跳到主要內容
Loading
Associate Professor Yu-Cheng Lin-Image
Associate Professor

Yu-Cheng Lin

Oral Genomics Data Science

DDS, MS, PhD

​​​​About Our Lab

Our lab lies at the intersection of machine learning, genomics and oral medicine, but essentially what we do every day is turning coffee into code :p

We believe biology is a “small” science; that’s why we adopt the principle of agile software development, bringing “wet” and “dry” labs together for novel biological insights

 

Research Focus

Oral Microbiome, Cancer Genomics, Precision Medicine

Specialty

Bioinformatics, Machine Learning, Genomics, Microbiology, Genetics

 

Education

  • PhD, Department of Biological Sciences, Columbia University, USA
  • MS, Institute of Microbiology and Biochemistry, National Taiwan University, Taiwan
  • DDS, Department of Dentistry, National Taiwan University, Taiwan

Work Experience

  • Computational Biologist, LifeMine Therapeutics, Boston, USA (2019 - 2021)
  • Postdoctoral Fellow, New England Biolabs, Boston, USA (2018 - 2019)

 

Publications

  1. Yang C-C, Washio J, Lin Y-C, Hsu M-L, Wang D-H, Tsai F-T, Lin Y-M, Tu H-F, Chang H-C & Takahashi N (2025) Microbiome Signatures and Dysbiotic Patterns in Oral Cancer and Precancerous Lesions. Oral Diseases, https://doi.org/10.1111/odi.15317.
  2. Florek LC, Lin X, Lin Y-C, Lin M-H, Chakraborty A, Price-Whelan A, Tong L, Rahme L & Dietrich LEP (2024) The L-lactate dehydrogenases of Pseudomonas aeruginosa are conditionally regulated but both contribute to survival during macrophage infection. mBio, https://doi.org/10.1128/mbio.00852-24.
  3. Chang H-C, Yang C-C, Loi L-K, Hung C-H, Wu C-H & Lin Y-C (2024) Interplay of p62-mTORC1 and EGFR Signaling Promotes Cisplatin Resistance in Oral Cancer. Heliyon, https://doi.org/10.1016/j.heliyon.2024.e28406.
  4. Tsai F-T, Yang C-C, Lin Y-C, Hsu M-L, Hong G, Yang M-C, Wang D-H, Huang L-J, Lin C-T, Hsu W-E & Tu H-F (2024) Temporal stability of tongue microbiota in older patients – A pilot study. Journal of Dental Sciences, https://doi.org/10.1016/j.jds.2024.01.012.
  5. *Loi L-K, *Yang C-C, Lin Y-C, Su Y-F, Juan Y-C, Chen Y-H & Chang H-C (2023) Decoy peptides effectively inhibit the binding of SARS-CoV-2 to ACE2 on oral epithelial cells. Heliyon, 9(12): e22614. *These authors contributed equally.
  6. Huang P-C, Chang C-W, Lin Y-C, Chen C-Y, Chen T-Y, Chuang L-T, Liu C-J, Huang C-L & Li W-C (2023) Pyruvate Kinase Differentially Alters Metabolic Signatures during Head and Neck Carcinogenesis. International Journal of Molecular Sciences, 24(23): 16639.
  7. Chansaenroj A, Kornsuthisopon C, Suwittayarak R, Rochanavibhata S, Loi L-K, Lin Y-C & Osathanon T (2023) IWP-2 modulates the immunomodulatory properties of human dental pulp stem cells in vitro. International Endodontic Journal, 2023;00:1–18.
  8. Wang D-H, Tsai F-T, Tu H-F, Yang C-C, Hsu M-L, Huang L-J, Lin C-T, Hsu W-E & Lin Y-C (2023) Profiles of oral microbiome associated with nasogastric tube feeding. Journal of Oral Microbiology, doi.org/10.1080/20002297.2023.2200898.
  9. Chang S-R, Chou C-H, Liu C-J, Lin Y-C, Tu H-F, Chang K-W & Lin S-C (2023) The Concordant Disruption of B7/CD28 Immune Regulators Predicts the Prognosis of Oral Carcinomas. International Journal of Molecular Sciences, 2023 Mar 21;24(6):5931.
  10. Tsai F-T, Wang D-H, Yang C-C, Lin Y-C, Huang L-J, Tsai W-Y, Li C-W, Hsu W-E, Tu H-F & Hsu M-L (2022) Locational effects on oral microbiota among long-term care patients. Journal of Oral Microbiology, 14(1): 2033003.
  11. *Yang W, *Lin Y-C, Johnson W, Dai N, Vaisvila R, Weigele PR, Lee Y-J, Corrêa IR Jr, Schildkraut I & Ettwiller L (2021) A Genome-Phenome Association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA. eLife, 10:e70021. *These authors contributed equally.
  12. Lee Y-J, Dai N, Muller SI, Guan C, Parker MJ, Fraser ME, Walsh SE, Sridar J, Mulholland A, Nayak K, Sun Z, Lin Y-C, Comb DG, Marks K, Gonzalez R, Dowling DP, Bandarian V, Saleh L, Corrêa IR Jr & Weigele PR (2021) Pathways of thymidine hypermodification. Nucleic Acids Research, 50(6), 3001–3017.
  13. Baum C, Lin Y-C, Fomenkov A, Anton BP, Chen L, Yan B, Evans TC, Roberts RJ, Tolonen AC, Ettwiller L (2021) Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes. Nucleic Acids Research, gkab705.
  14. Wang B, Lin Y-C, Vasquez-Rifo A, Jo J, Price-Whelan A, McDonald ST, Brown LM, Sieben C, Dietrich LEP (2021) Pseudomonas aeruginosa PA14 produces R-bodies, extendable protein polymers with roles in host colonization and virulence. Nature Communications, 12(1): 4613.
  15. Chen J-L, Lin Y-C, Fu H-Y, Yang C-S (2019) The Blue-Green Sensory Rhodopsin SRM from Haloarcula marismortui Attenuates Both Phototactic Responses Mediated by Sensory Rhodopsin I and II in Halobacterium salinarum. Scientific Reports, 9(1): 5672.
  16. Lin Y-C, Cornell W-C, Jo J, Price-Whelan A, Dietrich LEP (2018) The Pseudomonas aeruginosa Complement of Lactate Dehydrogenases Enables Use of D- and L-Lactate and Metabolic Cross-Feeding. mBio 9: e00961-18.
  17. Lin Y-C, Sekedat MD, Cornell WC, Silva GM, Okegbe C, Price-Whelan A, Vogel C, Dietrich LEP (2018) Phenazines regulate Nap-dependent denitrification in Pseudomonas aeruginosa biofilms. J. Bacteriol., JB.00031-18.
  18. Fong JC, Rogers A, Michael AK, Parsley NC, Cornell W-C, Lin Y-C, Singh PK, Hartmann R, Drescher K, Vinogradov E, Dietrich LE, Partch CL, Yildiz FH (2017) Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms. eLife, 6.
  19. Choi PH, Jo J, Lin Y-C, Lin M-H, Chou C-Y, Dietrich LEP, Tong L (2016) A distinct holoenzyme organization for two-subunit pyruvate carboxylase. Nat. Commun., 7, 12713.
  20. *Madsen JS, *Lin Y-C, *Squyres GR, Price-Whelan A, de Santiago Torio A, Song A, Cornell WC, Sørensen SJ, Xavier JB, Dietrich LEP (2015) Facultative control of matrix production optimizes competitive fitness in Pseudomonas aeruginosa PA14 biofilm models. Appl. Environ. Microbiol., 81(24), 8414–8426. *These authors contributed equally.
  21. *Hölscher T, *Bartels B, *Lin Y-C, Gallegos-Monterrosa R, Price-Whelan A, Kolter R, Dietrich LEP, Kovács ÁT (2015) Motility, chemotaxis and aerotaxis contribute to competitiveness during bacterial pellicle biofilm development. J. Mol. Biol. doi:10.1016/j.jmb.2015.06.014. *These authors contributed equally.
  22. Lin Y-C, Fu H-Y, Yang C-S (2010) Phototaxis of Haloarcula marismortui revealed through a novel microbial motion analysis algorithm. Photochem. Photobiol. 86(5):1084-90.
  23. Fu H-Y, Lin Y-C, Chang Y-N, Tseng H, Huang C-C, Liu K-C, Huang C-S, Su C-W, Weng RR, Lee Y-Y, Ng WV, Yang C-S (2010) A novel six-rhodopsin system in a single archaeon. J. Bacteriol. 192(22):5866-73.
     
:::