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Metavirome Sequencing to Evaluate Norovirus Diversity in Sewage and Related Bioaccumulated Oysters.

Strubbia S, Schaeffer J, Oude Munnink BB, Besnard A, Phan MVT, Nieuwenhuijse DF, de Graaf M, Schapendonk CME, Wacrenier C, Cotten M, Koopmans MPG, Le Guyader FS.

Front Microbiol. 2019 Oct 17;10:2394. doi: 10.3389/fmicb.2019.02394. eCollection 2019.


How Oxygen Availability Affects the Antimicrobial Efficacy of Host Defense Peptides: Lessons Learned from Studying the Copper-Binding Peptides Piscidins 1 and 3.

Oludiran A, Courson DS, Stuart MD, Radwan AR, Poutsma JC, Cotten ML, Purcell EB.

Int J Mol Sci. 2019 Oct 24;20(21). pii: E5289. doi: 10.3390/ijms20215289.


The host-defense peptide piscidin P1 reorganizes lipid domains in membranes and decreases activation energies in mechanosensitive ion channels.

Comert F, Greenwood A, Maramba J, Acevedo R, Lucas L, Kulasinghe T, Cairns LS, Wen Y, Fu R, Hammer J, Blazyk J, Sukharev S, Cotten ML, Mihailescu M.

J Biol Chem. 2019 Dec 6;294(49):18557-18570. doi: 10.1074/jbc.RA119.010232. Epub 2019 Oct 16.


A predictive model for extubation readiness in extremely preterm infants.

Gupta D, Greenberg RG, Sharma A, Natarajan G, Cotten M, Thomas R, Chawla S.

J Perinatol. 2019 Dec;39(12):1663-1669. doi: 10.1038/s41372-019-0475-x. Epub 2019 Aug 27.


Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next-Generation Sequencing.

Strubbia S, Phan MVT, Schaeffer J, Koopmans M, Cotten M, Le Guyader FS.

Food Environ Virol. 2019 Dec;11(4):400-409. doi: 10.1007/s12560-019-09402-3. Epub 2019 Aug 24.


Early Check: translational science at the intersection of public health and newborn screening.

Bailey DB Jr, Gehtland LM, Lewis MA, Peay H, Raspa M, Shone SM, Taylor JL, Wheeler AC, Cotten M, King NMP, Powell CM, Biesecker B, Bishop CE, Boyea BL, Duparc M, Harper BA, Kemper AR, Lee SN, Moultrie R, Okoniewski KC, Paquin RS, Pettit D, Porter KA, Zimmerman SJ.

BMC Pediatr. 2019 Jul 17;19(1):238. doi: 10.1186/s12887-019-1606-4.


Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant.

Agoti CN, Phan MVT, Munywoki PK, Githinji G, Medley GF, Cane PA, Kellam P, Cotten M, Nokes DJ.

Sci Rep. 2019 Jul 11;9(1):10076. doi: 10.1038/s41598-019-46509-w.


Structure and Function in Antimicrobial Piscidins: Histidine Position, Directionality of Membrane Insertion, and pH-Dependent Permeabilization.

Mihailescu M, Sorci M, Seckute J, Silin VI, Hammer J, Perrin BS Jr, Hernandez JI, Smajic N, Shrestha A, Bogardus KA, Greenwood AI, Fu R, Blazyk J, Pastor RW, Nicholson LK, Belfort G, Cotten ML.

J Am Chem Soc. 2019 Jun 26;141(25):9837-9853. doi: 10.1021/jacs.9b00440. Epub 2019 Jun 13.


The Utility of Data Transformation for Alignment, De Novo Assembly and Classification of Short Read Virus Sequences.

Tapinos A, Constantinides B, Phan MVT, Kouchaki S, Cotten M, Robertson DL.

Viruses. 2019 Apr 26;11(5). pii: E394. doi: 10.3390/v11050394.


Complete Genome Characterization of Eight Human Parainfluenza Viruses from the Netherlands.

Phan MVT, Arron G, GeurtsvanKessel CH, Huisman RC, Molenkamp R, Koopmans MPG, Cotten M.

Microbiol Resour Announc. 2019 Apr 11;8(15). pii: e00125-19. doi: 10.1128/MRA.00125-19.


Complete Genome Sequences of Dengue Virus Type 2 Strains from Kilifi, Kenya.

Kamau E, Agoti CN, Ngoi JM, de Laurent ZR, Gitonga J, Cotten M, Phan MVT, Nokes DJ, Delwart E, Sanders E, Warimwe GM.

Microbiol Resour Announc. 2019 Jan 24;8(4). pii: e01566-18. doi: 10.1128/MRA.01566-18. eCollection 2019 Jan.


Genomic sequence of yellow fever virus from a Dutch traveller returning from the Gambia-Senegal region, the Netherlands, November 2018.

Phan MV, Murad SD, van der Eijk AA, Metselaar HJ, Hartog H, Harinck F, GeurtsvanKessel CH, Molenkamp R, Cotten M, Koopmans MP.

Euro Surveill. 2019 Jan;24(4). doi: 10.2807/1560-7917.ES.2019.24.4.1800684.


Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains.

Phan MVT, Ngo Tri T, Hong Anh P, Baker S, Kellam P, Cotten M.

Virus Evol. 2018 Dec 15;4(2):vey035. doi: 10.1093/ve/vey035. eCollection 2018 Jul.


Evaluating the performance of tools used to call minority variants from whole genome short-read data.

Said Mohammed K, Kibinge N, Prins P, Agoti CN, Cotten M, Nokes DJ, Brand S, Githinji G.

Version 2. Wellcome Open Res. 2018 Sep 13 [revised 2018 Jan 1];3:21. doi: 10.12688/wellcomeopenres.13538.2. eCollection 2018.


Metal-ion Binding to Host Defense Peptide Piscidin 3 Observed in Phospholipid Bilayers by Magic Angle Spinning Solid-state NMR.

Rai RK, De Angelis A, Greenwood A, Opella SJ, Cotten ML.

Chemphyschem. 2019 Jan 21;20(2):295-301. doi: 10.1002/cphc.201800855. Epub 2018 Dec 19.


Erratum: Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains.

Otieno JR, Kamau EM, Oketch JW, Ngoi JM, Gichuki AM, Binter Š, Otieno GP, Ngama M, Agoti CN, Cane PA, Kellam P, Cotten M, Lemey P, Nokes DJ.

Virus Evol. 2018 Nov 16;4(2):vey036. doi: 10.1093/ve/vey036. eCollection 2018 Jul.


Virus discovery reveals frequent infection by diverse novel members of the Flaviviridae in wild lemurs.

Canuti M, Williams CV, Sagan SM, Oude Munnink BB, Gadi S, Verhoeven JTP, Kellam P, Cotten M, Lang AS, Junge RE, Cullen JM, van der Hoek L.

Arch Virol. 2019 Feb;164(2):509-522. doi: 10.1007/s00705-018-4099-9. Epub 2018 Nov 20.


Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains.

Otieno JR, Kamau EM, Oketch JW, Ngoi JM, Gichuki AM, Binter Š, Otieno GP, Ngama M, Agoti CN, Cane PA, Kellam P, Cotten M, Lemey P, Nokes DJ.

Virus Evol. 2018 Sep 24;4(2):vey027. doi: 10.1093/ve/vey027. eCollection 2018 Jul. Erratum in: Virus Evol. 2018 Nov 16;4(2):vey036.


Copper regulates the interactions of antimicrobial piscidin peptides from fish mast cells with formyl peptide receptors and heparin.

Kim SY, Zhang F, Gong W, Chen K, Xia K, Liu F, Gross R, Wang JM, Linhardt RJ, Cotten ML.

J Biol Chem. 2018 Oct 5;293(40):15381-15396. doi: 10.1074/jbc.RA118.001904. Epub 2018 Aug 29.


Human Coronavirus NL63 Molecular Epidemiology and Evolutionary Patterns in Rural Coastal Kenya.

Kiyuka PK, Agoti CN, Munywoki PK, Njeru R, Bett A, Otieno JR, Otieno GP, Kamau E, Clark TG, van der Hoek L, Kellam P, Nokes DJ, Cotten M.

J Infect Dis. 2018 May 5;217(11):1728-1739. doi: 10.1093/infdis/jiy098.


Complete Genome Sequences of Six Measles Virus Strains.

Phan MVT, Schapendonk CME, Oude Munnink BB, Koopmans MPG, de Swart RL, Cotten M.

Genome Announc. 2018 Mar 29;6(13). pii: e00184-18. doi: 10.1128/genomeA.00184-18.


HLA-associated polymorphisms in the HIV-2 capsid highlight key differences between HIV-1 and HIV-2 immune adaptation.

de Silva TI, Leligdowicz A, Carlson J, Garcia-Knight M, Onyango C, Miller N, Yindom LM, Hué S, Jaye A, Dong T, Cotten M, Rowland-Jones SL.

AIDS. 2018 Mar 27;32(6):709-714. doi: 10.1097/QAD.0000000000001753.


Milrinone in congenital diaphragmatic hernia - a randomized pilot trial: study protocol, review of literature and survey of current practices.

Lakshminrusimha S, Keszler M, Kirpalani H, Van Meurs K, Chess P, Ambalavanan N, Yoder B, Fraga MV, Hedrick H, Lally KP, Nelin L, Cotten M, Klein J, Guilford S, Williams A, Chaudhary A, Gantz M, Gabrio J, Chowdhury D, Zaterka-Baxter K, Das A, Higgins RD.

Matern Health Neonatol Perinatol. 2017 Nov 27;3:27. doi: 10.1186/s40748-017-0066-9. eCollection 2017. Review.


Whole-Genome Next-Generation Sequencing to Study Within-Host Evolution of Norovirus (NoV) Among Immunocompromised Patients With Chronic NoV Infection.

van Beek J, de Graaf M, Smits S, Schapendonk CME, Verjans GMGM, Vennema H, van der Eijk AA, Phan MVT, Cotten M, Koopmans M.

J Infect Dis. 2017 Dec 19;216(12):1513-1524. doi: 10.1093/infdis/jix520.


Characterization of Posa and Posa-like virus genomes in fecal samples from humans, pigs, rats, and bats collected from a single location in Vietnam.

Oude Munnink BB, Phan MVT; VIZIONS Consortium, Simmonds P, Koopmans MPG, Kellam P, van der Hoek L, Cotten M.

Virus Evol. 2017 Aug 23;3(2):vex022. doi: 10.1093/ve/vex022. eCollection 2017 Jul.


Nuclease activity gives an edge to host-defense peptide piscidin 3 over piscidin 1, rendering it more effective against persisters and biofilms.

Libardo MDJ, Bahar AA, Ma B, Fu R, McCormick LE, Zhao J, McCallum SA, Nussinov R, Ren D, Angeles-Boza AM, Cotten ML.

FEBS J. 2017 Nov;284(21):3662-3683. doi: 10.1111/febs.14263. Epub 2017 Sep 30.


Next-generation sequencing and norovirus.

Cotten M, Koopmans M.

Future Virol. 2016 Nov;11(11):719-722. doi: 10.2217/fvl-2016-0099. Epub 2016 Nov 11. No abstract available.


Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection.

Phan MVT, Anh PH, Cuong NV, Munnink BBO, van der Hoek L, My PT, Tri TN, Bryant JE, Baker S, Thwaites G, Woolhouse M, Kellam P, Rabaa MA, Cotten M; VIZIONS Consortium.

Virus Evol. 2016 Oct 3;2(2):vew027. doi: 10.1093/ve/vew027. eCollection 2016 Jul.


Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases.

Arias A, Watson SJ, Asogun D, Tobin EA, Lu J, Phan MVT, Jah U, Wadoum REG, Meredith L, Thorne L, Caddy S, Tarawalie A, Langat P, Dudas G, Faria NR, Dellicour S, Kamara A, Kargbo B, Kamara BO, Gevao S, Cooper D, Newport M, Horby P, Dunning J, Sahr F, Brooks T, Simpson AJH, Groppelli E, Liu G, Mulakken N, Rhodes K, Akpablie J, Yoti Z, Lamunu M, Vitto E, Otim P, Owilli C, Boateng I, Okoror L, Omomoh E, Oyakhilome J, Omiunu R, Yemisis I, Adomeh D, Ehikhiametalor S, Akhilomen P, Aire C, Kurth A, Cook N, Baumann J, Gabriel M, Wölfel R, Di Caro A, Carroll MW, Günther S, Redd J, Naidoo D, Pybus OG, Rambaut A, Kellam P, Goodfellow I, Cotten M.

Virus Evol. 2016 Jun 22;2(1):vew016. doi: 10.1093/ve/vew016. eCollection 2016 Jan.


Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis.

Agoti CN, Munywoki PK, Phan MVT, Otieno JR, Kamau E, Bett A, Kombe I, Githinji G, Medley GF, Cane PA, Kellam P, Cotten M, Nokes DJ.

Virus Evol. 2017 Mar 11;3(1):vex006. doi: 10.1093/ve/vex006. eCollection 2017 Jan.


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.


Genome Sequences of a Novel Vietnamese Bat Bunyavirus.

Oude Munnink BB, Phan MV, van der Hoek L, Kellam P, Cotten M; VIZIONS Consortium.

Genome Announc. 2016 Dec 22;4(6). pii: e01366-16. doi: 10.1128/genomeA.01366-16.


Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes.

Dolle DD, Liu Z, Cotten M, Simpson JT, Iqbal Z, Durbin R, McCarthy SA, Keane TM.

Genome Res. 2017 Feb;27(2):300-309. doi: 10.1101/gr.211748.116. Epub 2016 Dec 16.


Severe acute respiratory infection caused by swine influenza virus in a child necessitating extracorporeal membrane oxygenation (ECMO), the Netherlands, October 2016.

Fraaij PL, Wildschut ED, Houmes RJ, Swaan CM, Hoebe CJ, de Jonge HC, Tolsma P, de Kleer I, Pas SD, Oude Munnink BB, Phan MV, Bestebroer TM, Roosenhoff RS, van Kampen JJ, Cotten M, Beerens N, Fouchier RA, van den Kerkhof JH, Timen A, Koopmans MP.

Euro Surveill. 2016 Dec 1;21(48). pii: 30416. doi: 10.2807/1560-7917.ES.2016.21.48.30416.


Resurgence of Ebola Virus Disease in Guinea Linked to a Survivor With Virus Persistence in Seminal Fluid for More Than 500 Days.

Diallo B, Sissoko D, Loman NJ, Bah HA, Bah H, Worrell MC, Conde LS, Sacko R, Mesfin S, Loua A, Kalonda JK, Erondu NA, Dahl BA, Handrick S, Goodfellow I, Meredith LW, Cotten M, Jah U, Guetiya Wadoum RE, Rollin P, Magassouba N, Malvy D, Anglaret X, Carroll MW, Aylward RB, Djingarey MH, Diarra A, Formenty P, Keïta S, Günther S, Rambaut A, Duraffour S.

Clin Infect Dis. 2016 Nov 15;63(10):1353-1356. Epub 2016 Sep 1.


A Novel Astrovirus-Like RNA Virus Detected in Human Stool.

Oude Munnink BB, Cotten M, Canuti M, Deijs M, Jebbink MF, van Hemert FJ, Phan MV, Bakker M, Jazaeri Farsani SM, Kellam P, van der Hoek L.

Virus Evol. 2016 Mar 2;2(1):vew005. eCollection 2016 Jan.


Simulations of Membrane-Disrupting Peptides II: AMP Piscidin 1 Favors Surface Defects over Pores.

Perrin BS Jr, Fu R, Cotten ML, Pastor RW.

Biophys J. 2016 Sep 20;111(6):1258-1266. doi: 10.1016/j.bpj.2016.08.015.


Human Rhinovirus B and C Genomes from Rural Coastal Kenya.

Agoti CN, Kiyuka PK, Kamau E, Munywoki PK, Bett A, van der Hoek L, Kellam P, Nokes DJ, Cotten M.

Genome Announc. 2016 Jul 28;4(4). pii: e00751-16. doi: 10.1128/genomeA.00751-16.


Recent controversies on comparative effectiveness research investigations: Challenges, opportunities, and pitfalls.

Kirpalani H, Truog WE, D'Angio CT, Cotten M.

Semin Perinatol. 2016 Oct;40(6):341-347. doi: 10.1053/j.semperi.2016.05.004. Epub 2016 Aug 8.


Taking forward a 'One Health' approach for turning the tide against the Middle East respiratory syndrome coronavirus and other zoonotic pathogens with epidemic potential.

Zumla A, Dar O, Kock R, Muturi M, Ntoumi F, Kaleebu P, Eusebio M, Mfinanga S, Bates M, Mwaba P, Ansumana R, Khan M, Alagaili AN, Cotten M, Azhar EI, Maeurer M, Ippolito G, Petersen E.

Int J Infect Dis. 2016 Jun;47:5-9. doi: 10.1016/j.ijid.2016.06.012. Epub 2016 Jun 15.


Comparative Transcriptomics Reveals Key Gene Expression Differences between Diapausing and Non-Diapausing Adults of Culex pipiens.

Kang DS, Cotten MA, Denlinger DL, Sim C.

PLoS One. 2016 Apr 29;11(4):e0154892. doi: 10.1371/journal.pone.0154892. eCollection 2016.


Complete Genome Characterization of Two Wild-Type Measles Viruses from Vietnamese Infants during the 2014 Outbreak.

Oude Munnink BB, Phan MV, Kellam P, Cotten M; VIZIONS Consortium.

Genome Announc. 2016 Apr 14;4(2). pii: e00250-16. doi: 10.1128/genomeA.00250-16.


Zika virus outbreak and the case for building effective and sustainable rapid diagnostics laboratory capacity globally.

Zumla A, Goodfellow I, Kasolo F, Ntoumi F, Buchy P, Bates M, Azhar EI, Cotten M, Petersen E.

Int J Infect Dis. 2016 Apr;45:92-4. doi: 10.1016/j.ijid.2016.02.1007. Epub 2016 Mar 4. No abstract available.


Complementary Effects of Host Defense Peptides Piscidin 1 and Piscidin 3 on DNA and Lipid Membranes: Biophysical Insights into Contrasting Biological Activities.

Hayden RM, Goldberg GK, Ferguson BM, Schoeneck MW, Libardo MD, Mayeux SE, Shrestha A, Bogardus KA, Hammer J, Pryshchep S, Lehman HK, McCormick ML, Blazyk J, Angeles-Boza AM, Fu R, Cotten ML.

J Phys Chem B. 2015 Dec 10;119(49):15235-46. doi: 10.1021/acs.jpcb.5b09685. Epub 2015 Dec 1.


Point-of-Care Quantitative Measure of Glucose-6-Phosphate Dehydrogenase Enzyme Deficiency.

Bhutani VK, Kaplan M, Glader B, Cotten M, Kleinert J, Pamula V.

Pediatrics. 2015 Nov;136(5):e1268-75. doi: 10.1542/peds.2015-2122. Epub 2015 Oct 12.


The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases.

Rabaa MA, Tue NT, Phuc TM, Carrique-Mas J, Saylors K, Cotten M, Bryant JE, Nghia HD, Cuong NV, Pham HA, Berto A, Phat VV, Dung TT, Bao LH, Hoa NT, Wertheim H, Nadjm B, Monagin C, van Doorn HR, Rahman M, Tra MP, Campbell JI, Boni MF, Tam PT, van der Hoek L, Simmonds P, Rambaut A, Toan TK, Van Vinh Chau N, Hien TT, Wolfe N, Farrar JJ, Thwaites G, Kellam P, Woolhouse ME, Baker S.

Ecohealth. 2015 Dec;12(4):726-35. doi: 10.1007/s10393-015-1061-0. Epub 2015 Sep 24. Review.


A novel genus in the order Picornavirales detected in human stool.

Oude Munnink BB, Cotten M, Deijs M, Jebbink MF, Bakker M, Farsani SM, Canuti M, Kellam P, van der Hoek L.

J Gen Virol. 2015 Nov;96(11):3440-3.


Correction. The presence of prolines in the flanking region of an immunodominant HIV-2 gag epitope influences the quality and quantity of the epitope generated.

Jallow S, Leligdowicz A, Kramer HB, Onyango C, Cotten M, Wright C, Whittle HC, McMichael A, Dong T, Kessler BM, Rowland-Jones SL.

Eur J Immunol. 2015 Sep;45(9):2701. doi: 10.1002/eji.201570096. No abstract available.


Molecular Epidemiology and Evolution of Influenza Viruses Circulating within European Swine between 2009 and 2013.

Watson SJ, Langat P, Reid SM, Lam TT, Cotten M, Kelly M, Van Reeth K, Qiu Y, Simon G, Bonin E, Foni E, Chiapponi C, Larsen L, Hjulsager C, Markowska-Daniel I, Urbaniak K, Dürrwald R, Schlegel M, Huovilainen A, Davidson I, Dán Á, Loeffen W, Edwards S, Bublot M, Vila T, Maldonado J, Valls L; ESNIP3 Consortium, Brown IH, Pybus OG, Kellam P.

J Virol. 2015 Oct;89(19):9920-31. doi: 10.1128/JVI.00840-15. Epub 2015 Jul 22.

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