Author

Charles A. Ishak

University Health NetworkORCID 0000-0002-2287-6738Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Research Focus:gene regulatory network inference· 2 Approach:statistical model· 2 Approach:benchmark study· 1 Research Focus:benchmarking· 1 Assay:ChIP-seq· 1 Research Focus:differential expression· 1 Assay:DNA methylation· 1 Research Focus:variant calling· 1

Frequent Co-Authors

Coby VineriD· 2 shared Daniel Diniz De CarvalhoiD· 2 shared Michael M. HoffmaniD· 2 shared Sarah J. HaineriD· 2 shared Shu Yi SheniD· 2 shared Anne C. Ferguson‐SmithiD· 1 shared David J. AdamsiD· 1 shared Hui ShiiD· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 41 mutual co-author links

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2 shared papersBioinformatics

Coby VinerORCID

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2 papers

Recent·Most cited

Benchmarking CUT&RUN analysis using motif enrichment

Luomeng Tan, Coby Viner, Xing Hao Li, Michael Wrana, Charles A. Ishak, Shu Yi Shen, Daniel Diniz De Carvalho, Sarah J. Hainer, Michael M. Hoffman

This study benchmarks CUT&RUN peak callers using motif enrichment, finding that MACS2 outperforms SEACR in most scenarios with optimal preprocessing.

bioRxiv · Sep 14, 2026 · PreprintBioinformatics

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

Coby Viner, Charles A. Ishak, James Johnson, Nicolas J. Walker, Hui Shi, Marcela K. Sjöberg-Herrera, Shu Yi Shen, Santana M. Lardo, David J. Adams, Anne C. Ferguson‐Smith, Daniel Diniz De Carvalho, Sarah J. Hainer, Timothy L. Bailey, Michael M. Hoffman

The paper develops methods to model transcription factor binding in modified DNA by expanding the DNA alphabet and adapting existing tools to handle custom alphabets, identifying modification-sensitive motifs and validating them with experimental data.

Genome biology · Jan 8, 2024Peer-reviewedBioinformatics