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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Cancer Biology· 4 Biophysics· 3 Cell Biology· 3 Evolutionary Biology· 2 Ecology· 1 Microbiology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 8 Organism:human· 6 Approach:statistical model· 6 Research Focus:cell type annotation· 5 Research Focus:differential expression· 4 Assay:bulk RNA-seq· 3 Research Focus:drug response / drug discovery· 3 Research Focus:gene regulatory network inference· 3

Frequent Co-Authors

C. C. Collins· 4 shared H. Xue· 3 shared J. Lipfert· 3 shared S. Anderson· 3 shared S. Volik· 3 shared S.-Y. Chang· 3 shared W. Vanderlinden· 3 shared Y. Wang· 3 shared

Activity by Year

2018-2024 · peak 5/yr

Co-Author Collaboration Network

10 top collaborators · 16 mutual co-author links

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4 shared papersCancer Biology

C. C. Collins

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Author profile →

16 papers

Recent·Most cited

Deciphering the Transcription Factor Landscape in Neuroendocrine Prostate Cancer Progression: A Novel Approach to Understand NE Transdifferentiation

Y. Wang, H. Xue, X. Zhu, D. Lin, X. Dong, Z. Chen, J. Chen, M. Shi, Y. Ni, J. Cao, R. Wu, N. Kang, X. Pang, F. Crea, Y.-Y. Lin, , Y. Wang

This study identifies lineage-specific transcription factor profiles in prostate cancer progression, revealing dynamic shifts during NE transdifferentiation and proposing a three-phase model.

bioRxiv · Apr 27, 2024Cancer Biology

scMUSCL: Multi-Source Transfer Learning for Clustering scRNA-seq Data

A. Khoeini, F. Sar, Y.-Y. Lin, C. Collins, M. Ester

scMUSCL improves scRNA-seq clustering by transferring knowledge from multiple annotated datasets without requiring batch correction or prior cluster number knowledge.

bioRxiv · Apr 22, 2024Cell Biology

5'-S-(3-aminophenyl)-5'-thioadenosine, a novel chemoprotective agent for reducing toxic side effects of fluorouracil in treatment of MTAP-deficient cancers

S. Zhang, H. Xue, N. K. Y. Wong, T. Doerksen, F. Ban, S. Anderson, S. Volik, Y.-Y. Lin, Z. Dai, I. Bratanovic, H. Cheng, C. C. Collins, A. Cherkasov, J. Wulff, Y. Wang

This paper identifies m-APTA, an MTA analogue that reduces NBA toxicity without hypothermia, improving safety for MTAP-deficient cancer treatment.

bioRxiv · Apr 17, 2024Cancer Biology

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