Yu-Cheng Lin

Name: Yu-Cheng Lin

Assistant Professor

Department of Dentistry

College of Dentistry

National Yang Ming Chiao Tung University


DDS (National Taiwan University, Taiwan)

MS (National Taiwan University, Taiwan)
PhD (Columbia University, USA)


Appointment Status
Assistant Professor



Bioinformatics, Machine Learning, Genomics, Microbiology, Genetics



Oral cancer genomics, Precision medicine, Oral microbiome



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

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

Membership of Associated Professional Bodies








Columbia University


Department of Biological Sciences



National Taiwan University


Institute of Microbiology and Biochemistry



National Taiwan University


Department of Dentistry







Job Title


National Yang Ming Chiao Tung University, Taiwan

Department of Dentistry

Assistant Professor

2021 – Present

LifeMine Therapeutics

Genomics, Data Sciences Department

Computational Biologist II

2019 – 2021

New England Biolabs

Research Department

Postdoctoral Fellow

2018 – 2019







Interpretable Deep Learning on Cancer Genomics of Oral Squamous Cell Carcinoma

Principal investigator

8/1/2022 –7/31/2025

National Science and Technology Council, Taiwan

Pilot Project on Precision Oral Oncology

Principal investigator

7/1/2022 – 12/31/2022

Ministry of Health and Welfare, Taiwan

Publications (5-year, key author)

  1. 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.
  2. *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
  3. 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.
  4. 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.
  5. 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.
  6. 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: 5672.
  7. 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.
  8. 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 J. Bacteriol., JB.00031-18.
  9. 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 eLife, 6.
  10. 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. Commun., 7, 12713.
  11. *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. Environ. Microbiol., 81(24), 8414–8426. *These authors contributed equally
  12. *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
  13. Lin Y-C, Fu H-Y, Yang C-S (2010) Phototaxis of Haloarcula marismortui revealed through a novel microbial motion analysis algorithm. Photobiol. 86(5):1084-90.
  14. 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. Bacteriol. 192(22):5866-73.

Email Address: ylin@nycu.edu.tw