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Items: 31

1.

Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149.

Tkavc R, Matrosova VY, Grichenko OE, Gostinčar C, Volpe RP, Klimenkova P, Gaidamakova EK, Zhou CE, Stewart BJ, Lyman MG, Malfatti SA, Rubinfeld B, Courtot M, Singh J, Dalgard CL, Hamilton T, Frey KG, Gunde-Cimerman N, Dugan L, Daly MJ.

Front Microbiol. 2018 Jan 8;8:2528. doi: 10.3389/fmicb.2017.02528. eCollection 2017.

2.

A compendium of multi-omic sequence information from the Saanich Inlet water column.

Hawley AK, Torres-Beltrán M, Zaikova E, Walsh DA, Mueller A, Scofield M, Kheirandish S, Payne C, Pakhomova L, Bhatia M, Shevchuk O, Gies EA, Fairley D, Malfatti SA, Norbeck AD, Brewer HM, Pasa-Tolic L, Del Rio TG, Suttle CA, Tringe S, Hallam SJ.

Sci Data. 2017 Oct 31;4:170160. doi: 10.1038/sdata.2017.160.

3.

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.

Gontang EA, Aylward FO, Carlos C, Glavina Del Rio T, Chovatia M, Fern A, Lo CC, Malfatti SA, Tringe SG, Currie CR, Kolter R.

PLoS One. 2017 May 18;12(5):e0177189. doi: 10.1371/journal.pone.0177189. eCollection 2017.

4.

A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes.

Grady SL, Malfatti SA, Gunasekera TS, Dalley BK, Lyman MG, Striebich RC, Mayhew MB, Zhou CL, Ruiz ON, Dugan LC.

BMC Genomics. 2017 Apr 28;18(1):334. doi: 10.1186/s12864-017-3708-4.

5.

Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions.

He S, Malfatti SA, McFarland JW, Anderson FE, Pati A, Huntemann M, Tremblay J, Glavina del Rio T, Waldrop MP, Windham-Myers L, Tringe SG.

MBio. 2015 May 19;6(3):e00066-15. doi: 10.1128/mBio.00066-15.

6.

Convergent bacterial microbiotas in the fungal agricultural systems of insects.

Aylward FO, Suen G, Biedermann PH, Adams AS, Scott JJ, Malfatti SA, Glavina del Rio T, Tringe SG, Poulsen M, Raffa KF, Klepzig KD, Currie CR.

MBio. 2014 Nov 18;5(6):e02077. doi: 10.1128/mBio.02077-14.

7.

Metagenomes from two microbial consortia associated with Santa Barbara seep oil.

Hawley ER, Malfatti SA, Pagani I, Huntemann M, Chen A, Foster B, Copeland A, del Rio TG, Pati A, Jansson JR, Gilbert JA, Tringe SG, Lorenson TD, Hess M.

Mar Genomics. 2014 Dec;18 Pt B:97-9. doi: 10.1016/j.margen.2014.06.003. Epub 2014 Jun 20.

PMID:
24958360
8.

Tackling soil diversity with the assembly of large, complex metagenomes.

Howe AC, Jansson JK, Malfatti SA, Tringe SG, Tiedje JM, Brown CT.

Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4904-9. doi: 10.1073/pnas.1402564111. Epub 2014 Mar 14. Erratum in: Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):6115.

9.

The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling.

Lindemann SR, Moran JJ, Stegen JC, Renslow RS, Hutchison JR, Cole JK, Dohnalkova AC, Tremblay J, Singh K, Malfatti SA, Chen F, Tringe SG, Beyenal H, Fredrickson JK.

Front Microbiol. 2013 Nov 13;4:323. doi: 10.3389/fmicb.2013.00323. eCollection 2013.

10.

Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass.

D'haeseleer P, Gladden JM, Allgaier M, Chain PS, Tringe SG, Malfatti SA, Aldrich JT, Nicora CD, Robinson EW, Paša-Tolić L, Hugenholtz P, Simmons BA, Singer SW.

PLoS One. 2013 Jul 19;8(7):e68465. doi: 10.1371/journal.pone.0068465. Print 2013.

11.

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.

12.

Comparative genomics suggests an independent origin of cytoplasmic incompatibility in Cardinium hertigii.

Penz T, Schmitz-Esser S, Kelly SE, Cass BN, Müller A, Woyke T, Malfatti SA, Hunter MS, Horn M.

PLoS Genet. 2012;8(10):e1003012. doi: 10.1371/journal.pgen.1003012. Epub 2012 Oct 25.

13.

Mesophilic and thermophilic conditions select for unique but highly parallel microbial communities to perform carboxylate platform biomass conversion.

Hollister EB, Forrest AK, Wilkinson HH, Ebbole DJ, Tringe SG, Malfatti SA, Holtzapple MT, Gentry TJ.

PLoS One. 2012;7(6):e39689. doi: 10.1371/journal.pone.0039689. Epub 2012 Jun 22.

14.

The metagenome of an anaerobic microbial community decomposing poplar wood chips.

van der Lelie D, Taghavi S, McCorkle SM, Li LL, Malfatti SA, Monteleone D, Donohoe BS, Ding SY, Adney WS, Himmel ME, Tringe SG.

PLoS One. 2012;7(5):e36740. doi: 10.1371/journal.pone.0036740. Epub 2012 May 21.

15.

Complete genome sequence of Francisella philomiragia ATCC 25017.

Zeytun A, Malfatti SA, Vergez LM, Shin M, Garcia E, Chain PS.

J Bacteriol. 2012 Jun;194(12):3266. doi: 10.1128/JB.00413-12.

16.

Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill.

Baelum J, Borglin S, Chakraborty R, Fortney JL, Lamendella R, Mason OU, Auer M, Zemla M, Bill M, Conrad ME, Malfatti SA, Tringe SG, Holman HY, Hazen TC, Jansson JK.

Environ Microbiol. 2012 Sep;14(9):2405-16. doi: 10.1111/j.1462-2920.2012.02780.x. Epub 2012 May 23.

PMID:
22616650
17.

The metagenome of the marine anammox bacterium 'Candidatus Scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium.

van de Vossenberg J, Woebken D, Maalcke WJ, Wessels HJ, Dutilh BE, Kartal B, Janssen-Megens EM, Roeselers G, Yan J, Speth D, Gloerich J, Geerts W, van der Biezen E, Pluk W, Francoijs KJ, Russ L, Lam P, Malfatti SA, Tringe SG, Haaijer SC, Op den Camp HJ, Stunnenberg HG, Amann R, Kuypers MM, Jetten MS.

Environ Microbiol. 2013 May;15(5):1275-89. doi: 10.1111/j.1462-2920.2012.02774.x. Epub 2012 May 9.

18.

Microbial iron cycling in acidic geothermal springs of yellowstone national park: integrating molecular surveys, geochemical processes, and isolation of novel fe-active microorganisms.

Kozubal MA, Macur RE, Jay ZJ, Beam JP, Malfatti SA, Tringe SG, Kocar BD, Borch T, Inskeep WP.

Front Microbiol. 2012 Mar 26;3:109. doi: 10.3389/fmicb.2012.00109. eCollection 2012.

19.

Genome of Ochrobactrum anthropi ATCC 49188 T, a versatile opportunistic pathogen and symbiont of several eukaryotic hosts.

Chain PS, Lang DM, Comerci DJ, Malfatti SA, Vergez LM, Shin M, Ugalde RA, Garcia E, Tolmasky ME.

J Bacteriol. 2011 Aug;193(16):4274-5. doi: 10.1128/JB.05335-11. Epub 2011 Jun 17.

20.

The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes.

van Passel MW, Kant R, Zoetendal EG, Plugge CM, Derrien M, Malfatti SA, Chain PS, Woyke T, Palva A, de Vos WM, Smidt H.

PLoS One. 2011 Mar 3;6(3):e16876. doi: 10.1371/journal.pone.0016876.

21.

Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production.

Hollister EB, Forrest AK, Wilkinson HH, Ebbole DJ, Malfatti SA, Tringe SG, Holtzapple MT, Gentry TJ.

Appl Microbiol Biotechnol. 2010 Sep;88(1):389-99. doi: 10.1007/s00253-010-2789-7. Epub 2010 Jul 31.

PMID:
20676626
22.

Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores.

Pope PB, Denman SE, Jones M, Tringe SG, Barry K, Malfatti SA, McHardy AC, Cheng JF, Hugenholtz P, McSweeney CS, Morrison M.

Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14793-8. doi: 10.1073/pnas.1005297107. Epub 2010 Jul 28.

23.

Genomics. Genome project standards in a new era of sequencing.

Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, Gibbs R, Graves T, Han CS, Harrison SH, Highlander S, Hugenholtz P, Khouri HM, Kodira CD, Kolker E, Kyrpides NC, Lang D, Lapidus A, Malfatti SA, Markowitz V, Metha T, Nelson KE, Parkhill J, Pitluck S, Qin X, Read TD, Schmutz J, Sozhamannan S, Sterk P, Strausberg RL, Sutton G, Thomson NR, Tiedje JM, Weinstock G, Wollam A; Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium, Detter JC.

Science. 2009 Oct 9;326(5950):236-7. doi: 10.1126/science.1180614. No abstract available.

24.

The complete plastid genome sequence of the secondarily nonphotosynthetic alga Cryptomonas paramecium: reduction, compaction, and accelerated evolutionary rate.

Donaher N, Tanifuji G, Onodera NT, Malfatti SA, Chain PS, Hara Y, Archibald JM.

Genome Biol Evol. 2009 Nov 13;1:439-48. doi: 10.1093/gbe/evp047.

25.

Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans.

Sievert SM, Scott KM, Klotz MG, Chain PS, Hauser LJ, Hemp J, Hügler M, Land M, Lapidus A, Larimer FW, Lucas S, Malfatti SA, Meyer F, Paulsen IT, Ren Q, Simon J; USF Genomics Class.

Appl Environ Microbiol. 2008 Feb;74(4):1145-56. Epub 2007 Dec 7.

26.

The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2.

Scott KM, Sievert SM, Abril FN, Ball LA, Barrett CJ, Blake RA, Boller AJ, Chain PS, Clark JA, Davis CR, Detter C, Do KF, Dobrinski KP, Faza BI, Fitzpatrick KA, Freyermuth SK, Harmer TL, Hauser LJ, Hügler M, Kerfeld CA, Klotz MG, Kong WW, Land M, Lapidus A, Larimer FW, Longo DL, Lucas S, Malfatti SA, Massey SE, Martin DD, McCuddin Z, Meyer F, Moore JL, Ocampo LH Jr, Paul JH, Paulsen IT, Reep DK, Ren Q, Ross RL, Sato PY, Thomas P, Tinkham LE, Zeruth GT.

PLoS Biol. 2006 Nov;4(12):e383.

27.

Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility.

Chain PS, Denef VJ, Konstantinidis KT, Vergez LM, Agulló L, Reyes VL, Hauser L, Córdova M, Gómez L, González M, Land M, Lao V, Larimer F, LiPuma JJ, Mahenthiralingam E, Malfatti SA, Marx CJ, Parnell JJ, Ramette A, Richardson P, Seeger M, Smith D, Spilker T, Sul WJ, Tsoi TV, Ulrich LE, Zhulin IB, Tiedje JM.

Proc Natl Acad Sci U S A. 2006 Oct 17;103(42):15280-7. Epub 2006 Oct 9.

28.

Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707.

Klotz MG, Arp DJ, Chain PS, El-Sheikh AF, Hauser LJ, Hommes NG, Larimer FW, Malfatti SA, Norton JM, Poret-Peterson AT, Vergez LM, Ward BB.

Appl Environ Microbiol. 2006 Sep;72(9):6299-315.

29.

Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen.

Chain PS, Hu P, Malfatti SA, Radnedge L, Larimer F, Vergez LM, Worsham P, Chu MC, Andersen GL.

J Bacteriol. 2006 Jun;188(12):4453-63.

30.

Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255.

Starkenburg SR, Chain PS, Sayavedra-Soto LA, Hauser L, Land ML, Larimer FW, Malfatti SA, Klotz MG, Bottomley PJ, Arp DJ, Hickey WJ.

Appl Environ Microbiol. 2006 Mar;72(3):2050-63.

31.

Whole-genome analyses of speciation events in pathogenic Brucellae.

Chain PS, Comerci DJ, Tolmasky ME, Larimer FW, Malfatti SA, Vergez LM, Aguero F, Land ML, Ugalde RA, Garcia E.

Infect Immun. 2005 Dec;73(12):8353-61.

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