Timothy Clark, PhD

2026
Nourreddine S, Doctor Y, Dailamy A, Forget A, Lee YH, Chinn B, Khaliq H, Polaaco B, Muralidharan M, Pan E, Zhang Y, Sigaeva A, Hansen JN, Gao J, Parker J, Obernier K, Clark T, Metallo C, Lundberg E, Ideker T, Krogan N, Mali P. A Perturbation Cell Atlas of KOLF2.1J hiPSCs. Nature Biotechnology 2026 (in press).

Clark T, Caufield H, Parker JA, Al Manir S, Amorim E, Eddy J, Gim N, Gow B, Goar W, Haendel M, Hansen JN, Harris N, Hermjakob H, Joachimiak M, Jordan G, Lee IH, McWeeney SK, Nebeker C, Nikolov M, Shaffer J, Sheffield N, Sheynkman G, Stevenson J, Chen JY, Mungall C, Wagner A, Kong SW, Ghosh SS, Patel B, Williams A, Munoz-Torres MC. AI-readiness Criteria for Biomedical Data (2026). bioRxiv. 2024 Nov 24;2024.10.23.619844.

Al Manir S, Levinson MA, Niestroy J, Churas C, Parker JA, Clark T (2026). The FAIRSCAPE Ai-readiness Framework for Biomedical Research. bioRxiv 2026.12.23.629818; doi: https://doi.org/10.1101/2024.12.23.629818 

2025
Lenkiewicz J, Churas C, Hu M, Qian G, Jain M, Levinson MA, Al Manir S, Qin Y, Fong D, Ono K, Chen J, Gao C, Pratt D, Parker JA, Clark T, Ideker T, Schaffer LV. Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization. Bioinformatics. 2025 Jun 2;41(6):btaf205. doi: 10.1093/bioinformatics/btaf205. PMID: 40489639; PMCID: PMC12161986.

2024
Clark T, Mohan J, Schaffer L, Obernier K, Al Manir S, Churas CP, Dailamy A, Doctor Y, Forget A, Hansen JN, Hu M, Lenkiewicz J, Levinson MA, Marquez C, Nourreddine S, Niestroy J, Pratt D, Qian G, Thaker S, Bélisle-Pipon JC, Brandt C, Chen J, Ding Y, Fodeh S, Krogan N, Lundberg E, Mali P, Payne-Foster P, Ratcliffe S, Ravitsky V, Sali A, Schulz W, Ideker T (2024). Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines. bioRxiv 2024.05.21.589311; https://doi.org/10.1101/2024.05.21.589311

2022
Sheffield N, Bourne P, Grossman R, Yates A, Spjuth O, Clark T, Burdett T, Bonazzi V (2022) From biomedical cloud platforms to microservices: next steps in FAIR data and analysis. npj Scientific Data 9:553. Clark collaborated in writing and editing this article https://doi.org/10.1038/s41597-022-01619-5.  

Niestroy J, Levinson MA, Manir SA, Clark T, Moorman JR, Fairchild KD, Lake DE. (2022) Discovery of signatures of fatal neonatal illness in vital signs using highly comparative time-series analysis. npj Digital Medicine 2022 Dec;5(1):6. https://www.nature.com/articles/s41746-021-00551-z.

2020
Juty N, Wimalaratne S, Kunze J, Goble C, Clark T (2020). Unique, Persistent, Resolvable Identifiers as the foundation of FAIR. Data Intelligence. Special Issue on Emerging FAIR practices. https://doi.org/10.1162/dint_a_00025. 

2019
Bihlmeyer NA, Merrill E, Lambert Y, Srivastava GP, Clark T, Hyman BT, and Das S (2019). Novel methods for integration and visualization of genomics and genetics data in Alzheimer’s disease. Alzheimers Dement. J. Alzheimers Assoc. https://doi.org/10.1016/j.jalz.2019.01.011. 

2018
Cousijn H, Kenall A, Ganley E, Harrison M, Kernohan D, Murphy F, Polischuk P, Martone M, Clark T (2018) A Data Citation Roadmap for Scientific Publishers. npj Scientific Data 5:180259, 2018. DOI: https://doi.org/10.1038/sdata.2018.259.

Wimalaratne SM, Juty N, Kunze J, Janée G, McMurry JA, Beard N, Jimenez R, Grethe JS, Hermjakob H, Martone ME, Clark T. Uniform resolution of compact identifiers for biomedical data. Scientific Data 2018, 5:180029. DOI: https://doi.org/10.1038/sdata.2018.29. 

Bennett RE, Robbins AB, Hu M, Cao X, Betensky RA, Clark T, Das S, Hyman BT (2018) Tau Induces Blood Vessel Abnormalities and Angiogenesis-Related Gene Expression in P301L Transgenic Mice and Human Alzheimer’s Disease. Proceedings of the National Academy of Science. PMID: 29358399. DOI: https://doi.org/10.1073/pnas.1710329115. 

Fenner M, Crosas M, Grethe J, Kennedy D, Hermjakob H, Rocca-Serra P, Berjon R, Karcher S, Martone M, Clark T (2018). A Data Citation Roadmap for Scholarly Data Repositories. npj Scientific Data . https://doi.org/10.1162/dint_a_00030. 

Cousijn H, Kenall A, Ganley E, Harrison M, Kernohan D, Murphy F, Polischuk P, Martone M, Clark T (2018) A Data Citation Roadmap for Scientific Publishers. npj Scientific Data 5:180259, 2018. DOI: https://doi.org/10.1038/sdata.2018.259.

2016
Wilkinson M, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten J, da Silva Santos L, Bourne P, Bouwman J, Brookes A, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo C, Finkers R, Gonzalez-Beltran A, Gray A, Groth P, Goble C, Grethe J, Heringa J, t Hoen P, Hooft R, Kuhn T, Kok R, Kok J, Lusher S, Martone M, Mons A, Packer A, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone S, Schultes E, Sengstag T, Slater T, Strawn G, Swertz M, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B. (2016) The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data. 3:160018. PMID: 26978244; PMCID: PMC4792175; DOI: https://doi.org/10.1038/sdata.2016.18 

2014
Clark T, Ciccarese P, Goble C (2014) Micropublications: A Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications. Journal of Biomedical Semantics 5:28. http://www.jbiomedsem.com/content/5/1/28. PMID: 26261718;; PMCID:PMC4530550; DOI: https://doi.org/10.1186/2041-1480-5-28. 

2013
Ciccarese P, Soiland-Reyes S, Belhajjame K, Gray AJG, Goble CA, Clark T. (2013) PAV ontology: Provenance, Authoring and Versioning. Journal of Biomedical Semantics 013, 4:37  DOI:10.1186/2041-1480-4-37. PMID: 24267948; PMCID: PMC4177195; DOI: https://doi.org/10.1186/2041-1480-4-37

2012
McFarland KN, Das S, Sun TT, Leyfer D, Kim M-O, Xia E, Kuhn A, Luthi-Carter R, Clark T, Sadri-Vakili G, Cha JH*(2012) Genome-wide histone acetylation is altered in a transgenic mouse model of Huntington's disease. PLoS One 7(7):e41423. PMID: 22848491; PMCID: PMC3407195; DOI: https://doi.org/10.1371/journal.pone.0041423.