Author

Xiaopeng Zhu

Primary ORCID profile (0000-0003-2007-9820 · 4 papers)Unclaimed ORCID profile · follow to get notified of new preprints

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Same name, identified by ORCID

Xiaopeng ZhuiD4 papers · Carnegie Mellon University

Biology Disciplines

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Bioinformatics· 2 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Assay:bulk RNA-seq· 2 Approach:deep learning· 2 Research Focus:gene regulatory network inference· 2 Approach:statistical model· 2 Research Focus:cell type annotation· 1 Research Focus:differential expression· 1 Organism:multiple species· 1

Frequent Co-Authors

Alexander A. Shishkin· 1 shared Aviv RegeviD· 1 shared Boyang Bai· 1 shared Erxi WuiD· 1 shared Haozhe Wang· 1 shared Itay Maza· 1 shared Jacob H Hanna· 1 shared Jenny CheniD· 1 shared

Activity by Year

2015-2024 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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1 shared paperEvolutionary Biology

Alexander A. Shishkin

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3 papers

Recent·Most cited

MATES: A Deep Learning-Based Model for Locus-specific Quantification of Transposable Elements in Single Cell

Ruohan Wang, Yumin Zheng, Zijian Zhang, Kailu Song, Erxi Wu, Xiaopeng Zhu, Tao Wu, Jun Ding

MATES improves locus-specific transposable element quantification in single-cell data by accurately allocating multi-mapping reads using contextual alignment information.

Nature Communications · Oct 11, 2024Peer-reviewedBioinformatics

RSQ: a statistical method for quantification of isoform-specific structurome using transcriptome-wide structural profiling data

Yunfei Wang, Xiaopeng Zhu, Ming Sun, Yong Chen, Yiwen Chen, Shikui Tu, Boyang Bai, Min Chen, Qi Dai, Haozhe Wang, Michael Q. Zhang, Zhenyu Xuan

RSQ quantifies isoform-specific structurome by modeling read distribution across isoforms and RNA conformations, enabling comparison between conditions and analysis of conformational variation.

bioRxiv · Jun 18, 2016 · PreprintBioinformatics

Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs

Jenny Chen, Alexander A. Shishkin, Xiaopeng Zhu, Sabah Kadri, Itay Maza, Jacob H Hanna, Aviv Regev, Manuel Garber

The paper introduces a computational tool for lncRNA discovery and analysis, identifying two distinct classes of lncRNAs based on evolutionary patterns.

bioRxiv · Nov 11, 2015Evolutionary Biology