Author

Lucas R. van Dijk

Broad InstituteORCID 0000-0002-7565-5859Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Approach:statistical model· 3 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Assay:metagenomics· 2 Research Focus:variant calling· 2 Organism:bacteria (other)· 1 Assay:bulk RNA-seq· 1 Research Focus:cell-cell communication· 1

Frequent Co-Authors

Ashlee M. EarliD· 4 shared Abigail L. MansoniD· 3 shared Colin J. WorbyiD· 3 shared Scott J. HultgreniD· 3 shared Henry L. SchreiberiD· 2 shared Karen DodsoniD· 2 shared Philippe N. AzimzadehiD· 2 shared Thomas AbeeliD· 2 shared

Activity by Year

2022-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 41 mutual co-author links

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4 shared papersBioinformatics

Ashlee M. EarlORCID

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Author profile →

4 papers

Recent·Most cited

Strain Tracking with Uncertainty Quantification

Younhun Kim, Colin J. Worby, Sawal Acharya, Lucas R. van Dijk, Daniel Alfonsetti, Zackary Gromko, Philippe N. Azimzadeh, Karen Dodson, Georg Kurt Gerber, Scott J. Hultgren, Ashlee M. Earl, Bonnie Berger, Travis E. Gibson

ChronoStrain tracks low-abundance microbial strains over time with uncertainty quantification, outperforming existing methods on real and synthetic data.

Nature Microbiology · May 6, 2025Peer-reviewedBioinformatics

Fast and exact gap-affine partial order alignment with POASTA

Lucas R. van Dijk, Abigail L. Manson, Ashlee M. Earl, Kiran V. Garimella, Thomas Abeel

POASTA is an optimal algorithm for partial order alignment that improves speed and memory efficiency, enabling larger alignments in bacterial gene datasets.

Bioinformatics · Dec 26, 2024Peer-reviewedBioinformatics

Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection

M. G. Young, Timothy J. Straub, Colin J. Worby, Hayden C. Metsky, Andreas Gnirke, Ryan A. Bronson, Lucas R. van Dijk, Christopher A. Desjardins, Christian B. Matranga, James Qu, Jesús Bazán Villicaña, Philippe N. Azimzadeh, Andrew L. Kau, Karen Dodson, Henry L. Schreiber, , Ashlee M. Earl

This study identifies distinct E. coli transcriptional profiles in the guts of recurrent UTI sufferers using a novel pangenome hybrid selection method.

Nature Communications · Nov 2, 2024Peer-reviewedMicrobiology

StrainGE: A toolkit to track and characterize low-abundance strains in complex microbial communities

Lucas R. van Dijk, Bruce J. Walker, Timothy J. Straub, Colin J. Worby, Alexandra Grote, Henry L. Schreiber, Christine Anyansi, Amy J. Pickering, Scott J. Hultgren, Abigail L. Manson, Thomas Abeel, Ashlee M. Earl

StrainGE identifies low-abundance microbial strains from metagenomic data with higher sensitivity and resolution than existing tools.

Genome biology · Mar 7, 2022Peer-reviewedBioinformatics