The effect of scan length on the reliability of resting-state fMRI connectivity estimates. - Rasmus M. Birn; Erin K. Molloy; Rémi Patriat; Taurean Parker; Timothy B. Meier; Gregory R. Kirk; Veena A. Nair; Mary Elizabeth Meyerand; Vivek Prabhakaran (NeuroImage, 2013)

The effect of resting condition on resting-state fMRI reliability and consistency: A comparison between resting with eyes open, closed, and fixated. - Rémi Patriat; Erin K. Molloy; Timothy B. Meier; Gregory R. Kirk; Veena A. Nair; Mary E. Meyerand; Vivek Prabhakaran; Rasmus M. Birn (NeuroImage, 2013)

The Influence of Physiological Noise Correction on Test-Retest Reliability of Resting-State Functional Connectivity. - Rasmus M. Birn; Maria Daniela Cornejo; Erin K. Molloy; Rémi Patriat; Timothy B. Meier; Gregory R. Kirk; Veena A. Nair; Mary Elizabeth Meyerand; Vivek Prabhakaran (Brain Connect., 2014)

The influence of spatial resolution and smoothing on the detectability of resting-state and task fMRI. - Erin K. Molloy; Mary E. Meyerand; Rasmus M. Birn (NeuroImage, 2014)

Using Edge Voxel Information to Improve Motion Regression for rs-fMRI Connectivity Studies. - Rémi Patriat; Erin K. Molloy; Rasmus M. Birn (Brain Connect., 2015)

Optimal Completion of Incomplete Gene Trees in Polynomial Time Using OCTAL. - Sarah A. Christensen; Erin K. Molloy; Pranjal Vachaspati; Tandy J. Warnow (WABI, 2017)

NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees. - Erin K. Molloy; Tandy J. Warnow (RECOMB-CG, 2018)

OCTAL: Optimal Completion of gene trees in polynomial time. - Sarah A. Christensen; Erin K. Molloy; Pranjal Vachaspati; Tandy J. Warnow (Algorithms Mol. Biol., 2018)

Using INC Within Divide-and-Conquer Phylogeny Estimation. - Thien Le; Aaron Sy; Erin K. Molloy; Qiuyi (Richard) Zhang; Satish Rao; Tandy J. Warnow (AlCoB, 2019)

TRACTION: Fast Non-Parametric Improvement of Estimated Gene Trees. - Sarah A. Christensen; Erin K. Molloy; Pranjal Vachaspati; Tandy J. Warnow (WABI, 2019)

Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. - Erin K. Molloy; Tandy J. Warnow (Algorithms Mol. Biol., 2019)

TreeMerge: a new method for improving the scalability of species tree estimation methods. - Erin K. Molloy; Tandy J. Warnow (Bioinform., 2019)

Advancing Divide-And-Conquer Phylogeny Estimation Using Robinson-Foulds Supertrees. - Xilin Yu; Thien Le; Sarah A. Christensen; Erin K. Molloy; Tandy J. Warnow (WABI, 2020)

Non-parametric correction of estimated gene trees using TRACTION. - Sarah A. Christensen; Erin K. Molloy; Pranjal Vachaspati; Ananya Yammanuru; Tandy J. Warnow (Algorithms Mol. Biol., 2020)

FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models. - Erin K. Molloy; Tandy J. Warnow (Bioinform., 2020)

Supertree-like methods for genome-scale species tree estimation - Erin K. Molloy (2020)

Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation. - Xilin Yu; Thien Le; Sarah A. Christensen; Erin K. Molloy; Tandy J. Warnow (Algorithms Mol. Biol., 2021)

Advancing admixture graph estimation via maximum likelihood network orientation. - Erin K. Molloy; Arun Durvasula; Sriram Sankararaman (Bioinform., 2021)

TIPP2: metagenomic taxonomic profiling using phylogenetic markers. - Nidhi Shah; Erin K. Molloy; Mihai Pop; Tandy J. Warnow (Bioinform., 2021)

Using Constrained-INC for Large-Scale Gene Tree and Species Tree Estimation. - Thien Le; Aaron Sy; Erin K. Molloy; Qiuyi Zhang 001; Satish Rao; Tandy J. Warnow (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss. - Brandon Legried; Erin K. Molloy; Tandy J. Warnow; Sébastien Roch (J. Comput. Biol., 2021)

Leveraging Constraints Plus Dynamic Programming for the Large Dollo Parsimony Problem. - Junyan Dai; Tobias Rubel; Yunheng Han; Erin K. Molloy (WABI, 2023)

Quartets Enable Statistically Consistent Estimation of Cell Lineage Trees Under an Unbiased Error and Missingness Model (Abstract). - Yunheng Han; Erin K. Molloy (WABI, 2023)

Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model. - Yunheng Han; Erin K. Molloy (Algorithms Mol. Biol., 2023)

Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem. - Junyan Dai; Tobias Rubel; Yunheng Han; Erin K. Molloy (Algorithms Mol. Biol., 2024)

Fast, parallel, and cache-friendly suffix array construction. - Jamshed Khan; Tobias Rubel; Erin K. Molloy; Laxman Dhulipala; Rob Patro (Algorithms Mol. Biol., 2024)

Dynamic Programming Algorithms for Fast and Accurate Cell Lineage Tree Reconstruction from CRISPR-Based Lineage Tracing Data. - Junyan Dai; Erin K. Molloy (RECOMB, 2025)

A Partition Function Algorithm to Evaluate Inferred Subclonal Structures in Single-Cell Sequencing Data. - Farid Rashidi Mehrabadi; Erfan Sadeqi Azer; John D. Bridgers; Eva Pérez-Guijarro; Kerrie Marie; Howard H. Yang; Charli Gruen; Chih Hao Wu; Welles Robinson; Huaitian Liu; Can Kizilkale; Michael C. Kelly; et al. (RECOMB, 2025)