Author

Y.-Y. Lin

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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Biophysics· 3 Cancer Biology· 2 Cell Biology· 2 Evolutionary Biology· 2 Ecology· 1 Microbiology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 7 Organism:human· 5 Approach:statistical model· 5 Research Focus:cell type annotation· 4 Research Focus:differential expression· 3 Assay:bulk RNA-seq· 2 Research Focus:chromatin & epigenetic regulation· 2 Research Focus:drug response / drug discovery· 2

Frequent Co-Authors

J. Lipfert· 3 shared S.-Y. Chang· 3 shared W. Vanderlinden· 3 shared A. Haegert· 2 shared A. Kowala· 2 shared B. McConeghy· 2 shared C. C. Collins· 2 shared G. B. Morin· 2 shared

Activity by Year

2018-2024 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 9 mutual co-author links

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3 shared papersBiophysics

J. Lipfert

Mutual co-authors in cluster

Author profile →

13 papers

Recent·Most cited

Epigenetic histone modifications H3K36me3 and H4K5/8/12/16ac induce open polynucleosome conformations via different mechanisms

Y.-Y. Lin, P. Muller, E. Karagianni, W. Vanderlinden, J. Lipfert

This study examines how H3K36me3 and H4K5/8/12/16ac histone modifications affect nucleosome structure and interactions in tri-nucleosome arrays, revealing distinct mechanisms for inducing open conformations.

bioRxiv · Feb 19, 2024Biophysics

Cross-institutional HER2 assessment via a computer-aided system using federated learning and stain composition augmentation

C.-H. Yang, Y.-A. Chen, S.-Y. Chang, Y.-H. Hsieh, Y.-L. Hung, Y.-W. Lin, Y.-H. Lee, C.-H. Lin, Y.-C. Lin, Y.-S. Lu, Y.-Y. Lin

This paper develops a HER2 assessment system using federated learning and stain composition augmentation, achieving over 90% accuracy across two institutions with improved generalizability.

bioRxiv · Jan 17, 2024 · PreprintPathology

Engineered human myogenic cells in hydrogels generate functional myofibers within dystrophic mouse muscle

A. Kowala, J. Meng, O. Pourquie, J. Connelly, J. E. Morgan, Y.-Y. Lin

This study shows engineered human myogenic cells in hydrogels form functional myofibers in dystrophic mouse muscle, producing dystrophin and integrating with host nerves and blood vessels.

bioRxiv · Sep 5, 2023Cell Biology

Antagonistic pleiotropy plays an important role in governing the evolution and genetic diversity of SARS-CoV-2

D.-C. Lee, J.-H. Tai, H.-F. Lin, T.-L. Chao, Y. Ruan, Y.-W. Cheng, Y.-C. Chou, Y.-Y. Lin, S.-Y. Chang, P.-J. Chen, S.-H. Yeh, H.-Y. Wang

The paper examines how antagonistic pleiotropy influences SARS-CoV-2 evolution and genetic diversity by analyzing genomic mutations and their functional impacts.

bioRxiv · Feb 10, 2023Evolutionary Biology

High-yield, ligation-free assembly of DNA constructs with nucleosome positioning sequence repeats for single molecule manipulation assays

Y.-Y. Lin, T. Brouns, P. J. Kolbeck, W. Vanderlinden, J. Lipfert

This paper describes a method for high-yield DNA construct assembly with nucleosome positioning sequences for single-molecule manipulation assays, demonstrating stable tethers and proof-of-concept measurements on nucleosome dynamics.

bioRxiv · Jan 5, 2023Biophysics

Spatial and Temporal Origin of The Third SARS-Cov-2 Outbreak in Taiwan

J.-H. Tai, Y. K. Low, S. C.-L. Wang, H.-F. Lin, T.-Y. Wang, Y.-Y. Lin, C. Foster, S. J. van Hal, Y.-Y. Lai, S.-H. Yeh, S.-Y. Chang, P.-J. Chen, S.-M. Chaw

This study identifies the third SARS-CoV-2 outbreak in Taiwan as originating from a European lineage introduced in February 2021, not from the US as previously thought.

bioRxiv · Jul 4, 2022 · PreprintEvolutionary Biology

CRISPR-mediated correction of skeletal muscle Ca2+ handling in a novel DMD patient-derived pluripotent stem cell model

C. Morera, J. Kim, A. Paredes-Redondo, M. Nobles, D. Rybin, R. Moccia, A. Kowala, J. Meng, S. Garren, P. Liu, J. E. Morgan, F. Muntoni, N. Christoforou, J. Owens, A. Tinker, Y.-Y. Lin

This study uses CRISPR to correct dystrophin mutations in DMD patient-derived PSCs, revealing impaired Ca2+ handling and showing rescue through gene correction.

bioRxiv · Feb 17, 2022Cell Biology

Allometric scaling of RNA abundance from genes to communities

M. L. D. Lopez, Y.-y. Lin, S. Q. Schneider, R. J. Machida

This study tests RNA allometric scaling using mock community metatranscriptome analysis, finding that smaller, faster-growing species have higher RNA abundance per tissue mass.

bioRxiv · Oct 3, 2021 · PreprintEcology

A promiscuity locus confers Lotus burttii nodulation with rhizobia from five different genera

M. Zarrabian, J. Montiel, N. Sandal, H. Jin, Y.-Y. Lin, V. Klingl, M. Marin, E. K. James, M. Parniske, J. Stougaard, S. U. Andersen

This study identifies a genetic locus in Lotus burttii that enables nodulation with rhizobia from five different genera, suggesting a general mechanism for host-range expansion.

bioRxiv · Aug 26, 2021Plant Biology

Typhoid toxin sorting and exocytic transport from Salmonella Typhi infected cells

S.-J. Chang, Y.-Y. Lin, M. Lara-Tejero, J. E. Galan

This study identifies the cellular machinery and receptor involved in the exocytic transport of typhoid toxin from Salmonella Typhi-infected cells.

bioRxiv · Aug 10, 2021Microbiology

Twisting DNA by Salt

S. Cruz-León, W. Vanderlinden, P. Müller, T. Forster, G. Staudt, Y.-Y. Lin, J. Lipfert, N. Schwierz

This study investigates how DNA twist changes with ion concentration and identity using single-molecule experiments and simulations, revealing trends in cation-specific effects on DNA structure.

bioRxiv · Jul 14, 2021Biophysics

Multiomics Characterization of Potential Therapeutic Vulnerabilities in Low-grade Serous Ovarian Carcinoma

R. Shrestha, M. L. Fernandez, A. Dawson, J. Hoenisch, S. Volik, Y.-Y. Lin, S. Anderson, H. Kim, A. Haegert, S. Colborne, B. McConeghy, R. H. Bell, S. Brahmbhatt, G. E. DiMattia, S. Le Bihan, , M. S. Carey

This study uses multiomics analysis of LGSOC cell lines to identify therapeutic vulnerabilities and biomarkers for MEK inhibitor efficacy.

bioRxiv · Jun 18, 2020 · PreprintCancer Biology

BAP1 Haploinsufficiency Predicts a Distinct Immunogenic Class of Malignant Peritoneal Mesothelioma

R. Shrestha, N. Nabavi, Y.-Y. Lin, F. Mo, S. Anderson, S. Volik, H. H. Adomat, D. Lin, H. Xue, X. Dong, R. Shukin, R. H. Bell, B. McConeghy, A. Haegert, S. Brahmbhatt, , C. C. Collins

The paper identifies BAP1 loss as a marker for a distinct immunogenic PeM subtype, suggesting potential therapeutic targets like immune checkpoint inhibitors.

bioRxiv · Dec 13, 2018Cancer Biology