Author

Yi Zhu

Max Planck Institute for Multidisciplinary Sciences

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

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Bioengineering· 2 Genomics· 2 Cancer Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 3 Research Focus:gene regulatory network inference· 2 Assay:Hi-C· 2 Approach:benchmark study· 1 Research Focus:cancer & tumor microenvironment· 1 Research Focus:cell signaling & trafficking· 1 Assay:ChIP-seq· 1 Approach:deep learning· 1

Frequent Co-Authors

A. Marieke OudelaariD· 2 shared Magdalena A. KarpińskaiD· 2 shared Shyam RamasamyiD· 2 shared Abrar AljahaniiD· 1 shared Alex Smerkous· 1 shared Argyris PapantonisiD· 1 shared Belgin Caglar· 1 shared Bin YangiD· 1 shared

Activity by Year

2024-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 13 mutual co-author links

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2 shared papersGenomics

A. Marieke OudelaarORCID

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

T50 O-GlcNAc PKM2 promotes aerobic glycolysis and PDAC progression via ARNT-CDC27-AKT pathway

Bin Yang, Yi Zhu, Xiaopeng Zhan, Yun Zhang, Jianing Cui, Yu Zhou, Shikai Zhu

This study identifies an O-GlcNAc modification on PKM2 that promotes PDAC progression through the ARNT-CDC27-AKT pathway by enhancing aerobic glycolysis.

bioRxiv · Jul 29, 2026 · PreprintCancer Biology

Simultaneous regeneration of skin and bone in full-thickness cranial composite defects

Mirae Kim, Yi Zhu, Shivakalyani Adepu, Caralyn Paige Collins, Maria Mendez-Santos, Cheng Sun, Tong‐Chuan He, Russell Reid, Guillermo Antonio Ameer

This paper develops a 3D-printed composite scaffold that simultaneously regenerates skin and bone in cranial defects, achieving outcomes comparable to autografts and reducing surgical complexity.

bioRxiv · Jun 17, 2026 · PreprintBioengineering

Analysis of multi-way chromatin interactions at sub-nucleosome resolution identifies synergistic nano-scale interactions within super-enhancers

Shyam Ramasamy, Yi Zhu, Magdalena A. Karpińska, Ilya M. Flyamer, Johannes Söding, A. Marieke Oudelaar

The paper introduces mwMCC, a method to detect multi-way chromatin interactions at sub-nucleosome resolution, revealing synergistic nano-scale interactions within super-enhancers and their role in gene regulation.

bioRxiv · May 23, 2026 · PreprintGenomics

LabOS: The AI-XR Co-Scientist That Sees and Works With Humans

Le Cong, David Smerkous, Xiaotong Wang, Di Yin, Zaixi Zhang, Ruofan Jin, Yinkai Wang, Michal Gerasimiuk, Ravi K. Dinesh, Alex Smerkous, Lihan Shi, Joy Zheng, Ian Lam, Xuekun Wu, Shilong Liu, , Mengdi Wang

LabOS is an AI co-scientist that integrates computational reasoning with physical experimentation through multimodal perception and human-AI collaboration, enhancing scientific discovery in biomedical and materials science.

bioRxiv · Oct 16, 2025 · PreprintBioengineering

CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation during cellular differentiation

Magdalena A. Karpińska, Yi Zhu, Zahra Fakhraei Ghazvini, Shyam Ramasamy, Mariano Barbieri, T. B. Ngoc Cao, Natalie Varahram, Abrar Aljahani, Michael Lidschreiber, Argyris Papantonis, A. Marieke Oudelaar

The paper shows that CTCF depletion disrupts chromatin hub formation but not enhancer-promoter interactions, which still drive gene expression during differentiation.

bioRxiv · Nov 20, 2024 · PreprintGenomics