 Melissa A Haendel
| Title | Professor |
|---|
| Institution | University of Colorado Denver - Anschutz Medical Campus |
|---|
| Department | SOM-BIOMED Informatics Gen Ops |
|---|
|
|
|
 Research OT2OD036113 (HAENDEL, MELISSA A)Sep 2, 2023 - Mar 1, 2025 NIH
Iron-CLAD: securely advancing AoU participant characterization with provenplatforms and collaborations
Role: 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 |
| U2CHL156291 (CARROLL, ROBERT J;DIGIOVANNA, JACK ;ESPINOSA, JOAQUIN M.;FERRETTI, VINCENT ;HAENDEL, MELISSA A;O'CON)Sep 26, 2020 - Aug 31, 2025 NIH
Data Management and Portal for the INCLUDE (DAPI) Project
Role: Co-Principal Investigator |
| RM1HG010860 (HAENDEL, MELISSA A ;MUNGALL, CHRISTOPHER J)Aug 1, 2020 - May 31, 2025 NIH
A phenomics-first resource for interpretation of variants
Role: Principal Investigator |
| OT2TR003449 (HAENDEL, MELISSA A)Jan 23, 2020 - Nov 30, 2022 NIH
A Common Dialect for Infrastructure and Services in Translator
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 |
| U13CA221044 (HAENDEL, MELISSA A)Sep 18, 2017 - Sep 17, 2021 NIH
Forums for Integrative Phenomics
Role: 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 |
| 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 |
| R25EB020379 (DORR, DAVID A.)Sep 29, 2014 - Oct 31, 2017 NIH
OHSU Informatics Analytics BD2K Skill Course
Role: Co-Principal Investigator |
| R24OD011883 (HAENDEL, MELISSA A ;MUNGALL, CHRISTOPHER J;ROBINSON, PETER NICHOLAS)Jun 1, 2012 - Aug 31, 2025 NIH
The Monarch Initiative: Linking diseases to model organism resources
Role: Principal Investigator |
| F32NS011170 (HAENDEL, MELISSA A)Sep 30, 2000 NIH
DIFFERENTIATION FACTOR RECEPTORS AND NEURAL CELL FATE
Role: Principal Investigator |
| F31MH011560 (HAENDEL, MELISSA A)Jan 17, 1998 NIH
TRAPPING NOVEL GENES INVOLVED IN NEURAL DEVELOPMENT
Role: Principal Investigator |
Bibliographic
-
Putman TE, Schaper K, Matentzoglu N, Rubinetti VP, Alquaddoomi FS, Cox C, Caufield JH, Elsarboukh G, Gehrke S, Hegde H, Reese JT, Braun I, Bruskiewich RM, Cappelletti L, Carbon S, Caron AR, Chan LE, Chute CG, Cortes KG, De Souza V, Fontana T, Harris NL, Hartley EL, Hurwitz E, Jacobsen JOB, Krishnamurthy M, Laraway BJ, McLaughlin JA, McMurry JA, Moxon SAT, Mullen KR, O'Neil ST, Shefchek KA, Stefancsik R, Toro S, Vasilevsky NA, Walls RL, Whetzel PL, Osumi-Sutherland D, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC. The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes?and diseases across species. Nucleic Acids Res. 2024 Jan 05; 52(D1):D938-D949. PMID: 38000386.
-
Gargano MA, Matentzoglu N, Coleman B, Addo-Lartey EB, Anagnostopoulos AV, Anderton J, Avillach P, Bagley AM, Bak?tein E, Balhoff JP, Baynam G, Bello SM, Berk M, Bertram H, Bishop S, Blau H, Bodenstein DF, Botas P, Boztug K, Cady J, Callahan TJ, Cameron R, Carbon SJ, Castellanos F, Caufield JH, Chan LE, Chute CG, Cruz-Rojo J, Dahan-Oliel N, Davids JR, de Dieuleveult M, de Souza V, de Vries BBA, de Vries E, DePaulo JR, Derfalvi B, Dhombres F, Diaz-Byrd C, Dingemans AJM, Donadille B, Duyzend M, Elfeky R, Essaid S, Fabrizzi C, Fico G, Firth HV, Freudenberg-Hua Y, Fullerton JM, Gabriel DL, Gilmour K, Giordano J, Goes FS, Moses RG, Green I, Griese M, Groza T, Gu W, Guthrie J, Gyori B, Hamosh A, Hanauer M, Hanu?ov? K, He YO, Hegde H, Helbig I, Holasov? K, Hoyt CT, Huang S, Hurwitz E, Jacobsen JOB, Jiang X, Joseph L, Keramatian K, King B, Knoflach K, Koolen DA, Kraus ML, Kroll C, Kusters M, Ladewig MS, Lagorce D, Lai MC, Lapunzina P, Laraway B, Lewis-Smith D, Li X, Lucano C, Majd M, Marazita ML, Martinez-Glez V, McHenry TH, McInnis MG, McMurry JA, Mihulov? M, Millett CE, Mitchell PB, Moslerov? V, Narutomi K, Nematollahi S, Nevado J, Nierenberg AA, Cajbikov? NN, Nurnberger JI, Ogishima S, Olson D, Ortiz A, Pachajoa H, Perez de Nanclares G, Peters A, Putman T, Rapp CK, Rath A, Reese J, Rekerle L, Roberts AM, Roy S, Sanders SJ, Schuetz C, Schulte EC, Schulze TG, Schwarz M, Scott K, Seelow D, Seitz B, Shen Y, Similuk MN, Simon ES, Singh B, Smedley D, Smith CL, Smolinsky JT, Sperry S, Stafford E, Stefancsik R, Steinhaus R, Strawbridge R, Sundaramurthi JC, Talapova P, Tenorio Castano JA, Tesner P, Thomas RH, Thurm A, Turnovec M, van Gijn ME, Vasilevsky NA, Vlckov? M, Walden A, Wang K, Wapner R, Ware JS, Wiafe AA, Wiafe SA, Wiggins LD, Williams AE, Wu C, Wyrwoll MJ, Xiong H, Yalin N, Yamamoto Y, Yatham LN, Yocum AK, Young AH, Y?ksel Z, Zandi PP, Zankl A, Zarante I, Zvolsk? M, Toro S, Carmody LC, Harris NL, Munoz-Torres MC, Danis D, Mungall CJ, K?hler S, Haendel MA, Robinson PN. The Human Phenotype Ontology in 2024: phenotypes around the world. Nucleic Acids Res. 2024 Jan 05; 52(D1):D1333-D1346. PMID: 37953324.
-
Wei WQ, Guardo C, Gandireddy S, Yan C, Ong H, Kerchberger V, Dickson A, Pfaff E, Master H, Basford M, Tran N, Mancuso S, Syed T, Zhao Z, Feng Q, Haendel M, Lunt C, Ginsburg G, Chute C, Denny J, Roden D. Genetic and Survey Data Improves Performance of Machine Learning Model for Long COVID. Res Sq. 2023 Dec 19. PMID: 38196610.
-
Liu S, Wen A, Wang L, He H, Fu S, Miller R, Williams A, Harris D, Kavuluru R, Liu M, Abu-El-Rub N, Schutte D, Zhang R, Rouhizadeh M, Osborne JD, He Y, Topaloglu U, Hong SS, Saltz JH, Schaffter T, Pfaff E, Chute CG, Duong T, Haendel MA, Fuentes R, Szolovits P, Xu H, Liu H. An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C). J Am Med Inform Assoc. 2023 11 17; 30(12):2036-2040. PMID: 37555837.
-
Suver C, Harper J, Loomba J, Saltz M, Solway J, Anzalone AJ, Walters K, Pfaff E, Walden A, McMurry J, Chute CG, Haendel M. The N3C governance ecosystem: A model socio-technical partnership for the future of collaborative analytics at scale. J Clin Transl Sci. 2023; 7(1):e252. PMID: 38229902.
-
Carmody LC, Gargano MA, Toro S, Vasilevsky NA, Adam MP, Blau H, Chan LE, Gomez-Andres D, Horvath R, Kraus ML, Ladewig MS, Lewis-Smith D, Lochm?ller H, Matentzoglu NA, Munoz-Torres MC, Schuetz C, Seitz B, Similuk MN, Sparks TN, Strauss T, Swietlik EM, Thompson R, Zhang XA, Mungall CJ, Haendel MA, Robinson PN. The Medical Action Ontology: A tool for annotating and analyzing treatments and clinical management of human disease. Med. 2023 Dec 08; 4(12):913-927.e3. PMID: 37963467.
-
Hill EL, Mehta HB, Sharma S, Mane K, Singh SK, 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: an N3C and NIH RECOVER study. BMC Public Health. 2023 10 25; 23(1):2103. PMID: 37880596.
-
Hurwitz E, Butzin-Dozier Z, Master H, O'Neil ST, Walden A, Holko M, Patel RC, Haendel MA. Harnessing consumer wearable digital biomarkers for individualized recognition of postpartum depression using the All of Us Research Program dataset. medRxiv. 2023 Oct 14. PMID: 37873471.
-
Levitt EB, Patch DA, Hess MC, Terrero A, Jaeger B, Haendel MA, Chute CG, Yeager MT, Ponce BA, Theiss SM, Spitler CA, Johnson JP. Outcomes of SARS-CoV-2 infection among patients with orthopaedic fracture surgery in the National COVID Cohort Collaborative (N3C). Injury. 2023 Dec; 54(12):111092. PMID: 37871347.
-
L Mandel H, Colleen G, Abedian S, Ammar N, Charles Bailey L, Bennett TD, Daniel Brannock M, Brosnahan SB, Chen Y, Chute CG, Divers J, Evans MD, Haendel M, Hall MA, Hirabayashi K, Hornig M, Katz SD, Krieger AC, Loomba J, Lorman V, Mazzotti DR, McMurry J, Moffitt RA, Pajor NM, Pfaff E, Radwell J, Razzaghi H, Redline S, Seibert E, Sekar A, Sharma S, Thaweethai T, Weiner MG, Jae Yoo Y, Zhou A, Thorpe LE. Risk of post-acute sequelae of SARS-CoV-2 infection associated with pre-coronavirus disease obstructive sleep apnea diagnoses: an electronic health record-based analysis from the RECOVER initiative. Sleep. 2023 09 08; 46(9). PMID: 37166330.
-
Jones SE, Bradwell KR, Chan LE, McMurry JA, Olson-Chen C, Tarleton J, Wilkins KJ, Ly V, Ljazouli S, Qin Q, Faherty EG, Lau YK, Xie C, Kao YH, Liebman MN, Mariona F, Challa AP, Li L, Ratcliffe SJ, Haendel MA, Patel RC, Hill EL. Who is pregnant? Defining real-world data-based pregnancy episodes in the National COVID Cohort Collaborative (N3C). JAMIA Open. 2023 Oct; 6(3):ooad067. PMID: 37600074.
-
Chan LE, Casiraghi E, Putman T, Reese J, Harmon QE, Schaper K, Hedge H, Valentini G, Schmitt C, Motsinger-Reif A, Hall JE, Mungall CJ, Robinson PN, Haendel MA. Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests. medRxiv. 2023 Jul 16. PMID: 37502882.
-
Carmody LC, Gargano MA, Toro S, Vasilevsky NA, Adam MP, Blau H, Chan LE, Gomez-Andres D, Horvath R, Kraus ML, Ladewig MS, Lewis-Smith D, Lochm?ller H, Matentzoglu NA, Munoz-Torres MC, Schuetz C, Seitz B, Similuk MN, Sparks TN, Strauss T, Swietlik EM, Thompson R, Zhang XA, Mungall CJ, Haendel MA, Robinson PN. The Medical Action Ontology: A Tool for Annotating and Analyzing Treatments and Clinical Management of Human Disease. medRxiv. 2023 Jul 13. PMID: 37503136.
-
Caufield JH, Putman T, Schaper K, Unni DR, Hegde H, Callahan TJ, Cappelletti L, Moxon SAT, Ravanmehr V, Carbon S, Chan LE, Cortes K, Shefchek KA, Elsarboukh G, Balhoff J, Fontana T, Matentzoglu N, Bruskiewich RM, Thessen AE, Harris NL, Munoz-Torres MC, Haendel MA, Robinson PN, Joachimiak MP, Mungall CJ, Reese JT. KG-Hub-building and exchanging biological knowledge graphs. Bioinformatics. 2023 07 01; 39(7). PMID: 37389415.
-
Pfaff ER, Girvin AT, Crosskey M, Gangireddy S, Master H, Wei WQ, Kerchberger VE, Weiner M, Harris PA, Basford M, Lunt C, Chute CG, Moffitt RA, Haendel M. De-black-boxing health AI: demonstrating reproducible machine learning computable phenotypes using the N3C-RECOVER Long COVID model in the All of Us data repository. J Am Med Inform Assoc. 2023 06 20; 30(7):1305-1312. PMID: 37218289.
-
Brannock MD, Chew RF, Preiss AJ, Hadley EC, Redfield S, 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 in an EHR-based cohort study from the RECOVER program. Nat Commun. 2023 05 22; 14(1):2914. PMID: 37217471.
-
Callahan TJ, Stefanski AL, Wyrwa JM, Zeng C, Ostropolets A, Banda JM, Baumgartner WA, Boyce RD, Casiraghi E, Coleman BD, Collins JH, Deakyne Davies SJ, Feinstein JA, Lin AY, Martin B, Matentzoglu NA, Meeker D, Reese J, Sinclair J, Taneja SB, Trinkley KE, Vasilevsky NA, Williams AE, Zhang XA, Denny JC, Ryan PB, Hripcsak G, Bennett TD, Haendel MA, Robinson PN, Hunter LE, Kahn MG. Ontologizing health systems data at scale: making translational discovery a reality. NPJ Digit Med. 2023 May 19; 6(1):89. PMID: 37208468.
-
Leese P, Anand A, Girvin A, Manna A, Patel S, Yoo YJ, Wong R, Haendel M, Chute CG, Bennett T, Hajagos J, Pfaff E, Moffitt R. Clinical encounter heterogeneity and methods for resolving in networked EHR data: a study from N3C and RECOVER programs. J Am Med Inform Assoc. 2023 05 19; 30(6):1125-1136. PMID: 37087110.
-
Danis D, Jacobsen JOB, Wagner AH, Groza T, Beckwith MA, Rekerle L, Carmody LC, Reese J, Hegde H, Ladewig MS, Seitz B, Munoz-Torres M, Harris NL, Rambla J, Baudis M, Mungall CJ, Haendel MA, Robinson PN. Phenopacket-tools: Building and validating GA4GH Phenopackets. PLoS One. 2023; 18(5):e0285433. PMID: 37196000.
-
Bhatia A, Preiss AJ, Xiao X, Brannock MD, Alexander GC, Chew RF, Fitzgerald M, Hill E, Kelly EP, Mehta HB, Madlock-Brown C, Wilkins KJ, Chute CG, Haendel M, Moffitt R, Pfaff ER. Effect of Nirmatrelvir/Ritonavir (Paxlovid) on Hospitalization among Adults with COVID-19: an EHR-based Target Trial Emulation from N3C. medRxiv. 2023 May 04. PMID: 37205340.
-
Stefancsik R, Balhoff JP, Balk MA, Ball RL, Bello SM, Caron AR, Chesler EJ, de Souza V, Gehrke S, Haendel M, Harris LW, Harris NL, Ibrahim A, Koehler S, Matentzoglu N, McMurry JA, Mungall CJ, Munoz-Torres MC, Putman T, Robinson P, Smedley D, Sollis E, Thessen AE, Vasilevsky N, Walton DO, Osumi-Sutherland D. The Ontology of Biological Attributes (OBA)-computational traits for the life sciences. Mamm Genome. 2023 09; 34(3):364-378. PMID: 37076585.
-
Chan LE, Thessen AE, Duncan WD, Matentzoglu N, Schmitt C, Grondin CJ, Vasilevsky N, McMurry JA, Robinson PN, Mungall CJ, Haendel MA. The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond. J Biomed Semantics. 2023 02 24; 14(1):3. PMID: 36823605.
-
Pfaff ER, Madlock-Brown C, Baratta JM, Bhatia A, Davis H, Girvin A, Hill E, Kelly E, 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. BMC Med. 2023 02 16; 21(1):58. PMID: 36793086.
-
Stefancsik R, Balhoff JP, Balk MA, Ball R, Bello SM, Caron AR, Chessler E, de Souza V, Gehrke S, Haendel M, Harris LW, Harris NL, Ibrahim A, Koehler S, Matentzoglu N, McMurry JA, Mungall CJ, Munoz-Torres MC, Putman T, Robinson P, Smedley D, Sollis E, Thessen AE, Vasilevsky N, Walton DO, Osumi-Sutherland D. The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences. bioRxiv. 2023 Jan 27. PMID: 36747660.
-
Hadley E, Yoo YJ, Patel S, Zhou A, Laraway B, Wong R, Preiss A, Chew R, Davis H, Chute CG, Pfaff ER, Loomba J, Haendel M, Hill E, Moffitt R. SARS-CoV-2 Reinfection is Preceded by Unique Biomarkers and Related to Initial Infection Timing and Severity: an N3C RECOVER EHR-Based Cohort Study. medRxiv. 2023 Jan 05. PMID: 36656776.
-
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. 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. 2023 03; 16(3):398-411. 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. 2023 Jan; 87:104413. PMID: 36563487.
-
Hoyt CT, Balk M, Callahan TJ, Domingo-Fern?ndez 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 11 19; 9(1):714. PMID: 36402838.
-
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. PMID: 36400170.
-
Coleman B, Casiraghi E, Callahan TJ, Blau H, Chan L, Laraway B, Clark KB, Re? 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 01. PMID: 36380762.
-
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 10 08; 2022. PMID: 36208225.
-
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 07. PMID: 36238713.
-
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 02. PMID: 36093345.
-
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. PMID: 36093353.
-
Ladewig MS, Jacobsen JOB, Wagner AH, Danis D, El Kassaby B, Gargano M, Groza T, Baudis M, Steinhaus R, Seelow D, Bechrakis NE, Mungall CJ, Schofield PN, Elemento O, Smith L, McMurry JA, Munoz-Torres M, Haendel MA, Robinson PN. GA4GH Phenopackets: A Practical Introduction. Adv Genet (Hoboken). 2023 Mar; 4(1):2200016. PMID: 36910590.
-
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. 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 06. PMID: 35982668.
-
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 08 01; 176(8):819-821. PMID: 35426941.
-
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 06; 190(2):231-242. PMID: 35872606.
-
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. PMID: 35665012.
-
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 06 14; 29(7):1172-1182. PMID: 35435957.
-
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 06 13; 45(6). PMID: 35030631.
-
Unni DR, Moxon SAT, Bada M, Brush M, Bruskiewich R, Caufield JH, Clemons PA, Dancik V, Dumontier M, Fecho K, Glusman G, Hadlock JJ, Harris NL, Joshi A, Putman T, Qin G, Ramsey SA, Shefchek KA, Solbrig H, Soman K, Thessen AE, Haendel MA, Bizon C, Mungall CJ. Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science. Clin Transl Sci. 2022 08; 15(8):1848-1855. PMID: 36125173.
-
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, K?hler S, Laraway BJ, Lehv?slaiho 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. PMID: 35705716.
-
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. PMID: 35524622.
-
Matentzoglu N, Balhoff JP, Bello SM, Bizon C, Brush M, Callahan TJ, Chute CG, Duncan WD, Evelo CT, Gabriel D, Graybeal J, Gray A, Gyori BM, Haendel M, Harmse H, Harris NL, Harrow I, Hegde HB, Hoyt AL, Hoyt CT, Jiao D, Jim?nez-Ruiz E, Jupp S, Kim H, Koehler S, Liener T, Long Q, Malone J, McLaughlin JA, McMurry JA, Moxon S, Munoz-Torres MC, Osumi-Sutherland D, Overton JA, Peters B, Putman T, Queralt-Rosinach N, Shefchek K, Solbrig H, Thessen A, Tudorache T, Vasilevsky N, Wagner AH, Mungall CJ. A Simple Standard for Sharing Ontological Mappings (SSSOM). Database (Oxford). 2022 05 25; 2022. PMID: 35616100.
-
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 07; 4(7):e532-e541. 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 05 15; 19(1):84. PMID: 35570298.
-
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). PMID: 35754516.
-
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 07; 24(7):1512-1522. PMID: 35442193.
-
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 04; 19(4):695-697. PMID: 34788203.
-
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 03 15; 29(4):609-618. PMID: 34590684.
-
Thessen AE, Marvel S, Achenbach JC, Fischer S, Haendel MA, Hayward K, Kl?ver N, K?nemann S, Legradi J, Lein P, Leong C, Mylroie JE, Padilla S, Perone D, Planchart A, Prieto RM, Muriana A, Quevedo C, Reif D, Ryan K, Stinckens E, Truong L, Vergauwen L, Vom Berg C, Wilbanks M, Yaghoobi B, Hamm J. Implementation of Zebrafish Ontologies for Toxicology Screening. Front Toxicol. 2022; 4:817999. PMID: 35387429.
-
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. PMID: 35237737.
-
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 02 01; 5(2):e2143151. PMID: 35133437.
-
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.
-
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. NSAID use and clinical outcomes in COVID-19 patients: A 38-center retrospective cohort study. medRxiv. 2021 Dec 22. PMID: 33907758.
-
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. PMID: 35211336.
-
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.
-
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, K?hler 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 Dec; 74:103722. PMID: 34839263.
-
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, Rehmstr?m 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, Gr?f 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, N?meth 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.
-
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, Nyr?nen 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.
-
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, Guig? 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, Jen? 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, Moln?r-G?bor F, Mulder N, Munoz-Torres MC, Nag R, Nakagawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyr?nen 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, T?rnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Vamathevan J, Varma S, Vears DF, Viner C, Voisin C, Wagner AH, Wallace SE, Walsh BP, Williams MS, Winkler EC, Wold BJ, Wood GM, Woolley JP, Yamasaki C, Yates AD, Yung CK, Zass LJ, Zaytseva K, Zhang J, Goodhand P, North K, Birney E. GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genom. 2021 Nov 10; 1(2). PMID: 35072136.
-
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.
-
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 10 26; 2021. 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 10 22; 16(1):429. 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 11; 8(11):e690-e700. PMID: 34655550.
-
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.
-
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.
-
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.
-
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.
-
Kahkoska AR, Abrahamsen TJ, Alexander GC, Bennett TD, Chute CG, Haendel MA, Klein KR, Mehta H, Miller JD, Moffitt RA, St?rmer 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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
K?hler 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, Y?ksel 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.
-
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.
-
D'Angelo CS, Hermes A, McMaster CR, Prichep E, Richer ?, 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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
Robinson PN, Ravanmehr V, Jacobsen JOB, Danis D, Zhang XA, Carmody LC, Gargano MA, Thaxton CL, Karlebach G, Reese J, Holtgrewe M, K?hler 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.
-
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.
-
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.
-
Haendel M, Vasilevsky N, Unni D, Bologa C, Harris N, Rehm H, Hamosh A, Baynam G, Groza T, McMurry J, Dawkins H, Rath A, Thaxton C, Bocci G, Joachimiak MP, K?hler 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.
-
Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Della Rocca M, Dunn N, Essaid S, Fey P, Grove C, Gourdine JP, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, K?hler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D. The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 2020 01 08; 48(D1):D704-D715. PMID: 31701156.
-
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.
-
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.
-
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.
-
K?hler S, ?ien 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.
-
Nell?ker C, Alkuraya FS, Baynam G, Bernier RA, Bernier FPJ, Boulanger V, Brudno M, Brunner HG, Clayton-Smith J, Cogn? 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, K?ry S, Lees M, Lyon GJ, Lyonnet S, Marcadier JL, Meyn S, Moslerov? 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.
-
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.
-
Tang YA, Pichler K, F?llgrabe 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.
-
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, K?hler 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.
-
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, B?nnemann 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.
-
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.
-
K?hler 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, Y?ksel 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, G?mez-Andr?s D, Lochm?ller 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.
-
Gourdine JF, Brush MH, Vasilevsky NA, Shefchek K, K?hler 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.
-
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.
-
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.
-
Haendel MA, Chute CG, Robinson PN. Classification, Ontology, and Precision Medicine. N Engl J Med. 2018 10 11; 379(15):1452-1462. PMID: 30304648.
-
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.
-
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, K?hler S, Haendel MA. Plain-language medical vocabulary for precision diagnosis. Nat Genet. 2018 04; 50(4):474-476. PMID: 29632381.
-
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.
-
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.
-
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, H?rich? JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Nov?re N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, M?ller 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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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, Lochm?ller 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.
-
Mungall CJ, McMurry JA, K?hler 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.
-
K?hler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aym? 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, J?hn JA, James R, Krause R, F Laulederkind SJ, Lochm?ller 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, Z?chner 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.
-
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.
-
Smedley D, Schubach M, Jacobsen JOB, K?hler S, Zemojtel T, Spielmann M, J?ger 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.
-
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 Nov?re 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.
-
McMurry JA, K?hler 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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
Bone WP, Washington NL, Buske OJ, Adams DR, Davis J, Draper D, Flynn ED, Girdea M, Godfrey R, Golas G, Groden C, Jacobsen J, K?hler 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.
-
Smedley D, Jacobsen JO, J?ger M, K?hler 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.
-
Robinson PN, Mungall CJ, Haendel M. Capturing phenotypes for precision medicine. Cold Spring Harb Mol Case Stud. 2015 Oct; 1(1):a000372. PMID: 27148566.
-
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, Z?chner 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.
-
Mungall CJ, Washington NL, Nguyen-Xuan J, Condit C, Smedley D, K?hler 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.
-
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.
-
Groza T, K?hler 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.
-
Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, Mungall CJ, Washington N, K?hler 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.
-
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.
-
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.
-
Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Cs?sz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, K?hler S, Lecointre G, Lapp H, Lawrence CJ, Le Nov?re N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mik? I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ram?rez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P. Finding our way through phenotypes. PLoS Biol. 2015 Jan; 13(1):e1002033. PMID: 25562316.
-
Starr J, Castro E, Crosas M, Dumontier M, Downs RR, Duerr R, Haak LL, Haendel M, Herman I, Hodson S, Hourcl? 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.
-
K?hler 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.
-
Thacker RW, D?az 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.
-
Ibn-Salem J, K?hler 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.
-
Zemojtel T, K?hler S, Mackenroth L, J?ger M, Hecht J, Krawitz P, Graul-Neumann L, Doelken S, Ehmke N, Spielmann M, Oien NC, Schweiger MR, Kr?ger U, Frommer G, Fischer B, Kornak U, Fl?ttmann 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.
-
Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Sch?rer 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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
K?hler 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, J?hn 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.
-
Robinson PN, K?hler 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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
Haendel MA, Chesler EJ. Lost and found in behavioral informatics. Int Rev Neurobiol. 2012; 103:1-18. PMID: 23195118.
-
Chesler EJ, Haendel MA. The field of bioinformatics. Preface. Int Rev Neurobiol. 2012; 103:xi-xii. PMID: 23195125.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
Benjamin M, Haendel M. Cuba. A healthy revolution? Links. 1991; 8(3):3-6. PMID: 12159276.
-
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.
This graph shows the total number of publications by year, by first, middle/unknown, or last author.
To see the data from this visualization as text, click here.
| Year | Publications |
|---|
| 1996 | 1 | | 1997 | 1 | | 1999 | 1 | | 2000 | 1 | | 2004 | 2 | | 2005 | 1 | | 2006 | 1 | | 2007 | 5 | | 2009 | 1 | | 2010 | 2 | | 2012 | 6 | | 2013 | 9 | | 2014 | 10 | | 2015 | 13 | | 2016 | 14 | | 2017 | 10 | | 2018 | 5 | | 2019 | 12 | | 2020 | 14 | | 2021 | 25 | | 2022 | 31 | | 2023 | 24 | | 2024 | 2 |
To return to the timeline, click here.
|
Haendel's Networks
Click the "See All" links for more information and interactive visualizations!
Concepts  Derived automatically from this person's publications. _
Co-Authors People in Profiles who have published with this person. _
Similar People People who share similar concepts with this person. _
Same Department
People who are also in this person's primary department.
|