James McInerney

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Chris CreeveyProfessor of Computational Biology, Queen’s University BelfastVerified email at qub.ac.uk
Davide PisaniProfessor of Phylogenomics. Schools of Biological & Earth Sciences. University of Bristol (UK)Verified email at bristol.ac.uk
Dr Mary J. O'ConnellThe University Of NottinghamVerified email at nottingham.ac.uk
Thomas KeaneResearch Group Leader, and Head of European Genome-phenome Archive + European Variation ArchiveVerified email at ebi.ac.uk
Thomas J. NaughtonNational University of Ireland MaynoothVerified email at cs.nuim.ie
Eric BaptesteCNRS, Université Pierre et Marie CurieVerified email at snv.jussieu.fr
Mark WilkinsonThe Natural History MuseumVerified email at nhm.ac.uk
David FitzpatrickMaynooth UniversityVerified email at mu.ie
James CottonIBAHCM, University of GlasgowVerified email at glasgow.ac.uk
Alan McNallyUniversity of BirminghamVerified email at bham.ac.uk
Philippe LopezProfesseur de Biologie des Systèmes, Sorbonne UniversitéVerified email at upmc.fr
Giddy LandanChristian-Albrechts-University KielVerified email at ifam.uni-kiel.de
William MartinProfessor of Molecular Evolution, University of DüsseldorfVerified email at hhu.de
Shijulal Nelson-SathiRajiv Gandhi Centre for Biotechnology (RGCB) , Trivandrum, IndiaVerified email at rgcb.res.in
Martin EmbleyProfessor of Molecular Evolution, Newcastle UniversityVerified email at ncl.ac.uk
Prof. Mike SteelUniversity of Canterbury, New ZealandVerified email at canterbury.ac.nz
Joseph L. ThorleyPoisson Consulting Ltd.Verified email at poissonconsulting.ca
Peter G. FosterNatural History Museum, LondonVerified email at nhm.ac.uk
David Alvarez-PonceAssociate Professor, University of Nevada, RenoVerified email at unr.edu
Filipa L. SousaDepartment of Functional and Evolutionary Ecology, University of ViennaVerified email at univie.ac.at

James McInerney

Chair in Evolutionary Biology, University of Nottingham

Verified email at nottingham.ac.uk - Homepage

pangenomes prokaryotes eukaryotes phylogenetics


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Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified T Keane, C Creevey, M Pentony, T Naughton, JO Mclnerney BMC evolutionary biology 6 (1), 29, 2006	1132	2006
Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears S Liu, ED Lorenzen, M Fumagalli, B Li, K Harris, Z Xiong, L Zhou, ... Cell 157 (4), 785-794, 2014	303	2014
Replicational and transcriptional selection on codon usage in Borrelia burgdorferi JO McInerney Proceedings of the National Academy of Sciences 95 (18), 10698-10703, 1998	274	1998
GCUA: general codon usage analysis. JO McInerney Bioinformatics (Oxford, England) 14 (4), 372-373, 1998	266	1998
Endosymbiotic origin and differential loss of eukaryotic genes C Ku, S Nelson-Sathi, M Roettger, FL Sousa, PJ Lockhart, D Bryant, ... Nature 524 (7566), 427-432, 2015	260	2015
Why prokaryotes have pangenomes JO McInerney, A McNally, MJ O'Connell Nature Microbiology 2 (4), 1-5, 2017	243	2017
Origins of major archaeal clades correspond to gene acquisitions from bacteria S Nelson-Sathi, FL Sousa, M Roettger, N Lozada-Chávez, T Thiergart, ... Nature 517 (7532), 77-80, 2015	230	2015
Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea S Nelson-Sathi, T Dagan, G Landan, A Janssen, M Steel, JO McInerney, ... Proceedings of the National Academy of Sciences 109 (50), 20537-20542, 2012	228	2012
Clann: investigating phylogenetic information through supertree analyses CJ Creevey, JO McInerney Bioinformatics 21 (3), 390-392, 2005	217	2005
Supertrees disentangle the chimerical origin of eukaryotic genomes D Pisani, JA Cotton, JO McInerney Molecular biology and evolution 24 (8), 1752-1760, 2007	210	2007
Networks: expanding evolutionary thinking E Bapteste, L van Iersel, A Janke, S Kelchner, S Kelk, JO McInerney, ... Trends in Genetics 29 (8), 439-441, 2013	164	2013
Genome phylogenies indicate a meaningful α-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales DA Fitzpatrick, CJ Creevey, JO McInerney Molecular Biology and Evolution 23 (1), 74-85, 2006	162	2006
Metazoan opsin evolution reveals a simple route to animal vision R Feuda, SC Hamilton, JO McInerney, D Pisani Proceedings of the National Academy of Sciences 109 (46), 18868-18872, 2012	160	2012
The Opisthokonta and the Ecdysozoa may not be clades: stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata … GK Philip, CJ Creevey, JO McInerney Molecular biology and evolution 22 (5), 1175-1184, 2005	149	2005
Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations A McNally, Y Oren, D Kelly, B Pascoe, S Dunn, T Sreecharan, M Vehkala, ... PLoS genetics 12 (9), e1006280, 2016	144	2016
Does a tree–like phylogeny only exist at the tips in the prokaryotes? CJ Creevey, DA Fitzpatrick, GK Philip, RJ Kinsella, MJ O'Connell, ... Proceedings of the Royal Society of London. Series B: Biological Sciences …, 2004	143	2004
TOPD/FMTS: a new software to compare phylogenetic trees P Puigbò, S Garcia-Vallve, JO McInerney Bioinformatics 23 (12), 1556-1558, 2007	141	2007
A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases CA Cummins, JO McInerney Systematic biology 60 (6), 833-844, 2011	139	2011
The hybrid nature of the Eukaryota and a consilient view of life on Earth JO McInerney, MJ O'connell, D Pisani Nature Reviews Microbiology 12 (6), 449-455, 2014	137	2014
Recovery and phylogenetic analysis of novel archaeal rRNA sequences from a deep-sea deposit feeder JO McInerney, M Wilkinson, JW Patching, TM Embley, R Powell Applied and Environmental Microbiology 61 (4), 1646-1648, 1995	133	1995

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