Matthew R. Henn, Ph.D. - Publications

Affiliations: 
2003 University of California, Berkeley, Berkeley, CA 
Area:
Microbiology Biology, Ecology Biology, Biogeochemistry

59 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 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, et al. Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus. Plos Pathogens. 12: e1005619. PMID 27163788 DOI: 10.1371/Journal.Ppat.1005619  1
2014 Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, ... ... Henn MR, et al. Standardized metadata for human pathogen/vector genomic sequences. Plos One. 9: e99979. PMID 24936976 DOI: 10.1371/Journal.Pone.0099979  1
2014 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, et al. Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy. Plos One. 9: e90485. PMID 24603872 DOI: 10.1371/Journal.Pone.0090485  1
2013 Yang X, Charlebois P, Macalalad A, Henn MR, Zody MC. V-Phaser 2: variant inference for viral populations. Bmc Genomics. 14: 674. PMID 24088188 DOI: 10.1186/1471-2164-14-674  1
2013 Makhluf H, Buck MD, King K, Perry ST, Henn MR, Shresta S. Tracking the evolution of dengue virus strains D2S10 and D2S20 by 454 pyrosequencing. Plos One. 8: e54220. PMID 23342105 DOI: 10.1371/Journal.Pone.0054220  1
2013 Labrie SJ, Frois-Moniz K, Osburne MS, Kelly L, Roggensack SE, Sullivan MB, Gearin G, Zeng Q, Fitzgerald M, Henn MR, Chisholm SW. Genomes of marine cyanopodoviruses reveal multiple origins of diversity. Environmental Microbiology. 15: 1356-76. PMID 23320838 DOI: 10.1111/1462-2920.12053  1
2013 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. Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants. The Journal of Infectious Diseases. 208: 17-31. PMID 23136221 DOI: 10.1093/Infdis/Jis679  1
2013 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. Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification. Nucleic Acids Research. 41: e13. PMID 22962364 DOI: 10.1093/nar/gks794  1
2013 Malmstrom RR, Rodrigue S, Huang KH, Kelly L, Kern SE, Thompson A, Roggensack S, Berube PM, Henn MR, Chisholm SW. Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis. The Isme Journal. 7: 184-98. PMID 22895163 DOI: 10.1038/Ismej.2012.89  1
2013 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, et al. Complex dynamic of dengue virus serotypes 2 and 3 in Cambodia following series of climate disasters. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 15: 77-86. PMID 22677620 DOI: 10.1016/J.Meegid.2012.05.012  1
2013 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. Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 15: 59-68. PMID 21757030 DOI: 10.1016/J.Meegid.2011.06.019  1
2012 Yang X, Charlebois P, Gnerre S, Coole MG, Lennon NJ, Levin JZ, Qu J, Ryan EM, Zody MC, Henn MR. De novo assembly of highly diverse viral populations. Bmc Genomics. 13: 475. PMID 22974120 DOI: 10.1186/1471-2164-13-475  1
2012 Orozco S, Schmid MA, Parameswaran P, Lachica R, Henn MR, Beatty R, Harris E. Characterization of a model of lethal dengue virus 2 infection in C57BL/6 mice deficient in the alpha/beta interferon receptor Journal of General Virology. 93: 2152-2157. PMID 22815273 DOI: 10.1099/Vir.0.045088-0  1
2012 Santiago GA, McElroy-Horne K, Lennon NJ, Santiago LM, Birren BW, Henn MR, Muñoz-Jordán JL. Reemergence and decline of dengue virus serotype 3 in Puerto Rico. The Journal of Infectious Diseases. 206: 893-901. PMID 22740715 DOI: 10.1093/Infdis/Jis426  1
2012 Parameswaran P, Charlebois P, Tellez Y, Nunez A, Ryan EM, Malboeuf CM, Levin JZ, Lennon NJ, Balmaseda A, Harris E, Henn MR. Genome-wide patterns of intrahuman dengue virus diversity reveal associations with viral phylogenetic clade and interhost diversity. Journal of Virology. 86: 8546-58. PMID 22647702 DOI: 10.1128/Jvi.00736-12  1
2012 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, et al. Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data. Plos Computational Biology. 8: e1002417. PMID 22438797 DOI: 10.1371/Journal.Pcbi.1002417  1
2012 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, et al. Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. Plos Pathogens. 8: e1002529. PMID 22412369 DOI: 10.1371/Journal.Ppat.1002529  1
2012 Marston MF, Pierciey FJ, Shepard A, Gearin G, Qi J, Yandava C, Schuster SC, Henn MR, Martiny JB. Rapid diversification of coevolving marine Synechococcus and a virus. Proceedings of the National Academy of Sciences of the United States of America. 109: 4544-9. PMID 22388749 DOI: 10.1073/Pnas.1120310109  1
2012 Pesko KN, Fitzpatrick KA, Ryan EM, Shi PY, Zhang B, Lennon NJ, Newman RM, Henn MR, Ebel GD. Internally deleted WNV genomes isolated from exotic birds in New Mexico: function in cells, mosquitoes, and mice. Virology. 427: 10-7. PMID 22365325 DOI: 10.1016/J.Virol.2012.01.028  1
2012 Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ. Draft genome sequence of four coccolithoviruses: Emiliania huxleyi virus EhV-88, EhV-201, EhV-207, and EhV-208. Journal of Virology. 86: 2896-7. PMID 22328700 DOI: 10.1128/Jvi.07046-11  1
2012 Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ. Draft genome sequence of the coccolithovirus Emiliania huxleyi virus 202. Journal of Virology. 86: 2380-1. PMID 22282334 DOI: 10.1128/Jvi.06863-11  1
2012 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, et al. High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections. Journal of Virology. 86: 835-43. PMID 22090119 DOI: 10.1128/Jvi.05985-11  1
2011 OhAinle M, Balmaseda A, Macalalad AR, Tellez Y, Zody MC, Saborío S, Nuñez A, Lennon NJ, Birren BW, Gordon A, Henn MR, Harris E. Dynamics of dengue disease severity determined by the interplay between viral genetics and serotype-specific immunity. Science Translational Medicine. 3: 114ra128. PMID 22190239 DOI: 10.1126/Scitranslmed.3003084  1
2011 Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ. Draft genome sequence of the coccolithovirus EhV-84. Standards in Genomic Sciences. 5: 1-11. PMID 22180805 DOI: 10.4056/Sigs.1884581  1
2011 Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ. Draft genome sequence of the Coccolithovirus Emiliania huxleyi virus 203. Journal of Virology. 85: 13468-9. PMID 22106382 DOI: 10.1128/Jvi.06440-11  1
2011 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, et al. Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis. Plos Genetics. 7: e1002345. PMID 22046142 DOI: 10.1371/Journal.Pgen.1002345  1
2011 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, ... ... Henn MR, et al. Human leukocyte antigen B27 selects for rare escape mutations that significantly impair hepatitis C virus replication and require compensatory mutations. Hepatology (Baltimore, Md.). 54: 1157-66. PMID 22006856 DOI: 10.1002/Hep.24541  1
2011 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, ... ... Henn MR, et al. A phylogenetic analysis using full-length viral genomes of South American dengue serotype 3 in consecutive Venezuelan outbreaks reveals a novel NS5 mutation. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 11: 2011-9. PMID 21964598 DOI: 10.1016/J.Meegid.2011.09.010  1
2011 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, et al. Compensatory mutations restore the replication defects caused by cytotoxic T lymphocyte escape mutations in hepatitis C virus polymerase. Journal of Virology. 85: 11883-90. PMID 21880756 DOI: 10.1128/Jvi.00779-11  1
2011 Armstrong PM, Vossbrinck CR, Andreadis TG, Anderson JF, Pesko KN, Newman RM, Lennon NJ, Birren BW, Ebel GD, Henn MR. Molecular evolution of West Nile virus in a northern temperate region: Connecticut, USA 1999-2008. Virology. 417: 203-10. PMID 21723580 DOI: 10.1016/j.virol.2011.06.006  1
2011 Raghwani J, Rambaut A, Holmes EC, Hang VT, Hien TT, Farrar J, Wills B, Lennon NJ, Birren BW, Henn MR, Simmons CP. Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission Plos Pathogens. 7. PMID 21655108 DOI: 10.1371/Journal.Ppat.1002064  1
2011 Erlich RL, Jia X, Anderson S, Banks E, Gao X, Carrington M, Gupta N, DePristo MA, Henn MR, Lennon NJ, de Bakker PI. Next-generation sequencing for HLA typing of class I loci. Bmc Genomics. 12: 42. PMID 21244689 DOI: 10.1186/1471-2164-12-42  1
2011 McElroy KL, Santiago GA, Lennon NJ, Birren BW, Henn MR, Muñoz-Jordán JL. Endurance, refuge, and reemergence of dengue virus type 2, Puerto Rico, 1986-2007. Emerging Infectious Diseases. 17: 64-71. PMID 21192856 DOI: 10.3201/Eid1701.100961  1
2011 Yu Q, Ryan EM, Allen TM, Birren BW, Henn MR, Lennon NJ. PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes. Bioinformatics (Oxford, England). 27: 266-7. PMID 21068001 DOI: 10.1093/bioinformatics/btq624  1
2010 Reyes M, Mercado JC, Standish K, Matute JC, Ortega O, Moraga B, Avilés W, Henn MR, Balmaseda A, Kuan G, Harris E. Index cluster study of dengue virus infection in Nicaragua. The American Journal of Tropical Medicine and Hygiene. 83: 683-9. PMID 20810839 DOI: 10.4269/Ajtmh.2010.10-0023  1
2010 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, ... ... Henn MR, et al. Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments. Environmental Microbiology. 12: 3035-56. PMID 20662890 DOI: 10.1111/J.1462-2920.2010.02280.X  1
2010 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, et al. 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. Plos Neglected Tropical Diseases. 4: e757. PMID 20651932 DOI: 10.1371/Journal.Pntd.0000757  1
2010 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, ... ... Henn MR, et al. Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Research. 20: 938-46. PMID 20516208 DOI: 10.1101/Gr.103911.109  1
2010 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, et al. Analysis of high-throughput sequencing and annotation strategies for phage genomes. Plos One. 5: e9083. PMID 20140207 DOI: 10.1371/Journal.Pone.0009083  1
2010 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, ... ... Henn MR, et al. A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454. Genome Biology. 11: R15. PMID 20137071 DOI: 10.1186/Gb-2010-11-2-R15  1
2010 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. Trends in patterns of dengue transmission over 4 years in a pediatric cohort study in Nicaragua. The Journal of Infectious Diseases. 201: 5-14. PMID 19929380 DOI: 10.1086/648592  1
2009 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, et al. The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. Plos Computational Biology. 5: e1000593. PMID 20011103 DOI: 10.1371/Journal.Pcbi.1000593  1
2009 Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW. Whole genome amplification and de novo assembly of single bacterial cells. Plos One. 4: e6864. PMID 19724646 DOI: 10.1371/Journal.Pone.0006864  1
2009 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, ... ... Henn MR, et al. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Research. 19: 1722-31. PMID 19717792 DOI: 10.1101/Gr.087551.108  1
2009 Lambreghts R, Shi M, Belden WJ, Decaprio D, Park D, Henn MR, Galagan JE, Bastürkmen M, Birren BW, Sachs MS, Dunlap JC, Loros JJ. A high-density single nucleotide polymorphism map for Neurospora crassa. Genetics. 181: 767-81. PMID 19015548 DOI: 10.1534/Genetics.108.089292  1
2009 Henn MR, Boutwell C, Lennon N, Power K, Malboeuf C, Charlebois P, Gladden A, Levin J, Casali M, Philips L, Berlin A, Berical A, Erlich R, Anderson S, Streeck H, et al. P09-20 LB. Ultra-deep sequencing of full-length HIV-1 genomes identifies rapid viral evolution during acute infection Retrovirology. 6. DOI: 10.1186/1742-4690-6-S3-P400  1
2008 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, ... ... Henn MR, et al. Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients. Hepatology (Baltimore, Md.). 48: 1769-78. PMID 19026009 DOI: 10.1002/Hep.22549  1
2008 Quaiser A, López-García P, Zivanovic Y, Henn MR, Rodriguez-Valera F, Moreira D. Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton. Environmental Microbiology. 10: 2704-17. PMID 18627413 DOI: 10.1111/J.1462-2920.2008.01691.X  1
2008 Kuntzen T, Berical A, Ndjomou J, Bennett P, Schneidewind A, Lennon N, Birren BW, Kuiken C, Henn MR, Simmonds P, Allen TM. A set of reference sequences for the hepatitis C genotypes 4d, 4f, and 4k covering the full open reading frame. Journal of Medical Virology. 80: 1370-8. PMID 18551618 DOI: 10.1002/Jmv.21240  1
2008 White TC, Oliver BG, Gräser Y, Henn MR. Generating and testing molecular hypotheses in the dermatophytes. Eukaryotic Cell. 7: 1238-45. PMID 18539886 DOI: 10.1128/Ec.00100-08  1
2008 Martin-Cuadrado AB, Rodriguez-Valera F, Moreira D, Alba JC, Ivars-Martínez E, Henn MR, Talla E, López-García P. Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions. The Isme Journal. 2: 865-86. PMID 18463691 DOI: 10.1038/Ismej.2008.40  1
2007 Dunlap JC, Borkovich KA, Henn MR, Turner GE, Sachs MS, Glass NL, McCluskey K, Plamann M, Galagan JE, Birren BW, Weiss RL, Townsend JP, Loros JJ, Nelson MA, Lambreghts R, et al. Enabling a community to dissect an organism: overview of the Neurospora functional genomics project. Advances in Genetics. 57: 49-96. PMID 17352902 DOI: 10.1016/S0065-2660(06)57002-6  1
2005 Galagan JE, Henn MR, Ma LJ, Cuomo CA, Birren B. Genomics of the fungal kingdom: insights into eukaryotic biology. Genome Research. 15: 1620-31. PMID 16339359 DOI: 10.1101/087969807.46.41  1
2004 Henn MR, Chapela IH. Isotopic fractionation during ammonium assimilation by basidiomycete fungi and its implications for natural nitrogen isotope patterns New Phytologist. 162: 771-781. DOI: 10.1111/J.1469-8137.2004.01068.X  1
2002 Henn MR, Gleixner G, Chapela IH. Growth-dependent stable carbon isotope fractionation by basidiomycete fungi: delta(13)C pattern and physiological process. Applied and Environmental Microbiology. 68: 4956-64. PMID 12324344 DOI: 10.1128/Aem.68.10.4956-4964.2002  1
2001 Henn MR, Chapela IH. Ecophysiology of (13)C and (15)N isotopic fractionation in forest fungi and the roots of the saprotrophic-mycorrhizal divide. Oecologia. 128: 480-487. PMID 28547392 DOI: 10.1007/S004420100680  1
2001 Chapela IH, Osher LJ, Horton TR, Henn MR. Ectomycorrhizal fungi introduced with exotic pine plantations induce soil carbon depletion Soil Biology and Biochemistry. 33: 1733-1740. DOI: 10.1016/S0038-0717(01)00098-0  1
2001 Henn MR, Chapela IH. Ecophysiology of 13C and 15N isotopic fractionation in forest fungi and the roots of the saprotrophic-mycorrhizal divide Oecologia. 128: 480-487. DOI: 10.1007/s004420100680  1
2000 Henn MR, Chapela IH. Differential C isotope discrimination by fungi during decomposition of C(3)- and C(4)-derived sucrose. Applied and Environmental Microbiology. 66: 4180-6. PMID 11010857 DOI: 10.1128/Aem.66.10.4180-4186.2000  1
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