Author

Ida Shinder

Johns Hopkins UniversityORCID 0000-0002-1651-9347Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:gene regulatory network inference· 3 Organism:human· 3 Approach:statistical model· 3 Research Focus:variant calling· 3 Research Focus:benchmarking· 2 Assay:bulk RNA-seq· 2 Approach:experimental assay· 2 Research Focus:software / tool· 2

Frequent Co-Authors

Mihaela PerteaiD· 4 shared Alaina ShumateiD· 2 shared Daniela PuiuiD· 2 shared Jakob HeinziD· 2 shared Kuan-Hao ChaoiD· 2 shared Richard HuiD· 2 shared Steven L. SalzbergiD· 2 shared Aleksey V. ZiminiD· 1 shared

Activity by Year

2021-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 35 mutual co-author links

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4 shared papersGenomics

Mihaela PerteaORCID

Mutual co-authors in cluster

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4 papers

Recent·Most cited

StringTie3 Improves Total RNA-seq Assembly by Resolving Nascent and Mature Transcripts

Ida Shinder, Geo M. Pertea, Richard Hu, Zoe Rudnick, Mihaela Pertea

StringTie3 improves total RNA-seq assembly by resolving nascent and mature transcripts, reducing errors and enhancing precision and sensitivity in both short- and long-read data.

Nature Methods · May 19, 2026Peer-reviewedGenomics

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

EASTR: Correcting systematic alignment errors in multi-exon genes

Ida Shinder, Richard Hu, Hyun Joo Ji, Kuan-Hao Chao, Mihaela Pertea

EASTR corrects systematic alignment errors in multi-exon genes by detecting and removing falsely spliced transcripts, improving alignment accuracy across species.

bioRxiv · May 10, 2023 · PreprintGenomics

A reference-quality, fully annotated genome from a Puerto Rican individual

Aleksey V. Zimin, Alaina Shumate, Ida Shinder, Jakob Heinz, Daniela Puiu, Mihaela Pertea, Steven L. Salzberg

The paper presents a new reference genome, PR1, from a Puerto Rican individual, highlighting its completeness and annotations compared to existing genomes.

Genetics · Dec 13, 2021Peer-reviewedGenomics