Anne Thessen, PhD
Visiting Associate Professor, Biomedical Informatics

Professional Titles

• Visiting Associate Professor

Research Interests

Publications

• 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 Aug;15(8):1848-1855. PubMed PMID: 36125173
• 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, Jiménez-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 May 25;2022. PubMed PMID: 35616100
• 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, Dancík 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;15(8):1838-47. [Epub ahead of print] PubMed PMID: 35611543
• Thessen AE, Marvel S, Achenbach JC, Fischer S, Haendel MA, Hayward K, Klüver N, Könemann 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. PubMed PMID: 35387429
• Thessen, A. E., D. Mozzherin, D. P. Shorthouse, D. J. Patterson (2022) Improving the discoverability of biodiversity data using the Global Names Finder. Biodiversity Information Science and Standards 6:e90026. https://doi.org/10.3897/biss.6.90026
• 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 Mar;19(3):e3001129. PubMed PMID: 33770077
• 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 Jan 25;2021. PubMed PMID: 33507269
• 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 Aug 26;18(17). PubMed PMID: 34501574
• 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 Mar;19(3):e3001129. PubMed PMID: 33770077
• 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 Jan 25;2021. PubMed PMID: 33494105
• Groom Q, Güntsch 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 Nov 27;2020. PubMed PMID: 33439246
• 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 Nov;16(11):e1008376. PubMed PMID: 33232313
• 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, Köhler 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 Jan 8;48(D1):D704-D715. PubMed PMID: 31701156
• 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 Dec;128(12):125002. PubMed PMID: 33369481
• Campbell DL, Thessen AE, Ries L. A novel curation system to facilitate data integration across regional citizen science survey programs. PeerJ. 2020;8:e9219. PubMed PMID: 32821528
• 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. PubMed PMID: 30532623
• Lancaster AK, Thessen AE, Virapongse A. A new paradigm for the scientific enterprise: nurturing the ecosystem. F1000Res. 2018;7:803. PubMed PMID: 30345023
• 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. PubMed PMID: 33816817
• 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. PubMed PMID: 28645762
• 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. PubMed PMID: 28437440
• Patterson D, Mozzherin D, Shorthouse DP, Thessen A. Challenges with using names to link digital biodiversity information. Biodivers Data J. 2016;(4):e8080. PubMed PMID: 27346955
• Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz 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, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez 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. PubMed PMID: 25562316
• Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez 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. PubMed PMID: 26713234
• 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. PubMed PMID: 25548736
• Thessen AE, Parr CS. Knowledge extraction and semantic annotation of text from the encyclopedia of life. PLoS One. 2014;9(3):e89550. PubMed PMID: 24594988
• 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. PubMed PMID: 22940223
• 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. PubMed PMID: 22952856
• Thessen AE, Cui H, Mozzherin D. Applications of natural language processing in biodiversity science. Adv Bioinformatics. 2012;2012:391574. PubMed PMID: 22685456
• Thessen AE, Patterson DJ. Data issues in the life sciences. Zookeys. 2011;(150):15-51. PubMed PMID: 22207805
• 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. PubMed PMID: 19835902