Melissa Haendel, PhD
Professor, Biomedical Informatics

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Graduate School :
  • PhD, University of Wisconsin - Madison (1999)
Department: Biomedical Informatics

Professional Titles

  • Chief Research Informatics Officer
  • Professor

Publications

  • Anzalone AJ, Sun J, Vinson AJ, Beasley WH, Hillegass WB, Murray K, Hendricks BM, Haendel M, Geary CR, Bailey KL, Hanson CK, Miele L, Horswell R, McMurry JA, Porterfield JZ, Vest MT, Bunnell HT, Harper JR, Price BS, Santangelo SL, Rosen CJ, McClay JC, Hodder SL. Community risks for SARS-CoV-2 infection among fully vaccinated US adults by rurality: A retrospective cohort study from the National COVID Cohort Collaborative. PLoS One. 2023;18(1):e0279968. PubMed PMID: 36603014
  • Fu S, Wang L, Moon S, Zong N, He H, Pejaver V, Relevo R, Walden A, Haendel M, Chute CG, Liu H. Recommended Practices and Ethical Considerations for Natural Language Processing-Assisted Observational Research: A Scoping Review. Clin Transl Sci. 2022 Dec 7. [Epub ahead of print] PubMed PMID: 36478394
  • Reese JT, Blau H, Casiraghi E, Bergquist T, Loomba JJ, Callahan TJ, Laraway B, Antonescu C, Coleman B, Gargano M, Wilkins KJ, Cappelletti L, Fontana T, Ammar N, Antony B, Murali TM, Caufield JH, Karlebach G, McMurry JA, Williams A, Moffitt R, Banerjee J, Solomonides AE, Davis H, Kostka K, Valentini G, Sahner D, Chute CG, Madlock-Brown C, Haendel MA, Robinson PN. Generalisable long COVID subtypes: Findings from the NIH N3C and RECOVER programmes. EBioMedicine. 2022 Dec 21;87:104413. [Epub ahead of print] PubMed PMID: 36563487
  • Call JT, Lee AS, Haendel MA, Chute CG, Helgeson SA. The Effect of the COVID-19 Pandemic on Pulmonary Diagnostic Procedures. Ann Am Thorac Soc. 2022 Apr;19(4):695-697. PubMed PMID: 34788203
  • Hoyt CT, Balk M, Callahan TJ, Domingo-Fernández D, Haendel MA, Hegde HB, Himmelstein DS, Karis K, Kunze J, Lubiana T, Matentzoglu N, McMurry J, Moxon S, Mungall CJ, Rutz A, Unni DR, Willighagen E, Winston D, Gyori BM. Unifying the identification of biomedical entities with the Bioregistry. Sci Data. 2022 Nov 19;9(1):714. PubMed PMID: 36402838
  • Pfaff ER, Girvin AT, Gabriel DL, Kostka K, Morris M, Palchuk MB, Lehmann HP, Amor B, Bissell M, Bradwell KR, Gold S, Hong SS, Loomba J, Manna A, McMurry JA, Niehaus E, Qureshi N, Walden A, Zhang XT, Zhu RL, Moffitt RA, Haendel MA, Chute CG, Adams WG, Al-Shukri S, Anzalone A, Baghal A, Bennett TD, Bernstam EV, Bernstam EV, Bissell MM, Bush B, Campion TR, Castro V, Chang J, Chaudhari DD, Chen W, Chu S, Cimino JJ, Crandall KA, Crooks M, Davies SJD, DiPalazzo J, Dorr D, Eckrich D, Eltinge SE, Fort DG, Golovko G, Gupta S, Haendel MA, Hajagos JG, Hanauer DA, Harnett BM, Horswell R, Huang N, Johnson SG, Kahn M, Khanipov K, Kieler C, Luzuriaga KR, Maidlow S, Martinez A, Mathew J, McClay JC, McMahan G, Melancon B, Meystre S, Miele L, Morizono H, Pablo R, Patel L, Phuong J, Popham DJ, Pulgarin C, Santos C, Sarkar IN, Sazo N, Setoguchi S, Soby S, Surampalli S, Suver C, Vangala UMR, Visweswaran S, Oehsen JV, Walters KM, Wiley L, Williams DA, Zai A. Synergies between centralized and federated approaches to data quality: a report from the national COVID cohort collaborative. J Am Med Inform Assoc. 2022 Mar 15;29(4):609-618. PubMed PMID: 34590684
  • Chan LE, Casiraghi E, Laraway B, Coleman B, Blau H, Zaman A, Harris NL, Wilkins K, Antony B, Gargano M, Valentini G, Sahner D, Haendel M, Robinson PN, Bramante C, Reese J. Metformin is associated with reduced COVID-19 severity in patients with prediabetes. Diabetes Res Clin Pract. 2022 Dec;194:110157. PubMed PMID: 36400170
  • Coleman B, Casiraghi E, Callahan TJ, Blau H, Chan L, Laraway B, Clark KB, Reâ Em Y, Gersing KR, Wilkins K, Harris NL, Valentini G, Haendel MA, Reese J, Robinson PN. Post-COVID Phenotypic Manifestations are Associated with New-Onset Psychiatric Disease: Findings from the NIH N3C and RECOVER Studies. medRxiv. 2022 Nov 1. PubMed PMID: 36380762
  • Brannock MD, Chew RF, Preiss AJ, Hadley EC, McMurry JA, Leese PJ, Girvin AT, Crosskey M, Zhou AG, Moffitt RA, Funk MJ, Pfaff ER, Haendel MA, Chute CG. Long COVID Risk and Pre-COVID Vaccination: An EHR-Based Cohort Study from the RECOVER Program. medRxiv. 2022 Oct 7. PubMed PMID: 36238713
  • Matentzoglu N, Goutte-Gattat D, Tan SZK, Balhoff JP, Carbon S, Caron AR, Duncan WD, Flack JE, Haendel M, Harris NL, Hogan WR, Hoyt CT, Jackson RC, Kim H, Kir H, Larralde M, McMurry JA, Overton JA, Peters B, Pilgrim C, Stefancsik R, Robb SM, Toro S, Vasilevsky NA, Walls R, Mungall CJ, Osumi-Sutherland D. Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. Database (Oxford). 2022 Oct 8;2022. PubMed PMID: 36208225
  • 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
  • Chan LE, Casiraghi E, Laraway B, Coleman B, Blau H, Zaman A, Harris N, Wilkins K, Gargano M, Valentini G, Sahner D, Haendel M, Robinson PN, Bramante C, Reese J. Metformin is Associated with Reduced COVID-19 Severity in Patients with Prediabetes. medRxiv. 2022 Aug 30. PubMed PMID: 36093353
  • Pfaff ER, Madlock-Brown C, Baratta JM, Bhatia A, Davis H, Girvin A, Hill E, Kelly L, Kostka K, Loomba J, McMurry JA, Wong R, Bennett TD, Moffitt R, Chute CG, Haendel M. Coding Long COVID: Characterizing a new disease through an ICD-10 lens. medRxiv. 2022 Sep 2. PubMed PMID: 36093345
  • Hill E, Mehta H, Sharma S, Mane K, Xie C, Cathey E, Loomba J, Russell S, Spratt H, DeWitt PE, Ammar N, Madlock-Brown C, Brown D, McMurry JA, Chute CG, Haendel MA, Moffitt R, Pfaff ER, Bennett TD. Risk Factors Associated with Post-Acute Sequelae of SARS-CoV-2 in an EHR Cohort: A National COVID Cohort Collaborative (N3C) Analysis as part of the NIH RECOVER program. medRxiv. 2022 Aug 17. PubMed PMID: 36032983
  • Jones S, Bradwell KR, Chan LE, Olson-Chen C, Tarleton J, Wilkins KJ, Qin Q, Faherty EG, Lau YK, Xie C, Kao YH, Liebman MN, Mariona F, Challa A, Li L, Ratcliffe SJ, McMurry JA, Haendel MA, Patel RC, Hill EL. Who is pregnant? defining real-world data-based pregnancy episodes in the National COVID Cohort Collaborative (N3C). medRxiv. 2022 Aug 6. PubMed PMID: 35982668
  • Dhombres F, Morgan P, Chaudhari BP, Filges I, Sparks TN, Lapunzina P, Roscioli T, Agarwal U, Aggarwal S, Beneteau C, Cacheiro P, Carmody LC, Collardeau-Frachon S, Dempsey EA, Dufke A, Duyzend MH, El Ghosh M, Giordano JL, Glad R, Grinfelde I, Iliescu DG, Ladewig MS, Munoz-Torres MC, Pollazzon M, Radio FC, Rodo C, Silva RG, Smedley D, Sundaramurthi JC, Toro S, Valenzuela I, Vasilevsky NA, Wapner RJ, Zemet R, Haendel MA, Robinson PN. Prenatal phenotyping: A community effort to enhance the Human Phenotype Ontology. Am J Med Genet C Semin Med Genet. 2022 Jun;190(2):231-242. PubMed PMID: 35872606
  • Thaxton C, Goldstein J, DiStefano M, Wallace K, Witmer PD, Haendel MA, Hamosh A, Rehm HL, Berg JS. Lumping versus splitting: How to approach defining a disease to enable accurate genomic curation. Cell Genom. 2022 May 11;2(5). PubMed PMID: 35754516
  • Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Buske OJ, Callahan TJ, Chute CG, Courtot M, Danis D, Elemento O, Essenwanger A, Freimuth RR, Gargano MA, Groza T, Hamosh A, Harris NL, Kaliyaperumal R, Lloyd KCK, Khalifa A, Krawitz PM, Köhler S, Laraway BJ, Lehväslaiho H, Matalonga L, McMurry JA, Metke-Jimenez A, Mungall CJ, Munoz-Torres MC, Ogishima S, Papakonstantinou A, Piscia D, Pontikos N, Queralt-Rosinach N, Roos M, Sass J, Schofield PN, Seelow D, Siapos A, Smedley D, Smith LD, Steinhaus R, Sundaramurthi JC, Swietlik EM, Thun S, Vasilevsky NA, Wagner AH, Warner JL, Weiland C, Haendel MA, Robinson PN. The GA4GH Phenopacket schema defines a computable representation of clinical data. Nat Biotechnol. 2022 Jun;40(6):817-820. PubMed PMID: 35705716
  • Reese JT, Blau H, Bergquist T, Loomba JJ, Callahan T, Laraway B, Antonescu C, Casiraghi E, Coleman B, Gargano M, Wilkins KJ, Cappelletti L, Fontana T, Ammar N, Antony B, Murali TM, Karlebach G, McMurry JA, Williams A, Moffitt R, Banerjee J, Solomonides AE, Davis H, Kostka K, Valentini G, Sahner D, Chute CG, Madlock-Brown C, Haendel MA, Robinson PN. Generalizable Long COVID Subtypes: Findings from the NIH N3C and RECOVER Programs. medRxiv. 2022 Jul 20. PubMed PMID: 35665012
  • 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
  • Pfaff ER, Girvin AT, Bennett TD, Bhatia A, Brooks IM, Deer RR, Dekermanjian JP, Jolley SE, Kahn MG, Kostka K, McMurry JA, Moffitt R, Walden A, Chute CG, Haendel MA. Identifying who has long COVID in the USA: a machine learning approach using N3C data. Lancet Digit Health. 2022 Jul;4(7):e532-e541. PubMed PMID: 35589549
  • Reese JT, Coleman B, Chan L, Blau H, Callahan TJ, Cappelletti L, Fontana T, Bradwell KR, Harris NL, Casiraghi E, Valentini G, Karlebach G, Deer R, McMurry JA, Haendel MA, Chute CG, Pfaff E, Moffitt R, Spratt H, Singh JA, Mungall CJ, Williams AE, Robinson PN. NSAID use and clinical outcomes in COVID-19 patients: a 38-center retrospective cohort study. Virol J. 2022 May 15;19(1):84. PubMed PMID: 35570298
  • Coleman B, Casiraghi E, Blau H, Chan L, Haendel MA, Laraway B, Callahan TJ, Deer RR, Wilkins KJ, Reese J, Robinson PN. Risk of new-onset psychiatric sequelae of COVID-19 in the early and late post-acute phase. World Psychiatry. 2022 Jun;21(2):319-320. PubMed PMID: 35524622
  • Chin HL, Gazzaz N, Huynh S, Handra I, Warnock L, Moller-Hansen A, Boerkoel P, Jacobsen JOB, du Souich C, Zhang N, Shefchek K, Prentice LM, Washington N, Haendel M, Armstrong L, Clarke L, Li WL, Smedley D, Robinson PN, Boerkoel CF. The Clinical Variant Analysis Tool: Analyzing the evidence supporting reported genomic variation in clinical practice. Genet Med. 2022 Jul;24(7):1512-1522. PubMed PMID: 35442193
  • Bradwell KR, Wooldridge JT, Amor B, Bennett TD, Anand A, Bremer C, Yoo YJ, Qian Z, Johnson SG, Pfaff ER, Girvin AT, Manna A, Niehaus EA, Hong SS, Zhang XT, Zhu RL, Bissell M, Qureshi N, Saltz J, Haendel MA, Chute CG, Lehmann HP, Moffitt RA. Harmonizing units and values of quantitative data elements in a very large nationally pooled electronic health record (EHR) dataset. J Am Med Inform Assoc. 2022 Jun 14;29(7):1172-1182. PubMed PMID: 35435957
  • Martin B, DeWitt PE, Russell S, Sanchez-Pinto LN, Haendel MA, Moffitt R, Bennett TD. Acute Upper Airway Disease in Children With the Omicron (B.1.1.529) Variant of SARS-CoV-2-A Report From the US National COVID Cohort Collaborative. JAMA Pediatr. 2022 Aug 1;176(8):819-821. PubMed PMID: 35426941
  • 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
  • Pitts CC, Levitt EB, Patch DA, Mihas AK, Terrero A, Haendel MA, Chute CG, Ponce BA, Theiss SM, Spitler CA, Johnson MD. Ankle Fracture and Length of Stay in US Adult Population Using Data From the National COVID Cohort Collaborative. Foot Ankle Orthop. 2022 Jan;7(1):24730114221077282. PubMed PMID: 35237737
  • Pfaff ER, Haendel MA, Kostka K, Lee A, Niehaus E, Palchuk MB, Walters K, Chute CG. Ensuring a safe(r) harbor: Excising personally identifiable information from structured electronic health record data. J Clin Transl Sci. 2022;6(1):e10. PubMed PMID: 35211336
  • Martin B, DeWitt PE, Russell S, Anand A, Bradwell KR, Bremer C, Gabriel D, Girvin AT, Hajagos JG, McMurry JA, Neumann AJ, Pfaff ER, Walden A, Wooldridge JT, Yoo YJ, Saltz J, Gersing KR, Chute CG, Haendel MA, Moffitt R, Bennett TD. Characteristics, Outcomes, and Severity Risk Factors Associated With SARS-CoV-2 Infection Among Children in the US National COVID Cohort Collaborative. JAMA Netw Open. 2022 Feb 1;5(2):e2143151. PubMed PMID: 35133437
  • Mazzotti DR, Haendel MA, McMurry JA, Smith CJ, Buysse DJ, Roenneberg T, Penzel T, Purcell S, Redline S, Zhang Y, Merikangas KR, Menetski JP, Mullington J, Boudreau E. Sleep and circadian informatics data harmonization: a workshop report from the Sleep Research Society and Sleep Research Network. Sleep. 2022 Jun 13;45(6). PubMed PMID: 35030631
  • Levitt EB, Patch DA, Mabry S, Terrero A, Jaeger B, Haendel MA, Chute CG, Quade JH, Ponce B, Theiss S, Spitler CA, Johnson JP. Association Between COVID-19 and Mortality in Hip Fracture Surgery in the National COVID Cohort Collaborative (N3C): A Retrospective Cohort Study. J Am Acad Orthop Surg Glob Res Rev. 2022 Jan 4;6(1). PubMed PMID: 34982060
  • Haendel MA, Chute CG, Bennett TD, Eichmann DA, Guinney J, Kibbe WA, Payne PRO, Pfaff ER, Robinson PN, Saltz JH, Spratt H, Suver C, Wilbanks J, Wilcox AB, Williams AE, Wu C, Blacketer C, Bradford RL, Cimino JJ, Clark M, Colmenares EW, Francis PA, Gabriel D, Graves A, Hemadri R, Hong SS, Hripscak G, Jiao D, Klann JG, Kostka K, Lee AM, Lehmann HP, Lingrey L, Miller RT, Morris M, Murphy SN, Natarajan K, Palchuk MB, Sheikh U, Solbrig H, Visweswaran S, Walden A, Walters KM, Weber GM, Zhang XT, Zhu RL, Amor B, Girvin AT, Manna A, Qureshi N, Kurilla MG, Michael SG, Portilla LM, Rutter JL, Austin CP, Gersing KR. The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment. J Am Med Inform Assoc. 2021 Mar 1;28(3):427-443. PubMed PMID: 32805036
  • 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
  • Köhler S, Gargano M, Matentzoglu N, Carmody LC, Lewis-Smith D, Vasilevsky NA, Danis D, Balagura G, Baynam G, Brower AM, Callahan TJ, Chute CG, Est JL, Galer PD, Ganesan S, Griese M, Haimel M, Pazmandi J, Hanauer M, Harris NL, Hartnett MJ, Hastreiter M, Hauck F, He Y, Jeske T, Kearney H, Kindle G, Klein C, Knoflach K, Krause R, Lagorce D, McMurry JA, Miller JA, Munoz-Torres MC, Peters RL, Rapp CK, Rath AM, Rind SA, Rosenberg AZ, Segal MM, Seidel MG, Smedley D, Talmy T, Thomas Y, Wiafe SA, Xian J, Yüksel Z, Helbig I, Mungall CJ, Haendel MA, Robinson PN. The Human Phenotype Ontology in 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D1207-D1217. PubMed PMID: 33264411
  • Reese JT, Unni D, Callahan TJ, Cappelletti L, Ravanmehr V, Carbon S, Shefchek KA, Good BM, Balhoff JP, Fontana T, Blau H, Matentzoglu N, Harris NL, Munoz-Torres MC, Haendel MA, Robinson PN, Joachimiak MP, Mungall CJ. KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response. Patterns (N Y). 2021 Jan 8;2(1):100155. PubMed PMID: 33196056
  • Coleman B, Casiraghi E, Blau H, Chan L, Haendel M, Laraway B, Callahan TJ, Deer RR, Wilkins K, Reese J, Robinson PN. Increased risk of psychiatric sequelae of COVID-19 is highest early in the clinical course. medRxiv. 2021 Dec 2. PubMed PMID: 34909790
  • 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
  • Deer RR, Rock MA, Vasilevsky N, Carmody L, Rando H, Anzalone AJ, Basson MD, Bennett TD, Bergquist T, Boudreau EA, Bramante CT, Byrd JB, Callahan TJ, Chan LE, Chu H, Chute CG, Coleman BD, Davis HE, Gagnier J, Greene CS, Hillegass WB, Kavuluru R, Kimble WD, Koraishy FM, Köhler S, Liang C, Liu F, Liu H, Madhira V, Madlock-Brown CR, Matentzoglu N, Mazzotti DR, McMurry JA, McNair DS, Moffitt RA, Monteith TS, Parker AM, Perry MA, Pfaff E, Reese JT, Saltz J, Schuff RA, Solomonides AE, Solway J, Spratt H, Stein GS, Sule AA, Topaloglu U, Vavougios GD, Wang L, Haendel MA, Robinson PN. Characterizing Long COVID: Deep Phenotype of a Complex Condition. EBioMedicine. 2021 Nov 25;74:103722. [Epub ahead of print] PubMed PMID: 34839263
  • 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
  • Lawson J, Cabili MN, Kerry G, Boughtwood T, Thorogood A, Alper P, Bowers SR, Boyles RR, Brookes AJ, Brush M, Burdett T, Clissold H, Donnelly S, Dyke SOM, Freeberg MA, Haendel MA, Hata C, Holub P, Jeanson F, Jene A, Kawashima M, Kawashima S, Konopko M, Kyomugisha I, Li H, Linden M, Rodriguez LL, Morita M, Mulder N, Muller J, Nagaie S, Nasir J, Ogishima S, Ota Wang V, Paglione LD, Pandya RN, Parkinson H, Philippakis AA, Prasser F, Rambla J, Reinold K, Rushton GA, Saltzman A, Saunders G, Sofia HJ, Spalding JD, Swertz MA, Tulchinsky I, van Enckevort EJ, Varma S, Voisin C, Yamamoto N, Yamasaki C, Zass L, Guidry Auvil JM, Nyrönen TH, Courtot M. The Data Use Ontology to streamline responsible access to human biomedical datasets. Cell Genom. 2021 Nov 10;1(2):None. PubMed PMID: 34820659
  • Vasilevsky NA, Hosseini M, Teplitzky S, Ilik V, Mohammadi E, Schneider J, Kern B, Colomb J, Edmunds SC, Gutzman K, Himmelstein DS, White M, Smith B, O'Keefe L, Haendel M, Holmes KL. Is authorship sufficient for today's collaborative research? A call for contributor roles. Account Res. 2021 Jan;28(1):23-43. PubMed PMID: 32602379
  • Call JT, Lee AS, Haendel MA, Chute CG, Helgeson SA. The Effect of the COVID-19 Pandemic on Pulmonary Diagnostic Procedures. Ann Am Thorac Soc. 2021 Nov 17. [Epub ahead of print] PubMed PMID: 34788203
  • Smedley D, Smith KR, Martin A, Thomas EA, McDonagh EM, Cipriani V, Ellingford JM, Arno G, Tucci A, Vandrovcova J, Chan G, Williams HJ, Ratnaike T, Wei W, Stirrups K, Ibanez K, Moutsianas L, Wielscher M, Need A, Barnes MR, Vestito L, Buchanan J, Wordsworth S, Ashford S, Rehmström K, Li E, Fuller G, Twiss P, Spasic-Boskovic O, Halsall S, Floto RA, Poole K, Wagner A, Mehta SG, Gurnell M, Burrows N, James R, Penkett C, Dewhurst E, Gräf S, Mapeta R, Kasanicki M, Haworth A, Savage H, Babcock M, Reese MG, Bale M, Baple E, Boustred C, Brittain H, de Burca A, Bleda M, Devereau A, Halai D, Haraldsdottir E, Hyder Z, Kasperaviciute D, Patch C, Polychronopoulos D, Matchan A, Sultana R, Ryten M, Tavares ALT, Tregidgo C, Turnbull C, Welland M, Wood S, Snow C, Williams E, Leigh S, Foulger RE, Daugherty LC, Niblock O, Leong IUS, Wright CF, Davies J, Crichton C, Welch J, Woods K, Abulhoul L, Aurora P, Bockenhauer D, Broomfield A, Cleary MA, Lam T, Dattani M, Footitt E, Ganesan V, Grunewald S, Compeyrot-Lacassagne S, Muntoni F, Pilkington C, Quinlivan R, Thapar N, Wallis C, Wedderburn LR, Worth A, Bueser T, Compton C, Deshpande C, Fassihi H, Haque E, Izatt L, Josifova D, Mohammed S, Robert L, Rose S, Ruddy D, Sarkany R, Say G, Shaw AC, Wolejko A, Habib B, Burns G, Hunter S, Grocock RJ, Humphray SJ, Robinson PN, Haendel M, Simpson MA, Banka S, Clayton-Smith J, Douzgou S, Hall G, Thomas HB, O'Keefe RT, Michaelides M, Moore AT, Malka S, Pontikos N, Browning AC, Straub V, Gorman GS, Horvath R, Quinton R, Schaefer AM, Yu-Wai-Man P, Turnbull DM, McFarland R, Taylor RW, O'Connor E, Yip J, Newland K, Morris HR, Polke J, Wood NW, Campbell C, Camps C, Gibson K, Koelling N, Lester T, Németh AH, Palles C, Patel S, Roy NBA, Sen A, Taylor J, Cacheiro P, Jacobsen JO, Seaby EG, Davison V, Chitty L, Douglas A, Naresh K, McMullan D, Ellard S, Temple IK, Mumford AD, Wilson G, Beales P, Bitner-Glindzicz M, Black G, Bradley JR, Brennan P, Burn J, Chinnery PF, Elliott P, Flinter F, Houlden H, Irving M... 100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care - Preliminary Report. N Engl J Med. 2021 Nov 11;385(20):1868-1880. PubMed PMID: 34758253
  • Danis D, Jacobsen JOB, Carmody LC, Gargano MA, McMurry JA, Hegde A, Haendel MA, Valentini G, Smedley D, Robinson PN. Interpretable prioritization of splice variants in diagnostic next-generation sequencing. Am J Hum Genet. 2021 Nov 4;108(11):2205. PubMed PMID: 34739835
  • Jackson R, Matentzoglu N, Overton JA, Vita R, Balhoff JP, Buttigieg PL, Carbon S, Courtot M, Diehl AD, Dooley DM, Duncan WD, Harris NL, Haendel MA, Lewis SE, Natale DA, Osumi-Sutherland D, Ruttenberg A, Schriml LM, Smith B, Stoeckert CJ Jr, Vasilevsky NA, Walls RL, Zheng J, Mungall CJ, Peters B. OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. Database (Oxford). 2021 Oct 26;2021. PubMed PMID: 34697637
  • Tisdale A, Cutillo CM, Nathan R, Russo P, Laraway B, Haendel M, Nowak D, Hasche C, Chan CH, Griese E, Dawkins H, Shukla O, Pearce DA, Rutter JL, Pariser AR. The IDeaS initiative: pilot study to assess the impact of rare diseases on patients and healthcare systems. Orphanet J Rare Dis. 2021 Oct 22;16(1):429. PubMed PMID: 34674728
  • Yang X, Sun J, Patel RC, Zhang J, Guo S, Zheng Q, Olex AL, Olatosi B, Weissman SB, Islam JY, Chute CG, Haendel M, Kirk GD, Li X. Associations between HIV infection and clinical spectrum of COVID-19: a population level analysis based on US National COVID Cohort Collaborative (N3C) data. Lancet HIV. 2021 Nov;8(11):e690-e700. PubMed PMID: 34655550
  • Pfaff ER, Girvin AT, Gabriel DL, Kostka K, Morris M, Palchuk M, Lehmann HP, Amor B, Bissell M, Bradwell KR, Gold S, Hong SS, Loomba J, Manna A, McMurry J, Niehaus E, Quresh N, Walden A, Zhang XT, Zhu RL, Moffitt RA, Haendel MA, Chute CG. Synergies between Centralized and Federated Approaches to Data Quality: A Report from the National COVID Cohort Collaborative. J Am Med Inform Assoc. 2021 Sep 30. [Epub ahead of print] PubMed PMID: 34590684
  • Hamosh A, Amberger JS, Bocchini CA, Bodurtha J, Bult CJ, Chute CG, Cutting GR, Dietz HC, Firth HV, Gibbs RA, Grody WW, Haendel MA, Lupski JR, Posey JE, Robinson PN, Schriml LM, Scott AF, Sobreira NL, Valle D, Wu N, Rasmussen SA. Response to Biesecker et al. Am J Hum Genet. 2021 Sep 2;108(9):1807-1808. PubMed PMID: 34478655
  • Martin B, DeWitt PE, Russell S, Anand A, Bradwell KR, Bremer C, Gabriel D, Girvin AT, Hajagos JG, McMurry JA, Neumann AJ, Pfaff ER, Walden A, Wooldridge JT, Yoo YJ, Saltz J, Gersing KR, Chute CG, Haendel MA, Moffitt R, Bennett TD. Children with SARS-CoV-2 in the National COVID Cohort Collaborative (N3C). medRxiv. 2021 Jul 23. PubMed PMID: 34341796
  • Vasilevsky NA, Hosseini M, Teplitzky S, Ilik V, Mohammadi E, Schneider J, Kern B, Colomb J, Edmunds SC, Gutzman K, Himmelstein DS, White M, Smith B, O'Keefe L, Haendel M, Holmes KL. Is authorship sufficient for today's collaborative research? A call for contributor roles. Account Res. 2021 Jan;28(1):23-43. PubMed PMID: 32602379
  • Haendel MA, Chute CG, Bennett TD, Eichmann DA, Guinney J, Kibbe WA, Payne PRO, Pfaff ER, Robinson PN, Saltz JH, Spratt H, Suver C, Wilbanks J, Wilcox AB, Williams AE, Wu C, Blacketer C, Bradford RL, Cimino JJ, Clark M, Colmenares EW, Francis PA, Gabriel D, Graves A, Hemadri R, Hong SS, Hripscak G, Jiao D, Klann JG, Kostka K, Lee AM, Lehmann HP, Lingrey L, Miller RT, Morris M, Murphy SN, Natarajan K, Palchuk MB, Sheikh U, Solbrig H, Visweswaran S, Walden A, Walters KM, Weber GM, Zhang XT, Zhu RL, Amor B, Girvin AT, Manna A, Qureshi N, Kurilla MG, Michael SG, Portilla LM, Rutter JL, Austin CP, Gersing KR. The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment. J Am Med Inform Assoc. 2021 Mar 1;28(3):427-443. PubMed PMID: 32805036
  • Reese JT, Unni D, Callahan TJ, Cappelletti L, Ravanmehr V, Carbon S, Shefchek KA, Good BM, Balhoff JP, Fontana T, Blau H, Matentzoglu N, Harris NL, Munoz-Torres MC, Haendel MA, Robinson PN, Joachimiak MP, Mungall CJ. KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response. Patterns (N Y). 2021 Jan 8;2(1):100155. PubMed PMID: 33196056
  • Köhler S, Gargano M, Matentzoglu N, Carmody LC, Lewis-Smith D, Vasilevsky NA, Danis D, Balagura G, Baynam G, Brower AM, Callahan TJ, Chute CG, Est JL, Galer PD, Ganesan S, Griese M, Haimel M, Pazmandi J, Hanauer M, Harris NL, Hartnett MJ, Hastreiter M, Hauck F, He Y, Jeske T, Kearney H, Kindle G, Klein C, Knoflach K, Krause R, Lagorce D, McMurry JA, Miller JA, Munoz-Torres MC, Peters RL, Rapp CK, Rath AM, Rind SA, Rosenberg AZ, Segal MM, Seidel MG, Smedley D, Talmy T, Thomas Y, Wiafe SA, Xian J, Yüksel Z, Helbig I, Mungall CJ, Haendel MA, Robinson PN. The Human Phenotype Ontology in 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D1207-D1217. PubMed PMID: 33264411
  • Bennett TD, Moffitt RA, Hajagos JG, Amor B, Anand A, Bissell MM, Bradwell KR, Bremer C, Byrd JB, Denham A, DeWitt PE, Gabriel D, Garibaldi BT, Girvin AT, Guinney J, Hill EL, Hong SS, Jimenez H, Kavuluru R, Kostka K, Lehmann HP, Levitt E, Mallipattu SK, Manna A, McMurry JA, Morris M, Muschelli J, Neumann AJ, Palchuk MB, Pfaff ER, Qian Z, Qureshi N, Russell S, Spratt H, Walden A, Williams AE, Wooldridge JT, Yoo YJ, Zhang XT, Zhu RL, Austin CP, Saltz JH, Gersing KR, Haendel MA, Chute CG. The National COVID Cohort Collaborative: Clinical Characterization and Early Severity Prediction. medRxiv. 2021 Jan 23. PubMed PMID: 33469592
  • 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
  • Li J, Hojlo MA, Chennuri S, Gujral N, Paterson HL, Shefchek KA, Genetti CA, Cohn EL, Sewalk KC, Garvey EA, Buttermore ED, Anderson NC, Beggs AH, Agrawal PB, Brownstein JS, Haendel MA, Holm IA, Gonzalez-Heydrich J, Brownstein CA. Underrepresentation of Phenotypic Variability of 16p13.11 Microduplication Syndrome Assessed With an Online Self-Phenotyping Tool (Phenotypr): Cohort Study. J Med Internet Res. 2021 Mar 16;23(3):e21023. PubMed PMID: 33724192
  • 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
  • Rando HM, Bennett TD, Byrd JB, Bramante C, Callahan TJ, Chute CG, Davis HE, Deer R, Gagnier J, Koraishy FM, Liu F, McMurry JA, Moffitt RA, Pfaff ER, Reese JT, Relevo R, Robinson PN, Saltz JH, Solomonides A, Sule A, Topaloglu U, Haendel MA. Challenges in defining Long COVID: Striking differences across literature, Electronic Health Records, and patient-reported information. medRxiv. 2021 Mar 26. PubMed PMID: 33791733
  • Wilson SL, Way GP, Bittremieux W, Armache JP, Haendel MA, Hoffman MM. Sharing biological data: why, when, and how. FEBS Lett. 2021 Apr;595(7):847-863. PubMed PMID: 33843054
  • Alamgir J, Yajima M, Ergas R, Chen X, Hill N, Munir N, Saeed M, Gersing K, Haendel M, Chute CG, Abid MR. Drug repositioning candidates identified using in-silico quasi-quantum molecular simulation demonstrate reduced COVID-19 mortality in 1.5M patient records. medRxiv. 2021 Apr 6. PubMed PMID: 33851170
  • Reese JT, Coleman B, Chan L, Blau H, Callahan TJ, Cappelletti L, Fontana T, Bradwell KR, Harris NL, Casiraghi E, Valentini G, Karlebach G, Deer R, McMurry JA, Haendel MA, Chute CG, Pfaff E, Moffitt R, Spratt H, Singh J, Mungall CJ, Williams AE, Robinson PN. Cyclooxygenase inhibitor use is associated with increased COVID-19 severity. medRxiv. 2021 Apr 20. PubMed PMID: 33907758
  • Kahkoska AR, Abrahamsen TJ, Alexander GC, Bennett TD, Chute CG, Haendel MA, Klein KR, Mehta H, Miller JD, Moffitt RA, Stürmer T, Kvist K, Buse JB. Association Between Glucagon-Like Peptide 1 Receptor Agonist and Sodium-Glucose Cotransporter 2 Inhibitor Use and COVID-19 Outcomes. Diabetes Care. 2021 Jul;44(7):1564-1572. PubMed PMID: 34135013
  • Bennett TD, Moffitt RA, Hajagos JG, Amor B, Anand A, Bissell MM, Bradwell KR, Bremer C, Byrd JB, Denham A, DeWitt PE, Gabriel D, Garibaldi BT, Girvin AT, Guinney J, Hill EL, Hong SS, Jimenez H, Kavuluru R, Kostka K, Lehmann HP, Levitt E, Mallipattu SK, Manna A, McMurry JA, Morris M, Muschelli J, Neumann AJ, Palchuk MB, Pfaff ER, Qian Z, Qureshi N, Russell S, Spratt H, Walden A, Williams AE, Wooldridge JT, Yoo YJ, Zhang XT, Zhu RL, Austin CP, Saltz JH, Gersing KR, Haendel MA, Chute CG. Clinical Characterization and Prediction of Clinical Severity of SARS-CoV-2 Infection Among US Adults Using Data From the US National COVID Cohort Collaborative. JAMA Netw Open. 2021 Jul 1;4(7):e2116901. PubMed PMID: 34255046
  • Danis D, Jacobsen JOB, Carmody LC, Gargano MA, McMurry JA, Hegde A, Haendel MA, Valentini G, Smedley D, Robinson PN. Interpretable prioritization of splice variants in diagnostic next-generation sequencing. Am J Hum Genet. 2021 Sep 2;108(9):1564-1577. PubMed PMID: 34289339
  • Rehm HL, Page AJH, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJS, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SOM, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Auvil JMG, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CWL, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJM, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen R, Li S, Lin MF, Linden M, Liu X, Udara Liyanage I, Lopez J, Lucassen AM, Lukowski M, Mann AL, Marshall J, Mattioni M, Metke-Jimenez A, Middleton A, Milne RJ, Molnár-Gábor F, Mulder N, Munoz-Torres MC, Nag R, Nakagawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyrönen TH, O'Connor BD, Oesterle S, Ogishima S, Wang VO, Paglione LAD, Palumbo E, Parkinson HE, Philippakis AA, Pizarro AD, Prlic A, Rambla J, Rendon A, Rider RA, Robinson PN, Rodarmer KW, Rodriguez LL, Rubin AF, Rueda M, Rushton GA, Ryan RS, Saunders GI, Schuilenburg H, Schwede T, Scollen S, Senf A, Sheffield NC, Skantharajah N, Smith AV, Sofia HJ, Spalding D, Spurdle AB, Stark Z, Stein LD, Suematsu M, Tan P, Tedds JA, Thomson AA, Thorogood A, Tickle TL, Tokunaga K, Törnroos J, Torrents D, Upchurch S, Valencia ... GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genom. 2021 Nov 10;1(2). PubMed PMID: 35072136
  • Robinson PN, Ravanmehr V, Jacobsen JOB, Danis D, Zhang XA, Carmody LC, Gargano MA, Thaxton CL, Karlebach G, Reese J, Holtgrewe M, Köhler S, McMurry JA, Haendel MA, Smedley D. Interpretable Clinical Genomics with a Likelihood Ratio Paradigm. Am J Hum Genet. 2020 Sep 3;107(3):403-417. PubMed PMID: 32755546
  • Rubinstein YR, Robinson PN, Gahl WA, Avillach P, Baynam G, Cederroth H, Goodwin RM, Groft SC, Hansson MG, Harris NL, Huser V, Mascalzoni D, McMurry JA, Might M, Nellaker C, Mons B, Paltoo DN, Pevsner J, Posada M, Rockett-Frase AP, Roos M, Rubinstein TB, Taruscio D, van Enckevort E, Haendel MA. The case for open science: rare diseases. JAMIA Open. 2020 Oct;3(3):472-486. PubMed PMID: 33426479
  • 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
  • Tcheandjieu C, Aguirre M, Gustafsson S, Saha P, Potiny P, Haendel M, Ingelsson E, Rivas MA, Priest JR. A phenome-wide association study of 26 mendelian genes reveals phenotypic expressivity of common and rare variants within the general population. PLoS Genet. 2020 Nov;16(11):e1008802. PubMed PMID: 33226994
  • Ong E, Wang LL, Schaub J, O'Toole JF, Steck B, Rosenberg AZ, Dowd F, Hansen J, Barisoni L, Jain S, de Boer IH, Valerius MT, Waikar SS, Park C, Crawford DC, Alexandrov T, Anderton CR, Stoeckert C, Weng C, Diehl AD, Mungall CJ, Haendel M, Robinson PN, Himmelfarb J, Iyengar R, Kretzler M, Mooney S, He Y. Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project. Nat Rev Nephrol. 2020 Nov;16(11):686-696. PubMed PMID: 32939051
  • 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
  • Haendel M, Vasilevsky N, Unni D, Bologa C, Harris N, Rehm H, Hamosh A, Baynam G, Groza T, McMurry J, Dawkins H, Rath A, Thaxon C, Bocci G, Joachimiak MP, Köhler S, Robinson PN, Mungall C, Oprea TI. How many rare diseases are there?. Nat Rev Drug Discov. 2020 Feb;19(2):77-78. PubMed PMID: 32020066
  • 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
  • Robinson PN, Haendel MA. Ontologies, Knowledge Representation, and Machine Learning for Translational Research: Recent Contributions. Yearb Med Inform. 2020 Aug;29(1):159-162. PubMed PMID: 32823310
  • Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu-Pons J, Duren RP, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Pitel BA, Sezerman OU, Ellrott K, Warner JL, Rieke DT, Aittokallio T, Cerami E, Ritter DI, Schriml LM, Freimuth RR, Haendel M, Raca G, Madhavan S, Baudis M, Beckmann JS, Dienstmann R, Chakravarty D, Li XS, Mockus S, Elemento O, Schultz N, Lopez-Bigas N, Lawler M, Goecks J, Griffith M, Griffith OL, Margolin AA. A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Nat Genet. 2020 Apr;52(4):448-457. PubMed PMID: 32246132
  • D'Angelo CS, Hermes A, McMaster CR, Prichep E, Richer É, van der Westhuizen FH, Repetto GM, Mengchun G, Malherbe H, Reichardt JKV, Arbour L, Hudson M, du Plessis K, Haendel M, Wilcox P, Lynch SA, Rind S, Easteal S, Estivill X, Thomas Y, Baynam G. Barriers and Considerations for Diagnosing Rare Diseases in Indigenous Populations. Front Pediatr. 2020;8:579924. PubMed PMID: 33381478
  • Köhler S, Øien NC, Buske OJ, Groza T, Jacobsen JOB, McNamara C, Vasilevsky N, Carmody LC, Gourdine JP, Gargano M, McMurry JA, Danis D, Mungall CJ, Smedley D, Haendel M, Robinson PN. Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics. Curr Protoc Hum Genet. 2019 Sep;103(1):e92. PubMed PMID: 31479590
  • Mishra R, Burke A, Gitman B, Verma P, Engelstad M, Haendel MA, Alevizos I, Gahl WA, Collins MT, Lee JS, Sincan M. Data-driven method to enhance craniofacial and oral phenotype vocabularies. J Am Dent Assoc. 2019 Nov;150(11):933-939.e2. PubMed PMID: 31668172
  • Tang YA, Pichler K, Füllgrabe A, Lomax J, Malone J, Munoz-Torres MC, Vasant DV, Williams E, Haendel M. Ten quick tips for biocuration. PLoS Comput Biol. 2019 May;15(5):e1006906. PubMed PMID: 31048830
  • Cacheiro P, Haendel MA, Smedley D. New models for human disease from the International Mouse Phenotyping Consortium. Mamm Genome. 2019 Jun;30(5-6):143-150. PubMed PMID: 31127358
  • Köhler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine JP, Gargano M, Harris NL, Matentzoglu N, McMurry JA, Osumi-Sutherland D, Cipriani V, Balhoff JP, Conlin T, Blau H, Baynam G, Palmer R, Gratian D, Dawkins H, Segal M, Jansen AC, Muaz A, Chang WH, Bergerson J, Laulederkind SJF, Yüksel Z, Beltran S, Freeman AF, Sergouniotis PI, Durkin D, Storm AL, Hanauer M, Brudno M, Bello SM, Sincan M, Rageth K, Wheeler MT, Oegema R, Lourghi H, Della Rocca MG, Thompson R, Castellanos F, Priest J, Cunningham-Rundles C, Hegde A, Lovering RC, Hajek C, Olry A, Notarangelo L, Similuk M, Zhang XA, Gómez-Andrés D, Lochmüller H, Dollfus H, Rosenzweig S, Marwaha S, Rath A, Sullivan K, Smith C, Milner JD, Leroux D, Boerkoel CF, Klion A, Carter MC, Groza T, Smedley D, Haendel MA, Mungall C, Robinson PN. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. 2019 Jan 8;47(D1):D1018-D1027. PubMed PMID: 30476213
  • Gourdine JF, Brush MH, Vasilevsky NA, Shefchek K, Köhler S, Matentzoglu N, Munoz-Torres MC, McMurry JA, Zhang XA, Robinson PN, Haendel MA. Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery. Database (Oxford). 2019 Jan 1;2019. PubMed PMID: 31735951
  • Taylor DM, Aronow BJ, Tan K, Bernt K, Salomonis N, Greene CS, Frolova A, Henrickson SE, Wells A, Pei L, Jaiswal JK, Whitsett J, Hamilton KE, MacParland SA, Kelsen J, Heuckeroth RO, Potter SS, Vella LA, Terry NA, Ghanem LR, Kennedy BC, Helbig I, Sullivan KE, Castelo-Soccio L, Kreigstein A, Herse F, Nawijn MC, Koppelman GH, Haendel M, Harris NL, Rokita JL, Zhang Y, Regev A, Rozenblatt-Rosen O, Rood JE, Tickle TL, Vento-Tormo R, Alimohamed S, Lek M, Mar JC, Loomes KM, Barrett DM, Uapinyoying P, Beggs AH, Agrawal PB, Chen YW, Muir AB, Garmire LX, Snapper SB, Nazarian J, Seeholzer SH, Fazelinia H, Singh LN, Faryabi RB, Raman P, Dawany N, Xie HM, Devkota B, Diskin SJ, Anderson SA, Rappaport EF, Peranteau W, Wikenheiser-Brokamp KA, Teichmann S, Wallace D, Peng T, Ding YY, Kim MS, Xing Y, Kong SW, Bönnemann CG, Mandl KD, White PS. The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. Dev Cell. 2019 Apr 8;49(1):10-29. PubMed PMID: 30930166
  • Nellåker C, Alkuraya FS, Baynam G, Bernier RA, Bernier FPJ, Boulanger V, Brudno M, Brunner HG, Clayton-Smith J, Cogné B, Dawkins HJS, deVries BBA, Douzgou S, Dudding-Byth T, Eichler EE, Ferlaino M, Fieggen K, Firth HV, FitzPatrick DR, Gration D, Groza T, Haendel M, Hallowell N, Hamosh A, Hehir-Kwa J, Hitz MP, Hughes M, Kini U, Kleefstra T, Kooy RF, Krawitz P, Küry S, Lees M, Lyon GJ, Lyonnet S, Marcadier JL, Meyn S, Moslerová V, Politei JM, Poulton CC, Raymond FL, Reijnders MRF, Robinson PN, Romano C, Rose CM, Sainsbury DCG, Schofield L, Sutton VR, Turnovec M, Van Dijck A, Van Esch H, Wilkie AOM. Enabling Global Clinical Collaborations on Identifiable Patient Data: The Minerva Initiative. Front Genet. 2019;10:611. PubMed PMID: 31417602
  • Zhang XA, Yates A, Vasilevsky N, Gourdine JP, Callahan TJ, Carmody LC, Danis D, Joachimiak MP, Ravanmehr V, Pfaff ER, Champion J, Robasky K, Xu H, Fecho K, Walton NA, Zhu RL, Ramsdill J, Mungall CJ, Köhler S, Haendel MA, McDonald CJ, Vreeman DJ, Peden DB, Bennett TD, Feinstein JA, Martin B, Stefanski AL, Hunter LE, Chute CG, Robinson PN. Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery. NPJ Digit Med. 2019;2. PubMed PMID: 31119199
  • Carbon S, Champieux R, McMurry JA, Winfree L, Wyatt LR, Haendel MA. An analysis and metric of reusable data licensing practices for biomedical resources. PLoS One. 2019;14(3):e0213090. PubMed PMID: 30917137
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Professional Memberships

  • American Medical Informatics Association, Fellow of the American College of Medical Informatics

General Information

Graduate Schools:
  • PhD, University of Wisconsin - Madison (1999)
Department: Biomedical Informatics
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