SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data on bioRxiv

Our paper on a tool for simulating single-cell and bulk next-generation DNA sequencing data from hierarchcial experimental arrangements is now available on bioRxiv.

Targeted Metabolomic Profiling Reveals Association Between Altered Amino Acids and Poor Functional Recovery After Stroke

Our paper with Qing Mei Wang of Spaulding Rehabilitation Hospital was published in Frontiers in Neurology. There is a lot of opportunity to use statistics and machine learning to improve diagnosis and treatment of stroke and we’re happy to work on improving treatment.

Introduction to Foundations of Data Science Summer Course now open

We’re offering a 2-week summer course on Foundations of Data Science July 19 - Aug 1. If you are a high school student interested in learning more about data science with real-world applications, please join us!

Multiple Postdoc Positions Available

We have multiple postdoc openings to join the UMass TRIPODS Institute. If you’re interested in foundations of data science please apply.

MAP Clustering via Mixed Integer Nonlinear Programming Preprint on

A preprint of some of our recent work on MAP clustering is now on arXiv. Have a look — no paywalls. This is work with Andrew Trapp and Pitchaya Wiratchitisatian at WPI and Ji Ah Lee at UMass.

NIH R01 on Learning Conditionally Essential Networks in the Protein Homeostasis System is funded

Our R01 grant proposal on using Tn-seq to learn conditionally essential networks in the protein homeostasis system has been selected for funding by the NIH. This work build on our work on chemogenomics work indentifying essential genes here and here as well as our statistical methodology work on identifying subtypes in genomic data here, here, and here. More details are in this UMass News article and NIH RePORTer. We’re looking forward to doing this work!

NSF HDR TRIPODS Institute Funded

Our NSF HDR TRIPODS Institute was funded by the NSF. This project will develop the TRIPODS Institute for Theoretical Foundations of Data Science at UMass Amherst. The institute is collaborative effort between mathematics, statistics, and computer science. We have great PI team including Andrew McGregor, Arya Mazumder, Barnha Saha, and Markos Katsoulakis. We’re all excited for the workshops, programs, and research that will come from this opportunity.

Global Optimization for Sparse Mixed Membership Factorization is published

Our paper with lab PhD graduate Fan Zhang (now at Harvard Medical School/Broad Institute), Chuanqi Wang (former lab member now PhD student with Kwonmoo Lee at WPI), and Andrew Trapp on global optimization for sparse mixed membership matrix factorization is now online in Contemporary Biostatistics with Biopharmaceutical Applications. A preprint of the article is on arXiv.

Flaherty appointed as adjunct faculty in UMass College of Computer and Information Sciences

I’m happy to be joining the UMass College of Information and Computer Sciences as an Adjunct Assistant Professor.

Flaherty appointed as member of UMass MCB Program

I’m happy to be joining the UMass Graduate Program in Molecular and Cellular Biology. You can find the list of all program members here

Compact Representation of Uncertainty in Clustering at NeurIPS2018

NeurIPS paper with Craig Greenberg, Nick Monath, Ari Kobren, Andrew McGregor, and Andrew McCallum on exact clustering accepted to NIPS2018.

Summer REU students

Fusheng Yang and Collin Giguere join the lab for a summer REU working on single-cell variant calling.

Paper published in PLOS Genetics.

Paper in collaboration with Vidali lab at WPI is published in PLOS Genetics.

Submatrices Paper Published in Annals of Operations Research

Paper in collaboration with Trapp lab at WPI published.

Flaherty selected for Lilly Fellowship

I'm grateful to be selected for the 2017--2018 Lilly Fellowship.

VI for Variant Detection Paper Published

Variational inference for rare variant detection published.

GLAD-GOP paper on arXiv

Global optimization for mixed membership matrix factorization.

PLOS Genetics Paper Published

Study of mutations that modulate resistance to methotrexate.

Variational RVD2 Paper published to arXiv

Our paper on a variational inference for RVD2 is published to the arXiv.

New Website

We have a new lab website