Jeff Bailey, M.D. Ph.D. is the Mencoff Family Associate Professor of Translational Research in the Department of Pathology and Laboratory Medicine and a practicing physician in Transfusion Medicine and Coagulation at Miriam and Rhode Island Hospitals. He studies infectious disease genetics and genomics aiming to understand host and pathogen interactions within the context of immunity and human disease. His research is integrative combining experimental and computational approaches. The majority of his current research relates to the parasitic infection malaria—including the direct consequences of infection, parasite genome structure, tracking the spread of drug resistance, and the examination of related diseases including the cancer Burkitt lymphoma.
He has made major contributions to methods for analyzing whole genome sequencing in particular to study segmental duplication and copy number variation as well as more recent methods for high-throughput pathogen targeted sequencing to track pathogens across space and time.
Dr. Bailey obtained his B.A. in Biology from St. Olaf College and his MD and PhD at Case Western University working on analyzing segmental duplications and copy number variation as part of the initial Human Genome Project with his mentor Dr. Evan Eichler. His residency was in Clinical Pathology at Case Western Reserve University and his fellowship in Transfusion Medicine through the Cleveland Citywide Fellowship hosted at the American Red Cross, Cleveland Clinic, and University Hospitals. He is board certified in Clinical Pathology and Transfusion Medicine.
| Chauhan G, McClure J, Hekman J, Marsh PW, Bailey JA, Daniels RF, Genereux DP, Karlsson EK. "Combining Citizen Science and Genomics to Investigate Tick, Pathogen, and Commensal Microbiome at Single-Tick Resolution." Frontiers in genetics, vol. 10, 2020, pp. 1322. |
| Morgan AP, Brazeau NF, Ngasala B, Mhamilawa LE, Denton M, Msellem M, Morris U, Filer DL, Aydemir O, Bailey JA, Parr JB, Mårtensson A, Bjorkman A, Juliano JJ. "Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago." Malaria journal, vol. 19, no. 1, 2020, pp. 47. |
| Oluoch PO, Oduor CI, Forconi CS, Ong'echa JM, Münz C, Dittmer DP, Bailey JA, Moormann AM. "Kaposi Sarcoma-associated herpesvirus infection and endemic Burkitt's lymphoma." The Journal of Infectious Diseases, 2020. |
| Aydemir Ö, Noble JA, Bailey JA, Lernmark Å, Marsh P, Andersson Svärd A, Bearoff F, Blankenhorn EP, Mordes JP, Better Diabetes Diagnosis (BDD) Study Group. "Genetic Variation Within the HLA-DRA1 Gene Modulates Susceptibility to Type 1 Diabetes in HLA-DR3 Homozygotes." Diabetes, vol. 68, no. 7, 2019, pp. 1523-1527. |
| Sá JM, Kaslow SR, Moraes Barros RR, Brazeau NF, Parobek CM, Tao D, Salzman RE, Gibson TJ, Velmurugan S, Krause MA, Melendez-Muniz V, Kite WA, Han PK, Eastman RT, Kim A, Kessler EG, Abebe Y, James ER, Chakravarty S, Orr-Gonzalez S, Lambert LE, Engels T, Thomas ML, Fasinu PS, Serre D, Gwadz RW, Walker L, DeConti DK, Mu J, Bailey JA, Sim BKL, Hoffman SL, Fay MP, Dinglasan RR, Juliano JJ, Wellems TE. "Plasmodium vivax chloroquine resistance links to pvcrt transcription in a genetic cross." Nature Communications, vol. 10, no. 1, 2019, pp. 4300. |
| Brazeau NF, Assefa A, Mohammed H, Seme H, Tsadik AG, Parr JB, Keeler C, Hathaway NJ, Meshnick SR, Bailey JA, Kassa M, Juliano JJ, Woyessa A. "Pooled Deep Sequencing of Drug Resistance Loci from <i>Plasmodium falciparum</i> Parasites across Ethiopia." The American Journal of Tropical Medicine and Hygiene, vol. 101, no. 5, 2019, pp. 1139-1143. |
| Boyce RM, Brazeau N, Fulton T, Hathaway N, Matte M, Ntaro M, Mulogo E, Juliano JJ. "Prevalence of Molecular Markers of Antimalarial Drug Resistance across Altitudinal Transmission Zones in Highland Western Uganda." The American Journal of Tropical Medicine and Hygiene, vol. 101, no. 4, 2019, pp. 799-802. |
| Movassagh M, Oduor C, Forconi C, Moormann AM, Bailey JA. "Sensitive detection of EBV microRNAs across cancer spectrum reveals association with decreased survival in adult acute myelocytic leukemia." Scientific reports, vol. 9, no. 1, 2019, pp. 20321. |
| Ghansah A, Kamau E, Amambua-Ngwa A, Ishengoma DS, Maiga-Ascofare O, Amenga-Etego L, Deme A, Yavo W, Randrianarivelojosia M, Plasmodium Diversity Network Africa., Ochola-Oyier LI, Helegbe GK, Bailey J, Alifrangis M, Djimde A. "Targeted Next Generation Sequencing for malaria research in Africa: current status and outlook." Malaria journal, vol. 18, no. 1, 2019, pp. 324. |
| Deutsch-Feldman M, Aydemir O, Carrel M, Brazeau NF, Bhatt S, Bailey JA, Kashamuka M, Tshefu AK, Taylor SM, Juliano JJ, Meshnick SR, Verity R. "The changing landscape of Plasmodium falciparum drug resistance in the Democratic Republic of Congo." BMC infectious diseases, vol. 19, no. 1, 2019, pp. 872. |
| Panea RI, Love CL, Shingleton JR, Reddy A, Bailey JA, Moormann AM, Otieno JA, Ong'echa JM, Oduor CI, Schroeder KMS, Masalu N, Chao NJ, Agajanian M, Major MB, Fedoriw Y, Richards KL, Rymkiewicz G, Miles RR, Alobeid B, Bhagat G, Flowers CR, Ondrejka SL, Hsi ED, Choi WWL, Au-Yeung RKH, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig MA, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus BC, Seshadri V, Kim SY, Gascoyne RD, Levy S, Mukhopadhyay M, Dunson DB, Dave SS. "The whole genome landscape of Burkitt lymphoma subtypes." Blood, 2019. |
| Weinstein R, Haynes S, Zhao Y, Hickson E, Linden J, St Pierre P, Ducharme P, Sulmasy P, Graves M, Bailey JA, Welch L, Simard A, Vauthrin M, Greene M. "A liquid calcium+vitamin D<sub>3</sub> supplement is effective prophylaxis against hypocalcemic toxicity during apheresis platelet donation." Journal of clinical apheresis, vol. 33, no. 1, 2018, pp. 60-64. |
| Aydemir O, Janko M, Hathaway NJ, Verity R, Mwandagalirwa MK, Tshefu AK, Tessema SK, Marsh PW, Tran A, Reimonn T, Ghani AC, Ghansah A, Juliano JJ, Greenhouse BR, Emch M, Meshnick SR, Bailey JA. "Drug-Resistance and Population Structure of Plasmodium falciparum Across the Democratic Republic of Congo Using High-Throughput Molecular Inversion Probes." The Journal of Infectious Diseases, vol. 218, no. 6, 2018, pp. 946-955. |
| McDonald EA, Stuart R, Joshi A, Wu HW, Olveda RM, Acosta LP, Tallo V, Baltazar PI, Bailey JA, Kurtis JD, Friedman JF. "Endotoxin at the Maternal-Fetal Interface in a Resource-Constrained Setting: Risk Factors and Associated Birth Outcomes." The American Journal of Tropical Medicine and Hygiene, vol. 99, no. 2, 2018, pp. 495-501. |
| Wesolowski A, Taylor AR, Chang HH, Verity R, Tessema S, Bailey JA, Alex Perkins T, Neafsey DE, Greenhouse B, Buckee CO. "Mapping malaria by combining parasite genomic and epidemiologic data." BMC Medicine, vol. 16, no. 1, 2018, pp. 190. |
| Waltmann A, Patel JC, Thwai KL, Hathaway NJ, Parobek CM, Massougbodji A, Fievet N, Bailey JA, Deloron P, Juliano JJ, Ndam NT, Meshnick SR. "Matched Placental and Circulating <i>Plasmodium falciparum</i> Parasites are Genetically Homologous at the <i>var2csa</i> ID1-DBL2X Locus by Deep Sequencing." The American Journal of Tropical Medicine and Hygiene, vol. 98, no. 1, 2018, pp. 77-82. |
| Verity R, Hathaway NJ, Waltmann A, Doctor SM, Watson OJ, Patel JC, Mwandagalirwa K, Tshefu AK, Bailey JA, Ghani AC, Juliano JJ, Meshnick SR. "Plasmodium falciparum genetic variation of var2csa in the Democratic Republic of the Congo." Malaria journal, vol. 17, no. 1, 2018, pp. 46. |
| Zhao Y, Linden J, Welch L, St Pierre P, Graves M, Garrity D, Ducharme P, Bailey JA, Greene M, Vauthrin M, Weinstein R. "Prophylactic infusion of calcium gluconate to prevent a symptomatic fall in plasma ionized calcium during therapeutic plasma exchange: A comparison of two methods." Journal of clinical apheresis, vol. 33, no. 5, 2018, pp. 600-603. |
| Boyce RM, Hathaway N, Fulton T, Reyes R, Matte M, Ntaro M, Mulogo E, Waltmann A, Bailey JA, Siedner MJ, Juliano JJ. "Reuse of malaria rapid diagnostic tests for amplicon deep sequencing to estimate Plasmodium falciparum transmission intensity in western Uganda." Scientific reports, vol. 8, no. 1, 2018, pp. 10159. |
| Wang J, Song J, Zhou S, Fu Y, Bailey JA, Shen C. "Screening and identification of RhD antigen mimic epitopes from a phage display random peptide library for the serodiagnosis of haemolytic disease of the foetus and newborn." Blood transfusion = Trasfusione del sangue, 2018, pp. 1-7. |
| Hathaway NJ, Parobek CM, Juliano JJ, Bailey JA. "SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing." Nucleic acids research, vol. 46, no. 4, 2018, pp. e21. |
| Miller RH, Hathaway NJ, Kharabora O, Mwandagalirwa K, Tshefu A, Meshnick SR, Taylor SM, Juliano JJ, Stewart VA, Bailey JA. "A deep sequencing approach to estimate Plasmodium falciparum complexity of infection (COI) and explore apical membrane antigen 1 diversity." Malaria journal, vol. 16, no. 1, 2017, pp. 490. |
| Kaymaz Y, Oduor CI, Yu H, Otieno JA, Ong'echa JM, Moormann AM, Bailey JA. "Comprehensive Transcriptome and Mutational Profiling of Endemic Burkitt Lymphoma Reveals EBV Type-Specific Differences." Molecular Cancer Research, vol. 15, no. 5, 2017, pp. 563-576. |
| Purpura LJ, Rogers E, Baller A, White S, Soka M, Choi MJ, Mahmoud N, Wasunna C, Massaquoi M, Kollie J, Dweh S, Bemah P, Ladele V, Kpaka J, Jawara M, Mugisha M, Subah O, Faikai M, Bailey JA, Rollin P, Marston B, Nyenswah T, Gasasira A, Knust B, Nichol S, Williams D. "Ebola Virus RNA in Semen from an HIV-Positive Survivor of Ebola." Emerging infectious diseases, vol. 23, no. 4, 2017, pp. 714-715. |
| Ashar-Patel A, Kaymaz Y, Rajakumar A, Bailey JA, Karumanchi SA, Moore MJ. "FLT1 and transcriptome-wide polyadenylation site (PAS) analysis in preeclampsia." Scientific reports, vol. 7, no. 1, 2017, pp. 12139. |
| Falanga YT, Frascoli M, Kaymaz Y, Forconi C, Ong'echa JM, Bailey JA, Berg LJ, Moormann AM. "High pathogen burden in childhood promotes the development of unconventional innate-like CD8+ T cells." JCI insight, vol. 2, no. 15, 2017. |
| Oduor CI, Movassagh M, Kaymaz Y, Chelimo K, Otieno J, Ong'echa JM, Moormann AM, Bailey JA. "Human and Epstein-Barr Virus miRNA Profiling as Predictive Biomarkers for Endemic Burkitt Lymphoma." Frontiers in microbiology, vol. 8, 2017, pp. 501. |
| Patel JC, Hathaway NJ, Parobek CM, Thwai KL, Madanitsa M, Khairallah C, Kalilani-Phiri L, Mwapasa V, Massougbodji A, Fievet N, Bailey JA, Ter Kuile FO, Deloron P, Engel SM, Taylor SM, Juliano JJ, Tuikue Ndam N, Meshnick SR. "Increased risk of low birth weight in women with placental malaria associated with P. falciparum VAR2CSA clade." Scientific reports, vol. 7, no. 1, 2017, pp. 7768. |
| Oduor CI, Kaymaz Y, Chelimo K, Otieno JA, Ong'echa JM, Moormann AM, Bailey JA. "Integrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma." BMC cancer, vol. 17, no. 1, 2017, pp. 761. |
| Parobek CM, Parr JB, Brazeau NF, Lon C, Chaorattanakawee S, Gosi P, Barnett EJ, Norris LD, Meshnick SR, Spring MD, Lanteri CA, Bailey JA, Saunders DL, Lin JT, Juliano JJ. "Partner-Drug Resistance and Population Substructuring of Artemisinin-Resistant Plasmodium falciparum in Cambodia." Genome biology and evolution, vol. 9, no. 6, 2017, pp. 1673-1686. |
| Ngondi JM, Ishengoma DS, Doctor SM, Thwai KL, Keeler C, Mkude S, Munishi OM, Willilo RA, Lalji S, Kaspar N, Kitojo C, Paxton LA, Hathaway NJ, Bailey JA, Juliano JJ, Meshnick SR, Gutman J. "Surveillance for sulfadoxine-pyrimethamine resistant malaria parasites in the Lake and Southern Zones, Tanzania, using pooling and next-generation sequencing." Malaria journal, vol. 16, no. 1, 2017, pp. 236. |
| Zhao Y, Ibrahim H, Bailey JA, Linden J, Hickson E, Haynes S, Greene M, Vauthrin M, Weinstein R. "Therapeutic plasma exchange performed in tandem with hemodialysis without supplemental calcium in the apheresis circuit." Journal of clinical apheresis, vol. 32, no. 3, 2017, pp. 154-157. |
| Mideo N, Bailey JA, Hathaway NJ, Ngasala B, Saunders DL, Lon C, Kharabora O, Jamnik A, Balasubramanian S, Björkman A, Mårtensson A, Meshnick SR, Read AF, Juliano JJ. "A deep sequencing tool for partitioning clearance rates following antimalarial treatment in polyclonal infections." Evolution, medicine, and public health, vol. 2016, no. 1, 2016, pp. 21-36. |
| Lemieux JE, Tran AD, Freimark L, Schaffner SF, Goethert H, Andersen KG, Bazner S, Li A, McGrath G, Sloan L, Vannier E, Milner D, Pritt B, Rosenberg E, Telford S 3rd, Bailey JA, Sabeti PC. "A global map of genetic diversity in Babesia microti reveals strong population structure and identifies variants associated with clinical relapse." Nature Microbiology, vol. 1, no. 7, 2016, pp. 16079. |
| Buckle G, Maranda L, Skiles J, Ong'echa JM, Foley J, Epstein M, Vik TA, Schroeder A, Lemberger J, Rosmarin A, Remick SC, Bailey JA, Vulule J, Otieno JA, Moormann AM. "Factors influencing survival among Kenyan children diagnosed with endemic Burkitt lymphoma between 2003 and 2011: A historical cohort study." International Journal of Cancer, vol. 139, no. 6, 2016, pp. 1231-40. |
| Brazeau NF, Hathaway N, Parobek CM, Lin JT, Bailey JA, Lon C, Saunders DL, Juliano JJ. "Longitudinal Pooled Deep Sequencing of the Plasmodium vivax K12 Kelch Gene in Cambodia Reveals a Lack of Selection by Artemisinin." The American Journal of Tropical Medicine and Hygiene, vol. 95, no. 6, 2016, pp. 1409-1412. |
| Moormann AM, Bailey JA. "Malaria - how this parasitic infection aids and abets EBV-associated Burkitt lymphomagenesis." Current opinion in virology, vol. 20, 2016, pp. 78-84. |
| Soka MJ, Choi MJ, Baller A, White S, Rogers E, Purpura LJ, Mahmoud N, Wasunna C, Massaquoi M, Abad N, Kollie J, Dweh S, Bemah PK, Christie A, Ladele V, Subah OC, Pillai S, Mugisha M, Kpaka J, Kowalewski S, German E, Stenger M, Nichol S, Ströher U, Vanderende KE, Zarecki SM, Green HH, Bailey JA, Rollin P, Marston B, Nyenswah TG, Gasasira A, Knust B, Williams D. "Prevention of sexual transmission of Ebola in Liberia through a national semen testing and counselling programme for survivors: an analysis of Ebola virus RNA results and behavioural data." The Lancet. Global health, vol. 4, no. 10, 2016, pp. e736-43. |
| Parobek CM, Lin JT, Saunders DL, Barnett EJ, Lon C, Lanteri CA, Balasubramanian S, Brazeau N, DeConti DK, Garba DL, Meshnick SR, Spring MD, Chuor CM, Bailey JA, Juliano JJ. "Selective sweep suggests transcriptional regulation may underlie Plasmodium vivax resilience to malaria control measures in Cambodia." Proceedings of the National Academy of Sciences, vol. 113, no. 50, 2016, pp. E8096-E8105. |
| Taylor SM, Parobek CM, DeConti DK, Kayentao K, Coulibaly SO, Greenwood BM, Tagbor H, Williams J, Bojang K, Njie F, Desai M, Kariuki S, Gutman J, Mathanga DP, Mårtensson A, Ngasala B, Conrad MD, Rosenthal PJ, Tshefu AK, Moormann AM, Vulule JM, Doumbo OK, Ter Kuile FO, Meshnick SR, Bailey JA, Juliano JJ. "Absence of putative artemisinin resistance mutations among Plasmodium falciparum in Sub-Saharan Africa: a molecular epidemiologic study." The Journal of Infectious Diseases, vol. 211, no. 5, 2015, pp. 680-8. |
| Galera P, Martin HC, Welch L, Sulmasy P, Cerny J, Greene M, Vauthrin M, Bailey JA, Weinstein R. "Automated red blood cell exchange for acute drug removal in a patient with sirolimus toxicity." Journal of clinical apheresis, vol. 30, no. 6, 2015, pp. 367-70. |
| Weinstein R, Simard A, Ferschke J, Vauthrin M, Bailey JA, Greene M. "Prospective surveillance of D- recipients of D+ apheresis platelets: alloimmunization against D is not detected." Transfusion, vol. 55, no. 6, 2015, pp. 1327-30. |
| Lin JT, Hathaway NJ, Saunders DL, Lon C, Balasubramanian S, Kharabora O, Gosi P, Sriwichai S, Kartchner L, Chuor CM, Satharath P, Lanteri C, Bailey JA, Juliano JJ. "Using Amplicon Deep Sequencing to Detect Genetic Signatures of Plasmodium vivax Relapse." The Journal of Infectious Diseases, vol. 212, no. 6, 2015, pp. 999-1008. |
| Van Treuren W, Ponnusamy L, Brinkerhoff RJ, Gonzalez A, Parobek CM, Juliano JJ, Andreadis TG, Falco RC, Ziegler LB, Hathaway N, Keeler C, Emch M, Bailey JA, Roe RM, Apperson CS, Knight R, Meshnick SR. "Variation in the Microbiota of Ixodes Ticks with Regard to Geography, Species, and Sex." Applied and Environmental Microbiology, vol. 81, no. 18, 2015, pp. 6200-9. |
| Parobek CM, Bailey JA, Hathaway NJ, Socheat D, Rogers WO, Juliano JJ. "Differing patterns of selection and geospatial genetic diversity within two leading Plasmodium vivax candidate vaccine antigens." PLOS Neglected Tropical Diseases, vol. 8, no. 4, 2014, pp. e2796. |
| Simkin AT, Bailey JA, Gao FB, Jensen JD. "Inferring the evolutionary history of primate microRNA binding sites: overcoming motif counting biases." Molecular biology and evolution, vol. 31, no. 7, 2014, pp. 1894-901. |
| Oduor CI, Chelimo K, Ouma C, Mulama DH, Foley J, Vulule J, Bailey JA, Moormann AM. "Interleukin-6 and interleukin-10 gene promoter polymorphisms and risk of endemic Burkitt lymphoma." The American Journal of Tropical Medicine and Hygiene, vol. 91, no. 3, 2014, pp. 649-54. |
| Mulama DH, Bailey JA, Foley J, Chelimo K, Ouma C, Jura WG, Otieno J, Vulule J, Moormann AM. "Sickle cell trait is not associated with endemic Burkitt lymphoma: an ethnicity and malaria endemicity-matched case-control study suggests factors controlling EBV may serve as a predictive biomarker for this pediatric cancer." International Journal of Cancer, vol. 134, no. 3, 2014, pp. 645-53. |
| Mideo N, Kennedy DA, Carlton JM, Bailey JA, Juliano JJ, Read AF. "Ahead of the curve: next generation estimators of drug resistance in malaria infections." Trends in parasitology, vol. 29, no. 7, 2013, pp. 321-8. |
| Aragam NR, Thayer KM, Nge N, Hoffman I, Martinson F, Kamwendo D, Lin FC, Sutherland C, Bailey JA, Juliano JJ. "Diversity of T cell epitopes in Plasmodium falciparum circumsporozoite protein likely due to protein-protein interactions." PLoS ONE, vol. 8, no. 5, 2013, pp. e62427. |
| Bailey JA, Mvalo T, Aragam N, Weiser M, Congdon S, Kamwendo D, Martinson F, Hoffman I, Meshnick SR, Juliano JJ. "Use of massively parallel pyrosequencing to evaluate the diversity of and selection on Plasmodium falciparum csp T-cell epitopes in Lilongwe, Malawi." The Journal of Infectious Diseases, vol. 206, no. 4, 2012, pp. 580-7. |
| Xia A, Sharakhova MV, Leman SC, Tu Z, Bailey JA, Smith CD, Sharakhov IV. "Genome landscape and evolutionary plasticity of chromosomes in malaria mosquitoes." PLoS ONE, vol. 5, no. 5, 2010, pp. e10592. |
| Bailey JA, Kidd JM, Eichler EE. "Human copy number polymorphic genes." Cytogenetic and genome research, vol. 123, no. 1-4, 2008, pp. 234-43. |
| Bailey JA, Eichler EE. "Primate segmental duplications: crucibles of evolution, diversity and disease." Nature reviews. Genetics, vol. 7, no. 7, 2006, pp. 552-64. |
| Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, Olson MV, Eichler EE. "Fine-scale structural variation of the human genome." Nature Genetics, vol. 37, no. 7, 2005, pp. 727-32. |
| Alkan C, Tüzün E, Buard J, Lethiec F, Eichler EE, Bailey JA, Sahinalp SC. "Manipulating multiple sequence alignments via MaM and WebMaM." Nucleic acids research, vol. 33, no. Web Server issue, 2005, pp. W295-8. |
| Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU, Pertz LM, Clark RA, Schwartz S, Segraves R, Oseroff VV, Albertson DG, Pinkel D, Eichler EE. "Segmental duplications and copy-number variation in the human genome." The American Journal of Human Genetics, vol. 77, no. 1, 2005, pp. 78-88. |
| Bailey JA, Church DM, Ventura M, Rocchi M, Eichler EE. "Analysis of segmental duplications and genome assembly in the mouse." Genome Research, vol. 14, no. 5, 2004, pp. 789-801. |
| Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F, Rat Genome Sequencing Project Consortium. "Genome sequence of the Brown Norway rat yields insights into mammalian evolution." J. Geophys. Res., vol. 428, no. 6982, 2004, pp. 493-521. |
| Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE. "Hotspots of mammalian chromosomal evolution." Genome Biology, vol. 5, no. 4, 2004, pp. R23. |
| Tuzun E, Bailey JA, Eichler EE. "Recent segmental duplications in the working draft assembly of the brown Norway rat." Genome Research, vol. 14, no. 4, 2004, pp. 493-506. |
| Alkan C, Eichler EE, Bailey JA, Sahinalp SC, Tüzün E. "The role of unequal crossover in alpha-satellite DNA evolution: a computational analysis." Journal of Computational Biology, vol. 11, no. 5, 2004, pp. 933-44. |
| She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark R, Graves T, Gulden CL, Alkan C, Bailey JA, Sahinalp C, Rocchi M, Haussler D, Wilson RK, Miller W, Schwartz S, Eichler EE. "The structure and evolution of centromeric transition regions within the human genome." J. Geophys. Res., vol. 430, no. 7002, 2004, pp. 857-64. |
| Bailey JA, Liu G, Eichler EE. "An Alu transposition model for the origin and expansion of human segmental duplications." The American Journal of Human Genetics, vol. 73, no. 4, 2003, pp. 823-34. |
| Liu G, NISC Comparative Sequencing Program., Zhao S, Bailey JA, Sahinalp SC, Alkan C, Tuzun E, Green ED, Eichler EE. "Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome." Genome Research, vol. 13, no. 3, 2003, pp. 358-68. |
| Bailey JA, Eichler EE. "Genome-wide detection and analysis of recent segmental duplications within mammalian organisms." Cold Spring Harbor Symposia on Quantitative Biology, vol. 68, 2003, pp. 115-24. |
| Guy J, Hearn T, Crosier M, Mudge J, Viggiano L, Koczan D, Thiesen HJ, Bailey JA, Horvath JE, Eichler EE, Earthrowl ME, Deloukas P, French L, Rogers J, Bentley D, Jackson MS. "Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10p." Genome Research, vol. 13, no. 2, 2003, pp. 159-72. |
| Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J, Andrews S, Isak A, Vanbrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, Gish WR, Eddy SR, McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH, Wilson RK. "The DNA sequence of human chromosome 7." J. Geophys. Res., vol. 424, no. 6945, 2003, pp. 157-64. |
| Horvath JE, Gulden CL, Bailey JA, Yohn C, McPherson JD, Prescott A, Roe BA, de Jong PJ, Ventura M, Misceo D, Archidiacono N, Zhao S, Schwartz S, Rocchi M, Eichler EE. "Using a pericentromeric interspersed repeat to recapitulate the phylogeny and expansion of human centromeric segmental duplications." Molecular biology and evolution, vol. 20, no. 9, 2003, pp. 1463-79. |
| Alkan C, Bailey JA, Eichler EE, Sahinalp SC, Tuzun E. "An algorithmic analysis of the role of unequal crossover in alpha-satellite DNA evolution." Genome informatics. International Conference on Genome Informatics, vol. 13, 2002, pp. 93-102. |
| Bailey JA, Yavor AM, Viggiano L, Misceo D, Horvath JE, Archidiacono N, Schwartz S, Rocchi M, Eichler EE. "Human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22." The American Journal of Human Genetics, vol. 70, no. 1, 2002, pp. 83-100. |
| Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE. "Recent segmental duplications in the human genome." Science, vol. 297, no. 5583, 2002, pp. 1003-7. |
| Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J, International Human Genome Sequencing Consortium. "Initial sequencing and analysis of the human genome." J. Geophys. Res., vol. 409, no. 6822, 2001, pp. 860-921. |
| Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M, Conroy J, Kasprzyk A, Massa H, Yonescu R, Sait S, Thoreen C, Snijders A, Lemyre E, Bailey JA, Bruzel A, Burrill WD, Clegg SM, Collins S, Dhami P, Friedman C, Han CS, Herrick S, Lee J, Ligon AH, Lowry S, Morley M, Narasimhan S, Osoegawa K, Peng Z, Plajzer-Frick I, Quade BJ, Scott D, Sirotkin K, Thorpe AA, Gray JW, Hudson J, Pinkel D, Ried T, Rowen L, Shen-Ong GL, Strausberg RL, Birney E, Callen DF, Cheng JF, Cox DR, Doggett NA, Carter NP, Eichler EE, Haussler D, Korenberg JR, Morton CC, Albertson D, Schuler G, de Jong PJ, Trask BJ, BAC Resource Consortium. "Integration of cytogenetic landmarks into the draft sequence of the human genome." J. Geophys. Res., vol. 409, no. 6822, 2001, pp. 953-8. |
| Horvath JE, Bailey JA, Locke DP, Eichler EE. "Lessons from the human genome: transitions between euchromatin and heterochromatin." Human molecular genetics, vol. 10, no. 20, 2001, pp. 2215-23. |
| Johnson ME, Viggiano L, Bailey JA, Abdul-Rauf M, Goodwin G, Rocchi M, Eichler EE. "Positive selection of a gene family during the emergence of humans and African apes." J. Geophys. Res., vol. 413, no. 6855, 2001, pp. 514-9. |
| Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE. "Segmental duplications: organization and impact within the current human genome project assembly." Genome Research, vol. 11, no. 6, 2001, pp. 1005-17. |
| Bailey JA, Carrel L, Chakravarti A, Eichler EE. "Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis." Proceedings of the National Academy of Sciences, vol. 97, no. 12, 2000, pp. 6634-9. |
| Lynn A, Kashuk C, Petersen MB, Bailey JA, Cox DR, Antonarakis SE, Chakravarti A. "Patterns of meiotic recombination on the long arm of human chromosome 21." Genome Research, vol. 10, no. 9, 2000, pp. 1319-32. |
| Halushka MK, Mathews DJ, Bailey JA, Chakravarti A. "GIST: A web tool for collecting gene information." Physiological Genomics, vol. 1, no. 2, 1999, pp. 75-81. |
Dr. Bailey's research is focused on understanding the genetic interplay between host and pathogens. This includes how pathogens such the malaria parasite plasmodium and the virus EBV impact the host to cause disease and how the human host responds to either mitigate or potentiate pathology. He hAs a highly-collaborative and integrative experimental and computational laboratory which draws on a variety of disciplines including genetics, genomics, immunology, epidemiology bioinformatics and computational biology.
Major projects in the lab include:
Improving malaria vaccines by discovering new vaccine candidates and determining the impacts of landscape ecology, parasite strains, and human genetics on the current malaria vaccine R,TSS
Tracking the evolution and spread of recent malaria parasite drug resistance in the Democratic Republic of Congo and elsewhere in Africa and supporting malaria control programs in monitoring drug resistance
Determining the molecular underpinnings and role of the falciparum malaria and Epstein Barr Virus in etiology and pathology of Burkitt lymphoma
Understanding genetic variation and evolution of Epstein Barr Virus
The role of genetic variation and infectious agents in autoimmune disorders such as type 1 diabetes.
| Year | Degree | Institution |
|---|---|---|
| 2005 | MD | Case Western Reserve University |
| 2002 | PhD | Case Western Reserve University |
| 1989 | BA | Saint Olaf College |
| Fellowship | American Red Cross, Cleveland Clinic, University Hospitals, Cleveland, Transfusion Medicine / Blood Banking | 2007-2008 | |
| Residency | Case Western Reserve University, Cinical Pathology | 2005-2009 |
| Name | Title |
|---|---|
| Aydemir, Ozkan | Instructor in Pathology and Laboratory Medicine (Research) |
| Kurtis, Jonathan | Stanley M. Aronson Professor of Pathology and Laboratory Medicine, Chair of Pathology and Laboratory Medicine |
| Medical | State of Rhode Island | 2018- | |
| Medical | American Board of Pathology, Transfusion Medicine / Blood Banking | 2011- | |
| Medical | American Board of Pathology, Clinical Pathology | 2009- |
| Adjunct Professor. University of Ghana , 2018- |
| Associate Director Coagulation and Transfusion Medicine. Lifespan Academic Medical Center, 2018- |
