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Martin Wu - Publications

Affiliations: 
2005-2007 University of California, Davis, Davis, CA 
 2007- University of Virginia, Charlottesville, VA 
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55 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 Wang Z, Yang Y, Yan Z, Liu H, Chen B, Liang Z, Wang F, Miller BE, Tal-Singer R, Yi X, Li J, Stampfli MR, Zhou H, Brightling CE, Brown JR, ... Wu M, et al. Multi-omic meta-analysis identifies functional signatures of airway microbiome in chronic obstructive pulmonary disease. The Isme Journal. PMID 32719402 DOI: 10.1038/S41396-020-0727-Y  0.319
2020 Grippo RM, Tang Q, Zhang Q, Chadwick SR, Gao Y, Altherr EB, Sipe L, Purohit AM, Purohit NM, Sunkara MD, Cios KJ, Sidikpramana M, Spano AJ, Campbell JN, Steele AD, ... ... Wu M, et al. Dopamine Signaling in the Suprachiasmatic Nucleus Enables Weight Gain Associated with Hedonic Feeding. Current Biology : Cb. 30: 1352-1355. PMID 32259494 DOI: 10.1016/j.cub.2020.03.034  0.355
2019 Grippo RM, Tang Q, Zhang Q, Chadwick SR, Gao Y, Altherr EB, Sipe L, Purohit AM, Purohit NM, Sunkara MD, Cios KJ, Sidikpramana M, Spano AJ, Campbell JN, Steele AD, ... ... Wu M, et al. Dopamine Signaling in the Suprachiasmatic Nucleus Enables Weight Gain Associated with Hedonic Feeding. Current Biology : Cb. PMID 31902720 DOI: 10.1016/J.Cub.2019.11.029  0.444
2017 Wang Z, Wu M. Comparative Genomic Analysis of Acanthamoeba Endosymbionts Highlights the Role of Amoebae as a "Melting Pot" Shaping the Rickettsiales Evolution. Genome Biology and Evolution. 9: 3214-3224. PMID 29177480 DOI: 10.1093/Gbe/Evx246  0.472
2016 Cichewicz K, Garren EJ, Adiele C, Aso Y, Wang Z, Wu M, Birman S, Rubin GM, Hirsh J. A New Brain Dopamine Deficient Drosophila and its Pharmacological and Genetic Rescue. Genes, Brain, and Behavior. PMID 27762066 DOI: 10.1111/Gbb.12353  0.463
2016 Ren T, Kahrl AF, Wu M, Cox RM. Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards. Molecular Ecology. PMID 27497270 DOI: 10.1111/Mec.13796  0.326
2015 Wang Z, Wu M. An integrated phylogenomic approach toward pinpointing the origin of mitochondria. Scientific Reports. 5: 7949. PMID 25609566 DOI: 10.1038/Srep07949  0.438
2015 Weller C, Wu M. A generation-time effect on the rate of molecular evolution in bacteria Evolution. 69: 643-652. PMID 25564727 DOI: 10.1111/Evo.12597  0.387
2014 Wang Z, Wu M. Phylogenomic reconstruction indicates mitochondrial ancestor was an energy parasite. Plos One. 9: e110685. PMID 25333787 DOI: 10.1371/Journal.Pone.0110685  0.315
2014 Wang Z, Wu M. Complete Genome Sequence of the Endosymbiont of Acanthamoeba Strain UWC8, an Amoeba Endosymbiont Belonging to the "Candidatus Midichloriaceae" Family in Rickettsiales. Genome Announcements. 2. PMID 25103769 DOI: 10.1128/Genomea.00791-14  0.453
2014 Lin W, Deng A, Wang Z, Li Y, Wen T, Wu LF, Wu M, Pan Y. Genomic insights into the uncultured genus 'Candidatus Magnetobacterium' in the phylum Nitrospirae. The Isme Journal. 8: 2463-77. PMID 24914800 DOI: 10.1038/Ismej.2014.94  0.537
2014 Kopac S, Wang Z, Wiedenbeck J, Sherry J, Wu M, Cohan FM. Genomic heterogeneity and ecological speciation within one subspecies of Bacillus subtilis. Applied and Environmental Microbiology. 80: 4842-53. PMID 24907327 DOI: 10.1128/Aem.00576-14  0.479
2014 Sloan DB, Triant DA, Forrester NJ, Bergner LM, Wu M, Taylor DR. A recurring syndrome of accelerated plastid genome evolution in the angiosperm tribe Sileneae (Caryophyllaceae). Molecular Phylogenetics and Evolution. 72: 82-9. PMID 24373909 DOI: 10.1016/J.Ympev.2013.12.004  0.496
2014 Sloan DB, Triant DA, Wu M, Taylor DR. Cytonuclear interactions and relaxed selection accelerate sequence evolution in organelle ribosomes. Molecular Biology and Evolution. 31: 673-82. PMID 24336923 DOI: 10.1093/Molbev/Mst259  0.435
2014 Koeppel AF, Wu M. Species matter: the role of competition in the assembly of congeneric bacteria. The Isme Journal. 8: 531-40. PMID 24132075 DOI: 10.1038/Ismej.2013.180  0.343
2013 McNamara M, Tzeng SC, Maier C, Wu M, Bermudez LE. Surface-exposed proteins of pathogenic mycobacteria and the role of cu-zn superoxide dismutase in macrophages and neutrophil survival. Proteome Science. 11: 45. PMID 24283571 DOI: 10.1186/1477-5956-11-45  0.306
2013 Koeppel AF, Wu M. Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units. Nucleic Acids Research. 41: 5175-88. PMID 23571758 DOI: 10.1093/Nar/Gkt241  0.404
2013 Wang Z, Wu M. A phylum-level bacterial phylogenetic marker database. Molecular Biology and Evolution. 30: 1258-62. PMID 23519313 DOI: 10.1093/Molbev/Mst059  0.486
2013 Ren T, Glatt DU, Nguyen TN, Allen EK, Early SV, Sale M, Winther B, Wu M. 16S rRNA survey revealed complex bacterial communities and evidence of bacterial interference on human adenoids Environmental Microbiology. 15: 535-547. PMID 23113966 DOI: 10.1111/1462-2920.12000  0.33
2012 Kembel SW, Wu M, Eisen JA, Green JL. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. Plos Computational Biology. 8: e1002743. PMID 23133348 DOI: 10.1371/Journal.Pcbi.1002743  0.62
2012 Lu HP, Wang YB, Huang SW, Lin CY, Wu M, Hsieh CH, Yu HT. Metagenomic analysis reveals a functional signature for biomass degradation by cecal microbiota in the leaf-eating flying squirrel (Petaurista alborufus lena). Bmc Genomics. 13: 466. PMID 22963241 DOI: 10.1186/1471-2164-13-466  0.303
2012 Koeppel AF, Wu M. Lineage-dependent ecological coherence in bacteria. Fems Microbiology Ecology. 81: 574-82. PMID 22486161 DOI: 10.1111/J.1574-6941.2012.01387.X  0.333
2012 Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics (Oxford, England). 28: 1033-4. PMID 22332237 DOI: 10.1093/Bioinformatics/Bts079  0.482
2012 Wu M, Chatterji S, Eisen JA. Accounting for alignment uncertainty in phylogenomics. Plos One. 7: e30288. PMID 22272325 DOI: 10.1371/Journal.Pone.0030288  0.658
2012 Sloan DB, Alverson AJ, Chuckalovcak JP, Wu M, McCauley DE, Palmer JD, Taylor DR. Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates. Plos Biology. 10: e1001241. PMID 22272183 DOI: 10.1371/Journal.Pbio.1001241  0.474
2012 Sloan DB, Alverson AJ, Wu M, Palmer JD, Taylor DR. Recent acceleration of plastid sequence and structural evolution coincides with extreme mitochondrial divergence in the angiosperm genus Silene. Genome Biology and Evolution. 4: 294-306. PMID 22247429 DOI: 10.1093/Gbe/Evs006  0.476
2011 Coyne RS, Hannick L, Shanmugam D, Hostetler JB, Brami D, Joardar VS, Johnson J, Radune D, Singh I, Badger JH, Kumar U, Saier M, Wang Y, Cai H, Gu J, ... ... Wu M, et al. Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control. Genome Biology. 12: R100. PMID 22004680 DOI: 10.1186/Gb-2011-12-10-R100  0.696
2011 Wang Z, Kadouri DE, Wu M. Genomic insights into an obligate epibiotic bacterial predator: Micavibrio aeruginosavorus ARL-13. Bmc Genomics. 12: 453. PMID 21936919 DOI: 10.1186/1471-2164-12-453  0.524
2011 Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA. Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. Plos One. 6: e18011. PMID 21437252 DOI: 10.1371/Journal.Pone.0018011  0.733
2009 Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 462: 1056-60. PMID 20033048 DOI: 10.1038/Nature08656  0.772
2009 Rastogi R, Wu M, Dasgupta I, Fox GE. Visualization of ribosomal RNA operon copy number distribution. Bmc Microbiology. 9: 208. PMID 19781086 DOI: 10.1186/1471-2180-9-208  0.441
2009 Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J, Barabote RD, Bradley B, Brettin TS, Brinkac LM, Bruce D, et al. Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Applied and Environmental Microbiology. 75: 2046-56. PMID 19201974 DOI: 10.1128/Aem.02294-08  0.716
2009 Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb F, Colman A, Tallon LJ, Badger JH, Madupu R, Ward NL, Eisen JA. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. Plos One. 4: e4207. PMID 19148287 DOI: 10.1371/Journal.Pone.0004207  0.785
2008 Wu M, Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biology. 9: R151. PMID 18851752 DOI: 10.1186/Gb-2008-9-10-R151  0.585
2008 Harriff MJ, Wu M, Kent ML, Bermudez LE. Species of environmental mycobacteria differ in their abilities to grow in human, mouse, and carp macrophages and with regard to the presence of mycobacterial virulence genes, as observed by DNA microarray hybridization. Applied and Environmental Microbiology. 74: 275-85. PMID 17981953 DOI: 10.1128/Aem.01480-07  0.333
2007 Maresca JA, Graham JE, Wu M, Eisen JA, Bryant DA. Identification of a fourth family of lycopene cyclases in photosynthetic bacteria. Proceedings of the National Academy of Sciences of the United States of America. 104: 11784-9. PMID 17606904 DOI: 10.1073/Pnas.0702984104  0.589
2006 Seshadri R, Joseph SW, Chopra AK, Sha J, Shaw J, Graf J, Haft D, Wu M, Ren Q, Rosovitz MJ, Madupu R, Tallon L, Kim M, Jin S, Vuong H, et al. Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades. Journal of Bacteriology. 188: 8272-82. PMID 16980456 DOI: 10.1128/Jb.00621-06  0.513
2006 Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, et al. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. Plos Biology. 4: e286. PMID 16933976 DOI: 10.1371/Journal.Pbio.0040286  0.8
2006 Dunning Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Eisen J, Seshadri R, Ren Q, Wu M, Utterback TR, Smith S, Lewis M, Khouri H, Zhang C, et al. Comparative genomics of emerging human ehrlichiosis agents. Plos Genetics. 2: e21. PMID 16482227 DOI: 10.1371/Journal.Pgen.0020021  0.594
2006 Yamazaki Y, Danelishvili L, Wu M, Macnab M, Bermudez LE. Mycobacterium avium genes associated with the ability to form a biofilm. Applied and Environmental Microbiology. 72: 819-25. PMID 16391123 DOI: 10.1128/Aem.72.1.819-825.2006  0.336
2006 Dunning Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Seshadri R, Ren Q, Wu M, Utterback TR, Smith S, Lewis M, Khouri H, Zhang C, Niu H, et al. Correction: Comparative Genomics of Emerging Human Ehrlichiosis Agents Plos Genetics. 2: e213. DOI: 10.1371/Journal.Pgen.0020213  0.48
2006 Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Haft DH, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, et al. Correction: Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901 Plos Genetics. 2: e60. DOI: 10.1371/Journal.Pgen.0020060  0.593
2005 Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Haft DH, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, et al. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. Plos Genetics. 1: e65. PMID 16311624 DOI: 10.1371/Journal.Pgen.0010065  0.609
2005 Methé BA, Nelson KE, Deming JW, Momen B, Melamud E, Zhang X, Moult J, Madupu R, Nelson WC, Dodson RJ, Brinkac LM, Daugherty SC, Durkin AS, DeBoy RT, Kolonay JF, ... ... Wu M, et al. The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses Proceedings of the National Academy of Sciences of the United States of America. 102: 10913-10918. PMID 16043709 DOI: 10.1073/Pnas.0504766102  0.503
2004 Ward N, Larsen Ø, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH, Lewis M, Nelson KE, Methé B, Wu M, Heidelberg JF, et al. Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). Plos Biology. 2: e303. PMID 15383840 DOI: 10.1371/Journal.Pbio.0020303  0.746
2004 Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C, Ahmadinejad N, Wiegand C, Madupu R, Beanan MJ, Brinkac LM, Daugherty SC, et al. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. Plos Biology. 2: E69. PMID 15024419 DOI: 10.1371/Journal.Pbio.0020069  0.646
2003 Methé BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, Wu D, Wu M, Ward N, Beanan MJ, Dodson RJ, Madupu R, Brinkac LM, Daugherty SC, DeBoy RT, et al. Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science (New York, N.Y.). 302: 1967-9. PMID 14671304 DOI: 10.1126/Science.1088727  0.536
2003 Ermolaeva MD, Wu M, Eisen JA, Salzberg SL. The age of the Arabidopsis thaliana genome duplication. Plant Molecular Biology. 51: 859-66. PMID 12777046 DOI: 10.1023/A:1023001130337  0.584
2003 Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, et al. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature. 423: 81-6. PMID 12721629 DOI: 10.1038/Nature01586  0.587
2002 Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, ... ... Wu M, et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science (New York, N.Y.). 298: 129-49. PMID 12364791 DOI: 10.1126/Science.1076181  0.507
2002 Eisen JA, Wu M. Phylogenetic analysis and gene functional predictions: phylogenomics in action. Theoretical Population Biology. 61: 481-7. PMID 12167367 DOI: 10.1006/Tpbi.2002.1594  0.564
2002 Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, Deboy R, Gwinn ML, Nelson WC, Haft DH, Hickey EK, Peterson JD, Durkin AS, Kolonay JL, Yang F, et al. The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proceedings of the National Academy of Sciences of the United States of America. 99: 9509-14. PMID 12093901 DOI: 10.1073/Pnas.132181499  0.654
2001 Wu M, Schleif R. Mapping arm-DNA-binding domain interactions in AraC. Journal of Molecular Biology. 307: 1001-9. PMID 11286551 DOI: 10.1006/Jmbi.2001.4531  0.567
2001 Harmer T, Wu M, Schleif R. The role of rigidity in DNA looping-unlooping by AraC. Proceedings of the National Academy of Sciences of the United States of America. 98: 427-31. PMID 11209047 DOI: 10.1073/Pnas.98.2.427  0.712
2000 Wu M, Schleif R. Strengthened arm-dimerization domain interactions in AraC. The Journal of Biological Chemistry. 276: 2562-4. PMID 11069917 DOI: 10.1074/Jbc.M008705200  0.548
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