I gratefully acknowledge current support from NSF grants DMS-1902892, DMS-1916378, and DMS-2023239 (TRIPODS Phase II).

Past funding includes NSF grants DMS-1248176, DMS-1149312 (CAREER), DMS-1614242, and CCF-1740707 (TRIPODS Phase I), as well as an Alfred P. Sloan Research Fellowship, a Simons Fellowship, and a Vilas Associates Award.

Hongyi Huang

Max Hill

Yu Sun

Shuqi Yu

Brandon Legried
[graduated 2020; now postdoc at Georgia Institute of Technology]

Kun-Chieh (Jason) Wang [graduated 2017; now at Google]

Wai Tong (Louis) Fan
[2015-2018; now assistant professor at Indiana University Bloomington]

Modern Discrete Probability: an Essential Toolkit

To be published by Cambridge University Press.

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

Bulletin of the AMS, 56:527-533, 2019.

Hands-on introduction to sequence-length requirements in phylogenetics

Bioinformatics and Phylogenetics. Computational Biology, vol 29. Springer, 2019.

Statistically consistent rooting of species trees under the multi-species coalescent model

To appear in RECOMB 2023. With Yasamin Tabatabaee and Tandy Warnow.

Inconsistency of triplet-based and quartet-based species tree estimation under intralocus recombination

To appear in Journal of Computational Biology. With Max Hill.

Expanding the class of global objective functions for dissimilarity-based
hierarchical clustering

Submitted.

Pairwise sequence alignment at arbitrarily large evolutionary distance

Submitted. With Brandon Legried.

Estimating Graph Dimension with Cross-validated Eigenvalues

Submitted. With Fan Chen, Karl Rohe, Shuqi Yu.

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

Submitted. With Yilin Zhang and Karl Rohe.

Impossibility of phylogeny reconstruction from k-mer counts

Annals of Applied Probability, 32(6):4893-4913, 2022. With Wai-Tong Louis Fan and Brandon Legried.

Species tree estimation under joint modeling of coalescence and duplication:
sample complexity of quartet methods

Annals of Applied Probability, 32(6): 4681-4705, 2022. With Max Hill and Brandon Legried.

On the Effect of Intralocus Recombination on Triplet-Based Species Tree Estimation

RECOMB 2022. With Max Hill.

A stochastic Farris transform for genetic data under the multispecies coalescent with applications to data requirements

Journal of Mathematical Biology, 84(5):36, April 2022. With Gautam Dasarathy, Elchanan Mossel, Robert Nowak.

Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss

Journal of Computational Biology, 28(5):452-468, 2021. With Brandon Legried, Erin Molloy, and Tandy Warnow.

Conference version in Proceedings of RECOMB 2020, 120-135.

Conference version in Proceedings of RECOMB 2020, 120-135.

Sufficient condition for root reconstruction by parsimony on binary trees with general weights

Electronic Communications in Probability, 26:1-13, 2021. With Jason Wang.

Impossibility of consistent distance estimation from sequence lengths under
the TKF91 model

Bulletin of Mathematical Biology, 82(9):123, 2020. With Wai-Tong Louis Fan and Brandon Legried.

Asymptotic seed bias in respondent-driven sampling

Electronic Journal of Statistics, 14(1):1577-1610, 2020. With Yuling Yan, Bret Hanlon and Karl Rohe.

Statistically consistent and computationally efficient inference of
ancestral DNA sequences in the TKF91 model under dense taxon sampling.

Bulletin of Mathematical Biology, 82(2):21, 2020. With L. Fan.

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

Systematic Biology, Volume 68, Issue 2, March 2019, Pages 281-297. With Michael Nute and Tandy Warnow.

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.