Author

Joseph L. Lalli

University of Wisconsin–MadisonORCID 0000-0003-4703-0461Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Evolutionary Biology· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Organism:human· 2 Approach:statistical model· 2 Research Focus:variant calling· 2 Assay:whole-genome sequencing· 2 Research Focus:differential expression· 1 Research Focus:imputation· 1

Frequent Co-Authors

Amra UzicaniniD· 1 shared Andrew N. BortviniD· 1 shared Donna M. WerlingiD· 1 shared Hunter J. RiesiD· 1 shared Jonathan L. TemteiD· 1 shared Kelsey R. FlorekiD· 1 shared Maureen D. GossiD· 1 shared Rajiv C. McCoyiD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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1 shared paperEvolutionary Biology

Amra UzicaninORCID

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2 papers

Recent·Most cited

Evolutionary BiologyPLoS PathogensPeer-reviewedMay 7, 2026

Weak selection and stochastic processes limit the emergence of antigenic variants during household transmission of influenza A viruses

Hunter J. Ries, Joseph L. Lalli, Kelsey R. Florek…·Thomas C. Friedrich

This study examines influenza A virus evolution during household transmission, finding weak selection and stochastic processes dominate, with no clear evidence of antigenic variant selection during transmission.

DOI 10.1371/journal.ppat.1013689

humanwhole-genome sequencing

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GenomicsbioRxivPreprintFeb 24, 2025

A T2T-CHM13 recombination map and globally diverse haplotype reference panel improves phasing and imputation

Joseph L. Lalli, Andrew N. Bortvin, Rajiv C. McCoy, Donna M. Werling

This study shows that using a T2T-CHM13 recombination map and haplotype panel improves phasing and imputation accuracy compared to GRCh38.

6 citations

humanwhole-genome sequencing

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