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Comparative Genomics and Genome Evolution in birds-of-paradise
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Transposable elements: powerful facilitators of evolution
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Expression profile of Papss2 (3′‐phosphoadenosine 5′‐phosphosulfate synthase 2) during cartilage formation and skeletal development in the mouse embryo
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Transposable elements and viruses as factors in adaptation and evolution: an expansion and strengthening of the TE ‐Thrust hypothesis
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Phylogenetic Relationships among the Major Lineages of the Birds-of-Paradise (Paradisaeidae) Using Mitochondrial DNA Gene Sequences
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Polar amplification of climate change in coupled models
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Ovaries and Female Phenotype in a Girl with 46,XY Karyotype and Mutations in the CBX2 Gene
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Inhibition of lipolysis does not affect insulin sensitivity to glucose uptake in the mourning dove
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Glucose regulation in birds
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Glucose uptake in vivo in skeletal muscles of insulin-injected chicks
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Red Carotenoid Coloration in the Zebra Finch Is Controlled by a Cytochrome P450 Gene Cluster
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APOBEC2 mRNA and protein is predominantly expressed in skeletal and cardiac muscles of chickens
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Degenerative knee joint disease in mice lacking 3′-phosphoadenosine 5′-phosphosulfate synthetase 2 (Papss2) activity: a putative model of human PAPSS2 deficiency-associated arthrosis
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SLC5A9/SGLT4, a new Na+-dependent glucose transporter, is an essential transporter for mannose, 1,5-anhydro-D-glucitol, and fructose
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Evolutionary stasis: the stable chromosomes of birds
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Nature and localization of avian lens glycogen by electron microscopy and Raman spectroscopy
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The Color Loci of Mice – A Genetic Century
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Male development of chromosomally female mice transgenic for Sry
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Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
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The effects of life history and sexual selection on male and female plumage colouration
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Evolutionary analysis of the female-specific avian W chromosome
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Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle
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The molecular scaffold Gab2 is a crucial component of RANK signaling and osteoclastogenesis
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Essential role of Ca2+-binding protein 4, a Cav1.4 channel regulator, in photoreceptor synaptic function
inferredcites →https://doi.org/10.1038/nrg2337openalex-snapshot
Transposable elements and the evolution of regulatory networks
inferredcites →https://doi.org/10.1046/j.1365-2699.2001.00600.xopenalex-snapshot
Birds of paradise, biogeography and ecology in New Guinea: a review
inferredcites →https://doi.org/10.1046/j.1365-2699.2002.00667.xopenalex-snapshot
Birds of paradise, vicariance biogeography and terrane tectonics in New Guinea
inferredcites →https://doi.org/10.1071/zo9920343openalex-snapshot
Relationships Among the Birds-of-Paradise (Paradisaeidae) and Bowerbirds (Ptilonorhynchidae) - Protein Evidence
inferredcites →https://doi.org/10.1073/pnas.0409137102openalex-snapshot
An algorithm for progressive multiple alignment of sequences with insertions
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Stra8 and its inducer, retinoic acid, regulate meiotic initiation in both spermatogenesis and oogenesis in mice
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High-quality draft assemblies of mammalian genomes from massively parallel sequence data
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Sparkling feather reflections of a bird-of-paradise explained by finite-difference time-domain modeling
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Coloration strategies in peacock feathers
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Identification of a photoreceptor cell-specific nuclear receptor
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Five Members of a Novel Ca2+-binding Protein (CABP) Subfamily with Similarity to Calmodulin
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Inferring Phylogeny Despite Incomplete Lineage Sorting
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RANKL-induced DC-STAMP Is Essential for Osteoclastogenesis
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Sensory Drive, Color, and Color Vision
inferredcites →https://doi.org/10.1089/dna.1992.11.661openalex-snapshot
Molecular Cloning and Functional Characterization of Chicken Cathepsin D, a Key Enzyme for Yolk Formation
inferredcites →https://doi.org/10.1093/bib/bbn013openalex-snapshot
Recent developments in the MAFFT multiple sequence alignment program
inferredcites →https://doi.org/10.1093/bioinformatics/13.5.555openalex-snapshot
PAML: a program package for phylogenetic analysis by maximum likelihood
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r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
inferredcites →https://doi.org/10.1093/bioinformatics/btg1080openalex-snapshot
Gene prediction with a hidden Markov model and a new intron submodel
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CAFE: a computational tool for the study of gene family evolution
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TimeTree: a public knowledge-base of divergence times among organisms
inferredcites →https://doi.org/10.1093/bioinformatics/btm071openalex-snapshot
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
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bioDBnet: the biological database network
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Fast and accurate short read alignment with Burrows–Wheeler transform
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The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btq102openalex-snapshot
Genome-wide synteny through highly sensitive sequence alignment: Satsuma
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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ASTRAL: genome-scale coalescent-based species tree estimation
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ExaML version 3: a tool for phylogenomic analyses on supercomputers
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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
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Female Marmoset Monkeys (Callithrix jacchus) Can Be Identified from the Chemical Composition of their Scent Marks
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Histological Properties of the Nasal Cavity and Olfactory Bulb of the Japanese Jungle Crow Corvus macrorhynchos
inferredcites →https://doi.org/10.1093/gbe/evv005openalex-snapshot
Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates
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Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies
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A novel common variant in DCST2 is associated with length in early life and height in adulthood
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The Evolution of Avian Senescence Patterns: Implications for Understanding Primary Aging Processes
inferredcites →https://doi.org/10.1093/molbev/mst100openalex-snapshot
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inferredcites →https://doi.org/10.1093/molbev/msv035openalex-snapshot
Gene-Wide Identification of Episodic Selection
inferredcites →https://doi.org/10.1093/molbev/msv155openalex-snapshot
Olfactory Receptor Subgenomes Linked with Broad Ecological Adaptations in Sauropsida
inferredcites →https://doi.org/10.1093/molbev/msv239openalex-snapshot
DNA Editing of LTR Retrotransposons Reveals the Impact of APOBECs on Vertebrate Genomes
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/27.2.573openalex-snapshot
Tandem repeats finder: a program to analyze DNA sequences
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An efficient algorithm for large-scale detection of protein families
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Accelerated Ovarian Aging in the Absence of the Transcription Regulator TAF4B in Mice1
inferredcites →https://doi.org/10.1097/prs.0000000000000517openalex-snapshot
Functional Analysis of SPECC1L in Craniofacial Development and Oblique Facial Cleft Pathogenesis
inferredcites →https://doi.org/10.1098/rspb.2010.2293openalex-snapshot
Dramatic colour changes in a bird of paradise caused by uniquely structured breast feather barbules
inferredcites →https://doi.org/10.1098/rspb.2011.0238openalex-snapshot
Evolution of olfaction in non-avian theropod dinosaurs and birds
inferredcites →https://doi.org/10.1098/rspb.2014.2321openalex-snapshot
Evolution of opsin expression in birds driven by sexual selection and habitat
inferredcites →https://doi.org/10.1098/rspb.2016.1208openalex-snapshot
Seeing red to being red: conserved genetic mechanism for red cone oil droplets and co-option for red coloration in birds and turtles
inferredcites →https://doi.org/10.1098/rstb.2016.0338openalex-snapshot
Coevolution of coloration and colour vision?
inferredcites →https://doi.org/10.1101/gr.092759.109openalex-snapshot
Circos: An information aesthetic for comparative genomics
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1101/gr.126953.111openalex-snapshot
Efficient de novo assembly of large genomes using compressed data structures
inferredcites →https://doi.org/10.1101/gr.88502openalex-snapshot
Automated De Novo Identification of Repeat Sequence Families in Sequenced Genomes
inferredcites →https://doi.org/10.1101/pdb.prot5448openalex-snapshot
Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing
inferredcites →https://doi.org/10.1111/j.1463-6409.2006.00249.xopenalex-snapshot
Nuclear DNA from old collections of avian study skins reveals the evolutionary history of the Old World suboscines (Aves, Passeriformes)
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The role of chemical communication in mate choice
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ENMTools: a toolbox for comparative studies of environmental niche models
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Unlocking the vault: next‐generation museum population genomics
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Abundant recent activity of retrovirus‐like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes
inferredcites →https://doi.org/10.1111/nyas.13295openalex-snapshot
Evolution of bird genomes—a transposon's‐eye view
inferredcites →https://doi.org/10.1111/zsc.12213openalex-snapshot
The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves
inferredcites →https://doi.org/10.1113/jphysiol.2007.135582openalex-snapshot
Calcium‐dependent inactivation of calcium channels in cochlear hair cells of the chicken
inferredcites →https://doi.org/10.1126/science.1181369openalex-snapshot
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
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Three Periods of Regulatory Innovation During Vertebrate Evolution
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Reconstruction of Microraptor and the Evolution of Iridescent Plumage
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Statistical binning enables an accurate coalescent-based estimation of the avian tree
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Comparative genomics reveals insights into avian genome evolution and adaptation
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The genomic landscape underlying phenotypic integrity in the face of gene flow in crows
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Whole-genome analyses resolve early branches in the tree of life of modern birds
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Mice: Individual Recognition by Olfactory Cues
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Human Insulin-Degrading Enzyme Shares Structural and Functional Homologies with E. coli Protease III
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MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
inferredcites →https://doi.org/10.1186/1471-2148-9-235openalex-snapshot
An unexpectedly long history of sexual selection in birds-of-paradise
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Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees
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Families of transposable elements, population structure and the origin of species
inferredcites →https://doi.org/10.1186/1759-8753-4-21openalex-snapshot
Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera
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SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
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ANGSD: Analysis of Next Generation Sequencing Data
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De-novo emergence of SINE retroposons during the early evolution of passerine birds
inferredcites →https://doi.org/10.1210/en.2011-1055openalex-snapshot
Cbx2, a Polycomb Group Gene, Is Required for Sry Gene Expression in Mice
inferredcites →https://doi.org/10.1242/dev.127.23.5213openalex-snapshot
Delta 1-activated Notch inhibits muscle differentiation without affecting Myf5 and Pax3 expression in chick limb myogenesis
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The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds
inferredcites →https://doi.org/10.1371/journal.pgen.1000003openalex-snapshot
The Secreted Metalloprotease ADAMTS20 Is Required for Melanoblast Survival
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Spag16, an Axonemal Central Apparatus Gene, Encodes a Male Germ Cell Nuclear Speckle Protein that Regulates SPAG16 mRNA Expression
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Orthology Detection Combining Clustering and Synteny for Very Large Datasets
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Animal Biochromes and Structural Colours
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Effects of pancreatectomy, tolbutamide and insulin on glucose fluxes in chickens
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Glucose-6-Phosphatase Structure, Regulation, and Function: An Update
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Sex- and tissue-specific expression of “similar to nothepsin” and cathepsin D in relation to egg yolk formation in Gallus gallus
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Role of the P-Type ATPases, ATP7A and ATP7B in brain copper homeostasis
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/ece3.72962openalex-snapshot
The Genetic and Morphological Basis of Local Adaptation to Elevational Extremes in an Alpine Finch
inferred← citeshttps://doi.org/10.1038/s41437-020-0298-8openalex-snapshot
Rapid morphological divergence following a human-mediated introduction: the role of drift and directional selection
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