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Items: 33


Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes.

Wang Y, Youssef NH, Couger MB, Hanafy RA, Elshahed MS, Stajich JE.

mSystems. 2019 Aug 27;4(4). pii: e00247-19. doi: 10.1128/mSystems.00247-19.


Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage.

Murphy CL, Youssef NH, Hanafy RA, Couger MB, Stajich JE, Wang Y, Baker K, Dagar SS, Griffith GW, Farag IF, Callaghan TM, Elshahed MS.

Appl Environ Microbiol. 2019 Jul 18;85(15). pii: e00988-19. doi: 10.1128/AEM.00988-19. Print 2019 Aug 1.


Genome Sequence of a Bovine Isolate of Pasteurella multocida Strain 232.

Ayalew S, Confer AW, Couger MB.

Microbiol Resour Announc. 2019 May 16;8(20). pii: e00333-19. doi: 10.1128/MRA.00333-19.


Nanopore ultra-long read sequencing technology for antimicrobial resistance detection in Mannheimia haemolytica.

Lim A, Naidenov B, Bates H, Willyerd K, Snider T, Couger MB, Chen C, Ramachandran A.

J Microbiol Methods. 2019 Apr;159:138-147. doi: 10.1016/j.mimet.2019.03.001. Epub 2019 Mar 5.


A High Quality Genome for Mus spicilegus, a Close Relative of House Mice with Unique Social and Ecological Adaptations.

Couger MB, Arévalo L, Campbell P.

G3 (Bethesda). 2018 Jul 2;8(7):2145-2152. doi: 10.1534/g3.118.200318.


Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus Pecoramyces ruminantium strain C1A.

Calkins SS, Elledge NC, Mueller KE, Marek SM, Couger MB, Elshahed MS, Youssef NH.

PeerJ. 2018 Jan 30;6:e4276. doi: 10.7717/peerj.4276. eCollection 2018.


Thermal adaptation strategies of the extremophile bacterium Thermus filiformis based on multi-omics analysis.

Mandelli F, Couger MB, Paixão DAA, Machado CB, Carnielli CM, Aricetti JA, Polikarpov I, Prade R, Caldana C, Paes Leme AF, Mercadante AZ, Riaño-Pachón DM, Squina FM.

Extremophiles. 2017 Jul;21(4):775-788. doi: 10.1007/s00792-017-0942-2. Epub 2017 May 12.


Genome Sequence of Mannheimia haemolytica Serotype 1 Strain 16041065 BH.

Ayalew S, Confer AW, Hansen RD, Couger MB.

Genome Announc. 2017 Apr 6;5(14). pii: e01721-16. doi: 10.1128/genomeA.01721-16.


Genome Sequence of a Spontaneous Nonhemolytic Mutant of Mannheimia haemolytica 16041065 GH.

Ayalew S, Confer AW, Hansen RD, Couger MB.

Genome Announc. 2017 Apr 6;5(14). pii: e01720-16. doi: 10.1128/genomeA.01720-16.


A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors.

Bryant DM, Johnson K, DiTommaso T, Tickle T, Couger MB, Payzin-Dogru D, Lee TJ, Leigh ND, Kuo TH, Davis FG, Bateman J, Bryant S, Guzikowski AR, Tsai SL, Coyne S, Ye WW, Freeman RM Jr, Peshkin L, Tabin CJ, Regev A, Haas BJ, Whited JL.

Cell Rep. 2017 Jan 17;18(3):762-776. doi: 10.1016/j.celrep.2016.12.063.


Isolation and characterization of Rhizobium sp. strain YS-1r that degrades lignin in plant biomass.

Jackson CA, Couger MB, Prabhakaran M, Ramachandriya KD, Canaan P, Fathepure BZ.

J Appl Microbiol. 2017 Apr;122(4):940-952. doi: 10.1111/jam.13401. Epub 2017 Feb 27.


Draft genome sequence of Staphylococcus hominis strain Hudgins isolated from human skin implicates metabolic versatility and several virulence determinants.

Calkins S, Couger MB, Jackson C, Zandler J, Hudgins GC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef N.

Genom Data. 2016 Oct 7;10:91-96. eCollection 2016 Dec.


Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis.

Moghadam F, Couger MB, Russ B, Ramsey R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef N.

Genom Data. 2016 Sep 20;10:63-68. eCollection 2016 Dec.


Draft genome sequence of Microbacterium oleivorans strain Wellendorf implicates heterotrophic versatility and bioremediation potential.

Avramov AP, Couger MB, Hartley EL, Land C, Wellendorf R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef N.

Genom Data. 2016 Sep 17;10:54-60. eCollection 2016 Dec.


Draft genome sequence of Pseudomonas moraviensis strain Devor implicates metabolic versatility and bioremediation potential.

Miller NT, Fuller D, Couger MB, Bagazinski M, Boyne P, Devor RC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef N.

Genom Data. 2016 Aug 4;9:154-9. doi: 10.1016/j.gdata.2016.08.004. eCollection 2016 Sep.


Draft genome sequence of Micrococcus luteus strain O'Kane implicates metabolic versatility and the potential to degrade polyhydroxybutyrates.

Hanafy RA, Couger MB, Baker K, Murphy C, O'Kane SD, Budd C, French DP, Hoff WD, Youssef N.

Genom Data. 2016 Aug 8;9:148-53. doi: 10.1016/j.gdata.2016.08.006. eCollection 2016 Sep.


Penicillium echinulatum secretome analysis reveals the fungi potential for degradation of lignocellulosic biomass.

Schneider WDH, Gonçalves TA, Uchima CA, Couger MB, Prade R, Squina FM, Dillon AJP, Camassola M.

Biotechnol Biofuels. 2016 Mar 17;9:66. doi: 10.1186/s13068-016-0476-3. eCollection 2016.


Draft Genome Sequences of Five Pseudomonas aeruginosa Clinical Strains Isolated from Sputum Samples from Cystic Fibrosis Patients.

Couger MB, Wright A, Lutter EI, Youssef N.

Genome Announc. 2016 Jan 28;4(1). pii: e01528-15. doi: 10.1128/genomeA.01528-15.


Draft Genome of the Arthrobacter sp. Strain Edens01.

Couger MB, Hanafy RA, Edens C, Budd C, French DP, Hoff WD, Elshahed MS, Youssef NH.

Genome Announc. 2015 Dec 17;3(6). pii: e01475-15. doi: 10.1128/genomeA.01475-15.


The Draft Genome Sequence of Xanthomonas sp. Strain Mitacek01 Expands the Pangenome of a Genus of Plant Pathogens.

Couger MB, Hanafy RA, Mitacek RM, Budd C, French DP, Hoff WD, Elshahed MS, Youssef NH.

Genome Announc. 2015 Dec 10;3(6). pii: e01450-15. doi: 10.1128/genomeA.01450-15.


Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate Orpinomyces sp. strain C1A.

Couger MB, Youssef NH, Struchtemeyer CG, Liggenstoffer AS, Elshahed MS.

Biotechnol Biofuels. 2015 Dec 8;8:208. doi: 10.1186/s13068-015-0390-0. eCollection 2015.


Research Resource: The Dexamethasone Transcriptome in Hypothalamic Embryonic Neural Stem Cells.

Frahm KA, Peffer ME, Zhang JY, Luthra S, Chakka AB, Couger MB, Chandran UR, Monaghan AP, DeFranco DB.

Mol Endocrinol. 2016 Jan;30(1):144-54. doi: 10.1210/me.2015-1258. Epub 2015 Nov 25.


Genome Analysis of Staphylococcus agnetis, an Agent of Lameness in Broiler Chickens.

Al-Rubaye AA, Couger MB, Ojha S, Pummill JF, Koon JA 2nd, Wideman RF Jr, Rhoads DD.

PLoS One. 2015 Nov 25;10(11):e0143336. doi: 10.1371/journal.pone.0143336. eCollection 2015.


Draft Genome Sequence of the Environmental Isolate Chryseobacterium sp. Hurlbut01.

Couger MB, Hurlbut A, Murphy CL, Budd C, French DP, Hoff WD, Elshahed MS, Youssef NH.

Genome Announc. 2015 Sep 17;3(5). pii: e01071-15. doi: 10.1128/genomeA.01071-15.


Assessing the global phylum level diversity within the bacterial domain: A review.

Youssef NH, Couger MB, McCully AL, Criado AE, Elshahed MS.

J Adv Res. 2015 May;6(3):269-82. doi: 10.1016/j.jare.2014.10.005. Epub 2014 Nov 4. Review.


Draft Genome Sequence of the Thermophile Thermus filiformis ATCC 43280, Producer of Carotenoid-(Di)glucoside-Branched Fatty Acid (Di)esters and Source of Hyperthermostable Enzymes of Biotechnological Interest.

Mandelli F, Oliveira Ramires B, Couger MB, Paixão DA, Camilo CM, Polikarpov I, Prade R, Riaño-Pachón DM, Squina FM.

Genome Announc. 2015 May 14;3(3). pii: e00475-15. doi: 10.1128/genomeA.00475-15.


Genome Sequences of the Lignin-Degrading Pseudomonas sp. Strain YS-1p and Rhizobium sp. Strain YS-1r Isolated from Decaying Wood.

Prabhakaran M, Couger MB, Jackson CA, Weirick T, Fathepure BZ.

Genome Announc. 2015 Mar 5;3(2). pii: e00019-15. doi: 10.1128/genomeA.00019-15.


Survival of the anaerobic fungus Orpinomyces sp. strain C1A after prolonged air exposure.

Struchtemeyer CG, Ranganathan A, Couger MB, Liggenstoffer AS, Youssef NH, Elshahed MS.

Sci Rep. 2014 Nov 4;4:6892. doi: 10.1038/srep06892.


Enabling large-scale next-generation sequence assembly with Blacklight.

Couger MB, Pipes L, Squina F, Prade R, Siepel A, Palermo R, Katze MG, Mason CE, Blood PD.

Concurr Comput. 2014 Sep 10;26(13):2157-2166.


De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.

Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A.

Nat Protoc. 2013 Aug;8(8):1494-512. doi: 10.1038/nprot.2013.084. Epub 2013 Jul 11.


The genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader.

Youssef NH, Couger MB, Struchtemeyer CG, Liggenstoffer AS, Prade RA, Najar FZ, Atiyeh HK, Wilkins MR, Elshahed MS.

Appl Environ Microbiol. 2013 Aug;79(15):4620-34. doi: 10.1128/AEM.00821-13. Epub 2013 May 24.


Fine-scale bacterial beta diversity within a complex ecosystem (Zodletone Spring, OK, USA): the role of the rare biosphere.

Youssef NH, Couger MB, Elshahed MS.

PLoS One. 2010 Aug 26;5(8):e12414. doi: 10.1371/journal.pone.0012414.


Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores.

Liggenstoffer AS, Youssef NH, Couger MB, Elshahed MS.

ISME J. 2010 Oct;4(10):1225-35. doi: 10.1038/ismej.2010.49. Epub 2010 Apr 22.


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