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The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Anatomy of Amphibians and Reptiles
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CRISPR-Cas9 Gene Editing in Lizards through Microinjection of Unfertilized Oocytes
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Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages
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The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes
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Long walk to genomics: History and current approaches to genome sequencing and assembly
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The Deep Origin and Recent Loss of Venom Toxin Genes in Rattlesnakes
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Venomics of the Duvernoy's gland secretion of the false coral snake Rhinobothryum bovallii (Andersson, 1916) and assessment of venom lethality towards synapsid and diapsid animal models
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Attitudes and behaviour toward snakes on the part of Igbo people in southeastern Nigeria
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A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome
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How to choose your research organism
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Phylogenomics: the beginning of incongruence?
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Detecting Polygenic Evolution: Problems, Pitfalls, and Promises
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Transposable Element Domestication As an Adaptation to Evolutionary Conflicts
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Bradykinin-potentiating peptides: Beyond captopril
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Toxins and drug discovery
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Snake venoms: A brief treatise on etymology, origins of terminology, and definitions
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Coevolution of Genome Architecture and Social Behavior
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Phylogenetics is the New Genetics (for Most of Biodiversity)
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A reverse genetic approach in geckos with the CRISPR/Cas9 system by oocyte microinjection
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A phylogenomic analysis of turtles
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Adaptive evolution of animal toxin multigene families
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Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
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Initial sequencing and analysis of the human genome
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Initial sequencing and comparative analysis of the mouse genome
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Genome sequence of the Brown Norway rat yields insights into mammalian evolution
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
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Initial sequence of the chimpanzee genome and comparison with the human genome
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Early evolution of the venom system in lizards and snakes
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Changes in Hox genes’ structure and function during the evolution of the squamate body plan
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Climate-driven population divergence in sex-determining systems
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The genome of the green anole lizard and a comparative analysis with birds and mammals
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A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes
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Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper
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The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan
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Regulatory activities of transposable elements: from conflicts to benefits
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Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals
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Horizontal transfer and evolution of transposable elements in vertebrates
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Megaevolutionary dynamics and the timing of evolutionary innovation in reptiles
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Extensive introgression and mosaic genomes of Mediterranean endemic lizards
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Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila
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Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards
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Trends in peptide drug discovery
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The origin of squamates revealed by a Middle Triassic lizard from the Italian Alps
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The tuatara genome reveals ancient features of amniote evolution
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Dense sampling of bird diversity increases power of comparative genomics
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A comparative genomics multitool for scientific discovery and conservation
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Chromosome-scale genome assembly of the brown anole (Anolis sagrei), an emerging model species
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The Burmese python genome reveals the molecular basis for extreme adaptation in snakes
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The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system
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Rolling-circle transposons in eukaryotes
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Dynamics of genome size evolution in birds and mammals
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The Tiger Rattlesnake genome reveals a complex genotype underlying a simple venom phenotype
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The Earth BioGenome Project 2020: Starting the clock
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The Phylogenetic Definition of Reptilia
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Molecular Phylogenetics of Squamata: The Position of Snakes, Amphisbaenians, and Dibamids, and the Root of the Squamate Tree
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Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence
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Evil Animals in the Zoroastrian Religion
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Sex-specific effects of developmental temperature on morphology, growth and survival of offspring in a lizard with temperature-dependent sex determination
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Chromosome-Level Assembly of the Common Lizard (Zootoca vivipara) Genome
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Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing
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The Rattlesnake W Chromosome: A GC-Rich Retroelement Refugium with Retained Gene Function Across Ancient Evolutionary Strata
inferredcites →https://doi.org/10.1093/gbe/evq080openalex-snapshot
The Evolution and Diversity of DNA Transposons in the Genome of the Lizard Anolis carolinensis
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Lizards and LINEs: Selection and Demography Affect the Fate of L1 Retrotransposons in the Genome of the Green Anole (Anolis carolinensis)
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Multiple Lineages of Ancient CR1 Retroposons Shaped the Early Genome Evolution of Amniotes
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Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates
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Evolution and Diversity of Transposable Elements in Vertebrate Genomes
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Comparative Genomics Reveals Accelerated Evolution in Conserved Pathways during the Diversification of Anole Lizards
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Multiple and Independent Phases of Transposable Element Amplification in the Genomes of Piciformes (Woodpeckers and Allies)
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Genome size evolution in the diverse insect order Trichoptera
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How many species of mammals are there?
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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
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New Methods to Calculate Concordance Factors for Phylogenomic Datasets
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Genome-Scale Profiling Reveals Noncoding Loci Carry Higher Proportions of Concordant Data
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BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes
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Ancient Demographics Determine the Effectiveness of Genetic Purging in Endangered Lizards
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The Evolutionary Dynamics of Autonomous Non-LTR Retrotransposons in the Lizard Anolis Carolinensis Shows More Similarity to Fish Than Mammals
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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Large Numbers of Novel miRNAs Originate from DNA Transposons and Are Coincident with a Large Species Radiation in Bats
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Restriction Site-Associated DNA Sequencing (RAD-seq) Reveals an Extraordinary Number of Transitions among Gecko Sex-Determining Systems
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“Reverse Genomics” Predicts Function of Human Conserved Noncoding Elements
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Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
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TimeTree: A Resource for Timelines, Timetrees, and Divergence Times
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Quantity, Not Quality: Rapid Adaptation in a Polygenic Trait Proceeded Exclusively through Expression Differentiation
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Variations in mitochondrial tRNA gene organization of reptiles as phylogenetic markers.
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Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective
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A Genomic Perspective on the Evolutionary Diversification of Turtles
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Phylogenetic Analysis in the Anomaly Zone
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Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).
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Interrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships
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Facultative parthenogenesis discovered in wild vertebrates
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Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species
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Horizontal transfer and subsequent explosive expansion of a DNA transposon in sea kraits ( Laticauda )
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Accumulation of transposable elements inHoxgene clusters during adaptive radiation ofAnolislizards
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Genome size evolution: towards new model systems for old questions
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What's in a genome? The C-value enigma and the evolution of eukaryotic genome content
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Accurate Detection of Incomplete Lineage Sorting via Supervised Machine Learning
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Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
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The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes
inferredcites →https://doi.org/10.1101/gr.3715005openalex-snapshot
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
inferredcites →https://doi.org/10.1111/bij.12744openalex-snapshot
The emerging phylogenetic pattern of parthenogenesis in snakes
inferredcites →https://doi.org/10.1111/ele.12168openalex-snapshot
Early origin of viviparity and multiple reversions to oviparity in squamate reptiles
inferredcites →https://doi.org/10.1111/evo.12328openalex-snapshot
ANOLIS SEX CHROMOSOMES ARE DERIVED FROM A SINGLE ANCESTRAL PAIR
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IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?
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The Sequence of the Human Genome
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Unifying the Epidemiological and Evolutionary Dynamics of Pathogens
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Evolutionary and Biomedical Insights from the Rhesus Macaque Genome
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Who Speaks with a Forked Tongue?
inferredcites →https://doi.org/10.1126/science.1251385openalex-snapshot
Comparative genomics reveals insights into avian genome evolution and adaptation
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Genome Sequence of the Nematode C. elegans : A Platform for Investigating Biology
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The Genome Sequence of Drosophila melanogaster
inferredcites →https://doi.org/10.1126/science.aal3327openalex-snapshot
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
inferredcites →https://doi.org/10.1126/science.aat7244openalex-snapshot
Convergent regulatory evolution and loss of flight in paleognathous birds
inferredcites →https://doi.org/10.1126/science.abi8870openalex-snapshot
MIC-Drop: A platform for large-scale in vivo CRISPR screens
inferredcites →https://doi.org/10.1126/science.abn3943openalex-snapshot
Evolutionary constraint and innovation across hundreds of placental mammals
inferredcites →https://doi.org/10.1146/annurev-animal-090414-014900openalex-snapshot
The Genome 10K Project: A Way Forward
inferredcites →https://doi.org/10.1146/annurev.genet.40.110405.090448openalex-snapshot
DNA Transposons and the Evolution of Eukaryotic Genomes
inferredcites →https://doi.org/10.1146/annurev.genom.9.081307.164356openalex-snapshot
The Toxicogenomic Multiverse: Convergent Recruitment of Proteins Into Animal Venoms
inferredcites →https://doi.org/10.1159/000337126openalex-snapshot
The Evolutionary Dynamics of Transposable Elements in Eukaryote Genomes
inferredcites →https://doi.org/10.1159/000496416openalex-snapshot
The Mobilome of Reptiles: Evolution, Structure, and Function
inferredcites →https://doi.org/10.1186/1471-2148-13-93openalex-snapshot
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes
inferredcites →https://doi.org/10.1186/1745-6150-6-44openalex-snapshot
Families of transposable elements, population structure and the origin of species
inferredcites →https://doi.org/10.1186/gb-2012-13-6-r45openalex-snapshot
The genomic landscape shaped by selection on transposable elements across 18 mouse strains
inferredcites →https://doi.org/10.1186/gb-2013-14-3-r28openalex-snapshot
The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage
inferredcites →https://doi.org/10.1186/s12859-018-2129-yopenalex-snapshot
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
inferredcites →https://doi.org/10.1186/s12859-020-3382-4openalex-snapshot
Toward a more holistic method of genome assembly assessment
inferredcites →https://doi.org/10.1186/s12864-020-07227-0openalex-snapshot
A comprehensive evaluation of long read error correction methods
inferredcites →https://doi.org/10.1186/s13100-015-0041-9openalex-snapshot
Repbase Update, a database of repetitive elements in eukaryotic genomes
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Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome
inferredcites →https://doi.org/10.1186/s13100-020-00230-yopenalex-snapshot
The Dfam community resource of transposable element families, sequence models, and genome annotations
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Draft genome of the leopard gecko, Eublepharis macularius
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Cultural taboos as a factor in the participation rate of Native Americans in STEM
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Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
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Comparative Sex Chromosome Genomics in Snakes: Differentiation, Evolutionary Strata, and Lack of Global Dosage Compensation
inferredcites →https://doi.org/10.1371/journal.pgen.1002384openalex-snapshot
Repetitive Elements May Comprise Over Two-Thirds of the Human Genome
inferredcites →https://doi.org/10.1371/journal.pgen.1009082openalex-snapshot
Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations
inferredcites →https://doi.org/10.1371/journal.pone.0177708openalex-snapshot
The Agassiz’s desert tortoise genome provides a resource for the conservation of a threatened species
inferredcites →https://doi.org/10.1371/journal.pone.0204188openalex-snapshot
Warmer and wetter conditions will reduce offspring production of hawksbill turtles in Brazil under climate change
inferredcites →https://doi.org/10.1534/g3.115.020578openalex-snapshot
Post-transcriptional Mechanisms Contribute Little to Phenotypic Variation in Snake Venoms
inferredcites →https://doi.org/10.1638/2012-0022r.1openalex-snapshot
ANAEROBIC AND AEROBIC BACTERIOLOGY OF THE SALIVA AND GINGIVA FROM 16 CAPTIVE KOMODO DRAGONS (VARANUS KOMODOENSIS): NEW IMPLICATIONS FOR THE “BACTERIA AS VENOM” MODEL
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Snake Venom: From Deadly Toxins to Life-saving Therapeutics
inferredcites →https://doi.org/10.2174/1389202023350499openalex-snapshot
The Use of Phylogenetic Profiles for Gene Predictions
inferredcites →https://doi.org/10.3374/014.053.0101openalex-snapshot
Assembling the Squamate Tree of Life: Perspectives from the Phenotype and the Fossil Record
inferredcites →https://doi.org/10.3389/fphys.2018.00278openalex-snapshot
Skull Development, Ossification Pattern, and Adult Shape in the Emerging Lizard Model Organism Pogona vitticeps: A Comparative Analysis With Other Squamates
inferredcites →https://doi.org/10.3390/genes10060419openalex-snapshot
On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements
inferredcites →https://doi.org/10.3390/rel10080454openalex-snapshot
Cobra Deities and Divine Cobras: The Ambiguous Animality of Nāgas
inferredcites →https://doi.org/10.3390/toxins9080242openalex-snapshot
Enter the Dragon: The Dynamic and Multifunctional Evolution of Anguimorpha Lizard Venoms
inferredcites →https://doi.org/10.4161/mge.1.2.17733openalex-snapshot
The transposable element profile of the Anolis genome
inferredcites →https://doi.org/10.7717/peerj.1660openalex-snapshot
AMAS: a fast tool for alignment manipulation and computing of summary statistics
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.11646/zootaxa.5722.2.1zenodo-depositor-declared
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inferred← citeshttps://doi.org/10.1038/s41577-024-01083-9openalex-snapshot
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inferred← citeshttps://doi.org/10.1080/14772019.2026.2711806openalex-snapshot
Lepidosauria: history and relationships
inferred← citeshttps://doi.org/10.1093/g3journal/jkaf302openalex-snapshot
Telomere-to-telomere reference genome of the common five-lined skink, Plestiodon fasciatus (Squamata: Scincidae)
inferred← citeshttps://doi.org/10.1093/gbe/evae157openalex-snapshot
Differential Conservation and Loss of Chicken Repeat 1 (CR1) Retrotransposons in Squamates Reveal Lineage-Specific Genome Dynamics Across Reptiles
inferred← citeshttps://doi.org/10.1093/gbe/evaf196openalex-snapshot
Structural Rearrangements and Selection Promote Phenotypic Evolution in Anolis Lizards
inferred← citeshttps://doi.org/10.1093/gbe/evaf228openalex-snapshot
Ancestral Chromosome-Level Assemblies Reveal Posthybridization Genome Evolution in the New Mexico Whiptail Lizard ( Aspidoscelis neomexicanus )
inferred← citeshttps://doi.org/10.1093/gigascience/giaf079openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/jhered/esae026openalex-snapshot
Whole snake genomes from eighteen families of snakes (Serpentes: Caenophidia) and their applications to systematics
inferred← citeshttps://doi.org/10.1093/molbev/msag067openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/sysbio/syae032openalex-snapshot
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inferred← citeshttps://doi.org/10.1146/annurev-ecolsys-102723-050400openalex-snapshot
Origin and Early Evolution of Squamates and Their Kin: From Fossils to Genomes
inferred← citeshttps://doi.org/10.1186/s12915-026-02540-8openalex-snapshot
Chromosomal rearrangements and segmental deletions contribute to gene loss in squamates
inferred← citeshttps://doi.org/10.1371/journal.pone.0350380openalex-snapshot
Highly contiguous reference genome assembly of the endangered Orcés’ blue whiptail Holcosus orcesi
inferred← citeshttps://doi.org/10.2139/ssrn.6170240openalex-snapshot
Disagreement among Genomic Markers Profoundly Influences Phylogenetic Inference in Squamates
inferred← citeshttps://doi.org/10.3390/d17090638openalex-snapshot
Thermal Ecology of Hermann’s Tortoise, Testudo hermanni and Glass Lizard Pseudopus apodus in a Seasonal Environment
inferred← citeshttps://doi.org/10.3390/genes15030371openalex-snapshot
Karyotype Diversification and Chromosome Rearrangements in Squamate Reptiles
inferred← citeshttps://doi.org/10.3390/toxins16110458openalex-snapshot
Current Technologies in Snake Venom Analysis and Applications
inferred← citeshttps://doi.org/10.64898/2026.04.01.715795openalex-snapshot
A versatile cryopreservation method for peri-gastrulation squamate embryos optimised using the veiled chameleon ( C. calyptratus )
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