Publications

1. Lennon NJ, Kottyan LC, Kachulis C, Abul-Husn NS, Arias J, Belbin G, Below JE, Berndt SI, Chung WK, Cimino JJ, Clayton EW, Connolly JJ, Crosslin DR, Dikilitas O, Velez Edwards DR, Feng Q, Fisher M, Freimuth RR, Ge T, Glessner JT, Gordon AS, Patterson C, Hakonarson H, Harden M, Harr M, Hirschhorn JN, Hoggart C, Hsu L, Irvin MR, Jarvik GP, Karlson EW, Khan A, Khera A, Kiryluk K, Kullo I, Larkin K, Limdi N, Linder JE, Loos RJF, Luo Y, Malolepsza E, Manolio TA, Martin LJ, McCarthy L, McNally EM, Meigs JB, Mersha TB, Mosley JD, Musick A, Namjou B, Pai N, Pesce LL, Peters U, Peterson JF, Prows CA, Puckelwartz MJ, Rehm HL, Roden DM, Rosenthal EA, Rowley R, Sawicki KT, Schaid DJ, Smit RAJ, Smith JL, Smoller JW, Thomas M, Tiwari H, Toledo DM, Vaitinadin NS, Veenstra D, Walunas TL, Wang Z, Wei WQ, Weng C, Wiesner GL, Yin X, Kenny EE, GIANT Consortium//All of Us Research Program. Selection, optimization and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse US populations. Nat Med. 2024 Feb; 30 (2):480-487 Epub 2024 Feb 19
   View PubMed
2. Walton NA, Nagarajan R, Wang C, Sincan M, Freimuth RR, Everman DB, Walton DC, McGrath SP, Lemas DJ, Benos PV, Alekseyenko AV, Song Q, Gamsiz Uzun E, Taylor CO, Uzun A, Person TN, Rappoport N, Zhao Z, Williams MS. Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup. J Am Med Inform Assoc. 2024 Jan 18; 31 (2):536-541
   View PubMed
3. Khalifa A, Freimuth RR. Representing NIH Genetic Test Registry Data in the FHIR Genomic Study Resource. Stud Health Technol Inform. 2023 Jun 29; 305:398-401
   View PubMed
4. Bangash H, Elsekaily O, Saadatagah S, Sutton J, Johnsen P, Gundelach JH, Kamzabek A, Freimuth R, Caraballo PJ, Kullo IJ. Clinician Perspectives on Clinical Decision Support for Familial Hypercholesterolemia. J Pers Med. 2023 May 31; 13 (6)
   View PubMed
5. Linder JE, Allworth A, Bland HT, Caraballo PJ, Chisholm RL, Clayton EW, Crosslin DR, Dikilitas O, DiVietro A, Esplin ED, Forman S, Freimuth RR, Gordon AS, Green R, Harden MV, Holm IA, Jarvik GP, Karlson EW, Labrecque S, Lennon NJ, Limdi NA, Mittendorf KF, Murphy SN, Orlando L, Prows CA, Rasmussen LV, Rasmussen-Torvik L, Rowley R, Sawicki KT, Schmidlen T, Terek S, Veenstra D, Velez Edwards DR, Absher D, Abul-Husn NS, Alsip J, Bangash H, Beasley M, Below JE, Berner ES, Booth J, Chung WK, Cimino JJ, Connolly J, Davis P, Devine B, Fullerton SM, Guiducci C, Habrat ML, Hain H, Hakonarson H, Harr M, Haverfield E, Hernandez V, Hoell C, Horike-Pyne M, Hripcsak G, Irvin MR, Kachulis C, Karavite D, Kenny EE, Khan A, Kiryluk K, Korf B, Kottyan L, Kullo IJ, Larkin K, Liu C, Malolepsza E, Manolio TA, May T, McNally EM, Mentch F, Miller A, Mooney SD, Murali P, Mutai B, Muthu N, Namjou B, Perez EF, Puckelwartz MJ, Rakhra-Burris T, Roden DM, Rosenthal EA, Saadatagah S, Sabatello M, Schaid DJ, Schultz B, Seabolt L, Shaibi GQ, Sharp RR, Shirts B, Smith ME, Smoller JW, Sterling R, Suckiel SA, Thayer J, Tiwari HK, Trinidad SB, Walunas T, Wei WQ, Wells QS, Weng C, Wiesner GL, Wiley K, Peterson JF. Returning integrated genomic risk and clinical recommendations: The eMERGE study. Genet Med. 2023 Apr; 25 (4):100006 Epub 2023 Jan 06
   View PubMed
6. Zhao Y, Brush M, Wang C, Wagner AH, Liu H, Freimuth RR. Leveraging a pharmacogenomics knowledgebase to formulate a drug response phenotype terminology for genomic medicine. Bioinformatics. 2022 Nov 30; 38 (23):5279-5287
   View PubMed
7. Goar W, Babb L, Chamala S, Cline M, Freimuth RR, Hart RK, Kuzma K, Lee J, Nelson T, Prlic A, Riehle K, Smith A, Stahl K, Yates AD, Rehm HL, Wagner AH. Development and application of a computable genotype model in the GA4GH variation representation specification. Pacific Symposium on Biocomputing. 2022 Nov; (2023):383-94
   
8. Hui D, Xiao B, Dikilitas O, Freimuth RR, Irvin MR, Jarvik GP, Kottyan L, Kullo I, Limdi NA, Liu C, Luo Y, Namjou B, Puckelwartz MJ, Schaid D, Tiwari H, Wei WQ, Verma S, Kim D, Ritchie MD. Quantifying factors that affect polygenic risk score performance across diverse ancestries and age groups for body mass index. Pacific Symposium on Biocomputing. 2022 Nov; (2023):437-48
   
9. Wiley K, Findley L, Goldrich M, Rakhra-Burris TK, Stevens A, Williams P, Bult CJ, Chisholm R, Deverka P, Ginsburg GS, Green ED, Jarvik G, Mensah GA, Ramos E, Relling MV, Roden DM, Rowley R, Alterovitz G, Aronson S, Bastarache L, Cimino JJ, Crowgey EL, Del Fiol G, Freimuth RR, Hoffman MA, Jeff J, Johnson K, Kawamoto K, Madhavan S, Mendonca EA, Ohno-Machado L, Pratap S, Taylor CO, Ritchie MD, Walton N, Weng C, Zayas-Caban T, Manolio TA, Williams MS. A research agenda to support the development and implementation of genomics-based clinical informatics tools and resources. J Am Med Inform Assoc. 2022 Jul 12; 29 (8):1342-1349
   View PubMed
10. Wang L, Scherer SE, Bielinski SJ, Muzny DM, Jones LA, Black JL 3rd, Moyer AM, Giri J, Sharp RR, Matey ET, Wright JA, Oyen LJ, Nicholson WT, Wiepert M, Sullard T, Curry TB, Rohrer Vitek CR, McAllister TM, St Sauver JL, Caraballo PJ, Lazaridis KN, Venner E, Qin X, Hu J, Kovar CL, Korchina V, Walker K, Doddapaneni H, Wu TJ, Raj R, Denson S, Liu W, Chandanavelli G, Zhang L, Wang Q, Kalra D, Karow MB, Harris KJ, Sicotte H, Peterson SE, Barthel AE, Moore BE, Skierka JM, Kluge ML, Kotzer KE, Kloke K, Vander Pol JM, Marker H, Sutton JA, Kekic A, Ebenhoh A, Bierle DM, Schuh MJ, Grilli C, Erickson S, Umbreit A, Ward L, Crosby S, Nelson EA, Levey S, Elliott M, Peters SG, Pereira N, Frye M, Shamoun F, Goetz MP, Kullo IJ, Wermers R, Anderson JA, Formea CM, El Melik RM, Zeuli JD, Herges JR, Krieger CA, Hoel RW, Taraba JL, St Thomas SR, Absah I, Bernard ME, Fink SR, Gossard A, Grubbs PL, Jacobson TM, Takahashi P, Zehe SC, Buckles S, Bumgardner M, Gallagher C, Fee-Schroeder K, Nicholas NR, Powers ML, Ragab AK, Richardson DM, Stai A, Wilson J, Pacyna JE, Olson JE, Sutton EJ, Beck AT, Horrow C, Kalari KR, Larson NB, Liu H, Wang L, Lopes GS, Borah BJ, Freimuth RR, Zhu Y, Jacobson DJ, Hathcock MA, Armasu SM, McGree ME, Jiang R, Koep TH, Ross JL, Hilden MG, Bosse K, Ramey B, Searcy I, Boerwinkle E, Gibbs RA, Weinshilboum RM. Implementation of preemptive DNA sequence-based pharmacogenomics testing across a large academic medical center: The Mayo-Baylor RIGHT 10K Study. Genet Med. 2022 May; 24 (5):1062-1072 Epub 2022 Mar 21
    View PubMed
11. Yu J, Pacheco JA, Ghosh AS, Luo Y, Weng C, Shang N, Benoit B, Carrell DS, Carroll RJ, Dikilitas O, Freimuth RR, Gainer VS, Hakonarson H, Hripcsak G, Kullo IJ, Mentch F, Murphy SN, Peissig PL, Ramirez AH, Walton N, Wei WQ, Rasmussen LV. Under-specification as the source of ambiguity and vagueness in narrative phenotype algorithm definitions. BMC Med Inform Decis Mak. 2022 Jan 28; 22 (1):23
    View PubMed
12. Wagner AH, Babb L, Alterovitz G, Baudis M, Brush M, Cameron DL, Cline M, Griffith M, Griffith OL, Hunt SE, Kreda D, Lee JM, Li S, Lopez J, Moyer E, Nelson T, Patel RY, Riehle K, Robinson PN, Rynearson S, Schuilenburg H, Tsukanov K, Walsh B, Konopko M, Rehm HL, Yates AD, Freimuth RR, Hart RK. The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification. Cell Genom. 2021 Nov 10; 1 (2)
    View PubMed
13. 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, Guigo 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, Jene 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, Molnar-Gabor F, Mulder N, Munoz-Torres MC, Nag R, Nakagawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyronen 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, Tornroos 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)
    View PubMed
14. Murugan M, Babb LJ, Overby Taylor C, Rasmussen LV, Freimuth RR, Venner E, Yan F, Yi V, Granite SJ, Zouk H, Aronson SJ, Power K, Fedotov A, Crosslin DR, Fasel D, Jarvik GP, Hakonarson H, Bangash H, Kullo IJ, Connolly JJ, Nestor JG, Caraballo PJ, Wei W, Wiley K, Rehm HL, Gibbs RA. Genomic considerations for FHIR(R); eMERGE implementation lessons. J Biomed Inform. 2021 Jun; 118:103795 Epub 2021 Apr 28
    View PubMed
15. Petersen C, Smith J, Freimuth RR, Goodman KW, Jackson GP, Kannry J, Liu H, Madhavan S, Sittig DF, Wright A. Recommendations for the safe, effective use of adaptive CDS in the US healthcare system: an AMIA position paper. J Am Med Inform Assoc. 2021 Mar 18; 28 (4):677-684
    View PubMed
16. Rasmussen LV, Connolly JJ, Del Fiol G, Freimuth RR, Pet DB, Peterson JF, Shirts BH, Starren JB, Williams MS, Walton N, Taylor CO. Infobuttons for Genomic Medicine: Requirements and Barriers. Appl Clin Inform. 2021 Mar; 12 (2):383-390 Epub 2021 May 12
    View PubMed
17. Hoell C, Wynn J, Rasmussen LV, Marsolo K, Aufox SA, Chung WK, Connolly JJ, Freimuth RR, Kochan D, Hakonarson H, Harr M, Holm IA, Kullo IJ, Lammers PE, Leppig KA, Leslie ND, Myers MF, Sharp RR, Smith ME, Prows CA. Participant choices for return of genomic results in the eMERGE Network. Genet Med. 2020 Nov; 22 (11):1821-1829 Epub 2020 July 16
    View PubMed
18. Bangash H, Pencille L, Gundelach JH, Makkawy A, Sutton J, Makkawy L, Dikilitas O, Kopecky S, Freimuth R, Caraballo PJ, Kullo IJ. An Implementation Science Framework to Develop a Clinical Decision Support Tool for Familial Hypercholesterolemia. J Pers Med. 2020 Jul 23; 10(3).
    View PubMed
19. Bangash H, Sutton J, Gundelach JH, Pencille L, Makkawy A, Elsekaily O, Dikilitas O, Mir A, Freimuth R, Caraballo PJ, Kullo IJ. Deploying Clinical Decision Support for Familial Hypercholesterolemia. ACI open. 2020 Jul; 4 (2):e157-e161 Epub 2020 Dec 31
    View PubMed
20. Kochan DC, Winkler E, Lindor N, Shaibi GQ, Olson J, Caraballo PJ, Freimuth R, Pacyna JE, Breitkopf CR, Sharp RR, Kullo IJ. Challenges in returning results in a genomic medicine implementation study: the Return of Actionable Variants Empirical (RAVE) study. NPJ Genom Med. 2020 May 4; 5 (1):19 Epub 2020 May 04
    View PubMed
21. 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, Variant Interpretation for Cancer Consortium. A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Nat Genet. 2020 Apr; 52 (4):448-457 Epub 2020 Apr 03
    View PubMed
22. McDonough CW, Breitenstein MK, Shahin M, Empey PE, Freimuth RR, Li L, Liebman M, Tuteja S. Translational Informatics Connects Real-World Information to Knowledge in an Increasingly Data-Driven World. Clin Pharmacol Ther. 2020 Apr; 107 (4):738-741 Epub 2019 Dec 14
    View PubMed
23. Garcia SJ, Zayas-Caban T, Freimuth RR. Sync for Genes: Making Clinical Genomics Available for Precision Medicine at the Point-of-Care. Appl Clin Inform. 2020 Mar; 11 (2):295-302 Epub 2020 Apr 22
    View PubMed
24. Bielinski SJ, St Sauver JL, Olson JE, Larson NB, Black JL, Scherer SE, Bernard ME, Boerwinkle E, Borah BJ, Caraballo PJ, Curry TB, Doddapaneni H, Formea CM, Freimuth RR, Gibbs RA, Giri J, Hathcock MA, Hu J, Jacobson DJ, Jones LA, Kalla S, Koep TH, Korchina V, Kovar CL, Lee S, Liu H, Matey ET, McGree ME, McAllister TM, Moyer AM, Muzny DM, Nicholson WT, Oyen LJ, Qin X, Raj R, Roger VL, Rohrer Vitek CR, Ross JL, Sharp RR, Takahashi PY, Venner E, Walker K, Wang L, Wang Q, Wright JA, Wu TJ, Wang L, Weinshilboum RM. Cohort Profile: The Right Drug, Right Dose, Right Time: Using Genomic Data to Individualize Treatment Protocol (RIGHT Protocol). Int J Epidemiol. 2020 Feb 1; 49 (1):23-24k
    View PubMed
25. Kochan DC, Winkler E, Lindor N, Shaibi GQ, Olson J, Caraballo PJ, Freimuth R, Pacyna JE, Breitkopf CR, Sharp RR, Kullo IJ. Challenges in returning results in a genomic medicine implementation study: the Return of Actionable Variants Empirical (RAVE) study. NPJ Genom Med. 2020; 5:19 Epub 2020 May 04
    View PubMed
26. Romano JD, Bernauer M, McGrath SP, Nagar SD, Freimuth RR. A Decade of Translational Bioinformatics: A Retrospective Analysis of "Year-in-Review" Presentations. AMIA Jt Summits Transl Sci Proc. 2019; 2019:335-344 Epub 2019 May 06
    View PubMed
27. Williams MS, Taylor CO, Walton NA, Goehringer SR, Aronson S, Freimuth RR, Rasmussen LV, Hall ES, Prows CA, Chung WK, Fedotov A, Nestor J, Weng C, Rowley RK, Wiesner GL, Jarvik GP, Del Fiol G. Genomic Information for Clinicians in the Electronic Health Record: Lessons Learned From the Clinical Genome Resource Project and the Electronic Medical Records and Genomics Network. Front Genet. 2019; 10:1059 Epub 2019 Oct 29
    View PubMed
28. 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 Nov; 39 (11):1686-1689
    View PubMed
29. Kullo IJ, Olson J, Fan X, Jose M, Safarova M, Radecki Breitkopf C, Winkler E, Kochan DC, Snipes S, Pacyna JE, Carney M, Chute CG, Gupta J, Jose S, Venner E, Murugan M, Jiang Y, Zordok M, Farwati M, Philogene M, Smith E, Shaibi GQ, Caraballo P, Freimuth R, Lindor NM, Sharp R, Thibodeau SN. The Return of Actionable Variants Empirical (RAVE) Study, a Mayo Clinic Genomic Medicine Implementation Study: Design and Initial Results. Mayo Clin Proc. 2018 Nov; 93 (11):1600-1610
    View PubMed
30. Pawliczek P, Patel RY, Ashmore LR, Jackson AR, Bizon C, Nelson T, Powell B, Freimuth RR, Strande N, Shah N, Paithankar S, Wright MW, Dwight S, Zhen J, Landrum M, McGarvey P, Babb L, Plon SE, Milosavljevic A, Clinical Genome (ClinGen) Resource. ClinGen Allele Registry links information about genetic variants. Hum Mutat. 2018 Nov; 39 (11):1690-1701
    View PubMed
31. Aronson S, Babb L, Ames D, Gibbs RA, Venner E, Connelly JJ, Marsolo K, Weng C, Williams MS, Hartzler AL, Liang WH, Ralston JD, Devine EB, Murphy S, Chute CG, Caraballo PJ, Kullo IJ, Freimuth RR, Rasmussen LV, Wehbe FH, Peterson JF, Robinson JR, Wiley K, Overby Taylor C, eMERGE Network EHRI Working Group. Empowering genomic medicine by establishing critical sequencing result data flows: the eMERGE example. J Am Med Inform Assoc. 2018 Oct 1; 25 (10):1375-1381
    View PubMed
32. Crump JK, Del Fiol G, Williams MS, Freimuth RR. Prototype of a Standards-Based EHR and Genetic Test Reporting Tool Coupled with HL7-Compliant Infobuttons. AMIA Jt Summits Transl Sci Proc. 2018; 2017:330-339 Epub 2018 May 18
    View PubMed
33. Luzum JA, Pakyz RE, Elsey AR, Haidar CE, Peterson JF, Whirl-Carrillo M, Handelman SK, Palmer K, Pulley JM, Beller M, Schildcrout JS, Field JR, Weitzel KW, Cooper-DeHoff RM, Cavallari LH, O'Donnell PH, Altman RB, Pereira N, Ratain MJ, Roden DM, Embi PJ, Sadee W, Klein TE, Johnson JA, Relling MV, Wang L, Weinshilboum RM, Shuldiner AR, Freimuth RR, Pharmacogenomics Research Network Translational Pharmacogenetics Program. The Pharmacogenomics Research Network Translational Pharmacogenetics Program: Outcomes and Metrics of Pharmacogenetic Implementations Across Diverse Healthcare Systems. Clin Pharmacol Ther. 2017 Sep; 102 (3):502-510 Epub 2017 June 09
    View PubMed
34. Rasmussen-Torvik LJ, Almoguera B, Doheny KF, Freimuth RR, Gordon AS, Hakonarson H, Hawkins JB, Husami A, Ivacic LC, Kullo IJ, Linderman MD, Manolio TA, Obeng AO, Pellegrino R, Prows CA, Ritchie MD, Smith ME, Stallings SC, Wolf WA, Zhang K, Scott SA. Concordance between Research Sequencing and Clinical Pharmacogenetic Genotyping in the eMERGE-PGx Study. J Mol Diagn. 2017 Jul; 19 (4):561-566 Epub 2017 May 11
    View PubMed
35. Caudle KE, Dunnenberger HM, Freimuth RR, Peterson JF, Burlison JD, Whirl-Carrillo M, Scott SA, Rehm HL, Williams MS, Klein TE, Relling MV, Hoffman JM. Standardizing terms for clinical pharmacogenetic test results: consensus terms from the Clinical Pharmacogenetics Implementation Consortium (CPIC). Genet Med. 2017 Feb; 19 (2):215-223 Epub 2016 July 21
    View PubMed
36. Min H, Turner S, de Coronado S, Davis B, Whetzel T, Freimuth RR, Solbrig HR, Kiefer R, Riben M, Stafford GA, Wright L, Ohira R.. Towards a Standard Ontology Metadata Model. International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016). CEUR Workshop Proceedings.10/1/2016;1747:
    
37. Tenenbaum JD, Avillach P, Benham-Hutchins M, Breitenstein MK, Crowgey EL, Hoffman MA, Jiang X, Madhavan S, Mattison JE, Nagarajan R, Ray B, Shin D, Visweswaran S, Zhao Z, Freimuth RR. An informatics research agenda to support precision medicine: seven key areas. J Am Med Inform Assoc. 2016 Jul; 23 (4):791-5 Epub 2016 Apr 23
    View PubMed
38. Hoffman JM, Dunnenberger HM, Kevin Hicks J, Caudle KE, Whirl Carrillo M, Freimuth RR, Williams MS, Klein TE, Peterson JF. Developing knowledge resources to support precision medicine: principles from the Clinical Pharmacogenetics Implementation Consortium (CPIC). J Am Med Inform Assoc. 2016 Jul; 23 (4):796-801 Epub 2016 Mar 28
    View PubMed
39. Aziz A, Kawamoto K, Eilbeck K, Williams MS, Freimuth RR, Hoffman MA, Rasmussen LV, Overby CL, Shirts BH, Hoffman JM, Welch BM. The genomic CDS sandbox: An assessment among domain experts. J Biomed Inform. 2016 Apr; 60:84-94 Epub 2016 Jan 15
    View PubMed
40. Wiley LK, Tarczy-Hornoch P, Denny JC, Freimuth RR, Overby CL, Shah N, Martin RD, Sarkar IN. Harnessing next-generation informatics for personalizing medicine: a report from AMIA's 2014 Health Policy Invitational Meeting. J Am Med Inform Assoc. 2016 Mar; 23 (2):413-9 Epub 2016 Feb 05
    View PubMed
41. Kalman LV, Agundez J, Appell ML, Black JL, Bell GC, Boukouvala S, Bruckner C, Bruford E, Caudle K, Coulthard SA, Daly AK, Del Tredici A, den Dunnen JT, Drozda K, Everts RE, Flockhart D, Freimuth RR, Gaedigk A, Hachad H, Hartshorne T, Ingelman-Sundberg M, Klein TE, Lauschke VM, Maglott DR, McLeod HL, McMillin GA, Meyer UA, Muller DJ, Nickerson DA, Oetting WS, Pacanowski M, Pratt VM, Relling MV, Roberts A, Rubinstein WS, Sangkuhl K, Schwab M, Scott SA, Sim SC, Thirumaran RK, Toji LH, Tyndale RF, van Schaik R, Whirl-Carrillo M, Yeo K, Zanger UM. Pharmacogenetic allele nomenclature: International workgroup recommendations for test result reporting. Clin Pharmacol Ther. 2016 Feb; 99 (2):172-85 Epub 2015 Nov 20
    View PubMed
42. Rasmussen LV, Overby CL, Connolly J, Chute CG, Denny JC, Freimuth RR, Hartzler AL, Holm IA, Manzi S, Pathak J, Peissig PL, Smith M, Williams MS, Shirts BH, Stoffel EM, Tarczy-Hornoch P, Rohrer Vitek CR, Wolf WA, Starren J. Practical considerations for implementing genomic information resources: Experiences from eMERGE and CSER: Experiences from eMERGE and CSER Applied Clinical Informatics. 2016; 7: (3)870-82.
    
43. Heale BSE, Overby CL, Del Fiol G, Rubinstein WS, Maglott DR, Nelson TH, Milosavljevic A, Martin CL, Goehringer SR, Freimuth RR, Williams MS. Integrating genomic resources with electronic health records using the hl7 infobutton standard Applied Clinical Informatics. 2016; 7: (3)817-31.
    
44. Tenenbaum JD, Madhavan S, Freimuth RR, Denny JC, Frey L. Translational bioinformatics 101 Pacific Symposium on Biocomputing 2016, PSB 2016. 2016; 552-6.
    
45. Shellum JL, Freimuth RR, Peters SG, Nishimura RA, Chaudhry R, Demuth SJ, Knopp AL, Miksch TA, Milliner DS. Knowledge as a Service at the Point of Care. AMIA Annu Symp Proc. 2016; 2016:1139-1148 Epub 2017 Feb 10
    View PubMed
46. Shirts BH, Salama JS, Aronson SJ, Chung WK, Gray SW, Hindorff LA, Jarvik GP, Plon SE, Stoffel EM, Tarczy-Hornoch PZ, Van Allen EM, Weck KE, Chute CG, Freimuth RR, Grundmeier RW, Hartzler AL, Li R, Peissig PL, Peterson JF, Rasmussen LV, Starren JB, Williams MS, Overby CL. CSER and eMERGE: current and potential state of the display of genetic information in the electronic health record. J Am Med Inform Assoc. 2015 Nov; 22 (6):1231-42 Epub 2015 July 03
    View PubMed
47. Samwald M, Minarro Gimenez JA, Boyce RD, Freimuth RR, Adlassnig KP, Dumontier M. Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies. BMC Med Inform Decis Mak. 2015 Feb 22; 15:12
    View PubMed
48. Linan MK, Sottara D, Freimuth RR. Creating Shareable Clinical Decision Support Rules for a Pharmacogenomics Clinical Guideline Using Structured Knowledge Representation. AMIA Annu Symp Proc. 2015; 2015:1985-94 Epub 2015 Nov 05
    View PubMed
49. Samwald M, Blagec K, Hofer S, Freimuth RR. Analyzing the potential for incorrect haplotype calls with different pharmacogenomic assays in different populations: a simulation based on 1000 Genomes data. Pharmacogenomics. 2015; 16 (15):1713-21 Epub 2015 Sept 30
    View PubMed
50. Herr TM, Bielinski SJ, Bottinger E, Brautbar A, Brilliant M, Chute CG, Denny J, Freimuth RR, Hartzler A, Kannry J, Kohane IS, Kullo IJ, Lin S, Pathak J, Peissig P, Pulley J, Ralston J, Rasmussen L, Roden D, Tromp G, Williams MS, Starren J. A conceptual model for translating omic data into clinical action. J Pathol Inform. 2015; 6:46 Epub 2015 Aug 31
    View PubMed
51. Martin MA, Hoffman JM, Freimuth RR, Klein TE, Dong BJ, Pirmohamed M, Hicks JK, Wilkinson MR, Haas DW, Kroetz DL, Clinical Pharmacogenetics Implementation Consortium. Clinical Pharmacogenetics Implementation Consortium Guidelines for HLA-B Genotype and Abacavir Dosing: 2014 update. Clin Pharmacol Ther. 2014 May; 95 (5):499-500 Epub 2014 Feb 21
    View PubMed
52. Caudle KE, Klein TE, Hoffman JM, Muller DJ, Whirl-Carrillo M, Gong L, McDonagh EM, Sangkuhl K, Thorn CF, Schwab M, Agundez JAG, Freimuth RR, Huser V, Lee MTM, Iwuchukwu OF, Crews KR, Scott SA, Wadelius M, Swen JJ, Tyndale RF, Stein CM, Roden D, Relling MV, Williams MS, Johnson SG. Incorporation of pharmacogenomics into routine clinical practice: the clinical pharmacogenetics implementation consortium (cpic) guideline development process. Current Drug Metabolism. 2014 Feb; 15(2):209-17.
    View PubMed
53. Bell GC, Crews KR, Wilkinson MR, Haidar CE, Hicks JK, Baker DK, Kornegay NM, Yang W, Cross SJ, Howard SC, Freimuth RR, Evans WE, Broeckel U, Relling MV, Hoffman JM. Development and use of active clinical decision support for preemptive pharmacogenomics. J Am Med Inform Assoc. 2014 Feb; 21(e1):e93-9. Epub 2013 Aug 26.
    View PubMed
54. Freimuth RR, Zhu Q, Pathak J, Chute CG. Simplifying complex clinical element models to encourage adoption. AMIA Jt Summits Transl Sci Proc. 2014; 2014:26-31 Epub 2014 Apr 07
    View PubMed
55. Overby CL, Rasmussen LV, Hartzler A, Connolly JJ, Peterson JF, Hedberg RE, Freimuth RR, Shirts BH, Denny JC, Larson EB, Chute CG, Jarvik GP, Ralston JD, Shuldiner AR, Starren J, Kullo IJ, Tarczy-Hornoch P, Williams MS. A Template for Authoring and Adapting Genomic Medicine Content in the eMERGE Infobutton Project. AMIA Annu Symp Proc. 2014; 2014:944-53 Epub 2014 Nov 14
    View PubMed
56. Freimuth RR, Wix K, Zhu Q, Siska M, Chute CG. Evaluation of RxNorm for Medication Clinical Decision Support. AMIA Annu Symp Proc. 2014; 2014:554-63 Epub 2014 Nov 14
    View PubMed
57. Bielinski SJ, Olson JE, Pathak J, Weinshilboum RM, Wang L, Lyke KJ, Ryu E, Targonski PV, Van Norstrand MD, Hathcock MA, Takahashi PY, McCormick JB, Johnson KJ, Maschke KJ, Rohrer Vitek CR, Ellingson MS, Wieben ED, Farrugia G, Morrisette JA, Kruckeberg KJ, Bruflat JK, Peterson LM, Blommel JH, Skierka JM, Ferber MJ, Black JL, Baudhuin LM, Klee EW, Ross JL, Veldhuizen TL, Schultz CG, Caraballo PJ, Freimuth RR, Chute CG, Kullo IJ. Preemptive genotyping for personalized medicine: design of the right drug, right dose, right time-using genomic data to individualize treatment protocol. Mayo Clin Proc. 2014 Jan; 89 (1):25-33
    View PubMed
58. Winham SJ, Freimuth RR, Biernacka JM. A Weighted Random Forests Approach to Improve Predictive Performance. Stat Anal Data Min. 2013 Dec 1; 6 (6):496-505
    View PubMed
59. Zhu Q, Freimuth RR, Pathak J, Durski MJ, Chute CG. Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL. J Biomed Inform. 2013 Aug; 46 (4):690-6 Epub 2013 May 29
    View PubMed
60. Shuldiner AR, Relling MV, Peterson JF, Hicks JK, Freimuth RR, Sadee W, Pereira NL, Roden DM, Johnson JA, Klein TE, Shuldiner AR, Vesely M, Robinson SW, Ambulos N Jr, Stass SA, Kelemen MD, Brown LA, Pollin TI, Beitelshees AL, Zhao RY, Pakyz RE, Palmer K, Alestock T, O'Neill C, Maloney K, Branham A, Sewell D, Relling MV, Crews K, Hoffman J, Cross S, Haidar C, Baker D, Hicks JK, Bell G, Greeson F, Gaur A, Reiss U, Huettel A, Cheng C, Gajjar A, Pappo A, Howard S, Hudson M, Pui CH, Jeha S, Evans WE, Broeckel U, Altman RB, Gong L, Whirl-Carrillo M, Klein TE, Sadee W, Manickam K, Sweet KM, Embi PJ, Roden D, Peterson J, Denny J, Schildcrout J, Bowton E, Pulley J, Beller M, Mitchell J, Danciu I, Price L, Pereira NL, Weinshilboum R, Wang L, Johnson JA, Nelson D, Clare-Salzler M, Elsey A, Burkley B, Langaee T, Liu F, Nessl D, Dong HJ, Lesko L, Freimuth RR, Chute CG, Pharmacogenomics Research Network Translational Pharmacogenetics Program Group. The Pharmacogenomics Research Network Translational Pharmacogenetics Program: overcoming challenges of real-world implementation. Clin Pharmacol Ther. 2013 Aug; 94 (2):207-10 Epub 2013 Mar 19
    View PubMed
61. Tao C, Jiang G, Oniki TA, Freimuth RR, Zhu Q, Sharma D, Pathak J, Huff SM, Chute CG. A semantic-web oriented representation of the clinical element model for secondary use of electronic health records data. J Am Med Inform Assoc. 2013 May 01; 20(3):554-62. Epub 2012 Dec 25.
    View PubMed
62. Zhu Q, Freimuth RR, Lian Z, Bauer S, Pathak J, Tao C, Durski MJ, Chute CG. Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: a case study. J Biomed Inform. 2013 Apr; 46 (2):286-93 Epub 2012 Nov 29
    View PubMed
63. Zhu Q, Freimuth RR, Pathak J, Chute CG. Using clinical element models for pharmacogenomic study data standardization. AMIA Jt Summits Transl Sci Proc. 2013; 2013:292-6 Epub 2013 Mar 18
    View PubMed
64. Zhu Q, Freimuth RR, Pathak J, Chute CG. PharmGKB Drug Data Normalization with NDF-RT. AMIA Jt Summits Transl Sci Proc. 2013; 2013:180 Epub 2013 Mar 18
    View PubMed
65. Kiefer RC, Freimuth RR, Chute CG, Pathak J. Mining Genotype-Phenotype Associations from Public Knowledge Sources via Semantic Web Querying. AMIA Jt Summits Transl Sci Proc. 2013; 2013:118-22 Epub 2013 Mar 18
    View PubMed
66. Boyce RD, Freimuth RR, Romagnoli KM, Pummer T, Hochheiser H, Empey PE. Toward semantic modeling of pharmacogenomic knowledge for clinical and translational decision support. AMIA Summits Transl Sci Proc. 2013; 2013:28-32. Epub 2013 Mar 18.
    View PubMed
67. Samwald M, Freimuth R, Luciano JS, Lin S, Powers RL, Marshall MS, Adlassnig KP, Dumontier M, Boyce RD. An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics. Stud Health Technol Inform. 2013; 192:539-42.
    View PubMed
68. Hassanzadeh O, Zhu Q, Freimuth R, Boyce R. Extending the "web of drug identity" with knowledge extracted from United States product labels. AMIA Jt Summits Transl Sci Proc. 2013; 2013:64-8 Epub 2013 Mar 18
    View PubMed
69. Freimuth RR, Freund ET, Schick L, Sharma MK, Stafford GA, Suzek BE, Hernandez J, Hipp J, Kelley JM, Rokicki K, Pan S, Buckler A, Stokes TH, Fernandez A, Fore I, Buetow KH, Klemm JD. Life sciences domain analysis model. J Am Med Inform Assoc. 2012 Nov-Dec; 19 (6):1095-102 Epub 2012 June 28
    View PubMed
70. Winham SJ, Colby CL, Freimuth RR, Wang X, de Andrade M, Huebner M, Biernacka JM. SNP interaction detection with Random Forests in high-dimensional genetic data. BMC Bioinformatics. 2012 Jul 15; 13:164 Epub 2012 July 15
    View PubMed
71. Pathak J, Kiefer R, Freimuth R, Chute C. Validation and discovery of genotype-phenotype associations in chronic diseases using linked data. Stud Health Technol Inform. 2012; 180:549-53
    View PubMed
72. Samwald M, Coulet A, Huerga I, Powers RL, Luciano JS, Freimuth RR, Whipple F, Pichler E, Prud'hommeaux E, Dumontier M, Marshall MS. Semantically enabling pharmacogenomic data for the realization of personalized medicine. Pharmacogenomics. 2012 Jan; 13(2):201-12.
    View PubMed
73. Pathak J, Weiss LC, Durski MJ, Zhu Q, Freimuth RR, Chute CG. Integrating VA's NDF-RT drug terminology with PharmGKB: preliminary results. Pac Symp Biocomput. 2012; 400-9
    View PubMed
74. Fridley BL, Jenkins G, Deyo-Svendsen ME, Hebbring S, Freimuth R. Utilizing genotype imputation for the augmentation of sequence data. PLoS One. 2010 Jun 8; 5 (6):e11018 Epub 2010 June 08
    View PubMed
75. Freimuth RR, Schauer MW, Lodha P, Govindrao P, Nagarajan R, Chute CG. caBIG compatibility review system: software to support the evaluation of applications using defined interoperability criteria. AMIA Annu Symp Proc. 2008 Nov 6; 197-201 Epub 2008 Nov 06
    View PubMed
76. Yu J, Freimuth RR, Culverhouse R, Marsh S, Watson MA, McLeod HL. DNA methylotype analysis in colorectal cancer. Oncol Rep. 2008 Oct; 20(4):921-7.
    View PubMed
77. Ryu EJ, Yang M, Gustin JA, Chang LW, Freimuth RR, Nagarajan R, Milbrandt J. Analysis of peripheral nerve expression profiles identifies a novel myelin glycoprotein, MP11. J Neurosci. 2008 Jul 23; 28(30):7563-73.
    View PubMed
78. Yu J, Mallon MA, Zhang W, Freimuth RR, Marsh S, Watson MA, Goodfellow PJ, McLeod HL. DNA repair pathway profiling and microsatellite instability in colorectal cancer. Clin Cancer Res. 2006 Sep 1; 12(17):5104-11.
    View PubMed
79. Freimuth RR, Xiao M, Marsh S, Minton M, Addleman N, Van Booven DJ, McLeod HL, Kwok PY. Polymorphism discovery in 51 chemotherapy pathway genes. Hum Mol Genet. 2005 Dec 1; 14(23):3595-603. Epub 2005 Oct 20.
    View PubMed
80. Freimuth RR, Stormo GD, McLeod HL. PolyMAPr: programs for polymorphism database mining, annotation, and functional analysis. Hum Mutat. 2005 Feb; 25(2):110-7.
    View PubMed
81. King CR, Yu J, Freimuth RR, McLeod HL, Marsh S. Interethnic variability of ERCC2 polymorphisms. Pharmacogenomics J. 2005; 5(1):54-9.
    View PubMed
82. Marsh S, Xiao M, Yu J, Ahluwalia R, Minton M, Freimuth RR, Kwok PY, McLeod HL. Pharmacogenomic assessment of carboxylesterases 1 and 2. Genomics. 2004 Oct; 84(4):661-8.
    View PubMed
83. Blanchard RL, Freimuth RR, Buck J, Weinshilboum RM, Coughtrie MW. A proposed nomenclature system for the cytosolic sulfotransferase (SULT) superfamily. Pharmacogenetics. 2004 Mar; 14(3):199-211.
    View PubMed
84. Freimuth RR, Ameyaw M-M, Pritchard SC, Kwok P-Y, McLeod HL. High-Throughput Genotyping Methods for Pharmacogenomic Studies. Current Pharmacogenomics. 2004; 2:21-33.
    
85. Freimuth RR, Wiepert M, Chute CG, Wieben ED, Weinshilboum RM. Human cytosolic sulfotransferase database mining: identification of seven novel genes and pseudogenes. Pharmacogenomics J. 2004; 4 (1):54-65
    View PubMed
86. Ahluwalia R, Freimuth R, McLeod HL, Marsh S. Use of pyrosequencing to detect clinically relevant polymorphisms in dihydropyrimidine dehydrogenase. Clin Chem. 2003 Oct; 49(10):1661-4.
    View PubMed
87. Xu ZH, Freimuth RR, Eckloff B, Wieben E, Weinshilboum RM. Human 3'-phosphoadenosine 5'-phosphosulfate synthetase 2 (PAPSS2) pharmacogenetics: gene resequencing, genetic polymorphisms and functional characterization of variant allozymes. Pharmacogenetics. 2002 Jan; 12 (1):11-21
    View PubMed
88. Thomae BA, Eckloff BW, Freimuth RR, Wieben ED, Weinshilboum RM. Human sulfotransferase SULT2A1 pharmacogenetics: genotype-to-phenotype studies. Pharmacogenomics J. 2002; 2 (1):48-56
    View PubMed
89. Freimuth RR, Eckloff B, Wieben ED, Weinshilboum RM. Human sulfotransferase SULT1C1 pharmacogenetics: gene resequencing and functional genomic studies. Pharmacogenetics. 2001 Dec; 11 (9):747-56
    View PubMed
90. Freimuth RR, Raftogianis RB, Wood TC, Moon E, Kim UJ, Xu J, Siciliano MJ, Weinshilboum RM. Human sulfotransferases SULT1C1 and SULT1C2: cDNA characterization, gene cloning, and chromosomal localization. Genomics. 2000 Apr 15; 65(2):157-65.
    View PubMed
91. Xu ZH, Otterness DM, Freimuth RR, Carlini EJ, Wood TC, Mitchell S, Moon E, Kim UJ, Xu JP, Siciliano MJ, Weinshilboum RM. Human 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 (PAPSS1) and PAPSS2: gene cloning, characterization and chromosomal localization. Biochem Biophys Res Commun. 2000 Feb 16; 268(2):437-44.
    View PubMed