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Publications
2021
Model-based identification of conditionally-essential genes from transposon-insertion sequencing data
Vishal Sarsani
,
Berent Aldikacti
,
Shai He
,
Rilee Zeinert
,
Peter Chien
,
Patrick Flaherty
bioRxiv
July, 2021
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Project
Cluster Trellis: Data Structures & Algorithms for Exact Inference in Hierarchical Clustering
Sebastian Macaluso
,
Craig Greenberg
,
Nicholas Monath
,
Ji Ah Lee
,
Patrick Flaherty
,
Kyle Cranmer
,
Andrew McGregor
,
Andrew McCallum
AISTATS2021
April, 2021
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Project
A Bayesian Nonparametric Model for Inferring Subclonal Populations from Structured DNA Sequencing Data
Shai He
,
Aaron Schein
,
Vishal Sarsani
,
Patrick Flaherty
AOAS
January, 2021
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Project
2020
Multi-Biomarker Prediction Models for Multiple Infection Episodes Following Blunt Trauma
Amy Tsurumi
,
Patrick Flaherty
,
Yok-Ai Que
,
Colleen M. Ryan
,
April E. Mendoza
,
Marianna Almpani
,
Arunava Bandyopahhaya
,
Asako Ogura
,
Yashoda V. Dhole
,
Laura F. Goodfield
,
Ronald G. Tompkins
,
Laurence G. Rahme
iScience
November, 2020
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Project
SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data
Collin Giguere
,
Harsh Dubey
,
Vishal Sarsani
,
Shai He
,
Patrick Flaherty
BMC Bioinformatics
May, 2020
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Project
Targeted Metabolomic Profiling Reveals Association Between Altered Amino Acids and Poor Functional Recovery After Stroke
Xin Wang
,
Tao Liu
,
Haixin Song
,
Shaoyang Cui
,
Gang Liu
,
Andrea Christoforou
,
Patrick Flaherty
,
Xun Luo
,
Lisa Wood
,
Qing Mei Wang
Frontiers in Neurology
January, 2020
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Project
2019
A Global Optimization Algorithm for Sparse Mixed Membership Matrix Factorization
Fan Zhang
,
Chaunqi Wang
,
Andrew C. Trapp
,
Patrick Flaherty
Contemporary Biostatistics with Biopharmaceutical Applications
July, 2019
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2018
Compact Representation of Uncertainty in Clustering
Craig Greenberg
,
Nicholas Monath
,
Ari Kroben
,
Patrick Flaherty
,
Andrew McGregor
,
Andrew McCallum
NeurIPS
December, 2018
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Conditional genetic screen in Physcomitrella patens reveals a novel microtubule depolymerizing-end-tracking protein
Xinxin Ding
,
Leah Pervere
,
Carl Bascom Jr.
,
Jeffrey Bibeau
,
Sakshi Khurana
,
Allison Butt
,
Robert Orr
,
Patrick Flaherty
,
Magdelena Bezanilla
,
Luis Vidali
PLOS Genetics
May, 2018
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Recovering all generalized order-preserving submatrices: new exact formulations and algorithms
Andrew C. Trapp
,
Chao Li
,
Patrick Flaherty
Annals of Operations Research
April, 2018
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Project
2017
Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data
Fan Zhang
,
Patrick Flaherty
BMC Bioinformatics
January, 2017
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Project
2016
Reverse Chemical Genetics: Comprehensive Fitness Profiling Reveals the Spectrum of Drug Target Interactions
Lai H. Wong
,
Sunita Sinha
,
Julien Bergeron
,
Joseph Melor
,
Guri Giaever
,
Patrick Flaherty
,
Corey Nislow
PLOS Genetics
September, 2016
Details
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Project
GEMINI: a computationally-efficient search engine for large gene expression datasets
Timothy DeFreitas
,
Hachem Saddiki
,
Patrick Flaherty
BMC Bioinformatics
February, 2016
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Project