On the public citation graph

FastML: a web server for probabilistic reconstruction of ancestral sequences

0 signed · 367 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.

Claim with ORCID

Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.

See reference health

What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/bf00160154openalex-snapshot

Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods

inferredcites →https://doi.org/10.1007/bf02101694openalex-snapshot

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

inferredcites →https://doi.org/10.1007/bf02198858openalex-snapshot

Probabilistic reconstruction of ancestral protein sequences

inferredcites →https://doi.org/10.1007/bf02498640openalex-snapshot

Model of Amino Acid Substitution in Proteins Encoded by Mitochondrial DNA

inferredcites →https://doi.org/10.1007/s002399910038openalex-snapshot

Plastid Genome Phylogeny and a Model of Amino Acid Substitution for Proteins Encoded by Chloroplast DNA

inferredcites →https://doi.org/10.1016/b978-1-4832-3210-2.50006-6openalex-snapshot

Mammalian Protein Metabolism

inferredcites →https://doi.org/10.1016/j.cbpa.2011.03.005openalex-snapshot

Utilizing natural diversity to evolve protein function: applications towards thermostability

inferredcites →https://doi.org/10.1093/acprof:oso/9780199299188.001.0001openalex-snapshot

Ancestral Sequence Reconstruction

inferredcites →https://doi.org/10.1093/bioinformatics/18.8.1116openalex-snapshot

A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families

inferredcites →https://doi.org/10.1093/bioinformatics/8.3.275openalex-snapshot

The rapid generation of mutation data matrices from protein sequences

inferredcites →https://doi.org/10.1093/bioinformatics/bti191openalex-snapshot

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees

inferredcites →https://doi.org/10.1093/bioinformatics/btp033openalex-snapshot

Jalview Version 2—a multiple sequence alignment editor and analysis workbench

inferredcites →https://doi.org/10.1093/bioinformatics/btq651openalex-snapshot

maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences

inferredcites →https://doi.org/10.1093/bioinformatics/btr219openalex-snapshot

Accurate estimation of heritability in genome wide studies using random effects models

inferredcites →https://doi.org/10.1093/gbe/evr101openalex-snapshot

Inference of Gain and Loss Events from Phyletic Patterns Using Stochastic Mapping and Maximum Parsimony—A Simulation Study

inferredcites →https://doi.org/10.1093/genetics/141.4.1641openalex-snapshot

A new method of inference of ancestral nucleotide and amino acid sequences.

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/molbev/msh198openalex-snapshot

Ancestral Sequence Reconstruction in Primate Mitochondrial DNA: Compositional Bias and Effect on Functional Inference

inferredcites →https://doi.org/10.1093/molbev/msl175openalex-snapshot

A Combined Empirical and Mechanistic Codon Model

inferredcites →https://doi.org/10.1093/molbev/msn067openalex-snapshot

An Improved General Amino Acid Replacement Matrix

inferredcites →https://doi.org/10.1093/nar/gki198openalex-snapshot

MAFFT version 5: improvement in accuracy of multiple sequence alignment

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003851openalex-snapshot

A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004211openalex-snapshot

Recreating a Functional Ancestral Archosaur Visual Pigment

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026369openalex-snapshot

A Fast Algorithm for Joint Reconstruction of Ancestral Amino Acid Sequences

inferredcites →https://doi.org/10.1093/sysbio/49.2.369openalex-snapshot

Gaps as Characters in Sequence-Based Phylogenetic Analyses

inferredcites →https://doi.org/10.1098/rstb.2008.0177openalex-snapshot

A likelihood framework to analyse phyletic patterns

inferredcites →https://doi.org/10.1101/gr.2800104openalex-snapshot

Reconstructing large regions of an ancestral mammalian genome in silico

inferredcites →https://doi.org/10.1101/gr.849004openalex-snapshot

WebLogo: A Sequence Logo Generator: Figure 1

inferredcites →https://doi.org/10.1126/science.1070441openalex-snapshot

Diversity Considerations in HIV-1 Vaccine Selection

inferredcites →https://doi.org/10.1126/science.1086185openalex-snapshot

Resurrecting the Ancestral Steroid Receptor: Ancient Origin of Estrogen Signaling

inferredcites →https://doi.org/10.1128/jvi.02683-06openalex-snapshot

Reconstruction and Function of Ancestral Center-of-Tree Human Immunodeficiency Virus Type 1 Proteins

inferredcites →https://doi.org/10.1137/0128004openalex-snapshot

Minimal Mutation Trees of Sequences

inferredcites →https://doi.org/10.1186/1471-2105-5-123openalex-snapshot

GASP: Gapped Ancestral Sequence Prediction for proteins

inferredcites →https://doi.org/10.1186/1471-2105-6-134openalex-snapshot

Empirical codon substitution matrix

inferredcites →https://doi.org/10.1371/journal.pcbi.0020069openalex-snapshot

Assessing the Accuracy of Ancestral Protein Reconstruction Methods

inferredcites →https://doi.org/10.1371/journal.pcbi.1000214openalex-snapshot

Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes

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.3760.1.1zenodo-depositor-declared

An integrative appraisal of the diversification in the Atlantic forest genus Delomys (Rodentia: Cricetidae: Sigmodontinae) with the description of a new species

inferred← citeshttps://doi.org/10.1002/1873-3468.13356openalex-snapshot

Molecular evolution of proteins mediating mitochondrial fission–fusion dynamics

inferred← citeshttps://doi.org/10.1002/9783527844340.ch18openalex-snapshot

Recent Trends in Computational Tools for Industrially Important Enzymes

inferred← citeshttps://doi.org/10.1002/cbic.201700589openalex-snapshot

Unravelling the Carbohydrate‐Binding Preferences of the Carbohydrate‐Binding Modules of AMP‐Activated Protein Kinase

inferred← citeshttps://doi.org/10.1002/cbic.202200727openalex-snapshot

Definition of an Index Parameter To Screen Highly Functional Enzymes Derived from a Biochemical and Thermodynamic Analysis of Ancestral meso‐Diaminopimelate Dehydrogenases

inferred← citeshttps://doi.org/10.1002/cbic.202500155openalex-snapshot

Exploring the Stability and Substrate Profile of Transaminase from Silicibacter pomeroyi with Ancestral Sequence Reconstruction

inferred← citeshttps://doi.org/10.1002/cpz1.30openalex-snapshot

Fully Automated Ancestral Sequence Reconstruction using FireProtASR

inferred← citeshttps://doi.org/10.1002/pro.3494openalex-snapshot

The CaspBase: a curated database for evolutionary biochemical studies of caspase functional divergence and ancestral sequence inference

inferred← citeshttps://doi.org/10.1002/pro.4016openalex-snapshot

Hexamerization and thermostability emerged very early during geranylgeranylglyceryl phosphate synthase evolution

inferred← citeshttps://doi.org/10.1002/pro.4423openalex-snapshot

Characterization of ancestral Fe/Mn superoxide dismutases indicates their cambialistic origin

inferred← citeshttps://doi.org/10.1002/pro.5234openalex-snapshot

Evolutionary analysis of Quinone Reductases 1 and 2 suggests that NQO2 evolved to function as a pseudoenzyme

inferred← citeshttps://doi.org/10.1002/prot.25225openalex-snapshot

Combining ancestral sequence reconstruction with protein design to identify an interface hotspot in a key metabolic enzyme complex

inferred← citeshttps://doi.org/10.1007/978-1-0716-2349-7_12openalex-snapshot

Ancestral Sequence Reconstruction for Exploring Alkaloid Evolution

inferred← citeshttps://doi.org/10.1007/978-1-0716-2691-7_13openalex-snapshot

An Integrated Method to Reconstruct Ancient Proteins

inferred← citeshttps://doi.org/10.1007/978-1-4939-6637-0_16openalex-snapshot

Evolution-Inspired Computational Design of Symmetric Proteins

inferred← citeshttps://doi.org/10.1007/978-1-4939-6673-8_8openalex-snapshot

Reconstructing the Ancestral Relationships Between Bacterial Pathogen Genomes

inferred← citeshttps://doi.org/10.1007/978-1-4939-6940-1_5openalex-snapshot

Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors

inferred← citeshttps://doi.org/10.1007/978-1-4939-8736-8_8openalex-snapshot

High-Throughput Reconstruction of Ancestral Protein Sequence, Structure, and Molecular Function

inferred← citeshttps://doi.org/10.1007/978-1-4939-8736-8_9openalex-snapshot

Ancestral Sequence Reconstruction as a Tool for the Elucidation of a Stepwise Evolutionary Adaptation

inferred← citeshttps://doi.org/10.1007/978-981-19-4320-1_24openalex-snapshot

Metagenomic Approaches for the Discovery of Pollutant-Remediating Enzymes: Recent Trends and Challenges

inferred← citeshttps://doi.org/10.1007/s00203-022-03354-2openalex-snapshot

Analysis of multipartite bacterial genomes using alignment free and alignment-based pipelines

inferred← citeshttps://doi.org/10.1007/s00239-014-9611-6openalex-snapshot

The Phylogenetic Distribution and Evolution of Enzymes Within the Thymidine Kinase 2-like Gene Family in Metazoa

inferred← citeshttps://doi.org/10.1007/s00239-014-9639-7openalex-snapshot

One origin for metallo-β-lactamase activity, or two? An investigation assessing a diverse set of reconstructed ancestral sequences based on a sample of phylogenetic trees

inferred← citeshttps://doi.org/10.1007/s00239-020-09964-yopenalex-snapshot

Fewer Exposed Lysine Residues May Explain Relative Resistance of Chicken Serum Albumin to In Vitro Protein Glycation in Comparison to Bovine Serum Albumin

inferred← citeshttps://doi.org/10.1007/s00239-021-10010-8openalex-snapshot

Reenacting the Birth of a Function: Functional Divergence of HIUases and Transthyretins as Inferred by Evolutionary and Biophysical Studies

inferred← citeshttps://doi.org/10.1007/s00239-021-10034-0openalex-snapshot

Phylogenetic and Ancestral Sequence Reconstruction of SARS-CoV-2 Reveals Latent Capacity to Bind Human ACE2 Receptor

inferred← citeshttps://doi.org/10.1007/s00792-016-0859-1openalex-snapshot

HU histone-like DNA-binding protein from Thermus thermophilus: structural and evolutionary analyses

inferred← citeshttps://doi.org/10.1007/s11120-016-0307-1openalex-snapshot

Novel insights into the origin and diversification of photosynthesis based on analyses of conserved indels in the core reaction center proteins

inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.14650-5openalex-snapshot

Vertical Investigations of Enzyme Evolution Using Ancestral Sequence Reconstruction

inferred← citeshttps://doi.org/10.1016/j.bbabio.2021.148400openalex-snapshot

Time-resolved comparative molecular evolution of oxygenic photosynthesis

inferred← citeshttps://doi.org/10.1016/j.bbapap.2017.06.004openalex-snapshot

A glimpse into the specialization history of the lipases/acyltransferases family of CpLIP2

inferred← citeshttps://doi.org/10.1016/j.bidere.2025.100005openalex-snapshot

Recent advances on protein engineering for improved stability

inferred← citeshttps://doi.org/10.1016/j.biortech.2026.134261openalex-snapshot

Structural evolution-based ancestral sequence reconstruction of medium-chain alcohol dehydrogenase for efficient synthesis of fused-ring chiral alcohols

inferred← citeshttps://doi.org/10.1016/j.biotechadv.2021.107696openalex-snapshot

Computational design of enzymes for biotechnological applications

inferred← citeshttps://doi.org/10.1016/j.biotechadv.2023.108094openalex-snapshot

Role of distal sites in enzyme engineering

inferred← citeshttps://doi.org/10.1016/j.biotechadv.2025.108788openalex-snapshot

From traditional to AI-driven: The evolution of intelligent enzyme engineering for biocatalysis

inferred← citeshttps://doi.org/10.1016/j.canlet.2021.11.011openalex-snapshot

Premetastatic shifts of endogenous and exogenous mutational processes support consolidative therapy in EGFR-driven lung adenocarcinoma

inferred← citeshttps://doi.org/10.1016/j.cell.2015.12.024openalex-snapshot

De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints

inferred← citeshttps://doi.org/10.1016/j.cell.2020.08.052openalex-snapshot

A Global Map of G Protein Signaling Regulation by RGS Proteins

inferred← citeshttps://doi.org/10.1016/j.cell.2025.01.023openalex-snapshot

Design of CoQ10 crops based on evolutionary history

inferred← citeshttps://doi.org/10.1016/j.celrep.2020.108602openalex-snapshot

Sequence and Structure-Based Analysis of Specificity Determinants in Eukaryotic Protein Kinases

inferred← citeshttps://doi.org/10.1016/j.celrep.2022.111808openalex-snapshot

De novo birth of functional microproteins in the human lineage

inferred← citeshttps://doi.org/10.1016/j.cels.2024.05.005openalex-snapshot

The substrate quality of CK2 target sites has a determinant role on their function and evolution

inferred← citeshttps://doi.org/10.1016/j.chom.2020.01.027openalex-snapshot

VRC34-Antibody Lineage Development Reveals How a Required Rare Mutation Shapes the Maturation of a Broad HIV-Neutralizing Lineage

inferred← citeshttps://doi.org/10.1016/j.chom.2020.09.014openalex-snapshot

RTP4 Is a Potent IFN-Inducible Anti-flavivirus Effector Engaged in a Host-Virus Arms Race in Bats and Other Mammals

inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2019.107110openalex-snapshot

Landscape of ROD9 Island: Functional annotations and biological network of hypothetical proteins in Salmonella enterica

inferred← citeshttps://doi.org/10.1016/j.csbj.2017.05.002openalex-snapshot

Resurrecting the Dead (Molecules)

inferred← citeshttps://doi.org/10.1016/j.csbj.2020.10.040openalex-snapshot

Development and applications of artificial symmetrical proteins

inferred← citeshttps://doi.org/10.1016/j.csbj.2021.03.008openalex-snapshot

Ancestral sequence reconstruction - An underused approach to understand the evolution of gene function in plants?

inferred← citeshttps://doi.org/10.1016/j.cstres.2024.10.004openalex-snapshot

Functional similarities and differences among subunits of the nascent polypeptide-associated complex (NAC) of Saccharomyces cerevisiae

inferred← citeshttps://doi.org/10.1016/j.cub.2018.03.027openalex-snapshot

A Tandem Amino Acid Residue Motif in Guard Cell SLAC1 Anion Channel of Grasses Allows for the Control of Stomatal Aperture by Nitrate

inferred← citeshttps://doi.org/10.1016/j.cub.2022.02.018openalex-snapshot

Recurrent evolution of an inhibitor of ESCRT-dependent virus budding and LINE-1 retrotransposition in primates

inferred← citeshttps://doi.org/10.1016/j.cub.2022.07.059openalex-snapshot

A single residue confers selective loss of sugar sensing in wrynecks

inferred← citeshttps://doi.org/10.1016/j.cub.2026.05.021openalex-snapshot

Genomic and physiological changes in a sexually selected and frugivorous bird radiation

inferred← citeshttps://doi.org/10.1016/j.enzmictec.2022.109989openalex-snapshot

Ancestral sequence reconstruction and spatial structure analysis guided alteration of longer-chain substrate catalysis for Thermomicrobium roseum lipase

inferred← citeshttps://doi.org/10.1016/j.fob.2013.12.006openalex-snapshot

Ancestral mutations as a tool for solubilizing proteins: The case of a hydrophobic phosphate‐binding protein

inferred← citeshttps://doi.org/10.1016/j.gene.2012.08.046openalex-snapshot

The evolution of catalytic residues and enzyme mechanism within the bacterial nucleoside phosphorylase superfamily 1

inferred← citeshttps://doi.org/10.1016/j.gene.2020.144510openalex-snapshot

Deep mitochondrial DNA phylogeographic divergence in the threatened aoudad Ammotragus lervia (Bovidae, Caprini)

inferred← citeshttps://doi.org/10.1016/j.isci.2023.106043openalex-snapshot

A reversible mutation in a genomic hotspot saves bacterial swarms from extinction

inferred← citeshttps://doi.org/10.1016/j.jbc.2021.101043openalex-snapshot

Catalytic mechanism of ancestral L-lysine oxidase assigned by sequence data mining

inferred← citeshttps://doi.org/10.1016/j.jgg.2021.12.003openalex-snapshot

Evidence for a mouse origin of the SARS-CoV-2 Omicron variant

inferred← citeshttps://doi.org/10.1016/j.jmgm.2019.07.014openalex-snapshot

Visualization of protein sequence space with force-directed graphs, and their application to the choice of target-template pairs for homology modelling

inferred← citeshttps://doi.org/10.1016/j.mcat.2024.113874openalex-snapshot

Enzyme engineering for biocatalysis

inferred← citeshttps://doi.org/10.1016/j.meegid.2016.03.029openalex-snapshot

Phylogenetic analysis of canine distemper virus in South America clade 1 reveals unique molecular signatures of the local epidemic

inferred← citeshttps://doi.org/10.1016/j.trechm.2022.03.001openalex-snapshot

Computational enzyme redesign: large jumps in function

inferred← citeshttps://doi.org/10.1016/j.virol.2015.03.029openalex-snapshot

Ebolavirus is evolving but not changing: No evidence for functional change in EBOV from 1976 to the 2014 outbreak

inferred← citeshttps://doi.org/10.1016/j.xplc.2025.101381openalex-snapshot

Evolution of CYP71D drives the diversification of monoterpene indole alkaloid biosynthesis in Gentianales

inferred← citeshttps://doi.org/10.1016/j.ygcen.2021.113925openalex-snapshot

In silico evaluation of the downstream effect of mutated glucagon is consistent with higher blood glucose homeostasis in Galliformes and Strigiformes

inferred← citeshttps://doi.org/10.1016/j.ymben.2019.12.001openalex-snapshot

Methanol-free biosynthesis of fatty acid methyl ester (FAME) in Synechocystis sp. PCC 6803

inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107969openalex-snapshot

Coupling DNA barcodes and exon-capture to resolve the phylogeny of Turridae (Gastropoda, Conoidea)

inferred← citeshttps://doi.org/10.1016/s1872-2067(26)64991-1openalex-snapshot

Synergistic integration of ancestral sequence reconstruction and rational design empowers unspecific peroxygenase for efficient steroid core oxyfunctionalization

inferred← citeshttps://doi.org/10.1021/acs.jpcb.1c01253openalex-snapshot

Improving the Thermostability of Xylanase A from Bacillus subtilis by Combining Bioinformatics and Electrostatic Interactions Optimization

inferred← citeshttps://doi.org/10.1021/acscatal.5c01062openalex-snapshot

Discovery and Engineering of a Urethanase for Enhanced Depolymerization of Polyurethane

inferred← citeshttps://doi.org/10.1021/acscatal.6b01332openalex-snapshot

A Catalytically Competent Terpene Synthase Inferred Using Ancestral Sequence Reconstruction Strategy

inferred← citeshttps://doi.org/10.1021/acscatal.8b03613openalex-snapshot

Computational Design of Stable and Soluble Biocatalysts

inferred← citeshttps://doi.org/10.1021/acscatal.9b03418openalex-snapshot

Deracemization and Stereoinversion to Aromatic d -Amino Acid Derivatives with Ancestral l -Amino Acid Oxidase

inferred← citeshttps://doi.org/10.1021/acscentsci.7b00269openalex-snapshot

Absence of Selection for Quantum Coherence in the Fenna–Matthews–Olson Complex: A Combined Evolutionary and Excitonic Study

inferred← citeshttps://doi.org/10.1021/acschembio.0c00296openalex-snapshot

Three Recently Diverging Duplicated Methyltransferases Exhibit Substrate-Dependent Regioselectivity Essential for Xantholipin Biosynthesis

inferred← citeshttps://doi.org/10.1021/acschemneuro.0c00410openalex-snapshot

Contingency between Historical Substitutions in the Acetylcholine Receptor Pore

inferred← citeshttps://doi.org/10.1021/acsnano.6c04954openalex-snapshot

Design and Characterization of SAKe, a Building Block for Protein Self-Assembly

inferred← citeshttps://doi.org/10.1021/jacsau.4c00653openalex-snapshot

Ancestral Sequence Reconstruction for Designing Biocatalysts and Investigating their Functional Mechanisms

inferred← citeshttps://doi.org/10.1038/nature13036openalex-snapshot

Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies

inferred← citeshttps://doi.org/10.1038/ncomms12847openalex-snapshot

An experimental phylogeny to benchmark ancestral sequence reconstruction

inferred← citeshttps://doi.org/10.1038/s41467-017-01370-1openalex-snapshot

Tracing the origin and evolution of supergene mimicry in butterflies

inferred← citeshttps://doi.org/10.1038/s41467-018-05114-7openalex-snapshot

Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination

inferred← citeshttps://doi.org/10.1038/s41467-020-16182-zopenalex-snapshot

Molecular determinants underlying functional innovations of TBP and their impact on transcription initiation

inferred← citeshttps://doi.org/10.1038/s41467-020-20630-1openalex-snapshot

Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase

inferred← citeshttps://doi.org/10.1038/s41467-021-22073-8openalex-snapshot

Harnessing machine learning to guide phylogenetic-tree search algorithms

inferred← citeshttps://doi.org/10.1038/s41467-023-43451-4openalex-snapshot

Resurrecting ancestral antibiotics: unveiling the origins of modern lipid II targeting glycopeptides

inferred← citeshttps://doi.org/10.1038/s41467-023-44246-3openalex-snapshot

Multiple independent losses of the biosynthetic pathway for two tropane alkaloids in the Solanaceae family

inferred← citeshttps://doi.org/10.1038/s41467-024-44806-1openalex-snapshot

Evolution of optimal growth temperature in Asgard archaea inferred from the temperature dependence of GDP binding to EF-1A

inferred← citeshttps://doi.org/10.1038/s41467-025-56597-0openalex-snapshot

Cryptic genetic variation shapes the fate of gene duplicates in a protein interaction network

inferred← citeshttps://doi.org/10.1038/s41467-026-72977-6openalex-snapshot

Ground squirrel coprolites preserve complex archives of ancient environmental DNA over 700,000 years

inferred← citeshttps://doi.org/10.1038/s41477-019-0444-6openalex-snapshot

A stigmatic gene confers interspecies incompatibility in the Brassicaceae

inferred← citeshttps://doi.org/10.1038/s41559-020-1232-4openalex-snapshot

Birth of a pathway for sulfur metabolism in early amniote evolution

inferred← citeshttps://doi.org/10.1038/s41559-023-02012-0openalex-snapshot

An ancient metalloenzyme evolves through metal preference modulation

inferred← citeshttps://doi.org/10.1038/s41564-018-0304-6openalex-snapshot

Neofunctionalization of the secreted Tin2 effector in the fungal pathogen Ustilago maydis

inferred← citeshttps://doi.org/10.1038/s41586-022-04464-zopenalex-snapshot

ACE2 binding is an ancestral and evolvable trait of sarbecoviruses

inferred← citeshttps://doi.org/10.1038/s41587-019-0193-0openalex-snapshot

Continuous evolution of base editors with expanded target compatibility and improved activity

inferred← citeshttps://doi.org/10.1038/s41588-018-0117-9openalex-snapshot

Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam

inferred← citeshttps://doi.org/10.1038/s41589-018-0042-3openalex-snapshot

Evolution of chalcone isomerase from a noncatalytic ancestor

inferred← citeshttps://doi.org/10.1038/s41592-021-01100-yopenalex-snapshot

Low-N protein engineering with data-efficient deep learning

inferred← citeshttps://doi.org/10.1038/s41598-017-06332-7openalex-snapshot

Computational design of a symmetrical β-trefoil lectin with cancer cell binding activity

inferred← citeshttps://doi.org/10.1038/s41598-017-12619-6openalex-snapshot

Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions

inferred← citeshttps://doi.org/10.1038/s41598-018-34758-0openalex-snapshot

Deciphering the evolutionary signatures of pinnipeds using novel genome sequences: The first genomes of Phoca largha, Callorhinus ursinus, and Eumetopias jubatus

inferred← citeshttps://doi.org/10.1038/s41598-019-45532-1openalex-snapshot

Terpene Synthase Genes Originated from Bacteria through Horizontal Gene Transfer Contribute to Terpenoid Diversity in Fungi

inferred← citeshttps://doi.org/10.1038/s41598-019-56941-7openalex-snapshot

Duplication and parallel evolution of the pancreatic ribonuclease gene (RNASE1) in folivorous non-colobine primates, the howler monkeys (Alouatta spp.)

inferred← citeshttps://doi.org/10.1038/s41598-021-01736-yopenalex-snapshot

Protein innovation through template switching in the Saccharomyces cerevisiae lineage

inferred← citeshttps://doi.org/10.1038/s41598-021-93381-8openalex-snapshot

The coordination of major events in C4 photosynthesis evolution in the genus Flaveria

inferred← citeshttps://doi.org/10.1038/s42003-019-0677-yopenalex-snapshot

Highly thermostable carboxylic acid reductases generated by ancestral sequence reconstruction

inferred← citeshttps://doi.org/10.1038/srep16550openalex-snapshot

Convergent evolution of marine mammals is associated with distinct substitutions in common genes

inferred← citeshttps://doi.org/10.1039/d0cy00081gopenalex-snapshot

A new monooxygenase from Herbaspirillum huttiense catalyzed highly enantioselective epoxidation of allylbenzenes and allylic alcohols

inferred← citeshttps://doi.org/10.1039/d1np00006copenalex-snapshot

A roadmap for metagenomic enzyme discovery

inferred← citeshttps://doi.org/10.1039/d3gc04888hopenalex-snapshot

Computational design of an efficient and thermostable esterase for polylactic acid depolymerization

inferred← citeshttps://doi.org/10.1039/d4cy00090kopenalex-snapshot

Thermostable fatty acid hydroxylases from ancestral reconstruction of cytochrome P450 family 4 enzymes

inferred← citeshttps://doi.org/10.1042/bcj20160507openalex-snapshot

Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the ‘retro’ approach to protein engineering

inferred← citeshttps://doi.org/10.1042/bcj20190625openalex-snapshot

Resurrection of ancestral effector caspases identifies novel networks for evolution of substrate specificity

inferred← citeshttps://doi.org/10.1042/bj20121221openalex-snapshot

Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes

inferred← citeshttps://doi.org/10.1073/pnas.1412768111openalex-snapshot

Computational design of a self-assembling symmetrical β-propeller protein

inferred← citeshttps://doi.org/10.1073/pnas.1812865115openalex-snapshot

Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period

inferred← citeshttps://doi.org/10.1073/pnas.1912132117openalex-snapshot

Analysis of allosteric communication in a multienzyme complex by ancestral sequence reconstruction

inferred← citeshttps://doi.org/10.1073/pnas.2021516118openalex-snapshot

Loss of sweet taste despite the conservation of sweet receptor genes in insectivorous bats

inferred← citeshttps://doi.org/10.1073/pnas.2101276118openalex-snapshot

Evolution of bacterial steroid biosynthesis and its impact on eukaryogenesis

inferred← citeshttps://doi.org/10.1073/pnas.2312691121openalex-snapshot

Recurrent viral capture of cellular phosphodiesterases that antagonize OAS-RNase L

inferred← citeshttps://doi.org/10.1074/jbc.ra118.005695openalex-snapshot

Mechanistic basis for the evolution of chalcone synthase catalytic cysteine reactivity in land plants

inferred← citeshttps://doi.org/10.1074/jbc.ra120.013528openalex-snapshot

Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia

inferred← citeshttps://doi.org/10.1080/01614940.2024.2313603openalex-snapshot

Enzymatic synthesis of chiral alcohols using ketoreductases

inferred← citeshttps://doi.org/10.1080/15476286.2018.1493331openalex-snapshot

Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems

inferred← citeshttps://doi.org/10.1088/1361-6633/adea92openalex-snapshot

Fluctuations and the limit of predictability in protein evolution

inferred← citeshttps://doi.org/10.1093/bib/bbaa337openalex-snapshot

FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction

inferred← citeshttps://doi.org/10.1093/bioinformatics/btae043openalex-snapshot

Statistical framework to determine indel-length distribution

inferred← citeshttps://doi.org/10.1093/bioinformatics/bty1031openalex-snapshot

Ancestral sequence reconstruction: accounting for structural information by averaging over replacement matrices

inferred← citeshttps://doi.org/10.1093/bioinformatics/btz249openalex-snapshot

Accounting for ambiguity in ancestral sequence reconstruction

inferred← citeshttps://doi.org/10.1093/database/bay123openalex-snapshot

NBDC RDF portal: a comprehensive repository for semantic data in life sciences

inferred← citeshttps://doi.org/10.1093/gbe/evaa164openalex-snapshot

Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy

inferred← citeshttps://doi.org/10.1093/gbe/evab268openalex-snapshot

Adaptive Evolution in TRIF Leads to Discordance between Human and Mouse Innate Immune Signaling

inferred← citeshttps://doi.org/10.1093/gbe/evad112openalex-snapshot

Highly Abundant Proteins Are Highly Thermostable

inferred← citeshttps://doi.org/10.1093/gbe/evae151openalex-snapshot

Ancestral Sequence Reconstruction as a Tool to Detect and Study De Novo Gene Emergence

inferred← citeshttps://doi.org/10.1093/gbe/evaf119openalex-snapshot

Impact of Phylogenetic Method Choice on Indel Analyses in HIV-1 Subtype B

inferred← citeshttps://doi.org/10.1093/gbe/evt113openalex-snapshot

In Silico Resurrection of the Major Vault Protein Suggests It Is Ancestral in Modern Eukaryotes

inferred← citeshttps://doi.org/10.1093/gbe/evw211openalex-snapshot

Substitutions in the Glycogenin-1 Gene Are Associated with the Evolution of Endothermy in Sharks and Tunas

inferred← citeshttps://doi.org/10.1093/gbe/evw231openalex-snapshot

GC Content Heterogeneity Transition of Conserved Noncoding Sequences Occurred at the Emergence of Vertebrates

inferred← citeshttps://doi.org/10.1093/gbe/evx235openalex-snapshot

Structure-Related Differences between Cytochrome Oxidase I Proteins in a Stable Heteroplasmic Mitochondrial System

inferred← citeshttps://doi.org/10.1093/genetics/iyac074openalex-snapshot

Reconstruction of full-length LINE-1 progenitors from ancestral genomes

inferred← citeshttps://doi.org/10.1093/genetics/iyad175openalex-snapshot

Dissection of the role of a Src homology 3 domain in the evolution of binding preference of paralogous proteins

inferred← citeshttps://doi.org/10.1093/gigascience/giaa059openalex-snapshot

Genomic consequences of dietary diversification and parallel evolution due to nectarivory in leaf-nosed bats

inferred← citeshttps://doi.org/10.1093/molbev/msaa247openalex-snapshot

Biased Mutation and Selection in RNA Viruses

inferred← citeshttps://doi.org/10.1093/molbev/msaa312openalex-snapshot

The Molecular Determinants of Thermoadaptation:Methanococcalesas a Case Study

inferred← citeshttps://doi.org/10.1093/molbev/msab266openalex-snapshot

A Probabilistic Model for Indel Evolution: Differentiating Insertions from Deletions

inferred← citeshttps://doi.org/10.1093/molbev/msab367openalex-snapshot

Synergism, Bifunctionality, and the Evolution of a Gradual Sensory Trade-off in Hummingbird Taste Receptors

inferred← citeshttps://doi.org/10.1093/molbev/msab371openalex-snapshot

Placental Mammals Acquired Functional Sequences in NRK for Regulating the CK2–PTEN–AKT Pathway and Placental Cell Proliferation

inferred← citeshttps://doi.org/10.1093/molbev/msac250openalex-snapshot

Substrate Affinity Versus Catalytic Efficiency: Ancestral Sequence Reconstruction of tRNA Nucleotidyltransferases Solves an Enzyme Puzzle

inferred← citeshttps://doi.org/10.1093/molbev/msae109openalex-snapshot

Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels

inferred← citeshttps://doi.org/10.1093/molbev/msae177openalex-snapshot

Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications

inferred← citeshttps://doi.org/10.1093/molbev/msae203openalex-snapshot

soibean : High-Resolution Taxonomic Identification of Ancient Environmental DNA Using Mitochondrial Pangenome Graphs

inferred← citeshttps://doi.org/10.1093/molbev/msae262openalex-snapshot

A de novo Gene Promotes Seed Germination Under Drought Stress in Arabidopsis

inferred← citeshttps://doi.org/10.1093/molbev/msaf043openalex-snapshot

Widespread and Convergent Evolution of Cone Monochromacy in Galeomorph Sharks

inferred← citeshttps://doi.org/10.1093/molbev/msaf222openalex-snapshot

Introducing the Y-chromosomal Ancestral-like Reference Sequence—Improving the Capture of Human Evolutionary Information

inferred← citeshttps://doi.org/10.1093/molbev/msag031openalex-snapshot

Evolutionary remodeling of the FXR binding pocket drove functional divergence and ligand discrimination

inferred← citeshttps://doi.org/10.1093/molbev/msu243openalex-snapshot

The Early Expansion and Evolutionary Dynamics of POU Class Genes

inferred← citeshttps://doi.org/10.1093/molbev/msv203openalex-snapshot

High-Throughput Identification ofCis-Regulatory Rewiring Events in Yeast

inferred← citeshttps://doi.org/10.1093/molbev/msv234openalex-snapshot

Disentangling Sources of Selection on Exonic Transcriptional Enhancers

inferred← citeshttps://doi.org/10.1093/molbev/msw070openalex-snapshot

Conservation and Innovation of APOBEC3A Restriction Functions during Primate Evolution

inferred← citeshttps://doi.org/10.1093/molbev/msx096openalex-snapshot

Origin and Evolutionary Alteration of the Mitochondrial Import System in Eukaryotic Lineages

inferred← citeshttps://doi.org/10.1093/molbev/msx187openalex-snapshot

Increased Affinity for RNA Targets Evolved Early in Animal and Plant Dicer Lineages through Different Structural Mechanisms

inferred← citeshttps://doi.org/10.1093/molbev/msy055openalex-snapshot

Alignment Modulates Ancestral Sequence Reconstruction Accuracy

inferred← citeshttps://doi.org/10.1093/molbev/msy144openalex-snapshot

Exon-Capture-Based Phylogeny and Diversification of the Venomous Gastropods (Neogastropoda, Conoidea)

inferred← citeshttps://doi.org/10.1093/mtomcs/mfad057openalex-snapshot

Evolution of Cd2+ and Cu+ binding inHelix pomatiametallothioneins

inferred← citeshttps://doi.org/10.1093/nar/gkaf962openalex-snapshot

Structural and evolutionary determinants of Argonaute function

inferred← citeshttps://doi.org/10.1093/nar/gkt1369openalex-snapshot

Structural integrity of the PCI domain of eIF3a/TIF32 is required for mRNA recruitment to the 43S pre-initiation complexes

inferred← citeshttps://doi.org/10.1093/nar/gku1196openalex-snapshot

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

inferred← citeshttps://doi.org/10.1093/nar/gku240openalex-snapshot

Exonic splicing signals impose constraints upon the evolution of enzymatic activity

inferred← citeshttps://doi.org/10.1093/protein/gzv038openalex-snapshot

Assessing the prediction fidelity of ancestral reconstruction by a library approach

inferred← citeshttps://doi.org/10.1093/sysbio/syac050openalex-snapshot

ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process

inferred← citeshttps://doi.org/10.1093/sysbio/syw121openalex-snapshot

ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability

inferred← citeshttps://doi.org/10.1093/sysbio/syz016openalex-snapshot

Lack of Signal for the Impact of Conotoxin Gene Diversity on Speciation Rates in Cone Snails

inferred← citeshttps://doi.org/10.1093/ve/vead031openalex-snapshot

Selective events at individual sites underlie the evolution of monkeypox virus clades

inferred← citeshttps://doi.org/10.1093/ve/veae108openalex-snapshot

HIV-1 Vif global diversity and possible APOBEC-mediated response since 1980

inferred← citeshttps://doi.org/10.1093/ve/veag025openalex-snapshot

Getting to the root of HIV transmitted founder virus sequences

inferred← citeshttps://doi.org/10.1093/ve/vex019openalex-snapshot

Adaptive HIV-1 evolutionary trajectories are constrained by protein stability

inferred← citeshttps://doi.org/10.1098/rsob.220133openalex-snapshot

A synthetic ancestral kinesin-13 depolymerizes microtubules faster than any natural depolymerizing kinesin

inferred← citeshttps://doi.org/10.1098/rspb.2013.3251openalex-snapshot

A Bayesian approach for inferring the dynamics of partially observed endemic infectious diseases from space-time-genetic data

inferred← citeshttps://doi.org/10.1098/rspb.2019.0830openalex-snapshot

Of eyes and embryos: subfunctionalization of theCRXhomeobox gene in mammalian evolution

inferred← citeshttps://doi.org/10.1098/rstb.2021.0279openalex-snapshot

Molecular advances to study the function, evolution and spectral tuning of arthropod visual opsins

inferred← citeshttps://doi.org/10.1099/mgen.0.000694openalex-snapshot

SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments

inferred← citeshttps://doi.org/10.1101/195115openalex-snapshot

Global analysis of specificity determinants in eukaryotic protein kinases

inferred← citeshttps://doi.org/10.1101/2020.06.22.165787openalex-snapshot

Detailed phylogenetic analysis of SARS-CoV-2 reveals latent capacity to bind human ACE2 receptor

inferred← citeshttps://doi.org/10.1101/2020.10.13.337972openalex-snapshot

Higher temperatures worsen the effects of mutations on protein stability

inferred← citeshttps://doi.org/10.1101/2021.04.27.441704openalex-snapshot

Recurrent Emergence of an Antiviral Defense through Repeated Retrotransposition and Truncation of CHMP3

inferred← citeshttps://doi.org/10.1101/2021.09.22.461318openalex-snapshot

Placental mammals acquired the functional region and domain in NRK for regulating the CK2-PTEN-AKT pathway and placental cell proliferation

inferred← citeshttps://doi.org/10.1101/2021.10.01.462744openalex-snapshot

De novo birth of functional, human-specific microproteins

inferred← citeshttps://doi.org/10.1101/2022.04.11.487848openalex-snapshot

A synthetic ancestral Kinesin-13 depolymerises microtubules faster than any natural depolymerising kinesin

inferred← citeshttps://doi.org/10.1101/2022.06.09.495570openalex-snapshot

The evolutionary history of class I aminoacyl-tRNA synthetases indicates early statistical translation

inferred← citeshttps://doi.org/10.1101/2023.03.09.531510openalex-snapshot

Dissection of the role of a SH3 domain in the evolution of binding preference of paralogous proteins

inferred← citeshttps://doi.org/10.1101/2023.05.18.541272openalex-snapshot

Evolution towards simplicity in bacterial small heat shock protein system

inferred← citeshttps://doi.org/10.1101/2023.08.07.552269openalex-snapshot

Purifying selection and adaptive evolution proximate to the zoonosis of SARS-CoV-1 and SARS-CoV-2

inferred← citeshttps://doi.org/10.1101/2024.01.08.574609openalex-snapshot

Cytochrome P450 Enzyme Design by Constraining Catalytic Pocket in Diffusion model

inferred← citeshttps://doi.org/10.1101/2024.03.27.586611openalex-snapshot

Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment including Long Indels

inferred← citeshttps://doi.org/10.1101/2025.05.07.652589openalex-snapshot

Introducing the Y chromosome ancestral reference sequence - Improving the capture of human evolutionary information

inferred← citeshttps://doi.org/10.1101/2025.09.16.676541openalex-snapshot

Evolutionary remodeling of non-canonical ORF translation in mammals

showing the first 200 of 331

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.