Papers

Underline indicates member of Molloy Lab or trainee we mentored/co-mentored

See here for a running list of minor corrections

Preprints

38.

Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet
Sapoval, Liu, Curry, Kille, Huang, Kokroko, Nute, Tyshaieva, Dilthey, Molloy, Treangen

Refereed Papers

2025

37.

Dynamic programming algorithms for fast and accurate cell lineage tree reconstruction from CRISPR-based lineage tracing data
Dai and Molloy
RECOMB 2025
    Star-CDP

36.

A Partition Function Algorithm to Evaluate Inferred Subclonal Structures in Single-Cell Sequencing
Rashidi Mehrabadi, Sadeqi Azer, Bridgers, Pérez-Guijarro, Marie, Yang, Gruen, Wu, Robinson, Liu, Kizilkale, Kelly, Smith, Chin, Ebersole, Burkett, Buluç, Lee, Molloy, Przytycka, Merlino, Day, Malikić, Ergun, Sahinalp
RECOMB 2025

35.

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
Nature Biotechnology

34.

Complete sequencing of ape genomes
Yoo et al.
Nature

33.

Improved robustness to gene tree incompleteness, estimation errors, and systematic homology errors with weighted TREE-QMC
Han and Molloy
Systematic Biology
    TREE-QMC

32.

Stochastic modelling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones
Hirsch, Pal, Rashidi Mehrabadi, Malikić, Gruen, Sassano, Pérez-Guijarro, Merlino, Sahinalp, Molloy, Day, Przytycka
Cell Systems

2024

31.

Detectability of Varied Hybridization Scenarios using Genome-Scale Hybrid Detection Methods
Bjorner, Molloy, Dewey, Solís-Lemus
The Bulletin of the Society of Systematic Biologists

30.

Genetic and behavioral differences between above and below ground Culex pipiens bioforms
Bell, Noreuil, Molloy, Fritz
Heredity

29.

Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem
Dai, Rubel, Han, Molloy
WABI 2023 / Algorithms Mol Biol
    Dollo-CDP

28.

Fast, Parallel, and Cache-friendly Suffix Array Construction
Kahn, Rubel, Molloy, Dhulipala, Patro
WABI 2023 / Algorithms Mol Biol
  CaPS-SA

2023

27.

Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model
Han and Molloy
WABI 2023 / Algorithms Mol Biol

26.

Improving quartet graph construction for scalable and accurate species tree estimation from gene trees
Han and Molloy
RECOMB 2023 / Genome Research
      TREE-QMC

25.

Single-cell methylation sequencing data reveals succinct metastatic migration histories and tumor progression models
Liu, Li, Rashidi Mehrabadi, Schäffer, Pratt, Crawford, Malikić, Molloy, Gopalan, Mount, Ruppin, Aldape, Sahinalp
RECOMB 2023 / Genome Research
 

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, Pightling, Hoffmann, Pop, Jayeola, Foley, Luo
BMC Genomics

2022

23.

Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone
Molloy, Gatesy, Springer
Systematic Biology
  + ASTRAL-BP MLE branch estimator

Postdoc @ UCLA

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
ISMB 2021 / Bioinformatics
  (and )     OrientAGraph  

Phd @ UIUC

20.

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

19.

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

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
AlCoB 2019 / IEEE/ACM TCBB 2021

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
ISMB 2020 / Bioinformatics 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
WABI 2019 / Algorithms Mol Biol 2020
 

12.

TreeMerge: A new method for improving the scalability of species tree estimation methods
Molloy and Warnow
ISMB 2019 / Bioinformatics 2019
    TreeMerge + pipeline

11.

Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge
Molloy and Warnow
RECOMB-CG 2018 / Algorithms Mol Biol 2019
    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
WABI 2017 / Algorithms Mol Biol 2018
 

7.

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

REU + Postbac @ UW-Madison

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, Nair, Meyerand, Prabhakaran
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, Nair, Meyerand, Prabhakaranan
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, Meyerand, Prabhakaran, Birn
Neuroimage 2013

1.

Developmental pathways to amygdala-prefrontal function and internalizing symptoms in adolescence
Burghy, Stodola, Ruttle, Molloy, Armstrong, Oler, Fox, Hayes, Kalin, Essex, Davidson, Birn
Nature Neuroscience 2012