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Ramy Arnaout, M.D., Ph.D.

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  1. K08AI114958 (ARNAOUT, RAMY) Jan 1, 2015 - Dec 31, 2019
    NIH/NIAID
    Demographics Causes and Consequences of B Cell Repertoire Diversity
    Role: Principal Investigator

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Arnaout R. Machine Learning in Clinical Pathology: Seeing the Forest for the Trees. Clin Chem. 2018 Nov; 64(11):1553-1554. PMID: 30237151.
    Citations:    Fields:    
  2. Krishnan V, Stoppel DC, Nong Y, Johnson MA, Nadler MJ, Ozkaynak E, Teng BL, Nagakura I, Mohammad F, Silva MA, Peterson S, Cruz TJ, Kasper EM, Arnaout R, Anderson MP. Autism gene Ube3a and seizures impair sociability by repressing VTA Cbln1. Nature. 2017 03 23; 543(7646):507-512. PMID: 28297715.
    Citations: 10     Fields:    Translation:AnimalsCells
  3. Kaplinsky J, Arnaout R. Robust estimates of overall immune-repertoire diversity from high-throughput measurements on samples. Nat Commun. 2016 06 15; 7:11881. PMID: 27302887.
    Citations: 5     Fields:    Translation:HumansCells
  4. Harris RM, Arnaout R, Koziel H, Folch E, Majid A, Kirby JE. Utility of microbiological testing of thoracic lymph nodes sampled by endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) in patients with mediastinal lymphadenopathy. Diagn Microbiol Infect Dis. 2016 Feb; 84(2):170-4. PMID: 26602949.
    Citations: 1     Fields:    Translation:Humans
  5. de Baca ME, Arnaout R, Brodsky V, Birdsong GG. Ordo ab Chao: framework for an integrated disease report. Arch Pathol Lab Med. 2015 Feb; 139(2):165-70. PMID: 25611099.
    Citations: 1     Fields:    Translation:Humans
  6. Kaplinsky J, Li A, Sun A, Coffre M, Koralov SB, Arnaout R. Antibody repertoire deep sequencing reveals antigen-independent selection in maturing B cells. Proc Natl Acad Sci U S A. 2014 Jun 24; 111(25):E2622-9. PMID: 24927543; PMCID: PMC4078805.
    Citations: 12     Fields:    Translation:AnimalsCells
  7. Theisen-Toupal J, Breu AC, Mattison ML, Arnaout R. Diagnostic yield of head computed tomography for the hospitalized medical patient with delirium. J Hosp Med. 2014 Aug; 9(8):497-501. PMID: 24733711.
    Citations:    Fields:    Translation:Humans
  8. Mohammad F, Theisen-Toupal JC, Arnaout R. Advantages and limitations of anticipating laboratory test results from regression- and tree-based rules derived from electronic health-record data. PLoS One. 2014; 9(4):e92199. PMID: 24732572; PMCID: PMC3986061.
    Citations:    Fields:    Translation:Humans
  9. Baron JM, Dighe AS, Arnaout R, Balis UJ, Black-Schaffer WS, Carter AB, Henricks WH, Higgins JM, Jackson BR, Kim J, Klepeis VE, Le LP, Louis DN, Mandelker D, Mermel CH, Michaelson JS, Nagarajan R, Platt ME, Quinn AM, Rao L, Shirts BH, Gilbertson JR. The 2013 symposium on pathology data integration and clinical decision support and the current state of field. J Pathol Inform. 2014; 5(1):2. PMID: 24672737; PMCID: PMC3952400.
    Citations: 2     
  10. Zhi M, Ding EL, Theisen-Toupal J, Whelan J, Arnaout R. The landscape of inappropriate laboratory testing: a 15-year meta-analysis. PLoS One. 2013; 8(11):e78962. PMID: 24260139; PMCID: PMC3829815.
    Citations: 35     Fields:    Translation:Humans
  11. Tapper EB, Rahni DO, Arnaout R, Lai M. The overuse of serum ceruloplasmin measurement. Am J Med. 2013 Oct; 126(10):926.e1-5. PMID: 23953876.
    Citations: 4     Fields:    Translation:Humans
  12. Arnaout R. Economic modelling could aid brain map. Nature. 2013 May 23; 497(7450):439. PMID: 23698434.
    Citations:    Fields:    
  13. Lakhani KR, Boudreau KJ, Loh PR, Backstrom L, Baldwin C, Lonstein E, Lydon M, MacCormack A, Arnaout RA, Guinan EC. Prize-based contests can provide solutions to computational biology problems. Nat Biotechnol. 2013 Feb; 31(2):108-11. PMID: 23392504; PMCID: PMC4527172.
    Citations: 25     Fields:    Translation:Humans
  14. Arnaout R, Buck TP, Roulette P, Sukhatme VP. Predicting the cost and pace of pharmacogenomic advances: an evidence-based study. Clin Chem. 2013 Apr; 59(4):649-57. PMID: 23230323.
    Citations: 3     Fields:    
  15. Arnaout R. Elementary, my dear Doctor Watson. Clin Chem. 2012 Jun; 58(6):986-8. PMID: 22522222.
    Citations: 3     Fields:    
  16. Arnaout R, Lee W, Cahill P, Honan T, Sparrow T, Weiand M, Nusbaum C, Rajewsky K, Koralov SB. High-resolution description of antibody heavy-chain repertoires in humans. PLoS One. 2011; 6(8):e22365. PMID: 21829618; PMCID: PMC3150326.
    Citations: 78     Fields:    Translation:HumansCells
  17. Buck TP, Connor IM, Horowitz GL, Arnaout RA. CallWall: tracking resident calls to improve clinical utilization of pathology laboratories. Arch Pathol Lab Med. 2011 Jul; 135(7):920-4. PMID: 21732784.
    Citations: 1     Fields:    Translation:Humans
  18. Haspel RL, Arnaout R, Briere L, Kantarci S, Marchand K, Tonellato P, Connolly J, Boguski MS, Saffitz JE. A call to action: training pathology residents in genomics and personalized medicine. Am J Clin Pathol. 2010 Jun; 133(6):832-4. PMID: 20472839.
    Citations: 18     Fields:    Translation:Humans
  19. Boguski MS, Arnaout R, Hill C. Customized care 2020: how medical sequencing and network biology will enable personalized medicine. F1000 Biol Rep. 2009 Sep 28; 1:73. PMID: 20948615; PMCID: PMC2948270.
    Citations: 5     
  20. Tsibris AM, Korber B, Arnaout R, Russ C, Lo CC, Leitner T, Gaschen B, Theiler J, Paredes R, Su Z, Hughes MD, Gulick RM, Greaves W, Coakley E, Flexner C, Nusbaum C, Kuritzkes DR. Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo. PLoS One. 2009 May 25; 4(5):e5683. PMID: 19479085.
    Citations: 112     Fields:    Translation:HumansCells
  21. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C, Green RD, Dekker J. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 Oct; 16(10):1299-309. PMID: 16954542; PMCID: PMC1581439.
    Citations: 339     Fields:    Translation:HumansCells
  22. Björn Sällström, Ramy A Arnaout, Wagied Davids, Pär Bjelkmar and Siv G E Andersson. J Mol Evol. Protein evolutionary rates correlate with expression independently of synonymous substitutions in Helicobacter pylori. 2006; 62(5):600-14. View Publication.
  23. Josée Dostie, Todd A Richmond, Ramy A Arnaout, Rebecca R Selzer, William L Lee, Tracey A Honan, Eric D Rubio, Anton Krumm, Justin Lamb, Chad Nusbaum, Roland D Green and Job Dekker. Genome Research. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. 2006; 16(10):1299-309. View Publication.
  24. Ramy A Arnaout. BMC Genomics. Specificity and overlap in gene segment-defined antibody repertoires. 2005; 6:148. View Publication.
  25. Wodarz D, Arnaout RA, Nowak MA, Lifson JD. Transient antiretroviral treatment during acute simian immunodeficiency virus infection facilitates long-term control of the virus. Philos Trans R Soc Lond B Biol Sci. 2000 Aug 29; 355(1400):1021-9. PMID: 11186303; PMCID: PMC1692816.
    Citations: 10     Fields:    Translation:HumansAnimalsCells
  26. Arnaout RA, Nowak MA, Wodarz D. HIV-1 dynamics revisited: biphasic decay by cytotoxic T lymphocyte killing? Proc Biol Sci. 2000 Jul 07; 267(1450):1347-54. PMID: 10972131; PMCID: PMC1690670.
    Citations: 14     Fields:    Translation:HumansCells
  27. Arnaout RA, Nowak MA. Competitive coexistence in antiviral immunity. J Theor Biol. 2000 Jun 07; 204(3):431-41. PMID: 10816366.
    Citations: 3     Fields:    Translation:Animals
  28. Masel J, Arnaout RA, O'Brien TR, Goedert JJ, Lloyd AL. Fluctuations in HIV-1 viral load are correlated to CD4+ T-lymphocyte count during the natural course of infection. J Acquir Immune Defic Syndr. 2000 Apr 15; 23(5):375-9. PMID: 10866229.
    Citations: 3     Fields:    Translation:HumansCells
  29. Wodarz D, Page KM, Arnaout RA, Thomsen AR, Lifson JD, Nowak MA. A new theory of cytotoxic T-lymphocyte memory: implications for HIV treatment. Philos Trans R Soc Lond B Biol Sci. 2000 Mar 29; 355(1395):329-43. PMID: 10794051; PMCID: PMC1692738.
    Citations: 17     Fields:    Translation:HumansAnimalsCells
  30. Lifson JD, Rossio JL, Arnaout R, Li L, Parks TL, Schneider DK, Kiser RF, Coalter VJ, Walsh G, Imming RJ, Fisher B, Flynn BM, Bischofberger N, Piatak M, Hirsch VM, Nowak MA, Wodarz D. Containment of simian immunodeficiency virus infection: cellular immune responses and protection from rechallenge following transient postinoculation antiretroviral treatment. J Virol. 2000 Mar; 74(6):2584-93. PMID: 10684272; PMCID: PMC111746.
    Citations: 57     Fields:    Translation:AnimalsCells
  31. D Wodarz, K M Page, R A Arnaout, A R Thomsen, J D Lifson and M A Nowak. Philos Trans R Soc Lond B Biol Sci. A new theory of cytotoxic T-lymphocyte memory: implications for HIV treatment. 2000; 355(1395):329-43. View Publication.
  32. R A Arnaout. Immunol Today. Perforin deficiency: fighting unarmed?. 2000; 21(11):592. View Publication.
  33. D Wodarz, R A Arnaout, M A Nowak and J D Lifson. Philos Trans R Soc Lond B Biol Sci. Transient antiretroviral treatment during acute simian immunodeficiency virus infection facilitates long-term control of the virus. 2000; 355(1400):1021-9. View Publication.
  34. J Masel, R A Arnaout, T R O'Brien, J J Goedert and A L Lloyd. J Acquir Immune Defic Syndr Hum Retrovirol. Fluctuations in HIV-1 viral load are correlated to CD4+ T-lymphocyte count during the natural course of infection. 2000; 23(5):375-9. View Publication.
  35. R A Arnaout, M A Nowak and D Wodarz. Proc Biol Sci. HIV-1 dynamics revisited: biphasic decay by cytotoxic T lymphocyte killing?. 2000; 267(1450):1347-54. View Publication.
  36. R A Arnaout and M A Nowak. J Theor Biol. Competitive coexistence in antiviral immunity. 2000; 204(3):431-41. View Publication.
  37. Arnaout RA, Lloyd AL, O'Brien TR, Goedert JJ, Leonard JM, Nowak MA. A simple relationship between viral load and survival time in HIV-1 infection. Proc Natl Acad Sci U S A. 1999 Sep 28; 96(20):11549-53. PMID: 10500214; PMCID: PMC18071.
    Citations: 10     Fields:    Translation:HumansCells
  38. R A Arnaout, A L Lloyd, T R O'Brien, J J Goedert, J M Leonard and M A Nowak. Proc Natl Acad Sci. A simple relationship between viral load and survival time in HIV-1 infection. 1999; 96(20):11549-53. View Publication.
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Funded by the NIH/NCATS Clinical and Translational Science Award (CTSA) program, grant number UL1TR001102, and through institutional support from Harvard University, Harvard Medical School, Harvard T.H. Chan School of Public Health, Beth Israel Deaconess Medical Center, Boston Children's Hospital, Brigham and Women's Hospital, Massachusetts General Hospital and the Dana Farber Cancer Institute.