I gratefully acknowledge current support from NSF grants DMS-1614242 and CCF-1740707 (TRIPODS), and a Simons Fellowship. Past funding includes NSF grants DMS-1248176 and DMS-1149312 (CAREER), and an Alfred P. Sloan Research Fellowship.

arXiv, Google Scholar, dblp, PubMed

Reducing Seed Bias in Respondent-Driven Sampling by Estimating Block Transition
Probabilities

Preprint, 2018. With Yilin Zhang and Karl Rohe.

Hands-on introduction to sequence-length requirements in phylogenetics

Preprint, 2018.

Asymptotic seed bias in respondent-driven sampling

Preprint, 2018. With Yuling Yan, Bret Hanlon and Karl Rohe.

Long-branch attraction in species tree estimation: inconsistency of
partitioned likelihood and topology-based summary methods

To appear in Systematic Biology, 2018. With Michael Nute and Tandy Warnow.

Book review of "Phylogeny-Discrete and random processes in evolution by Mike Steel"

To appear in Bulletin of the AMS, 2018.

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.

Species trees are recoverable from unrooted gene tree topologies under a constant rate of
horizontal gene transfer

Preprint, 2017. With C. Daskalakis.

Generalized least squares can overcome the critical threshold in respondent-driven sampling

Proceedings of the National Academy of Sciences, 115(41):10299-10304, 2018. With Karl Rohe.

Species tree estimation using ASTRAL: how many genes are enough?

IEEE/ACM Trans. Comput. Biology Bioinform., 15(5):1738--1747, 2018. With S. Shekhar and S. Mirarab.

Conference abstract in Proceedings of RECOMB 2017, 393-395.

Conference abstract in Proceedings of RECOMB 2017, 393-395.

Geometry of the sample frequency spectrum and the perils of demographic inference

Genetics, 210(2):665-682, 2018. With Zvi Rosen, Anand Bhaskar, Yun S. Song.

(Featured in ISSUE HIGHLIGHTS in Genetics, October 1, 2018.)

(Featured in ISSUE HIGHLIGHTS in Genetics, October 1, 2018.)

Necessary and sufficient conditions for consistent root reconstruction in Markov models
on trees

Electronic Journal of Probability, Volume 23, paper no. 47, 24 pp., 2018. With L. Fan.

On the Variance of Internode Distance Under the Multispecies Coalescent

Proceedings of RECOMB-CG 2018, 196-206.

Circular Networks from Distorted Metrics

Proceedings of RECOMB 2018, 167-176. With J. Wang.

(Best Paper Award, RECOMB 2018)

(Best Paper Award, RECOMB 2018)

Distance-based species tree estimation
under the coalescent: information-theoretic trade-off between number of loci and sequence length

Ann. Appl. Probab., 27(5)-2926-2955, 2017. With E. Mossel.

Conference abstract in Proceedings of RANDOM 2015, 931-942.

Conference abstract in Proceedings of RANDOM 2015, 931-942.

Phase transition in the sample complexity of likelihood-based
phylogeny inference

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.

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.

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.

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.

(Honorable Mention, 2018 Marcus W. Feldman Prize in Theoretical Population Biology.)

(Honorable Mention, 2018 Marcus W. Feldman Prize in Theoretical Population Biology.)

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.

Journal version in IEEE/ACM Trans. Comput. Biology Bioinform., 12(2):422-432, 2015.

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.

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.

Conference abstract in Proceedings of RECOMB 2010, 123-137.

An analytical comparison of coalescent-based multilocus methods: The three-taxon case

Proceedings of PSB 2013, 297-306.

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.

Conference abstract in Proceedings of ICS 2010, 358-369.

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.

Journal version in Journal of Computational Biology, 20(2):93-112, 2013.

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.

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.

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.

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.)

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.

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.

Journal version in Stochastic Processes and their Applications, 122(12):3852-3874, 2012.

Shrinkage Effect in Ancestral Maximum Likelihood

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6(1):126-133, 2009.
With E. Mossel, M. Steel.

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.

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 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

Review in The Daily Telegraph

Review in PhysOrg.com

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.

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.

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.

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.

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.

Journal version in Probability Theory and Related Fields, 149(1-2):149-189, 2011.

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.

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.

Journal version in Annals of Applied Probability, 16(2):583-614, 2006.

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.

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.

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.

Journal version in Physics of Fluids, 14(10), 2002.

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