Photo of Ramy Arnaout,  MD, PhD

Ramy Arnaout, MD, PhD

Beth Israel Deaconess Medical Center

Beth Israel Deaconess Medical Center
Phone: (617) 538-5681


rarnaout@bidmc.harvard.edu

Ramy Arnaout, MD, PhD

Beth Israel Deaconess Medical Center

EDUCATIONAL TITLES

  • Assistant Professor, Pathology, Harvard Medical School
  • Associate Director, Clinical Microbiology, Pathology, Beth Israel Deaconess Medical Center
  • Faculty, Division of Clinical Informatics, Medicine, Beth Israel Deaconess Medical Center
  • Faculty, Systems Biology PhD Program, Systems Biology, Harvard Medical School
  • Staff Pathologist, Pathology, Beth Israel Deaconess Medical Center

DF/HCC PROGRAM AFFILIATION

Research Abstract

B and T cells are important in vaccines, infections, autoimmunity, aging, and cancer. There are millions of these cells in a typical blood sample. High-throughput sequencing and big-data computational biology make it possible to investigate how this unique set of cells carries out its functions—and raise the possibility of using them as early diagnostics and biological therapeutics for a range of conditions. In our lab, we are sequencing and analyzing antibodies and T cell receptors across species and medical conditions to understand this complex system. Specific projects include sequencing and analysis of B- and T-cell repertoires in melanoma and cancer and other vaccines.

Publications

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  • de Baca ME, Arnaout R, Brodsky V, Birdsong GG. Ordo ab Chao: framework for an integrated disease report. Arch Pathol Lab Med 2015; 139:165-70. PubMed
  • 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. PubMed
  • 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. PubMed
  • 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:e92199. PubMed
  • 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; 5:2. PubMed
  • Tapper EB, Rahni DO, Arnaout R, Lai M. The overuse of serum ceruloplasmin measurement. Am J Med 2013; 126:926.e1-5. PubMed
  • Arnaout R. Economic modelling could aid brain map. Nature 2013; 497:439. PubMed
  • Arnaout R, Buck TP, Roulette P, Sukhatme VP. Predicting the cost and pace of pharmacogenomic advances: an evidence-based study. Clin Chem 2013; 59:649-57. PubMed
  • 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; 31:108-11. PubMed
  • 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:e78962. PubMed
  • Arnaout R. Elementary, my dear Doctor Watson. Clin Chem 2012; 58:986-8. PubMed
  • Buck TP, Connor IM, Horowitz GL, Arnaout RA. CallWall: tracking resident calls to improve clinical utilization of pathology laboratories. Arch Pathol Lab Med 2011; 135:920-4. PubMed
  • 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:e22365. PubMed
  • 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; 4:e5683. PubMed
  • Boguski MS, Arnaout R, Hill C. Customized care 2020: how medical sequencing and network biology will enable personalized medicine. F1000 Biol Rep 2010; 1:73. PubMed
  • 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; 16:1299-309. PubMed
  • Sällström B, Arnaout RA, Davids W, Bjelkmar P, Andersson SG. Protein evolutionary rates correlate with expression independently of synonymous substitutions in Helicobacter pylori. J Mol Evol 2006; 62:600-14. PubMed
  • Arnaout RA. Specificity and overlap in gene segment-defined antibody repertoires. BMC Genomics 2005; 6:148. PubMed
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