Phylogenetic Mixtures: Concentration of Measure in the Large-Tree Limit
Annals of Applied Probability, 22(6):2429-2459, 2012. With E. Mossel.
Global Alignment of Molecular Sequences via Ancestral State Reconstruction
Stochastic Processes and their Applications, 122(12):3852-3874, 2012. With A. Andoni, C. Daskalakis, and A. Hassidim.
Conference abstract in Proceedings of ICS 2010, 358-369.
Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep
SIAM J. Discrete Math., 25(2):872-893, 2011. With C. Daskalakis, E. Mossel.
Conference abstract in Proceedings of RECOMB 2009, 451-465.
On the inference of large phylogenies with long branches: How long is too long?
Bulletin of Mathematical Biology, 73(7):1627-1644, 2011. With E. Mossel and A. Sly.
Reconstruction on Trees: Exponential Moment Bounds for Linear Estimators
Electronic Communications in Probability, 16:251-261, 2011. With Y. Peres.
Evolutionary Trees and the Ising Model on the Bethe Lattice: A Proof of Steel's Conjecture
Probability Theory and Related Fields, 149(1-2):149-189, 2011. With C. Daskalakis, E. Mossel.
Conference abstract in Proceedings of ACM STOC 2006, 159-168.
Network Delay Inference from Additive Metrics
Random Structures and Algorithms, 37(2):176-203, 2010. With S. Bhamidi and R. Rajagopal.
Incomplete Lineage Sorting: Consistent Phylogeny Estimation from Multiple Loci
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(1):166-171 , 2010. With E. Mossel.
Submodularity of Influence in Social Networks: From Local to Global
SIAM J. Comput., 39(6):2176-2188, 2010. With E. Mossel.
Conference abstract in Proceedings of ACM STOC 2007, 128-134.
Toward Extracting All Phylogenetic Information from Matrices of Evolutionary Distances
Science, 327(5971):1376 - 1379, 2010. (Posted by permission of the AAAS for personal use, not for redistribution.)
Shrinkage Effect in Ancestral Maximum Likelihood
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6(1):126-133, 2009. With E. Mossel, M. Steel.
On Learning Thresholds of Parities and Unions of Rectangles in Random Walk Models
Random Structures and Algorithms, 31(4):406-417, 2007.
Slow Emergence of Cooperation for Win-Stay Lose-Shift on Trees
Machine Learning 67(1-2):7-22, 2007. (Special Issue on Learning and Computational Game Theory) With E. Mossel.
Upstream Reciprocity and the Evolution of Gratitude
Proceedings of the Royal Society B: Biological Sciences, 274(1610):605-609, 2007. With M. Nowak.
Review in The Daily Telegraph
Review in PhysOrg.com
Learning nonsingular phylogenies and hidden Markov models
Annals of Applied Probability, 16(2):583-614, 2006. With E. Mossel.
Conference abstract in Proceedings of ACM STOC 2005, 366-375.
A smoothing heuristic for a bilevel pricing problem
European Journal of Operational Research, 174(3):1396-1413, 2006. With J.P. Dussault, P.Marcotte, G. Savard.
A Short Proof that Phylogenetic Tree Reconstruction by Maximum Likelihood is Hard
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(1):92-94, 2006.
Bounding Fastest Mixing
Electronic Communications in Probability, 10:282-296, 2005.
Design and Analysis of an Approximation Algorithm for Stackelberg Network Pricing
Networks, 46(1):57-67, 2005. With P. Marcotte, G. Savard.
Transient Growth in Taylor-Couette Flow
Physics of Fluids, 14(10), 2002. With H. Hristova, P. Schmid, L. Tuckerman.
Conference abstract in Theoretical and Computational Fluid Dynamics 16:43-48, 2002.
Non-colliding Random Walks, Tandem Queues and Discrete Orthogonal Polynomial Ensembles
Electronic Journal of Probability, 7:1-24, 2002. With W. Koenig, Neil O'Connell.

Conference Papers

Species tree estimation using ASTRAL: how many genes are enough?
Proceedings of RECOMB 2017, 393-395. With S. Shekhar and S. Mirarab.
Species trees from gene trees despite a high rate of lateral genetic transfer: A tight bound
Proceedings of ACM-SIAM SODA 2016, 1621-1630. With C. Daskalakis.
Distance-based species tree estimation under the coalescent: information-theoretic trade-off between number of loci and sequence length
Proceedings of RANDOM 2015, 931-942. With E. Mossel.
New sample complexity bounds for phylogenetic inference from multiple loci
Proceedings of ISIT 2014, 2037-2041. With G. Dasarathy and R. Nowak.
Journal version in IEEE/ACM Trans. Comput. Biology Bioinform., 12(2):422-432, 2015.
An analytical comparison of coalescent-based multilocus methods: The three-taxon case
Proceedings of PSB 2013, 297-306.
On Fixed-Price Marketing for Goods with Positive Network Externalities
Proceedings of WINE 2012, 532-538. With V. Mirrokni and M. Sundararajan.
Recovering the tree-like trend of evolution despite extensive lateral genetic transfer: A probabilistic analysis
Proceedings of RECOMB 2012, 224-238. With S. Snir.
Journal version in Journal of Computational Biology, 20(2):93-112, 2013.
Alignment-Free Phylogenetic Reconstruction
Proceedings of RECOMB 2010, 123-137. With C. Daskalakis.
Journal version in Annals of Applied Probability, 23(2):693-721, 2013.
Global Alignment of Molecular Sequences via Ancestral State Reconstruction
Proceedings of ICS 2010, 358-369. With A. Andoni, C. Daskalakis, and A. Hassidim.
Journal version in Stochastic Processes and their Applications, 122(12):3852-3874, 2012.
Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep
Proceedings of RECOMB 2009, 451-465. With C. Daskalakis, E. Mossel.
Journal version in SIAM J. Discrete Math., 25(2):872-893, 2011.
Sequence-Length Requirement of Distance-Based Phylogeny Reconstruction: Breaking the Polynomial Barrier
Proceedings of IEEE FOCS 2008, 729-738.
On the Submodularity of Influence in Social Networks
Proceedings of ACM STOC 2007, 128-134. With E. Mossel.
Journal version in SIAM J. Comput. 39(6):2176-2188, 2010.
First to Market is not Everything: an Analysis of Preferential Attachment with Fitness
Proceedings of ACM STOC 2007, 135-144. With C. Borgs, J. Chayes and C. Daskalakis.
The Kesten-Stigum Reconstruction Bound Is Tight for Roughly Symmetric Binary Channels
Proceedings of IEEE FOCS 2006, 518-530. With C. Borgs, J. Chayes, and E. Mossel.
Optimal Phylogenetic Reconstruction
Proceedings of ACM STOC 2006, 159-168. With C. Daskalakis, E. Mossel.
Journal version in Probability Theory and Related Fields, 149(1-2):149-189, 2011.
Learning nonsingular phylogenies and hidden Markov models
Proceedings of ACM STOC 2005, 366-375. With E. Mossel.
Journal version in Annals of Applied Probability, 16(2):583-614, 2006.
Transient growth in exactly counter-rotating Couette-Taylor flow
Theoretical and Computational Fluid Dynamics 16:43-48, 2002. With H. Hristova, P. Schmid, L. Tuckerman.
Journal version in Physics of Fluids, 14(10), 2002.

Theses

Markov Models on Trees: Reconstruction and Applications
Ph.D. Thesis, University of California, Berkeley, 2007.
Tarification optimale: Complexite et approximation [Optimal pricing: Complexity and approximation]
Master's Thesis, Ecole Polytechnique, Montreal, 2003.

Coauthors

Alexandr Andoni, Cecile Ane, Shankar Bhamidi, Christian Borgs, Jennifer Chayes, Jennifer Chayes, Constantinos Daskalakis, Jean-Pierre Dussault, Wai-Tong (Louis) Fan, Avinatan Hassidim, Lam Ho, Hristina Hristova, Wolfgang Koenig, Patrice Marcotte, Siavash Mirarab, Vahab Mirrokni, Elchanan Mossel, Martin Nowak, Robert Nowak, Neil O'Connell, Yuval Peres, Ram Rajagopal, Karl Rohe, Gilles Savard, Peter Schmid, Shubhanshu Shekhar, Allan Sly, Sagi Snir, Mike Steel, Mukund Sundararajan, Laurette Tuckerman, Kun-Chieh (Jason) Wang, Tandy Warnow


last modified: aug 25, 2017