Publications

TW Coleman, J Bittner. Heuristics: Cognitive Strategies for Decisions Under Constraint. Joint Ontology Workshops (JOWO) at the Formal Ontology in Information Systems (FOIS 2025) PHASES: Workshop on Promoting Healthy Aging through the Semantic Enrichment of Social Sciences. Sep 8, 2025. https://ceur-ws.org/Vol-4176/phases-5.pdf

Bittner, J. H., Beverley, J., & Coleman, T. W. (2025). Shadows to Referents: An Ontological Interpretation of Plato’s Cave for Anomaly Resolution. Joint Ontology Workshops (JOWO) - Episode XI: The Sicilian Summer under the Etna, co-located with the 15th International Conference on Formal Ontology in Information Systems (FOIS 2025) CAOS: Cognition And OntologieS Workshop. Sep 8, 2025. https://ceur-ws.org/Vol-4176/caos-8.pdf

L. Burtnyak, Y. Yuan, E. Stojek, X. Pan, L. Gunaratne, G. Silveira d’Almeida, C. Fergus, M. Martinelli, C. J. Reed, J. Fernandez, B.I. Patel, I. Marquez, A.E. Ehrenhofer-Murray, M.A. Swairjo, J.D. Alfonzo, B.D. Green, V.P. Kelly, & V. de Crécy-Lagard, The oncogene SLC35F2 is a high-specificity transporter for the micronutrients queuine and queuosine, Proc. Natl. Acad. Sci. U.S.A. 122 (25) e2425364122, https://doi.org/10.1073/pnas.2425364122 (2025).

Jaroch M, Sun G, Tsui HT, Reed C, Sun J, Jörg M, Winkler ME, Rice KC, Dziergowska A, Stich TA, Dedon PC, Dos Santos PC, de Crécy-Lagard V. 2024. Alternate routes to mnm5s2U synthesis in Gram-positive bacteria. J Bacteriol 206:e00452-23. https://doi.org/10.1128/jb.00452-23

Colbie J. Reed, Rémi Denise, Jacob Hourihan, Jill Babor, Marshall Jaroch, Maria Martinelli Geoffrey Hutinet and Valérie de Crécy-Lagard. 2024. Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families. Microbial Genomics 10 (2), 001183. https://doi.org/10.1099/mgen.0.001183

Colbie J. Reed. Contemporary Challenges of Protein Functional Annotation in the Era of Big Biodata: Investigating the Balance of Quality & Quantity in Today’s Biological Sciences. Doctoral Thesis. Department of Microbiology and Cell Science. University of Florida. 2023. ProQuest.

Lombard, M., Reed, C. J., Pecqueur, L., Faivre, B., Toubdji, S., Sudol, C., Brégeon, D., de Crécy-Lagard, V., & Hamdane, D. (2022). Evolutionary Diversity of Dus2 Enzymes Reveals Novel Structural and Functional Features among Members of the RNA Dihydrouridine Synthases Family. Biomolecules, 12(12), 1760. https://doi.org/10.3390/biom12121760

Valérie de Crécy-lagard, Rocio Amorin de Hegedus, Cecilia Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan J Bridge, Stephen K Burley, Stacey Cleveland, Lucy J Colwell, Ana Conesa, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang, Iddo Friedberg, John Gerlt, Joshua Goldford, Mark Gorelik, Benjamin M Gyori, Christopher Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria-Jesus Martin, Claire McWhite, Gaurav D Moghe, Paul Monaghan, Anne Morgat, Christopher J Mungall, Darren A Natale, William C Nelson, Seán O’Donoghue, Christine Orengo, Katherine H O’Toole, Predrag Radivojac, Colbie Reed, Richard J Roberts, Dmitri Rodionov, Irina A Rodionova, Jeffrey D Rudolf, Lana Saleh, Gloria Sheynkman, Francoise Thibaud-Nissen, Paul D Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter R Weigele, Valerie Wood, Elisha M Wood-Charlson, Jin Xu, A roadmap for the functional annotation of protein families: a community perspective, Database, Volume 2022, 2022, baac062, https://doi.org/10.1093/database/baac062

Reed, C. J., Hutinet, G., & de Crécy-Lagard, V. (2021). Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase. Biomolecules, 11(9), 1282. https://doi.org/10.3390/biom11091282