Author

Shai He

University of Massachusetts Amherst

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Bioinformatics· 3 Systems Biology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:benchmarking· 2 Organism:C. elegans· 2 Approach:statistical model· 2 Research Focus:variant calling· 2 Assay:whole-exome sequencing· 2 Assay:whole-genome sequencing· 2 Approach:Bayesian inference· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Patrick FlahertyiD· 4 shared Vishal SarsaniiD· 4 shared Berent AldikactiiD· 2 shared Peter ChieniD· 2 shared Aaron ScheiniD· 1 shared Collin Giguere· 1 shared Hachem SaddikiiD· 1 shared Harsh Vardhan DubeyiD· 1 shared

Activity by Year

2020-2024 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

4 shared papersBioinformatics

Patrick FlahertyORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

Discovering Genetic Modulators of the Protein Homeostasis System through Multilevel Analysis

Vishal Sarsani, Berent Aldikacti, Tingting Zhao, Shai He, Peter Chien, Patrick Flaherty

The paper uses transposon mutagenesis and computational analysis to identify genetic modulators of protein homeostasis in Caulobacter crescentus, finding limited overlap in essential genes across environmental and genetic perturbations.

PNAS Nexus · Dec 23, 2024Peer-reviewedSystems Biology

Model-based identification of conditionally-essential genes from transposon-insertion sequencing data

Vishal Sarsani, Berent Aldikacti, Shai He, Rilee Zeinert, Peter Chien, Patrick Flaherty

The paper introduces a model-based method to identify conditionally-essential genes using transposon-insertion sequencing data, finding a set of genes essential under specific stress conditions in Caulobacter crescentus.

PLoS Computational Biology · Mar 7, 2022Peer-reviewedBioinformatics

A Bayesian Nonparametric Model for Inferring Subclonal Populations from Structured DNA Sequencing Data

Shai He, Aaron Schein, Vishal Sarsani, Patrick Flaherty

This paper introduces a Bayesian nonparametric model to infer subclonal populations from structured DNA sequencing data, showing improved performance over existing methods.

The Annals of Applied Statistics · Jun 1, 2021Peer-reviewedBioinformatics

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

Collin Giguere, Harsh Vardhan Dubey, Vishal Sarsani, Hachem Saddiki, Shai He, Patrick Flaherty

SCSIM simulates correlated single-cell and bulk DNA sequencing data for testing variant callers and analysis tools.

BMC Bioinformatics · May 26, 2020Peer-reviewedBioinformatics