2023
QR-STAR: A Polynomial-Time Statistically Consistent Method for Rooting Species Trees Under the Coalescent.
J. Comput. Biol., November, 2023

Expanding the Class of Global Objective Functions for Dissimilarity-Based Hierarchical Clustering.
J. Classif., November, 2023

Statistically Consistent Rooting of Species Trees Under the Multispecies Coalescent Model.
Proceedings of the Research in Computational Molecular Biology, 2023

2022
Inconsistency of Triplet-Based and Quartet-Based Species Tree Estimation under Intralocus Recombination.
J. Comput. Biol., 2022

Pairwise sequence alignment at arbitrarily large evolutionary distance.
CoRR, 2022

On the Effect of Intralocus Recombination on Triplet-Based Species Tree Estimation.
Proceedings of the Research in Computational Molecular Biology, 2022

2021
Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss.
J. Comput. Biol., May, 2021

Estimating Graph Dimension with Cross-validated Eigenvalues.
CoRR, 2021

2020
Impossibility of phylogeny reconstruction from k-mer counts.
CoRR, 2020

2018
Species Tree Estimation Using ASTRAL: How Many Genes Are Enough?
IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Reducing Seed Bias in Respondent-Driven Sampling by Estimating Block Transition Probabilities.
CoRR, 2018

Asymptotic Seed Bias in Respondent-driven Sampling.
CoRR, 2018

Long-branch attraction in species tree estimation: inconsistency of partitioned likelihood and topology-based summary methods.
CoRR, 2018

Circular Networks from Distorted Metrics.
Proceedings of the Research in Computational Molecular Biology, 2018

On the Variance of Internode Distance Under the Multispecies Coalescent.
Proceedings of the Comparative Genomics - 16th International Conference, 2018

2017
Generalized least squares can overcome the critical threshold in respondent-driven sampling.
CoRR, 2017

Critical threshold for ancestral reconstruction by maximum parsimony on general phylogenies.
CoRR, 2017

Efficient and consistent inference of ancestral sequences in an evolutionary model with insertions and deletions under dense taxon sampling.
CoRR, 2017

Necessary and sufficient conditions for consistent root reconstruction in Markov models on trees.
CoRR, 2017

Coalescent-based species tree estimation: a stochastic Farris transform.
CoRR, 2017

2016
Species Trees from Gene Trees Despite a High Rate of Lateral Genetic Transfer: A Tight Bound (Extended Abstract).
Proceedings of the Twenty-Seventh Annual ACM-SIAM Symposium on Discrete Algorithms, 2016

2015
Data Requirement for Phylogenetic Inference from Multiple Loci: A New Distance Method.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

Species Trees from Gene Trees Despite a High Rate of Lateral Genetic Transfer: A Tight Bound.
CoRR, 2015

Distance-based Species Tree Estimation: Information-Theoretic Trade-off between Number of Loci and Sequence Length under the Coalescent.
Proceedings of the Approximation, 2015

2014
Likelihood-based tree reconstruction on a concatenation of alignments can be positively misleading.
CoRR, 2014

Phase transition on the convergence rate of parameter estimation under an Ornstein-Uhlenbeck diffusion on a tree.
CoRR, 2014

New sample complexity bounds for phylogenetic inference from multiple loci.
Proceedings of the 2014 IEEE International Symposium on Information Theory, Honolulu, HI, USA, June 29, 2014

2013
Robust Estimation of Latent Tree Graphical Models: Inferring Hidden States With Inexact Parameters.
IEEE Trans. Inf. Theory, 2013

Recovering the Treelike Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis.
J. Comput. Biol., 2013

An Analytical Comparison of Multilocus Methods Under the Multispecies Coalescent: The Three-Taxon Case.
Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

2012
An analytical comparison of coalescent-based multilocus methods: The three-taxon case
CoRR, 2012

On Fixed-Price Marketing for Goods with Positive Network Externalities.
Proceedings of the Internet and Network Economics - 8th International Workshop, 2012

Recovering the Tree-Like Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis.
Proceedings of the Research in Computational Molecular Biology, 2012

2011
Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep.
SIAM J. Discret. Math., 2011

Alignment-Free Phylogenetic Reconstruction: Sample Complexity via a Branching Process Analysis
CoRR, 2011

Phase Transition in Distance-Based Phylogeny Reconstruction
CoRR, 2011

Phylogenetic mixtures: Concentration of measure in the large-tree limit.
CoRR, 2011

Identifiability and inference of non-parametric rates-across-sites models on large-scale phylogenies.
CoRR, 2011

2010
Incomplete Lineage Sorting: Consistent Phylogeny Estimation from Multiple Loci.
IEEE ACM Trans. Comput. Biol. Bioinform., 2010

Submodularity of Influence in Social Networks: From Local to Global.
SIAM J. Comput., 2010

Network delay inference from additive metrics.
Random Struct. Algorithms, 2010

On the inference of large phylogenies with long branches: How long is too long?
CoRR, 2010

Alignment-Free Phylogenetic Reconstruction.
Proceedings of the Research in Computational Molecular Biology, 2010

Global Alignment of Molecular Sequences via Ancestral State Reconstruction.
Proceedings of the Innovations in Computer Science, 2010

2009
Shrinkage Effect in Ancestral Maximum Likelihood.
IEEE ACM Trans. Comput. Biol. Bioinform., 2009

Reconstruction on Trees: Exponential Moment Bounds for Linear Estimators.
CoRR, 2009

2008
Sequence Length Requirement of Distance-Based Phylogeny Reconstruction: Breaking the Polynomial Barrier.
Proceedings of the 49th Annual IEEE Symposium on Foundations of Computer Science, 2008

2007
On learning thresholds of parities and unions of rectangles in random walk models.
Random Struct. Algorithms, 2007

Slow emergence of cooperation for win-stay lose-shift on trees.
Mach. Learn., 2007

On the submodularity of influence in social networks.
Proceedings of the 39th Annual ACM Symposium on Theory of Computing, 2007

First to market is not everything: an analysis of preferential attachment with fitness.
Proceedings of the 39th Annual ACM Symposium on Theory of Computing, 2007

2006
A Short Proof that Phylogenetic Tree Reconstruction by Maximum Likelihood Is Hard.
IEEE ACM Trans. Comput. Biol. Bioinform., 2006

A smoothing heuristic for a bilevel pricing problem.
Eur. J. Oper. Res., 2006

Optimal phylogenetic reconstruction.
Proceedings of the 38th Annual ACM Symposium on Theory of Computing, 2006

The Kesten-Stigum Reconstruction Bound Is Tight for Roughly Symmetric Binary Channels.
Proceedings of the 47th Annual IEEE Symposium on Foundations of Computer Science (FOCS 2006), 2006

2005
An approximation algorithm for Stackelberg network pricing.
Networks, 2005

Evolutionary Trees and the Ising Model on the Bethe Lattice: a Proof of Steel's Conjecture.
CoRR, 2005

Learning nonsingular phylogenies and hidden Markov models.
Proceedings of the 37th Annual ACM Symposium on Theory of Computing, 2005