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    22833 Publications
    3073 Total Profiles
    24 Edited Profiles

    LaButti, Kurt

    TitleBusiness/Systems Analyst 4
    SchoolLawrence Berkeley National Lab
    DepartmentGenomics
    Address
    Phone925/330-7439

       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can sign in to make corrections and additions, or contact us for help.
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      1. Olsen MT, Nowack S, Wood JM, Becraft ED, LaButti K, Lipzen A, Martin J, Schackwitz WS, Rusch DB, Cohan FM, Bryant DA, Ward DM. The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat. Front Microbiol. 2015; 6:604.
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      2. Lam KK, LaButti K, Khalak A, Tse D. FinisherSC: a repeat-aware tool for upgrading de novo assembly using long reads. Bioinformatics. 2015 Oct 1; 31(19):3207-9.
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      3. Chang Y, Wang S, Sekimoto S, Aerts AL, Choi C, Clum A, LaButti KM, Lindquist EA, Yee Ngan C, Ohm RA, Salamov AA, Grigoriev IV, Spatafora JW, Berbee ML. Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants. Genome Biol Evol. 2015; 7(6):1590-601.
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      4. Branco S, Gladieux P, Ellison CE, Kuo A, LaButti K, Lipzen A, Grigoriev IV, Liao HL, Vilgalys R, Peay KG, Taylor JW, Bruns TD. Genetic isolation between two recently diverged populations of a symbiotic fungus. Mol Ecol. 2015 Jun; 24(11):2747-58.
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      5. Baker SE, Schackwitz W, Lipzen A, Martin J, Haridas S, LaButti K, Grigoriev IV, Simmons BA, McCluskey K. Draft Genome Sequence of Neurospora crassa Strain FGSC 73. Genome Announc. 2015; 3(2).
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      6. Dhillon B, Feau N, Aerts AL, Beauseigle S, Bernier L, Copeland A, Foster A, Gill N, Henrissat B, Herath P, LaButti KM, Levasseur A, Lindquist EA, Majoor E, Ohm RA, Pangilinan JL, Pribowo A, Saddler JN, Sakalidis ML, de Vries RP, Grigoriev IV, Goodwin SB, Tanguay P, Hamelin RC. Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen. Proc Natl Acad Sci U S A. 2015 Mar 17; 112(11):3451-6.
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      7. 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. Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nat Genet. 2015 Apr; 47(4):410-5.
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      8. Floudas D, Held BW, Riley R, Nagy LG, Koehler G, Ransdell AS, Younus H, Chow J, Chiniquy J, Lipzen A, Tritt A, Sun H, Haridas S, LaButti K, Ohm RA, Kües U, Blanchette RA, Grigoriev IV, Minto RE, Hibbett DS. Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii. Fungal Genet Biol. 2015 Mar; 76:78-92.
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      9. Riley R, Salamov AA, Brown DW, Nagy LG, Floudas D, Held BW, Levasseur A, Lombard V, Morin E, Otillar R, Lindquist EA, Sun H, LaButti KM, Schmutz J, Jabbour D, Luo H, Baker SE, Pisabarro AG, Walton JD, Blanchette RA, Henrissat B, Martin F, Cullen D, Hibbett DS, Grigoriev IV. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proc Natl Acad Sci U S A. 2014 Jul 8; 111(27):9923-8.
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      10. Hess J, Skrede I, Wolfe BE, LaButti K, Ohm RA, Grigoriev IV, Pringle A. Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi. Genome Biol Evol. 2014; 6(7):1564-78.
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      11. Weiss M, Kesberg AI, Labutti KM, Pitluck S, Bruce D, Hauser L, Copeland A, Woyke T, Lowry S, Lucas S, Land M, Goodwin L, Kjelleberg S, Cook AM, Buhmann M, Thomas T, Schleheck D. Permanent draft genome sequence of Comamonas testosteroni KF-1. Stand Genomic Sci. 2013; 8(2):239-54.
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      12. Condon BJ, Leng Y, Wu D, Bushley KE, Ohm RA, Otillar R, Martin J, Schackwitz W, Grimwood J, MohdZainudin N, Xue C, Wang R, Manning VA, Dhillon B, Tu ZJ, Steffenson BJ, Salamov A, Sun H, Lowry S, LaButti K, Han J, Copeland A, Lindquist E, Barry K, Schmutz J, Baker SE, Ciuffetti LM, Grigoriev IV, Zhong S, Turgeon BG. Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens. PLoS Genet. 2013; 9(1):e1003233.
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      13. 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. Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathog. 2012; 8(12):e1003037.
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      14. Kontur WS, Schackwitz WS, Ivanova N, Martin J, Labutti K, Deshpande S, Tice HN, Pennacchio C, Sodergren E, Weinstock GM, Noguera DR, Donohue TJ. Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome. J Bacteriol. 2012 Dec; 194(24):7016-7.
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      15. Morin E, Kohler A, Baker AR, Foulongne-Oriol M, Lombard V, Nagy LG, Ohm RA, Patyshakuliyeva A, Brun A, Aerts AL, Bailey AM, Billette C, Coutinho PM, Deakin G, Doddapaneni H, Floudas D, Grimwood J, Hildén K, Kües U, Labutti KM, Lapidus A, Lindquist EA, Lucas SM, Murat C, Riley RW, Salamov AA, Schmutz J, Subramanian V, Wösten HA, Xu J, Eastwood DC, Foster GD, Sonnenberg AS, Cullen D, de Vries RP, Lundell T, Hibbett DS, Henrissat B, Burton KS, Kerrigan RW, Challen MP, Grigoriev IV, Martin F. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proc Natl Acad Sci U S A. 2012 Oct 23; 109(43):17501-6.
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      16. Suzuki H, MacDonald J, Syed K, Salamov A, Hori C, Aerts A, Henrissat B, Wiebenga A, VanKuyk PA, Barry K, Lindquist E, LaButti K, Lapidus A, Lucas S, Coutinho P, Gong Y, Samejima M, Mahadevan R, Abou-Zaid M, de Vries RP, Igarashi K, Yadav JS, Grigoriev IV, Master ER. Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize. BMC Genomics. 2012; 13:444.
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      17. Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martínez AT, Otillar R, Spatafora JW, Yadav JS, Aerts A, Benoit I, Boyd A, Carlson A, Copeland A, Coutinho PM, de Vries RP, Ferreira P, Findley K, Foster B, Gaskell J, Glotzer D, Górecki P, Heitman J, Hesse C, Hori C, Igarashi K, Jurgens JA, Kallen N, Kersten P, Kohler A, Kües U, Kumar TK, Kuo A, LaButti K, Larrondo LF, Lindquist E, Ling A, Lombard V, Lucas S, Lundell T, Martin R, McLaughlin DJ, Morgenstern I, Morin E, Murat C, Nagy LG, Nolan M, Ohm RA, Patyshakuliyeva A, Rokas A, Ruiz-Dueñas FJ, Sabat G, Salamov A, Samejima M, Schmutz J, Slot JC, St John F, Stenlid J, Sun H, Sun S, Syed K, Tsang A, Wiebenga A, Young D, Pisabarro A, Eastwood DC, Martin F, Cullen D, Grigoriev IV, Hibbett DS. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science. 2012 Jun 29; 336(6089):1715-9.
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      18. Piškur J, Ling Z, Marcet-Houben M, Ishchuk OP, Aerts A, LaButti K, Copeland A, Lindquist E, Barry K, Compagno C, Bisson L, Grigoriev IV, Gabaldón T, Phister T. The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties. Int J Food Microbiol. 2012 Jul 2; 157(2):202-9.
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      19. 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, San RJ, 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. Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. Proc Natl Acad Sci U S A. 2012 Apr 3; 109(14):5458-63.
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      20. Padamsee M, Kumar TK, Riley R, Binder M, Boyd A, Calvo AM, Furukawa K, Hesse C, Hohmann S, James TY, LaButti K, Lapidus A, Lindquist E, Lucas S, Miller K, Shantappa S, Grigoriev IV, Hibbett DS, McLaughlin DJ, Spatafora JW, Aime MC. The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction. Fungal Genet Biol. 2012 Mar; 49(3):217-26.
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      21. Kallimanis A, Karabika E, Mavromatis K, Lapidus A, Labutti KM, Liolios K, Ivanova N, Goodwin L, Woyke T, Velentzas AD, Perisynakis A, Ouzounis CC, Kyrpides NC, Koukkou AI, Drainas C. Complete genome sequence of Mycobacterium sp. strain (Spyr1) and reclassification to Mycobacterium gilvum Spyr1. Stand Genomic Sci. 2011 Oct 15; 5(1):144-53.
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      22. 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. Comparative genomics of xylose-fermenting fungi for enhanced biofuel production. Proc Natl Acad Sci U S A. 2011 Aug 9; 108(32):13212-7.
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      23. Eastwood DC, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A, Asiegbu FO, Baker SE, Barry K, Bendiksby M, Blumentritt M, Coutinho PM, Cullen D, de Vries RP, Gathman A, Goodell B, Henrissat B, Ihrmark K, Kauserud H, Kohler A, LaButti K, Lapidus A, Lavin JL, Lee YH, Lindquist E, Lilly W, Lucas S, Morin E, Murat C, Oguiza JA, Park J, Pisabarro AG, Riley R, Rosling A, Salamov A, Schmidt O, Schmutz J, Skrede I, Stenlid J, Wiebenga A, Xie X, Kües U, Hibbett DS, Hoffmeister D, Högberg N, Martin F, Grigoriev IV, Watkinson SC. The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science. 2011 Aug 5; 333(6043):762-5.
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      24. Lapidus A, Clum A, Labutti K, Kaluzhnaya MG, Lim S, Beck DA, Glavina Del Rio T, Nolan M, Mavromatis K, Huntemann M, Lucas S, Lidstrom ME, Ivanova N, Chistoserdova L. Genomes of three methylotrophs from a single niche reveal the genetic and metabolic divergence of the methylophilaceae. J Bacteriol. 2011 Aug; 193(15):3757-64.
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      25. Kallimanis A, Labutti KM, Lapidus A, Clum A, Lykidis A, Mavromatis K, Pagani I, Liolios K, Ivanova N, Goodwin L, Pitluck S, Chen A, Palaniappan K, Markowitz V, Bristow J, Velentzas AD, Perisynakis A, Ouzounis CC, Kyrpides NC, Koukkou AI, Drainas C. Complete genome sequence of Arthrobacter phenanthrenivorans type strain (Sphe3). Stand Genomic Sci. 2011 Apr 29; 4(2):123-30.
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      26. Labutti K, Mayilraj S, Clum A, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207). Stand Genomic Sci. 2010; 3(1):85-92.
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      27. Labutti K, Sikorski J, Schneider S, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Tindall BJ, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Planctomyces limnophilus type strain (Mü 290). Stand Genomic Sci. 2010; 3(1):47-56.
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      28. Pukall R, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Labutti K, Pati A, Ivanova N, Mavromatis K, Mikhailova N, Pitluck S, Bruce D, Goodwin L, Land M, Hauser L, Chang YJ, Jeffries CD, Chen A, Palaniappan K, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Brettin T. Complete genome sequence of Kribbella flavida type strain (IFO 14399). Stand Genomic Sci. 2010; 2(2):186-93.
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      29. Pati A, Labutti K, Pukall R, Nolan M, Glavina Del Rio T, Tice H, Cheng JF, Lucas S, Chen F, Copeland A, Ivanova N, Mavromatis K, Mikhailova N, Pitluck S, Bruce D, Goodwin L, Land M, Hauser L, Chang YJ, Jeffries CD, Chen A, Palaniappan K, Chain P, Brettin T, Sikorski J, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022). Stand Genomic Sci. 2010; 2(1):49-56.
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      30. Labutti K, Pukall R, Steenblock K, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Saunders E, Brettin T, Detter JC, Han C, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Anaerococcus prevotii type strain (PC1). Stand Genomic Sci. 2009; 1(2):159-65.
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      31. Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, Debruyn B, Decaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, Labutti K, Lee E, Li S, Lovin DD, Mao C, Mauceli E, Menck CF, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JM, Vanzee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng Q, Zhao Q, Zhao Y, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Birren B, Fraser-Liggett CM, Severson DW. Genome sequence of Aedes aegypti, a major arbovirus vector. Science. 2007 Jun 22; 316(5832):1718-23.
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      32. Zody MC, Garber M, Adams DJ, Sharpe T, Harrow J, Lupski JR, Nicholson C, Searle SM, Wilming L, Young SK, Abouelleil A, Allen NR, Bi W, Bloom T, Borowsky ML, Bugalter BE, Butler J, Chang JL, Chen CK, Cook A, Corum B, Cuomo CA, de Jong PJ, DeCaprio D, Dewar K, FitzGerald M, Gilbert J, Gibson R, Gnerre S, Goldstein S, Grafham DV, Grocock R, Hafez N, Hagopian DS, Hart E, Norman CH, Humphray S, Jaffe DB, Jones M, Kamal M, Khodiyar VK, LaButti K, Laird G, Lehoczky J, Liu X, Lokyitsang T, Loveland J, Lui A, Macdonald P, Major JE, Matthews L, Mauceli E, McCarroll SA, Mihalev AH, Mudge J, Nguyen C, Nicol R, O'Leary SB, Osoegawa K, Schwartz DC, Shaw-Smith C, Stankiewicz P, Steward C, Swarbreck D, Venkataraman V, Whittaker CA, Yang X, Zimmer AR, Bradley A, Hubbard T, Birren BW, Rogers J, Lander ES, Nusbaum C. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. Nature. 2006 Apr 20; 440(7087):1045-9.
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      33. Taylor TD, Noguchi H, Totoki Y, Toyoda A, Kuroki Y, Dewar K, Lloyd C, Itoh T, Takeda T, Kim DW, She X, Barlow KF, Bloom T, Bruford E, Chang JL, Cuomo CA, Eichler E, FitzGerald MG, Jaffe DB, LaButti K, Nicol R, Park HS, Seaman C, Sougnez C, Yang X, Zimmer AR, Zody MC, Birren BW, Nusbaum C, Fujiyama A, Hattori M, Rogers J, Lander ES, Sakaki Y. Human chromosome 11 DNA sequence and analysis including novel gene identification. Nature. 2006 Mar 23; 440(7083):497-500.
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