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Northwestern University Feinberg School of Medicine
Rex Chisholm Lab

Publications

  1. Manolio TA, Narula J, Rupert A, Bult CJ, Chisholm RL, Ginsburg GS, Green ED, Hooker G, Jarvik GP, Mensah GA  et al.  Genomic medicine year in review: 2024.  Am J Hum Genet  2024 Dec 05;111(12):2585-2588. doi:10.1016/j.ajhg.2024.11.002
  2. Fakhari H, Scherr CL, Moe S, Hoell C, Smith ME, Rasmussen-Torvik LJ, Chisholm RL, McNally EM  From Calculation to Communication: Using Risk Score Calculators to Inform Clinical Decision Making and Facilitate Patient Engagement.  Med Decis Making  2024 Nov;44(8):900-913. doi:10.1177/0272989X241285036
  3. Luo Y, Mao C, Sanchez-Pinto LN, Ahmad FS, Naidech A, Rasmussen L, Pacheco JA, Schneider D, Mithal LB, Dresden S  et al.  Northwestern University resource and education development initiatives to advance collaborative artificial intelligence across the learning health system.  Learn Health Syst  2024 Jul;8(3):e10417. pii:e10417
  4. Lewis ACF, Chisholm RL, Connolly JJ, Esplin ED, Glessner J, Gordon A, Green RC, Hakonarson H, Harr M, Holm IA  et al.  Managing differential performance of polygenic risk scores across groups: Real-world experience of the eMERGE Network.  Am J Hum Genet  2024 Jun 06;111(6):999-1005. doi:10.1016/j.ajhg.2024.04.005
  5. Manolio TA, Narula J, Bult CJ, Chisholm RL, Deverka PA, Ginsburg GS, Green ED, Hooker G, Jarvik GP, Mensah GA  et al.  Genomic medicine year in review: 2023.  Am J Hum Genet  2023 Dec 07;110(12):1992-1995. doi:10.1016/j.ajhg.2023.11.001
  6. Linder JE, Tao R, Chung WK, Kiryluk K, Liu C, Weng C, Connolly JJ, Hakonarson H, Harr M, Leppig KA  et al.  Prospective, multi-site study of healthcare utilization after actionable monogenic findings from clinical sequencing.  Am J Hum Genet  2023 Nov 02;110(11):1950-1958. doi:10.1016/j.ajhg.2023.10.006
  7. Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP  et al.  Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets.  Nat Commun  2023 Sep 27;14(1):6030. pii:6030
  8. Connolly JJ, Berner ES, Smith M, Levy S, Terek S, Harr M, Karavite D, Suckiel S, Holm IA, Dufendach K  et al.  Education and electronic medical records and genomics network, challenges, and lessons learned from a large-scale clinical trial using polygenic risk scores.  Genet Med  2023 Sep;25(9):100906. doi:10.1016/j.gim.2023.100906
  9. Joo YY, Pacheco JA, Thompson WK, Rasmussen-Torvik LJ, Rasmussen LV, Lin FTJ, Andrade M, Borthwick KM, Bottinger E, Cagan A  et al.  Multi-ancestry genome- and phenome-wide association studies of diverticular disease in electronic health records with natural language processing enriched phenotyping algorithm.  PLoS One  2023;18(5):e0283553. pii:e0283553
  10. Linder JE, Allworth A, Bland HT, Caraballo PJ, Chisholm RL, Clayton EW, Crosslin DR, Dikilitas O, DiVietro A, Esplin ED  et al.  Returning integrated genomic risk and clinical recommendations: The eMERGE study.  Genet Med  2023 Apr;25(4):100006. doi:10.1016/j.gim.2023.100006
  11. Manolio TA, Narula J, Bult CJ, Chisholm RL, Deverka PA, Ginsburg GS, Goldrich M, Green ED, Jarvik GP, Mensah GA  et al.  Genomic Medicine Year in Review: 2022.  Am J Hum Genet  2022 Dec 01;109(12):2101-2104. doi:10.1016/j.ajhg.2022.11.003
  12. Banday AR, Stanifer ML, Florez-Vargas O, Onabajo OO, Papenberg BW, Zahoor MA, Mirabello L, Ring TJ, Lee CH, Albert PS  et al.  Genetic regulation of OAS1 nonsense-mediated decay underlies association with COVID-19 hospitalization in patients of European and African ancestries.  Nat Genet  2022 Aug;54(8):1103-1116. doi:10.1038/s41588-022-01113-z
  13. Weiss J, Hockberger P, Shamaly T, Rosen A, Lewandosky L, Chisholm RL  NUcore at 10: A Decade of Experience Developing a Core Facilities Management Application.  J Biomol Tech  2021 Dec 15;32(4). pii:3fc1f5fe.3a4b405c
  14. Manolio TA, Bult CJ, Chisholm RL, Deverka PA, Ginsburg GS, Goldrich M, Jarvik GP, Mensah GA, Ramos EM, Relling MV  et al.  Genomic medicine year in review: 2021.  Am J Hum Genet  2021 Dec 02;108(12):2210-2214. doi:10.1016/j.ajhg.2021.11.006
  15. Chisholm RL  Is genetic ancestry a tool to combat health disparities?  Cell  2021 Apr 15;184(8):1964-1965. doi:10.1016/j.cell.2021.03.038
  16. Manolio TA, Bult CJ, Chisholm RL, Deverka PA, Ginsburg GS, Goldrich M, Jarvik GP, Mensah GA, Relling MV, Roden DM  et al.  Genomic Medicine Year in Review: 2020.  Am J Hum Genet  2020 Dec 03;107(6):1007-1010. doi:10.1016/j.ajhg.2020.11.005
  17. Joo YY, Actkins K, Pacheco JA, Basile AO, Carroll R, Crosslin DR, Day F, Denny JC, Velez Edwards DR, Hakonarson H  et al.  A Polygenic and Phenotypic Risk Prediction for Polycystic Ovary Syndrome Evaluated by Phenome-Wide Association Studies.  J Clin Endocrinol Metab  2020 Jun 01;105(6):1918-36. pii:dgz326
  18. Manolio TA, Bult CJ, Chisholm RL, Deverka PA, Ginsburg GS, Jarvik GP, McLeod HL, Mensah GA, Relling MV, Roden DM  et al.  Genomic Medicine Year in Review: 2019.  Am J Hum Genet  2019 Dec 05;105(6):1072-1075. doi:10.1016/j.ajhg.2019.11.006
  19. Manolio TA, Rowley R, Williams MS, Roden D, Ginsburg GS, Bult C, Chisholm RL, Deverka PA, McLeod HL, Mensah GA  et al.  Opportunities, resources, and techniques for implementing genomics in clinical care.  Lancet  2019 Aug 10;394(10197):511-520. doi:10.1016/S0140-6736(19)31140-7
  20. Rasmussen LV, Smith ME, Almaraz F, Persell SD, Rasmussen-Torvik LJ, Pacheco JA, Chisholm RL, Christensen C, Herr TM, Wehbe FH  et al.  An ancillary genomics system to support the return of pharmacogenomic results.  J Am Med Inform Assoc  2019 Apr 01;26(4):306-310. doi:10.1093/jamia/ocy187
  21. Fey P, Dodson RJ, Basu S, Hartline EC, Chisholm RL  dictyBase and the Dicty Stock Center (version 2.0) - a progress report.  Int J Dev Biol  2019;63(8-9-10):563-572. doi:10.1387/ijdb.190226pf
  22. Volpi S, Bult CJ, Chisholm RL, Deverka PA, Ginsburg GS, Jacob HJ, Kasapi M, McLeod HL, Roden DM, Williams MS  et al.  Research Directions in the Clinical Implementation of Pharmacogenomics: An Overview of US Programs and Projects.  Clin Pharmacol Ther  2018 May;103(5):778-786. doi:10.1002/cpt.1048
  23. Nadkarni GN, Galarneau G, Ellis SB, Nadukuru R, Zhang J, Scott SA, Schurmann C, Li R, Rasmussen-Torvik LJ, Kho AN  et al.  Apolipoprotein L1 Variants and Blood Pressure Traits in African Americans.  J Am Coll Cardiol  2017 Mar 28;69(12):1564-1574. doi:10.1016/j.jacc.2017.01.040
  24. Manolio TA, Fowler DM, Starita LM, Haendel MA, MacArthur DG, Biesecker LG, Worthey E, Chisholm RL, Green ED, Jacob HJ  et al.  Bedside Back to Bench: Building Bridges between Basic and Clinical Genomic Research.  Cell  2017 Mar 23;169(1):6-12. doi:10.1016/j.cell.2017.03.005
  25. Dumitrescu L, Ritchie MD, Denny JC, El Rouby NM, McDonough CW, Bradford Y, Ramirez AH, Bielinski SJ, Basford MA, Chai HS  et al.  Genome-wide study of resistant hypertension identified from electronic health records.  PLoS One  2017;12(2):e0171745. pii:e0171745
  26. Bush WS, Crosslin DR, Owusu-Obeng A, Wallace J, Almoguera B, Basford MA, Bielinski SJ, Carrell DS, Connolly JJ, Crawford D  et al.  Genetic variation among 82 pharmacogenes: The PGRNseq data from the eMERGE network.  Clin Pharmacol Ther  2016 Aug;100(2):160-9. doi:10.1002/cpt.350
  27. Mosley JD, Shaffer CM, Van Driest SL, Weeke PE, Wells QS, Karnes JH, Velez Edwards DR, Wei WQ, Teixeira PL, Bastarache L  et al.  A genome-wide association study identifies variants in KCNIP4 associated with ACE inhibitor-induced cough.  Pharmacogenomics J  2016 Jun;16(3):231-7. doi:10.1038/tpj.2015.51
  28. Simonti CN, Vernot B, Bastarache L, Bottinger E, Carrell DS, Chisholm RL, Crosslin DR, Hebbring SJ, Jarvik GP, Kullo IJ  et al.  The phenotypic legacy of admixture between modern humans and Neandertals.  Science  2016 Feb 12;351(6274):737-41. doi:10.1126/science.aad2149
  29. Van Driest SL, Wells QS, Stallings S, Bush WS, Gordon A, Nickerson DA, Kim JH, Crosslin DR, Jarvik GP, Carrell DS  et al.  Association of Arrhythmia-Related Genetic Variants With Phenotypes Documented in Electronic Medical Records.  JAMA  2016 Jan 05;315(1):47-57. doi:10.1001/jama.2015.17701
  30. Burton PR, Murtagh MJ, Boyd A, Williams JB, Dove ES, Wallace SE, Tassé AM, Little J, Chisholm RL, Gaye A  et al.  Data Safe Havens in health research and healthcare.  Bioinformatics  2015 Oct 15;31(20):3241-8. doi:10.1093/bioinformatics/btv279
  31. Basu S, Fey P, Jimenez-Morales D, Dodson RJ, Chisholm RL  dictyBase 2015: Expanding data and annotations in a new software environment.  Genesis  2015 Aug;53(8):523-534. doi:10.1002/dvg.22867
  32. Manolio TA, Abramowicz M, Al-Mulla F, Anderson W, Balling R, Berger AC, Bleyl S, Chakravarti A, Chantratita W, Chisholm RL  et al.  Global implementation of genomic medicine: We are not alone.  Sci Transl Med  2015 Jun 03;7(290):290ps13. doi:10.1126/scitranslmed.aab0194
  33. Malinowski JR, Denny JC, Bielinski SJ, Basford MA, Bradford Y, Peissig PL, Carrell D, Crosslin DR, Pathak J, Rasmussen L  et al.  Genetic variants associated with serum thyroid stimulating hormone (TSH) levels in European Americans and African Americans from the eMERGE Network.  PLoS One  2014;9(12):e111301. pii:e111301
  34. Rasmussen-Torvik LJ, Stallings SC, Gordon AS, Almoguera B, Basford MA, Bielinski SJ, Brautbar A, Brilliant MH, Carrell DS, Connolly JJ  et al.  Design and anticipated outcomes of the eMERGE-PGx project: a multicenter pilot for preemptive pharmacogenomics in electronic health record systems.  Clin Pharmacol Ther  2014 Oct;96(4):482-9. doi:10.1038/clpt.2014.137
  35. Jeff JM, Armstrong LL, Ritchie MD, Denny JC, Kho AN, Basford MA, Wolf WA, Pacheco JA, Li R, Chisholm RL  et al.  Admixture mapping and subsequent fine-mapping suggests a biologically relevant and novel association on chromosome 11 for type 2 diabetes in African Americans.  PLoS One  2014;9(3):e86931. pii:e86931
  36. Jeff JM, Brown-Gentry K, Goodloe R, Ritchie MD, Denny JC, Kho AN, Armstrong LL, McClellan B, Mayo P, Allen M  et al.  Replication of SCN5A Associations with Electrocardio-graphic Traits in African Americans from Clinical and Epidemiologic Studies.  Evol Comput Mach Learn Data Min Bioinform  2014;2014:939-951
  37. Chisholm RL  The opportunities and challenges of implementing genomics-informed personalized medicine.  Clin Pharmacol Ther  2013 Aug;94(2):181-2. doi:10.1038/clpt.2013.71
  38. Chisholm RL  At the Interface between Medical Informatics and Personalized Medicine: The eMERGE Network Experience.  Healthc Inform Res  2013 Jun;19(2):67-8. doi:10.4258/hir.2013.19.2.67
  39. Fey P, Dodson RJ, Basu S, Chisholm RL  One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012.  Methods Mol Biol  2013;983:59-92. doi:10.1007/978-1-62703-302-2_4
  40. Basu S, Fey P, Pandit Y, Dodson R, Kibbe WA, Chisholm RL  DictyBase 2013: integrating multiple Dictyostelid species.  Nucleic Acids Res  2013 Jan;41(Database issue):D676-83. doi:10.1093/nar/gks1064
  41. Rasmussen-Torvik LJ, Pacheco JA, Wilke RA, Thompson WK, Ritchie MD, Kho AN, Muthalagu A, Hayes MG, Armstrong LL, Scheftner DA  et al.  High density GWAS for LDL cholesterol in African Americans using electronic medical records reveals a strong protective variant in APOE.  Clin Transl Sci  2012 Oct;5(5):394-9. doi:10.1111/j.1752-8062.2012.00446.x
  42. Kho AN, Hayes MG, Rasmussen-Torvik L, Pacheco JA, Thompson WK, Armstrong LL, Denny JC, Peissig PL, Miller AW, Wei WQ  et al.  Use of diverse electronic medical record systems to identify genetic risk for type 2 diabetes within a genome-wide association study.  J Am Med Inform Assoc  2012;19(2):212-8. doi:10.1136/amiajnl-2011-000439
  43. Kowal AS, Chisholm RL  Uncovering a role for the tail of the Dictyostelium discoideum SadA protein in cell-substrate adhesion.  Eukaryot Cell  2011 May;10(5):662-71. doi:10.1128/EC.00221-10
  44. Kho AN, Pacheco JA, Peissig PL, Rasmussen L, Newton KM, Weston N, Crane PK, Pathak J, Chute CG, Bielinski SJ  et al.  Electronic medical records for genetic research: results of the eMERGE consortium.  Sci Transl Med  2011 Apr 20;3(79):79re1. doi:10.1126/scitranslmed.3001807
  45. Gaudet P, Fey P, Basu S, Bushmanova YA, Dodson R, Sheppard KA, Just EM, Kibbe WA, Chisholm RL  dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa.  Nucleic Acids Res  2011 Jan;39(Database issue):D620-4. doi:10.1093/nar/gkq1103
  46. Ormond KE, Cirino AL, Helenowski IB, Chisholm RL, Wolf WA  Assessing the understanding of biobank participants.  Am J Med Genet A  2009 Feb;149A(2):188-98. doi:10.1002/ajmg.a.32635
  47. Gaudet P, Lane L, Fey P, Bridge A, Poux S, Auchincloss A, Axelsen K, Braconi Quintaje S, Boutet E, Brown P  et al.  Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase.  Database (Oxford)  2009;2009:bap016. pii:bap016
  48. Fey P, Gaudet P, Curk T, Zupan B, Just EM, Basu S, Merchant SN, Bushmanova YA, Shaulsky G, Kibbe WA  et al.  dictyBase--a Dictyostelium bioinformatics resource update.  Nucleic Acids Res  2009 Jan;37(Database issue):D515-9. doi:10.1093/nar/gkn844
  49. Gaudet P, Williams JG, Fey P, Chisholm RL  An anatomy ontology to represent biological knowledge in Dictyostelium discoideum.  BMC Genomics  2008 Mar 18;9:130. doi:10.1186/1471-2164-9-130
  50. Pilcher KE, Gaudet P, Fey P, Kowal AS, Chisholm RL  A general purpose method for extracting RNA from Dictyostelium cells.  Nat Protoc  2007;2(6):1329-32