Author

Dongyue Xie

University of Chicago

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Bioengineering· 1 Bioinformatics· 1 Genetics· 1 Genomics· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Approach:statistical model· 4 Organism:human· 2 Organism:rat· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:differential expression· 1 Assay:DNA methylation· 1 Research Focus:fine-mapping· 1

Frequent Co-Authors

Matthew StephensiD· 3 shared Gao T. WangiD· 2 shared Peter S. CarbonettoiD· 2 shared Carlos F. Buen Abad NajariD· 1 shared Charlotte JalouxiD· 1 shared Houcheng LiiD· 1 shared Jake E. BarraletiD· 1 shared Kushal K. DeyiD· 1 shared

Activity by Year

2018-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 19 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

3 shared papersBioinformatics

Matthew StephensORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

Reference-free isoform discovery links unannotated RNA processing to disease risk

Carlos F. Buen Abad Najar, Dongyue Xie, Ru Feng, Peter S. Carbonetto, Xuewei Cao, Houcheng Li, Lingzhao Fang, Gao T. Wang, Matthew Stephens, Yang Li

Torino, a reference-free framework for isoform discovery, identifies RNA processing patterns linked to disease risk by analyzing read coverage variation across species and disease states.

bioRxiv · Oct 23, 2026 · PreprintBioinformatics

Venous Angiogenesis and Dermal Fibroblast Augmentation of Decellularized Dermis: Towards Transplantable Dermal Substitutes

Sze Wai Lau, Yu Ling Zhang, Dongyue Xie, Nicholas Maroun Makhoul, Charlotte Jaloux, Jake E. Barralet

This study shows that a flexible decellularized dermis can be vascularized around a single vein, with fibroblasts enhancing vascularization, and demonstrates improved vascular outcomes compared to subcutaneous implantation.

bioRxiv · Oct 2, 2026 · PreprintBioengineering

Fast and flexible joint fine-mapping of multiple traits via the Sum of Single Effects model

Yuxin Zou, Peter S. Carbonetto, Dongyue Xie, Gao T. Wang, Matthew Stephens

The paper introduces mvSuSiE, a multi-trait fine-mapping method that improves causal SNP identification by jointly analyzing multiple traits, discovering more causal SNPs and narrower credible sets compared to single-trait approaches.

Nature Genetics · Feb 1, 2026Peer-reviewedGenomics

A new sequence logo plot to highlight enrichment and depletion

Kushal K. Dey, Dongyue Xie, Matthew Stephens

The paper introduces a new sequence logo plot, EDLogo, that visualizes both enrichment and depletion of characters in biological sequences and provides an R package for its implementation.

BMC Bioinformatics · Dec 1, 2018Peer-reviewedGenetics