Author

Allysia J. Mak

University of California, Santa Cruz

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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Bioinformatics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 2 Assay:bulk RNA-seq· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1 Research Focus:variant calling· 1 Research Focus:variant effect prediction· 1 Assay:whole-exome sequencing· 1 Assay:whole-genome sequencing· 1

Frequent Co-Authors

Angela Norie BrooksiD· 1 shared Brian Y Lin· 1 shared Colette FeltoniD· 1 shared Jon AkutagawaiD· 1 shared Julie L. AspdeniD· 1 shared Patricia P. ChaniD· 1 shared Tanvi Damle· 1 shared Todd M. LoweiD· 1 shared

Activity by Year

2021-2022 · peak 1/yr

Co-Author Collaboration Network

8 top collaborators · 13 mutual co-author links

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1 shared paperGenomics

Angela Norie BrooksORCID

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2 papers

Recent·Most cited

GenomicsbioRxivPreprintMay 10, 2022

RNA-sequencing as an expression-informed alternative for somatic variant detection and cancer driver identification

Jon Akutagawa, Allysia J. Mak, Tanvi Damle…·Angela Norie Brooks

This study uses RNA-seq data to detect somatic variants and identify cancer drivers in 1,359 samples, showing RNA-seq can effectively replace WES/WGS for this task.

1 citation

humanwhole-exome sequencing

𝕏 PostBluesky

BioinformaticsNucleic Acids ResearchPeer-reviewedJul 27, 2021

tRNAscan-SE 2.0: Improved Detection and Functional Classification of Transfer RNA Genes

Patricia P. Chan, Brian Y Lin, Allysia J. Mak, Todd M. Lowe

The paper improves tRNAscan-SE for better detection and classification of tRNA genes across diverse genomes and introduces mitochondrial tRNA detection.

1,962 citationstop 1%

statistical modelgene regulatory network inference

𝕏 PostBluesky