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 is a core member of the Center for Computational Molecular Biology and co-director of their PhD program. 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.
| Sadler JM, Simkin A, Tchuenkam VPK, Gerdes Gyuricza I, Fola AA, Wamae K, Assefa A, Niaré K, Thwai K, White SJ, Moss WJ, Dinglasan RR, Nsango SE, Tume CB, Parr JB, Ali IM, Bailey JA, Juliano JJ. "Application of a new highly multiplexed amplicon sequencing tool to evaluate Plasmodium falciparum antimalarial resistance and relatedness in individual and pooled samples from Dschang, Cameroon." Frontiers in parasitology, vol. 3, 2025, pp. 1509261. |
| Martin AC, Sadler JM, Simkin A, Musonda M, Katowa B, Matoba J, Schue J, Simulundu E, Bailey JA, Moss WJ, Juliano JJ, Fola AA. "Emergence and Rising Prevalence of Artemisinin Partial Resistance Marker Kelch13 P441L in a Low Malaria Transmission Setting in Southern Zambia." medRxiv : the preprint server for health sciences, 2025. |
| Wernsman Young N, Gashema P, Giesbrecht D, Munyaneza T, Maisha F, Mwebembezi F, Budodo R, Leonetti A, Crudale R, Iradukunda V, Jean Bosco N, Kirby RI, Boyce RM, Mandara CI, Kanyankole GK, Ntaro M, Okell LC, Watson OJ, Mulogo E, Ishengoma DS, Hangi S, Karema C, Mazarati JB, Juliano JJ, Bailey JA. "High Frequency of Artemisinin Partial Resistance Mutations in the Great Lakes Region Revealed Through Rapid Pooled Deep Sequencing." The Journal of Infectious Diseases, vol. 231, no. 1, 2025, pp. 269-280. |
| Kim IE Jr, Oduor C, Stamp J, Luftig MA, Moormann AM, Crawford L, Bailey JA. "Incorporation of Epstein-Barr viral variation implicates significance of Latent Membrane Protein 1 in survival prediction and prognostic subgrouping in Burkitt lymphoma." International Journal of Cancer, 2025. |
| Katairo T, Asua V, Nsengimaana B, Tukwasibwe S, Semakuba FD, Wiringilimaana I, Garg S, Kiyaga S, Mbabazi M, Kabbale KD, Ayitewala A, Nsobya SL, Kamya MR, Ssewanyana I, Bailey JA, Aranda-Díaz A, Rosenthal PJ, Greenhouse B, Briggs J, Conrad MD. "Performance of Molecular Inversion Probe DR23K and Paragon MAD4HatTeR Amplicon Sequencing Panels for Detection of Plasmodium falciparum Mutations Associated with Antimalarial Drug Resistance." Research square, 2025. |
| Meier-Scherling CPG, Watson OJ, Asua V, Ghinai I, Katairo T, Garg S, Conrad MD, Rosenthal PJ, Okell LC, Bailey JA. "Selection of Plasmodium falciparum kelch13 mutations in Uganda in comparison with southeast Asia: a modelling study." The Lancet. Microbe, 2025, pp. 101027. |
| Sadler JM, Simkin A, Tchuenkam VPK, Gyuricza IG, Fola AA, Wamae K, Assefa A, Niaré K, Thwai K, White SJ, Moss WJ, Dinglasan RR, Nsango S, Tume CB, Parr JB, Ali IM, Bailey JA, Juliano JJ. "Application of a new highly multiplexed amplicon sequencing tool to evaluate Plasmodium falciparum antimalarial resistance and relatedness in individual and pooled samples from Dschang, Cameroon." medRxiv : the preprint server for health sciences, 2024. |
| Mitchell CL, Janko MM, Verity R, Kashamuka MM, Bailey JA, Tshefu AK, Parr JB, Juliano JJ. "Close Proximity to Mining Is Associated with Increased Prevalence of the Drug Resistance-Associated Mutation dhps540E in Eastern Democratic Republic of the Congo." The American Journal of Tropical Medicine and Hygiene, vol. 111, no. 2, 2024, pp. 361-364. |
| Ishengoma DS, Mandara CI, Bakari C, Fola AA, Madebe RA, Seth MD, Francis F, Buguzi CC, Moshi R, Garimo I, Lazaro S, Lusasi A, Aaron S, Chacky F, Mohamed A, Njau RJA, Kitau J, Rasmussen C, Bailey JA, Juliano JJ, Warsame M. "Evidence of artemisinin partial resistance in northwestern Tanzania: clinical and molecular markers of resistance." The Lancet Infectious Diseases, vol. 24, no. 11, 2024, pp. 1225-1233. |
| Somé AF, Conrad MD, Kabré Z, Fofana A, Yerbanga RS, Bazié T, Neya C, Somé M, Kagambega TJ, Legac J, Garg S, Bailey JA, Ouédraogo J-B, Rosenthal PJ, Cooper RA. "Ex vivo drug susceptibility and resistance mediating genetic polymorphisms of Plasmodium falciparum in Bobo-Dioulasso, Burkina Faso." Antimicrobial Agents and Chemotherapy, vol. 68, no. 4, 2024, pp. e0153423. |
| Kreutzfeld O, Orena S, Okitwi M, Tumwebaze PK, Byaruhanga O, Katairo T, Conrad MD, Legac J, Garg S, Crudale R, Aydemir O, Giesbrecht D, Nsobya SL, Blasco B, Duffey M, Rouillier M, Bailey JA, Cooper RA, Rosenthal PJ. "Ex vivo susceptibilities to ganaplacide and diversity in potential resistance mediators in Ugandan Plasmodium falciparum isolates." Antimicrobial Agents and Chemotherapy, vol. 68, no. 9, 2024, pp. e0046624. |
| Rosado J, Fola AA, Cojean S, Sarrasin V, Coppée R, Zaffaroulah R, Bouzayene A, Cicéron L, Houzé L, Crudale R, Musset L, Thellier M, Pradines B, Clain J, Bailey JA, Houzé S, Investigation Study Group. "Ex vivo susceptibility to antimalarial drugs and polymorphisms in drug resistance genes of African Plasmodium falciparum, 2016-2023: a genotype-phenotype association study." medRxiv : the preprint server for health sciences, 2024. |
| Schreidah C, Giesbrecht D, Gashema P, Young NW, Munyaneza T, Muvunyi CM, Thwai K, Mazarati JB, Bailey JA, Juliano JJ, Karema C. "Expansion of artemisinin partial resistance mutations and lack of histidine rich protein-2 and -3 deletions in Plasmodium falciparum infections from Rukara, Rwanda." Malaria journal, vol. 23, no. 1, 2024, pp. 150. |
| de Cesare M, Mwenda M, Jeffreys AE, Chirwa J, Drakeley C, Schneider K, Mambwe B, Glanz K, Ntalla C, Carrasquilla M, Portugal S, Verity RJ, Bailey JA, Ghinai I, Busby GB, Hamainza B, Hawela M, Bridges DJ, Hendry JA. "Flexible and cost-effective genomic surveillance of P. falciparum malaria with targeted nanopore sequencing." Nature Communications, vol. 15, no. 1, 2024, pp. 1413. |
| Lyimo BM, Bakari C, Popkin-Hall ZR, Giesbrecht DJ, Seth MD, Pereus D, Shabani ZI, Moshi R, Boniface R, Mandara CI, Madebe R, Juliano JJ, Bailey JA, Ishengoma DS. "Genetic polymorphism and evidence of signatures of selection in the Plasmodium falciparum circumsporozoite protein gene in Tanzanian regions with different malaria endemicity." Malaria journal, vol. 23, no. 1, 2024, pp. 139. |
| Watson OJ, Tran TN, Zupko RJ, Symons T, Thomson R, Visser T, Rumisha S, Dzianach PA, Hathaway N, Kim I, Juliano JJ, Bailey JA, Slater H, Okell L, Gething P, Ghani A, Boni MF, Parr JB, Cunningham J. "Global risk of selection and spread of Plasmodium falciparum histidine-rich protein 2 and 3 gene deletions." medRxiv : the preprint server for health sciences, 2024. |
| Popkin-Hall ZR, Niaré K, Crudale R, Simkin A, Fola AA, Sanchez JF, Pannebaker DL, Giesbrecht DJ, Kim IE Jr, Aydemir Ö, Bailey JA, Valdivia HO, Juliano JJ. "High-throughput genotyping of Plasmodium vivax in the Peruvian Amazon via molecular inversion probes." Nature Communications, vol. 15, no. 1, 2024, pp. 10219. |
| Hathaway NJ, Kim IE, WernsmanYoung N, Hui ST, Crudale R, Liang EY, Nixon CP, Giesbrecht D, Juliano JJ, Parr JB, Bailey JA. "Interchromosomal segmental duplication drives translocation and loss of P. falciparum histidine-rich protein 3." eLife, vol. 13, 2024. |
| Paquette SE, Oduor CI, Gaulke A, Stefan S, Bronk P, Dafonseca V, Barulin N, Lee C, Carley R, Morrison AR, Choi BR, Bailey JA, Plavicki JS. "Loss of developmentally derived Irf8+ macrophages promotes hyperinnervation and arrhythmia in the adult zebrafish heart." bioRxiv : the preprint server for biology, 2024. |
| Popkin Hall ZR, Seth MD, Madebe RA, Budodo R, Bakari C, Francis F, Pereus D, Giesbrecht DJ, Mandara CI, Mbwambo D, Aaron S, Lusasi A, Lazaro S, Bailey JA, Juliano JJ, Ishengoma DS. "Malaria species positivity rates among symptomatic individuals across regions of differing transmission intensities in Mainland Tanzania." The Journal of Infectious Diseases, vol. 229, no. 4, 2024, pp. 959-968. |
| Ishengoma DS, Mandara CI, Madebe RA, Warsame M, Ngasala B, Kabanywanyi AM, Mahende MK, Kamugisha E, Kavishe RA, Muro F, Mandike R, Mkude S, Chacky F, Njau R, Martin T, Mohamed A, Bailey JA, Fola AA. "Microsatellites reveal high polymorphism and high potential for use in anti-malarial efficacy studies in areas with different transmission intensities in mainland Tanzania." Malaria journal, vol. 23, no. 1, 2024, pp. 79. |
| Rogier E, Battle N, Bakari C, Seth MD, Nace D, Herman C, Barakoti A, Madebe RA, Mandara CI, Lyimo BM, Giesbrecht DJ, Popkin-Hall ZR, Francis F, Mbwambo D, Garimo I, Aaron S, Lusasi A, Molteni F, Njau R, Cunningham JA, Lazaro S, Mohamed A, Juliano JJ, Bailey JA, Udhayakumar V, Ishengoma DS. "Plasmodium falciparum pfhrp2 and pfhrp3 gene deletions among patients enrolled at 100 health facilities throughout Tanzania: February to July 2021." Scientific reports, vol. 14, no. 1, 2024, pp. 8158. |
| Popkin-Hall ZR, Carey-Ewend K, Aghakhanian F, Oriero EC, Seth MD, Kashamuka MM, Ngasala B, Ali IM, Mukomena ES, Mandara CI, Kharabora O, Sendor R, Simkin A, Amambua-Ngwa A, Tshefu A, Fola AA, Ishengoma DS, Bailey JA, Parr JB, Lin JT, Juliano JJ. "Population Genomics of Plasmodium malariae from Four African Countries." medRxiv : the preprint server for health sciences, 2024. |
| Carey-Ewend K, Popkin-Hall ZR, Simkin A, Muller M, Hennelly C, He W, Moser KA, Gaither C, Niaré K, Aghakanian F, Feleke S, Brhane BG, Phanzu F, Kashamuka MM, Aydemir O, Sutherland CJ, Ishengoma DS, Ali IM, Ngasala B, Kalonji A, Tshefu A, Parr JB, Bailey JA, Juliano JJ, Lin JT. "Population genomics of Plasmodium ovale species in sub-Saharan Africa." Nature Communications, vol. 15, no. 1, 2024, pp. 10297. |
| Gaither C, Morgan C, Kirby R, Karema C, Gashema P, White SJ, Topazian HM, Geibrecht D, Thwai K, Young NW, Boyter K, Munyaneza T, Muvunyi CM, Butera JD, Bailey JA, Mazarati JB, Juliano JJ. "Prevalence of Asymptomatic non-Falciparum and Falciparum Malaria in the 2014-15 Rwanda Demographic Health Survey." medRxiv : the preprint server for health sciences, 2024. |
| Juliano JJ, Giesbrecht DJ, Simkin A, Fola AA, Lyimo BM, Pereus D, Bakari C, Madebe RA, Seth MD, Mandara CI, Popkin-Hall ZR, Moshi R, Mbwambo RB, Niaré K, MacInnis B, Francis F, Mbwambo D, Garimo I, Chacky F, Aaron S, Lusasi A, Molteni F, Njau RJA, Nhiga SL, Mohamed A, Bailey JA, Ishengoma DS. "Prevalence of mutations associated with artemisinin partial resistance and sulfadoxine-pyrimethamine resistance in 13 regions in Tanzania in 2021: a cross-sectional survey." The Lancet. Microbe, vol. 5, no. 10, 2024, pp. 100920. |
| Popkin-Hall ZR, Seth MD, Madebe RA, Budodo R, Bakari C, Francis F, Pereus D, Giesbrecht DJ, Mandara CI, Mbwambo D, Aaron S, Lusasi A, Lazaro S, Bailey JA, Juliano JJ, Gutman JR, Ishengoma DS. "Prevalence of non-falciparum malaria infections among asymptomatic individuals in four regions of Mainland Tanzania." Parasites & vectors, vol. 17, no. 1, 2024, pp. 153. |
| Tebit DM, Nickel G, Gibson R, Rodriguez M, Hathaway NJ, Bain K, Reyes-Rodriguez AL, Ondoa P, Heeney JL, Li Y, Bongorno J, Canaday D, McDonald D, Bailey JA, Arts EJ. "Replicative fitness and pathogenicity of primate lentiviruses in lymphoid tissue, primary human and chimpanzee cells: relation to possible jumps to humans." EBioMedicine, vol. 100, 2024, pp. 104965. |
| Watson OJ, Muchiri S, Ward A, Meier-Sherling C, Asua V, Katairo T, Brewer T, Cuomo-Dannenburg G, Winskill P, Bailey JA, Okell L, Scudu G, Woolsey AM. "Risk of selection and timelines for the continued spread of artemisinin and partner drug resistance in Africa." medRxiv : the preprint server for health sciences, 2024. |
| Oduor CI, Connelly SV, Cunningham C, Rustamzade N, Zuromski J, Chin DM, Nixon C, Kurtis J, Juliano JJ, Bailey JA. "Single cell transcriptional changes across the blood stages of artemisinin resistant K13(580Y) Plasmodium falciparum upon dihydroartemisinin exposure." bioRxiv : the preprint server for biology, 2024. |
| Connelly SV, Brazeau NF, Msellem M, Ngasala BE, Aydemir O, Goel V, Niaré K, Giesbrecht DJ, Popkin-Hall ZR, Hennelly C, Park Z, Moormann AM, Ong'echa JM, Verity R, Mohammed S, Shija SJ, Mhamilawa LE, Morris U, Mårtensson A, Lin JT, Björkman A, Juliano JJ, Bailey JA. "Strong isolation by distance and evidence of population microstructure reflect ongoing Plasmodium falciparum transmission in Zanzibar." eLife, vol. 12, 2024. |
| Wamae K, Ndwiga L, Kharabora O, Kimenyi K, Osoti V, de Laurent Z, Wambua J, Musyoki J, Ngetsa C, Kalume P, Mwambingu G, Hamaluba M, van der Pluijm R, Dondorp AM, Bailey J, Juliano J, Bejon P, Ochola-Oyier L. "Targeted amplicon deep sequencing of ama1 and mdr1 to track within-host P. falciparum diversity throughout treatment in a clinical drug trial." Wellcome open research, vol. 7, 2024, pp. 95. |
| Fola AA, Kobayashi T, Hamapumbu H, Musonda M, Katowa B, Matoba J, Stevenson JC, Norris DE, Thuma PE, Wesolowski A, Moss WJ, Juliano JJ, Bailey JA. "Temporal genomics in Southern Zambia shows rising prevalence of Plasmodium falciparum mutations linked to delayed clearance after artemisinin-lumefantrine treatment." Scientific reports, vol. 14, no. 1, 2024, pp. 26789. |
| Rosenthal PJ, Asua V, Bailey JA, Conrad MD, Ishengoma DS, Kamya MR, Rasmussen C, Tadesse FG, Uwimana A, Fidock DA. "The emergence of artemisinin partial resistance in Africa: how do we respond?." The Lancet Infectious Diseases, vol. 24, no. 9, 2024, pp. e591-e600. |
| Okitwi M, Shoue DA, Checkley LA, Orena S, Ceja FG, Taremwa Y, Tumwebaze PK, Katairo T, Byaruhanga O, Sievert MA, Garg S, Kreutzfeld OK, Legac J, Bailey JA, Nsobya SL, Conrad MD, Rosenthal PJ, Ferdig MT, Cooper RA. "The extended recovery ring-stage survival assay is a scalable alternative for artemisinin susceptibility phenotyping of fresh Plasmodium falciparum isolates." Antimicrobial Agents and Chemotherapy, vol. 68, no. 12, 2024, pp. e0118324. |
| Ishengoma DS, Gosling R, Martinez-Vega R, Beshir KB, Bailey JA, Chimumbwa J, Sutherland C, Conrad MD, Tadesse FG, Juliano JJ, Kamya MR, Mbacham WF, Ménard D, Rosenthal PJ, Raman J, Tatarsky A, Tessema SK, Fidock DA, Djimde AA. "Urgent action is needed to confront artemisinin partial resistance in African malaria parasites." Nature Medicine, vol. 30, no. 7, 2024, pp. 1807-1808. |
| Tukwasibwe S, Garg S, Katairo T, Asua V, Kagurusi BA, Mboowa G, Crudale R, Tumusiime G, Businge J, Alula D, Kasozi J, Wadembere I, Ssewanyana I, Arinaitwe E, Nankabirwa JI, Nsobya SL, Kamya MR, Greenhouse B, Dorsey G, Bailey JA, Briggs J, Conrad MD, Rosenthal PJ. "Varied Prevalence of Antimalarial Drug Resistance Markers in Different Populations of Newly Arrived Refugees in Uganda." The Journal of Infectious Diseases, vol. 230, no. 2, 2024, pp. 497-504. |
| Niaré K, Greenhouse B, Bailey JA. "An optimized GATK4 pipeline for Plasmodium falciparum whole genome sequencing variant calling and analysis." Malaria journal, vol. 22, no. 1, 2023, pp. 207. |
| Bell GJ, Gyaase S, Goel V, Adu B, Mensah B, Essone P, Dosoo D, Osei M, Niare K, Wiru K, Brandt K, Emch M, Ghansah A, Asante KP, Mvalo T, Agnandji ST, Juliano JJ, Bailey JA. "Background malaria incidence and parasitemia during the three-dose RTS,S/AS01 vaccination series do not reduce magnitude of antibody response nor efficacy against the first case of malaria." BMC infectious diseases, vol. 23, no. 1, 2023, pp. 716. |
| Paschalidis A, Watson OJ, Aydemir O, Verity R, Bailey JA. "coiaf: Directly estimating complexity of infection with allele frequencies." PLOS Computational Biology, vol. 19, no. 6, 2023, pp. e1010247. |
| Oluoch PO, Forconi CS, Oduor CI, Ritacco DA, Akala HM, Bailey JA, Juliano JJ, Ong'echa JM, Münz C, Moormann AM. "Distinctive Kaposi Sarcoma-Associated Herpesvirus Serological Profile during Acute Plasmodium falciparum Malaria Episodes." International Journal of Molecular Sciences, vol. 24, no. 7, 2023. |
| Saikumar Lakshmi P, Oduor CI, Forconi CS, M'Bana V, Bly C, Gerstein RM, Otieno JA, Ong'echa JM, Münz C, Luftig MA, Brehm MA, Bailey JA, Moormann AM. "Endemic Burkitt lymphoma avatar mouse models for exploring inter-patient tumor variation and testing targeted therapies." Life science alliance, vol. 6, no. 5, 2023. |
| Sendor R, Banek K, Kashamuka MM, Mvuama N, Bala JA, Nkalani M, Kihuma G, Atibu J, Thwai KL, Svec WM, Goel V, Nseka T, Lin JT, Bailey JA, Emch M, Carrel M, Juliano JJ, Tshefu A, Parr JB. "Epidemiology of Plasmodium malariae and Plasmodium ovale spp. in Kinshasa Province, Democratic Republic of Congo." Nature Communications, vol. 14, no. 1, 2023, pp. 6618. |
| Muriuki BM, Forconi CS, Kirwa EK, Maina TK, Ariera BO, Bailey JA, Ghansah A, Moormann AM, Ong'echa JM. "Evaluation of KIR3DL1/KIR3DS1 allelic polymorphisms in Kenyan children with endemic Burkitt lymphoma." PLoS ONE, vol. 18, no. 8, 2023, pp. e0275046. |
| Conrad MD, Asua V, Garg S, Giesbrecht D, Niaré K, Smith S, Namuganga JF, Katairo T, Legac J, Crudale RM, Tumwebaze PK, Nsobya SL, Cooper RA, Kamya MR, Dorsey G, Bailey JA, Rosenthal PJ. "Evolution of Partial Resistance to Artemisinins in Malaria Parasites in Uganda." New England Journal of Medicine, vol. 389, no. 8, 2023, pp. 722-732. |
| Kirby R, Giesbrecht D, Karema C, Watson O, Lewis S, Munyaneza T, Butera JD, Juliano JJ, Bailey JA, Mazarati JB. "Examining the Early Distribution of the Artemisinin-Resistant Plasmodium falciparum kelch13 R561H Mutation in Areas of Higher Transmission in Rwanda." Open Forum Infectious Diseases, vol. 10, no. 4, 2023, pp. ofad149. |
| Jenike AE, Bunkelman B, Perzel Mandell KA, Oduor CI, Chin D, Mair D, Jenike KM, Kim DH, Bailey JA, Rafailovich MH, Rosenberg AZ, Halushka MK. "Expression Microdissection for the Analysis of miRNA in a Single-Cell Type." Laboratory investigation; a journal of technical methods and pathology, vol. 103, no. 7, 2023, pp. 100133. |
| Andolina C, Ramjith J, Rek J, Lanke K, Okoth J, Grignard L, Arinaitwe E, Briggs J, Bailey J, Aydemir O, Kamya MR, Greenhouse B, Dorsey G, Staedke SG, Drakeley C, Jonker M, Bousema T. "Plasmodium falciparum gametocyte carriage in longitudinally monitored incident infections is associated with duration of infection and human host factors." Scientific reports, vol. 13, no. 1, 2023, pp. 7072. |
| Fola AA, Feleke SM, Mohammed H, Brhane BG, Hennelly CM, Assefa A, Crudal RM, Reichert E, Juliano JJ, Cunningham J, Mamo H, Solomon H, Tasew G, Petros B, Parr JB, Bailey JA. "Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia." Nature Microbiology, vol. 8, no. 10, 2023, pp. 1911-1919. |
| François R, Kashamuka MM, Banek K, Bala JA, Nkalani M, Kihuma G, Atibu J, Mahilu GE, Thwai KL, Assefa A, Bailey JA, Dinglasan RR, Juliano JJ, Tshefu AK, Parr JB. "Plasmodium falciparum with pfhrp2/3 Deletion Not Detected in a 2018-2021 Malaria Longitudinal Cohort Study in Kinshasa Province, Democratic Republic of the Congo." The American Journal of Tropical Medicine and Hygiene, vol. 109, no. 2, 2023, pp. 273-276. |
| Binder RA, Fujimori GF, Forconi CS, Reed GW, Silva LS, Lakshmi PS, Higgins A, Cincotta L, Dutta P, Salive MC, Mangolds V, Anya O, Calvo Calle JM, Nixon T, Tang Q, Wessolossky M, Wang Y, Ritacco DA, Bly CS, Fischinger S, Atyeo C, Oluoch PO, Odwar B, Bailey JA, Maldonado-Contreras A, Haran JP, Schmidt AG, Cavacini L, Alter G, Moormann AM. "SARS-CoV-2 Serosurveys: How Antigen, Isotype and Threshold Choices Affect the Outcome." The Journal of Infectious Diseases, vol. 227, no. 3, 2023, pp. 371-380. |
| Kreutzfeld O, Tumwebaze PK, Okitwi M, Orena S, Byaruhanga O, Katairo T, Conrad MD, Rasmussen SA, Legac J, Aydemir O, Giesbrecht D, Forte B, Campbell P, Smith A, Kano H, Nsobya SL, Blasco B, Duffey M, Bailey JA, Cooper RA, Rosenthal PJ. "Susceptibility of Ugandan Plasmodium falciparum Isolates to the Antimalarial Drug Pipeline." Microbiology spectrum, vol. 11, no. 3, 2023, pp. e0523622. |
| Fola AA, Moser KA, Aydemir O, Hennelly C, Kobayashi T, Shields T, Hamapumbu H, Musonda M, Katowa B, Matoba J, Stevenson JC, Norris DE, Thuma PE, Wesolowski A, Moss WJ, Bailey JA, Juliano JJ, Southern, Central Africa International Center of Excellence for Malaria Research (ICEMR). "Temporal and spatial analysis of Plasmodium falciparum genomics reveals patterns of parasite connectivity in a low-transmission district in Southern Province, Zambia." Malaria journal, vol. 22, no. 1, 2023, pp. 208. |
| Willard KA, Barry AP, Oduor CI, Ong'echa JM, Bailey JA, Moormann AM, Luftig MA. "Viral and host factors drive a type 1 Epstein-Barr virus spontaneous lytic phenotype." mBio, vol. 14, no. 6, 2023, pp. e0220423. |
| Wamae K, Kimenyi KM, Osoti V, de Laurent ZR, Ndwiga L, Kharabora O, Hathaway NJ, Bailey JA, Juliano JJ, Bejon P, Ochola-Oyier LI. "Amplicon Sequencing as a Potential Surveillance Tool for Complexity of Infection and Drug Resistance Markers in Plasmodium falciparum Asymptomatic Infections." The Journal of Infectious Diseases, vol. 226, no. 5, 2022, pp. 920-927. |
| Balasubramanian S, Curtis-Robles R, Chirra B, Auckland LD, Mai A, Bocanegra-Garcia V, Clark P, Clark W, Cottingham M, Fleurie G, Johnson CD, Metz RP, Wang S, Hathaway NJ, Bailey JA, Hamer GL, Hamer SA. "Characterization of triatomine bloodmeal sources using direct Sanger sequencing and amplicon deep sequencing methods." Scientific reports, vol. 12, no. 1, 2022, pp. 10234. |
| Tumwebaze PK, Conrad MD, Okitwi M, Orena S, Byaruhanga O, Katairo T, Legac J, Garg S, Giesbrecht D, Smith SR, Ceja FG, Nsobya SL, Bailey JA, Cooper RA, Rosenthal PJ. "Decreased susceptibility of Plasmodium falciparum to both dihydroartemisinin and lumefantrine in northern Uganda." Nature Communications, vol. 13, no. 1, 2022, pp. 6353. |
| Kreutzfeld O, Tumwebaze PK, Byaruhanga O, Katairo T, Okitwi M, Orena S, Rasmussen SA, Legac J, Conrad MD, Nsobya SL, Aydemir O, Bailey JA, Duffey M, Cooper RA, Rosenthal PJ. "Decreased Susceptibility to Dihydrofolate Reductase Inhibitors Associated With Genetic Polymorphisms in Ugandan Plasmodium falciparum Isolates." The Journal of Infectious Diseases, vol. 225, no. 4, 2022, pp. 696-704. |
| Topazian HM, Moser KA, Ngasala B, Oluoch PO, Forconi CS, Mhamilawa LE, Aydemir O, Kharabora O, Deutsch-Feldman M, Read AF, Denton M, Lorenzo A, Mideo N, Ogutu B, Moormann AM, Mårtensson A, Odwar B, Bailey JA, Akala H, Ong'echa JM, Juliano JJ. "Low Complexity of Infection Is Associated With Molecular Persistence of Plasmodium falciparum in Kenya and Tanzania." Frontiers in epidemiology, vol. 2, 2022, pp. 852237. |
| Bell GJ, Goel V, Essone P, Dosoo D, Adu B, Mensah BA, Gyaase S, Wiru K, Mougeni F, Osei M, Minsoko P, Sinai C, Niaré K, Juliano JJ, Hudgens M, Ghansah A, Kamthunzi P, Mvalo T, Agnandji ST, Bailey JA, Asante KP, Emch M. "Malaria Transmission Intensity Likely Modifies RTS, S/AS01 Efficacy Due to a Rebound Effect in Ghana, Malawi, and Gabon." The Journal of Infectious Diseases, 2022. |
| Movassagh M, Morton SU, Hehnly C, Smith J, Doan TT, Irizarry R, Broach JR, Schiff SJ, Bailey JA, Paulson JN. "mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis." BMC genomics, vol. 23, no. 1, 2022, pp. 439. |
| Wesolowski A, Ippolito MM, Gebhardt ME, Ferriss E, Schue JL, Kobayashi T, Chaponda M, Kabuya JB, Muleba M, Mburu M, Matoba J, Musonda M, Katowa B, Lubinda M, Hamapumbu H, Simubali L, Mudenda T, Shields TM, Hackman A, Shiff C, Coetzee M, Koekemoer LL, Munyati S, Gwanzura L, Mutambu S, Stevenson JC, Thuma PE, Norris DE, Bailey JA, Juliano JJ, Chongwe G, Mulenga M, Simulundu E, Mharakurwa S, Agre P, Moss WJ, Southern and Central Africa International Center of Excellence for Malaria Research. "Policy Implications of the Southern and Central Africa International Center of Excellence for Malaria Research: Ten Years of Malaria Control Impact Assessments in Hypo-, Meso-, and Holoendemic Transmission Zones in Zambia and Zimbabwe." The American Journal of Tropical Medicine and Hygiene, vol. 107, no. 4_Suppl, 2022, pp. 68-74. |
| Lyimo BM, Popkin-Hall ZR, Giesbrecht DJ, Mandara CI, Madebe RA, Bakari C, Pereus D, Seth MD, Ngamba RM, Mbwambo RB, MacInnis B, Mbwambo D, Garimo I, Chacky F, Aaron S, Lusasi A, Molteni F, Njau R, Cunningham JA, Lazaro S, Mohamed A, Juliano JJ, Bailey JA, Ishengoma DS. "Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa." Frontiers in cellular and infection microbiology, vol. 12, 2022, pp. 757844. |
| Agwati EO, Oduor CI, Ayieko C, Ong'echa JM, Moormann AM, Bailey JA. "Profiling genome-wide recombination in Epstein Barr virus reveals type-specific patterns and associations with endemic-Burkitt lymphoma." Virology Journal, vol. 19, no. 1, 2022, pp. 208. |
| Ippolito MM, Gebhardt ME, Ferriss E, Schue JL, Kobayashi T, Chaponda M, Kabuya JB, Muleba M, Mburu M, Matoba J, Musonda M, Katowa B, Lubinda M, Hamapumbu H, Simubali L, Mudenda T, Wesolowski A, Shields TM, Hackman A, Shiff C, Coetzee M, Koekemoer LL, Munyati S, Gwanzura L, Mutambu S, Stevenson JC, Thuma PE, Norris DE, Bailey JA, Juliano JJ, Chongwe G, Mulenga M, Simulundu E, Mharakurwa S, Agre PC, Moss WJ, Southern and Central Africa International Center of Excellence for Malaria Research. "Scientific Findings of the Southern and Central Africa International Center of Excellence for Malaria Research: Ten Years of Malaria Control Impact Assessments in Hypo-, Meso-, and Holoendemic Transmission Zones in Zambia and Zimbabwe." The American Journal of Tropical Medicine and Hygiene, vol. 107, no. 4_Suppl, 2022, pp. 55-67. |
| Garg S, Kreutzfeld O, Chelebieva S, Tumwebaze PK, Byaruhanga O, Okitwi M, Orena S, Katairo T, Nsobya SL, Conrad MD, Aydemir O, Legac J, Gould AE, Bayles BR, Bailey JA, Duffey M, Lin G, Kirkman LA, Cooper RA, Rosenthal PJ. "Susceptibilities of Ugandan Plasmodium falciparum Isolates to Proteasome Inhibitors." Antimicrobial Agents and Chemotherapy, 2022, pp. e0081722. |
| Tong Y, Orang'o E, Nakalembe M, Tonui P, Itsura P, Muthoka K, Titus M, Kiptoo S, Mwangi A, Ong'echa J, Tonui R, Odongo B, Mpamani C, Rosen B, Moormann A, Cu-Uvin S, Bailey JA, Oduor CI, Ermel A, Yiannoutsos C, Musick B, Sang E, Ngeresa A, Banturaki G, Kiragga A, Zhang J, Song Y, Chintala S, Katzenellenbogen R, Loehrer P, Brown DR. "The East Africa Consortium for human papillomavirus and cervical cancer in women living with HIV/AIDS." Annals of medicine, vol. 54, no. 1, 2022, pp. 1202-1211. |
| Dosoo DK, Bailey JA, Asante KP, Oppong FB, Niaré K, Opoku-Mensah J, Owusu-Agyei S, Greenwood B, Chandramohan D. "The prevalence of molecular markers of resistance to sulfadoxine-pyrimethamine among pregnant women at first antenatal clinic attendance and delivery in the forest-savannah area of Ghana." PLoS ONE, vol. 17, no. 8, 2022, pp. e0271489. |
| Ippolito MM, Kabuya JB, Hauser M, Kamavu LK, Banda PM, Yanek LR, Malik R, Mulenga M, Bailey JA, Chongwe G, Louis TA, Shapiro TA, Moss WJ, Southern and Central Africa International Centers of Excellence for Malaria Research. "Whole blood transfusion for severe malarial anemia in a high Plasmodium falciparum transmission setting." Clinical Infectious Diseases, 2022. |
| Muriuki BM, Forconi CS, Oluoch PO, Bailey JA, Ghansah A, Moormann AM, Ong'echa JM. "Association of killer cell immunoglobulin-like receptors with endemic Burkitt lymphoma in Kenyan children." Scientific reports, vol. 11, no. 1, 2021, pp. 11343. |
| Kreutzfeld O, Rasmussen SA, Ramanathan AA, Tumwebaze PK, Byaruhanga O, Katairo T, Asua V, Okitwi M, Orena S, Legac J, Conrad MD, Nsobya SL, Aydemir O, Bailey J, Duffey M, Bayles BR, Vaidya AB, Cooper RA, Rosenthal PJ. "Associations between Varied Susceptibilities to PfATP4 Inhibitors and Genotypes in Ugandan Plasmodium falciparum Isolates." Antimicrobial Agents and Chemotherapy, vol. 65, no. 10, 2021, pp. e0077121. |
| Asua V, Conrad MD, Aydemir O, Duvalsaint M, Legac J, Duarte E, Tumwebaze P, Chin DM, Cooper RA, Yeka A, Kamya MR, Dorsey G, Nsobya SL, Bailey J, Rosenthal PJ. "Changing Prevalence of Potential Mediators of Aminoquinoline, Antifolate, and Artemisinin Resistance Across Uganda." The Journal of Infectious Diseases, vol. 223, no. 6, 2021, pp. 985-994. |
| Rogers R, Shehadeh F, Mylona EK, Rich J, Neill M, Touzard-Romo F, Geffert S, Larkin J, Bailey JA, Lu S, Sweeney J, Mylonakis E. "Convalescent Plasma for Patients With Severe Coronavirus Disease 2019 (COVID-19): A Matched Cohort Study." Clinical Infectious Diseases, vol. 73, no. 1, 2021, pp. e208-e214. |
| Klein K, Nankya I, Nickel G, Ratcliff AN, Meadows AAJ, Hathaway N, Bailey JA, Stieh DJ, Cheeseman HM, Carias AM, Lobritz MA, Mann JFS, Gao Y, Hope TJ, Shattock RJ, Arts EJ. "Deep Gene Sequence Cluster Analyses of Multi-Virus-Infected Mucosal Tissue Reveal Enhanced Transmission of Acute HIV-1." Journal of Virology, vol. 95, no. 3, 2021. |
| Moser KA, Madebe RA, Aydemir O, Chiduo MG, Mandara CI, Rumisha SF, Chaky F, Denton M, Marsh PW, Verity R, Watson OJ, Ngasala B, Mkude S, Molteni F, Njau R, Warsame M, Mandike R, Kabanywanyi AM, Mahende MK, Kamugisha E, Ahmed M, Kavishe RA, Greer G, Kitojo CA, Reaves EJ, Mlunde L, Bishanga D, Mohamed A, Juliano JJ, Ishengoma DS, Bailey JA. "Describing the current status of Plasmodium falciparum population structure and drug resistance within mainland Tanzania using molecular inversion probes." Molecular Ecology, vol. 30, no. 1, 2021, pp. 100-113. |
| Tumwebaze PK, Katairo T, Okitwi M, Byaruhanga O, Orena S, Asua V, Duvalsaint M, Legac J, Chelebieva S, Ceja FG, Rasmussen SA, Conrad MD, Nsobya SL, Aydemir O, Bailey JA, Bayles BR, Rosenthal PJ, Cooper RA. "Drug susceptibility of Plasmodium falciparum in eastern Uganda: a longitudinal phenotypic and genotypic study." The Lancet. Microbe, vol. 2, no. 9, 2021, pp. e441-e449. |
| Aydemir O, Mensah B, Marsh PW, Abuaku B, Myers-Hansen JL, Bailey JA, Ghansah A. "Immediate pools of malaria infections at diagnosis combined with targeted deep sequencing accurately quantifies frequency of drug resistance mutations." PeerJ, vol. 9, 2021, pp. e11794. |
| Bell GJ, Agnandji ST, Asante KP, Ghansah A, Kamthunzi P, Emch M, Bailey JA. "Impacts of Ecology, Parasite Antigenic Variation, and Human Genetics on RTS,S/AS01e Malaria Vaccine Efficacy." Current epidemiology reports, vol. 8, no. 3, 2021, pp. 79-88. |
| Feleke SM, Reichert EN, Mohammed H, Brhane BG, Mekete K, Mamo H, Petros B, Solomon H, Abate E, Hennelly C, Denton M, Keeler C, Hathaway NJ, Juliano JJ, Bailey JA, Rogier E, Cunningham J, Aydemir O, Parr JB. "Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia." Nature Microbiology, vol. 6, no. 10, 2021, pp. 1289-1299. |
| Lin JT, Waltmann A, Moser KA, Park Z, Na YB, Aydemir O, Brazeau NF, Gosi P, Marsh PW, Muller MS, Spring M, Sok S, Bailey JA, Saunders DL, Lon C, Wojnarski M. "Selection of Cytochrome b Mutants Is Rare among Plasmodium falciparum Patients Failing Treatment with Atovaquone-Proguanil in Cambodia." Antimicrobial Agents and Chemotherapy, vol. 65, no. 3, 2021. |
| SoRelle ED, Dai J, Bonglack EN, Heckenberg EM, Zhou JY, Giamberardino SN, Bailey JA, Gregory SG, Chan C, Luftig MA. "Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host-pathogen dynamics in lymphoblastoid cell lines." eLife, vol. 10, 2021. |
| Naeem S, Gohh R, Bayliss G, Cosgrove C, Farmakiotis D, Merhi B, Morrissey P, Osband A, Bailey JA, Sweeney J, Rogers R. "Successful recovery from COVID-19 in three kidney transplant recipients who received convalescent plasma therapy." Transplant Infectious Disease, vol. 23, no. 1, 2021, pp. e13451. |
| Torrevillas BK, Garrison SM, McKeeken AJ, Patel D, Van Leuven JT, Dizon NI, Rivas KI, Hathaway NJ, Bailey JA, Waitumbi JN, Kifude CM, Oyieko J, Stewart VA, Luckhart S. "Plasmodium falciparum DHFR and DHPS Mutations Are Associated With HIV-1 Co-Infection and a Novel DHPS Mutation I504T Is Identified in Western Kenya." Frontiers in cellular and infection microbiology, vol. 10, 2020, pp. 600112. |
| Forconi CS, Oduor CI, Oluoch PO, Ong'echa JM, Münz C, Bailey JA, Moormann AM. "A New Hope for CD56negCD16pos NK Cells as Unconventional Cytotoxic Mediators: An Adaptation to Chronic Diseases." Frontiers in cellular and infection microbiology, vol. 10, 2020, pp. 162. |
| Mathai V, Das A, Bailey JA, Breuer K. "Airflows inside passenger cars and implications for airborne disease transmission." Science Advances, vol. 7, no. 1, 2020. |
| Mensah BA, Aydemir O, Myers-Hansen JL, Opoku M, Hathaway NJ, Marsh PW, Anto F, Bailey J, Abuaku B, Ghansah A. "Antimalarial Drug Resistance Profiling of Plasmodium falciparum Infections in Ghana Using Molecular Inversion Probes and Next-Generation Sequencing." Antimicrobial Agents and Chemotherapy, vol. 64, no. 4, 2020. |
| Bell GJ, Loop M, Topazian HM, Hudgens M, Mvalo T, Juliano JJ, Kamthunzi P, Tegha G, Mofolo I, Hoffman I, Bailey JA, Emch M. "Case reduction and cost-effectiveness of the RTS,S/AS01 malaria vaccine alongside bed nets in Lilongwe, Malawi." Vaccine, vol. 38, no. 25, 2020, pp. 4079-4087. |
| 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. |
| Bloch EM, Shoham S, Casadevall A, Sachais BS, Shaz B, Winters JL, van Buskirk C, Grossman BJ, Joyner M, Henderson JP, Pekosz A, Lau B, Wesolowski A, Katz L, Shan H, Auwaerter PG, Thomas D, Sullivan DJ, Paneth N, Gehrie E, Spitalnik S, Hod EA, Pollack L, Nicholson WT, Pirofski LA, Bailey JA, Tobian AA. "Deployment of convalescent plasma for the prevention and treatment of COVID-19." Journal of Clinical Investigation, vol. 130, no. 6, 2020, pp. 2757-2765. |
| Bell GJ, Loop MS, Mvalo T, Juliano JJ, Mofolo I, Kamthunzi P, Tegha G, Lievens M, Bailey J, Emch M, Hoffman I. "Environmental modifiers of RTS,S/AS01 malaria vaccine efficacy in Lilongwe, Malawi." BMC Public Health, vol. 20, no. 1, 2020, pp. 910. |
| Kaymaz Y, Oduor CI, Aydemir O, Luftig MA, Otieno JA, Ong'echa JM, Bailey JA, Moormann AM. "Epstein-Barr Virus Genomes Reveal Population Structure and Type 1 Association with Endemic Burkitt Lymphoma." Journal of Virology, vol. 94, no. 17, 2020. |
| 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. |
| Tessema SK, Hathaway NJ, Teyssier NB, Murphy M, Chen A, Aydemir O, Duarte EM, Simone W, Colborn J, Saute F, Crawford E, Aide P, Bailey JA, Greenhouse B. "Sensitive, highly multiplexed sequencing of microhaplotypes from the Plasmodium falciparum heterozygome." The Journal of Infectious Diseases, 2020. |
| Deutsch-Feldman M, Brazeau NF, Parr JB, Thwai KL, Muwonga J, Kashamuka M, Tshefu Kitoto A, Aydemir O, Bailey JA, Edwards JK, Verity R, Emch M, Gower EW, Juliano JJ, Meshnick SR. "Spatial and epidemiological drivers of Plasmodium falciparum malaria among adults in the Democratic Republic of the Congo." BMJ global health, vol. 5, no. 6, 2020. |
| Verity R, Aydemir O, Brazeau NF, Watson OJ, Hathaway NJ, Mwandagalirwa MK, Marsh PW, Thwai K, Fulton T, Denton M, Morgan AP, Parr JB, Tumwebaze PK, Conrad M, Rosenthal PJ, Ishengoma DS, Ngondi J, Gutman J, Mulenga M, Norris DE, Moss WJ, Mensah BA, Myers-Hansen JL, Ghansah A, Tshefu AK, Ghani AC, Meshnick SR, Bailey JA, Juliano JJ. "The impact of antimalarial resistance on the genetic structure of Plasmodium falciparum in the DRC." Nature Communications, vol. 11, no. 1, 2020, pp. 2107. |
| Ippolito MM, Pringle JC, Siame M, Katowa B, Aydemir O, Oluoch PO, Huang L, Aweeka FT, Bailey JA, Juliano JJ, Meshnick SR, Shapiro TA, Moss WJ, Thuma PE. "Therapeutic Efficacy of Artemether-Lumefantrine for Uncomplicated Falciparum Malaria in Northern Zambia." The American Journal of Tropical Medicine and Hygiene, vol. 103, no. 6, 2020, pp. 2224-2232. |
| 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. |
| Wesolowski A, Taylor AR, Chang HH, Verity R, Tessema S, Bailey JA, Alex Perkins T, Neafsey DE, Greenhouse B, Buckee CO. "Correction to: Mapping malaria by combining parasite genomic and epidemiologic data." BMC Medicine, vol. 16, no. 1, 2018, pp. 241. |
| 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. |
| Bozzay J, Bradley M, Kindvall A, Humphries A, Jessie E, Logeman J, Bailey J, Elster E, Rodriguez C. "Review of an emergency general surgery process improvement program at a verified military trauma center." Surgical Endoscopy, vol. 32, no. 10, 2018, pp. 4321-4328. |
| 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. |
| Meyerson HJ, Bailey J, Miedler J, Olobatuyi F. "Marginal zone B cell lymphomas with extensive plasmacytic differentiation are neoplasms of precursor plasma cells." Cytometry. Part B, Clinical cytometry, vol. 80, no. 2, 2011, pp. 71-82. |
| 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. |
| Sharakhova MV, George P, Brusentsova IV, Leman SC, Bailey JA, Smith CD, Sharakhov IV. "Genome mapping and characterization of the Anopheles gambiae heterochromatin." BMC genomics, vol. 11, 2010, pp. 459. |
| Bailey JA, Kidd JM, Eichler EE. "Human copy number polymorphic genes." Cytogenetic and genome research, vol. 123, no. 1-4, 2008, pp. 234-43. |
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"Origins and consequences of primate segmental duplications: crucibles of evolution, diversity and disease." 2006.
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| 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. |
| Bailey JA, Virgo KS, DiPiro JT, Nathens AB, Sawyer RG, Mazuski JE. "Aminoglycosides for intra-abdominal infection: equal to the challenge?." Surgical infections, vol. 3, no. 4, 2002, pp. 315-35. |
| 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." Nature, 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. |
| Kariuki HC, Mbugua G, Magak P, Bailey JA, Muchiri EM, Thiongo FW, King CH, Butterworth AE, Ouma JH, Blanton RE. "Prevalence and familial aggregation of schistosomal liver morbidity in Kenya: evaluation by new ultrasound criteria." The Journal of Infectious Diseases, vol. 183, no. 6, 2001, pp. 960-6. |
| 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 RTS,S as well as collaborating on systesm immunomics/genomics approaches to understadnign response in endemic regions.
Tracking the evolution and spread of recent malaria parasite drug resistance in Rwanda, Eithiopia, Kenya, Tanzania, Uganda and the Democratic Republic of Congo. Major efforts revolve around emerging artemisinin partial resistance -- a key component of all frontline drugs.
Determining the molecular underpinnings and role of the falciparum malaria and Epstein Barr Virus in etiology and pathology of Burkitt lymphoma.
The role of genetic variation and infectious agents in autoimmune disorders such as type 1 diabetes or other cancers.
| 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 |
|---|---|
| Friedman, Jennifer | Professor of Pediatrics, Professor of Epidemiology |
| Kurtis, Jonathan | Stanley M. Aronson Professor of Pathology and Laboratory Medicine, Chair of Pathology and Laboratory Medicine, Executive Director of the MD-PhD Program |
| McDonald, Emily | Assistant Professor of Pathology and Laboratory Medicine (Research), Assistant Professor of Pediatrics (Research) |
| Nixon, Christian | Associate Professor of Pathology and Laboratory Medicine |
| Ollila, Thomas | Assistant Professor of Medicine |
| Plavicki, Jessica | Associate Professor 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- |
