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List of works by James O. McInerney

"Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis

scientific article

A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases

scientific article

Adaptive evolution of the human fatty acid synthase gene: support for the cancer selection and fat utilization hypotheses?

scientific article

An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences

scientific article published in October 2002

Analysis of gene expression in the bovine corpus luteum through generation and characterisation of 960 ESTs

scientific article published in July 2004

Bipartite network analysis of gene sharings in the microbial world

scientific article published on 15 January 2018

Building Large Phylogenetic Trees on Coarse-Grained Parallel Machines

scholarly article by Thomas M. Keane et al published 18 April 2006 in Algorithmica

Characterization of endospore-forming bacteria associated with entomopathogenic nematodes, Heterorhabditis spp., and description of Paenibacillus nematophilus sp. nov.

scientific article

Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations

scientific article

Detecting adaptive molecular evolution: additional tools for the parasitologist

scientific article published on January 2003

Does a tree-like phylogeny only exist at the tips in the prokaryotes?

scholarly article by Christopher J. Creevey et al published 22 December 2004 in Proceedings of the Royal Society B

EGN: a wizard for construction of gene and genome similarity networks ⬇️

scientific article published on July 11, 2013

Endosymbiotic origin and differential loss of eukaryotic genes

scientific article published on 19 August 2015

Eukaryotic genes in Mycobacterium tuberculosis? Possible alternative explanations

scientific article published on 01 December 2003

Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function

scientific article (publication date: 5 October 2010)

Evidence for heterogeneous selective pressures in the evolution of the env gene in different human immunodeficiency virus type 1 subtypes

scientific article

Evidence of positive Darwinian selection in putative meningococcal vaccine antigens

scientific article published on 29 June 2005

Evolution: A four billion year old metabolism

scientific article

Evolutionary analyses of non-genealogical bonds produced by introgressive descent

scientific article

Evolutionary developmental biology: Ghost locus appears

scientific article published in October 2014

Fatty acid biosynthesis in Mycobacterium tuberculosis: lateral gene transfer, adaptive evolution, and gene duplication

scientific article published on 13 August 2003

Formation of chimeric genes with essential functions at the origin of eukaryotes.

scientific article published on 13 March 2018

Function-related replacement of bacterial siderophore pathways. ⬇️

scientific article published on 15 August 2017

Gene evolution and drug discovery

scientific article

Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models

scientific article

Gene similarity networks provide tools for understanding eukaryote origins and evolution

scientific article published on April 2013

Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility

scientific article published in 2021

Genetics. Paradigm for life

scientific article published in November 2007

Genome Phylogenies Indicate a Meaningful α-Proteobacterial Phylogeny and Support a Grouping of the Mitochondria with the Rickettsiales

scholarly article by David A. Fitzpatrick et al published 8 September 2005 in Molecular Biology and Evolution

Heterogeneous models place the root of the placental mammal phylogeny ⬇️

scientific article (publication date: September 2013)

Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis

scientific article

Horizontal gene transfer is less frequent in eukaryotes than prokaryotes but can be important (retrospective on DOI 10.1002/bies.201300095).

scientific article published on 18 April 2017

Increased genome sampling reveals a dynamic relationship between gene duplicability and the structure of the primate protein-protein interaction network

scientific article published on 21 June 2012

Integration of two ancestral chaperone systems into one: the evolution of eukaryotic molecular chaperones in light of eukaryogenesis

scientific article

Metazoan opsin evolution reveals a simple route to animal vision ⬇️

scientific article published on October 29, 2012

Microbiology: Mind the gaps in cellular evolution ⬇️

scientific article published on 11 January 2017

Molecular evidence for dim-light vision in the last common ancestor of the vertebrates

article

Molecular phylogeny of the Drosophila tripunctata and closely related species groups (Diptera: Drosophilidae).

scientific article published on 11 March 2009

More than tree dimensions: inter-lineage evolution's ecological importance

scientific article published on 12 September 2013

MultiPhyl: a high-throughput phylogenomics webserver using distributed computing

scientific article published on 6 June 2007

Networks: expanding evolutionary thinking ⬇️

scientific article published on June 11, 2013

New approaches for unravelling reassortment pathways

scientific article

On the desirability of models for inferring genome phylogenies

scientific article published on 03 November 2005

Origins of major archaeal clades correspond to gene acquisitions from bacteria

scientific article

Planctomycetes and eukaryotes: a case of analogy not homology

scientific article (publication date: November 2011)

Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears

scientific article

Recurring cluster and operon assembly for Phenylacetate degradation genes

scientific article

Reply to 'The population genetics of pangenomes'.

scientific article published in December 2017

SMBE Satellite meeting on reticulated microbial evolution 2014--meeting report

scientific article published on 12 August 2014

Society for Molecular Biology and Evolution, Council and Business Meetings, 2015, Vienna Austria

scientific article published on 28 December 2015

Supertrees disentangle the chimerical origin of eukaryotic genomes

scientific article

Systemic effects of deep brain stimulation on synergic control in Parkinson's disease

scientific article published on 9 March 2018

TOPD/FMTS: a new software to compare phylogenetic trees

scientific article published on 25 April 2007

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 than Ecdysozoa

scientific article

The causes of protein evolutionary rate variation

scientific article published on 24 March 2006

The human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differences

scientific article (publication date: 2011)

The molecular phylogeny of a nematode-specific clade of heterotrimeric G-protein alpha-subunit genes

scientific article published on 16 June 2006

The network of life: genome beginnings and evolution. Introduction

scientific article (publication date: 12 August 2009)

The prokaryotic tree of life: past, present... and future?

scientific article published on 25 March 2008

The public goods hypothesis for the evolution of life on Earth ⬇️

scientific article published on August 23, 2011

The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data

scientific article

The role of public goods in planetary evolution

scientific article

The shape of supertrees to come: tree shape related properties of fourteen supertree methods

scientific article published in June 2005

The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods

scientific article published on 12 November 2008

Timing and reconstruction of the most recent common ancestor of the subtype C clade of human immunodeficiency virus type 1.

scientific article published on October 2004

Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates

scientific article published on 24 July 2013

Trees from trees: construction of phylogenetic supertrees using clann

scientific article published in January 2009

Why prokaryotes have pangenomes ⬇️

scientific article published on 28 March 2017

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