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Matthew R. Henn, Ph.D. - Publications

Affiliations: 
2003 University of California, Berkeley, Berkeley, CA, United States 
Area:
Microbiology Biology, Ecology Biology, Biogeochemistry
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38 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
2020 McGovern BH, Ford CB, Henn MR, Pardi DS, Khanna S, Hohmann EL, O'Brien EJ, Desjardins CA, Bernardo P, Wortman JR, Lombardo MJ, Litcofsky KD, Winkler JA, McChalicher CWJ, Li SS, et al. SER-109, an Investigational Microbiome Drug to Reduce Recurrence after Clostridioides difficile infection: Lessons Learned from a Phase 2 Trial. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 32255488 DOI: 10.1093/Cid/Ciaa387  0.312
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  0.327
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  0.322
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  0.346
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  0.31
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  0.322
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  0.317
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  0.318
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  0.361
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  0.325
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  0.316
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  0.339
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  0.32
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  0.32
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  0.319
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  0.321
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  0.367
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  0.334
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  0.302
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  0.324
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  0.323
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  0.324
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  0.367
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  0.322
2010 Henn MR, Lennon NJ, Newman R, Charlebois P, Boutwell C, OhAinle M, Berlin A, Ryan E, Malboeuf C, Macalalad A, Casali M, Erlich R, Bigelow H, Green L, Gnerre S, et al. Sensitive population profiling and genome assembly of HIV and Flaviviruses using ultra-deep sequencing technologies Genome Biology. 11: P18. DOI: 10.1186/Gb-2010-11-S1-P18  0.348
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  0.345
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  0.308
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  0.387
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  0.338
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  0.305
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  0.332
2004 Henn MR, Chapela IH. Isotopic fractionation during ammonium assimilation by basidiomycete fungi and its implications for natural nitrogen isotope patterns. The New Phytologist. 162: 771-781. PMID 33873759 DOI: 10.1111/j.1469-8137.2004.01068.x  0.657
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  0.663
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  0.662
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  0.69
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  0.675
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  0.662
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  0.68
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