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Evolutionary Fingerprinting of Genes
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1007/978-3-540-39189-0_1openalex-snapshot
Lecture Notes on Optimal Transport Problems
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Kernel principal component analysis
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On the Translocation of Masses
inferredcites →https://doi.org/10.1016/0303-2647(83)90031-xopenalex-snapshot
Evidence that natural selection acts on silent mutation
inferredcites →https://doi.org/10.1016/j.gde.2003.10.007openalex-snapshot
Adaptive evolution of genes and gene families
inferredcites →https://doi.org/10.1016/j.virol.2005.03.014openalex-snapshot
Codon volatility does not reflect selective pressure on the HIV-1 genome
inferredcites →https://doi.org/10.1016/s0168-9525(00)02173-9openalex-snapshot
Evidence for purifying selection acting on silent sites in BRCA1
inferredcites →https://doi.org/10.1017/cbo9780511809682openalex-snapshot
Kernel Methods for Pattern Analysis
inferredcites →https://doi.org/10.1017/s0016672303006128openalex-snapshot
Potential impact of recombination on sitewise approaches for detecting positive natural selection
inferredcites →https://doi.org/10.1017/s1355838202554066openalex-snapshot
Thermodynamic and phylogenetic prediction of RNA secondary structures in the coding region of hepatitis C virus
inferredcites →https://doi.org/10.1038/nrg1770openalex-snapshot
Hearing silence: non-neutral evolution at synonymous sites in mammals
inferredcites →https://doi.org/10.1073/pnas.0508279103openalex-snapshot
A Dirichlet process model for detecting positive selection in protein-coding DNA sequences
inferredcites →https://doi.org/10.1093/bioinformatics/bti079openalex-snapshot
HyPhy: hypothesis testing using phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/bti320openalex-snapshot
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
inferredcites →https://doi.org/10.1093/bioinformatics/btl427openalex-snapshot
Robust inference of positive selection from recombining coding sequences
inferredcites →https://doi.org/10.1093/genetics/138.1.191openalex-snapshot
Selection on silent sites in the rodent H3 histone gene family.
inferredcites →https://doi.org/10.1093/genetics/148.3.929openalex-snapshot
Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene
inferredcites →https://doi.org/10.1093/genetics/155.1.431openalex-snapshot
Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites
inferredcites →https://doi.org/10.1093/genetics/164.3.1229openalex-snapshot
Effect of Recombination on the Accuracy of the Likelihood Method for Detecting Positive Selection at Amino Acid Sites
inferredcites →https://doi.org/10.1093/molbev/msi031openalex-snapshot
A Genetic Algorithm Approach to Detecting Lineage-Specific Variation in Selection Pressure
inferredcites →https://doi.org/10.1093/molbev/msi097openalex-snapshot
Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection
inferredcites →https://doi.org/10.1093/molbev/msi105openalex-snapshot
Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection
inferredcites →https://doi.org/10.1093/molbev/msi232openalex-snapshot
Site-to-Site Variation of Synonymous Substitution Rates
inferredcites →https://doi.org/10.1093/molbev/msl051openalex-snapshot
Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm
inferredcites →https://doi.org/10.1093/molbev/msl144openalex-snapshot
Evolutionary Model Selection with a Genetic Algorithm: A Case Study Using Stem RNA
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/oxfordjournals.molbev.a003981openalex-snapshot
Codon-Substitution Models to Detect Adaptive Evolution that Account for Heterogeneous Selective Pressures Among Site Classes
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004233openalex-snapshot
Pervasive Adaptive Evolution in Mammalian Fertilization Proteins
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040023openalex-snapshot
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040152openalex-snapshot
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040200openalex-snapshot
Positive selection is a general phenomenon in the evolution of abalone sperm lysin.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040454openalex-snapshot
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
inferredcites →https://doi.org/10.1099/vir.0.80141-0openalex-snapshot
Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods
inferredcites →https://doi.org/10.1109/iccv.1998.710701openalex-snapshot
A metric for distributions with applications to image databases
inferredcites →https://doi.org/10.1128/jvi.02005-07openalex-snapshot
The Influenza Virus Resource at the National Center for Biotechnology Information
inferredcites →https://doi.org/10.1128/jvi.73.12.10489-10502.1999openalex-snapshot
Consistent Viral Evolutionary Changes Associated with the Progression of Human Immunodeficiency Virus Type 1 Infection
inferredcites →https://doi.org/10.1128/jvi.78.4.1962-1970.2004openalex-snapshot
Comparative Study of Adaptive Molecular Evolution in Different Human Immunodeficiency Virus Groups and Subtypes
inferredcites →https://doi.org/10.1136/bmj.295.6599.646openalex-snapshot
Methods in molecular medicine.
inferredcites →https://doi.org/10.1371/journal.pbio.0020275openalex-snapshot
Ancient Adaptive Evolution of the Primate Antiviral DNA-Editing Enzyme APOBEC3G
inferredcites →https://doi.org/10.1371/journal.pbio.0030170openalex-snapshot
A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees
inferredcites →https://doi.org/10.1371/journal.pcbi.0020038openalex-snapshot
Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome
inferredcites →https://doi.org/10.1371/journal.pcbi.0020062openalex-snapshot
Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses
inferredcites →https://doi.org/10.1385/0-89603-521-2:133openalex-snapshot
Hepatitis C Virus: Types, Subtypes, and Beyond
inferredcites →https://doi.org/10.2307/1911491openalex-snapshot
A Method for Minimizing the Impact of Distributional Assumptions in Econometric Models for Duration Data
inferredcites →https://doi.org/10.2307/2289460openalex-snapshot
The Calculation of Posterior Distributions by Data Augmentation: Comment: A Noniterative Sampling/Importance Resampling Alternative to the Data Augmentation Algorithm for Creating a Few Imputations When Fractions of Missing Information Are Modest: The SIR Algorithm
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/ece3.2919openalex-snapshot
Adaptive molecular evolution of MC 1R gene reveals the evidence for positive diversifying selection in indigenous goat populations
inferred← citeshttps://doi.org/10.1007/s11434-011-4380-8openalex-snapshot
Prediction of sites under adaptive evolution in flavin-containing monooxygenases: Selection pattern revisited
inferred← citeshttps://doi.org/10.1007/s13258-021-01188-8openalex-snapshot
Deduction and exploration of the evolution and function of vertebrate GFPT family
inferred← citeshttps://doi.org/10.1016/b978-0-12-820472-6.00100-6openalex-snapshot
Personalized Medicine Through GPCR Pharmacogenomics
inferred← citeshttps://doi.org/10.1016/j.jprot.2014.01.013openalex-snapshot
Intraspecific venom variation in the medically significant Southern Pacific Rattlesnake (Crotalus oreganus helleri): Biodiscovery, clinical and evolutionary implications
inferred← citeshttps://doi.org/10.1016/j.jprot.2014.02.024openalex-snapshot
Multifunctional warheads: Diversification of the toxin arsenal of centipedes via novel multidomain transcripts
inferred← citeshttps://doi.org/10.1016/j.margen.2019.03.001openalex-snapshot
Extremophile deep-sea viral communities from hydrothermal vents: Structural and functional analysis
inferred← citeshttps://doi.org/10.1016/j.virusres.2024.199397openalex-snapshot
Cassava brown streak virus evolves with a nucleotide-substitution rate that is typical for the family Potyviridae
inferred← citeshttps://doi.org/10.1016/j.ympev.2012.09.030openalex-snapshot
Capsid protein evolution and comparative phylogeny of novel porcine parvoviruses
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.04.024openalex-snapshot
Evolution of circoviruses in lorikeets lags behind its hosts
inferred← citeshttps://doi.org/10.1038/ncomms4521openalex-snapshot
Evolution of separate predation- and defence-evoked venoms in carnivorous cone snails
inferred← citeshttps://doi.org/10.1038/s41598-017-10245-wopenalex-snapshot
REST, a master regulator of neurogenesis, evolved under strong positive selection in humans and in non human primates
inferred← citeshttps://doi.org/10.1039/c2ib20081copenalex-snapshot
The coordinated expression, interaction and evolution of the neuroendocrine genes
inferred← citeshttps://doi.org/10.1074/mcp.m112.023135openalex-snapshot
Differential Evolution and Neofunctionalization of Snake Venom Metalloprotease Domains
inferred← citeshttps://doi.org/10.1093/acprof:osobl/9780199601165.003.0006openalex-snapshot
Detecting and understanding natural selection
inferred← citeshttps://doi.org/10.1093/bioinformatics/btq429openalex-snapshot
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology
inferred← citeshttps://doi.org/10.1093/infdis/jix184openalex-snapshot
Molecular Features of the V1–V4 Coding Region of Sexually Transmitted Human Immunodeficiency Virus Type 1
inferred← citeshttps://doi.org/10.1093/molbev/msr125openalex-snapshot
A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection
inferred← citeshttps://doi.org/10.1093/molbev/msr170openalex-snapshot
Purifying Selection Can Obscure the Ancient Age of Viral Lineages
inferred← citeshttps://doi.org/10.1093/molbev/msr202openalex-snapshot
Statistics and Truth in Phylogenomics
inferred← citeshttps://doi.org/10.1093/molbev/msr266openalex-snapshot
Inconsistencies in Estimating the Age of HIV-1 Subtypes Due to Heterotachy
inferred← citeshttps://doi.org/10.1093/molbev/mss058openalex-snapshot
Evolution of CRISPs Associated with Toxicoferan-Reptilian Venom and Mammalian Reproduction
inferred← citeshttps://doi.org/10.1093/molbev/mss217openalex-snapshot
Integrating Sequence Variation and Protein Structure to Identify Sites under Selection
inferred← citeshttps://doi.org/10.1093/molbev/msu185openalex-snapshot
Evolutionary Origins of Human Herpes Simplex Viruses 1 and 2
inferred← citeshttps://doi.org/10.1093/molbev/msu400openalex-snapshot
RELAX: Detecting Relaxed Selection in a Phylogenetic Framework
inferred← citeshttps://doi.org/10.1093/molbev/msv022openalex-snapshot
Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection
inferred← citeshttps://doi.org/10.1093/molbev/msx335openalex-snapshot
Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes
inferred← citeshttps://doi.org/10.1093/molbev/msz197openalex-snapshot
HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies
inferred← citeshttps://doi.org/10.1098/rspb.2013.0965openalex-snapshot
Suppressors of RNAi from plant viruses are subject to episodic positive selection
inferred← citeshttps://doi.org/10.1098/rspb.2015.3115openalex-snapshot
Adaptive tolerance to a pathogenic fungus drives major histocompatibility complex evolution in natural amphibian populations
inferred← citeshttps://doi.org/10.1098/rstb.2014.0244openalex-snapshot
Quantifying evolutionary constraints on B-cell affinity maturation
inferred← citeshttps://doi.org/10.1101/2020.06.25.170688openalex-snapshot
Molecular Evolution of SARS-CoV-2 Structural Genes: Evidence of Positive Selection in Spike Glycoprotein
inferred← citeshttps://doi.org/10.1111/1755-0998.13511openalex-snapshot
Improved high‐throughput MHC typing for non‐model species using long‐read sequencing
inferred← citeshttps://doi.org/10.1111/cla.12100openalex-snapshot
Phylogeny and historical biogeography of the cocosoid palms ( A recaceae, A recoideae, C ocoseae) inferred from sequences of six WRKY gene family loci
inferred← citeshttps://doi.org/10.1111/imb.12068openalex-snapshot
Positive selection drives accelerated evolution of mosquito salivary genes associated with blood‐feeding
inferred← citeshttps://doi.org/10.1111/j.1467-9868.2011.01018.xopenalex-snapshot
The Phylogenetic Kantorovich–Rubinstein Metric for Environmental Sequence Samples
inferred← citeshttps://doi.org/10.1128/jvi.00972-16openalex-snapshot
The Evolutionary Histories of Antiretroviral Proteins SERINC3 and SERINC5 Do Not Support an Evolutionary Arms Race in Primates
inferred← citeshttps://doi.org/10.1128/jvi.03273-12openalex-snapshot
A Case for the Ancient Origin of Coronaviruses
inferred← citeshttps://doi.org/10.1145/2700293openalex-snapshot
Parallel Massive Clustering of Discrete Distributions
inferred← citeshttps://doi.org/10.1186/1471-2148-12-179openalex-snapshot
Modeling coding-sequence evolution within the context of residue solvent accessibility
inferred← citeshttps://doi.org/10.1186/1471-2148-13-164openalex-snapshot
Synonymous site conservation in the HIV-1 genome
inferred← citeshttps://doi.org/10.1186/1471-2148-13-76openalex-snapshot
Hippo pathway genes developed varied exon numbers and coevolved functional domains in metazoans for species specific growth control
inferred← citeshttps://doi.org/10.1186/1741-7015-10-140openalex-snapshot
Mammalian NPC1 genes may undergo positive selection and human polymorphisms associate with type 2 diabetes
inferred← citeshttps://doi.org/10.1186/s12859-015-0688-8openalex-snapshot
Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix
inferred← citeshttps://doi.org/10.1186/s12862-015-0411-4openalex-snapshot
Positive selection in octopus haemocyanin indicates functional links to temperature adaptation
inferred← citeshttps://doi.org/10.1186/s13059-015-0603-7openalex-snapshot
FRESCo: finding regions of excess synonymous constraint in diverse viruses
inferred← citeshttps://doi.org/10.1186/s13071-024-06545-6openalex-snapshot
Low nucleotide diversity of the Plasmodium falciparum AP2-EXP2 gene among clinical samples from Ghana
inferred← citeshttps://doi.org/10.1371/annotation/accecc73-91b2-45d4-bb33-774b1f394ca1openalex-snapshot
Correction: Molecular Evolution of Vertebrate Neurotrophins: Co-Option of the Highly Conserved Nerve Growth Factor Gene into the Advanced Snake Venom Arsenalf
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1000885openalex-snapshot
CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences
inferred← citeshttps://doi.org/10.1371/journal.pgen.1002764openalex-snapshot
Detecting Individual Sites Subject to Episodic Diversifying Selection
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Nmf9 Encodes a Highly Conserved Protein Important to Neurological Function in Mice and Flies
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Molecular Evolution of Vertebrate Neurotrophins: Co-Option of the Highly Conserved Nerve Growth Factor Gene into the Advanced Snake Venom Arsenalf
inferred← citeshttps://doi.org/10.1371/journal.ppat.1000884openalex-snapshot
Phylodynamic Reconstruction Reveals Norovirus GII.4 Epidemic Expansions and their Molecular Determinants
inferred← citeshttps://doi.org/10.1371/journal.ppat.1014457openalex-snapshot
Selection profiles in RNA viruses reflect the characteristics of viruses more than individual proteins
inferred← citeshttps://doi.org/10.20944/preprints201905.0002.v1openalex-snapshot
Why the Monophyly of Nymphaeaceae Currently Remains Indeterminate: An Assessment Based on Gene-Wise Plastid Phylogenomics
inferred← citeshttps://doi.org/10.21203/rs.3.rs-42498/v2openalex-snapshot
Molecular Evolution of SARS-CoV-2 Structural Genes: Evidence of Positive Selection in the Spike Glycoprotein
inferred← citeshttps://doi.org/10.3389/fvets.2021.794228openalex-snapshot
Molecular Characterization of Infectious Bronchitis Virus Strain HH06 Isolated in a Poultry Farm in Northeastern China
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Atractaspis aterrima Toxins: The First Insight into the Molecular Evolution of Venom in Side-Stabbers
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Three-Fingered RAVERs: Rapid Accumulation of Variations in Exposed Residues of Snake Venom Toxins
inferred← citeshttps://doi.org/10.3390/toxins5122456openalex-snapshot
Evolution Stings: The Origin and Diversification of Scorpion Toxin Peptide Scaffolds
inferred← citeshttps://doi.org/10.3390/toxins5122621openalex-snapshot
Venom Down Under: Dynamic Evolution of Australian Elapid Snake Toxins
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Complete Genome Sequence of Germline Chromosomally Integrated Human Herpesvirus 6A and Analyses Integration Sites Define a New Human Endogenous Virus with Potential to Reactivate as an Emerging Infection
inferred← citeshttps://doi.org/10.3929/ethz-a-010380340openalex-snapshot
Investigations into the relationship between evolutionary rate variation, protein structure and codon usage
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Quantifying evolutionary constraints on B cell affinity maturation
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Evolutionary fingerprinting of protein-coding genes in RNA viruses
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