Funding

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.


Students and Postdocs

Current Ph.D. Students

Shuqi Yu
Max Bacharach
Yu Sun

Former Ph.D. Students

Brandon Legried [graduated 2020; now postdoc at University of Michigan]
Kun-Chieh (Jason) Wang [graduated 2017; now at Google]

Former Postdocs

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


Surveys

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.

Preprints

On the Effect of Intralocus Recombination on Triplet-Based Species Tree Estimation
To appear in RECOMB 2022. With Max Hill.
Estimating Graph Dimension with Cross-validated Eigenvalues
Submitted, 2021. With Fan Chen, Karl Rohe, Shuqi Yu.
Impossibility of phylogeny reconstruction from k-mer counts
To appear in Annals of Applied Probability. With Wai-Tong Louis Fan and Brandon Legried.
Species tree estimation under joint modeling of coalescence and duplication: sample complexity of quartet methods
To appear in Annals of Applied Probability. With Max Hill and Brandon Legried.
Reducing Seed Bias in Respondent-Driven Sampling by Estimating Block Transition Probabilities
Submitted, 2020. With Yilin Zhang and Karl Rohe.
Coalescent-based species tree estimation: a stochastic Farris transform
To appear in Journal of Mathematical Biology. With Gautam Dasarathy, Elchanan Mossel, Robert Nowak.

Journal Papers and Refereed Proceedings

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.
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.
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.)
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)
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.
Phase transition in the sample complexity of likelihood-based phylogeny inference
Probability Theory and Related Fields, 169(1), 3-62, 2017. With A. Sly.
Access the recommendation on F1000Prime
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.
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.)
Access the recommendation on F1000Prime
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.
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.
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.
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.
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.)
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.
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.
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
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.
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.
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.
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.
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.
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.

updated: 03/01/22