Gao Y, Abdullah A, Wu M. A unifying model of species abundance distribution. bioRxiv 2024.06.14.599104; doi: https://doi.org/10.1101/2024.06.14.599104
Halhed A, Petrullo L, Boutin S, Dantzer B, McAdam A, Wu M, Cottenie K. Consistent spatial patterns in microbial taxa of red squirrel gut microbiomes. Environ Microbiol Rep. 2023 Nov 9;. doi: 10.1111/1758-2229.13209. [Epub ahead of print] PubMed PMID: 37943285.
Warren CA, Shin JH, Bansal EN, Costa DVDS, Wang XQ, Wu M, Swann JR, Behm BW, Targonski PV, Archbald-Pannone L. Alanyl-glutamine supplementation for Clostridioides difficile infection treatment (ACT): a double-blind randomised controlled trial study protocol. BMJ Open. 2023 Jul 19;13(7):e075721. doi: 10.1136/bmjopen-2023-075721. PubMed PMID: 37474181; PubMed Central PMCID: PMC10357635.
Gao Y, Wu M. Accounting for 16S rRNA copy number prediction uncertainty and its implications in bacterial diversity analyses. ISME Commun. 2023 Jun 10;3(1):59. doi: 10.1038/s43705-023-00266-0. PMID: 37301942; PMCID: PMC10257666.
Li-Gao R, Grubbs K, Bertoni AG, Hoffman KL, Petrosino JF, Ramesh G, Wu M, Rotter JI, Chen YI, Evans AM, Robinson RJ, Sommerville L, Mook-Kanamori D, Goodarzi MO, Michelotti GA, Sheridan PA. The Roles of Gut Microbiome and Plasma Metabolites in the Associations between ABO Blood Groups and Insulin Homeostasis: The Microbiome and Insulin Longitudinal Evaluation Study (MILES). Metabolites. 2022 Aug 25;12(9):787. doi: 10.3390/metabo12090787. PMID: 36144194; PMCID: PMC9505353.
Cui J, Ramesh G, Wu M, Jensen ET, Crago O, Bertoni AG, Gao C, Hoffman KL, Sheridan PA, Wong KE, Wood AC, Chen YI, Rotter JI, Petrosino JF, Rich SS, Goodarzi MO. Butyrate-Producing Bacteria and Insulin Homeostasis: The Microbiome and Insulin Longitudinal Evaluation Study (MILES). Diabetes. 2022 Nov 1;71(11):2438-2446. doi: 10.2337/db22-0168. PMID: 35972231; PMCID: PMC9630078.
Gao Y, Wu M. Microbial genomic trait evolution is dominated by frequent and rare pulsed evolution. Sci Adv. 2022 Jul 15;8(28):eabn1916. doi: 10.1126/sciadv.abn1916. Epub 2022 Jul 15. PMID: 35857501.
Gao Y, Wu M. Modeling Pulsed Evolution and Time-independent Variation Improves the Confidence Level of Ancestral and Hidden State Predictions. Syst Biol. 2022 Feb 25:syac016. doi: 10.1093/sysbio/syac016. Epub ahead of print. PMID: 35212761.
Costa DVS, Pham NVS, Hays RA, Bolick DT, Goldbeck SM, Poulter MD, Hoang SC, Shin JH, Wu M, Warren CA. Influence of Binary Toxin Gene Detection and Decreased Susceptibility to Antibiotics among Clostridioides difficile Strains on Disease Severity: a Single-Center Study. Antimicrob Agents Chemother. 2022 Aug 16;66(8):e0048922. doi: 10.1128/aac.00489-22. Epub 2022 Jul 21. PMID: 35861541; PMCID: PMC9380565.
Shanmugakani RK, Wu M. An isothermal amplification-coupled dipstick for the rapid detection of COVID-19. J Med Microbiol. 2022 Apr;71(4). doi: 10.1099/jmm.0.001519. PMID: 35451947.
Petrullo L, Ren T, Wu M, Boonstra R, Palme R, Boutin S, McAdam AG, Dantzer B. Glucocorticoids coordinate changes in gut microbiome composition in wild North American red squirrels. Sci Rep. 2022 Feb 16;12(1):2605. doi: 10.1038/s41598-022-06359-5. PubMed PMID: 35173201.
Murray CS, Gao Y, Wu M. Re-evaluating the evidence for a universal genetic boundary among microbial species. Nat Commun 12, 4059 (2021). https://doi.org/10.1038/s41467-021-24128-2
Luu LA, Flowers RH, Gao Y, Wu M, Gasperino S, Kellams AL, Preston DC, Zlotoff BJ, Wisniewski JA, Zeichner SL. Apple cider vinegar soaks do not alter the skin bacterial microbiome in atopic dermatitis. PLoS One. 2021 Jun 2;16(6):e0252272. doi: 10.1371/journal.pone.0252272. PMID: 34077434; PMCID: PMC8172074.
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, Chen R, Shu W. Multi-omic meta-analysis identifies functional signatures of airway microbiome in chronic obstructive pulmonary disease. ISME J. 2020 Jul 27. doi: 10.1038/s41396-020-0727-y. Epub ahead of print. PMID: 32719402.
Jensen ET, Bertoni AG, Crago OL, Hoffman KL, Wood AC, Arzumanyan Z, Lam LK, Roll K, Sandow K, Wu M, Rich SS, Rotter JI, Chen YI, Petrosino JF, Goodarzi MO. Rationale, design and baseline characteristics of the Microbiome and Insulin Longitudinal Evaluation Study (MILES). Diabetes Obes Metab. 2020 Jul 20. doi: 10.1111/dom.14145. Epub ahead of print. PMID: 32687239.
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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, Hirsh J, Deppmann CD, Wu M, Scott MM, Güler AD. Dopamine Signaling in the Suprachiasmatic Nucleus Enables Weight Gain Associated with Hedonic Feeding. Curr Biol. 2020 Jan 20;30(2):196-208.e8. doi: 10.1016/j.cub.2019.11.029. Epub 2020 Jan 2.
Chhabra P, Spano AJ, Bowers D, Ren T, Moore DJ, Timko MP, Wu M, Brayman KL. Evidence for the Role of the Cecal Microbiome in Maintenance of Immune Regulation and Homeostasis. Ann Surg. 2018 Sep;268(3):541-549. doi: 10.1097/SLA.0000000000002930.
Ren T, Boutin S, Humphries MM, Dantzer B, Gorrell JC, Coltman DW, McAdam AG, Wu M. Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels. Microbiome. 2017 Dec 21;5(1):163. doi: 10.1186/s40168-017-0382-3.
Wang Z, Wu M. Comparative genomic analysis of acanthamoeba endosymbionts highlights the role of amoebae as a "melting pot" shaping the Rickettsiales evolution. Genome Biol Evol. 2017 Nov 1;9(11):3214-3224. doi: 10.1093/gbe/evx246.
Shin JH, Gao Y, Moore JH, Bolick DT, Kolling GL, Wu M, Warren CA. Innate immune response and outcome of Clostridium difficile infection are dependent on fecal bacterial composition in the aged host. J Infect Dis. 2017 Aug 22. doi: 10.1093/infdis/jix414.
Marin IA, Goertz JE, Ren T, Rich SS, Onengut-Gumuscu S, Farber E, Wu M, Overall CC, Kipnis J, Gaultier A. Microbiota alteration is associated with the development of stress-induced despair behavior. Sci Rep. 2017 Mar 7;7:43859. doi: 10.1038/srep43859.
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 Behav. 2016 Oct 19. doi: 10.1111/gbb.12353. [Epub ahead of print]
Ren T, Wu M. PhyloCore: A phylogenetic approach to identifying core taxa in microbial communities.Gene. 2016 Nov 30;593(2):330-3. doi: 10.1016/j.gene.2016.08.032. Epub 2016 Aug 24.
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. Mol Ecol. 2016 Oct;25(19):4793-804. doi: 10.1111/mec.13796. Epub 2016 Sep 13.
Ren T, Grieneisen LE, Alberts SC, Archie EA, Wu M. Development, diet and dynamism: longitudinal and cross-sectional predictors of gut microbial communities in wild baboons. Environ Microbiol. 2015 Mar 26. doi:10.1111/1462-2920.12852. [Epub ahead of print]
Weller C and Wu M. A generation-time effect on the rate of molecular evolution in bacteria. Evolution. 2015 Jan 7. doi: 10.1111/evo.12597.
Wang Z and Wu M. An integrated phylogenomic approach toward pinpointing the origin of mitochondria. Scientific Reports. 2015 Jan 22;5:7949. doi: 10.1038/srep07949
Wang Z and Wu M. Phylogenomic reconstruction indicates mitochondrial ancestor was an energy parasite. PLoS One. 2014;9(10):e110685. doi:10.1371/journal.pone.0110685.
Wang Z and Wu M. Complete genome sequence of the endosymbiont of Acanthamoeba strain UWC8, an amoeba endosymbiont belonging to the "Candidatus Midichloriaceae" family in Rickettsiales. Genome Announc. 2014 Aug 7;2(4). pii: e00791-14. doi: 10.1128/genomeA.00791-14.
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. ISME J. 2014 Jun 10. doi: 10.1038/ismej.2014.94. [Epub ahead of print]
Kopac S, Wang Z, Wiedenbeck J, Sherry J, Wu M, Cohan FM. Genomic heterogeneity and ecological speciation within one subspecies of Bacillus subtilis. Appl Environ Microbiol. 2014 Jun 6. pii: AEM.00576-14. [Epub ahead of print]
Sloan DB, Triant DA, Wu M, Taylor DR. Cytonuclear interactions and relaxed selection accelerate sequence evolution in organelle ribosomes. Mol Biol Evol. 2014 Mar;31(3):673-82. doi: 10.1093/molbev/mst259. Epub 2013 Dec 13.
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). Mol Phylogenet Evol. 2014 Mar;72:82-9. doi: 10.1016/j.ympev.2013.12.004. Epub 2013 Dec 25.
Koeppel AF and Wu M. Species matter: the role of competition in the assembly of congeneric bacteria. ISME J. 2014 Mar;8(3):531-40. doi: 10.1038/ismej.2013.180. Epub 2013 Oct 17.
Sears MT, Zhang H, Rushton PJ, Wu M, Han S, Spano AJ, Timko MP. NtERF32: a non-NIC2 locus AP2/ERF transcription factor required in jasmonate-inducible nicotine biosynthesis in tobacco. Plant Mol Biol. 2014 Jan;84(1-2):49-66. doi: 10.1007/s11103-013-0116-2. Epub 2013 Aug 11.
Wu M. Protein-coding genes as alternative markers in microbial diversity studies. In: Nelson K. (Ed.) Encyclopedia of Metagenomics. SpringerReference (www.springerreference.com). Springer-Verlag Berlin Heidelberg, 2013. doi:10.1007/SpringerReference_343804 2013-03-06 16:02:26 UTC
Koeppel AF and Wu M. Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units. Nucleic Acids Res. 2013, 1-14 doi:10.1093/nar/gkt241.
Wang Z and Wu M. A phylum-level bacterial phylogenetic marker database. Mol. Biol. Evol. 2013 Jun;30(6):1258-62. doi: 10.1093/molbev/mst059. Epub 2013 Mar 21.
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 2013 Feb;15(2):535-47. doi: 10.1111/1462-2920.12000. Epub 2012 Oct 31.
Kembel SW, Wu M, Eisen JA, Green JL. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Comput Biol. 2012. 8(10): e1002743. doi:10.1371/journal.pcbi.1002743.
Kolling GL, Wu M, Alcantara-Warren C, Durmaz E, Klaenhammer TR, Guerrant RL. Lactic acid production by Streptococcus thermophilus alters Clostridium difficile infection and in vitro Toxin A production. Gut Microbes 2012, 3:6,1-7. doi:10.4161/gutmicrobes.21757.
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. 2012,13:466. doi:10.1186/1471-2164-13-466.
Kolling G, Wu M, Guerrant RL. Enteric pathogens through life stages. Frontiers in Cellular and Infection Microbiology. 2012, 2:114. doi:10.3389/fcimb.2012.00114.
Koeppel AF and Wu M. Lineage-dependent ecological coherence in bacteria. FEMS Microbiology Ecology. 2012, Sep;81(3):574-82. doi: 10.1111/j.1574-6941.2012.01387.x.
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 Biol Evol. 2012, Jan;4(3):294-306. Epub 2012 Jan 12.
Wu M and Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012, 28:1033-1034.
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 Biol. 2012 Jan;10(1):e1001241. Epub 2012 Jan 17.
Wu M, Chatterji S, Eisen JA. Accounting for alignment uncertainty in phylogenomics. PLoS ONE 2012, 7(1): e30288. doi:10.1371/journal.pone.0030288
Coyne RS, Hannick L, Shanmugam D, Hostetler JB, Brami D, Joardar VS, Johnson J, Radune D, Singh I, Kumar U, Saier M, Wang Y, Cai H, Gu J, Mather MW, Vaidya AB, Wilkes DE, Rajagopalan V, Asai DJ, Pearson CG, Findly RC, Dickerson HW, Badger JH, Wu M, Martens C, Van de Peer Y, Roos DS, Cassidy-Hanley DM, Clark TG. 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 Biol 2011 Oct 17;12(10):R100.
Wang Z, Kadouri DE and Wu M. Genomic insights into an obligate epibiotic bacterial predator: Micavibrio aeruginosavorus ARL-13. BMC Genomics 2011, 12:453. doi:10.1186/1471-2164-12-453
Wu M and Eisen JA. Towards Automated Phylogenomic Inference in Bruijn, F.J.d., Handbook of molecular microbial ecology I : metagenomics and complementary approaches. 2011, Hoboken, N.J.: Wiley-Blackwell.
Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC and Eisen JA. Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees. PLoS One 2011 6(3): e18011. doi:10.1371/journal.pone.0018011.
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, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, and Eisen JA. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009 Dec 24; 462(7276) 1056-60.
Rastogi R, Wu M, Dasgupta I, Fox GE. Visualization of ribosomal RNA operon copy number distribution. BMC Microbiol. 2009 Sep 25;9(1):208. [highly accessed]
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, Creasy T, Daugherty SC, Davidsen TM, DeBoy RT, Detter JC, Dodson RJ, Durkin AS, Ganapathy A, Gwinn-Giglio M, Han CS, Khouri H, Kiss H, Kothari SP, Madupu R, Nelson KE, Nelson WC, Paulsen I, Penn K, Ren Q, Rosovitz MJ, Selengut JD, Shrivastava S, Sullivan SA, Tapia R, Thompson LS, Watkins KL, Yang Q, Yu C, Zafar N, Zhou L, Kuske CR. Three genomes from the phylum acidobacteria provide insight into their lifestyles in soils. Appl Environ Microbiol. 2009; 75(7) 2046-56
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, and Eisen JA. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS ONE 2009; 4(1) e4207.
Wu M and Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biol 2008 Oct 13; 9(10) R151.
Maresca JA, Graham JE, Wu M, Eisen JA, and Bryant DA. Identification of a fourth family of lycopene cyclases in photosynthetic bacteria. Proc Natl Acad Sci U S A 2007 Jul 10; 104(28) 11784-9.
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, Stine OC, Ali A, Horneman AJ, and Heidelberg JF. Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades. J Bacteriol 2006 Dec; 188(23) 8272-82.
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, Majoros WH, Farzad M, Carlton JM, Smith RK Jr, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, and Orias E. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol 2006 Sep; 4(9) e286.
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, Lin Q, Ohashi N, Zhi N, Nelson W, Brinkac LM, Dodson RJ, Rosovitz MJ, Sundaram J, Daugherty SC, Davidsen T, Durkin AS, Gwinn M, Haft DH, Selengut JD, Sullivan SA, Zafar N, Zhou L, Benahmed F, Forberger H, Halpin R, Mulligan S, Robinson J, White O, Rikihisa Y, and Tettelin H. Comparative genomics of emerging human ehrlichiosis agents. PLoS Genet 2006 Feb; 2(2) e21.
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, Zhulin IB, Robb FT, and Eisen JA. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genet 2005 Nov; 1(5) e65.
Ward N, Larsen , Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH, Lewis M, Nelson KE, Meth B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, DeBoy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, and Eisen JA. Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol 2004 Oct; 2(10) e303.
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, Durkin AS, Kolonay JF, Nelson WC, Mohamoud Y, Lee P, Berry K, Young MB, Utterback T, Weidman J, Nierman WC, Paulsen IT, Nelson KE, Tettelin H, O'Neill SL, and Eisen JA. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol 2004 Mar; 2(3) E69.
Meth 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, Durkin AS, Gwinn M, Kolonay JF, Sullivan SA, Haft DH, Selengut J, Davidsen TM, Zafar N, White O, Tran B, Romero C, Forberger HA, Weidman J, Khouri H, Feldblyum TV, Utterback TR, Van Aken SE, Lovley DR, and Fraser CM. Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science 2003 Dec 12; 302(5652) 1967-9.
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, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, Plaut RD, Wolf AM, Watkins KL, Nierman WC, Hazen A, Cline R, Redmond C, Thwaite JE, White O, Salzberg SL, Thomason B, Friedlander AM, Koehler TM, Hanna PC, Kolst AB, and Fraser CM. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 2003 May 1; 423(6935) 81-6.
Ermolaeva MD, Wu M, Eisen JA, and Salzberg SL. The age of the Arabidopsis thaliana genome duplication. Plant Mol Biol 2003 Apr; 51(6) 859-66.
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, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, Zhao S, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, and Hoffman SL. The genome sequence of the malaria mosquito Anopheles gambiae. Science 2002 Oct 4; 298(5591) 129-49.
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, Holt I, Umayam LA, Mason T, Brenner M, Shea TP, Parksey D, Nierman WC, Feldblyum TV, Hansen CL, Craven MB, Radune D, Vamathevan J, Khouri H, White O, Gruber TM, Ketchum KA, Venter JC, Tettelin H, Bryant DA, and Fraser CM. The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc Natl Acad Sci U S A 2002 Jul 9; 99(14) 9509-14.
Eisen JA and Wu M. Phylogenetic analysis and gene functional predictions: phylogenomics in action. Theor Popul Biol 2002 Jun; 61(4) 481-7.
Wu M and Schleif R. Mapping arm-DNA-binding domain interactions in AraC. J Mol Biol 2001 Apr 6; 307(4) 1001-9.
Wu M and Schleif R. Strengthened arm-dimerization domain interactions in AraC. J Biol Chem 2001 Jan 26; 276(4) 2562-4.
Harmer T, Wu M, and Schleif R. The role of rigidity in DNA looping-unlooping by AraC. Proc Natl Acad Sci U S A 2001 Jan 16; 98(2) 427-31.
Halhed A, Petrullo L, Boutin S, Dantzer B, McAdam A, Wu M, Cottenie K. Consistent spatial patterns in microbial taxa of red squirrel gut microbiomes. Environ Microbiol Rep. 2023 Nov 9;. doi: 10.1111/1758-2229.13209. [Epub ahead of print] PubMed PMID: 37943285.
Warren CA, Shin JH, Bansal EN, Costa DVDS, Wang XQ, Wu M, Swann JR, Behm BW, Targonski PV, Archbald-Pannone L. Alanyl-glutamine supplementation for Clostridioides difficile infection treatment (ACT): a double-blind randomised controlled trial study protocol. BMJ Open. 2023 Jul 19;13(7):e075721. doi: 10.1136/bmjopen-2023-075721. PubMed PMID: 37474181; PubMed Central PMCID: PMC10357635.
Gao Y, Wu M. Accounting for 16S rRNA copy number prediction uncertainty and its implications in bacterial diversity analyses. ISME Commun. 2023 Jun 10;3(1):59. doi: 10.1038/s43705-023-00266-0. PMID: 37301942; PMCID: PMC10257666.
Li-Gao R, Grubbs K, Bertoni AG, Hoffman KL, Petrosino JF, Ramesh G, Wu M, Rotter JI, Chen YI, Evans AM, Robinson RJ, Sommerville L, Mook-Kanamori D, Goodarzi MO, Michelotti GA, Sheridan PA. The Roles of Gut Microbiome and Plasma Metabolites in the Associations between ABO Blood Groups and Insulin Homeostasis: The Microbiome and Insulin Longitudinal Evaluation Study (MILES). Metabolites. 2022 Aug 25;12(9):787. doi: 10.3390/metabo12090787. PMID: 36144194; PMCID: PMC9505353.
Cui J, Ramesh G, Wu M, Jensen ET, Crago O, Bertoni AG, Gao C, Hoffman KL, Sheridan PA, Wong KE, Wood AC, Chen YI, Rotter JI, Petrosino JF, Rich SS, Goodarzi MO. Butyrate-Producing Bacteria and Insulin Homeostasis: The Microbiome and Insulin Longitudinal Evaluation Study (MILES). Diabetes. 2022 Nov 1;71(11):2438-2446. doi: 10.2337/db22-0168. PMID: 35972231; PMCID: PMC9630078.
Gao Y, Wu M. Microbial genomic trait evolution is dominated by frequent and rare pulsed evolution. Sci Adv. 2022 Jul 15;8(28):eabn1916. doi: 10.1126/sciadv.abn1916. Epub 2022 Jul 15. PMID: 35857501.
Gao Y, Wu M. Modeling Pulsed Evolution and Time-independent Variation Improves the Confidence Level of Ancestral and Hidden State Predictions. Syst Biol. 2022 Feb 25:syac016. doi: 10.1093/sysbio/syac016. Epub ahead of print. PMID: 35212761.
Costa DVS, Pham NVS, Hays RA, Bolick DT, Goldbeck SM, Poulter MD, Hoang SC, Shin JH, Wu M, Warren CA. Influence of Binary Toxin Gene Detection and Decreased Susceptibility to Antibiotics among Clostridioides difficile Strains on Disease Severity: a Single-Center Study. Antimicrob Agents Chemother. 2022 Aug 16;66(8):e0048922. doi: 10.1128/aac.00489-22. Epub 2022 Jul 21. PMID: 35861541; PMCID: PMC9380565.
Shanmugakani RK, Wu M. An isothermal amplification-coupled dipstick for the rapid detection of COVID-19. J Med Microbiol. 2022 Apr;71(4). doi: 10.1099/jmm.0.001519. PMID: 35451947.
Petrullo L, Ren T, Wu M, Boonstra R, Palme R, Boutin S, McAdam AG, Dantzer B. Glucocorticoids coordinate changes in gut microbiome composition in wild North American red squirrels. Sci Rep. 2022 Feb 16;12(1):2605. doi: 10.1038/s41598-022-06359-5. PubMed PMID: 35173201.
Murray CS, Gao Y, Wu M. Re-evaluating the evidence for a universal genetic boundary among microbial species. Nat Commun 12, 4059 (2021). https://doi.org/10.1038/s41467-021-24128-2
Luu LA, Flowers RH, Gao Y, Wu M, Gasperino S, Kellams AL, Preston DC, Zlotoff BJ, Wisniewski JA, Zeichner SL. Apple cider vinegar soaks do not alter the skin bacterial microbiome in atopic dermatitis. PLoS One. 2021 Jun 2;16(6):e0252272. doi: 10.1371/journal.pone.0252272. PMID: 34077434; PMCID: PMC8172074.
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, Chen R, Shu W. Multi-omic meta-analysis identifies functional signatures of airway microbiome in chronic obstructive pulmonary disease. ISME J. 2020 Jul 27. doi: 10.1038/s41396-020-0727-y. Epub ahead of print. PMID: 32719402.
Jensen ET, Bertoni AG, Crago OL, Hoffman KL, Wood AC, Arzumanyan Z, Lam LK, Roll K, Sandow K, Wu M, Rich SS, Rotter JI, Chen YI, Petrosino JF, Goodarzi MO. Rationale, design and baseline characteristics of the Microbiome and Insulin Longitudinal Evaluation Study (MILES). Diabetes Obes Metab. 2020 Jul 20. doi: 10.1111/dom.14145. Epub ahead of print. PMID: 32687239.
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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, Hirsh J, Deppmann CD, Wu M, Scott MM, Güler AD. Dopamine Signaling in the Suprachiasmatic Nucleus Enables Weight Gain Associated with Hedonic Feeding. Curr Biol. 2020 Jan 20;30(2):196-208.e8. doi: 10.1016/j.cub.2019.11.029. Epub 2020 Jan 2.
Chhabra P, Spano AJ, Bowers D, Ren T, Moore DJ, Timko MP, Wu M, Brayman KL. Evidence for the Role of the Cecal Microbiome in Maintenance of Immune Regulation and Homeostasis. Ann Surg. 2018 Sep;268(3):541-549. doi: 10.1097/SLA.0000000000002930.
Ren T, Boutin S, Humphries MM, Dantzer B, Gorrell JC, Coltman DW, McAdam AG, Wu M. Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels. Microbiome. 2017 Dec 21;5(1):163. doi: 10.1186/s40168-017-0382-3.
Wang Z, Wu M. Comparative genomic analysis of acanthamoeba endosymbionts highlights the role of amoebae as a "melting pot" shaping the Rickettsiales evolution. Genome Biol Evol. 2017 Nov 1;9(11):3214-3224. doi: 10.1093/gbe/evx246.
Shin JH, Gao Y, Moore JH, Bolick DT, Kolling GL, Wu M, Warren CA. Innate immune response and outcome of Clostridium difficile infection are dependent on fecal bacterial composition in the aged host. J Infect Dis. 2017 Aug 22. doi: 10.1093/infdis/jix414.
Marin IA, Goertz JE, Ren T, Rich SS, Onengut-Gumuscu S, Farber E, Wu M, Overall CC, Kipnis J, Gaultier A. Microbiota alteration is associated with the development of stress-induced despair behavior. Sci Rep. 2017 Mar 7;7:43859. doi: 10.1038/srep43859.
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 Behav. 2016 Oct 19. doi: 10.1111/gbb.12353. [Epub ahead of print]
Ren T, Wu M. PhyloCore: A phylogenetic approach to identifying core taxa in microbial communities.Gene. 2016 Nov 30;593(2):330-3. doi: 10.1016/j.gene.2016.08.032. Epub 2016 Aug 24.
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. Mol Ecol. 2016 Oct;25(19):4793-804. doi: 10.1111/mec.13796. Epub 2016 Sep 13.
Ren T, Grieneisen LE, Alberts SC, Archie EA, Wu M. Development, diet and dynamism: longitudinal and cross-sectional predictors of gut microbial communities in wild baboons. Environ Microbiol. 2015 Mar 26. doi:10.1111/1462-2920.12852. [Epub ahead of print]
Weller C and Wu M. A generation-time effect on the rate of molecular evolution in bacteria. Evolution. 2015 Jan 7. doi: 10.1111/evo.12597.
Wang Z and Wu M. An integrated phylogenomic approach toward pinpointing the origin of mitochondria. Scientific Reports. 2015 Jan 22;5:7949. doi: 10.1038/srep07949
Wang Z and Wu M. Phylogenomic reconstruction indicates mitochondrial ancestor was an energy parasite. PLoS One. 2014;9(10):e110685. doi:10.1371/journal.pone.0110685.
Wang Z and Wu M. Complete genome sequence of the endosymbiont of Acanthamoeba strain UWC8, an amoeba endosymbiont belonging to the "Candidatus Midichloriaceae" family in Rickettsiales. Genome Announc. 2014 Aug 7;2(4). pii: e00791-14. doi: 10.1128/genomeA.00791-14.
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. ISME J. 2014 Jun 10. doi: 10.1038/ismej.2014.94. [Epub ahead of print]
Kopac S, Wang Z, Wiedenbeck J, Sherry J, Wu M, Cohan FM. Genomic heterogeneity and ecological speciation within one subspecies of Bacillus subtilis. Appl Environ Microbiol. 2014 Jun 6. pii: AEM.00576-14. [Epub ahead of print]
Sloan DB, Triant DA, Wu M, Taylor DR. Cytonuclear interactions and relaxed selection accelerate sequence evolution in organelle ribosomes. Mol Biol Evol. 2014 Mar;31(3):673-82. doi: 10.1093/molbev/mst259. Epub 2013 Dec 13.
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). Mol Phylogenet Evol. 2014 Mar;72:82-9. doi: 10.1016/j.ympev.2013.12.004. Epub 2013 Dec 25.
Koeppel AF and Wu M. Species matter: the role of competition in the assembly of congeneric bacteria. ISME J. 2014 Mar;8(3):531-40. doi: 10.1038/ismej.2013.180. Epub 2013 Oct 17.
Sears MT, Zhang H, Rushton PJ, Wu M, Han S, Spano AJ, Timko MP. NtERF32: a non-NIC2 locus AP2/ERF transcription factor required in jasmonate-inducible nicotine biosynthesis in tobacco. Plant Mol Biol. 2014 Jan;84(1-2):49-66. doi: 10.1007/s11103-013-0116-2. Epub 2013 Aug 11.
Wu M. Protein-coding genes as alternative markers in microbial diversity studies. In: Nelson K. (Ed.) Encyclopedia of Metagenomics. SpringerReference (www.springerreference.com). Springer-Verlag Berlin Heidelberg, 2013. doi:10.1007/SpringerReference_343804 2013-03-06 16:02:26 UTC
Koeppel AF and Wu M. Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units. Nucleic Acids Res. 2013, 1-14 doi:10.1093/nar/gkt241.
Wang Z and Wu M. A phylum-level bacterial phylogenetic marker database. Mol. Biol. Evol. 2013 Jun;30(6):1258-62. doi: 10.1093/molbev/mst059. Epub 2013 Mar 21.
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 2013 Feb;15(2):535-47. doi: 10.1111/1462-2920.12000. Epub 2012 Oct 31.
Kembel SW, Wu M, Eisen JA, Green JL. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Comput Biol. 2012. 8(10): e1002743. doi:10.1371/journal.pcbi.1002743.
Kolling GL, Wu M, Alcantara-Warren C, Durmaz E, Klaenhammer TR, Guerrant RL. Lactic acid production by Streptococcus thermophilus alters Clostridium difficile infection and in vitro Toxin A production. Gut Microbes 2012, 3:6,1-7. doi:10.4161/gutmicrobes.21757.
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. 2012,13:466. doi:10.1186/1471-2164-13-466.
Kolling G, Wu M, Guerrant RL. Enteric pathogens through life stages. Frontiers in Cellular and Infection Microbiology. 2012, 2:114. doi:10.3389/fcimb.2012.00114.
Koeppel AF and Wu M. Lineage-dependent ecological coherence in bacteria. FEMS Microbiology Ecology. 2012, Sep;81(3):574-82. doi: 10.1111/j.1574-6941.2012.01387.x.
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 Biol Evol. 2012, Jan;4(3):294-306. Epub 2012 Jan 12.
Wu M and Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012, 28:1033-1034.
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 Biol. 2012 Jan;10(1):e1001241. Epub 2012 Jan 17.
Wu M, Chatterji S, Eisen JA. Accounting for alignment uncertainty in phylogenomics. PLoS ONE 2012, 7(1): e30288. doi:10.1371/journal.pone.0030288
Coyne RS, Hannick L, Shanmugam D, Hostetler JB, Brami D, Joardar VS, Johnson J, Radune D, Singh I, Kumar U, Saier M, Wang Y, Cai H, Gu J, Mather MW, Vaidya AB, Wilkes DE, Rajagopalan V, Asai DJ, Pearson CG, Findly RC, Dickerson HW, Badger JH, Wu M, Martens C, Van de Peer Y, Roos DS, Cassidy-Hanley DM, Clark TG. 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 Biol 2011 Oct 17;12(10):R100.
Wang Z, Kadouri DE and Wu M. Genomic insights into an obligate epibiotic bacterial predator: Micavibrio aeruginosavorus ARL-13. BMC Genomics 2011, 12:453. doi:10.1186/1471-2164-12-453
Wu M and Eisen JA. Towards Automated Phylogenomic Inference in Bruijn, F.J.d., Handbook of molecular microbial ecology I : metagenomics and complementary approaches. 2011, Hoboken, N.J.: Wiley-Blackwell.
Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC and Eisen JA. Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees. PLoS One 2011 6(3): e18011. doi:10.1371/journal.pone.0018011.
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, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, and Eisen JA. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009 Dec 24; 462(7276) 1056-60.
Rastogi R, Wu M, Dasgupta I, Fox GE. Visualization of ribosomal RNA operon copy number distribution. BMC Microbiol. 2009 Sep 25;9(1):208. [highly accessed]
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, Creasy T, Daugherty SC, Davidsen TM, DeBoy RT, Detter JC, Dodson RJ, Durkin AS, Ganapathy A, Gwinn-Giglio M, Han CS, Khouri H, Kiss H, Kothari SP, Madupu R, Nelson KE, Nelson WC, Paulsen I, Penn K, Ren Q, Rosovitz MJ, Selengut JD, Shrivastava S, Sullivan SA, Tapia R, Thompson LS, Watkins KL, Yang Q, Yu C, Zafar N, Zhou L, Kuske CR. Three genomes from the phylum acidobacteria provide insight into their lifestyles in soils. Appl Environ Microbiol. 2009; 75(7) 2046-56
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, and Eisen JA. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS ONE 2009; 4(1) e4207.
Wu M and Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biol 2008 Oct 13; 9(10) R151.
Maresca JA, Graham JE, Wu M, Eisen JA, and Bryant DA. Identification of a fourth family of lycopene cyclases in photosynthetic bacteria. Proc Natl Acad Sci U S A 2007 Jul 10; 104(28) 11784-9.
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, Stine OC, Ali A, Horneman AJ, and Heidelberg JF. Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades. J Bacteriol 2006 Dec; 188(23) 8272-82.
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, Majoros WH, Farzad M, Carlton JM, Smith RK Jr, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, and Orias E. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol 2006 Sep; 4(9) e286.
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, Lin Q, Ohashi N, Zhi N, Nelson W, Brinkac LM, Dodson RJ, Rosovitz MJ, Sundaram J, Daugherty SC, Davidsen T, Durkin AS, Gwinn M, Haft DH, Selengut JD, Sullivan SA, Zafar N, Zhou L, Benahmed F, Forberger H, Halpin R, Mulligan S, Robinson J, White O, Rikihisa Y, and Tettelin H. Comparative genomics of emerging human ehrlichiosis agents. PLoS Genet 2006 Feb; 2(2) e21.
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, Zhulin IB, Robb FT, and Eisen JA. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genet 2005 Nov; 1(5) e65.
Ward N, Larsen , Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH, Lewis M, Nelson KE, Meth B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, DeBoy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, and Eisen JA. Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol 2004 Oct; 2(10) e303.
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, Durkin AS, Kolonay JF, Nelson WC, Mohamoud Y, Lee P, Berry K, Young MB, Utterback T, Weidman J, Nierman WC, Paulsen IT, Nelson KE, Tettelin H, O'Neill SL, and Eisen JA. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol 2004 Mar; 2(3) E69.
Meth 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, Durkin AS, Gwinn M, Kolonay JF, Sullivan SA, Haft DH, Selengut J, Davidsen TM, Zafar N, White O, Tran B, Romero C, Forberger HA, Weidman J, Khouri H, Feldblyum TV, Utterback TR, Van Aken SE, Lovley DR, and Fraser CM. Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science 2003 Dec 12; 302(5652) 1967-9.
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, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, Plaut RD, Wolf AM, Watkins KL, Nierman WC, Hazen A, Cline R, Redmond C, Thwaite JE, White O, Salzberg SL, Thomason B, Friedlander AM, Koehler TM, Hanna PC, Kolst AB, and Fraser CM. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 2003 May 1; 423(6935) 81-6.
Ermolaeva MD, Wu M, Eisen JA, and Salzberg SL. The age of the Arabidopsis thaliana genome duplication. Plant Mol Biol 2003 Apr; 51(6) 859-66.
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, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, Zhao S, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, and Hoffman SL. The genome sequence of the malaria mosquito Anopheles gambiae. Science 2002 Oct 4; 298(5591) 129-49.
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, Holt I, Umayam LA, Mason T, Brenner M, Shea TP, Parksey D, Nierman WC, Feldblyum TV, Hansen CL, Craven MB, Radune D, Vamathevan J, Khouri H, White O, Gruber TM, Ketchum KA, Venter JC, Tettelin H, Bryant DA, and Fraser CM. The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc Natl Acad Sci U S A 2002 Jul 9; 99(14) 9509-14.
Eisen JA and Wu M. Phylogenetic analysis and gene functional predictions: phylogenomics in action. Theor Popul Biol 2002 Jun; 61(4) 481-7.
Wu M and Schleif R. Mapping arm-DNA-binding domain interactions in AraC. J Mol Biol 2001 Apr 6; 307(4) 1001-9.
Wu M and Schleif R. Strengthened arm-dimerization domain interactions in AraC. J Biol Chem 2001 Jan 26; 276(4) 2562-4.
Harmer T, Wu M, and Schleif R. The role of rigidity in DNA looping-unlooping by AraC. Proc Natl Acad Sci U S A 2001 Jan 16; 98(2) 427-31.
