(Q28754651)

Rute R da Fonseca

1

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Warren E. Johnson

Warren E Johnson

2

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Maria J. Ramos

Maria João Ramos

4

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Stephen J. O'Brien

3

Proboscidean mitogenomics: chronology and mode of elephant evolution using mastodon as outgroup

Stephen J O'Brien

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language of work or name

English

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publication date

4 March 2008

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published in

BMC Genomics

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volume

9

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issue

1

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page(s)

119

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cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Proton-coupled electron transfer drives the proton pump of cytochrome c oxidase

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

MrBayes 3: Bayesian phylogenetic inference under mixed models

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Understanding ATP synthesis: structure and mechanism of the F1-ATPase (Review)

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Natural selection shaped regional mtDNA variation in humans

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Mammalian mitogenomic relationships and the root of the eutherian tree

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Resolution of the early placental mammal radiation using Bayesian phylogenetics

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

A missense mutation of cytochrome oxidase subunit II causes defective assembly and myopathy

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

MODELTEST: testing the model of DNA substitution

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Principles governing amino acid composition of integral membrane proteins: application to topology prediction

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

VMD: visual molecular dynamics

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

The protonmotive Q cycle. Energy transduction by coupling of proton translocation to electron transfer by the cytochrome bc1 complex

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Possible molecular mechanisms of the protonmotive function of cytochrome systems

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Bayesian inference of phylogeny and its impact on evolutionary biology

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

A hidden Markov model for predicting transmembrane helices in protein sequences

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

The incomplete natural history of mitochondria

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Mitochondrial diseases in man and mouse

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Understanding proboscidean evolution: a formidable task

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

The human gene map for performance and health-related fitness phenotypes: the 2005 update

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Differences in reactive oxygen species production explain the phenotypes associated with common mouse mitochondrial DNA variants

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Surface-modulated motion switch: capture and release of iron-sulfur protein in the cytochrome bc1 complex

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Energy converting NADH:quinone oxidoreductase (complex I).

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Cytonuclear coevolution: the genomics of cooperation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Population size does not influence mitochondrial genetic diversity in animals

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Binding of the respiratory chain inhibitor antimycin to the mitochondrial bc1 complex: a new crystal structure reveals an altered intramolecular hydrogen-bonding pattern

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Historical demography, selection, and coalescence of mitochondrial and nuclear (genes in Prochilodus species of northern South America

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Metabolic scaling: a many-splendoured thing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Defining the limits of diving biochemistry in marine mammals

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Effects of purifying and adaptive selection on regional variation in human mtDNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

A discrete water exit pathway in the membrane protein cytochrome c oxidase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Mechanics of coupling proton movements to c-ring rotation in ATP synthase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Afrotherian phylogeny as inferred from complete mitochondrial genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

The root of the mammalian tree inferred from whole mitochondrial genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Cytochrome c oxidase--structure, function, and physiology of a redox-driven molecular machine

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Mammalian basal metabolic rate is proportional to body mass2/3.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Standard energetics of leaf-nosed bats (Hipposideridae): its relationship to intermittent- and protracted-foraging tactics in bats and birds

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Physiology: the pitfalls of power laws

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Septo-optic dysplasia associated with a new mitochondrial cytochrome b mutation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Allometric scaling of metabolic rate from molecules and mitochondria to cells and mammals

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Partial assembly of the yeast mitochondrial ATP synthase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

The reconstruction of Kleiber's law at the organ-tissue level

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Natural selection and the evolution of mtDNA-encoded peptides: evidence for intergenomic co-adaptation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Recurrent myoglobinuria due to a nonsense mutation in the COX I gene of mitochondrial DNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Cryo-electron crystallography of two sub-complexes of bovine complex I reveals the relationship between the membrane and peripheral arms.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Uncovering the [2Fe2S] domain movement in cytochrome bc1 and its implications for energy conversion

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Divergent evolution of membrane protein topology: the Escherichia coli RnfA and RnfE homologues

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Oxidative phosphorylation at the fin de siècle

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Cytochrome c oxidase deficiency associated with the first stop-codon point mutation in human mtDNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Metabolic meaning of elevated levels of oxidative enzymes in high altitude adapted animals: an interpretive hypothesis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

An allometric comparison of the mitochondria of mammalian and reptilian tissues: the implications for the evolution of endothermy

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Analysis of mitochondrial DNA sequences in patients with isolated or combined oxidative phosphorylation system deficiency.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

The three-dimensional structure of complex I from Yarrowia lipolytica: a highly dynamic enzyme

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Physicochemical evolution and molecular adaptation of the cetacean and artiodactyl cytochrome b proteins.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Accelerated evolution of the electron transport chain in anthropoid primates.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Congruent Mammalian Trees from Mitochondrial and Nuclear Genes Using Bayesian Methods

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

A heteroplasmic mitochondrial complex I gene mutation in adult-onset dystonia

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Physiology: Why does metabolic rate scale with body size?

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Transmembrane topology of the NuoL, M and N subunits of NADH:quinone oxidoreductase and their homologues among membrane-bound hydrogenases and bona fide antiporters

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Childhood onset mitochondrial myopathy and lactic acidosis caused by a stop mutation in the mitochondrial cytochrome c oxidase III gene

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Allometric cascade as a unifying principle of body mass effects on metabolism

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Functional characterization of novel mutations in the human cytochrome b gene.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Estimating the influence of selection on the variable amino acid sites of the cytochrome B protein functional domains

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Rates of nuclear and cytoplasmic mitochondrial DNA sequence divergence in mammals.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375446

Energy constraints on carnivore diet

27 November 2018

1 reference

12 December 2020

Influence of base composition on quantitative estimates of gene evolution

1 reference

12 December 2020

TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees

1 reference

12 December 2020

A missense mutation in the mitochondrial cytochrome b gene in a revisited case with histiocytoid cardiomyopathy

1 reference

12 December 2020

The comparative energetics of 'caviomorph' rodents

1 reference

12 December 2020

Molecular evolution of cytochrome c oxidase in high-performance fish (teleostei: Scombroidei)

1 reference

12 December 2020

A novel gly290asp mitochondrial cytochrome b mutation linked to a complex III deficiency in progressive exercise intolerance

1 reference

12 December 2020

The effect of amino acid substitutions in the conserved aromatic region of subunit II of cytochrome c oxidase in Saccharomyces cerevisiae

1 reference

12 December 2020

Exercise intolerance due to a nonsense mutation in the mtDNA ND4 gene

1 reference

12 December 2020

Exercise intolerance due to mutations in the cytochrome b gene of mitochondrial DNA

1 reference

12 December 2020

The definition of mitochondrial H+ ATPase assembly defects in mit- mutants of Saccharomyces cerevisiae with a monoclonal antibody to the enzyme complex as an assembly probe

1 reference

12 December 2020

Oxygen and proton pathways in cytochrome c oxidase

1 reference

12 December 2020

Consensus predictions of membrane protein topology

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2164-9-119

1 reference

Dimensions Publication ID

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/1471-2164-9-119

Fatcat ID

release_wzmk3jlmyffonot5sn4rxzvuxy

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/wzmk3jlmyffonot5sn4rxzvuxy

24 November 2022

mapped directly with Wikidata item

1 reference

1 reference

PubMed publication ID

18318906

1 reference