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Items: 32


Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases.

Priyam A, Woodcroft BJ, Rai V, Moghul I, Munagala A, Ter F, Chowdhary H, Pieniak I, Maynard LJ, Gibbins MA, Moon H, Davis-Richardson A, Uludag M, Watson-Haigh NS, Challis R, Nakamura H, Favreau E, Gómez EA, Pluskal T, Leonard G, Rumpf W, Wurm Y.

Mol Biol Evol. 2019 Dec 1;36(12):2922-2924. doi: 10.1093/molbev/msz185.


An evolving view of methane metabolism in the Archaea.

Evans PN, Boyd JA, Leu AO, Woodcroft BJ, Parks DH, Hugenholtz P, Tyson GW.

Nat Rev Microbiol. 2019 Apr;17(4):219-232. doi: 10.1038/s41579-018-0136-7. Epub 2019 Jan 21. Review.


Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi.

Boyd JA, Jungbluth SP, Leu AO, Evans PN, Woodcroft BJ, Chadwick GL, Orphan VJ, Amend JP, Rappé MS, Tyson GW.

ISME J. 2019 May;13(5):1269-1279. doi: 10.1038/s41396-018-0343-2. Epub 2019 Jan 16.


Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov.

Martinez MA, Woodcroft BJ, Ignacio Espinoza JC, Zayed AA, Singleton CM, Boyd JA, Li YF, Purvine S, Maughan H, Hodgkins SB, Anderson D, Sederholm M, Temperton B, Bolduc B, Saleska SR, Tyson GW, Rich VI; IsoGenie Project Coordinators, Saleska SR, Tyson GW, Rich VI.

Syst Appl Microbiol. 2019 Jan;42(1):54-66. doi: 10.1016/j.syapm.2018.12.003. Epub 2018 Dec 14.


Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing.

Trubl G, Jang HB, Roux S, Emerson JB, Solonenko N, Vik DR, Solden L, Ellenbogen J, Runyon AT, Bolduc B, Woodcroft BJ, Saleska SR, Tyson GW, Wrighton KC, Sullivan MB, Rich VI.

mSystems. 2018 Oct 2;3(5). pii: e00076-18. doi: 10.1128/mSystems.00076-18. eCollection 2018 Sep-Oct.


Host-linked soil viral ecology along a permafrost thaw gradient.

Emerson JB, Roux S, Brum JR, Bolduc B, Woodcroft BJ, Jang HB, Singleton CM, Solden LM, Naas AE, Boyd JA, Hodgkins SB, Wilson RM, Trubl G, Li C, Frolking S, Pope PB, Wrighton KC, Crill PM, Chanton JP, Saleska SR, Tyson GW, Rich VI, Sullivan MB.

Nat Microbiol. 2018 Aug;3(8):870-880. doi: 10.1038/s41564-018-0190-y. Epub 2018 Jul 16.


Genome-centric view of carbon processing in thawing permafrost.

Woodcroft BJ, Singleton CM, Boyd JA, Evans PN, Emerson JB, Zayed AAF, Hoelzle RD, Lamberton TO, McCalley CK, Hodgkins SB, Wilson RM, Purvine SO, Nicora CD, Li C, Frolking S, Chanton JP, Crill PM, Saleska SR, Rich VI, Tyson GW.

Nature. 2018 Aug;560(7716):49-54. doi: 10.1038/s41586-018-0338-1. Epub 2018 Jul 16.


Methanotrophy across a natural permafrost thaw environment.

Singleton CM, McCalley CK, Woodcroft BJ, Boyd JA, Evans PN, Hodgkins SB, Chanton JP, Frolking S, Crill PM, Saleska SR, Rich VI, Tyson GW.

ISME J. 2018 Oct;12(10):2544-2558. doi: 10.1038/s41396-018-0065-5. Epub 2018 Jun 28.


GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes.

Boyd JA, Woodcroft BJ, Tyson GW.

Nucleic Acids Res. 2018 Jun 1;46(10):e59. doi: 10.1093/nar/gky174.


Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.

Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, Hugenholtz P, Tyson GW.

Nat Microbiol. 2018 Feb;3(2):253. doi: 10.1038/s41564-017-0083-5.


Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.

Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, Hugenholtz P, Tyson GW.

Nat Microbiol. 2017 Nov;2(11):1533-1542. doi: 10.1038/s41564-017-0012-7. Epub 2017 Sep 11. Erratum in: Nat Microbiol. 2017 Dec 12;:.


Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota.

Vanwonterghem I, Evans PN, Parks DH, Jensen PD, Woodcroft BJ, Hugenholtz P, Tyson GW.

Nat Microbiol. 2016 Oct 3;1:16170. doi: 10.1038/nmicrobiol.2016.170.


Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics.

Rinke C, Low S, Woodcroft BJ, Raina JB, Skarshewski A, Le XH, Butler MK, Stocker R, Seymour J, Tyson GW, Hugenholtz P.

PeerJ. 2016 Sep 22;4:e2486. doi: 10.7717/peerj.2486. eCollection 2016.


The Widespread Prevalence and Functional Significance of Silk-Like Structural Proteins in Metazoan Biological Materials.

McDougall C, Woodcroft BJ, Degnan BM.

PLoS One. 2016 Jul 14;11(7):e0159128. doi: 10.1371/journal.pone.0159128. eCollection 2016.


OrfM: a fast open reading frame predictor for metagenomic data.

Woodcroft BJ, Boyd JA, Tyson GW.

Bioinformatics. 2016 Sep 1;32(17):2702-3. doi: 10.1093/bioinformatics/btw241. Epub 2016 May 3.


Archaeal and bacterial communities across a chronosequence of drained lake basins in Arctic Alaska.

Kao-Kniffin J, Woodcroft BJ, Carver SM, Bockheim JG, Handelsman J, Tyson GW, Hinkel KM, Mueller CW.

Sci Rep. 2015 Dec 18;5:18165. doi: 10.1038/srep18165.


Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus.

Soo RM, Woodcroft BJ, Parks DH, Tyson GW, Hugenholtz P.

PeerJ. 2015 May 21;3:e968. doi: 10.7717/peerj.968. eCollection 2015.


Methane dynamics regulated by microbial community response to permafrost thaw.

McCalley CK, Woodcroft BJ, Hodgkins SB, Wehr RA, Kim EH, Mondav R, Crill PM, Chanton JP, Rich VI, Tyson GW, Saleska SR.

Nature. 2014 Oct 23;514(7523):478-81. doi: 10.1038/nature13798.


GroopM: an automated tool for the recovery of population genomes from related metagenomes.

Imelfort M, Parks D, Woodcroft BJ, Dennis P, Hugenholtz P, Tyson GW.

PeerJ. 2014 Sep 30;2:e603. doi: 10.7717/peerj.603. eCollection 2014.


Discovery of a novel methanogen prevalent in thawing permafrost.

Mondav R, Woodcroft BJ, Kim EH, McCalley CK, Hodgkins SB, Crill PM, Chanton J, Hurst GB, VerBerkmoes NC, Saleska SR, Hugenholtz P, Rich VI, Tyson GW.

Nat Commun. 2014;5:3212. doi: 10.1038/ncomms4212.


Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum.

Oehring SC, Woodcroft BJ, Moes S, Wetzel J, Dietz O, Pulfer A, Dekiwadia C, Maeser P, Flueck C, Witmer K, Brancucci NM, Niederwieser I, Jenoe P, Ralph SA, Voss TS.

Genome Biol. 2012 Nov 26;13(11):R108. doi: 10.1186/gb-2012-13-11-r108.


Determination of protein subcellular localization in apicomplexan parasites.

Woodcroft BJ, McMillan PJ, Dekiwadia C, Tilley L, Ralph SA.

Trends Parasitol. 2012 Dec;28(12):546-54. doi: 10.1016/ Epub 2012 Sep 17. Review.


Marked changes in neuropeptide expression accompany broadcast spawnings in the gastropod Haliotis asinina.

York PS, Cummins SF, Degnan SM, Woodcroft BJ, Degnan BM.

Front Zool. 2012 May 9;9(1):9. doi: 10.1186/1742-9994-9-9.


Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.

Bonnal RJ, Aerts J, Githinji G, Goto N, MacLean D, Miller CA, Mishima H, Pagani M, Ramirez-Gonzalez R, Smant G, Strozzi F, Syme R, Vos R, Wennblom TJ, Woodcroft BJ, Katayama T, Prins P.

Bioinformatics. 2012 Apr 1;28(7):1035-7. doi: 10.1093/bioinformatics/bts080. Epub 2012 Feb 12.


NUMTs in the sponge genome reveal conserved transposition mechanisms in metazoans.

Erpenbeck D, Voigt O, Adamski M, Woodcroft BJ, Hooper JN, Wörheide G, Degnan BM.

Mol Biol Evol. 2011 Jan;28(1):1-5. doi: 10.1093/molbev/msq217. Epub 2010 Aug 18.


The Amphimedon queenslandica genome and the evolution of animal complexity.

Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier ME, Mitros T, Richards GS, Conaco C, Dacre M, Hellsten U, Larroux C, Putnam NH, Stanke M, Adamska M, Darling A, Degnan SM, Oakley TH, Plachetzki DC, Zhai Y, Adamski M, Calcino A, Cummins SF, Goodstein DM, Harris C, Jackson DJ, Leys SP, Shu S, Woodcroft BJ, Vervoort M, Kosik KS, Manning G, Degnan BM, Rokhsar DS.

Nature. 2010 Aug 5;466(7307):720-6. doi: 10.1038/nature09201.


Drug target prediction and prioritization: using orthology to predict essentiality in parasite genomes.

Doyle MA, Gasser RB, Woodcroft BJ, Hall RS, Ralph SA.

BMC Genomics. 2010 Apr 3;11:222. doi: 10.1186/1471-2164-11-222.


Automated organelle-based colocalization in whole-cell imaging.

Woodcroft BJ, Hammond L, Stow JL, Hamilton NA.

Cytometry A. 2009 Nov;75(11):941-50. doi: 10.1002/cyto.a.20786.


REX1 and Pf62: are they one and the same?

Gardiner DL, Woodcroft BJ, Dixon MW, Ralph SA, Trenholme KR.

Parasitol Res. 2009 Apr;104(5):967-8. doi: 10.1007/s00436-009-1382-4. Review. No abstract available.


Widespread transcriptional changes pre-empt the critical pelagic-benthic transition in the vetigastropod Haliotis asinina.

Williams EA, Degnan BM, Gunter H, Jackson DJ, Woodcroft BJ, Degnan SM.

Mol Ecol. 2009 Mar;18(5):1006-25. doi: 10.1111/j.1365-294X.2008.04078.x. Epub 2009 Jan 29.


Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals.

Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, King N, Degnan BM, Rokhsar DS, Bartel DP.

Nature. 2008 Oct 30;455(7217):1193-7. doi: 10.1038/nature07415. Epub 2008 Oct 1.


Does the high gene density in the sponge NK homeobox gene cluster reflect limited regulatory capacity?

Fahey B, Larroux C, Woodcroft BJ, Degnan BM.

Biol Bull. 2008 Jun;214(3):205-17.


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