Publications

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 line Elife. 2021 Jan 27;10:e62586. doi: 10.7554/eLife.62586.PMID: 33501914

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. Antimicrob Agents Chemother. 2021 Feb 17;65(3):e01249-20. doi: 10.1128/AAC.01249-20. Print 2021 Feb 17. 

Mathai V, Das A, Bailey JA, Breuer K. Airflows inside passenger cars and implications for airborne disease transmission. Sci Adv. 2021 Jan 1;7(1):eabe0166. doi: 10.1126/sciadv.abe0166. Print 2021 Jan. 

2020

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. Am J Trop Med Hyg2020 Dec;103(6):2224-2232

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. J Virol2020 Nov 11

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. Mol Ecol. 2021 Jan;30(1):100-113. doi: 10.1111/mec.15706. Epub 2020 Nov 29. 

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 COVID-19: a matched cohort study. Clin Infect Dis2020 Oct 10

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. J Infect Dis2020 Aug 25

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. Transpl Infect Dis2020 Aug 19;:e13451

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. J Virol2020 Aug 17;94(17)

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 Lymphoma. J Infect Dis2020 Jun 16;222(1):111-120

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. J Clin Invest2020 Jun 1;130(6):2757-2765 

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 Glob Health2020 Jun;5(6)

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. Vaccine2020 May 22;38(25):4079-4087

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. Nat Commun2020 Apr 30;11(1):2107

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. Front Cell Infect Microbiol2020;10:162.

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. Antimicrob Agents Chemother2020 Mar 24;64(4)

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. Malar J2020 Jan 28;19(1):47

2019

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. Front Genet2019;10:1322


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, Mukhopadyay M, Dunson DB, Dave SS. The whole-genome landscape of Burkitt lymphoma subtypes. Blood2019 Nov 7;134(19):1598-1607

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 Plasmodium falciparum Parasites across Ethiopia. Am J Trop Med Hyg2019 Nov;101(5):1139-1143

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 Infect Dis2019 Oct 22;19(1):872

Ghansah A, Kamau E, Amambua-Ngwa A, Ishengoma DS, Maiga-Ascofare O, Amenga-Etego L, Deme A, Yavo W, Randrianarivelojosia M, Ochola-Oyier LI, Helegbe GK, Bailey J, Alifrangis M, Djimde A. Targeted Next Generation Sequencing for malaria research in Africa: current status and outlook. Malar J2019 Sep 23;18(1):324

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. Nat Commun2019 Sep 20;10(1):4300

Aydemir Ö, Noble JA, Bailey JA, Lernmark Å, Marsh P, Andersson Svärd A, Bearoff F, Blankenhorn EP, Mordes JP. Genetic Variation Within the HLA-DRA1 Gene Modulates Susceptibility to Type 1 Diabetes in HLA-DR3 Homozygotes. Diabetes2019 Jul;68(7):1523-1527

2018


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 Med2018 Oct 18;16(1):190

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. J Clin Apher2018 Oct;33(5):600-603

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. J Infect Dis2018 Aug 14;218(6):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. Am J Trop Med Hyg2018 Aug;99(2):495-501

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. Am J Trop Med Hyg. 2018 Aug;99(2):495-501

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. Sci Rep2018 Jul 5;8(1):10159

Zhao Y, Bailey JA, Linden J, St Pierre P, Cerny J, Vauthrin M, Greene M, Weinstein R. Automated red blood cell exchange in preparation for filgrastim mobilization of autologous peripheral blood hematopoietic progenitor cells in a patient with sickle cell anemia. J Clin Apher2018 Jun;33(3):431-435

Hathaway NJ, Parobek CM, Juliano JJ, Bailey JASeekDeep: single-base resolution de novo clustering for amplicon deep sequencing. Nucleic Acids Res2018 Feb 28;46(4):e21

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 Plasmodium falciparum Parasites are Genetically Homologous at the var2csa ID1-DBL2X Locus by Deep Sequencing.  Am J Trop Med Hyg. 2018 Jan;98(1):77-82

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 D3 supplement is effective prophylaxis against hypocalcemic toxicity during apheresis platelet donation. J Clin Apher2018 Feb;33(1):60-64

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. Malar J2018 Jan 24;17(1):46

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 Plasmodium falciparum Parasites are Genetically Homologous at the var2csa ID1-DBL2X Locus by Deep Sequencing. Am J Trop Med Hyg2018 Jan;98(1):77-82

2017

Miller RH, Hathaway NJ, Kharabora O, Mwandagalirwa K, Tshefu A, Meshnick SR, Taylor SM, Juliano JJ, Stewart VA, Bailey JAA deep sequencing approach to estimate Plasmodium falciparum complexity of infection (COI) and explore apical membrane antigen 1 diversity. Malar J2017 Dec 16;16(1):490

Oduor CI, Kaymaz Y, Chelimo K, Otieno JA, Ong'echa JM, Moormann AM, Bailey JAIntegrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma. BMC Cancer2017 Nov 13;17(1):761

Ashar-Patel A, Kaymaz Y, Rajakumar A, Bailey JA, Karumanchi SA, Moore MJ. FLT1 and transcriptome-wide polyadenylation site (PAS) analysis in preeclampsia. Sci Rep2017 Sep 22;7(1):12139

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. Sci Rep2017 Aug 11;7(1):7768

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 Insight2017 Aug 3;2(15)

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. Malar J2017 Jun 5;16(1):236

Zhao Y, Alexander B, Bailey JA, Welch L, Greene M, Vauthrin M, Mitchell M, Weinstein R. Therapeutic apheresis using a mononuclear cell program to lower the microfilaria burden of a 23-year-old African woman with loiasis. J Clin Apher2017 Jun;32(3):200-202

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 Biol Evol2017 Jun 1;9(6):1673-1686

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. J Clin Apher2017 Jun;32(3):154-157

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. Mol Cancer Res2017 May;15(5):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. Emerg Infect Dis2017 Apr;23(4):714-715

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. Front Microbiol2017;8:501

2016

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. Front Microbiol2017;8:501

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. Am J Trop Med Hyg2016 Dec 7;95(6):1409-1412

Moormann AM, Bailey JA. Malaria - how this parasitic infection aids and abets EBV-associated Burkitt lymphomagenesis. Curr Opin Virol2016 Oct;20:78-84

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. Lancet Glob Health2016 Oct;4(10):e736-43

Purpura LJ, Soka M, Baller A, White S, Rogers E, Choi MJ, Mahmoud N, Wasunna C, Massaquoi M, Vanderende K, Kollie J, Dweh S, Bemah P, Christie A, Ladele V, Subah O, Pillai S, Mugisha M, Kpaka J, Nichol S, Ströher U, Abad N, Mettee-Zarecki S, Bailey JA, Rollin P, Marston B, Nyenswah T, Gasasira A, Knust B, Williams D. Implementation of a National Semen Testing and Counseling Program for Male Ebola Survivors - Liberia, 2015-2016. MMWR Morb Mortal Wkly Rep2016 Sep 16;65(36):963-6

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. Int J Cancer2016 Sep 15;139(6):1231-40

Galera P, Haynes S, Sulmasy P, Bailey JA, Greene M, Vauthrin M, Brettler D, Liebmann J, Mark Madison J, Weinstein R. Physiological measurements corroborate symptomatic improvement after therapeutic leukapheresis in a pregnant woman with chronic myelogenous leukemia. J Clin Apher2016 Aug;31(4):393-7

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. Nat Microbiol2016 Jun 13;1(7):16079

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. Evol Med Public Health2016 Jan 27;2016(1):21-36

 2015 

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. J Clin Apher2015 Dec;30(6):367-70

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. J Infect Dis2015 Sep 15;212(6):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. Appl Environ Microbiol2015 Sep;81(18):6200-9

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. Transfusion2015 Jun;55(6):1327-30

2014 

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. J Infect Dis. 2015 Mar 1;211(5):680-8

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. Am J Trop Med Hyg2014 Sep;91(3):649-54

Simkin AT, Bailey JA, Gao FB, Jensen JD. Inferring the evolutionary history of primate microRNA binding sites: overcoming motif counting biases. Mol Biol Evol2014 Jul;31(7):1894-901

Chhibber V, Greene M, Vauthrin M, Bailey J, Weinstein R. Is group A thawed plasma suitable as the first option for emergency release transfusion? (CME). Transfusion2014 Jul;54(7):1751-5

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 Negl Trop Dis2014 Apr;8(4):e2796

Weinstein R, Kershaw G, Bailey J, Greene M, Chhibber V, Vauthrin M, Nath R, Galvin Karr E. Safety and efficacy of autologous hemopoietic progenitor cell collection in tandem with hemodialysis in multiple myeloma with myeloma cast nephropathy. J Clin Apher2014 Apr;29(2):83-9

2013

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 Parasitol2013 Jul;29(7):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 One2013;8(5):e62427

Johnson ME, Rowsey RA, Shirley S, Vandevoort C, Bailey J, Hassold T. A specific family of interspersed repeats (SINEs) facilitates meiotic synapsis in mammals. Mol Cytogenet2013 Jan 1;6(1):1

2012

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. J Infect Dis2012 Aug 15;206(4):580-7

2011 

Meyerson HJ, Bailey J, Miedler J, Olobatuyi F. Marginal zone B cell lymphomas with extensive plasmacytic differentiation are neoplasms of precursor plasma cells. Cytometry B Clin Cytom2011 Mar;80(2):71-82

Sharakhova MV, George P, Brusentsova IV, Leman SC, Bailey JA, Smith CD, Sharakhov IV. Genome mapping and characterization of the Anopheles gambiae heterochromatin. BMC Genomics2010 Aug 4;11:459

2010

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 One2010 May 12;5(5):e10592doi: 10.1371/journal.pone.0010592. PubMed PMID: 20485676; PubMed Central PMCID: PMC2868863

Klapper E, Zhang Y, Figueroa P, Ness P, Stubbs J, Abumuhor I, Bailey J, Epperson L, Tauscher C, Enriquez E, Hashmi G, Seul M. Toward extended phenotype matching: a new operational paradigm for the transfusion service. Transfusion2010 Mar;50(3):536-46

2009

Bailey JA, Kidd JM, Eichler EE. Human copy number polymorphic genes. Cytogenet Genome Res2008;123(1-4):234-43

2006

Bailey JA, Eichler EE. Primate segmental duplications: crucibles of evolution, diversity and disease. Nat Rev Genet. 2006 Jul;7(7):552-64

2005 

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. Nat Genet2005 Jul;37(7):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 Res2005 Jul 1;33(Web Server issue):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. Am J Hum Genet2005 Jul;77(1):78-88

2004

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. Nature2004 Aug 19;430(7002):857-64doi: 10.1038/nature02806. PubMed PMID: 15318213

Bailey JA, Church DM, Ventura M, Rocchi M, Eichler EE. Analysis of segmental duplications and genome assembly in the mouse. Genome Res2004 May;14(5):789-801doi: 10.1101/gr.2238404. PubMed PMID: 15123579; PubMed Central PMCID: PMC479105

Tuzun E, Bailey JA, Eichler EE. Recent segmental duplications in the working draft assembly of the brown Norway rat. Genome Res2004 Apr;14(4):493-506doi: 10.1101/gr.1907504. PubMed PMID: 15059990; PubMed Central PMCID: PMC383293

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. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature2004 Apr 1;428(6982):493-521doi: 10.1038/nature02426. PubMed PMID: 15057822; NIHMSID:NIHMS291392

Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE. Hotspots of mammalian chromosomal evolution. Genome Biol2004;5(4):R23doi: 10.1186/gb-2004-5-4-r23. Epub 2004 Mar 8. PubMed PMID: 15059256; PubMed Central PMCID: PMC395782

Alkan C, Eichler EE, Bailey JA, Sahinalp SC, Tüzün E. The role of unequal crossover in alpha-satellite DNA evolution: a computational analysis. J Comput Biol2004;11(5):933-44 

2003

Bailey JA, Liu G, Eichler EE. An Alu transposition model for the origin and expansion of human segmental duplications. Am J Hum Genet2003 Oct;73(4):823-34 

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. Mol Biol Evol2003 Sep;20(9):1463-79

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. Nature2003 Jul 10;424(6945):157-64doi: 10.1038/nature01782. PubMed PMID: 12853948

Liu G, 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 Res2003 Mar;13(3):358-68doi: 10.1101/gr.923303. PubMed PMID: 12618366; PubMed Central PMCID: PMC430288

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 Res2003 Feb;13(2):159-72doi: 10.1101/gr.644503. PubMed PMID: 12566394; PubMed Central PMCID: PMC420363

Bailey JA, Eichler EE. Genome-wide detection and analysis of recent segmental duplications within mammalian organisms. Cold Spring Harb Symp Quant Biol2003;68:115-24doi: 10.1101/sqb.2003.68.115. Review. PubMed PMID: 15338609

2002

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. Science2002 Aug 9;297(5583):1003-7doi: 10.1126/science.1072047. PubMed PMID: 12169732

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. Am J Hum Genet2002 Jan;70(1):83-100doi: 10.1086/338458. Epub 2001 Nov 30. PubMed PMID: 11731936; PubMed Central PMCID: PMC419985

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 Inform2002;13:93-102PubMed PMID: 14571378

2001

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. Nature2001 Oct 4;413(6855):514-9doi: 10.1038/35097067. PubMed PMID: 11586358

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. Nature2001 Oct 4;413(6855):514-9doi: 10.1038/35097067. PubMed PMID: 11586358

Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE. Segmental duplications: organization and impact within the current human genome project assembly. Genome Res2001 Jun;11(6):1005-17doi: 10.1101/gr.gr-1871r. PubMed PMID: 11381028; PubMed Central PMCID: PMC311093

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. J Infect Dis2001 Mar 15;183(6):960-6doi: 10.1086/319247. Epub 2001 Feb 13. PubMed PMID: 11237814

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. Initial sequencing and analysis of the human genome. Nature2001 Feb 15;409(6822):860-921doi: 10.1038/35057062. PubMed PMID: 11237011

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. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature2001 Feb 15;409(6822):953-8doi: 10.1038/35057192. PubMed PMID: 11237021

2000

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 Res2000 Sep;10(9):1319-32doi: 10.1101/gr.138100. PubMed PMID: 10984450

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. Proc Natl Acad Sci U S A2000 Jun 6;97(12):6634-9doi: 10.1073/pnas.97.12.6634. PubMed PMID: 10841562; PubMed Central PMCID: PMC18684

1999

Halushka MK, Mathews DJ, Bailey JA, Chakravarti A. GIST: A web tool for collecting gene information. Physiol Genomics1999 Aug 31;1(2):75-81doi: 10.1152/physiolgenomics.1999.1.2.75. PubMed PMID: 11015564