Author

Ilia Minkin

Johns Hopkins UniversityORCID 0000-0002-0807-347XUnclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Organism:human· 3 Approach:statistical model· 3 Assay:bulk RNA-seq· 2 Research Focus:database / resource· 2 Approach:experimental assay· 2 Research Focus:gene regulatory network inference· 2 Research Focus:variant calling· 2 Assay:whole-genome sequencing· 2

Frequent Co-Authors

Steven L. SalzbergiD· 3 shared Ales VarabyouiD· 2 shared Markus J. SommeriD· 2 shared Martin SteineggeriD· 2 shared Mihaela PerteaiD· 2 shared Natalia RinconiD· 2 shared Sukhwan ParkiD· 2 shared Alaina ShumateiD· 1 shared

Activity by Year

2020-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersGenomics

Steven L. SalzbergORCID

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Author profile →

4 papers

Recent·Most cited

Conservation assessment of human splice site annotation based on a 470-genome alignment

Ilia Minkin, Steven L. Salzberg

The paper assesses the conservation of human splice site annotations across 470 genomes, finding that MANE-annotated splice sites are highly conserved and better supported than others.

Nucleic Acids Research · Feb 25, 2025Peer-reviewedBioinformatics

CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure

Ales Varabyou, Markus J. Sommer, Beril Erdogdu, Ida Shinder, Ilia Minkin, Kuan-Hao Chao, Sukhwan Park, Jakob Heinz, Christopher Pockrandt, Alaina Shumate, Natalia Rincon, Daniela Puiu, Martin Steinegger, Steven L. Salzberg, Mihaela Pertea

CHESS 3 improves upon previous versions by using better algorithms and filtering to create a more accurate catalog of human genes and transcripts.

Genome biology · Oct 30, 2023Peer-reviewedGenomics

Highly accurate isoform identification for the human transcriptome

Markus J. Sommer, Sooyoung Cha, Ales Varabyou, Natalia Rincon, Sukhwan Park, Ilia Minkin, Mihaela Pertea, Martin Steinegger, Steven L. Salzberg

The paper uses 3D protein structures to evaluate human protein isoforms for biological functionality, refining genome annotations.

eLife · Dec 15, 2022Peer-reviewedGenomics

Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ

Ilia Minkin, Paul Medvedev

SibeliaZ improves scalability of multiple whole-genome alignment and collinear block reconstruction on a single machine.

Nature Communications · Dec 10, 2020Peer-reviewedBioinformatics