Author

Bence Kotis

Scripps Research Institute

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

Biology Disciplines

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Genetic & Genomic Medicine· 1 Genetics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 3 Organism:human· 3 Approach:statistical model· 3 Research Focus:differential expression· 2 Research Focus:variant effect prediction· 2 Research Focus:benchmarking· 1 Research Focus:eQTL / molecular QTL mapping· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Pejman MohammadiiD· 3 shared Stephane E. CasteliD· 2 shared Tuuli LappalaineniD· 2 shared Aaron GraubertiD· 1 shared Adolfo CorreaiD· 1 shared Alan M. KwongiD· 1 shared Alexandra J. ScottiD· 1 shared Alexis J. BattleiD· 1 shared

Activity by Year

2020-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 38 mutual co-author links

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3 shared papersGenetic & Genomic Medicine

Pejman MohammadiORCID

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3 papers

Recent·Most cited

Improved Identification of Large-effect Rare Genetic Variants using Haplotype Aggregated Allele-specific Expression Data

Kaushik Ram Ganapathy, Martin Broly, Sarah Silverstein, Marcela Mendoza, Eric Song, Bence Kotis, Paul Hoffman, Ali Torkamani, David R. Adams, Carsten G. Bönnemann, Tuuli Lappalainen, Pejman Mohammadi

ANEVA-h improves detection of rare regulatory variants by analyzing haplotype-level ASE data, increasing testable genes and reducing false positives in GTEx and clinical cohorts.

medRxiv · Dec 18, 2025 · PreprintGenetic & Genomic Medicine

Haplotype-aware modeling of cis-regulatory effects highlights the gaps remaining in eQTL data

Nava Ehsan, Bence Kotis, Stephane E. Castel, Eric J. Song, Nicholas Mancuso, Pejman Mohammadi

The paper introduces aFC-n, a method to improve eQTL effect size estimation and gene expression prediction, revealing significant residual allelic imbalance in many genes.

Nature Communications · Jan 15, 2024Peer-reviewedGenetics

Diverse transcriptomic signatures across human tissues identify functional rare genetic variation

Nicole M. Ferraro, Benjamin J. Strober, Jonah E. Einson, Nathan S. Abell, François Aguet, Alvaro Barbeira, Margot K. Brandt, Maja Bućan, Stephane E. Castel, Joe R. Davis, Emily Greenwald, Gaelen T. Hess, Austin T. Hilliard, Rachel L. Kember, Bence Kotis, , Andrew B. Nobel

Integrating expression, allelic expression and splicing across tissues identifies rare variants with relevance to traits.

Science · Sep 10, 2020Peer-reviewedGenomics