Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
Keywords
Last Name
Institution

Contact Us
If you have any questions or feedback please contact us.

Melissa A Haendel

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

    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.
    List All   |   Timeline
    1. 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.
      View in: PubMed
    2. 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
    3. 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. PMID: 33843054.
      View in: PubMed
    4. 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.
      View in: PubMed
    5. 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. PMID: 33770077.
      View in: PubMed
    6. 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. PMID: 33724192.
      View in: PubMed
    7. 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.
      View in: PubMed
    8. 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. PMID: 33507269.
      View in: PubMed
    9. 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. PMID: 33494105.
      View in: PubMed
    10. 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 J, 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 13. PMID: 33469592.
      View in: PubMed
    11. 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
    12. 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.
      View in: PubMed
    13. 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.
      View in: PubMed
    14. 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.
      View in: PubMed
    15. 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.
      View in: PubMed
    16. 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.
      View in: PubMed
    17. 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.
      View in: PubMed
    18. 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.
      View in: PubMed
    19. 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.
      View in: PubMed
    20. 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.
      View in: PubMed
    21. 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.
      View in: PubMed
    22. 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.
      View in: PubMed
    23. 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.
      View in: PubMed
    24. 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.
      View in: PubMed
    25. 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.
      View in: PubMed
    26. 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.
      View in: PubMed
    27. 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.
      View in: PubMed
    28. 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.
      View in: PubMed
    29. 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 09; 103(1):e92. PMID: 31479590.
      View in: PubMed
    30. 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. PMID: 31417602.
      View in: PubMed
    31. Cacheiro P, Haendel MA, Smedley D. New models for human disease from the International Mouse Phenotyping Consortium. Mamm Genome. 2019 06; 30(5-6):143-150. PMID: 31127358.
      View in: PubMed
    32. 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 05; 15(5):e1006906. PMID: 31048830.
      View in: PubMed
    33. 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. PMID: 31119199.
      View in: PubMed
    34. 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 04 08; 49(1):10-29. PMID: 30930166.
      View in: PubMed
    35. 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. PMID: 30917137.
      View in: PubMed
    36. 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 01 08; 47(D1):D1018-D1027. PMID: 30476213.
      View in: PubMed
    37. 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 01 01; 2019. PMID: 31735951.
      View in: PubMed
    38. Fukushima M, Austin C, Sato N, Maruyama T, Navarro E, Rocca M, Demotes J, Haendel M, Volchenboum SL, Cowperthwaite M, Silverstein JC, Webb C, Sim I, Chase M, Speakman J, Augustine E, Ford DE, Kush R. The Global academic research organization network: Data sharing to cure diseases and enable learning health systems. Learn Health Syst. 2019 Jan; 3(1):e10073. PMID: 31245596.
      View in: PubMed
    39. Dolman L, Page A, Babb L, Freimuth RR, Arachchi H, Bizon C, Brush M, Fiume M, Haendel M, Hansen DP, Milosavljevic A, Patel RY, Pawliczek P, Yates AD, Rehm HL. ClinGen advancing genomic data-sharing standards as a GA4GH driver project. Hum Mutat. 2018 11; 39(11):1686-1689. PMID: 30311379.
      View in: PubMed
    40. Haendel MA, Chute CG, Robinson PN. Classification, Ontology, and Precision Medicine. N Engl J Med. 2018 10 11; 379(15):1452-1462. PMID: 30304648.
      View in: PubMed
    41. Arachchi H, Wojcik MH, Weisburd B, Jacobsen JOB, Valkanas E, Baxter S, Byrne AB, O'Donnell-Luria AH, Haendel M, Smedley D, MacArthur DG, Philippakis AA, Rehm HL. matchbox: An open-source tool for patient matching via the Matchmaker Exchange. Hum Mutat. 2018 12; 39(12):1827-1834. PMID: 30240502.
      View in: PubMed
    42. Vasilevsky NA, Foster ED, Engelstad ME, Carmody L, Might M, Chambers C, Dawkins HJS, Lewis J, Della Rocca MG, Snyder M, Boerkoel CF, Rath A, Terry SF, Kent A, Searle B, Baynam G, Jones E, Gavin P, Bamshad M, Chong J, Groza T, Adams D, Resnick AC, Heath AP, Mungall C, Holm IA, Rageth K, Brownstein CA, Shefchek K, McMurry JA, Robinson PN, Köhler S, Haendel MA. Plain-language medical vocabulary for precision diagnosis. Nat Genet. 2018 04; 50(4):474-476. PMID: 29632381.
      View in: PubMed
    43. Meehan TF, Conte N, Goldstein T, Inghirami G, Murakami MA, Brabetz S, Gu Z, Wiser JA, Dunn P, Begley DA, Krupke DM, Bertotti A, Bruna A, Brush MH, Byrne AT, Caldas C, Christie AL, Clark DA, Dowst H, Dry JR, Doroshow JH, Duchamp O, Evrard YA, Ferretti S, Frese KK, Goodwin NC, Greenawalt D, Haendel MA, Hermans E, Houghton PJ, Jonkers J, Kemper K, Khor TO, Lewis MT, Lloyd KCK, Mason J, Medico E, Neuhauser SB, Olson JM, Peeper DS, Rueda OM, Seong JK, Trusolino L, Vinolo E, Wechsler-Reya RJ, Weinstock DM, Welm A, Weroha SJ, Amant F, Pfister SM, Kool M, Parkinson H, Butte AJ, Bult CJ. PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models. Cancer Res. 2017 11 01; 77(21):e62-e66. PMID: 29092942.
      View in: PubMed
    44. Sobreira NLM, Arachchi H, Buske OJ, Chong JX, Hutton B, Foreman J, Schiettecatte F, Groza T, Jacobsen JOB, Haendel MA, Boycott KM, Hamosh A, Rehm HL. Matchmaker Exchange. Curr Protoc Hum Genet. 2017 10 18; 95:9.31.1-9.31.15. PMID: 29044468.
      View in: PubMed
    45. McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H. Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biol. 2017 Jun; 15(6):e2001414. PMID: 28662064.
      View in: PubMed
    46. Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, Warren J, Chen CK, Tudose I, Relac M, Matthews P, Karp N, Santos L, Fiegel T, Ring N, Westerberg H, Greenaway S, Sneddon D, Morgan H, Codner GF, Stewart ME, Brown J, Horner N, Haendel M, Washington N, Mungall CJ, Reynolds CL, Gallegos J, Gailus-Durner V, Sorg T, Pavlovic G, Bower LR, Moore M, Morse I, Gao X, Tocchini-Valentini GP, Obata Y, Cho SY, Seong JK, Seavitt J, Beaudet AL, Dickinson ME, Herault Y, Wurst W, de Angelis MH, Lloyd KCK, Flenniken AM, Nutter LMJ, Newbigging S, McKerlie C, Justice MJ, Murray SA, Svenson KL, Braun RE, White JK, Bradley A, Flicek P, Wells S, Skarnes WC, Adams DJ, Parkinson H, Mallon AM, Brown SDM, Smedley D. Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium. Nat Genet. 2017 Aug; 49(8):1231-1238. PMID: 28650483.
      View in: PubMed
    47. Gall T, Valkanas E, Bello C, Markello T, Adams C, Bone WP, Brandt AJ, Brazill JM, Carmichael L, Davids M, Davis J, Diaz-Perez Z, Draper D, Elson J, Flynn ED, Godfrey R, Groden C, Hsieh CK, Fischer R, Golas GA, Guzman J, Huang Y, Kane MS, Lee E, Li C, Links AE, Maduro V, Malicdan MCV, Malik FS, Nehrebecky M, Park J, Pemberton P, Schaffer K, Simeonov D, Sincan M, Smedley D, Valivullah Z, Wahl C, Washington N, Wolfe LA, Xu K, Zhu Y, Gahl WA, Tifft CJ, Toro C, Adams DR, He M, Robinson PN, Haendel MA, Zhai RG, Boerkoel CF. Defining Disease, Diagnosis, and Translational Medicine within a Homeostatic Perturbation Paradigm: The National Institutes of Health Undiagnosed Diseases Program Experience. Front Med (Lausanne). 2017; 4:62. PMID: 28603714.
      View in: PubMed
    48. Lawler M, Haussler D, Siu LL, Haendel MA, McMurry JA, Knoppers BM, Chanock SJ, Calvo F, The BT, Walia G, Banks I, Yu PP, Staudt LM, Sawyers CL. Sharing Clinical and Genomic Data on Cancer - The Need for Global Solutions. N Engl J Med. 2017 05 25; 376(21):2006-2009. PMID: 28538124.
      View in: PubMed
    49. Vasilevsky NA, Minnier J, Haendel MA, Champieux RE. Reproducible and reusable research: are journal data sharing policies meeting the mark? PeerJ. 2017; 5:e3208. PMID: 28462024.
      View in: PubMed
    50. Manolio TA, Fowler DM, Starita LM, Haendel MA, MacArthur DG, Biesecker LG, Worthey E, Chisholm RL, Green ED, Jacob HJ, McLeod HL, Roden D, Rodriguez LL, Williams MS, Cooper GM, Cox NJ, Herman GE, Kingsmore S, Lo C, Lutz C, MacRae CA, Nussbaum RL, Ordovas JM, Ramos EM, Robinson PN, Rubinstein WS, Seidman C, Stranger BE, Wang H, Westerfield M, Bult C. Bedside Back to Bench: Building Bridges between Basic and Clinical Genomic Research. Cell. 2017 03 23; 169(1):6-12. PMID: 28340351.
      View in: PubMed
    51. Bada M, Vasilevsky N, Baumgartner WA, Haendel M, Hunter LE. Gold-standard ontology-based anatomical annotation in the CRAFT Corpus. Database (Oxford). 2017 Jan 01; 2017. PMID: 31725864.
      View in: PubMed
    52. Baynam G, Bowman F, Lister K, Walker CE, Pachter N, Goldblatt J, Boycott KM, Gahl WA, Kosaki K, Adachi T, Ishii K, Mahede T, McKenzie F, Townshend S, Slee J, Kiraly-Borri C, Vasudevan A, Hawkins A, Broley S, Schofield L, Verhoef H, Groza T, Zankl A, Robinson PN, Haendel M, Brudno M, Mattick JS, Dinger ME, Roscioli T, Cowley MJ, Olry A, Hanauer M, Alkuraya FS, Taruscio D, Posada de la Paz M, Lochmüller H, Bushby K, Thompson R, Hedley V, Lasko P, Mina K, Beilby J, Tifft C, Davis M, Laing NG, Julkowska D, Le Cam Y, Terry SF, Kaufmann P, Eerola I, Norstedt I, Rath A, Suematsu M, Groft SC, Austin CP, Draghia-Akli R, Weeramanthri TS, Molster C, Dawkins HJS. Improved Diagnosis and Care for Rare Diseases through Implementation of Precision Public Health Framework. Adv Exp Med Biol. 2017; 1031:55-94. PMID: 29214566.
      View in: PubMed
    53. Mungall CJ, McMurry JA, Köhler S, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, Lewis SE, NguyenXuan J, Shefchek K, Vasilevsky N, Yuan Z, Washington N, Hochheiser H, Groza T, Smedley D, Robinson PN, Haendel MA. The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 2017 01 04; 45(D1):D712-D722. PMID: 27899636.
      View in: PubMed
    54. Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins HJ, DeMare LE, Devereau AD, de Vries BB, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jähn JA, James R, Krause R, F Laulederkind SJ, Lochmüller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott RH, Segal M, Sergouniotis PI, Sever R, Smith CL, Straub V, Thompson R, Turner C, Turro E, Veltman MW, Vulliamy T, Yu J, von Ziegenweidt J, Zankl A, Züchner S, Zemojtel T, Jacobsen JO, Groza T, Smedley D, Mungall CJ, Haendel M, Robinson PN. The Human Phenotype Ontology in 2017. Nucleic Acids Res. 2017 01 04; 45(D1):D865-D876. PMID: 27899602.
      View in: PubMed
    55. Links AE, Draper D, Lee E, Guzman J, Valivullah Z, Maduro V, Lebedev V, Didenko M, Tomlin G, Brudno M, Girdea M, Dumitriu S, Haendel MA, Mungall CJ, Smedley D, Hochheiser H, Arnold AM, Coessens B, Verhoeven S, Bone W, Adams D, Boerkoel CF, Gahl WA, Sincan M. Distributed Cognition and Process Management Enabling Individualized Translational Research: The NIH Undiagnosed Diseases Program Experience. Front Med (Lausanne). 2016; 3:39. PMID: 27785453.
      View in: PubMed
    56. Smedley D, Schubach M, Jacobsen JOB, Köhler S, Zemojtel T, Spielmann M, Jäger M, Hochheiser H, Washington NL, McMurry JA, Haendel MA, Mungall CJ, Lewis SE, Groza T, Valentini G, Robinson PN. A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease. Am J Hum Genet. 2016 09 01; 99(3):595-606. PMID: 27569544.
      View in: PubMed
    57. Dumontier M, Gray AJG, Marshall MS, Alexiev V, Ansell P, Bader G, Baran J, Bolleman JT, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz EA, Gonzalez-Beltran AN, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayama T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall CJ, Rietveld L, Wimalaratne SM, Yamaguchi A. The health care and life sciences community profile for dataset descriptions. PeerJ. 2016; 4:e2331. PMID: 27602295.
      View in: PubMed
    58. McMurry JA, Köhler S, Washington NL, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, Xuan JN, Shefchek K, Vasilevsky NA, Yuan Z, Lewis SE, Hochheiser H, Groza T, Smedley D, Robinson PN, Mungall CJ, Haendel MA. Navigating the Phenotype Frontier: The Monarch Initiative. Genetics. 2016 08; 203(4):1491-5. PMID: 27516611.
      View in: PubMed
    59. Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, He Y, Osumi-Sutherland D, Ruttenberg A, Sarntivijai S, Van Slyke CE, Vasilevsky NA, Haendel MA, Blake JA, Mungall CJ. The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J Biomed Semantics. 2016 07 04; 7(1):44. PMID: 27377652.
      View in: PubMed
    60. Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J. The Ontology for Biomedical Investigations. PLoS One. 2016; 11(4):e0154556. PMID: 27128319.
      View in: PubMed
    61. Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SS, Washington N, Zudilova-Seinstra E, Vasilevsky N. The Resource Identification Initiative: A Cultural Shift in Publishing. Neuroinformatics. 2016 Apr; 14(2):169-82. PMID: 26589523.
      View in: PubMed
    62. Mulder N, Nembaware V, Adekile A, Anie KA, Inusa B, Brown B, Campbell A, Chinenere F, Chunda-Liyoka C, Derebail VK, Geard A, Ghedira K, Hamilton CM, Hanchard NA, Haendel M, Huggins W, Ibrahim M, Jupp S, Kamga KK, Knight-Madden J, Lopez-Sall P, Mbiyavanga M, Munube D, Nirenberg D, Nnodu O, Ofori-Acquah SF, Ohene-Frempong K, Opap KB, Panji S, Park M, Pule G, Royal C, Sangeda R, Tayo B, Treadwell M, Tshilolo L, Wonkam A. Proceedings of a Sickle Cell Disease Ontology workshop - Towards the first comprehensive ontology for Sickle Cell Disease. Appl Transl Genom. 2016 Jun; 9:23-9. PMID: 27354937.
      View in: PubMed
    63. Druzinsky RE, Balhoff JP, Crompton AW, Done J, German RZ, Haendel MA, Herrel A, Herring SW, Lapp H, Mabee PM, Muller HM, Mungall CJ, Sternberg PW, Van Auken K, Vinyard CJ, Williams SH, Wall CE. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PLoS One. 2016; 11(2):e0149102. PMID: 26870952.
      View in: PubMed
    64. Mattingly CJ, Boyles R, Lawler CP, Haugen AC, Dearry A, Haendel M. Laying a Community-Based Foundation for Data-Driven Semantic Standards in Environmental Health Sciences. Environ Health Perspect. 2016 08; 124(8):1136-40. PMID: 26871594.
      View in: PubMed
    65. Vita R, Vasilevsky N, Bandrowski A, Haendel M, Sette A, Peters B. Reproducibility and conflicts in immune epitope data. Immunology. 2016 Mar; 147(3):349-54. PMID: 26678806.
      View in: PubMed
    66. Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova-Seinstra E, Vasilevsky N. The Resource Identification Initiative: A Cultural Shift in Publishing. J Comp Neurol. 2016 Jan 01; 524(1):8-22. PMID: 26599696.
      View in: PubMed
    67. Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova-Seinstra E, Vasilevsky N. The Resource Identification Initiative: a cultural shift in publishing. Brain Behav. 2016 01; 6(1):e00417. PMID: 27110440.
      View in: PubMed
    68. Bone WP, Washington NL, Buske OJ, Adams DR, Davis J, Draper D, Flynn ED, Girdea M, Godfrey R, Golas G, Groden C, Jacobsen J, Köhler S, Lee EM, Links AE, Markello TC, Mungall CJ, Nehrebecky M, Robinson PN, Sincan M, Soldatos AG, Tifft CJ, Toro C, Trang H, Valkanas E, Vasilevsky N, Wahl C, Wolfe LA, Boerkoel CF, Brudno M, Haendel MA, Gahl WA, Smedley D. Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency. Genet Med. 2016 06; 18(6):608-17. PMID: 26562225.
      View in: PubMed
    69. Smedley D, Jacobsen JO, Jäger M, Köhler S, Holtgrewe M, Schubach M, Siragusa E, Zemojtel T, Buske OJ, Washington NL, Bone WP, Haendel MA, Robinson PN. Next-generation diagnostics and disease-gene discovery with the Exomiser. Nat Protoc. 2015 Dec; 10(12):2004-15. PMID: 26562621.
      View in: PubMed
    70. Robinson PN, Mungall CJ, Haendel M. Capturing phenotypes for precision medicine. Cold Spring Harb Mol Case Stud. 2015 Oct; 1(1):a000372. PMID: 27148566.
      View in: PubMed
    71. Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL. The Matchmaker Exchange: a platform for rare disease gene discovery. Hum Mutat. 2015 Oct; 36(10):915-21. PMID: 26295439.
      View in: PubMed
    72. Mungall CJ, Washington NL, Nguyen-Xuan J, Condit C, Smedley D, Köhler S, Groza T, Shefchek K, Hochheiser H, Robinson PN, Lewis SE, Haendel MA. Use of model organism and disease databases to support matchmaking for human disease gene discovery. Hum Mutat. 2015 Oct; 36(10):979-84. PMID: 26269093.
      View in: PubMed
    73. Buske OJ, Girdea M, Dumitriu S, Gallinger B, Hartley T, Trang H, Misyura A, Friedman T, Beaulieu C, Bone WP, Links AE, Washington NL, Haendel MA, Robinson PN, Boerkoel CF, Adams D, Gahl WA, Boycott KM, Brudno M. PhenomeCentral: a portal for phenotypic and genotypic matchmaking of patients with rare genetic diseases. Hum Mutat. 2015 Oct; 36(10):931-40. PMID: 26251998.
      View in: PubMed
    74. Groza T, Köhler S, Moldenhauer D, Vasilevsky N, Baynam G, Zemojtel T, Schriml LM, Kibbe WA, Schofield PN, Beck T, Vasant D, Brookes AJ, Zankl A, Washington NL, Mungall CJ, Lewis SE, Haendel MA, Parkinson H, Robinson PN. The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. Am J Hum Genet. 2015 Jul 02; 97(1):111-24. PMID: 26119816.
      View in: PubMed
    75. Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, Mungall CJ, Washington N, Köhler S, Lewis SE, Robinson PN, Smedley D. Disease insights through cross-species phenotype comparisons. Mamm Genome. 2015 Oct; 26(9-10):548-55. PMID: 26092691.
      View in: PubMed
    76. Ochs C, Perl Y, Geller J, Haendel M, Brush M, Arabandi S, Tu S. Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network. J Biomed Inform. 2015 Aug; 56:127-44. PMID: 26048076.
      View in: PubMed
    77. Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan S, Washington N, Zudilova-Seinstra E, Vasilevsky N. The Resource Identification Initiative: A cultural shift in publishing. F1000Res. 2015; 4:134. PMID: 26594330.
      View in: PubMed
    78. 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.
      View in: PubMed
    79. 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.
      View in: PubMed
    80. 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.
      View in: PubMed
    81. 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.
      View in: PubMed
    82. 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.
      View in: PubMed
    83. 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.
      View in: PubMed
    84. 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.
      View in: PubMed
    85. 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.
      View in: PubMed
    86. 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.
      View in: PubMed
    87. 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.
      View in: PubMed
    88. 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.
      View in: PubMed
    89. 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.
      View in: PubMed
    90. 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.
      View in: PubMed
    91. 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.
      View in: PubMed
    92. 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.
      View in: PubMed
    93. 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.
      View in: PubMed
    94. 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.
      View in: PubMed
    95. 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.
      View in: PubMed
    96. 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.
      View in: PubMed
    97. 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.
      View in: PubMed
    98. 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.
      View in: PubMed
    99. 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.
      View in: PubMed
    100. 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.
      View in: PubMed
    101. 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.
      View in: PubMed
    102. 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.
      View in: PubMed
    103. Chesler EJ, Haendel MA. The field of bioinformatics. Preface. Int Rev Neurobiol. 2012; 103:xi-xii. PMID: 23195125.
      View in: PubMed
    104. Haendel MA, Chesler EJ. Lost and found in behavioral informatics. Int Rev Neurobiol. 2012; 103:1-18. PMID: 23195118.
      View in: PubMed
    105. 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.
      View in: PubMed
    106. 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.
      View in: PubMed
    107. 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.
      View in: PubMed
    108. 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.
      View in: PubMed
    109. 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.
      View in: PubMed
    110. 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.
      View in: PubMed
    111. 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.
      View in: PubMed
    112. 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.
      View in: PubMed
    113. 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.
      View in: PubMed
    114. 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.
      View in: PubMed
    115. 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.
      View in: PubMed
    116. 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.
      View in: PubMed
    117. 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.
      View in: PubMed
    118. 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.
      View in: PubMed
    119. 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.
      View in: PubMed
    120. 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.
      View in: PubMed
    121. Benjamin M, Haendel M. Cuba. A healthy revolution? Links. 1991; 8(3):3-6. PMID: 12159276.
      View in: PubMed
    122. 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.
      View in: PubMed
    Haendel's Networks
    Click the "See All" links for more information and interactive visualizations!
    Concepts Expand Description
    _
    Co-Authors Expand Description
    _
    Similar People Expand Description
    _
    Same Department Expand Description

    Copyright © 2021 The Regents of the University of Colorado, a body corporate. All rights reserved. (Harvard PROFILES RNS software version: 2.11.1)