Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
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Melissa A Haendel

TitleProfessor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-BioChem&Molecular Genetics

    Collapse Research 
    Collapse research activities and funding
    R24OD011883     (HAENDEL, MELISSA A)Jun 1, 2012 - Aug 31, 2025
    NIH
    The Monarch Initiative: Linking Diseases to Model Organism Resources
    Role: Principal Investigator

    R25EB020379     (DORR, DAVID A.)Sep 29, 2014 - Oct 31, 2017
    NIH
    OHSU Informatics Analytics BD2K Skill Course
    Role: Co-Principal Investigator

    R25GM114820     (HERSH, WILLIAM R)Sep 29, 2014 - Jun 30, 2018
    NIH
    Adding Big Data Open Educational Resources to the ONC Health IT Curriculum
    Role: Co-Principal Investigator

    OT3TR002019     (CHUTE, CHRISTOPHER G)Sep 23, 2016 - Mar 31, 2020
    NIH
    Biomedical Data Translator Technical Feasibility Assessment and Architecture Design
    Role: Co-Principal Investigator

    U13CA221044     (HAENDEL, MELISSA A)Sep 18, 2017 - Sep 17, 2021
    NIH
    Forums for Integrative Phenomics
    Role: Principal Investigator

    U24TR002306     (HAENDEL, MELISSA A)Sep 20, 2017 - Jun 30, 2022
    NIH
    A National Center for Digital Health Informatics Innovation
    Role: Principal Investigator

    OT2TR003449     (HAENDEL, MELISSA A)Jan 23, 2020 - Jan 22, 2022
    NIH
    A Common Dialect for Infrastructure and Services in Translator
    Role: Principal Investigator

    RM1HG010860     (HAENDEL, MELISSA A)Aug 1, 2020 - May 31, 2025
    NIH
    A phenomics-first resource for interpretation of variants
    Role: Principal Investigator

    U2CHL156291     (RESNICK, ADAM CAIN)Sep 26, 2020 - Aug 31, 2025
    NIH
    Data Management and Portal for the INCLUDE (DAPI) Project
    Role: Co-Principal Investigator

    U24HG011449     (ROBINSON, PETER NICHOLAS)Sep 20, 2021 - Jun 30, 2026
    NIH
    The Human Phenotype Ontology: Accelerating Computational Integration of Clinical Data for Genomics
    Role: Co-Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    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. Mazzotti DR, Haendel M, McMurry J, 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 Jan 14. PMID: 35030631.
      View in: PubMed
    2. 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 01 04; 6(1). PMID: 34982060.
      View in: PubMed
    3. 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 02. PMID: 34909790.
      View in: PubMed
    4. 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. PMID: 34839263.
      View in: PubMed
    5. 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. PMID: 34788203.
      View in: PubMed
    6. 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, Newman W, Rahman S, Sayer JA, Taylor JC, Webster AR, Wilkie AOM, Ouwehand WH, Raymond FL, Chisholm J, Hill S, Bentley D, Scott RH, Fowler T, Rendon A, Caulfield M. 100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care - Preliminary Report. N Engl J Med. 2021 11 11; 385(20):1868-1880. PMID: 34758253.
      View in: PubMed
    7. 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. PMID: 34820659.
      View in: PubMed
    8. 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 04; 108(11):2205. PMID: 34739835.
      View in: PubMed
    9. 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, 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. PMID: 34697637.
      View in: PubMed
    10. 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 10 22; 16(1):429. PMID: 34674728.
      View in: PubMed
    11. 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 11; 8(11):e690-e700. PMID: 34655550.
      View in: PubMed
    12. 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. PMID: 34590684.
      View in: PubMed
    13. 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 09 02; 108(9):1807-1808. PMID: 34478655.
      View in: PubMed
    14. 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. PMID: 34341796.
      View in: PubMed
    15. 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 09 02; 108(9):1564-1577. PMID: 34289339.
      View in: PubMed
    16. 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 07 01; 4(7):e2116901. PMID: 34255046.
      View in: PubMed
    17. 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 07; 44(7):1564-1572. PMID: 34135013.
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    18. 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. PMID: 33907758.
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    19. 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 06. PMID: 33851170.
      View in: PubMed
    20. Wilson SL, Way GP, Bittremieux W, Armache JP, Haendel MA, Hoffman MM. Sharing biological data: why, when, and how. FEBS Lett. 2021 04; 595(7):847-863. PMID: 33843054.
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    21. 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. PMID: 33791733.
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    22. 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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    23. 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 03 16; 23(3):e21023. PMID: 33724192.
      View in: PubMed
    24. 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 03 01; 28(3):427-443. PMID: 32805036.
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    25. 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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    26. 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. PMID: 33469592.
      View in: PubMed
    27. 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 01 08; 49(D1):D1207-D1217. PMID: 33264411.
      View in: PubMed
    28. 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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    29. 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. PMID: 33381478.
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    30. 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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    31. 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 11; 16(11):e1008802. PMID: 33226994.
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    32. 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 08; 2(1):100155. PMID: 33196056.
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    33. 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 11; 16(11):686-696. PMID: 32939051.
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    34. 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. PMID: 33426479.
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    35. Robinson PN, Haendel MA. Ontologies, Knowledge Representation, and Machine Learning for Translational Research: Recent Contributions. Yearb Med Inform. 2020 Aug; 29(1):159-162. PMID: 32823310.
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    36. Duncan WD, Thyvalikakath T, Haendel M, Torniai C, Hernandez P, Song M, Acharya A, Caplan DJ, Schleyer T, Ruttenberg A. Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology. J Biomed Semantics. 2020 08 20; 11(1):8. PMID: 32819435.
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    37. 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 09 03; 107(3):403-417. PMID: 32755546.
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    38. 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 01; 28(1):23-43. PMID: 32602379.
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    39. 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 04; 52(4):448-457. PMID: 32246132.
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    40. 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 02; 19(2):77-78. PMID: 32020066.
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    41. 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 01 08; 48(D1):D704-D715. PMID: 31701156.
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    42. Hotchkiss J, Manyisa N, Adadey SM, Oluwole OG, Wonkam E, Mnika K, Yalcouye A, Nembaware V, Haendel M, Vasilevsky N, Mulder NJ, Jupp S, Wonkam A, Mazandu GK. The Hearing Impairment Ontology: A Tool for Unifying Hearing Impairment Knowledge to Enhance Collaborative Research. Genes (Basel). 2019 11 21; 10(12). PMID: 31766582.
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    43. 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 11; 150(11):933-939.e2. PMID: 31668172.
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    44. Clarke DJB, Wang L, Jones A, Wojciechowicz ML, Torre D, Jagodnik KM, Jenkins SL, McQuilton P, Flamholz Z, Silverstein MC, Schilder BM, Robasky K, Castillo C, Idaszak R, Ahalt SC, Williams J, Schurer S, Cooper DJ, de Miranda Azevedo R, Klenk JA, Haendel MA, Nedzel J, Avillach P, Shimoyama ME, Harris RM, Gamble M, Poten R, Charbonneau AL, Larkin J, Brown CT, Bonazzi VR, Dumontier MJ, Sansone SA, Ma'ayan A. FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources. Cell Syst. 2019 11 27; 9(5):417-421. PMID: 31677972.
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    94. 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. PMID: 25562316.
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    95. Starr J, Castro E, Crosas M, Dumontier M, Downs RR, Duerr R, Haak LL, Haendel M, Herman I, Hodson S, Hourclé J, Kratz JE, Lin J, Nielsen LH, Nurnberger A, Proell S, Rauber A, Sacchi S, Smith A, Taylor M, Clark T. Achieving human and machine accessibility of cited data in scholarly publications. PeerJ Comput Sci. 2015; 1. PMID: 26167542.
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    96. Köhler S, Schoeneberg U, Czeschik JC, Doelken SC, Hehir-Kwa JY, Ibn-Salem J, Mungall CJ, Smedley D, Haendel MA, Robinson PN. Clinical interpretation of CNVs with cross-species phenotype data. J Med Genet. 2014 Nov; 51(11):766-772. PMID: 25280750.
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    97. Thacker RW, Díaz MC, Kerner A, Vignes-Lebbe R, Segerdell E, Haendel MA, Mungall CJ. The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. J Biomed Semantics. 2014; 5(1):39. PMID: 25276334.
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    98. Ibn-Salem J, Köhler S, Love MI, Chung HR, Huang N, Hurles ME, Haendel M, Washington NL, Smedley D, Mungall CJ, Lewis SE, Ott CE, Bauer S, Schofield PN, Mundlos S, Spielmann M, Robinson PN. Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biol. 2014 Sep 04; 15(9):423. PMID: 25315429.
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    99. Zemojtel T, Köhler S, Mackenroth L, Jäger M, Hecht J, Krawitz P, Graul-Neumann L, Doelken S, Ehmke N, Spielmann M, Oien NC, Schweiger MR, Krüger U, Frommer G, Fischer B, Kornak U, Flöttmann R, Ardeshirdavani A, Moreau Y, Lewis SE, Haendel M, Smedley D, Horn D, Mundlos S, Robinson PN. Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. Sci Transl Med. 2014 Sep 03; 6(252):252ra123. PMID: 25186178.
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    100. Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y. CLO: The cell line ontology. J Biomed Semantics. 2014; 5:37. PMID: 25852852.
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    101. Dahdul WM, Cui H, Mabee PM, Mungall CJ, Osumi-Sutherland D, Walls RL, Haendel MA. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. J Biomed Semantics. 2014; 5:34. PMID: 25140222.
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    102. Oellrich A, Koehler S, Washington N, Mungall C, Lewis S, Haendel M, Robinson PN, Smedley D. The influence of disease categories on gene candidate predictions from model organism phenotypes. J Biomed Semantics. 2014; 5(Suppl 1 Proceedings of the Bio-Ontologies Spec Interest G):S4. PMID: 25093073.
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    103. Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall CJ. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J Biomed Semantics. 2014; 5:21. PMID: 25009735.
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    104. Hoehndorf R, Haendel M, Stevens R, Rebholz-Schuhmann D. Thematic series on biomedical ontologies in JBMS: challenges and new directions. J Biomed Semantics. 2014; 5:15. PMID: 24602198.
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    105. Van Slyke CE, Bradford YM, Westerfield M, Haendel MA. The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. J Biomed Semantics. 2014 Feb 25; 5(1):12. PMID: 24568621.
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    106. Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jähn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Van Vooren S, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout AT, de Leeuw N, de Vries BB, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 2014 Jan; 42(Database issue):D966-74. PMID: 24217912.
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    107. Robinson PN, Köhler S, Oellrich A, Wang K, Mungall CJ, Lewis SE, Washington N, Bauer S, Seelow D, Krawitz P, Gilissen C, Haendel M, Smedley D. Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Res. 2014 Feb; 24(2):340-8. PMID: 24162188.
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    108. Druzinsky R, Mungall C, Haendel M, Lapp H, Mabee P. What is an anatomy ontology? Anat Rec (Hoboken). 2013 Dec; 296(12):1797-9. PMID: 24127438.
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    109. Tenenbaum JD, Sansone SA, Haendel M. A sea of standards for omics data: sink or swim? J Am Med Inform Assoc. 2014 Mar-Apr; 21(2):200-3. PMID: 24076747.
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    110. Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA. On the reproducibility of science: unique identification of research resources in the biomedical literature. PeerJ. 2013; 1:e148. PMID: 24032093.
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    111. Meehan TF, Vasilevsky NA, Mungall CJ, Dougall DS, Haendel MA, Blake JA, Diehl AD. Ontology based molecular signatures for immune cell types via gene expression analysis. BMC Bioinformatics. 2013 Aug 30; 14:263. PMID: 24004649.
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    112. Schleyer TK, Ruttenberg A, Duncan W, Haendel M, Torniai C, Acharya A, Song M, Thyvalikakath TP, Liu K, Hernandez P. An ontology-based method for secondary use of electronic dental record data. AMIA Jt Summits Transl Sci Proc. 2013; 2013:234-8. PMID: 24303273.
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    113. Torniai C, Essaid S, Barnes C, Conlon M, Williams S, Hajagos JG, Bremer E, Corson-Rikert J, Haendel M. From EHRs to Linked Data: representing and mining encounter data for clinical expertise evaluation. AMIA Jt Summits Transl Sci Proc. 2013; 2013:165. PMID: 24303330.
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    114. Arighi CN, Carterette B, Cohen KB, Krallinger M, Wilbur WJ, Fey P, Dodson R, Cooper L, Van Slyke CE, Dahdul W, Mabee P, Li D, Harris B, Gillespie M, Jimenez S, Roberts P, Matthews L, Becker K, Drabkin H, Bello S, Licata L, Chatr-aryamontri A, Schaeffer ML, Park J, Haendel M, Van Auken K, Li Y, Chan J, Muller HM, Cui H, Balhoff JP, Chi-Yang Wu J, Lu Z, Wei CH, Tudor CO, Raja K, Subramani S, Natarajan J, Cejuela JM, Dubey P, Wu C. An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database (Oxford). 2013; 2013:bas056. PMID: 23327936.
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    115. Dahdul WM, Balhoff JP, Blackburn DC, Diehl AD, Haendel MA, Hall BK, Lapp H, Lundberg JG, Mungall CJ, Ringwald M, Segerdell E, Van Slyke CE, Vickaryous MK, Westerfield M, Mabee PM. A unified anatomy ontology of the vertebrate skeletal system. PLoS One. 2012; 7(12):e51070. PMID: 23251424.
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    116. Haendel MA, Vasilevsky NA, Wirz JA. Dealing with data: a case study on information and data management literacy. PLoS Biol. 2012; 10(5):e1001339. PMID: 22666180.
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    117. Vasilevsky N, Johnson T, Corday K, Torniai C, Brush M, Segerdell E, Wilson M, Shaffer C, Robinson D, Haendel M. Research resources: curating the new eagle-i discovery system. Database (Oxford). 2012; 2012:bar067. PMID: 22434835.
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    118. Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA. Uberon, an integrative multi-species anatomy ontology. Genome Biol. 2012 Jan 31; 13(1):R5. PMID: 22293552.
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    119. Haendel MA, Chesler EJ. Lost and found in behavioral informatics. Int Rev Neurobiol. 2012; 103:1-18. PMID: 23195118.
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    120. Chesler EJ, Haendel MA. The field of bioinformatics. Preface. Int Rev Neurobiol. 2012; 103:xi-xii. PMID: 23195125.
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    121. Dahdul WM, Lundberg JG, Midford PE, Balhoff JP, Lapp H, Vision TJ, Haendel MA, Westerfield M, Mabee PM. The teleost anatomy ontology: anatomical representation for the genomics age. Syst Biol. 2010 Jul; 59(4):369-83. PMID: 20547776.
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    122. Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M. Integrating phenotype ontologies across multiple species. Genome Biol. 2010 Jan 08; 11(1):R2. PMID: 20064205.
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    123. Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, Lewis SE. Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol. 2009 Nov; 7(11):e1000247. PMID: 19956802.
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    124. Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Haendel M, Howe DG, Knight J, Mani P, Moxon SA, Pich C, Ramachandran S, Schaper K, Segerdell E, Shao X, Singer A, Song P, Sprunger B, Van Slyke CE, Westerfield M. The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res. 2008 Jan; 36(Database issue):D768-72. PMID: 17991680.
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    125. Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, Westerfield M. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zool B Mol Dev Evol. 2007 Sep 15; 308(5):655-68. PMID: 17599725.
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    126. Day-Richter J, Harris MA, Haendel M, Lewis S. OBO-Edit--an ontology editor for biologists. Bioinformatics. 2007 Aug 15; 23(16):2198-200. PMID: 17545183.
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    127. Takayama S, Hostick U, Haendel M, Eisen J, Darimont B. An F-domain introduced by alternative splicing regulates activity of the zebrafish thyroid hormone receptor alpha. Gen Comp Endocrinol. 2008 Jan 01; 155(1):176-89. PMID: 17583703.
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    128. Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol. 2007 Jul; 22(7):345-50. PMID: 17416439.
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    129. Sprague J, Bayraktaroglu L, Clements D, Conlin T, Fashena D, Frazer K, Haendel M, Howe DG, Mani P, Ramachandran S, Schaper K, Segerdell E, Song P, Sprunger B, Taylor S, Van Slyke CE, Westerfield M. The Zebrafish Information Network: the zebrafish model organism database. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D581-5. PMID: 16381936.
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    130. Metcalfe SM, Muthukumarana PA, Thompson HL, Haendel MA, Lyons GE. Leukaemia inhibitory factor (LIF) is functionally linked to axotrophin and both LIF and axotrophin are linked to regulatory immune tolerance. FEBS Lett. 2005 Jan 31; 579(3):609-14. PMID: 15670816.
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    131. Haendel MA, Tilton F, Bailey GS, Tanguay RL. Developmental toxicity of the dithiocarbamate pesticide sodium metam in zebrafish. Toxicol Sci. 2004 Oct; 81(2):390-400. PMID: 15201444.
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    132. Reyes R, Haendel M, Grant D, Melancon E, Eisen JS. Slow degeneration of zebrafish Rohon-Beard neurons during programmed cell death. Dev Dyn. 2004 Jan; 229(1):30-41. PMID: 14699575.
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    133. Lyons GE, Swanson BJ, Haendel MA, Daniels J. Gene trapping in embryonic stem cells in vitro to identify novel developmentally regulated genes in the mouse. Methods Mol Biol. 2000; 136:297-307. PMID: 10840719.
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    134. Hunter PJ, Swanson BJ, Haendel MA, Lyons GE, Cross JC. Mrj encodes a DnaJ-related co-chaperone that is essential for murine placental development. Development. 1999 Mar; 126(6):1247-58. PMID: 10021343.
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    135. Baker RK, Haendel MA, Swanson BJ, Shambaugh JC, Micales BK, Lyons GE. In vitro preselection of gene-trapped embryonic stem cell clones for characterizing novel developmentally regulated genes in the mouse. Dev Biol. 1997 May 15; 185(2):201-14. PMID: 9187083.
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    136. Haendel MA, Bollinger KE, Baas PW. Cytoskeletal changes during neurogenesis in cultures of avain neural crest cells. J Neurocytol. 1996 Apr; 25(4):289-301. PMID: 8793733.
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    137. Benjamin M, Haendel M. Cuba. A healthy revolution? Links. 1991; 8(3):3-6. PMID: 12159276.
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    138. Gehring J, Koenig W, Haendel M, Sund M, Mathes P. Noninvasive detection of anterior wall asynergies by cardiokymography compared to electrocardiography. Cardiology. 1988; 75(2):100-7. PMID: 3370652.
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