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Anne Thessen

TitleAssociate Professor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-BIOMED Informatics Gen Ops
ORCID ORCID Icon0000-0002-2908-3327 Additional info

    Collapse Bibliographic 
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Clarke JL, Cooper LD, Poelchau MF, Berardini TZ, Elser J, Farmer AD, Ficklin S, Kumari S, Laporte MA, Nelson RT, Sadohara R, Selby P, Thessen AE, Whitehead B, Sen TZ. Data sharing and?ontology use among agricultural genetics, genomics, and?breeding databases and?resources of?the Agbiodata Consortium. Database (Oxford). 2023 11 15; 2023. PMID: 37971715.
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    2. Fecho K, Bizon C, Issabekova T, Moxon S, Thessen AE, Abdollahi S, Baranzini SE, Belhu B, Byrd WE, Chung L, Crouse A, Duby MP, Ferguson S, Foksinska A, Forero L, Friedman J, Gardner V, Glusman G, Hadlock J, Hanspers K, Hinderer E, Hobbs C, Hyde G, Huang S, Koslicki D, Mease P, Muller S, Mungall CJ, Ramsey SA, Roach J, Rubin I, Schurman SH, Shalev A, Smith B, Soman K, Stemann S, Su AI, Ta C, Watkins PB, Williams MD, Wu C, Xu CH. An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges. J Clin Transl Sci. 2023; 7(1):e214. PMID: 37900350.
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    3. Caufield JH, Putman T, Schaper K, Unni DR, Hegde H, Callahan TJ, Cappelletti L, Moxon SAT, Ravanmehr V, Carbon S, Chan LE, Cortes K, Shefchek KA, Elsarboukh G, Balhoff J, Fontana T, Matentzoglu N, Bruskiewich RM, Thessen AE, Harris NL, Munoz-Torres MC, Haendel MA, Robinson PN, Joachimiak MP, Mungall CJ, Reese JT. KG-Hub-building and exchanging biological knowledge graphs. Bioinformatics. 2023 07 01; 39(7). PMID: 37389415.
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    4. Thessen AE, Cooper L, Swetnam TL, Hegde H, Reese J, Elser J, Jaiswal P. Using knowledge graphs to infer gene expression in plants. Front Artif Intell. 2023; 6:1201002. PMID: 37384147.
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    5. Stefancsik R, Balhoff JP, Balk MA, Ball RL, Bello SM, Caron AR, Chesler EJ, de Souza V, Gehrke S, Haendel M, Harris LW, Harris NL, Ibrahim A, Koehler S, Matentzoglu N, McMurry JA, Mungall CJ, Munoz-Torres MC, Putman T, Robinson P, Smedley D, Sollis E, Thessen AE, Vasilevsky N, Walton DO, Osumi-Sutherland D. The Ontology of Biological Attributes (OBA)-computational traits for the life sciences. Mamm Genome. 2023 09; 34(3):364-378. PMID: 37076585.
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    6. Gosline SJC, Kim DN, Pande P, Thomas DG, Truong L, Hoffman P, Barton M, Loftus J, Moran A, Hampton S, Dowson S, Franklin L, Degnan D, Anderson L, Thessen A, Tanguay RL, Anderson KA, Waters KM. The Superfund Research Program Analytics Portal: linking environmental chemical exposure to biological phenotypes. Sci Data. 2023 03 21; 10(1):151. PMID: 36944655.
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    7. Chan LE, Thessen AE, Duncan WD, Matentzoglu N, Schmitt C, Grondin CJ, Vasilevsky N, McMurry JA, Robinson PN, Mungall CJ, Haendel MA. The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond. J Biomed Semantics. 2023 02 24; 14(1):3. PMID: 36823605.
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    8. Holmgren S, Bell SM, Wignall J, Duncan CG, Kwok RK, Cronk R, Osborn K, Black S, Thessen A, Schmitt C. Workshop Report: Catalyzing Knowledge-Driven Discovery in Environmental Health Sciences through a Harmonized Language. Int J Environ Res Public Health. 2023 01 28; 20(3). PMID: 36767684.
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    9. Stefancsik R, Balhoff JP, Balk MA, Ball R, Bello SM, Caron AR, Chessler E, de Souza V, Gehrke S, Haendel M, Harris LW, Harris NL, Ibrahim A, Koehler S, Matentzoglu N, McMurry JA, Mungall CJ, Munoz-Torres MC, Putman T, Robinson P, Smedley D, Sollis E, Thessen AE, Vasilevsky N, Walton DO, Osumi-Sutherland D. The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences. bioRxiv. 2023 Jan 27. PMID: 36747660.
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    10. Unni DR, Moxon SAT, Bada M, Brush M, Bruskiewich R, Caufield JH, Clemons PA, Dancik V, Dumontier M, Fecho K, Glusman G, Hadlock JJ, Harris NL, Joshi A, Putman T, Qin G, Ramsey SA, Shefchek KA, Solbrig H, Soman K, Thessen AE, Haendel MA, Bizon C, Mungall CJ. Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science. Clin Transl Sci. 2022 08; 15(8):1848-1855. PMID: 36125173.
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    11. Matentzoglu N, Balhoff JP, Bello SM, Bizon C, Brush M, Callahan TJ, Chute CG, Duncan WD, Evelo CT, Gabriel D, Graybeal J, Gray A, Gyori BM, Haendel M, Harmse H, Harris NL, Harrow I, Hegde HB, Hoyt AL, Hoyt CT, Jiao D, Jim?nez-Ruiz E, Jupp S, Kim H, Koehler S, Liener T, Long Q, Malone J, McLaughlin JA, McMurry JA, Moxon S, Munoz-Torres MC, Osumi-Sutherland D, Overton JA, Peters B, Putman T, Queralt-Rosinach N, Shefchek K, Solbrig H, Thessen A, Tudorache T, Vasilevsky N, Wagner AH, Mungall CJ. A Simple Standard for Sharing Ontological Mappings (SSSOM). Database (Oxford). 2022 05 25; 2022. PMID: 35616100.
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    12. Fecho K, Thessen AE, Baranzini SE, Bizon C, Hadlock JJ, Huang S, Roper RT, Southall N, Ta C, Watkins PB, Williams MD, Xu H, Byrd W, Danc?k V, Duby MP, Dumontier M, Glusman G, Harris NL, Hinderer EW, Hyde G, Johs A, Su AI, Qin G, Zhu Q. Progress toward a universal biomedical data translator. Clin Transl Sci. 2022 May 25. PMID: 35611543.
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    13. Thessen AE, Marvel S, Achenbach JC, Fischer S, Haendel MA, Hayward K, Kl?ver N, K?nemann S, Legradi J, Lein P, Leong C, Mylroie JE, Padilla S, Perone D, Planchart A, Prieto RM, Muriana A, Quevedo C, Reif D, Ryan K, Stinckens E, Truong L, Vergauwen L, Vom Berg C, Wilbanks M, Yaghoobi B, Hamm J. Implementation of Zebrafish Ontologies for Toxicology Screening. Front Toxicol. 2022; 4:817999. PMID: 35387429.
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    14. Holmgren SD, Boyles RR, Cronk RD, Duncan CG, Kwok RK, Lunn RM, Osborn KC, Thessen AE, Schmitt CP. Catalyzing Knowledge-Driven Discovery in Environmental Health Sciences through a Community-Driven Harmonized Language. Int J Environ Res Public Health. 2021 08 26; 18(17). PMID: 34501574.
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    15. Thessen AE, Bogdan P, Patterson DJ, Casey TM, Hinojo-Hinojo C, de Lange O, Haendel MA. From Reductionism to Reintegration: Solving society's most pressing problems requires building bridges between data types across the life sciences. PLoS Biol. 2021 03; 19(3):e3001129. PMID: 33770077.
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    16. Chan L, Vasilevsky N, Thessen A, McMurry J, Haendel M. The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research. Database (Oxford). 2021 01 25; 2021. PMID: 33494105.
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    17. Thessen AE, Grondin CJ, Kulkarni RD, Brander S, Truong L, Vasilevsky NA, Callahan TJ, Chan LE, Westra B, Willis M, Rothenberg SE, Jarabek AM, Burgoon L, Korrick SA, Haendel MA. Community Approaches for Integrating Environmental Exposures into Human Models of Disease. Environ Health Perspect. 2020 12; 128(12):125002. PMID: 33369481.
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    18. Groom Q, G?ntsch A, Huybrechts P, Kearney N, Leachman S, Nicolson N, Page RDM, Shorthouse DP, Thessen AE, Haston E. People are essential to linking biodiversity data. Database (Oxford). 2020 11 27; 2020. PMID: 33439246.
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    19. Thessen AE, Walls RL, Vogt L, Singer J, Warren R, Buttigieg PL, Balhoff JP, Mungall CJ, McGuinness DL, Stucky BJ, Yoder MJ, Haendel MA. Transforming the study of organisms: Phenomic data models and knowledge bases. PLoS Comput Biol. 2020 11; 16(11):e1008376. PMID: 33232313.
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    20. Campbell DL, Thessen AE, Ries L. A novel curation system to facilitate data integration across regional citizen science survey programs. PeerJ. 2020; 8:e9219. PMID: 32821528.
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    21. Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Della Rocca M, Dunn N, Essaid S, Fey P, Grove C, Gourdine JP, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, K?hler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D. The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 2020 01 08; 48(D1):D704-D715. PMID: 31701156.
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    22. Endara L, Thessen AE, Cole HA, Walls R, Gkoutos G, Cao Y, Chong SS, Cui H. Modifier Ontologies for frequency, certainty, degree, and coverage phenotype modifier. Biodivers Data J. 2018; (6):e29232. PMID: 30532623.
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    23. Thessen AE, Poelen JH, Collins M, Hammock J. 20 GB in 10 minutes: a case for linking major biodiversity databases using an open socio-technical infrastructure and a pragmatic, cross-institutional collaboration. PeerJ Comput Sci. 2018; 4:e164. PMID: 33816817.
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    24. Lancaster AK, Thessen AE, Virapongse A. A new paradigm for the scientific enterprise: nurturing the ecosystem. F1000Res. 2018; 7:803. PMID: 30345023.
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    25. Thessen AE, North EW. Calculating in situ degradation rates of hydrocarbon compounds in deep waters of the Gulf of Mexico. Mar Pollut Bull. 2017 Sep 15; 122(1-2):77-84. PMID: 28645762.
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    26. Gandy LM, Gumm J, Fertig B, Thessen A, Kennish MJ, Chavan S, Marchionni L, Xia X, Shankrit S, Fertig EJ. Synthesizer: Expediting synthesis studies from context-free data with information retrieval techniques. PLoS One. 2017; 12(4):e0175860. PMID: 28437440.
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    27. Patterson D, Mozzherin D, Shorthouse DP, Thessen A. Challenges with using names to link digital biodiversity information. Biodivers Data J. 2016; (4):e8080. PMID: 27346955.
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    28. Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ram?rez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. Emerging semantics to link phenotype and environment. PeerJ. 2015; 3:e1470. PMID: 26713234.
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    29. Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Cs?sz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, K?hler S, Lecointre G, Lapp H, Lawrence CJ, Le Nov?re N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mik? I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ram?rez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P. Finding our way through phenotypes. PLoS Biol. 2015 Jan; 13(1):e1002033. PMID: 25562316.
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    30. Quintero E, Thessen AE, Arias-Caballero P, Ayala-Orozco B. A statistical assessment of population trends for data deficient Mexican amphibians. PeerJ. 2014; 2:e703. PMID: 25548736.
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    31. Thessen AE, Parr CS. Knowledge extraction and semantic annotation of text from the encyclopedia of life. PLoS One. 2014; 9(3):e89550. PMID: 24594988.
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    32. Murray SA, Patterson DJ, Thessen AE. Transcriptomics and microbial eukaryote diversity: a way forward. Trends Ecol Evol. 2012 Dec; 27(12):651-2; author reply 652-3. PMID: 22940223.
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    33. Thessen AE, Patterson DJ, Murray SA. The taxonomic significance of species that have only been observed once: the genus Gymnodinium (Dinoflagellata) as an example. PLoS One. 2012; 7(8):e44015. PMID: 22952856.
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    34. Thessen AE, Cui H, Mozzherin D. Applications of natural language processing in biodiversity science. Adv Bioinformatics. 2012; 2012:391574. PMID: 22685456.
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    35. Thessen AE, Patterson DJ. Data issues in the life sciences. Zookeys. 2011; (150):15-51. PMID: 22207805.
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    36. Field D, Sansone S, Delong EF, Sterk P, Friedberg I, Gaudet P, Lewis S, Kottmann R, Hirschman L, Garrity G, Cochrane G, Wooley J, Meyer F, Hunter S, White O, Bramlett B, Gregurick S, Lapp H, Orchard S, Rocca-Serra P, Ruttenberg A, Shah N, Taylor C, Thessen A. Meeting Report: BioSharing at ISMB 2010. Stand Genomic Sci. 2010 Dec 04; 3(3):254-8. PMID: 21304729.
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    37. Thessen AE, Soniat TM, Dortch Q, Doucette GJ. Crassostrea virginica grazing on toxic and non-toxic diatoms. Toxicon. 2010 Feb-Mar; 55(2-3):570-9. PMID: 19835902.
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