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Items: 32

1.

Automatic choroidal segmentation in OCT images using supervised deep learning methods.

Kugelman J, Alonso-Caneiro D, Read SA, Hamwood J, Vincent SJ, Chen FK, Collins MJ.

Sci Rep. 2019 Sep 16;9(1):13298. doi: 10.1038/s41598-019-49816-4.

2.

Medical countermeasures during the 2018 Ebola virus disease outbreak in the North Kivu and Ituri Provinces of the Democratic Republic of the Congo: a rapid genomic assessment.

Mbala-Kingebeni P, Aziza A, Di Paola N, Wiley MR, Makiala-Mandanda S, Caviness K, Pratt CB, Ladner JT, Kugelman JR, Prieto K, Chitty JA, Larson PA, Beitzel B, Ayouba A, Vidal N, Karhemere S, Diop M, Diagne MM, Faye M, Faye O, Aruna A, Nsio J, Mulangu F, Mukadi D, Mukadi P, Kombe J, Mulumba A, Villabona-Arenas CJ, Pukuta E, Gonzalez J, Bartlett ML, Sozhamannan S, Gross SM, Schroth GP, Tim R, Zhao JJ, Kuhn JH, Diallo B, Yao M, Fall IS, Ndjoloko B, Mossoko M, Lacroix A, Delaporte E, Sanchez-Lockhart M, Sall AA, Muyembe-Tamfum JJ, Peeters M, Palacios G, Ahuka-Mundeke S.

Lancet Infect Dis. 2019 Jun;19(6):648-657. doi: 10.1016/S1473-3099(19)30118-5. Epub 2019 Apr 15.

PMID:
31000464
3.

Automatic segmentation of OCT retinal boundaries using recurrent neural networks and graph search.

Kugelman J, Alonso-Caneiro D, Read SA, Vincent SJ, Collins MJ.

Biomed Opt Express. 2018 Oct 26;9(11):5759-5777. doi: 10.1364/BOE.9.005759. eCollection 2018 Nov 1.

4.

Qualitative Profiling of the Humoral Immune Response Elicited by rVSV-ΔG-EBOV-GP Using a Systems Serology Assay, Domain Programmable Arrays.

Sanchez-Lockhart M, Reyes DS, Gonzalez JC, Garcia KY, Villa EC, Pfeffer BP, Trefry JC, Kugelman JR, Pitt ML, Palacios GF.

Cell Rep. 2018 Jul 24;24(4):1050-1059.e5. doi: 10.1016/j.celrep.2018.06.077.

5.

Virus genomes reveal factors that spread and sustained the Ebola epidemic.

Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D'Ambrozio J, Dellicour S, Di Caro A, Diclaro JW, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll MW, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A.

Nature. 2017 Apr 20;544(7650):309-315. doi: 10.1038/nature22040. Epub 2017 Apr 12.

6.

Error baseline rates of five sample preparation methods used to characterize RNA virus populations.

Kugelman JR, Wiley MR, Nagle ER, Reyes D, Pfeffer BP, Kuhn JH, Sanchez-Lockhart M, Palacios GF.

PLoS One. 2017 Feb 9;12(2):e0171333. doi: 10.1371/journal.pone.0171333. eCollection 2017.

7.

Reduced evolutionary rate in reemerged Ebola virus transmission chains.

Blackley DJ, Wiley MR, Ladner JT, Fallah M, Lo T, Gilbert ML, Gregory C, D'ambrozio J, Coulter S, Mate S, Balogun Z, Kugelman J, Nwachukwu W, Prieto K, Yeiah A, Amegashie F, Kearney B, Wisniewski M, Saindon J, Schroth G, Fakoli L, Diclaro JW 2nd, Kuhn JH, Hensley LE, Jahrling PB, Ströher U, Nichol ST, Massaquoi M, Kateh F, Clement P, Gasasira A, Bolay F, Monroe SS, Rambaut A, Sanchez-Lockhart M, Scott Laney A, Nyenswah T, Christie A, Palacios G.

Sci Adv. 2016 Apr 29;2(4):e1600378. doi: 10.1126/sciadv.1600378. eCollection 2016 Apr.

8.

Clinical Survey of Dengue Virus Circulation in the Republic of Djibouti between 2011 and 2014 Identifies Serotype 3 Epidemic and Recommends Clinical Diagnosis Guidelines for Resource Limited Settings.

Le Gonidec E, Maquart M, Duron S, Savini H, Cazajous G, Vidal PO, Chenilleau MC, Roseau JB, Benois A, Dehan C, Kugelman J, Leparc-Goffart I, Védy S.

PLoS Negl Trop Dis. 2016 Jun 20;10(6):e0004755. doi: 10.1371/journal.pntd.0004755. eCollection 2016 Jun.

9.

The Structure-Specific Recognition Protein 1 Associates with Lens Epithelium-Derived Growth Factor Proteins and Modulates HIV-1 Replication.

Lopez AP, Kugelman JR, Garcia-Rivera J, Urias E, Salinas SA, Fernandez-Zapico ME, Llano M.

J Mol Biol. 2016 Jul 17;428(14):2814-31. doi: 10.1016/j.jmb.2016.05.013. Epub 2016 May 21.

10.

Informing the Historical Record of Experimental Nonhuman Primate Infections with Ebola Virus: Genomic Characterization of USAMRIID Ebola Virus/H.sapiens-tc/COD/1995/Kikwit-9510621 Challenge Stock "R4368" and Its Replacement "R4415".

Kugelman JR, Rossi CA, Wiley MR, Ladner JT, Nagle ER, Pfeffer BP, Garcia K, Prieto K, Wada J, Kuhn JH, Palacios G.

PLoS One. 2016 Mar 22;11(3):e0150919. doi: 10.1371/journal.pone.0150919. eCollection 2016.

11.

Therapeutic efficacy of the small molecule GS-5734 against Ebola virus in rhesus monkeys.

Warren TK, Jordan R, Lo MK, Ray AS, Mackman RL, Soloveva V, Siegel D, Perron M, Bannister R, Hui HC, Larson N, Strickley R, Wells J, Stuthman KS, Van Tongeren SA, Garza NL, Donnelly G, Shurtleff AC, Retterer CJ, Gharaibeh D, Zamani R, Kenny T, Eaton BP, Grimes E, Welch LS, Gomba L, Wilhelmsen CL, Nichols DK, Nuss JE, Nagle ER, Kugelman JR, Palacios G, Doerffler E, Neville S, Carra E, Clarke MO, Zhang L, Lew W, Ross B, Wang Q, Chun K, Wolfe L, Babusis D, Park Y, Stray KM, Trancheva I, Feng JY, Barauskas O, Xu Y, Wong P, Braun MR, Flint M, McMullan LK, Chen SS, Fearns R, Swaminathan S, Mayers DL, Spiropoulou CF, Lee WA, Nichol ST, Cihlar T, Bavari S.

Nature. 2016 Mar 17;531(7594):381-5. doi: 10.1038/nature17180. Epub 2016 Mar 2. Erratum in: ACS Chem Biol. 2016 May 20;11(5):1463.

12.

Ebola Virus Infections in Nonhuman Primates Are Temporally Influenced by Glycoprotein Poly-U Editing Site Populations in the Exposure Material.

Trefry JC, Wollen SE, Nasar F, Shamblin JD, Kern SJ, Bearss JJ, Jefferson MA, Chance TB, Kugelman JR, Ladner JT, Honko AN, Kobs DJ, Wending MQ, Sabourin CL, Pratt WD, Palacios GF, Pitt ML.

Viruses. 2015 Dec 19;7(12):6739-54. doi: 10.3390/v7122969.

13.

Evolution and Spread of Ebola Virus in Liberia, 2014-2015.

Ladner JT, Wiley MR, Mate S, Dudas G, Prieto K, Lovett S, Nagle ER, Beitzel B, Gilbert ML, Fakoli L, Diclaro JW 2nd, Schoepp RJ, Fair J, Kuhn JH, Hensley LE, Park DJ, Sabeti PC, Rambaut A, Sanchez-Lockhart M, Bolay FK, Kugelman JR, Palacios G.

Cell Host Microbe. 2015 Dec 9;18(6):659-69. doi: 10.1016/j.chom.2015.11.008.

14.

Molecular Evidence of Sexual Transmission of Ebola Virus.

Mate SE, Kugelman JR, Nyenswah TG, Ladner JT, Wiley MR, Cordier-Lassalle T, Christie A, Schroth GP, Gross SM, Davies-Wayne GJ, Shinde SA, Murugan R, Sieh SB, Badio M, Fakoli L, Taweh F, de Wit E, van Doremalen N, Munster VJ, Pettitt J, Prieto K, Humrighouse BW, Ströher U, DiClaro JW, Hensley LE, Schoepp RJ, Safronetz D, Fair J, Kuhn JH, Blackley DJ, Laney AS, Williams DE, Lo T, Gasasira A, Nichol ST, Formenty P, Kateh FN, De Cock KM, Bolay F, Sanchez-Lockhart M, Palacios G.

N Engl J Med. 2015 Dec 17;373(25):2448-54. doi: 10.1056/NEJMoa1509773. Epub 2015 Oct 14.

15.

Emergence of Ebola Virus Escape Variants in Infected Nonhuman Primates Treated with the MB-003 Antibody Cocktail.

Kugelman JR, Kugelman-Tonos J, Ladner JT, Pettit J, Keeton CM, Nagle ER, Garcia KY, Froude JW, Kuehne AI, Kuhn JH, Bavari S, Zeitlin L, Dye JM, Olinger GG, Sanchez-Lockhart M, Palacios GF.

Cell Rep. 2015 Sep 29;12(12):2111-20. doi: 10.1016/j.celrep.2015.08.038. Epub 2015 Sep 10.

16.

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone.

Park DJ, Dudas G, Wohl S, Goba A, Whitmer SL, Andersen KG, Sealfon RS, Ladner JT, Kugelman JR, Matranga CB, Winnicki SM, Qu J, Gire SK, Gladden-Young A, Jalloh S, Nosamiefan D, Yozwiak NL, Moses LM, Jiang PP, Lin AE, Schaffner SF, Bird B, Towner J, Mamoh M, Gbakie M, Kanneh L, Kargbo D, Massally JL, Kamara FK, Konuwa E, Sellu J, Jalloh AA, Mustapha I, Foday M, Yillah M, Erickson BR, Sealy T, Blau D, Paddock C, Brault A, Amman B, Basile J, Bearden S, Belser J, Bergeron E, Campbell S, Chakrabarti A, Dodd K, Flint M, Gibbons A, Goodman C, Klena J, McMullan L, Morgan L, Russell B, Salzer J, Sanchez A, Wang D, Jungreis I, Tomkins-Tinch C, Kislyuk A, Lin MF, Chapman S, MacInnis B, Matthews A, Bochicchio J, Hensley LE, Kuhn JH, Nusbaum C, Schieffelin JS, Birren BW, Forget M, Nichol ST, Palacios GF, Ndiaye D, Happi C, Gevao SM, Vandi MA, Kargbo B, Holmes EC, Bedford T, Gnirke A, Ströher U, Rambaut A, Garry RF, Sabeti PC.

Cell. 2015 Jun 18;161(7):1516-26. doi: 10.1016/j.cell.2015.06.007.

17.

Monitoring of Ebola Virus Makona Evolution through Establishment of Advanced Genomic Capability in Liberia.

Kugelman JR, Wiley MR, Mate S, Ladner JT, Beitzel B, Fakoli L, Taweh F, Prieto K, Diclaro JW, Minogue T, Schoepp RJ, Schaecher KE, Pettitt J, Bateman S, Fair J, Kuhn JH, Hensley L, Park DJ, Sabeti PC, Sanchez-Lockhart M, Bolay FK, Palacios G; US Army Medical Research Institute of Infectious Diseases; National Institutes of Health; Integrated Research Facility–Frederick Ebola Response Team 2014–2015.

Emerg Infect Dis. 2015 Jul;21(7):1135-43. doi: 10.3201/eid2107.150522.

18.

Possible sexual transmission of Ebola virus - Liberia, 2015.

Christie A, Davies-Wayne GJ, Cordier-Lassalle T, Blackley DJ, Laney AS, Williams DE, Shinde SA, Badio M, Lo T, Mate SE, Ladner JT, Wiley MR, Kugelman JR, Palacios G, Holbrook MR, Janosko KB, de Wit E, van Doremalen N, Munster VJ, Pettitt J, Schoepp RJ, Verhenne L, Evlampidou I, Kollie KK, Sieh SB, Gasasira A, Bolay F, Kateh FN, Nyenswah TG, De Cock KM; Centers for Disease Control and Prevention (CDC).

MMWR Morb Mortal Wkly Rep. 2015 May 8;64(17):479-81. Erratum in: MMWR Morb Mortal Wkly Rep. 2015 Oct 23;64(41):1180. Cordier-Lasalle, Thierry [Corrected to Cordier-Lassalle, Thierry].

19.

Complete coding sequences of eastern equine encephalitis virus and venezuelan equine encephalitis virus strains isolated from human cases.

Yu GY, Wiley MR, Kugelman JR, Ladner JT, Beitzel BF, Eccleston LT, Morazzani EM, Glass PJ, Palacios GF.

Genome Announc. 2015 Apr 23;3(2). pii: e00243-15. doi: 10.1128/genomeA.00243-15.

20.

Evaluation of the potential impact of Ebola virus genomic drift on the efficacy of sequence-based candidate therapeutics.

Kugelman JR, Sanchez-Lockhart M, Andersen KG, Gire S, Park DJ, Sealfon R, Lin AE, Wohl S, Sabeti PC, Kuhn JH, Palacios GF.

MBio. 2015 Jan 20;6(1). pii: e02227-14. doi: 10.1128/mBio.02227-14.

21.

Viral diversity and clonal evolution from unphased genomic data.

Khiabanian H, Carpenter Z, Kugelman J, Chan J, Trifonov V, Nagle E, Warren T, Iversen P, Bavari S, Palacios G, Rabadan R.

BMC Genomics. 2014;15 Suppl 6:S17. doi: 10.1186/1471-2164-15-S6-S17. Epub 2014 Oct 17.

22.

Nomenclature- and database-compatible names for the two Ebola virus variants that emerged in Guinea and the Democratic Republic of the Congo in 2014.

Kuhn JH, Andersen KG, Baize S, Bào Y, Bavari S, Berthet N, Blinkova O, Brister JR, Clawson AN, Fair J, Gabriel M, Garry RF, Gire SK, Goba A, Gonzalez JP, Günther S, Happi CT, Jahrling PB, Kapetshi J, Kobinger G, Kugelman JR, Leroy EM, Maganga GD, Mbala PK, Moses LM, Muyembe-Tamfum JJ, N'Faly M, Nichol ST, Omilabu SA, Palacios G, Park DJ, Paweska JT, Radoshitzky SR, Rossi CA, Sabeti PC, Schieffelin JS, Schoepp RJ, Sealfon R, Swanepoel R, Towner JS, Wada J, Wauquier N, Yozwiak NL, Formenty P.

Viruses. 2014 Nov 24;6(11):4760-99. doi: 10.3390/v6114760.

23.

Reidentification of Ebola Virus E718 and ME as Ebola Virus/H.sapiens-tc/COD/1976/Yambuku-Ecran.

Kuhn JH, Lofts LL, Kugelman JR, Smither SJ, Lever MS, van der Groen G, Johnson KM, Radoshitzky SR, Bavari S, Jahrling PB, Towner JS, Nichol ST, Palacios G.

Genome Announc. 2014 Nov 20;2(6). pii: e01178-14. doi: 10.1128/genomeA.01178-14.

24.

Transcriptome reconstruction and annotation of cynomolgus and African green monkey.

Lee A, Khiabanian H, Kugelman J, Elliott O, Nagle E, Yu GY, Warren T, Palacios G, Rabadan R.

BMC Genomics. 2014 Oct 3;15:846. doi: 10.1186/1471-2164-15-846.

25.

A Yersinia pestis tat mutant is attenuated in bubonic and small-aerosol pneumonic challenge models of infection but not as attenuated by intranasal challenge.

Bozue J, Cote CK, Chance T, Kugelman J, Kern SJ, Kijek TK, Jenkins A, Mou S, Moody K, Fritz D, Robinson CG, Bell T, Worsham P.

PLoS One. 2014 Aug 7;9(8):e104524. doi: 10.1371/journal.pone.0104524. eCollection 2014.

26.

Standards for sequencing viral genomes in the era of high-throughput sequencing.

Ladner JT, Beitzel B, Chain PS, Davenport MG, Donaldson EF, Frieman M, Kugelman JR, Kuhn JH, O'Rear J, Sabeti PC, Wentworth DE, Wiley MR, Yu GY; Threat Characterization Consortium, Sozhamannan S, Bradburne C, Palacios G.

MBio. 2014 Jun 17;5(3):e01360-14. doi: 10.1128/mBio.01360-14.

27.

Genomic variability of monkeypox virus among humans, Democratic Republic of the Congo.

Kugelman JR, Johnston SC, Mulembakani PM, Kisalu N, Lee MS, Koroleva G, McCarthy SE, Gestole MC, Wolfe ND, Fair JN, Schneider BS, Wright LL, Huggins J, Whitehouse CA, Wemakoy EO, Muyembe-Tamfum JJ, Hensley LE, Palacios GF, Rimoin AW.

Emerg Infect Dis. 2014 Feb;20(2):232-9. doi: 10.3201/eid2002.130118.

28.

Ebola virus genome plasticity as a marker of its passaging history: a comparison of in vitro passaging to non-human primate infection.

Kugelman JR, Lee MS, Rossi CA, McCarthy SE, Radoshitzky SR, Dye JM, Hensley LE, Honko A, Kuhn JH, Jahrling PB, Warren TK, Whitehouse CA, Bavari S, Palacios G.

PLoS One. 2012;7(11):e50316. doi: 10.1371/journal.pone.0050316. Epub 2012 Nov 28.

29.

HIV-1 integrase modulates the interaction of the HIV-1 cellular cofactor LEDGF/p75 with chromatin.

Astiazaran P, Bueno MT, Morales E, Kugelman JR, Garcia-Rivera JA, Llano M.

Retrovirology. 2011 Apr 21;8:27. doi: 10.1186/1742-4690-8-27.

30.

SUMOylation of the lens epithelium-derived growth factor/p75 attenuates its transcriptional activity on the heat shock protein 27 promoter.

Bueno MT, Garcia-Rivera JA, Kugelman JR, Morales E, Rosas-Acosta G, Llano M.

J Mol Biol. 2010 Jun 4;399(2):221-39. doi: 10.1016/j.jmb.2010.03.063. Epub 2010 Apr 9.

31.

Implication of serine residues 271, 273, and 275 in the human immunodeficiency virus type 1 cofactor activity of lens epithelium-derived growth factor/p75.

Garcia-Rivera JA, Bueno MT, Morales E, Kugelman JR, Rodriguez DF, Llano M.

J Virol. 2010 Jan;84(2):740-52. doi: 10.1128/JVI.01043-09. Epub 2009 Nov 4.

32.

The phylogeny and evolution of deoxyribonuclease II: an enzyme essential for lysosomal DNA degradation.

Shpak M, Kugelman JR, Varela-Ramirez A, Aguilera RJ.

Mol Phylogenet Evol. 2008 May;47(2):841-54. doi: 10.1016/j.ympev.2007.11.033. Epub 2007 Dec 14.

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