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List of works by Edward L. Braun

A Phylogenomic Supertree of Birds

scientific article published on 10 July 2019

A macroevolutionary perspective on multiple sexual traits in the phasianidae (galliformes)

scientific article

A molecular phylogeny of the pheasants and partridges suggests that these lineages are not monophyletic

scientific article

A novel exome probe set captures phototransduction genes across birds (Aves) enabling efficient analysis of vision evolution

scientific article published in 2021

A phylogenomic study of birds reveals their evolutionary history

scientific article

A phylogenomic supermatrix of Galliformes (Landfowl) reveals biased branch lengths

A simple strategy for recovering ultraconserved elements, exons, and introns from low coverage shotgun sequencing of museum specimens: Placement of the partridge genus Tropicoperdix within the galliformes

scientific article published on 07 September 2018

A stationary-phase gene in Saccharomyces cerevisiae is a member of a novel, highly conserved gene family.

scientific article published on December 1996

A well-tested set of primers to amplify regions spread across the avian genome

article

An evolutionary model motivated by physicochemical properties of amino acids reveals variation among proteins.

scientific article published in July 2018

An unbiased approach to identify genes involved in development in a turtle with temperature-dependent sex determination

scientific article

Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods.

scientific article published on 10 February 2016

Ancestral range reconstruction of Galliformes: the effects of topology and taxon sampling

Are transposable element insertions homoplasy free?: an examination using the avian tree of life

scientific article

Assessing parameter identifiability in phylogenetic models using data cloning

scientific article

Assessing phylogenetic relationships among galliformes: a multigene phylogeny with expanded taxon sampling in Phasianidae

scientific article (publication date: 2013)

Author Correction: Dense sampling of bird diversity increases power of comparative genomics

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes).

scientific article

Building the avian tree of life using a large-scale, sparse supermatrix

scientific article published on 27 December 2014

Calibrating the genomic clock of modern birds using fossils

scientific article published on 16 September 2024

Categorical edge-based analyses of phylogenomic data reveal conflicting signals for difficult relationships in the avian tree

Chapter Five Transcription factors and metabolic engineering: Novel applications for ancient tools

Comparative Genomics Reveals a Burst of Homoplasy-Free Numt Insertions

scientific article published on 01 August 2018

Comparative genomics reveals insights into avian genome evolution and adaptation

scientific article

Comparative molecular evolution and phylogenetic utility of 3′-UTRs and introns in Galliformes

scientific article published on 14 April 2010

Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution.

scientific article

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

scientific article published on 29 April 2021

Complexity of avian evolution revealed by family-level genomes

scientific article published in April 2024

Data Types and the Phylogeny of Neoaves

Data Types and the Phylogeny of Neoaves

Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation

scientific article published in 2020

Dense sampling of bird diversity increases power of comparative genomics

scientific article published on 11 November 2020

Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements

Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix

scientific article published in 2014

Duplication of accelerated evolution and growth hormone gene in passerine birds

scientific article

Duplications and functional divergence of ADP-glucose pyrophosphorylase genes in plants

scientific article (publication date: 12 August 2008)

Dynamic Patterns of Sex Chromosome Evolution in Neognath Birds: Many Independent Barriers to Recombination at the ATP5F1A Locus

Dynamic Patterns of Sex Chromosome Evolution in Neognath Birds: Many Independent Barriers to Recombination at the ATP5F1A Locus

Early mesozoic coexistence of amniotes and hepadnaviridae

scientific article

Earth history and the passerine superradiation

scientific article published on 01 April 2019

Error in Phylogenetic Estimation for Bushes in the Tree of Life

scholarly article by Swati Patel published 2013 in Journal of phylogenetics & evolutionary biology

Evolution of the 3R-MYB Gene Family in Plants

scientific article

Evolution of the mitochondrial DNA control region and cytochrome b genes and the inference of phylogenetic relationships in the avian genus Lophura (Galliformes).

scientific article published in May 2001

Evolutionary and comparative analysis of MYB and bHLH plant transcription factors

scientific article published on April 2011

Evolutionary genomics implies a specific function of Ant4 in mammalian and anole lizard male germ cells

scientific article

Examining Basal Avian Divergences with Mitochondrial Sequences: Model Complexity, Taxon Sampling, and Sequence Length

article

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication

scientific article

Exploring Conflicts in Whole Genome Phylogenetics: A Case Study Within Manakins (Aves: Pipridae)

scientific article published in 2022

Expressed sequences from conidial, mycelial, and sexual stages of Neurospora crassa.

scientific article published on June 1997

Fungal Zuotin Proteins Evolved from MIDA1-like Factors by Lineage-Specific Loss of MYB Domains

scientific article published in 2001

GENOMIC INSIGHTS INTO EVOLUTIONARY RELATIONSHIPS AMONG HETEROKONT LINEAGES EMPHASIZING THE PHAEOPHYCEAE(1).

scientific article

Gene tree quality affects empirical coalescent branch length estimation

scientific article published in 2021

Genomics in Neurospora crassa: From One-Gene-One-Enzyme to 10,000 Genes

article

High association strengths are linked to phenotypic similarity, including plumage color and patterns, of participants in mixed-species bird flocks of southwestern China

scientific article published in 2022

Historical relationships of three enigmatic phasianid genera (Aves: Galliformes) inferred using phylogenomic and mitogenomic data

scientific article

Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)

Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)

Homoplastic microinversions and the avian tree of life

scientific article (publication date: 25 May 2011)

How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes).

scientific article

Identification of the first fungal annexin: analysis of annexin gene duplications and implications for eukaryotic evolution.

scientific article

Identifying localized biases in large datasets: a case study using the avian tree of life

scientific article

Incongruence among different mitochondrial regions: a case study using complete mitogenomes.

scientific article

Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes

scientific article

Land connectivity changes and global cooling shaped the colonization history and diversification of New World quail (Aves: Galliformes: Odontophoridae)

scientific article published in 2015

Large-scale comparison of fungal sequence information: mechanisms of innovation in Neurospora crassa and gene loss in Saccharomyces cerevisiae

scientific article

Mitochondrial DNA Phylogeny and Speciation in the Tragopans

scholarly article by Ettore Randi et al published October 2000 in The Auk

Mitochondrial genome diversity and population structure of two western honey bee subspecies in the Republic of South Africa

scientific article

Mitochondrial genome of <i>Apis mellifera anatoliaca</i> (Hymenoptera: Apidae) – the Anatolian honey bee

scientific article published on 16 April 2020

Mitochondrial genomes and avian phylogeny: complex characters and resolvability without explosive radiations

scientific article

Molecular cloning of the estrogen and progesterone receptors of the American alligator

scientific article published on March 2004

Molecular early burst associated with the diversification of birds at the K–Pg boundary

Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes

scientific article

Newly discovered plant c-myb-like genes rewrite the evolution of the plant myb gene family.

scientific article published in September 1999

PHYLOGENETIC POSITION OF THE NEW WORLD QUAIL (ODONTOPHORIDAE): EIGHT NUCLEAR LOCI AND THREE MITOCHONDRIAL REGIONS CONTRADICT MORPHOLOGY AND THE SIBLEY-AHLQUIST TAPESTRY

scholarly article by W. Andrew Cox et al published 2007 in The Auk

PHYLOGENOMICS AND SECONDARY PLASTIDS: A LOOK BACK AND A LOOK AHEAD(1).

scientific article published on February 2008

POLYTOMIES, THE POWER OF PHYLOGENETIC INFERENCE, AND THE STOCHASTIC NATURE OF MOLECULAR EVOLUTION: A COMMENT ON WALSH ET AL. (1999)

scientific article published on 01 June 2001

Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals

scientific article (publication date: 13 March 2013)

Patterns of Vertebrate Isochore Evolution Revealed by Comparison of Expressed Mammalian, Avian, and Crocodilian Genes

article

Phylogenetic Analyses of Sites in Different Protein Structural Environments Result in Distinct Placements of the Metazoan Root

scientific article published on 28 March 2020

Phylogenetic Analyses of Sites in Different Protein Structural Environments Result in Distinct Placements of the Metazoan Root

Phylogenetic Signal of Indels and the Neoavian Radiation

Phylogenetic definitions for 25 higher-level clade names of birds

scientific article published in 2022

Phylogenomic analyses data of the avian phylogenomics project

scientific article

Phylogenomic analyses reveal the evolutionary origin of the inhibin alpha-subunit, a unique TGFbeta superfamily antagonist

scientific article (publication date: 2010)

Phylogenomic analysis supports multiple instances of polyphyly in the oomycete peronosporalean lineage

scientific article

Phylogenomic evidence for multiple losses of flight in ratite birds

scientific article

Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness

scientific article published on 17 November 2020

Phylogeny and diversification of the gallopheasants (Aves: Galliformes): Testing roles of sexual selection and environmental niche divergence

scientific article published in 2020

Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds

Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds

Protein evolution is structure dependent and non-homogeneous across the tree of life

Protein synthesis in long-term stationary-phase cultures of Saccharomyces cerevisiae

scientific article

Rapid and recent diversification of curassows, guans, and chachalacas (Galliformes: Cracidae) out of Mesoamerica: Phylogeny inferred from mitochondrial, intron, and ultraconserved element sequences

scientific article

Ratite nonmonophyly: independent evidence from 40 novel Loci

scientific article

Recently duplicated maize R2R3 Myb genes provide evidence for distinct mechanisms of evolutionary divergence after duplication

scientific article

Report from the first snake genomics and integrative biology meeting

scientific article published on 24 September 2012

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

scientific article published on September 2015

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes

scientific article

Sorting out relationships among the grouse and ptarmigan using intron, mitochondrial, and ultra-conserved element sequences

scientific article

Stationary phase in Saccharomyces cerevisiae

scientific article

TAPER: Pinpointing errors in multiple sequence alignments despite varying rates of evolution

scientific article published in 2021

TAPER: Pinpointing errors in multiple sequence alignments despite varying rates of evolution

Tempo and Pattern of Avian Brain Size Evolution

scientific article published on 18 April 2020

Testing hypotheses about the sister group of the passeriformes using an independent 30-locus data set.

scientific article

The Roles of Protein Structure, Taxon Sampling, and Model Complexity in Phylogenomics: A Case Study Focused on Early Animal Divergences

The Roles of Protein Structure, Taxon Sampling, and Model Complexity in Phylogenomics: A Case Study Focused on Early Animal Divergences

The Structure of Evolutionary Model Space for Proteins Across the Tree of Life

The Structure of Evolutionary Model Space for Proteins across the Tree of Life

The complete mitochondrial genome and phylogenetic placement of Apis nigrocincta Smith (Insecta: Hymenoptera: Apidae), an Asian, cavity-nesting honey bee

The complete mitochondrial genome of (Insecta: Hymenoptera: Apidae)

The complete mitochondrial genome of <i>Apis mellifera jemenitica</i> (Insecta: Hymenoptera: Apidae), the Arabian honey bee

scientific article published on 27 January 2020

The complete mitochondrial genome of <i>Apis mellifera unicolor</i> (Insecta: Hymenoptera: Apidae), the Malagasy honey bee

scientific article published on 30 September 2019

The complete mitochondrial genome of <i>Apis nuluensis</i> Tingek, an Asian honey bee (Insecta: Hymenoptera: Apidae)

scientific article published on 17 August 2017

The complete mitochondrial genome of an east African honey bee, <i>Apis mellifera monticola</i> Smith (Insecta: Hymenoptera: Apidae)

scientific article published on 01 September 2017

The complete mitochondrial genome of the Cape honey bee, Apis mellifera capensis Esch. (Insecta: hymenoptera: apidae)

scholarly article by Amin Eimanifar et al published January 2016 in Mitochondrial DNA. Part B, Resources

The complete mitochondrial genome of the Egyptian honey bee, Apis mellifera lamarckii (Insecta: Hymenoptera: Apidae)

The complete mitochondrial genome of the West African honey bee <i>Apis mellifera adansonii</i> (Insecta: Hymenoptera: Apidae)

scientific article published on 09 December 2019

The complete mitochondrial genome of the hybrid honey bee, Apis mellifera capensis × Apis mellifera scutellata, from South Africa

article

The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach.

scientific article published in September 2014

The evolution of seminal ribonuclease: pseudogene reactivation or multiple gene inactivation events?

scientific article

The genome sequence of the filamentous fungus Neurospora crassa

scientific article

The mitochondrial genome of <i>Apis mellifera simensis</i> (Hymenoptera: Apidae), an Ethiopian honey bee

scientific article published on 10 December 2019

The mitochondrial genome of the Carniolan honey bee, <i>Apis mellifera carnica</i> (Insecta: Hymenoptera: Apidae)

scientific article published on 30 September 2019

The mitochondrial genome of the Maltese honey bee, <i>Apis mellifera ruttneri</i> (Insecta: Hymenoptera: Apidae)

scientific article published on 27 January 2020

The mitochondrial genome of the Spanish honey bee, <i>Apis mellifera iberiensis</i> (Insecta: Hymenoptera: Apidae), from Portugal

scientific article published on 09 December 2019

The nop-1 gene of Neurospora crassa encodes a seven transmembrane helix retinal-binding protein homologous to archaeal rhodopsins

scientific article

The two AGPase subunits evolve at different rates in angiosperms, yet they are equally sensitive to activity-altering amino acid changes when expressed in bacteria

scientific article published on 11 May 2007

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage.

scientific article

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

scientific article

Turtle isochore structure is intermediate between amphibians and other amniotes

scientific article published on 24 June 2008

Updating splits, lumps, and shuffles: Reconciling GenBank names with standardized avian taxonomies

scientific article published in 2022

What are the roles oftaxon sampling and model fit in tests ofcyto-nuclear discordance using avian mitogenomic data?

scientific article published on 12 October 2018

When good mitochondria go bad: Cyto-nuclear discordance in landfowl (Aves: Galliformes)

Whole genome phylogeny of Gallus: introgression and data-type effects

Whole genome sequence of the emerging oomycete pathogen Pythium insidiosum strain CDC-B5653 isolated from an infected human in the USA.

scientific article

Whole-genome analyses resolve early branches in the tree of life of modern birds

scientific article

Why do phylogenomic analyses of early animal evolution continue to disagree? Sites in different structural environments yield different answers

Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling

scientific article

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