Author

Kohei Hagiwara

St. Jude Children's Research HospitalORCID 0000-0001-7787-2008Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Cancer Biology· 1

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 2 Organism:human· 2 Research Focus:variant calling· 2 Assay:ChIP-seq· 1 Research Focus:chromatin & epigenetic regulation· 1 Approach:deep learning· 1 Approach:machine learning (classical)· 1 Approach:statistical model· 1

Frequent Co-Authors

Jinghui ZhangiD· 2 shared John B. EastoniD· 2 shared Nadezhda V. TerekhanovaiD· 2 shared Alfred Thomas LookiD· 1 shared Andrew ThrasheriD· 1 shared Bensheng JuiD· 1 shared David T. TeacheyiD· 1 shared Haseeb ZubairiD· 1 shared

Activity by Year

2019-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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2 shared papersBioinformatics

Jinghui ZhangORCID

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3 papers

Recent·Most cited

Reactivation of a TAL1 progenitor cell enhancer region by non-coding somatic variants in T-lineage acute lymphoblastic leukemia

Nadezhda V. Terekhanova, Xiaolong Chen, Kin-Hoe Chow, Yu Liu, Ying Shao, Li Dong, Bensheng Ju, Vinesh Vinayachandran, Haseeb Zubair, Kohei Hagiwara, Wentao Yang, X X, Sivaraman Natarajan, John B. Easton, David T. Teachey, , Jinghui Zhang

The paper identifies non-coding somatic variants in TAL1 regulatory regions that reactivate enhancers normally active in hematopoietic stem cells in T-lineage acute lymphoblastic leukemia.

bioRxiv · May 6, 2026 · PreprintCancer Biology

Confounding factors in assessing the enriched expression of somatic mutant allele in bulk tumor samples

Kohei Hagiwara, Andrew Thrasher, Nadezhda V. Terekhanova, Jinghui Zhang

The paper shows that mutant allele enrichment in bulk tumor RNA can be confounded by tumor purity and NMD, and demonstrates RNA-Seq can improve driver indel detection.

Genome Research · Mar 4, 2026Peer-reviewedBioinformatics

RNAIndel: a machine-learning framework for discovery of somatic coding indels using tumor RNA-Seq data

Kohei Hagiwara, Liang Ding, Michael N. Edmonson, Stephen V. Rice, Scott Newman, John B. Easton, Juncheng Dai, Soheil Meshinchi, Rhonda E. Ries, Michael Rusch, Jinghui Zhang

RNAIndel identifies somatic coding indels in tumor RNA-Seq data with high sensitivity and low false positives, outperforming existing methods.

Bioinformatics · Oct 1, 2019Peer-reviewedBioinformatics