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Items: 1 to 50 of 58

1.

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.

Nat Biotechnol. 2019 Aug 9. doi: 10.1038/s41587-019-0252-6. [Epub ahead of print]

PMID:
31399723
2.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.

Nat Biotechnol. 2019 Aug;37(8):852-857. doi: 10.1038/s41587-019-0209-9. No abstract available. Erratum in: Nat Biotechnol. 2019 Aug 9;:.

PMID:
31341288
3.

redbiom: a Rapid Sample Discovery and Feature Characterization System.

McDonald D, Kaehler B, Gonzalez A, DeReus J, Ackermann G, Marotz C, Huttley G, Knight R.

mSystems. 2019 Jun 25;4(4). pii: e00215-19. doi: 10.1128/mSystems.00215-19.

4.

Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages.

Ying H, Cooke I, Sprungala S, Wang W, Hayward DC, Tang Y, Huttley G, Ball EE, Forêt S, Miller DJ.

Genome Biol. 2018 Nov 2;19(1):175. doi: 10.1186/s13059-018-1552-8.

5.

Did aculeate silk evolve as an antifouling material?

Sutherland TD, Sriskantha A, Rapson TD, Kaehler BD, Huttley GA.

PLoS One. 2018 Sep 21;13(9):e0203948. doi: 10.1371/journal.pone.0203948. eCollection 2018.

6.

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin.

Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, Huttley GA, Gregory Caporaso J.

Microbiome. 2018 May 17;6(1):90. doi: 10.1186/s40168-018-0470-z.

7.

Standard Codon Substitution Models Overestimate Purifying Selection for Nonstationary Data.

Kaehler BD, Yap VB, Huttley GA.

Genome Biol Evol. 2017 Jan 1;9(1):134-149. doi: 10.1093/gbe/evw308.

8.

Statistical Methods for Identifying Sequence Motifs Affecting Point Mutations.

Zhu Y, Neeman T, Yap VB, Huttley GA.

Genetics. 2017 Feb;205(2):843-856. doi: 10.1534/genetics.116.195677. Epub 2016 Dec 14.

9.

The PHF21B gene is associated with major depression and modulates the stress response.

Wong ML, Arcos-Burgos M, Liu S, Vélez JI, Yu C, Baune BT, Jawahar MC, Arolt V, Dannlowski U, Chuah A, Huttley GA, Fogarty R, Lewis MD, Bornstein SR, Licinio J.

Mol Psychiatry. 2017 Jul;22(7):1015-1025. doi: 10.1038/mp.2016.174. Epub 2016 Oct 25.

10.

Novel and rare functional genomic variants in multiple autoimmune syndrome and Sjögren's syndrome.

Johar AS, Mastronardi C, Rojas-Villarraga A, Patel HR, Chuah A, Peng K, Higgins A, Milburn P, Palmer S, Silva-Lara MF, Velez JI, Andrews D, Field M, Huttley G, Goodnow C, Anaya JM, Arcos-Burgos M.

J Transl Med. 2015 Jun 2;13:173. doi: 10.1186/s12967-015-0525-x.

11.

Transcriptome sequencing of two phenotypic mosaic Eucalyptus trees reveals large scale transcriptome re-modelling.

Padovan A, Patel HR, Chuah A, Huttley GA, Krause ST, Degenhardt J, Foley WJ, Külheim C.

PLoS One. 2015 May 15;10(5):e0123226. doi: 10.1371/journal.pone.0123226. eCollection 2015.

12.

Folding behavior of four silks of giant honey bee reflects the evolutionary conservation of aculeate silk proteins.

Maitip J, Trueman HE, Kaehler BD, Huttley GA, Chantawannakul P, Sutherland TD.

Insect Biochem Mol Biol. 2015 Apr;59:72-9. doi: 10.1016/j.ibmb.2015.02.007. Epub 2015 Feb 21.

PMID:
25712559
13.

Draft Genome of Australian Environmental Strain WM 09.24 of the Opportunistic Human Pathogen Scedosporium aurantiacum.

Pérez-Bercoff Å, Papanicolaou A, Ramsperger M, Kaur J, Patel HR, Harun A, Duan SY, Elbourne L, Bouchara JP, Paulsen IT, Nevalainen H, Meyer W, Huttley GA.

Genome Announc. 2015 Feb 12;3(1). pii: e01526-14. doi: 10.1128/genomeA.01526-14.

14.

Genetic distance for a general non-stationary markov substitution process.

Kaehler BD, Yap VB, Zhang R, Huttley GA.

Syst Biol. 2015 Mar;64(2):281-93. doi: 10.1093/sysbio/syu106. Epub 2014 Dec 9.

15.

Whole exome sequencing of extreme morbid obesity patients: translational implications for obesity and related disorders.

Paz-Filho G, Boguszewski MC, Mastronardi CA, Patel HR, Johar AS, Chuah A, Huttley GA, Boguszewski CL, Wong ML, Arcos-Burgos M, Licinio J.

Genes (Basel). 2014 Aug 25;5(3):709-25. doi: 10.3390/genes5030709.

16.

Cryptococcus gattii in North American Pacific Northwest: whole-population genome analysis provides insights into species evolution and dispersal.

Engelthaler DM, Hicks ND, Gillece JD, Roe CC, Schupp JM, Driebe EM, Gilgado F, Carriconde F, Trilles L, Firacative C, Ngamskulrungroj P, Castañeda E, Lazera Mdos S, Melhem MS, Pérez-Bercoff A, Huttley G, Sorrell TC, Voelz K, May RC, Fisher MC, Thompson GR 3rd, Lockhart SR, Keim P, Meyer W.

MBio. 2014 Jul 15;5(4):e01464-14. doi: 10.1128/mBio.01464-14.

17.

The "naked coral" hypothesis revisited--evidence for and against scleractinian monophyly.

Kitahara MV, Lin MF, Forêt S, Huttley G, Miller DJ, Chen CA.

PLoS One. 2014 Apr 16;9(4):e94774. doi: 10.1371/journal.pone.0094774. eCollection 2014.

18.

The embedding problem for markov models of nucleotide substitution.

Verbyla KL, Yap VB, Pahwa A, Shao Y, Huttley GA.

PLoS One. 2013 Jul 30;8(7):e69187. doi: 10.1371/journal.pone.0069187. Print 2013.

19.

Infection with a Virulent Strain of Wolbachia Disrupts Genome Wide-Patterns of Cytosine Methylation in the Mosquito Aedes aegypti.

Ye YH, Woolfit M, Huttley GA, Rancès E, Caragata EP, Popovici J, O'Neill SL, McGraw EA.

PLoS One. 2013 Jun 19;8(6):e66482. doi: 10.1371/journal.pone.0066482. Print 2013.

20.

Histone H2A.Z inheritance during the cell cycle and its impact on promoter organization and dynamics.

Nekrasov M, Amrichova J, Parker BJ, Soboleva TA, Jack C, Williams R, Huttley GA, Tremethick DJ.

Nat Struct Mol Biol. 2012 Nov;19(11):1076-83. doi: 10.1038/nsmb.2424. Epub 2012 Oct 21.

PMID:
23085713
21.

Dynamic evolution of venom proteins in squamate reptiles.

Casewell NR, Huttley GA, Wüster W.

Nat Commun. 2012;3:1066. doi: 10.1038/ncomms2065.

PMID:
22990862
22.

A unique H2A histone variant occupies the transcriptional start site of active genes.

Soboleva TA, Nekrasov M, Pahwa A, Williams R, Huttley GA, Tremethick DJ.

Nat Struct Mol Biol. 2011 Dec 4;19(1):25-30. doi: 10.1038/nsmb.2161.

PMID:
22139013
23.

Statistical methods for detecting periodic fragments in DNA sequence data.

Epps J, Ying H, Huttley GA.

Biol Direct. 2011 Apr 28;6:21. doi: 10.1186/1745-6150-6-21.

24.

Exploiting CpG hypermutability to identify phenotypically significant variation within human protein-coding genes.

Ying H, Huttley G.

Genome Biol Evol. 2011;3:938-49. doi: 10.1093/gbe/evr021. Epub 2011 Mar 11.

25.

Regional context in the alignment of biological sequence pairs.

Sammut R, Huttley G.

J Mol Evol. 2011 Feb;72(2):147-59. doi: 10.1007/s00239-010-9409-0. Epub 2010 Nov 24.

26.

QIIME allows analysis of high-throughput community sequencing data.

Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R.

Nat Methods. 2010 May;7(5):335-6. doi: 10.1038/nmeth.f.303. Epub 2010 Apr 11. No abstract available.

27.

Expansion of circulating T cells resembling follicular helper T cells is a fixed phenotype that identifies a subset of severe systemic lupus erythematosus.

Simpson N, Gatenby PA, Wilson A, Malik S, Fulcher DA, Tangye SG, Manku H, Vyse TJ, Roncador G, Huttley GA, Goodnow CC, Vinuesa CG, Cook MC.

Arthritis Rheum. 2010 Jan;62(1):234-44. doi: 10.1002/art.25032.

28.

Evidence that localized variation in primate sequence divergence arises from an influence of nucleosome placement on DNA repair.

Ying H, Epps J, Williams R, Huttley G.

Mol Biol Evol. 2010 Mar;27(3):637-49. doi: 10.1093/molbev/msp253. Epub 2009 Oct 20.

29.

Estimates of the effect of natural selection on protein-coding content.

Yap VB, Lindsay H, Easteal S, Huttley G.

Mol Biol Evol. 2010 Mar;27(3):726-34. doi: 10.1093/molbev/msp232. Epub 2009 Oct 8.

30.

Pathological rate matrices: from primates to pathogens.

Schranz HW, Yap VB, Easteal S, Knight R, Huttley GA.

BMC Bioinformatics. 2008 Dec 19;9:550. doi: 10.1186/1471-2105-9-550.

31.

Pitfalls of the most commonly used models of context dependent substitution.

Lindsay H, Yap VB, Ying H, Huttley GA.

Biol Direct. 2008 Dec 16;3:52. doi: 10.1186/1745-6150-3-52. Erratum in: Biol Direct. 2009;(4). doi: 10.1186/1745-6150-4-10.

32.

Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics.

Caporaso JG, Smit S, Easton BC, Hunter L, Huttley GA, Knight R.

BMC Evol Biol. 2008 Dec 3;8:327. doi: 10.1186/1471-2148-8-327.

33.

Comparison of methods for estimating the nucleotide substitution matrix.

Oscamou M, McDonald D, Yap VB, Huttley GA, Lladser ME, Knight R.

BMC Bioinformatics. 2008 Dec 1;9:511. doi: 10.1186/1471-2105-9-511.

34.

Genome analysis of the platypus reveals unique signatures of evolution.

Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, Wilson RK.

Nature. 2008 May 8;453(7192):175-83. doi: 10.1038/nature06936. Erratum in: Nature. 2008 Sep 11;455(7210):256. Nefedov, Mikhail [added]; de Jong, Pieter J [added].

35.

Loss of ACTN3 gene function alters mouse muscle metabolism and shows evidence of positive selection in humans.

MacArthur DG, Seto JT, Raftery JM, Quinlan KG, Huttley GA, Hook JW, Lemckert FA, Kee AJ, Edwards MR, Berman Y, Hardeman EC, Gunning PW, Easteal S, Yang N, North KN.

Nat Genet. 2007 Oct;39(10):1261-5. Epub 2007 Sep 9.

PMID:
17828264
36.

PyCogent: a toolkit for making sense from sequence.

Knight R, Maxwell P, Birmingham A, Carnes J, Caporaso JG, Easton BC, Eaton M, Hamady M, Lindsay H, Liu Z, Lozupone C, McDonald D, Robeson M, Sammut R, Smit S, Wakefield MJ, Widmann J, Wikman S, Wilson S, Ying H, Huttley GA.

Genome Biol. 2007;8(8):R171.

37.

RCPdb: An evolutionary classification and codon usage database for repeat-containing proteins.

Faux NG, Huttley GA, Mahmood K, Webb GI, de la Banda MG, Whisstock JC.

Genome Res. 2007 Jul;17(7):1118-27. Epub 2007 Jun 13.

38.

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.

Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC; Broad Institute Genome Sequencing Platform; Broad Institute Whole Genome Assembly Team, Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K.

Nature. 2007 May 10;447(7141):167-77.

PMID:
17495919
39.

Rates of genome evolution and branching order from whole genome analysis.

Huttley GA, Wakefield MJ, Easteal S.

Mol Biol Evol. 2007 Aug;24(8):1722-30. Epub 2007 May 9.

PMID:
17494028
40.

Vestige: maximum likelihood phylogenetic footprinting.

Wakefield MJ, Maxwell P, Huttley GA.

BMC Bioinformatics. 2005 May 29;6:130.

41.

Modeling the impact of DNA methylation on the evolution of BRCA1 in mammals.

Huttley GA.

Mol Biol Evol. 2004 Sep;21(9):1760-8. Epub 2004 Jun 9.

PMID:
15190129
43.

PyEvolve: a toolkit for statistical modelling of molecular evolution.

Butterfield A, Vedagiri V, Lang E, Lawrence C, Wakefield MJ, Isaev A, Huttley GA.

BMC Bioinformatics. 2004 Jan 5;5:1.

44.

Association of polymorphisms of the estrogen receptor gene with anxiety-related traits in children and adolescents: a longitudinal study.

Prichard Z, Jorm AF, Prior M, Sanson A, Smart D, Zhang Y, Huttley G, Easteal S.

Am J Med Genet. 2002 Mar 8;114(2):169-76.

PMID:
11857578
45.

The human melanocortin-1 receptor locus: analysis of transcription unit, locus polymorphism and haplotype evolution.

Smith AG, Box NF, Marks LH, Chen W, Smit DJ, Wyeth JR, Huttley GA, Easteal S, Sturm RA.

Gene. 2001 Dec 27;281(1-2):81-94.

PMID:
11750130
46.

Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins.

Adcock GJ, Dennis ES, Easteal S, Huttley GA, Jermiin LS, Peacock WJ, Thorne A.

Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):537-42. Erratum in: Proc Natl Acad Sci U S A 2002 Jan 8;99(1):541.

47.

Testing for concordant equilibria between population samples.

Huttley GA, Wilson SR.

Genetics. 2000 Dec;156(4):2127-35.

48.

Adaptive evolution of the tumour suppressor BRCA1 in humans and chimpanzees. Australian Breast Cancer Family Study.

Huttley GA, Easteal S, Southey MC, Tesoriero A, Giles GG, McCredie MR, Hopper JL, Venter DJ.

Nat Genet. 2000 Aug;25(4):410-3.

PMID:
10932184
49.

How important is DNA replication for mutagenesis?

Huttley GA, Jakobsen IB, Wilson SR, Easteal S.

Mol Biol Evol. 2000 Jun;17(6):929-37.

PMID:
10833199
50.

A scan for linkage disequilibrium across the human genome.

Huttley GA, Smith MW, Carrington M, O'Brien SJ.

Genetics. 1999 Aug;152(4):1711-22.

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