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Items: 44

1.

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.

2.

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.

3.

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.

4.

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.

5.

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.

6.

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
7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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
13.

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
14.

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
15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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].

23.

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
24.

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.

25.

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.

26.

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
27.

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
28.

Vestige: maximum likelihood phylogenetic footprinting.

Wakefield MJ, Maxwell P, Huttley GA.

BMC Bioinformatics. 2005 May 29;6:130.

29.

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
31.

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.

32.

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
33.

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.

34.

Testing for concordant equilibria between population samples.

Huttley GA, Wilson SR.

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

35.

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
36.

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
37.

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.

38.

Dating the origin of the CCR5-Delta32 AIDS-resistance allele by the coalescence of haplotypes.

Stephens JC, Reich DE, Goldstein DB, Shin HD, Smith MW, Carrington M, Winkler C, Huttley GA, Allikmets R, Schriml L, Gerrard B, Malasky M, Ramos MD, Morlot S, Tzetis M, Oddoux C, di Giovine FS, Nasioulas G, Chandler D, Aseev M, Hanson M, Kalaydjieva L, Glavac D, Gasparini P, Kanavakis E, Claustres M, Kambouris M, Ostrer H, Duff G, Baranov V, Sibul H, Metspalu A, Goldman D, Martin N, Duffy D, Schmidtke J, Estivill X, O'Brien SJ, Dean M.

Am J Hum Genet. 1998 Jun;62(6):1507-15.

39.

CCR5-delta 32 gene deletion in HIV-1 infected patients.

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

Lancet. 1997 Sep 6;350(9079):741; author reply 742. No abstract available.

PMID:
9291930
40.

Contrasting genetic influence of CCR2 and CCR5 variants on HIV-1 infection and disease progression. Hemophilia Growth and Development Study (HGDS), Multicenter AIDS Cohort Study (MACS), Multicenter Hemophilia Cohort Study (MHCS), San Francisco City Cohort (SFCC), ALIVE Study.

Smith MW, Dean M, Carrington M, Winkler C, Huttley GA, Lomb DA, Goedert JJ, O'Brien TR, Jacobson LP, Kaslow R, Buchbinder S, Vittinghoff E, Vlahov D, Hoots K, Hilgartner MW, O'Brien SJ.

Science. 1997 Aug 15;277(5328):959-65.

41.

Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study.

Dean M, Carrington M, Winkler C, Huttley GA, Smith MW, Allikmets R, Goedert JJ, Buchbinder SP, Vittinghoff E, Gomperts E, Donfield S, Vlahov D, Kaslow R, Saah A, Rinaldo C, Detels R, O'Brien SJ.

Science. 1996 Sep 27;273(5283):1856-62. Erratum in: Science 1996 Nov 15;274(5290):1069.

PMID:
8791590
42.

Evolution of the chalcone synthase gene family in the genus Ipomoea.

Durbin ML, Learn GH Jr, Huttley GA, Clegg MT.

Proc Natl Acad Sci U S A. 1995 Apr 11;92(8):3338-42.

43.

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