Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 58

1.

Reply to Lagier et al.

Khanna S, Button JE, Lombardo MJ, Vulic M, Henn MR, Cook DN, Pomerantz RJ, Hohmann EL.

J Infect Dis. 2017 Jan 1;215(1):162-164. doi: 10.1093/infdis/jiw490. Epub 2016 Oct 20. No abstract available.

PMID:
28077592
2.

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.

Tully DC, Ogilvie CB, Batorsky RE, Bean DJ, Power KA, Ghebremichael M, Bedard HE, Gladden AD, Seese AM, Amero MA, Lane K, McGrath G, Bazner SB, Tinsley J, Lennon NJ, Henn MR, Brumme ZL, Norris PJ, Rosenberg ES, Mayer KH, Jessen H, Kosakovsky Pond SL, Walker BD, Altfeld M, Carlson JM, Allen TM.

PLoS Pathog. 2016 May 10;12(5):e1005619. doi: 10.1371/journal.ppat.1005619. eCollection 2016 May.

3.

A Novel Microbiome Therapeutic Increases Gut Microbial Diversity and Prevents Recurrent Clostridium difficile Infection.

Khanna S, Pardi DS, Kelly CR, Kraft CS, Dhere T, Henn MR, Lombardo MJ, Vulic M, Ohsumi T, Winkler J, Pindar C, McGovern BH, Pomerantz RJ, Aunins JG, Cook DN, Hohmann EL.

J Infect Dis. 2016 Jul 15;214(2):173-81. doi: 10.1093/infdis/jiv766. Epub 2016 Feb 8.

PMID:
26908752
4.

Standardized metadata for human pathogen/vector genomic sequences.

Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ Jr, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH.

PLoS One. 2014 Jun 17;9(6):e99979. doi: 10.1371/journal.pone.0099979. eCollection 2014.

5.

Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy.

Li JZ, Chapman B, Charlebois P, Hofmann O, Weiner B, Porter AJ, Samuel R, Vardhanabhuti S, Zheng L, Eron J, Taiwo B, Zody MC, Henn MR, Kuritzkes DR, Hide W; ACTG A5262 Study Team, Wilson CC, Berzins BI, Acosta EP, Bastow B, Kim PS, Read SW, Janik J, Meres DS, Lederman MM, Mong-Kryspin L, Shaw KE, Zimmerman LG, Leavitt R, De La Rosa G, Jennings A.

PLoS One. 2014 Mar 6;9(3):e90485. doi: 10.1371/journal.pone.0090485. eCollection 2014.

6.

V-Phaser 2: variant inference for viral populations.

Yang X, Charlebois P, Macalalad A, Henn MR, Zody MC.

BMC Genomics. 2013 Oct 3;14:674. doi: 10.1186/1471-2164-14-674.

7.

Tracking the evolution of dengue virus strains D2S10 and D2S20 by 454 pyrosequencing.

Makhluf H, Buck MD, King K, Perry ST, Henn MR, Shresta S.

PLoS One. 2013;8(1):e54220. doi: 10.1371/journal.pone.0054220. Epub 2013 Jan 14.

8.

Genomes of marine cyanopodoviruses reveal multiple origins of diversity.

Labrie SJ, Frois-Moniz K, Osburne MS, Kelly L, Roggensack SE, Sullivan MB, Gearin G, Zeng Q, Fitzgerald M, Henn MR, Chisholm SW.

Environ Microbiol. 2013 May;15(5):1356-76. doi: 10.1111/1462-2920.12053. Epub 2013 Jan 16.

PMID:
23320838
9.

Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants.

Newman RM, Kuntzen T, Weiner B, Berical A, Charlebois P, Kuiken C, Murphy DG, Simmonds P, Bennett P, Lennon NJ, Birren BW, Zody MC, Allen TM, Henn MR.

J Infect Dis. 2013 Jul;208(1):17-31. doi: 10.1093/infdis/jis679. Epub 2012 Nov 6.

10.

De novo assembly of highly diverse viral populations.

Yang X, Charlebois P, Gnerre S, Coole MG, Lennon NJ, Levin JZ, Qu J, Ryan EM, Zody MC, Henn MR.

BMC Genomics. 2012 Sep 13;13:475. doi: 10.1186/1471-2164-13-475.

11.

Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification.

Malboeuf CM, Yang X, Charlebois P, Qu J, Berlin AM, Casali M, Pesko KN, Boutwell CL, DeVincenzo JP, Ebel GD, Allen TM, Zody MC, Henn MR, Levin JZ.

Nucleic Acids Res. 2013 Jan 7;41(1):e13. doi: 10.1093/nar/gks794. Epub 2012 Sep 8.

12.

Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis.

Malmstrom RR, Rodrigue S, Huang KH, Kelly L, Kern SE, Thompson A, Roggensack S, Berube PM, Henn MR, Chisholm SW.

ISME J. 2013 Jan;7(1):184-98. doi: 10.1038/ismej.2012.89. Epub 2012 Aug 16.

13.

Characterization of a model of lethal dengue virus 2 infection in C57BL/6 mice deficient in the alpha/beta interferon receptor.

Orozco S, Schmid MA, Parameswaran P, Lachica R, Henn MR, Beatty R, Harris E.

J Gen Virol. 2012 Oct;93(Pt 10):2152-7. doi: 10.1099/vir.0.045088-0. Epub 2012 Jul 18.

14.

Reemergence and decline of dengue virus serotype 3 in Puerto Rico.

Santiago GA, McElroy-Horne K, Lennon NJ, Santiago LM, Birren BW, Henn MR, Muñoz-Jordán JL.

J Infect Dis. 2012 Sep 15;206(6):893-901. doi: 10.1093/infdis/jis426. Epub 2012 Jun 27.

15.

Complex dynamic of dengue virus serotypes 2 and 3 in Cambodia following series of climate disasters.

Duong V, Henn MR, Simmons C, Ngan C, Y B, Gavotte L, Viari A, Ong S, Huy R, Lennon NJ, Ly S, Vong S, Birren BW, Farrar JJ, Deubel V, Frutos R, Buchy P.

Infect Genet Evol. 2013 Apr;15:77-86. doi: 10.1016/j.meegid.2012.05.012. Epub 2012 Jun 5.

PMID:
22677620
16.

Genome-wide patterns of intrahuman dengue virus diversity reveal associations with viral phylogenetic clade and interhost diversity.

Parameswaran P, Charlebois P, Tellez Y, Nunez A, Ryan EM, Malboeuf CM, Levin JZ, Lennon NJ, Balmaseda A, Harris E, Henn MR.

J Virol. 2012 Aug;86(16):8546-58. doi: 10.1128/JVI.00736-12. Epub 2012 May 30.

17.

Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data.

Macalalad AR, Zody MC, Charlebois P, Lennon NJ, Newman RM, Malboeuf CM, Ryan EM, Boutwell CL, Power KA, Brackney DE, Pesko KN, Levin JZ, Ebel GD, Allen TM, Birren BW, Henn MR.

PLoS Comput Biol. 2012;8(3):e1002417. doi: 10.1371/journal.pcbi.1002417. Epub 2012 Mar 15.

18.

Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection.

Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, Macalalad AR, Berlin AM, Malboeuf CM, Ryan EM, Gnerre S, Zody MC, Erlich RL, Green LM, Berical A, Wang Y, Casali M, Streeck H, Bloom AK, Dudek T, Tully D, Newman R, Axten KL, Gladden AD, Battis L, Kemper M, Zeng Q, Shea TP, Gujja S, Zedlack C, Gasser O, Brander C, Hess C, Günthard HF, Brumme ZL, Brumme CJ, Bazner S, Rychert J, Tinsley JP, Mayer KH, Rosenberg E, Pereyra F, Levin JZ, Young SK, Jessen H, Altfeld M, Birren BW, Walker BD, Allen TM.

PLoS Pathog. 2012;8(3):e1002529. doi: 10.1371/journal.ppat.1002529. Epub 2012 Mar 8.

19.

Rapid diversification of coevolving marine Synechococcus and a virus.

Marston MF, Pierciey FJ Jr, Shepard A, Gearin G, Qi J, Yandava C, Schuster SC, Henn MR, Martiny JB.

Proc Natl Acad Sci U S A. 2012 Mar 20;109(12):4544-9. doi: 10.1073/pnas.1120310109. Epub 2012 Mar 2.

20.

Internally deleted WNV genomes isolated from exotic birds in New Mexico: function in cells, mosquitoes, and mice.

Pesko KN, Fitzpatrick KA, Ryan EM, Shi PY, Zhang B, Lennon NJ, Newman RM, Henn MR, Ebel GD.

Virology. 2012 May 25;427(1):10-7. doi: 10.1016/j.virol.2012.01.028. Epub 2012 Feb 23.

21.

Draft genome sequence of four coccolithoviruses: Emiliania huxleyi virus EhV-88, EhV-201, EhV-207, and EhV-208.

Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ.

J Virol. 2012 Mar;86(5):2896-7. doi: 10.1128/JVI.07046-11.

22.

Draft genome sequence of the coccolithovirus Emiliania huxleyi virus 202.

Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ.

J Virol. 2012 Feb;86(4):2380-1. doi: 10.1128/JVI.06863-11.

23.

Dynamics of dengue disease severity determined by the interplay between viral genetics and serotype-specific immunity.

OhAinle M, Balmaseda A, Macalalad AR, Tellez Y, Zody MC, Saborío S, Nuñez A, Lennon NJ, Birren BW, Gordon A, Henn MR, Harris E.

Sci Transl Med. 2011 Dec 21;3(114):114ra128. doi: 10.1126/scitranslmed.3003084.

24.

Draft genome sequence of the coccolithovirus EhV-84.

Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ.

Stand Genomic Sci. 2011 Oct 15;5(1):1-11. doi: 10.4056/sigs.1884581. Epub 2011 Sep 23.

25.

Draft genome sequence of the Coccolithovirus Emiliania huxleyi virus 203.

Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ.

J Virol. 2011 Dec;85(24):13468-9. doi: 10.1128/JVI.06440-11.

26.

High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections.

Thai KT, Henn MR, Zody MC, Tricou V, Nguyet NM, Charlebois P, Lennon NJ, Green L, de Vries PJ, Hien TT, Farrar J, van Doorn HR, de Jong MD, Birren BW, Holmes EC, Simmons CP.

J Virol. 2012 Jan;86(2):835-43. doi: 10.1128/JVI.05985-11. Epub 2011 Nov 16.

27.

Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis.

Desjardins CA, Champion MD, Holder JW, Muszewska A, Goldberg J, Bailão AM, Brigido MM, Ferreira ME, Garcia AM, Grynberg M, Gujja S, Heiman DI, Henn MR, Kodira CD, León-Narváez H, Longo LV, Ma LJ, Malavazi I, Matsuo AL, Morais FV, Pereira M, Rodríguez-Brito S, Sakthikumar S, Salem-Izacc SM, Sykes SM, Teixeira MM, Vallejo MC, Walter ME, Yandava C, Young S, Zeng Q, Zucker J, Felipe MS, Goldman GH, Haas BJ, McEwen JG, Nino-Vega G, Puccia R, San-Blas G, Soares CM, Birren BW, Cuomo CA.

PLoS Genet. 2011 Oct;7(10):e1002345. doi: 10.1371/journal.pgen.1002345. Epub 2011 Oct 27.

28.

Human leukocyte antigen B27 selects for rare escape mutations that significantly impair hepatitis C virus replication and require compensatory mutations.

Neumann-Haefelin C, Oniangue-Ndza C, Kuntzen T, Schmidt J, Nitschke K, Sidney J, Caillet-Saguy C, Binder M, Kersting N, Kemper MW, Power KA, Ingber S, Reyor LL, Hills-Evans K, Kim AY, Lauer GM, Lohmann V, Sette A, Henn MR, Bressanelli S, Thimme R, Allen TM.

Hepatology. 2011 Oct;54(4):1157-66. doi: 10.1002/hep.24541.

29.

A phylogenetic analysis using full-length viral genomes of South American dengue serotype 3 in consecutive Venezuelan outbreaks reveals a novel NS5 mutation.

Schmidt DJ, Pickett BE, Camacho D, Comach G, Xhaja K, Lennon NJ, Rizzolo K, de Bosch N, Becerra A, Nogueira ML, Mondini A, da Silva EV, Vasconcelos PF, Muñoz-Jordán JL, Santiago GA, Ocazionez R, Gehrke L, Lefkowitz EJ, Birren BW, Henn MR, Bosch I.

Infect Genet Evol. 2011 Dec;11(8):2011-9. doi: 10.1016/j.meegid.2011.09.010. Epub 2011 Sep 23.

30.

Compensatory mutations restore the replication defects caused by cytotoxic T lymphocyte escape mutations in hepatitis C virus polymerase.

Oniangue-Ndza C, Kuntzen T, Kemper M, Berical A, Wang YE, Neumann-Haefelin C, Foote PK, Hills-Evans K, Reyor LL, Kane K, Gladden AD, Bloom AK, Power KA, Thimme R, Lauer GM, Henn MR, Kim AY, Allen TM.

J Virol. 2011 Nov;85(22):11883-90. doi: 10.1128/JVI.00779-11. Epub 2011 Aug 31.

31.

Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia.

Duong V, Simmons C, Gavotte L, Viari A, Ong S, Chantha N, Lennon NJ, Birren BW, Vong S, Farrar JJ, Henn MR, Deubel V, Frutos R, Buchy P.

Infect Genet Evol. 2013 Apr;15:59-68. doi: 10.1016/j.meegid.2011.06.019. Epub 2011 Jul 2.

PMID:
21757030
32.

Molecular evolution of West Nile virus in a northern temperate region: Connecticut, USA 1999-2008.

Armstrong PM, Vossbrinck CR, Andreadis TG, Anderson JF, Pesko KN, Newman RM, Lennon NJ, Birren BW, Ebel GD, Henn MR.

Virology. 2011 Aug 15;417(1):203-10. doi: 10.1016/j.virol.2011.06.006. Epub 2011 Jul 1.

33.

Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission.

Raghwani J, Rambaut A, Holmes EC, Hang VT, Hien TT, Farrar J, Wills B, Lennon NJ, Birren BW, Henn MR, Simmons CP.

PLoS Pathog. 2011 Jun;7(6):e1002064. doi: 10.1371/journal.ppat.1002064. Epub 2011 Jun 2.

34.

Next-generation sequencing for HLA typing of class I loci.

Erlich RL, Jia X, Anderson S, Banks E, Gao X, Carrington M, Gupta N, DePristo MA, Henn MR, Lennon NJ, de Bakker PI.

BMC Genomics. 2011 Jan 18;12:42. doi: 10.1186/1471-2164-12-42.

35.

Endurance, refuge, and reemergence of dengue virus type 2, Puerto Rico, 1986-2007.

McElroy KL, Santiago GA, Lennon NJ, Birren BW, Henn MR, Muñoz-Jordán JL.

Emerg Infect Dis. 2011 Jan;17(1):64-71. doi: 10.3201/eid1701.100961.

36.

PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes.

Yu Q, Ryan EM, Allen TM, Birren BW, Henn MR, Lennon NJ.

Bioinformatics. 2011 Jan 15;27(2):266-7. doi: 10.1093/bioinformatics/btq624. Epub 2010 Nov 9.

37.

The major genetic determinants of HIV-1 control affect HLA class I peptide presentation.

International HIV Controllers Study, Pereyra F, Jia X, McLaren PJ, Telenti A, de Bakker PI, Walker BD, Ripke S, Brumme CJ, Pulit SL, Carrington M, Kadie CM, Carlson JM, Heckerman D, Graham RR, Plenge RM, Deeks SG, Gianniny L, Crawford G, Sullivan J, Gonzalez E, Davies L, Camargo A, Moore JM, Beattie N, Gupta S, Crenshaw A, Burtt NP, Guiducci C, Gupta N, Gao X, Qi Y, Yuki Y, Piechocka-Trocha A, Cutrell E, Rosenberg R, Moss KL, Lemay P, O'Leary J, Schaefer T, Verma P, Toth I, Block B, Baker B, Rothchild A, Lian J, Proudfoot J, Alvino DM, Vine S, Addo MM, Allen TM, Altfeld M, Henn MR, Le Gall S, Streeck H, Haas DW, Kuritzkes DR, Robbins GK, Shafer RW, Gulick RM, Shikuma CM, Haubrich R, Riddler S, Sax PE, Daar ES, Ribaudo HJ, Agan B, Agarwal S, Ahern RL, Allen BL, Altidor S, Altschuler EL, Ambardar S, Anastos K, Anderson B, Anderson V, Andrady U, Antoniskis D, Bangsberg D, Barbaro D, Barrie W, Bartczak J, Barton S, Basden P, Basgoz N, Bazner S, Bellos NC, Benson AM, Berger J, Bernard NF, Bernard AM, Birch C, Bodner SJ, Bolan RK, Boudreaux ET, Bradley M, Braun JF, Brndjar JE, Brown SJ, Brown K, Brown ST, Burack J, Bush LM, Cafaro V, Campbell O, Campbell J, Carlson RH, Carmichael JK, Casey KK, Cavacuiti C, Celestin G, Chambers ST, Chez N, Chirch LM, Cimoch PJ, Cohen D, Cohn LE, Conway B, Cooper DA, Cornelson B, Cox DT, Cristofano MV, Cuchural G Jr, Czartoski JL, Dahman JM, Daly JS, Davis BT, Davis K, Davod SM, DeJesus E, Dietz CA, Dunham E, Dunn ME, Ellerin TB, Eron JJ, Fangman JJ, Farel CE, Ferlazzo H, Fidler S, Fleenor-Ford A, Frankel R, Freedberg KA, French NK, Fuchs JD, Fuller JD, Gaberman J, Gallant JE, Gandhi RT, Garcia E, Garmon D, Gathe JC Jr, Gaultier CR, Gebre W, Gilman FD, Gilson I, Goepfert PA, Gottlieb MS, Goulston C, Groger RK, Gurley TD, Haber S, Hardwicke R, Hardy WD, Harrigan PR, Hawkins TN, Heath S, Hecht FM, Henry WK, Hladek M, Hoffman RP, Horton JM, Hsu RK, Huhn GD, Hunt P, Hupert MJ, Illeman ML, Jaeger H, Jellinger RM, John M, Johnson JA, Johnson KL, Johnson H, Johnson K, Joly J, Jordan WC, Kauffman CA, Khanlou H, Killian RK, Kim AY, Kim DD, Kinder CA, Kirchner JT, Kogelman L, Kojic EM, Korthuis PT, Kurisu W, Kwon DS, LaMar M, Lampiris H, Lanzafame M, Lederman MM, Lee DM, Lee JM, Lee MJ, Lee ET, Lemoine J, Levy JA, Llibre JM, Liguori MA, Little SJ, Liu AY, Lopez AJ, Loutfy MR, Loy D, Mohammed DY, Man A, Mansour MK, Marconi VC, Markowitz M, Marques R, Martin JN, Martin HL Jr, Mayer KH, McElrath MJ, McGhee TA, McGovern BH, McGowan K, McIntyre D, Mcleod GX, Menezes P, Mesa G, Metroka CE, Meyer-Olson D, Miller AO, Montgomery K, Mounzer KC, Nagami EH, Nagin I, Nahass RG, Nelson MO, Nielsen C, Norene DL, O'Connor DH, Ojikutu BO, Okulicz J, Oladehin OO, Oldfield EC 3rd, Olender SA, Ostrowski M, Owen WF Jr, Pae E, Parsonnet J, Pavlatos AM, Perlmutter AM, Pierce MN, Pincus JM, Pisani L, Price LJ, Proia L, Prokesch RC, Pujet HC, Ramgopal M, Rathod A, Rausch M, Ravishankar J, Rhame FS, Richards CS, Richman DD, Rodes B, Rodriguez M, Rose RC 3rd, Rosenberg ES, Rosenthal D, Ross PE, Rubin DS, Rumbaugh E, Saenz L, Salvaggio MR, Sanchez WC, Sanjana VM, Santiago S, Schmidt W, Schuitemaker H, Sestak PM, Shalit P, Shay W, Shirvani VN, Silebi VI, Sizemore JM Jr, Skolnik PR, Sokol-Anderson M, Sosman JM, Stabile P, Stapleton JT, Starrett S, Stein F, Stellbrink HJ, Sterman FL, Stone VE, Stone DR, Tambussi G, Taplitz RA, Tedaldi EM, Telenti A, Theisen W, Torres R, Tosiello L, Tremblay C, Tribble MA, Trinh PD, Tsao A, Ueda P, Vaccaro A, Valadas E, Vanig TJ, Vecino I, Vega VM, Veikley W, Wade BH, Walworth C, Wanidworanun C, Ward DJ, Warner DA, Weber RD, Webster D, Weis S, Wheeler DA, White DJ, Wilkins E, Winston A, Wlodaver CG, van't Wout A, Wright DP, Yang OO, Yurdin DL, Zabukovic BW, Zachary KC, Zeeman B, Zhao M.

Science. 2010 Dec 10;330(6010):1551-7. doi: 10.1126/science.1195271. Epub 2010 Nov 4.

38.

Index cluster study of dengue virus infection in Nicaragua.

Reyes M, Mercado JC, Standish K, Matute JC, Ortega O, Moraga B, Avilés W, Henn MR, Balmaseda A, Kuan G, Harris E.

Am J Trop Med Hyg. 2010 Sep;83(3):683-9. doi: 10.4269/ajtmh.2010.10-0023.

39.

Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments.

Sullivan MB, Huang KH, Ignacio-Espinoza JC, Berlin AM, Kelly L, Weigele PR, DeFrancesco AS, Kern SE, Thompson LR, Young S, Yandava C, Fu R, Krastins B, Chase M, Sarracino D, Osburne MS, Henn MR, Chisholm SW.

Environ Microbiol. 2010 Nov;12(11):3035-56. doi: 10.1111/j.1462-2920.2010.02280.x.

40.

Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia.

Vu TT, Holmes EC, Duong V, Nguyen TQ, Tran TH, Quail M, Churcher C, Parkhill J, Cardosa J, Farrar J, Wills B, Lennon NJ, Birren BW, Buchy P, Henn MR, Simmons CP.

PLoS Negl Trop Dis. 2010 Jul 20;4(7):e757. doi: 10.1371/journal.pntd.0000757.

41.

Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control.

Neafsey DE, Barker BM, Sharpton TJ, Stajich JE, Park DJ, Whiston E, Hung CY, McMahan C, White J, Sykes S, Heiman D, Young S, Zeng Q, Abouelleil A, Aftuck L, Bessette D, Brown A, FitzGerald M, Lui A, Macdonald JP, Priest M, Orbach MJ, Galgiani JN, Kirkland TN, Cole GT, Birren BW, Henn MR, Taylor JW, Rounsley SD.

Genome Res. 2010 Jul;20(7):938-46. doi: 10.1101/gr.103911.109. Epub 2010 Jun 1.

42.

Analysis of high-throughput sequencing and annotation strategies for phage genomes.

Henn MR, Sullivan MB, Stange-Thomann N, Osburne MS, Berlin AM, Kelly L, Yandava C, Kodira C, Zeng Q, Weiand M, Sparrow T, Saif S, Giannoukos G, Young SK, Nusbaum C, Birren BW, Chisholm SW.

PLoS One. 2010 Feb 5;5(2):e9083. doi: 10.1371/journal.pone.0009083.

43.

A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454.

Lennon NJ, Lintner RE, Anderson S, Alvarez P, Barry A, Brockman W, Daza R, Erlich RL, Giannoukos G, Green L, Hollinger A, Hoover CA, Jaffe DB, Juhn F, McCarthy D, Perrin D, Ponchner K, Powers TL, Rizzolo K, Robbins D, Ryan E, Russ C, Sparrow T, Stalker J, Steelman S, Weiand M, Zimmer A, Henn MR, Nusbaum C, Nicol R.

Genome Biol. 2010;11(2):R15. doi: 10.1186/gb-2010-11-2-r15. Epub 2010 Feb 5.

44.

The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes.

Angly FE, Willner D, Prieto-Davó A, Edwards RA, Schmieder R, Vega-Thurber R, Antonopoulos DA, Barott K, Cottrell MT, Desnues C, Dinsdale EA, Furlan M, Haynes M, Henn MR, Hu Y, Kirchman DL, McDole T, McPherson JD, Meyer F, Miller RM, Mundt E, Naviaux RK, Rodriguez-Mueller B, Stevens R, Wegley L, Zhang L, Zhu B, Rohwer F.

PLoS Comput Biol. 2009 Dec;5(12):e1000593. doi: 10.1371/journal.pcbi.1000593. Epub 2009 Dec 11.

45.

Trends in patterns of dengue transmission over 4 years in a pediatric cohort study in Nicaragua.

Balmaseda A, Standish K, Mercado JC, Matute JC, Tellez Y, Saborío S, Hammond SN, Nuñez A, Avilés W, Henn MR, Holmes EC, Gordon A, Coloma J, Kuan G, Harris E.

J Infect Dis. 2010 Jan 1;201(1):5-14. doi: 10.1086/648592.

46.

Whole genome amplification and de novo assembly of single bacterial cells.

Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW.

PLoS One. 2009 Sep 2;4(9):e6864. doi: 10.1371/journal.pone.0006864.

47.

Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives.

Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, Maiti R, Kodira CD, Neafsey DE, Zeng Q, Hung CY, McMahan C, Muszewska A, Grynberg M, Mandel MA, Kellner EM, Barker BM, Galgiani JN, Orbach MJ, Kirkland TN, Cole GT, Henn MR, Birren BW, Taylor JW.

Genome Res. 2009 Oct;19(10):1722-31. doi: 10.1101/gr.087551.108. Epub 2009 Aug 28.

48.

Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients.

Kuntzen T, Timm J, Berical A, Lennon N, Berlin AM, Young SK, Lee B, Heckerman D, Carlson J, Reyor LL, Kleyman M, McMahon CM, Birch C, Schulze Zur Wiesch J, Ledlie T, Koehrsen M, Kodira C, Roberts AD, Lauer GM, Rosen HR, Bihl F, Cerny A, Spengler U, Liu Z, Kim AY, Xing Y, Schneidewind A, Madey MA, Fleckenstein JF, Park VM, Galagan JE, Nusbaum C, Walker BD, Lake-Bakaar GV, Daar ES, Jacobson IM, Gomperts ED, Edlin BR, Donfield SM, Chung RT, Talal AH, Marion T, Birren BW, Henn MR, Allen TM.

Hepatology. 2008 Dec;48(6):1769-78. doi: 10.1002/hep.22549.

49.

A high-density single nucleotide polymorphism map for Neurospora crassa.

Lambreghts R, Shi M, Belden WJ, Decaprio D, Park D, Henn MR, Galagan JE, Bastürkmen M, Birren BW, Sachs MS, Dunlap JC, Loros JJ.

Genetics. 2009 Feb;181(2):767-81. doi: 10.1534/genetics.108.089292. Epub 2008 Nov 17.

50.

Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton.

Quaiser A, López-García P, Zivanovic Y, Henn MR, Rodriguez-Valera F, Moreira D.

Environ Microbiol. 2008 Oct;10(10):2704-17. doi: 10.1111/j.1462-2920.2008.01691.x. Epub 2008 Jul 8.

PMID:
18627413

Supplemental Content

Support Center