Publications
Also see Jeff’s Google Scholar Page and MyNCBI
2023
Susceptibility of Ugandan Plasmodium falciparum Isolates to the Antimalarial Drug Pipeline. 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.Microbiol Spectr. 2023 May 9:e0523622. doi: 10.1128/spectrum.05236-22. Online ahead of print. PMID: 37158739
Plasmodium falciparum gametocyte carriage in longitudinally monitored incident infections is associated with duration of infection and human host factors. 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.Sci Rep. 2023 May 1;13(1):7072. doi: 10.1038/s41598-023-33657-3.PMID: 37127688
Examining the Early Distribution of the Artemisinin-Resistant Plasmodium falciparum kelch13 R561H Mutation in Areas of Higher Transmission in Rwanda. Kirby R, Giesbrecht D, Karema C, Watson O, Lewis S, Munyaneza T, Butera JD, Juliano JJ, Bailey JA, Mazarati JB.Open Forum Infect Dis. 2023 Mar 21;10(4):ofad149. doi: 10.1093/ofid/ofad149. eCollection 2023 Apr. PMID: 37096145
Distinctive Kaposi Sarcoma-Associated Herpesvirus Serological Profile during Acute Plasmodium falciparum Malaria Episodes. Oluoch PO, Forconi CS, Oduor CI, Ritacco DA, Akala HM, Bailey JA, Juliano JJ, Ong'echa JM, Münz C, Moormann AM.Int J Mol Sci. 2023 Apr 4;24(7):6711. doi: 10.3390/ijms24076711.PMID: 37047683
Expression Microdissection for the Analysis of miRNA in a Single-Cell Type. 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.Lab Invest. 2023 Mar 28;103(7):100133. doi: 10.1016/j.labinv.2023.100133. Online ahead of print.PMID: 36990152
Endemic Burkitt lymphoma avatar mouse models for exploring inter-patient tumor variation and testing targeted therapies. 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.Life Sci Alliance. 2023 Mar 6;6(5):e202101355. doi: 10.26508/lsa.202101355. Print 2023 May.PMID: 36878637
SARS-CoV-2 Serosurveys: How Antigen, Isotype and Threshold Choices Affect the Outcome. 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.J Infect Dis. 2023 Feb 1;227(3):371-380. doi: 10.1093/infdis/jiac431.PMID: 36314635
2022
Profiling genome-wide recombination in Epstein Barr virus reveals type-specific patterns and associations with endemic-Burkitt lymphoma. Agwati EO, Oduor CI, Ayieko C, Ong'echa JM, Moormann AM, Bailey JA.Virol J. 2022 Dec 8;19(1):208. doi: 10.1186/s12985-022-01942-8.PMID: 36482473
Decreased susceptibility of Plasmodium falciparum to both dihydroartemisinin and lumefantrine in northern Uganda. 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.Nat Commun. 2022 Oct 26;13(1):6353. doi: 10.1038/s41467-022-33873-x.PMID: 36289202
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. 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.Am J Trop Med Hyg. 2022 Oct 11;107(4_Suppl):68-74. doi: 10.4269/ajtmh.21-1288. Print 2022 Oct 11.PMID: 36228913
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. 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.Am J Trop Med Hyg. 2022 Oct 11;107(4_Suppl):55-67. doi: 10.4269/ajtmh.21-1287. Print 2022 Oct 11.PMID: 36228903
Susceptibilities of Ugandan Plasmodium falciparum Isolates to Proteasome Inhibitors. 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.Antimicrob Agents Chemother. 2022 Oct 18;66(10):e0081722. doi: 10.1128/aac.00817-22. Epub 2022 Sep 12.PMID: 36094216
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. Dosoo DK, Bailey JA, Asante KP, Oppong FB, Niaré K, Opoku-Mensah J, Owusu-Agyei S, Greenwood B, Chandramohan D.PLoS One. 2022 Aug 8;17(8):e0271489. doi: 10.1371/journal.pone.0271489. eCollection 2022.PMID: 35939419
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. 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.Front Cell Infect Microbiol. 2022 Jul 13;12:757844. doi: 10.3389/fcimb.2022.757844. eCollection 2022.PMID: 35909968
Malaria Transmission Intensity Likely Modifies RTS, S/AS01 Efficacy Due to a Rebound Effect in Ghana, Malawi, and Gabon. 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.J Infect Dis. 2022 Nov 1;226(9):1646-1656. doi: 10.1093/infdis/jiac322.PMID: 35899811
Characterization of triatomine bloodmeal sources using direct Sanger sequencing and amplicon deep sequencing methods. 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.Sci Rep. 2022 Jun 17;12(1):10234. doi: 10.1038/s41598-022-14208-8.PMID: 35715521
The East Africa Consortium for human papillomavirus and cervical cancer in women living with HIV/AIDS. 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. Ann Med. 2022 Dec;54(1):1202-1211.
mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis. Movassagh M, Morton SU, Hehnly C, Smith J, Doan TT, Irizarry R, Broach JR, Schiff SJ, Bailey JA, Paulson JN. BMC Genomics. 2022 Jun 13;23(1):439. doi: 10.1186/s12864-022-08558-w.PMID: 35698050
Whole blood transfusion for severe malarial anemia in a high Plasmodium falciparum transmission setting. 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.Clin Infect Dis. 2022 Apr 19:ciac304. doi: 10.1093/cid/ciac304. Online ahead of print.PMID: 35439307
Amplicon Sequencing as a Potential Surveillance Tool for Complexity of Infection and Drug Resistance Markers in Plasmodium falciparum Asymptomatic Infections. Wamae K, Kimenyi KM, Osoti V, de Laurent ZR, Ndwiga L, Kharabora O, Hathaway NJ, Bailey JA, Juliano JJ, Bejon P, Ochola-Oyier LI.J Infect Dis. 2022 Sep 13;226(5):920-927. doi: 10.1093/infdis/jiac144.PMID: 3542939
2021
Immediate pools of malaria infections at diagnosis combined with targeted deep sequencing accurately quantifies frequency of drug resistance mutations. Aydemir O, Mensah B, Marsh PW, Abuaku B, Myers-Hansen JL, Bailey JA, Ghansah A. PeerJ. 2021 Nov 9;9:e11794. doi: 10.7717/peerj.11794. eCollection 2021.PMID: 34820155
Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia. 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.Nat Microbiol. 2021 Oct;6(10):1289-1299. doi: 10.1038/s41564-021-00962-4. Epub 2021 Sep 27.PMID: 34580442
Drug susceptibility of Plasmodium falciparum in eastern Uganda: a longitudinal phenotypic and genotypic study. 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. Lancet Microbe. 2021 Sep;2(9):e441-e449. doi: 10.1016/s2666-5247(21)00085-9. Epub 2021 Jun 18.PMID: 34553183
Decreased Susceptibility to Dihydrofolate Reductase Inhibitors Associated With Genetic Polymorphisms in Ugandan Plasmodium falciparum Isolates. 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. J Infect Dis. 2022 Feb 15;225(4):696-704. doi: 10.1093/infdis/jiab435.PMID: 34460932
Impacts of Ecology, Parasite Antigenic Variation, and Human Genetics on RTS,S/AS01e Malaria Vaccine Efficacy. Bell GJ, Agnandji ST, Asante KP, Ghansah A, Kamthunzi P, Emch M, Bailey JA. Curr Epidemiol Rep. 2021;8(3):79-88. doi: 10.1007/s40471-021-00271-8. Epub 2021 Jul 30.PMID: 34367877
Association of killer cell immunoglobulin-like receptors with endemic Burkitt lymphoma in Kenyan children. Muriuki BM, Forconi CS, Oluoch PO, Bailey JA, Ghansah A, Moormann AM, Ong'echa JM.Sci Rep. 2021 May 31;11(1):11343. doi: 10.1038/s41598-021-90596-7.PMID: 34059753
Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host-pathogen dynamics in lymphoblastoid cell lines. SoRelle ED, Dai J, Bonglack EN, Heckenberg EM, Zhou JY, Giamberardino SN, Bailey JA, Gregory SG, Chan C, Luftig MA. Elife. 2021 Jan 27;10:e62586. doi: 10.7554/eLife.62586.PMID: 33501914
Selection of Cytochrome b Mutants Is Rare among Plasmodium falciparum Patients Failing Treatment with Atovaquone-Proguanil in Cambodia. 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.Antimicrob Agents Chemother. 2021 Feb 17;65(3):e01249-20. doi: 10.1128/AAC.01249-20. Print 2021 Feb 17.PMID: 33361308
Airflows inside passenger cars and implications for airborne disease transmission. Mathai V, Das A, Bailey JA, Breuer K.Sci Adv. 2021 Jan 1;7(1):eabe0166. doi: 10.1126/sciadv.abe0166. Print 2021 Jan.PMID: 33277325
Deep Gene Sequence Cluster Analyses of Multi-Virus-Infected Mucosal Tissue Reveal Enhanced Transmission of Acute HIV-1. 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.J Virol. 2021 Jan 13;95(3):e01737-20. doi: 10.1128/JVI.01737-20. Print 2021 Jan 13.PMID: 33177204
2020
Plasmodium falciparum DHFR and DHPS Mutations Are Associated With HIV-1 Co-Infection and a Novel DHPS Mutation I504T Is Identified in Western Kenya. 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. Front Cell Infect Microbiol. 2020 Nov 26;10:600112. doi: 10.3389/fcimb.2020.600112. eCollection 2020.PMID: 33324580
Describing the current status of Plasmodium falciparum population structure and drug resistance within mainland Tanzania using molecular inversion probes. 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.Mol Ecol. 2021 Jan;30(1):100-113. doi: 10.1111/mec.15706. Epub 2020 Nov 29.PMID: 33107096
Therapeutic Efficacy of Artemether-Lumefantrine for Uncomplicated Falciparum Malaria in Northern Zambia. 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. Am J Trop Med Hyg. 2020 Dec;103(6):2224-2232. doi: 10.4269/ajtmh.20-0852. Epub 2020 Oct 15.PMID: 33078701
Convalescent Plasma for Patients With Severe Coronavirus Disease 2019 (COVID-19): A Matched Cohort Study. 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.Clin Infect Dis. 2021 Jul 1;73(1):e208-e214. doi: 10.1093/cid/ciaa1548.PMID: 33038227 (epub 2020)
Sensitive, Highly Multiplexed Sequencing of Microhaplotypes From the Plasmodium falciparum Heterozygome. 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.J Infect Dis. 2022 Apr 1;225(7):1227-1237. doi: 10.1093/infdis/jiaa527.PMID: 32840625 (online J Infect Dis. 2020 Aug 25)
Successful recovery from COVID-19 in three kidney transplant recipients who received convalescent plasma therapy. Naeem S, Gohh R, Bayliss G, Cosgrove C, Farmakiotis D, Merhi B, Morrissey P, Osband A, Bailey JA, Sweeney J, Rogers R.Transpl Infect Dis. 2021 Feb;23(1):e13451. doi: 10.1111/tid.13451. Epub 2020 Sep 3.PMID: 32815238
Epstein-Barr Virus Genomes Reveal Population Structure and Type 1 Association with Endemic Burkitt Lymphoma. Kaymaz Y, Oduor CI, Aydemir O, Luftig MA, Otieno JA, Ong'echa JM, Bailey JA, Moormann AM.J Virol. 2020 Aug 17;94(17):e02007-19. doi: 10.1128/JVI.02007-19. Print 2020 Aug 17.PMID: 32581102
Kaposi Sarcoma-Associated Herpesvirus Infection and Endemic Burkitt Lymphoma. Oluoch PO, Oduor CI, Forconi CS, Ong'echa JM, Münz C, Dittmer DP, Bailey JA, Moormann AM.J Infect Dis. 2020 Jun 16;222(1):111-120. doi: 10.1093/infdis/jiaa060.PMID: 32072172
Deployment of convalescent plasma for the prevention and treatment of COVID-19. 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.J Clin Invest. 2020 Jun 1;130(6):2757-2765. doi: 10.1172/JCI138745.PMID: 3225406
Spatial and epidemiological drivers of Plasmodium falciparum malaria among adults in the Democratic Republic of the Congo. 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.BMJ Glob Health. 2020 Jun;5(6):e002316. doi: 10.1136/bmjgh-2020-002316.PMID: 32601091
Case reduction and cost-effectiveness of the RTS,S/AS01 malaria vaccine alongside bed nets in Lilongwe, Malawi. Bell GJ, Loop M, Topazian HM, Hudgens M, Mvalo T, Juliano JJ, Kamthunzi P, Tegha G, Mofolo I, Hoffman I, Bailey JA, Emch M.Vaccine. 2020 May 22;38(25):4079-4087. doi: 10.1016/j.vaccine.2020.04.031. Epub 2020 Apr 30.PMID: 32362527
A New Hope for CD56negCD16pos NK Cells as Unconventional Cytotoxic Mediators: An Adaptation to Chronic Diseases. Forconi CS, Oduor CI, Oluoch PO, Ong'echa JM, Münz C, Bailey JA, Moormann AM.Front Cell Infect Microbiol. 2020 Apr 21;10:162. doi: 10.3389/fcimb.2020.00162. eCollection 2020.PMID: 32373555
The impact of antimalarial resistance on the genetic structure of Plasmodium falciparum in the DRC. 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. Nat Commun. 2020 Apr 30;11(1):2107. doi: 10.1038/s41467-020-15779-8.PMID: 32355199
Antimalarial Drug Resistance Profiling of Plasmodium falciparum Infections in Ghana Using Molecular Inversion Probes and Next-Generation Sequencing. Mensah BA, Aydemir O, Myers-Hansen JL, Opoku M, Hathaway NJ, Marsh PW, Anto F, Bailey J, Abuaku B, Ghansah A.Antimicrob Agents Chemother. 2020 Mar 24;64(4):e01423-19. doi: 10.1128/AAC.01423-19. Print 2020 Mar 24.PMID: 31932374
2019
Combining Citizen Science and Genomics to Investigate Tick, Pathogen, and Commensal Microbiome at Single-Tick Resolution. Chauhan G, McClure J, Hekman J, Marsh PW, Bailey JA, Daniels RF, Genereux DP, Karlsson EK.Front Genet. 2020 Jan 21;10:1322. doi: 10.3389/fgene.2019.01322. eCollection 2019.PMID: 32038704
Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago. 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.Malar J. 2020 Jan 28;19(1):47. doi: 10.1186/s12936-020-3137-8.PMID: 31992305
Sensitive detection of EBV microRNAs across cancer spectrum reveals association with decreased survival in adult acute myelocytic leukemia. Movassagh M, Oduor C, Forconi C, Moormann AM, Bailey JA. Sci Rep. 2019 Dec 30;9(1):20321. doi: 10.1038/s41598-019-56472-1.PMID: 31889055
The whole-genome landscape of Burkitt lymphoma subtypes. 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.Blood. 2019 Nov 7;134(19):1598-1607. doi: 10.1182/blood.2019001880.PMID: 31558468
Pooled Deep Sequencing of Drug Resistance Loci from Plasmodium falciparum Parasites across Ethiopia. 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.Am J Trop Med Hyg. 2019 Nov;101(5):1139-1143. doi: 10.4269/ajtmh.19-0142.PMID: 31516103
The changing landscape of Plasmodium falciparum drug resistance in the Democratic Republic of Congo. 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. BMC Infect Dis. 2019 Oct 22;19(1):872. doi: 10.1186/s12879-019-4523-0.PMID: 31640574
Targeted Next Generation Sequencing for malaria research in Africa: current status and outlook. 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.Malar J. 2019 Sep 23;18(1):324. doi: 10.1186/s12936-019-2944-2.PMID: 31547818
Plasmodium vivax chloroquine resistance links to pvcrt transcription in a genetic cross. 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. Nat Commun. 2019 Sep 20;10(1):4300. doi: 10.1038/s41467-019-12256-9.PMID: 31541097
Genetic Variation Within the HLA-DRA1 Gene Modulates Susceptibility to Type 1 Diabetes in HLA-DR3 Homozygotes. 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.Diabetes. 2019 Jul;68(7):1523-1527. doi: 10.2337/db18-1128. Epub 2019 Apr 8.PMID: 30962219
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. Wang J, Song J, Zhou S, Fu Y, Bailey JA, Shen C.Blood Transfus. 2019 Jan;17(1):53-59. doi: 10.2450/2018.0176-17. Epub 2018 Jan 16.PMID: 29517966
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 Med. 2018 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 Apher. 2018 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 Dis. 2018 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 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 Rep. 2018 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 Apher. 2018 Jun;33(3):431-435
Hathaway NJ, Parobek CM, Juliano JJ, Bailey JA. SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing. Nucleic Acids Res. 2018 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 Apher. 2018 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 J. 2018 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 Hyg. 2018 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 JA. A deep sequencing approach to estimate Plasmodium falciparum complexity of infection (COI) and explore apical membrane antigen 1 diversity. Malar J. 2017 Dec 16;16(1):490
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. 2017 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 Rep. 2017 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 Rep. 2017 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 Insight. 2017 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 J. 2017 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 Apher. 2017 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 Evol. 2017 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 Apher. 2017 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 Res. 2017 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 Dis. 2017 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 Microbiol. 2017;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 Microbiol. 2017;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 Hyg. 2016 Dec 7;95(6):1409-1412
Moormann AM, Bailey JA. Malaria - how this parasitic infection aids and abets EBV-associated Burkitt lymphomagenesis. Curr Opin Virol. 2016 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 Health. 2016 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 Rep. 2016 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 Cancer. 2016 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 Apher. 2016 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 Microbiol. 2016 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 Health. 2016 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 Apher. 2015 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 Dis. 2015 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 Microbiol. 2015 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. Transfusion. 2015 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 Hyg. 2014 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 Evol. 2014 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). Transfusion. 2014 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 Dis. 2014 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 Apher. 2014 Apr;29(2):83-9
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. Int J Cancer. 2014 Feb 1;134(3):645-53
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 Parasitol. 2013 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 One. 2013;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 Cytogenet. 2013 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 Dis. 2012 Aug 15;206(4):580-7
2011
Medical School and Residency
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 Cytom. 2011 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 Genomics. 2010 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 One. 2010 May 12;5(5):e10592. doi: 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. Transfusion. 2010 Mar;50(3):536-46
2009
Bailey JA, Kidd JM, Eichler EE. Human copy number polymorphic genes. Cytogenet Genome Res. 2008;123(1-4):234-43
2006
Primate segmental duplications: crucibles of evolution, diversity and disease. Bailey JA, Eichler EE.Nat Rev Genet. 2006 Jul;7(7):552-64. doi: 10.1038/nrg1895. Epub 2006 Jun 13.PMID: 16770338
Postdoctoral Fellowship
Manipulating multiple sequence alignments via MaM and WebMaM. Alkan C, Tüzün E, Buard J, Lethiec F, Eichler EE, Bailey JA, Sahinalp SC.Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W295-8. doi: 10.1093/nar/gki406.PMID: 15980474
Segmental duplications and copy-number variation in the human genome. 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.Am J Hum Genet. 2005 Jul;77(1):78-88. doi: 10.1086/431652. Epub 2005 May 25.PMID: 15918152
Fine-scale structural variation of the human genome. Tuzun E*, Sharp AJ*, Bailey JA*, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, Olson MV, Eichler EE.Nat Genet. 2005 Jul;37(7):727-32. doi: 10.1038/ng1562. Epub 2005 May 15.PMID: 15895083
The structure and evolution of centromeric transition regions within the human genome. 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.Nature. 2004 Aug 19;430(7002):857-64. doi: 10.1038/nature02806.PMID: 15318213
Genome-wide detection and analysis of recent segmental duplications within mammalian organisms. Bailey JA, Eichler EE.Cold Spring Harb Symp Quant Biol. 2003;68:115-24. doi: 10.1101/sqb.2003.68.115.PMID: 15338609
Hots of mammalian chromosomal evolution. Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE.Genome Biol. 2004;5(4):R23. doi: 10.1186/gb-2004-5-4-r23. Epub 2004 Mar 8.PMID: 15059256
Recent segmental duplications in the working draft assembly of the brown Norway rat. Tuzun E, Bailey JA, Eichler EE.Genome Res. 2004 Apr;14(4):493-506. doi: 10.1101/gr.1907504.PMID: 15059990
PhD
The role of unequal crossover in alpha-satellite DNA evolution: a computational analysis. Alkan C, Eichler EE, Bailey JA, Sahinalp SC, Tüzün E.J Comput Biol. 2004;11(5):933-44. doi: 10.1089/cmb.2004.11.933.PMID: 15700410
The structure and evolution of centromeric transition regions within the human genome. 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.Nature. 2004 Aug 19;430(7002):857-64. doi: 10.1038/nature02806.PMID: 15318213
Analysis of segmental duplications and genome assembly in the mouse. Bailey JA, Church DM, Ventura M, Rocchi M, Eichler EE.Genome Res. 2004 May;14(5):789-801. doi: 10.1101/gr.2238404.PMID: 15123579
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. 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.Nature. 2004 Apr 1;428(6982):493-521. doi: 10.1038/nature02426.PMID: 15057822
An Alu transposition model for the origin and expansion of human segmental duplications. Bailey JA, Liu G, Eichler EE.Am J Hum Genet. 2003 Oct;73(4):823-34. doi: 10.1086/378594. Epub 2003 Sep 22.PMID: 14505274
An algorithmic analysis of the role of unequal crossover in alpha-satellite DNA evolution. Alkan C, Bailey JA, Eichler EE, Sahinalp SC, Tuzun E.Genome Inform. 2002;13:93-102.PMID: 14571378
Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE. Hotspots of mammalian chromosomal evolution. Genome Biol. 2004;5(4):R23. doi: 10.1186/gb-2004-5-4-r23. Epub 2004 Mar 8. PubMed PMID: 15059256; PubMed Central PMCID: PMC395782
Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. iu G; NISC Comparative Sequencing Program, Zhao S, Bailey JA, Sahinalp SC, Alkan C, Tuzun E, Green ED, Eichler EE.Genome Res. 2003 Mar;13(3):358-68. doi: 10.1101/gr.923303.PMID: 12618366
The DNA sequence of human chromosome 7. 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.Nature. 2003 Jul 10;424(6945):157-64. doi: 10.1038/nature01782.PMID: 12853948
Using a pericentromeric interspersed repeat to recapitulate the phylogeny and expansion of human centromeric segmental duplications. 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.Mol Biol Evol. 2003 Sep;20(9):1463-79. doi: 10.1093/molbev/msg158. Epub 2003 May 30.PMID: 12777517
Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10p. 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.Genome Res. 2003 Feb;13(2):159-72. doi: 10.1101/gr.644503.PMID: 12566394
Recent segmental duplications in the human genome. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE.Science. 2002 Aug 9;297(5583):1003-7. doi: 10.1126/science.1072047.PMID: 12169732
Human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22. Bailey JA, Yavor AM, Viggiano L, Misceo D, Horvath JE, Archidiacono N, Schwartz S, Rocchi M, Eichler EE.Am J Hum Genet. 2002 Jan;70(1):83-100. doi: 10.1086/338458. Epub 2001 Nov 30.PMID: 11731936
Lessons from the human genome: transitions between euchromatin and heterochromatin. Horvath JE, Bailey JA, Locke DP, Eichler EE.Hum Mol Genet. 2001 Oct 1;10(20):2215-23. doi: 10.1093/hmg/10.20.2215.PMID: 11673404
Positive selection of a gene family during the emergence of humans and African apes. Johnson ME, Viggiano L, Bailey JA, Abdul-Rauf M, Goodwin G, Rocchi M, Eichler EE.Nature. 2001 Oct 4;413(6855):514-9. doi: 10.1038/35097067.PMID: 11586358
Segmental duplications: organization and impact within the current human genome project assembly. Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE.Genome Res. 2001 Jun;11(6):1005-17. doi: 10.1101/gr.gr-1871r.PMID: 11381028
Prevalence and familial aggregation of schistosomal liver morbidity in Kenya: evaluation by new ultrasound criteria. Kariuki HC, Mbugua G, Magak P, Bailey JA, Muchiri EM, Thiongo FW, King CH, Butterworth AE, Ouma JH, Blanton RE.J Infect Dis. 2001 Mar 15;183(6):960-6. doi: 10.1086/319247. Epub 2001 Feb 13.PMID: 11237814
Initial sequencing and analysis of the human genome. 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.Nature. 2001 Feb 15;409(6822):860-921. doi: 10.1038/35057062.PMID: 11237011
Integration of cytogenetic landmarks into the draft sequence of the human genome. 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.Nature. 2001 Feb 15;409(6822):953-8. doi: 10.1038/35057192.PMID: 11237021
Patterns of meiotic recombination on the long arm of human chromosome 21. Lynn A, Kashuk C, Petersen MB, Bailey JA, Cox DR, Antonarakis SE, Chakravarti A.Genome Res. 2000 Sep;10(9):1319-32. doi: 10.1101/gr.138100.PMID: 10984450
Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis. Bailey JA, Carrel L, Chakravarti A, Eichler EE.Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6634-9. doi: 10.1073/pnas.97.12.6634.PMID: 10841562
GIST: A web tool for collecting gene information. Halushka MK, Mathews DJ, Bailey JA, Chakravarti A.Physiol Genomics. 1999 Aug 31;1(2):75-81. doi: 10.1152/physiolgenomics.1999.1.2.75.PMID: 11015564