Publications

  1. 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 2016 Jul 21 Epub 2016 July 21
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  2. 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
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  3. 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
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  4. 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
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  5. 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
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  6. 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.undberg 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 R, v Pharmacogenetic allele nomenclature: International workgroup recommendations for test result reporting. Clin Pharmacol Ther 2016 Feb; 99 (2):172-85 Epub 2015 Nov 20
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  7. 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. 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
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  8. 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; 15:12 Epub 2015 Feb 22
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  9. 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
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  10. 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
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  11. 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
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  12. Clinical Pharmacogenetics Implementation Consortium, Martin MA, Hoffman JM, Freimuth RR, Klein TE, Dong BJ, Pirmohamed M, Hicks JK, Wilkinson MR, Haas DW, Kroetz DL. 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
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  13. 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.
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  14. 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. 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.
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  15. 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. 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.
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  16. 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
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  17. 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
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  18. 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.
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  19. 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.
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  20. 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.
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  21. Shuldiner AR, Relling MV, Peterson JF, Hicks JK, Freimuth RR, Sadee W, Pereira NL, Roden DM, Johnson JA, Klein TE, Pharmacogenomics Research Network Translational Pharmacogenetics Program Group, 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. 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, et al. 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.
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  22. 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 1; 20(3):554-62. Epub 2012 Dec 25.
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  23. 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.
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  24. 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.
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  25. Hassanzadeh O, Zhu Q, Freimuth R, Boyce R. Extending the "web of drug identity" with knowledge extracted from United States product labels. AMIA Summits Transl Sci Proc. 2013; 2013:64-8. Epub 2013 Mar 18.
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  26. 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.
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  27. 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
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  28. 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
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  29. 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
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  30. 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 Jun 28.
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  31. 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.
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  32. 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.
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  33. 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.
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  34. Winham SJ, Colby CL, Freimuth RR, Wang X, de Andrade, Huebner M, Biernacka JM. SNP interaction detection with Random Forests in high-dimensional genetic data. BMC Bioinformatics. 2012; 13:164. Epub 2012 Jul 15
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  35. Fridley BL, Jenkins G, Deyo-Svendsen ME, Hebbring S, Freimuth R. Utilizing genotype imputation for the augmentation of sequence data. PLoS One. 2010; 5(6):e11018. Epub 2010 Jun 08.
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  36. 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.
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  37. 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.
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  38. 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; 197-201. Epub 2008 Nov 06.
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  39. 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.
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  40. 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.
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  41. Freimuth RR, Stormo GD, McLeod HL. PolyMAPr: programs for polymorphism database mining, annotation, and functional analysis. Hum Mutat. 2005 Feb; 25(2):110-7.
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  42. King CR, Yu J, Freimuth RR, McLeod HL, Marsh S. Interethnic variability of ERCC2 polymorphisms. Pharmacogenomics J. 2005; 5(1):54-9.
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  43. 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.
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  44. 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.
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  45. 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.
  46. 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.
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  47. 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.
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  48. 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.
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  49. 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.
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  50. 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.
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  51. 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.
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  52. 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.
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