Biomedical and Translational Informatics Laboratory

Publications - 2016

  • Hall MA, Moore JH, Ritchie MD. Embracing Complex Associations in Common Traits: Critical Considerations for Precision Medicine. Trends Genet. 2016 Aug;32(8):470-84. doi: 10.1016/j.tig.2016.06.001. Review. PMID: 27392675
  • van 't Hof FN, Ruigrok YM, Lee CH, Ripke S, Anderson G, de Andrade M, Baas AF, Blankensteijn JD, Böttinger EP, Bown MJ, Broderick J, Bijlenga P, Carrell DS, Crawford DC, Crosslin DR, Ebeling C, Eriksson JG, Fornage M, Foroud T, von Und Zu Fraunberg M, Friedrich CM, Gaál EI, Gottesman O, Guo DC, Harrison SC, Hernesniemi J, Hofman A, Inoue I, Jääskeläinen JE, Jones GT, Kiemeney LA, Kivisaari R, Ko N, Koskinen S, Kubo M, Kullo IJ, Kuivaniemi H, Kurki MI, Laakso A, Lai D, Leal SM, Lehto H, LeMaire SA, Low SK, Malinowski J, McCarty CA, Milewicz DM, Mosley TH, Nakamura Y, Nakaoka H, Niemelä M, Pacheco J, Peissig PL, Pera J, Rasmussen-Torvik L, Ritchie MD, Rivadeneira F, van Rij AM, Santos-Cortez RL, Saratzis A, Slowik A, Takahashi A, Tromp G, Uitterlinden AG, Verma SS, Vermeulen SH, Wang GT; Aneurysm Consortium; Vascular Research Consortium of New Zealand., Han B, Rinkel GJ, de Bakker PI. Shared Genetic Risk Factors of Intracranial, Abdominal, and Thoracic Aneurysms. J Am Heart Assoc. 2016 Jul 14;5(7). pii: e002603. doi: 10.1161/JAHA.115.002603. PMID: 2741816, PMCID: PMC5015357 
  • Verma A, Basile AO, Bradford Y, Kuivaniemi H, Tromp G, Carey D, Gerhard GS, Crowe JE Jr, Ritchie MD, Pendergrass SA. Phenome-Wide Association Study to Explore Relationships between Immune System Related Genetic Loci and Complex Traits and Diseases. PLoS One. 2016 Aug 10;11(8):e0160573. doi: 10.1371/journal.pone.0160573. PMID: 27508393, PMCID: PMC4980020 
  • Verma A, Verma SS, Pendergrass SA, Crawford DC, Crosslin DR, Kuivaniemi H, Bush WS, Bradford Y, Kullo I, Bielinski SJ, Li R, Denny JC, Peissig P, Hebbring S, De Andrade M, Ritchie MD, Tromp G. eMERGE Phenome-Wide Association Study (PheWAS) identifies clinical associations and pleiotropy for stop-gain variants. BMC Med Genomics. 2016 Aug 12;9 Suppl 1:32. doi: 10.1186/s12920-016-0191-8. PMID: 27535653, PMCID: PMC4989894 
  • Moore CC, Basile AO, Wallace JR, Frase AT, Ritchie MD. A biologically informed method for detecting rare variant associations. BioData Min. 2016 Aug 30;9(1):27. doi: 10.1186/s13040-016-0107-3. PMID: 27582876, PMCID: PMC5006419
  • Verma SS, Cooke Bailey JN, Lucas A, Bradford Y, Linneman JG, Hauser MA, Pasquale LR, Peissig PL, Brilliant MH, McCarty CA, Haines JL, Wiggs JL, Vrabec TR, Tromp G, Ritchie MD; eMERGE Network.; NEIGHBOR Consortium. Epistatic Gene-Based Interaction Analyses for Glaucoma in eMERGE and NEIGHBOR Consortium. PLoS Genet. 2016 Sep 13;12(9):e1006186. doi: 10.1371/journal.pgen.1006186. PMID: 27623284, PMCID: PMC5021356
  • Verma SS, Lucas AM, Lavage DR, Leader JB, Metpally R, Krishnamurthy S, Dewey F, Borecki I, Lopez A, Overton J, Penn J, Reid J, Pendergrass SA, Breitwieser G, Ritchie MD. IDENTIFYING GENETIC ASSOCIATIONS WITH VARIABILITY IN METABOLIC HEALTH AND BLOOD COUNT LABORATORY VALUES: DIVING INTO THE QUANTITATIVE TRAITS BY LEVERAGING LONGITUDINAL DATA FROM AN EHR. Pac Symp Biocomput. 2016;22:533-544. PMID: 27897004
  • Dewey FE, Murray MF, Overton JD, Habegger L, Leader JB, Fetterolf SN, O'Dushlaine C, Van Hout CV, Staples J, Gonzaga-Jauregui C, Metpally R, Pendergrass SA, Giovanni MA, Kirchner HL, Balasubramanian S, Abul-Husn NS, Hartzel DN, Lavage DR, Kost KA, Packer JS, Lopez AE, Penn J, Mukherjee S, Gosalia N, Kanagaraj M, Li AH, Mitnaul LJ, Adams LJ, Person TN, Praveen K, Marcketta A, Lebo MS, Austin-Tse CA, Mason-Suares HM, Bruse S, Mellis S, Phillips R, Stahl N, Murphy A, Economides A, Skelding KA, Still CD, Elmore JR, Borecki IB, Yancopoulos GD, Davis FD, Faucett WA, Gottesman O, Ritchie MD, Shuldiner AR, Reid JG, Ledbetter DH, Baras A, Carey DJ. Distribution and clinical impact of functional variants in 50,726 whole-exome sequences from the DiscovEHR study. Science. 2016 Dec 23;354(6319). pii: aaf6814. doi: 10.1126/science.aaf6814. PMID: 28008009
  • Abul-Husn NS, Manickam K, Jones LK, Wright EA, Hartzel DN, Gonzaga-Jauregui C, O'Dushlaine C, Leader JB, Lester Kirchner H, Lindbuchler DM, Barr ML, Giovanni MA, Ritchie MD, Overton JD, Reid JG, Metpally RP, Wardeh AH, Borecki IB, Yancopoulos GD, Baras A, Shuldiner AR, Gottesman O, Ledbetter DH, Carey DJ, Dewey FE, Murray MF. Genetic identification of familial hypercholesterolemia within a single U.S. health care system. Science. 2016 Dec 23;354(6319). pii: aaf7000. doi: 10.1126/science.aaf7000. PMID: 28008010
  • Kim D, Li R, Lucas A, Verma SS, Dudek SM, Ritchie MD. Using knowledge-driven genomic interactions for multi-omics data analysis: metadimensional models for predicting clinical outcomes in ovarian carcinoma. J Am Med Inform Assoc. 2016 Dec 31. pii: ocw165. doi: 10.1093/jamia/ocw165. [Epub ahead of print] PMID: 28040685, PMCID: PMC5391734
  • Van Driest SL, Wells QS, Stallings S, Bush WS, Gordon A, Nickerson DA, Kim JH, Crosslin DR, Jarvik GP, Carrell DS, Ralston JD, Larson EB, Bielinski SJ, Olson JE, Ye Z, Kullo IJ, Abul-Husn NS, Scott SA, Bottinger E, Almoguera B, Connolly J, Chiavacci R, Hakonarson H, Rasmussen-Torvik LJ, Pan V, Persell SD, Smith M, Chisholm RL, Kitchner TE, He MM, Brilliant MH, Wallace JR, Doheny KF, Shoemaker MB, Li R, Manolio TA, Callis TE, Macaya D, Williams MS, Carey D, Kapplinger JD, Ackerman MJ, Ritchie MD, Denny JC, Roden DM. Association of Arrhythmia-Related Genetic Variants With Phenotypes Documented in Electronic Medical Records. JAMA. 2016 Jan 5;315(1):47-57. doi: 10.1001/jama.2015.17701. PubMed PMID: 26746457; PubMed Central PMCID: PMC4758131.
  • Verma SS, Frase AT, Verma A, Pendergrass SA, Mahony S, Haas DW, Ritchie MD. PHENOME-WIDE INTERACTION STUDY (PheWIS) IN AIDS CLINICAL TRIALS GROUP DATA (ACTG). Pac Symp Biocomput. 2016;21:57-68. PubMed PMID: 26776173; PubMed Central PMCID: PMC4722952.
  • Verma A, Leader JB, Verma SS, Frase A, Wallace J, Dudek S, Lavage DR, Van Hout CV, Dewey FE, Penn J, Lopez A, Overton JD, Carey DJ, Ledbetter DH, Kirchner HL, Ritchie MD, Pendergrass SA. INTEGRATING CLINICAL LABORATORY MEASURES AND ICD-9 CODE DIAGNOSES IN PHENOME-WIDE ASSOCIATION STUDIES. Pac Symp Biocomput. 2016;21:168-79. PubMed PMID: 26776183; PubMed Central PMCID: PMC4718547.
  • Basile AO, Wallace JR, Peissig P, McCarty CA, Brilliant M, Ritchie MD. KNOWLEDGE DRIVEN BINNING AND PHEWAS ANALYSIS IN MARSHFIELD PERSONALIZED MEDICINE RESEARCH PROJECT USING BIOBIN. Pac Symp Biocomput. 2016;21:249-60. PubMed PMID: 26776191; PubMed Central PMCID: PMC4824557.
  • Kim D, Lucas A, Glessner J, Verma SS, Bradford Y, Li R, Frase AT, Hakonarson H, Peissig P, Brilliant M, Ritchie MD. BIOFILTER AS A FUNCTIONAL ANNOTATION PIPELINE FOR COMMON AND RARE COPY NUMBER BURDEN. Pac Symp Biocomput. 2016;21:357-68. PubMed PMID: 26776200; PubMed Central PMCID: PMC4722964.
  • Hohman TJ, Bush WS, Jiang L, Brown-Gentry KD, Torstenson ES, Dudek SM, Mukherjee S, Naj A, Kunkle BW, Ritchie MD, Martin ER, Schellenberg GD, Mayeux R, Farrer LA, Pericak-Vance MA, Haines JL, Thornton-Wells TA; Alzheimer's Disease Genetics Consortium. Discovery of gene-gene interactions across multiple independent data sets of late onset Alzheimer disease from the Alzheimer Disease Genetics Consortium. Neurobiol Aging. 2016 Feb;38:141-50. doi: 10.1016/j.neurobiolaging.2015.10.031. Epub 2015 Nov 6. PubMed PMID: 26827652; PubMed Central PMCID: PMC4735733.
  • Bush WS, Crosslin DR, Obeng AO, Wallace J, Almoguera B, Basford MA, Bielinski SJ, Carrell DS, Connolly JJ, Crawford D, Doheny KF, Gallego CJ, Gordon AS, Keating B, Kirby J, Kitchner T, Manzi S, Mejia AR, Pan V, Perry CL, Peterson JF, Prows CA, Ralston J, Scott SA, Scrol A, Smith M, Stallings SC, Veldhuizen T, Wolf W, Volpi S, Wiley K, Li R, Manolio T, Bottinger E, Brilliant MH, Carey D, Chisholm RL, Chute CG, Haines JL, Hakonarson H, Harley JB, Holm IA, Kullo IJ, Jarvik GP, Larson EB, McCarty CA, Williams MS, Denny JC, Rasmussen-Torvik LJ, Roden DM, Ritchie MD. Genetic Variation among 82 Pharmacogenes: the PGRN-Seq data from the eMERGE Network. Clin Pharmacol Ther. 2016 Feb 9. doi: 10.1002/cpt.350. [Epub ahead of print] PubMed PMID: 26857349.
  • Simonti CN, Vernot B, Bastarache L, Bottinger E, Carrell DS, Chisholm RL, Crosslin DR, Hebbring SJ, Jarvik GP, Kullo IJ, Li R, Pathak J, Ritchie MD, Roden DM, Verma SS, Tromp G, Prato JD, Bush WS, Akey JM, Denny JC, Capra JA. The phenotypic legacy of admixture between modern humans and Neandertals. Science. 2016 Feb 12;351(6274):737-41. doi: 10.1126/science.aad2149. PubMed PMID: 26912863; PubMed Central PMCID: PMC4849557.
  • Dewey FE, Gusarova V, O'Dushlaine C, Gottesman O, Trejos J, Hunt C, Van Hout CV, Habegger L, Buckler D, Lai KM, Leader JB, Murray MF, Ritchie MD, Kirchner HL, Ledbetter DH, Penn J, Lopez A, Borecki IB, Overton JD, Reid JG, Carey DJ, Murphy AJ, Yancopoulos GD, Baras A, Gromada J, Shuldiner AR. Inactivating Variants in ANGPTL4 and Risk of Coronary Artery Disease. N Engl J Med. 2016 Mar 24;374(12):1123-33. doi: 10.1056/NEJMoa1510926. Epub 2016 Mar 2. PubMed PMID: 26933753; PubMed Central PMCID: PMC4900689.
  • Williams MS, Ritchie MD, Payne PR. Interdisciplinary training to build an informatics workforce for precision medicine. Appl Transl Genom. 2015 Aug 4;6:28-30. doi: 10.1016/j.atg.2015.07.003. eCollection 2015 Sep. PubMed PMID: 27054076; PubMed Central PMCID: PMC4803783.
  • Butkiewicz M, Cooke Bailey JN, Frase A, Dudek S, Yaspan BL, Ritchie MD, Pendergrass SA, Haines JL. Pathway analysis by randomization incorporating structure-PARIS: an update. Bioinformatics. 2016 Mar 7. pii: btw130. [Epub ahead of print] PubMed PMID: 27153576.
  • Li R, Dudek SM, Kim D, Hall MA, Bradford Y, Peissig PL, Brilliant MH, Linneman JG, McCarty CA, Bao L, Ritchie MD. Identification of genetic interaction networks via an evolutionary algorithm evolved Bayesian network. BioData Min. 2016 May 10;9:18. doi: 10.1186/s13040-016-0094-4. eCollection 2016. PubMed PMID: 27168765; PubMed Central PMCID: PMC4862166.
  • Oetjens MT, Bush WS, Denny JC, Birdwell K, Kodaman N, Verma A, Dilks HH, Pendergrass SA, Ritchie MD, Crawford DC. Evidence for extensive pleiotropy among pharmacogenes. Pharmacogenomics. 2016 Jun;17(8):853-66. doi: 10.2217/pgs-2015-0007. Epub 2016 Jun 1. PubMed PMID: 27249515.

Publications