Author

Wenduo Cheng

Carnegie Mellon University

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

Biology Disciplines

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Bioinformatics· 3 Animal Behavior & Cognition· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 3 Approach:deep learning· 3 Research Focus:differential expression· 2 Research Focus:gene regulatory network inference· 2 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Research Focus:cell-cell communication· 1 Research Focus:database / resource· 1

Frequent Co-Authors

Jian MaiD· 3 shared Yang ZhangiD· 2 shared Ameet TalwalkariD· 1 shared Andrew MahiD· 1 shared Danqing WangiD· 1 shared Darrell MooreiD· 1 shared Jun-Hong SheniD· 1 shared Junjie TangiD· 1 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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3 shared papersBioinformatics

Jian MaORCID

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Author profile →

4 papers

Recent·Most cited

A meta-interaction basis for cell-cell communication in tissues

Junjie Tang, Shaoheng Liang, Shahul Alam, Wenduo Cheng, Yang Zhang, Jian Ma

SpiderNet identifies cell-cell communication programs from spatial transcriptomics data, revealing key interactions and their associations with phenotypes and therapeutic responses.

bioRxiv · Sep 27, 2026 · PreprintBioinformatics

Phase response curve and RNA-sequencing demonstrate spiders' sensitivity to light and pinpoint candidate light-responsive genes

Natalia Toporikova, Wenduo Cheng, Leyuan Qian, Andrew Mah, Thomas Clarke, Thomas C. Jones, Darrell Moore, Nadia A. Ayoub

The paper uses phase response curves and RNA-sequencing to show spiders' sensitivity to light and identify candidate light-responsive genes.

PLoS ONE · Sep 23, 2026Peer-reviewedAnimal Behavior & Cognition

DNALONGBENCH: A Benchmark Suite for Long-Range DNA Prediction Tasks

Wenduo Cheng, Zhenqiao Song, Yang Zhang, Shike Wang, Danqing Wang, Muyu Yang, Lei Li, Jian Ma

The paper introduces DNALO_SCPLOWONGC_SCPLOWBO_SCPLOWENCHC_SCPLOW, a benchmark suite for long-range DNA prediction tasks, and evaluates five methods on five genomics tasks.

Nature Communications · Nov 18, 2025Peer-reviewedBioinformatics

L2G: Repurposing Language Models for Genomics Tasks

Wenduo Cheng, Jun-Hong Shen, Mikhail Khodak, Jian Ma, Ameet Talwalkar

This paper introduces L2G, a method that repurposes pre-trained language models for genomics tasks, achieving better performance than specialized models on multiple benchmarks.

bioRxiv · Dec 9, 2024 · PreprintBioinformatics