Author

Thomas C. Biondi

Los Alamos National LaboratoryORCID 0000-0003-3125-3222Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genomics· 2 Biochemistry· 1 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Assay:DNA methylation· 3 Assay:whole-genome sequencing· 3 Approach:experimental assay· 2 Organism:human· 2 Research Focus:variant calling· 2 Research Focus:benchmarking· 1 Approach:deep learning· 1 Research Focus:drug response / drug discovery· 1

Frequent Co-Authors

Jonathan D. FinniD· 3 shared Anne M. Bara· 2 shared Dane Z. HazelbakeriD· 2 shared Daniel J. O’ConnelliD· 2 shared Didac SantesmassesiD· 2 shared Japan B. Mehta· 2 shared Jesse C. CochraneiD· 2 shared Matthew H. BakalariD· 2 shared

Activity by Year

2022-2024 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersBiochemistry

Jonathan D. FinnORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

BiochemistrybioRxivPreprintOct 21, 2024

Engineered Bxb1 variants improve integrase activity and fidelity

Joshua Rose, Hyaeyeong Kim, Jessica R. Von Stetina…·Jesse C. Cochrane

The paper develops Bxb1 variants with improved integrase activity and fidelity, enhancing in vivo efficiency and reducing off-target effects.

4 citations

genetic perturbation / CRISPRprotein folding & dynamics

𝕏 PostBluesky

BioinformaticsbioRxivPreprintOct 10, 2024

Large Serine Integrase Off-Target Discovery with Deep Learning for Genome Wide Prediction

Matthew H. Bakalar, Thomas C. Biondi, Xiaoyu Liang…·Daniel J. O’Connell

The paper introduces IntQuery, a deep learning model that predicts LSI off-target activity genome-wide using data from Cryptic-seq.

3 citations

humanDNA methylation

𝕏 PostBluesky

GenomicsbioRxivPreprintAug 23, 2024

Large Serine Integrase Off-target Discovery and Validation for Therapeutic Genome Editing

Dane Z. Hazelbaker, Japan B. Mehta, Connor McGinnis…·Daniel J. O’Connell

The paper develops and validates methods to detect off-target recombination by Large Serine Integrases, finding higher sensitivity than whole genome sequencing.

8 citations

humanDNA methylation

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GenomicsbioRxivPreprintNov 30, 2022

The telomere-to-telomere, gapless, phased diploid genome and methylome of the green alga Scenedesmus obliquus UTEX 3031 reveals significant heterozygosity and functional separation of the haplotypes

Thomas C. Biondi, Colin P. S. Kruse, Samuel I. Koehler…·Shawn R. Starkenburg

The paper presents a gapless, phased diploid genome and methylome of Scenedesmus obliquus, revealing haplotype heterogeneity and functional divergence.

DOI 10.1101/2022.11.30.518549

plant (other)whole-genome sequencing

𝕏 PostBluesky