Author

Beril Erdogdu

Johns Hopkins UniversityORCID 0000-0002-9284-1522Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Signature Assays, Organisms & Methods

Click to filter · or open tag

Assay:bulk RNA-seq· 4 Organism:human· 4 Research Focus:differential expression· 3 Approach:statistical model· 3 Research Focus:database / resource· 2 Research Focus:gene regulatory network inference· 1 Approach:machine learning (classical)· 1 Organism:rat· 1

Frequent Co-Authors

Mihaela PerteaiD· 4 shared Steven L. SalzbergiD· 4 shared Ales VarabyouiD· 3 shared Alaina ShumateiD· 1 shared Christopher PockrandtiD· 1 shared Daniela PuiuiD· 1 shared Hyun Joo JiiD· 1 shared Ida ShinderiD· 1 shared

Activity by Year

2023-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 38 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

4 shared papersGenomics

Mihaela PerteaORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

Isoswitching in human brain development and aging

Beril Erdogdu, Hyun Joo Ji, Zoe Rudnick, Mihaela Pertea, Steven L. Salzberg

The paper identifies isoswitching, a phenomenon of isoform usage changes in human brain development and aging, and shows it can predict age across the lifespan using RNA-seq data.

bioRxiv · May 5, 2025 · PreprintGenomics

Detecting differential transcript usage in complex diseases with SPIT

Beril Erdogdu, Ales Varabyou, Stephanie C. Hicks, Steven L. Salzberg, Mihaela Pertea

SPIT detects differential transcript usage in complex diseases by quantifying population heterogeneity and identifying subgroups with distinct DTU events, revealing new events in schizophrenia brain samples.

Cell Reports Methods · Mar 1, 2024Peer-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

Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage

Ales Varabyou, Beril Erdogdu, Steven L. Salzberg, Mihaela Pertea

ORFanage identifies ORFs in known and novel transcripts, improving annotations in RefSeq and GENCODE databases and enabling analysis of large RNA-seq datasets.

Nature Computational Science · Jul 31, 2023Peer-reviewedBioinformatics