Publications by authors named "Gavin A Huttley"

36Publications

Machine Learning Techniques for Classifying the Mutagenic Origins of Point Mutations.

Genetics 2020 05 19;215(1):25-40. Epub 2020 Mar 19.

Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia

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http://dx.doi.org/10.1534/genetics.120.303093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7198283PMC
May 2020

Species abundance information improves sequence taxonomy classification accuracy.

Nat Commun 2019 10 11;10(1):4643. Epub 2019 Oct 11.

Research School of Biology, Australian National University, Canberra, Australia.

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http://dx.doi.org/10.1038/s41467-019-12669-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6789115PMC
October 2019

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

Authors:
Evan Bolyen Jai Ram Rideout Matthew R Dillon Nicholas A Bokulich Christian C Abnet Gabriel A Al-Ghalith Harriet Alexander Eric J Alm Manimozhiyan Arumugam Francesco Asnicar Yang Bai Jordan E Bisanz Kyle Bittinger Asker Brejnrod Colin J Brislawn C Titus Brown Benjamin J Callahan Andrés Mauricio Caraballo-Rodríguez John Chase Emily K Cope Ricardo Da Silva Christian Diener Pieter C Dorrestein Gavin M Douglas Daniel M Durall Claire Duvallet Christian F Edwardson Madeleine Ernst Mehrbod Estaki Jennifer Fouquier Julia M Gauglitz Sean M Gibbons Deanna L Gibson Antonio Gonzalez Kestrel Gorlick Jiarong Guo Benjamin Hillmann Susan Holmes Hannes Holste Curtis Huttenhower Gavin A Huttley Stefan Janssen Alan K Jarmusch Lingjing Jiang Benjamin D Kaehler Kyo Bin Kang Christopher R Keefe Paul Keim Scott T Kelley Dan Knights Irina Koester Tomasz Kosciolek Jorden Kreps Morgan G I Langille Joslynn Lee Ruth Ley Yong-Xin Liu Erikka Loftfield Catherine Lozupone Massoud Maher Clarisse Marotz Bryan D Martin Daniel McDonald Lauren J McIver Alexey V Melnik Jessica L Metcalf Sydney C Morgan Jamie T Morton Ahmad Turan Naimey Jose A Navas-Molina Louis Felix Nothias Stephanie B Orchanian Talima Pearson Samuel L Peoples Daniel Petras Mary Lai Preuss Elmar Pruesse Lasse Buur Rasmussen Adam Rivers Michael S Robeson Patrick Rosenthal Nicola Segata Michael Shaffer Arron Shiffer Rashmi Sinha Se Jin Song John R Spear Austin D Swafford Luke R Thompson Pedro J Torres Pauline Trinh Anupriya Tripathi Peter J Turnbaugh Sabah Ul-Hasan Justin J J van der Hooft Fernando Vargas Yoshiki Vázquez-Baeza Emily Vogtmann Max von Hippel William Walters Yunhu Wan Mingxun Wang Jonathan Warren Kyle C Weber Charles H D Williamson Amy D Willis Zhenjiang Zech Xu Jesse R Zaneveld Yilong Zhang Qiyun Zhu Rob Knight J Gregory Caporaso

Nat Biotechnol 2019 Sep;37(9):1091

Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.

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http://dx.doi.org/10.1038/s41587-019-0252-6DOI Listing
September 2019

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

Authors:
Evan Bolyen Jai Ram Rideout Matthew R Dillon Nicholas A Bokulich Christian C Abnet Gabriel A Al-Ghalith Harriet Alexander Eric J Alm Manimozhiyan Arumugam Francesco Asnicar Yang Bai Jordan E Bisanz Kyle Bittinger Asker Brejnrod Colin J Brislawn C Titus Brown Benjamin J Callahan Andrés Mauricio Caraballo-Rodríguez John Chase Emily K Cope Ricardo Da Silva Christian Diener Pieter C Dorrestein Gavin M Douglas Daniel M Durall Claire Duvallet Christian F Edwardson Madeleine Ernst Mehrbod Estaki Jennifer Fouquier Julia M Gauglitz Sean M Gibbons Deanna L Gibson Antonio Gonzalez Kestrel Gorlick Jiarong Guo Benjamin Hillmann Susan Holmes Hannes Holste Curtis Huttenhower Gavin A Huttley Stefan Janssen Alan K Jarmusch Lingjing Jiang Benjamin D Kaehler Kyo Bin Kang Christopher R Keefe Paul Keim Scott T Kelley Dan Knights Irina Koester Tomasz Kosciolek Jorden Kreps Morgan G I Langille Joslynn Lee Ruth Ley Yong-Xin Liu Erikka Loftfield Catherine Lozupone Massoud Maher Clarisse Marotz Bryan D Martin Daniel McDonald Lauren J McIver Alexey V Melnik Jessica L Metcalf Sydney C Morgan Jamie T Morton Ahmad Turan Naimey Jose A Navas-Molina Louis Felix Nothias Stephanie B Orchanian Talima Pearson Samuel L Peoples Daniel Petras Mary Lai Preuss Elmar Pruesse Lasse Buur Rasmussen Adam Rivers Michael S Robeson Patrick Rosenthal Nicola Segata Michael Shaffer Arron Shiffer Rashmi Sinha Se Jin Song John R Spear Austin D Swafford Luke R Thompson Pedro J Torres Pauline Trinh Anupriya Tripathi Peter J Turnbaugh Sabah Ul-Hasan Justin J J van der Hooft Fernando Vargas Yoshiki Vázquez-Baeza Emily Vogtmann Max von Hippel William Walters Yunhu Wan Mingxun Wang Jonathan Warren Kyle C Weber Charles H D Williamson Amy D Willis Zhenjiang Zech Xu Jesse R Zaneveld Yilong Zhang Qiyun Zhu Rob Knight J Gregory Caporaso

Nat Biotechnol 2019 08;37(8):852-857

Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.

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http://dx.doi.org/10.1038/s41587-019-0209-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7015180PMC
August 2019

Did aculeate silk evolve as an antifouling material?

PLoS One 2018 21;13(9):e0203948. Epub 2018 Sep 21.

Research School of Biology, Australian National University, Australian Capital Territory, Australia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0203948PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6150510PMC
March 2019

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

Microbiome 2018 05 17;6(1):90. Epub 2018 May 17.

The Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ, 86011-4073, USA.

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http://dx.doi.org/10.1186/s40168-018-0470-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5956843PMC
May 2018

q2-sample-classifier: machine-learning tools for microbiome classification and regression.

J Open Res Softw 2018 23;3(30). Epub 2018 Oct 23.

The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.

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http://dx.doi.org/10.21105/joss.00934DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6759219PMC
October 2018

Standard Codon Substitution Models Overestimate Purifying Selection for Nonstationary Data.

Genome Biol Evol 2017 01;9(1):134-149

Research School of Biology, College of Medicine, Biology, and Environment, Australian National University, Canberra, ACT, Australia.

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http://dx.doi.org/10.1093/gbe/evw308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381540PMC
January 2017

Statistical Methods for Identifying Sequence Motifs Affecting Point Mutations.

Genetics 2017 02 14;205(2):843-856. Epub 2016 Dec 14.

Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia

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http://dx.doi.org/10.1534/genetics.116.195677DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5289855PMC
February 2017

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

Insect Biochem Mol Biol 2015 Apr 21;59:72-9. Epub 2015 Feb 21.

CSIRO, (The Commonwealth Scientific and Industrial Research Organization), Food and Nutrition Flagship, Canberra, Australian Capital Territory, Australia.

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http://dx.doi.org/10.1016/j.ibmb.2015.02.007DOI Listing
April 2015

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

Syst Biol 2015 Mar 9;64(2):281-93. Epub 2014 Dec 9.

John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2600, Australia; and

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http://dx.doi.org/10.1093/sysbio/syu106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380038PMC
March 2015

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

Genes (Basel) 2014 Aug 25;5(3):709-25. Epub 2014 Aug 25.

Mind and Brain Theme, South Australian Health and Medical Research Institute, and Department of Psychiatry, School of Medicine, Flinders University, PO Box 11060 Adelaide SA 5001, Adelaide, Australia.

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http://dx.doi.org/10.3390/genes5030709DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198926PMC
August 2014

The embedding problem for markov models of nucleotide substitution.

PLoS One 2013 30;8(7):e69187. Epub 2013 Jul 30.

Computational Genomics Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, Australian.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069187PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728303PMC
April 2014

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

Nat Struct Mol Biol 2012 Nov 21;19(11):1076-83. Epub 2012 Oct 21.

The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.

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http://dx.doi.org/10.1038/nsmb.2424DOI Listing
November 2012

Dynamic evolution of venom proteins in squamate reptiles.

Nat Commun 2012 ;3:1066

Alistair Reid Venom Research Unit, Liverpool School of Tropical Medicine, Liverpool, UK.

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http://dx.doi.org/10.1038/ncomms2065DOI Listing
February 2013

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

Nat Struct Mol Biol 2011 Dec 4;19(1):25-30. Epub 2011 Dec 4.

The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.

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http://www.nature.com/articles/nsmb.2161
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http://dx.doi.org/10.1038/nsmb.2161DOI Listing
December 2011

Statistical methods for detecting periodic fragments in DNA sequence data.

Biol Direct 2011 Apr 28;6:21. Epub 2011 Apr 28.

School of Electrical Engineering and Telecommunications, The University of New South Wales, Sydney, NSW 2052, Australia.

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http://dx.doi.org/10.1186/1745-6150-6-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111405PMC
April 2011

Pathological rate matrices: from primates to pathogens.

BMC Bioinformatics 2008 Dec 19;9:550. Epub 2008 Dec 19.

John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.

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http://dx.doi.org/10.1186/1471-2105-9-550DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639438PMC
December 2008

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

Biol Direct 2008 Dec 16;3:52. Epub 2008 Dec 16.

Computational Genomics Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, Australia.

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http://dx.doi.org/10.1186/1745-6150-3-52DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2628887PMC
December 2008

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

BMC Evol Biol 2008 Dec 3;8:327. Epub 2008 Dec 3.

Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA.

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http://dx.doi.org/10.1186/1471-2148-8-327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2637866PMC
December 2008

Comparison of methods for estimating the nucleotide substitution matrix.

BMC Bioinformatics 2008 Dec 1;9:511. Epub 2008 Dec 1.

Department of Applied Mathematics, University of Colorado, Boulder, CO, USA.

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http://dx.doi.org/10.1186/1471-2105-9-511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655096PMC
December 2008

Genome analysis of the platypus reveals unique signatures of evolution.

Authors:
Wesley C Warren LaDeana W Hillier Jennifer A Marshall Graves Ewan Birney Chris P Ponting Frank Grützner Katherine Belov Webb Miller Laura Clarke Asif T Chinwalla Shiaw-Pyng Yang Andreas Heger Devin P Locke Pat Miethke Paul D Waters Frédéric Veyrunes Lucinda Fulton Bob Fulton Tina Graves John Wallis Xose S Puente Carlos López-Otín Gonzalo R Ordóñez Evan E Eichler Lin Chen Ze Cheng Janine E Deakin Amber Alsop Katherine Thompson Patrick Kirby Anthony T Papenfuss Matthew J Wakefield Tsviya Olender Doron Lancet Gavin A Huttley Arian F A Smit Andrew Pask Peter Temple-Smith Mark A Batzer Jerilyn A Walker Miriam K Konkel Robert S Harris Camilla M Whittington Emily S W Wong Neil J Gemmell Emmanuel Buschiazzo Iris M Vargas Jentzsch Angelika Merkel Juergen Schmitz Anja Zemann Gennady Churakov Jan Ole Kriegs Juergen Brosius Elizabeth P Murchison Ravi Sachidanandam Carly Smith Gregory J Hannon Enkhjargal Tsend-Ayush Daniel McMillan Rosalind Attenborough Willem Rens Malcolm Ferguson-Smith Christophe M Lefèvre Julie A Sharp Kevin R Nicholas David A Ray Michael Kube Richard Reinhardt Thomas H Pringle James Taylor Russell C Jones Brett Nixon Jean-Louis Dacheux Hitoshi Niwa Yoko Sekita Xiaoqiu Huang Alexander Stark Pouya Kheradpour Manolis Kellis Paul Flicek Yuan Chen Caleb Webber Ross Hardison Joanne Nelson Kym Hallsworth-Pepin Kim Delehaunty Chris Markovic Pat Minx Yucheng Feng Colin Kremitzki Makedonka Mitreva Jarret Glasscock Todd Wylie Patricia Wohldmann Prathapan Thiru Michael N Nhan Craig S Pohl Scott M Smith Shunfeng Hou Mikhail Nefedov Pieter J de Jong Marilyn B Renfree Elaine R Mardis Richard K Wilson

Nature 2008 May;453(7192):175-83

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature06936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803040PMC
May 2008

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

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

Institute for Neuromuscular Research, Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia.

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http://dx.doi.org/10.1038/ng2122DOI Listing
October 2007

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

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

Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia.

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http://www.genome.org/cgi/doi/10.1101/gr.6255407
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http://dx.doi.org/10.1101/gr.6255407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899123PMC
July 2007

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

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

John Curtin School of Medical Research, The Australian National University, Canberra, Australia.

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http://dx.doi.org/10.1093/molbev/msm094DOI Listing
August 2007

Vestige: maximum likelihood phylogenetic footprinting.

BMC Bioinformatics 2005 May 29;6:130. Epub 2005 May 29.

John Curtin School of Medical Research, The Australian National University, Canberra 0200 ACT, Australia.

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http://dx.doi.org/10.1186/1471-2105-6-130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1156870PMC
May 2005

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

Authors:
Gavin A Huttley

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

Centre for Bioinformation Science, John Curtin School of Medical Research and Mathematical Sciences Institute, Australian National University, Australia.

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http://dx.doi.org/10.1093/molbev/msh187DOI Listing
September 2004

PyEvolve: a toolkit for statistical modelling of molecular evolution.

BMC Bioinformatics 2004 Jan 5;5. Epub 2004 Jan 5.

Centre for Bioinformation Science, John Curtin School of Medical Research and Mathematical Sciences Institute, Australian National University, Canberra, ACT 0200, Australia.

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http://dx.doi.org/10.1186/1471-2105-5-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC317364PMC
January 2004