Author

Shu Yang

University of Pennsylvania

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

Same name, identified by ORCID

Biology Disciplines

Click to filter author papers

Bioinformatics· 3 Bioengineering· 2 Developmental Biology· 1 Ecology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Approach:statistical model· 4 Research Focus:benchmarking· 3 Organism:human· 3 Assay:bulk RNA-seq· 2 Approach:experimental assay· 2 Research Focus:protein structure prediction· 2 Assay:ATAC-seq· 1 Approach:benchmark study· 1

Frequent Co-Authors

Anton M. SimeonoviD· 1 shared Binbin YingiD· 1 shared Binyang LiiD· 1 shared Can YangiD· 1 shared Carlos A. TristaniD· 1 shared Chaitali Sen· 1 shared Cheng JiniD· 1 shared Christopher A. LeClairiD· 1 shared

Activity by Year

2023-2026 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 16 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

1 shared paperDevelopmental Biology

Anton M. SimeonovORCID

Mutual co-authors in cluster

Author profile →

7 papers

Recent·Most cited

Precision cooling assists electrical stimulation: Breaking selectivity barriers in nerve control

Shu Yang, Xiao Yu, Shihao Yang, Qianqian Wang, Guo‐Qiang Bi, Yun Liu, Zhanhong Jeff Du

The paper shows that local cooling improves the selectivity of electrical stimulation in nerves by reducing unwanted activity and enabling directional control.

bioRxiv · Sep 16, 2026 · PreprintBioengineering

Scalable Hypothalamic Arcuate Neuron Differentiation from Human Pluripotent Stem Cells Suitable for Modeling Metabolic and Reproductive Disorders

Vukasin M. Jovanovic, Narisu Narisu, Lori L. Bonnycastle, David Castellano, Seungmi Ryu, Ravi Tharakan, Kendall T. Mesch, Qiang Chen, F.M. Betül Erol, Hannah J. Glover, Tingfen Yan, Neelam Sinha, Chaitali Sen, Shu Yang, Dvir Blivis, , Carlos A. Tristan

This paper describes a scalable method to differentiate human pluripotent stem cells into hypothalamic arcuate neurons, which can model metabolic and reproductive disorders.

Stem Cell Reports · Jun 11, 2026Peer-reviewedDevelopmental Biology

Electroadhesion of polymer networks by polycation interfacial bridging: sticky electrophoresis, ionic complexation, and chain entanglement

Binbin Ying, Kun-Hao Yu, Shu Yang, Jiawei Yang

The paper develops a theoretical model to describe electroadhesion of polymer networks via polycation interfacial bridging and validates it with experimental data.

bioRxiv · Jun 10, 2026 · PreprintBioengineering

Global Trends and Hotspots in Grassland Root Functional Traits Research (2000-2025)

Yongxue Feng, Yang Gao, qin jin Li, Ting Yu Yang, Jing Yin, Shu Yang, hua zhi Jiang, Xiangtao Wang, Puchang Wang, Li Li Zhao

This study analyzes global trends and research hotspots in grassland root functional traits from 2000 to 2025 using bibliometric methods and identifies six key research areas.

bioRxiv · Feb 3, 2026 · PreprintEcology

Genomic Touchstone: Benchmarking Genomic Language Models in the Context of the Central Dogma

Yihui Wang, Zhiyuan Cai, Qian Zeng, Yihang Gao, Jiarui Ouyang, Yingxue Xu, Shu Yang, Sunan He, Yuxiang Nie, Yu Cai, Fengtao Zhou, Cheng Jin, Xi Wang, Zhi Xie, Danqing Zhu, , Hao Chen

Genomic Touchstone evaluates genomic language models across 36 tasks and 88 datasets, revealing insights on model performance, scaling, and pretraining strategies.

bioRxiv · Jun 25, 2025 · PreprintBioinformatics

QOT: Efficient Computation of Sample Level Distance Matrix from Single-Cell Omics Data through Quantized Optimal Transport

Zexuan Wang, Qipeng Zhan, Shu Yang, Shizhuo Mu, Jiong Chen, Sumita Garai, Patryk Orzechowski, Joost Wagenaar, Li Shen

This paper introduces QOT, a method for efficiently computing sample-level distance matrices from single-cell omics data, showing improved accuracy and robustness over existing OT-based approaches.

bioRxiv · Feb 6, 2024 · PreprintBioinformatics

BiATNovo: An Attention-based Bidirectional De Novo Sequencing Framework for Data-Independent-Acquisition Mass Spectrometry

Shu Yang, Siyu Wu, Binyang Li, Y Liu, Fei Li, Jing Qi, Qunying Wang, Xiaohui Liang, Tiannan Guo, Zhongzhi Luan

BiATNovo improves de novo peptide sequencing from DIA mass spectrometry data by using attention-based bidirectional models and post-processing, achieving better accuracy for long peptides and amino acid-level predictions.

bioRxiv · May 11, 2023 · PreprintBioinformatics