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Items: 32

1.

Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle.

Murat C, Payen T, Noel B, Kuo A, Morin E, Chen J, Kohler A, Krizsán K, Balestrini R, Da Silva C, Montanini B, Hainaut M, Levati E, Barry KW, Belfiori B, Cichocki N, Clum A, Dockter RB, Fauchery L, Guy J, Iotti M, Le Tacon F, Lindquist EA, Lipzen A, Malagnac F, Mello A, Molinier V, Miyauchi S, Poulain J, Riccioni C, Rubini A, Sitrit Y, Splivallo R, Traeger S, Wang M, Žifčáková L, Wipf D, Zambonelli A, Paolocci F, Nowrousian M, Ottonello S, Baldrian P, Spatafora JW, Henrissat B, Nagy LG, Aury JM, Wincker P, Grigoriev IV, Bonfante P, Martin FM.

Nat Ecol Evol. 2018 Dec;2(12):1956-1965. doi: 10.1038/s41559-018-0710-4. Epub 2018 Nov 12.

PMID:
30420746
2.

Draft Genome Sequence of Tuber borchii Vittad., a Whitish Edible Truffle.

Murat C, Kuo A, Barry KW, Clum A, Dockter RB, Fauchery L, Iotti M, Kohler A, LaButti K, Lindquist EA, Lipzen A, Morin E, Wang M, Grigoriev IV, Zambonelli A, Martin FM.

Genome Announc. 2018 Jun 21;6(25). pii: e00537-18. doi: 10.1128/genomeA.00537-18.

3.

Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.).

Bahri BA, Daverdin G, Xu X, Cheng JF, Barry KW, Brummer EC, Devos KM.

BMC Evol Biol. 2018 Jun 14;18(1):91. doi: 10.1186/s12862-018-1193-2.

4.

Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors.

Lopez D, Ribeiro S, Label P, Fumanal B, Venisse JS, Kohler A, de Oliveira RR, Labutti K, Lipzen A, Lail K, Bauer D, Ohm RA, Barry KW, Spatafora J, Grigoriev IV, Martin FM, Pujade-Renaud V.

Front Microbiol. 2018 Mar 2;9:276. doi: 10.3389/fmicb.2018.00276. eCollection 2018.

5.

Annotation of the Corymbia terpene synthase gene family shows broad conservation but dynamic evolution of physical clusters relative to Eucalyptus.

Butler JB, Freeman JS, Potts BM, Vaillancourt RE, Grattapaglia D, Silva-Junior OB, Simmons BA, Healey AL, Schmutz J, Barry KW, Lee DJ, Henry RJ, King GJ, Baten A, Shepherd M.

Heredity (Edinb). 2018 Jul;121(1):87-104. doi: 10.1038/s41437-018-0058-1. Epub 2018 Mar 10.

PMID:
29523839
6.

Secretome Analysis from the Ectomycorrhizal Ascomycete Cenococcum geophilum.

de Freitas Pereira M, Veneault-Fourrey C, Vion P, Guinet F, Morin E, Barry KW, Lipzen A, Singan V, Pfister S, Na H, Kennedy M, Egli S, Grigoriev I, Martin F, Kohler A, Peter M.

Front Microbiol. 2018 Feb 13;9:141. doi: 10.3389/fmicb.2018.00141. eCollection 2018.

7.

Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists.

Martino E, Morin E, Grelet GA, Kuo A, Kohler A, Daghino S, Barry KW, Cichocki N, Clum A, Dockter RB, Hainaut M, Kuo RC, LaButti K, Lindahl BD, Lindquist EA, Lipzen A, Khouja HR, Magnuson J, Murat C, Ohm RA, Singer SW, Spatafora JW, Wang M, Veneault-Fourrey C, Henrissat B, Grigoriev IV, Martin FM, Perotto S.

New Phytol. 2018 Feb;217(3):1213-1229. doi: 10.1111/nph.14974. Epub 2018 Jan 7.

8.

Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta).

Brawley SH, Blouin NA, Ficko-Blean E, Wheeler GL, Lohr M, Goodson HV, Jenkins JW, Blaby-Haas CE, Helliwell KE, Chan CX, Marriage TN, Bhattacharya D, Klein AS, Badis Y, Brodie J, Cao Y, Collén J, Dittami SM, Gachon CMM, Green BR, Karpowicz SJ, Kim JW, Kudahl UJ, Lin S, Michel G, Mittag M, Olson BJSC, Pangilinan JL, Peng Y, Qiu H, Shu S, Singer JT, Smith AG, Sprecher BN, Wagner V, Wang W, Wang ZY, Yan J, Yarish C, Zäuner-Riek S, Zhuang Y, Zou Y, Lindquist EA, Grimwood J, Barry KW, Rokhsar DS, Schmutz J, Stiller JW, Grossman AR, Prochnik SE.

Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):E6361-E6370. doi: 10.1073/pnas.1703088114. Epub 2017 Jul 17.

9.

The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies.

Li G, Jain R, Chern M, Pham NT, Martin JA, Wei T, Schackwitz WS, Lipzen AM, Duong PQ, Jones KC, Jiang L, Ruan D, Bauer D, Peng Y, Barry KW, Schmutz J, Ronald PC.

Plant Cell. 2017 Jun;29(6):1218-1231. doi: 10.1105/tpc.17.00154. Epub 2017 Jun 2.

10.

Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments.

Daly P, van Munster JM, Blythe MJ, Ibbett R, Kokolski M, Gaddipati S, Lindquist E, Singan VR, Barry KW, Lipzen A, Ngan CY, Petzold CJ, Chan LJG, Pullan ST, Delmas S, Waldron PR, Grigoriev IV, Tucker GA, Simmons BA, Archer DB.

Biotechnol Biofuels. 2017 Feb 7;10:35. doi: 10.1186/s13068-017-0700-9. eCollection 2017.

11.

Draft Genome Sequence of Coniochaeta ligniaria NRRL 30616, a Lignocellulolytic Fungus for Bioabatement of Inhibitors in Plant Biomass Hydrolysates.

Jiménez DJ, Hector RE, Riley R, Lipzen A, Kuo RC, Amirebrahimi M, Barry KW, Grigoriev IV, van Elsas JD, Nichols NN.

Genome Announc. 2017 Jan 26;5(4). pii: e01476-16. doi: 10.1128/genomeA.01476-16.

12.

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

Mock T, Otillar RP, Strauss J, McMullan M, Paajanen P, Schmutz J, Salamov A, Sanges R, Toseland A, Ward BJ, Allen AE, Dupont CL, Frickenhaus S, Maumus F, Veluchamy A, Wu T, Barry KW, Falciatore A, Ferrante MI, Fortunato AE, Glöckner G, Gruber A, Hipkin R, Janech MG, Kroth PG, Leese F, Lindquist EA, Lyon BR, Martin J, Mayer C, Parker M, Quesneville H, Raymond JA, Uhlig C, Valas RE, Valentin KU, Worden AZ, Armbrust EV, Clark MD, Bowler C, Green BR, Moulton V, van Oosterhout C, Grigoriev IV.

Nature. 2017 Jan 26;541(7638):536-540. doi: 10.1038/nature20803. Epub 2017 Jan 16.

13.

Fungal and plant gene expression in the Tulasnella calospora-Serapias vomeracea symbiosis provides clues about nitrogen pathways in orchid mycorrhizas.

Fochi V, Chitarra W, Kohler A, Voyron S, Singan VR, Lindquist EA, Barry KW, Girlanda M, Grigoriev IV, Martin F, Balestrini R, Perotto S.

New Phytol. 2017 Jan;213(1):365-379. doi: 10.1111/nph.14279. Epub 2016 Nov 11.

14.

Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum.

Peter M, Kohler A, Ohm RA, Kuo A, Krützmann J, Morin E, Arend M, Barry KW, Binder M, Choi C, Clum A, Copeland A, Grisel N, Haridas S, Kipfer T, LaButti K, Lindquist E, Lipzen A, Maire R, Meier B, Mihaltcheva S, Molinier V, Murat C, Pöggeler S, Quandt CA, Sperisen C, Tritt A, Tisserant E, Crous PW, Henrissat B, Nehls U, Egli S, Spatafora JW, Grigoriev IV, Martin FM.

Nat Commun. 2016 Sep 7;7:12662. doi: 10.1038/ncomms12662.

15.

Comparative genomics of biotechnologically important yeasts.

Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, Deshpande S, Douglass AP, Hanson SJ, Klenk HP, LaButti KM, Lapidus A, Lindquist EA, Lipzen AM, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW.

Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9882-7. doi: 10.1073/pnas.1603941113. Epub 2016 Aug 17.

16.

Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data.

Grabowski PP, Evans J, Daum C, Deshpande S, Barry KW, Kennedy M, Ramstein G, Kaeppler SM, Buell CR, Jiang Y, Casler MD.

New Phytol. 2017 Jan;213(1):154-169. doi: 10.1111/nph.14101. Epub 2016 Jul 22.

17.

Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation.

Li G, Chern M, Jain R, Martin JA, Schackwitz WS, Jiang L, Vega-Sánchez ME, Lipzen AM, Barry KW, Schmutz J, Ronald PC.

Mol Plant. 2016 Jul 6;9(7):1078-81. doi: 10.1016/j.molp.2016.03.009. Epub 2016 Mar 24. No abstract available.

18.

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.

Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot F, Canbäck B, Choi C, Cichocki N, Clum A, Colpaert J, Copeland A, Costa MD, Doré J, Floudas D, Gay G, Girlanda M, Henrissat B, Herrmann S, Hess J, Högberg N, Johansson T, Khouja HR, LaButti K, Lahrmann U, Levasseur A, Lindquist EA, Lipzen A, Marmeisse R, Martino E, Murat C, Ngan CY, Nehls U, Plett JM, Pringle A, Ohm RA, Perotto S, Peter M, Riley R, Rineau F, Ruytinx J, Salamov A, Shah F, Sun H, Tarkka M, Tritt A, Veneault-Fourrey C, Zuccaro A; Mycorrhizal Genomics Initiative Consortium, Tunlid A, Grigoriev IV, Hibbett DS, Martin F.

Nat Genet. 2015 Apr;47(4):410-5. doi: 10.1038/ng.3223. Epub 2015 Feb 23.

19.

Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential.

Hurley JM, Dasgupta A, Emerson JM, Zhou X, Ringelberg CS, Knabe N, Lipzen AM, Lindquist EA, Daum CG, Barry KW, Grigoriev IV, Smith KM, Galagan JE, Bell-Pedersen D, Freitag M, Cheng C, Loros JJ, Dunlap JC.

Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):16995-7002. doi: 10.1073/pnas.1418963111. Epub 2014 Oct 31.

20.

The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii.

Lowry DB, Hernandez K, Taylor SH, Meyer E, Logan TL, Barry KW, Chapman JA, Rokhsar DS, Schmutz J, Juenger TE.

New Phytol. 2015 Jan;205(1):402-14. doi: 10.1111/nph.13027. Epub 2014 Sep 23.

21.

Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle.

Scully ED, Geib SM, Hoover K, Tien M, Tringe SG, Barry KW, Glavina del Rio T, Chovatia M, Herr JR, Carlson JE.

PLoS One. 2013 Sep 4;8(9):e73827. doi: 10.1371/journal.pone.0073827. eCollection 2013.

22.

Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens.

Aylward FO, Burnum-Johnson KE, Tringe SG, Teiling C, Tremmel DM, Moeller JA, Scott JJ, Barry KW, Piehowski PD, Nicora CD, Malfatti SA, Monroe ME, Purvine SO, Goodwin LA, Smith RD, Weinstock GM, Gerardo NM, Suen G, Lipton MS, Currie CR.

Appl Environ Microbiol. 2013 Jun;79(12):3770-8. doi: 10.1128/AEM.03833-12. Epub 2013 Apr 12.

23.

Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi.

Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, Barry KW, Condon BJ, Copeland AC, Dhillon B, Glaser F, Hesse CN, Kosti I, LaButti K, Lindquist EA, Lucas S, Salamov AA, Bradshaw RE, Ciuffetti L, Hamelin RC, Kema GH, Lawrence C, Scott JA, Spatafora JW, Turgeon BG, de Wit PJ, Zhong S, Goodwin SB, Grigoriev IV.

PLoS Pathog. 2012;8(12):e1003037. doi: 10.1371/journal.ppat.1003037. Epub 2012 Dec 6. Erratum in: PLoS Pathog. 2013 Mar 5;9(3):.

24.

Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis.

Fernandez-Fueyo E, Ruiz-Dueñas FJ, Ferreira P, Floudas D, Hibbett DS, Canessa P, Larrondo LF, James TY, Seelenfreund D, Lobos S, Polanco R, Tello M, Honda Y, Watanabe T, Watanabe T, Ryu JS, Kubicek CP, Schmoll M, Gaskell J, Hammel KE, St John FJ, Vanden Wymelenberg A, Sabat G, Splinter BonDurant S, Syed K, Yadav JS, Doddapaneni H, Subramanian V, Lavín JL, Oguiza JA, Perez G, Pisabarro AG, Ramirez L, Santoyo F, Master E, Coutinho PM, Henrissat B, Lombard V, Magnuson JK, Kües U, Hori C, Igarashi K, Samejima M, Held BW, Barry KW, LaButti KM, Lapidus A, Lindquist EA, Lucas SM, Riley R, Salamov AA, Hoffmeister D, Schwenk D, Hadar Y, Yarden O, de Vries RP, Wiebenga A, Stenlid J, Eastwood D, Grigoriev IV, Berka RM, Blanchette RA, Kersten P, Martinez AT, Vicuna R, Cullen D.

Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5458-63. doi: 10.1073/pnas.1119912109. Epub 2012 Mar 20. Erratum in: Proc Natl Acad Sci U S A. 2012 May 22;109(21):8352. San, Ryu Jae [corrected to Ryu, Jae San].

25.

Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens.

Aylward FO, Burnum KE, Scott JJ, Suen G, Tringe SG, Adams SM, Barry KW, Nicora CD, Piehowski PD, Purvine SO, Starrett GJ, Goodwin LA, Smith RD, Lipton MS, Currie CR.

ISME J. 2012 Sep;6(9):1688-701. doi: 10.1038/ismej.2012.10. Epub 2012 Mar 1.

26.

Comparative genomics of xylose-fermenting fungi for enhanced biofuel production.

Wohlbach DJ, Kuo A, Sato TK, Potts KM, Salamov AA, Labutti KM, Sun H, Clum A, Pangilinan JL, Lindquist EA, Lucas S, Lapidus A, Jin M, Gunawan C, Balan V, Dale BE, Jeffries TW, Zinkel R, Barry KW, Grigoriev IV, Gasch AP.

Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13212-7. doi: 10.1073/pnas.1103039108. Epub 2011 Jul 25.

27.

Complete genome sequence of Candidatus Ruthia magnifica.

Roeselers G, Newton IL, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, Eisen JA, Cavanaugh CM.

Stand Genomic Sci. 2010 Oct 27;3(2):163-73. doi: 10.4056/sigs.1103048.

28.

An insect herbivore microbiome with high plant biomass-degrading capacity.

Suen G, Scott JJ, Aylward FO, Adams SM, Tringe SG, Pinto-Tomás AA, Foster CE, Pauly M, Weimer PJ, Barry KW, Goodwin LA, Bouffard P, Li L, Osterberger J, Harkins TT, Slater SC, Donohue TJ, Currie CR.

PLoS Genet. 2010 Sep 23;6(9):e1001129. doi: 10.1371/journal.pgen.1001129.

29.

The Calyptogena magnifica chemoautotrophic symbiont genome.

Newton IL, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, Eisen JA, Cavanaugh CM.

Science. 2007 Feb 16;315(5814):998-1000.

30.

Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities.

García Martín H, Ivanova N, Kunin V, Warnecke F, Barry KW, McHardy AC, Yeates C, He S, Salamov AA, Szeto E, Dalin E, Putnam NH, Shapiro HJ, Pangilinan JL, Rigoutsos I, Kyrpides NC, Blackall LL, McMahon KD, Hugenholtz P.

Nat Biotechnol. 2006 Oct;24(10):1263-9. Epub 2006 Sep 24.

PMID:
16998472
31.

Symbiosis insights through metagenomic analysis of a microbial consortium.

Woyke T, Teeling H, Ivanova NN, Huntemann M, Richter M, Gloeckner FO, Boffelli D, Anderson IJ, Barry KW, Shapiro HJ, Szeto E, Kyrpides NC, Mussmann M, Amann R, Bergin C, Ruehland C, Rubin EM, Dubilier N.

Nature. 2006 Oct 26;443(7114):950-5. Epub 2006 Sep 17.

PMID:
16980956
32.

Sequencing genomes from single cells by polymerase cloning.

Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, Church GM.

Nat Biotechnol. 2006 Jun;24(6):680-6. Epub 2006 May 28.

PMID:
16732271

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