Underline indicates member of Molloy Lab or trainee we supervised/co-supervised
33.
32.
Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads
Keskus, Bryant, Ahmad, Yoo, Aganezov, Goretsky, Donmez, Lansdon, Rodriguez, Park, Liu, Cui, Gardner, McNulty, Sacco, Shetty, Zhao, Tran, Narzisi, Helland, Cook, Chang, Kolesnikov, Carroll, Molloy, Pushel, Guest, Pastinen, Shafin, Miga, Malikić, Day, Robine, Sahinalp, Dean, Farooqi, Paten, Kolmogorov
bioRiv
31.
30.
29.
Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony
Dai, Rubel, Han, Molloy
Algorithms Mol Biol / WABI 2023
Dollo-CDP
28.
Fast, Parallel, and Cache-friendly Suffix Array Construction
Kahn, Rubel, Dhulipala, Molloy, Patro
WABI 2023
CaPS-SA
27.
26.
Improving quartet graph construction for scalable and accurate species tree estimation from gene trees
Han and Molloy
Genome Res / RECOMB 2023
TREE-QMC
25.
24.
23.
Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone
Molloy, Gatesy, Springer
Systematic Biology 2022
+
ASTRAL-BP MLE branch estimator
22.
Inferring population structure in biobank-scale genomic data
Chiu, Molloy, Tan, Talwalkar,
American J Human Genetics 2022
 
SCOPE
21.
Advancing admixture graph estimation via maximum likelihood network orientation
Molloy, Durvasula, Sankararaman
Bioinformatics / ISMB 2021
 
(and )
 
 
OrientAGraph
 
20.
19.
18.
TIPP2: Metagenomic taxonomic profiling using phylogenetic markers
Shah, Molloy, Pop, Warnow
Bioinformatics 2021
 
 
TIPP v2
17.
16.
ASTRAL-Pro: Quartet-based species tree inference despite paralogy
Zhang, Scornavacca, Molloy, Mirarab
Molecular Biology and Evolution 2020
 
 
ASTRAL-pro
15.
FastMulRFS: Fast and highly accurate species tree estimation under generic gene duplication and loss models
Molloy and Warnow
Bioinformatics / ISMB 2020
 
 
(and )
 
FastMulRFS
14.
ILS-Aware analysis of low-homoplasy retroelement insertions: Inference of species trees and introgression using quartets
Springer, Molloy, Sloan, Simmons, Gatesy
Journal of Heredity 2020
Editor's choice
 
 
ASTRAL-BP pipeline
13.
12.
TreeMerge: A new method for improving the scalability of species tree estimation methods
Molloy and Warnow
Bioinformatics / ISMB 2019
 
 
TreeMerge + pipeline
11.
Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge
Molloy and Warnow
Algorithms Mol Biol 2019 & RECOMB-CG 2018
 
 
NJMerge + pipeline
10.
9.
8.
7.
6.
5.
4.
3.
2.