Author

Alan J. Collins

University of Illinois Urbana-ChampaignORCID 0000-0003-4960-5716Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Microbiology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 2 Organism:human· 2 Research Focus:software / tool· 2 Approach:statistical model· 2 Assay:whole-genome sequencing· 2 Organism:bacteria (other)· 1 Research Focus:benchmarking· 1 Research Focus:chromatin & epigenetic regulation· 1

Frequent Co-Authors

Rachel J. WhitakeriD· 2 shared Alix AshareiD· 1 shared Daniel SchultziD· 1 shared David RitziD· 1 shared Deborah A. HoganiD· 1 shared Dev MashruwalaiD· 1 shared Emily T. NorrisiD· 1 shared Jay Goddard· 1 shared

Activity by Year

2023-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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2 shared papersMicrobiology

Rachel J. WhitakerORCID

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3 papers

Recent·Most cited

MicrobiologymSystemsPeer-reviewedAug 25, 2026

Within-host population structure, migration, and parallel adaptive evolution of Pseudomonas aeruginosa in cystic fibrosis lung disease

David Ritz, Michelle E. Clay, Ted Kim…·Deborah A. Hogan

This study analyzes 450 Pseudomonas aeruginosa isolates from CF patients to show structured population dynamics, migration, and parallel adaptive evolution within lung infections.

DOI 10.1128/msystems.00238-26

humanwhole-genome sequencing

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BioinformaticsbioRxivPreprintMar 23, 2026

Epidemiology of Legionella: Genome-bAsed Typing (el_gato) - a new bioinformatic tool for identifying sequence-based types of Legionella pneumophila from whole genome sequencing data

Alan J. Collins, Dev Mashruwala, Vasanta Chivukula…·Will A. Overholt

el_gato is a new bioinformatic tool that improves sequence-based typing of Legionella pneumophila from whole genome sequencing data, achieving high accuracy comparable to traditional Sanger sequencing.

DOI 10.64898/2026.03.20.713011

humanwhole-genome sequencing

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BioinformaticsThe CRISPR JournalPeer-reviewedJul 17, 2023

CRISPR comparison toolkit (CCTK): Rapid identification, visualization, and analysis of CRISPR array diversity

Alan J. Collins, Rachel J. Whitaker

The paper introduces CCTK, a toolkit for analyzing CRISPR array diversity, including tools for identifying arrays, visualizing similarities, and inferring phylogenetic trees.

24 citations

bacteria (other)CRISPR screen

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