Papers

25.

Single-cell methylation sequencing data reveals succinct metastatic migration histories and tumor progression models
Liu, Li, Rashidi Mehrabadi, , Sahinalp
Genome Res / RECOMB 2023
 

24.

Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation
Commichaux, Rand, Javkar, Molloy, Pettengill,
BMC Genomics 2023

2022

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, Sankararaman
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.

Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation
Yu, Le, Christensen, Molloy, Warnow
Algorithms Mol Biol 2021 & WABI 2020

19.

Polynomial-time statistical estimation of species trees under gene duplication and loss
Legried, Molloy, Warnow, Roch
J Comp Biol 2021 & RECOMB 2020
   

18.

TIPP2: Metagenomic taxonomic profiling using phylogenetic markers
Shah, Molloy, Pop, Warnow
Bioinformatics 2021
    TIPP v2

17.

Using Constrained-INC for large-scale gene tree and species tree estimation
Le, Sy, Molloy, Zhang, Rao, Warnow
IEEE/ACM TCBB 2021 & AlCoB 2019

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.

Non-parametric correction of estimated gene trees using TRACTION
Christensen, Molloy, Vachaspati, Yammanuru, Warnow
Algorithms Mol Biol 2020 & WABI 2019
 

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.

The performance of coalescent-based species tree estimation methods under models of missing data
Nute, Chou, Molloy, Warnow
BMC Genomics 2018
 

9.

To include or not to include: The impact of gene filtering on species tree estimation methods
Molloy and Warnow
Systematic Biology 2018
 

8.

OCTAL: Optimal completion of gene trees in polynomial time
Christensen, Molloy, Vachaspati, Warnow
Algorithms Mol Biol 2018 & WABI 2017
 

7.

A brief assessment tool for investigating facets of moral judgment from realistic moral vignettes
Kruepke, Molloy, Bresin, Barbey, Verona
Behavior Research Methods 2017

6.

Using edge voxel information to improve motion regression for rs-fMRI connectivity studies
Patriat, Molloy, Birn
Brain Connectivity 2015

5.

The influence of physiological noise correction on test-retest reliability of resting-state functional connectivity
Birn, Cornejo, Molloy, Patriat, Meier, Kirk,
Brain Connectivity 2014

4.

The influence of spatial resolution and smoothing on the detectability of resting-state and task fMRI
Molloy, Meyerand, Birn
Neuroimage 2014

3.

The effect of scan length on the reliability of resting-state fMRI connectivity estimates
Birn, Molloy, Patriat, Parker, Meier, Kirk,
Neuroimage 2013

2.

The effect of resting condition on resting-state fMRI reliability and consistency: A comparison between resting with eyes opened, closed, and fixated
Patriat, Molloy, Meier, Kirk, Nair, , Birn
Neuroimage 2013

1.

Developmental pathways to amygdala-prefrontal function and internalizing symptoms in adolescence
Burghy, Stodola, Ruttle, Molloy, , Davidson, Birn
Nature Neuroscience 2012