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