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List of works by Gustavo Caetano-Anollés

A Dynamic Model for the Evolution of Protein Structure

scientific article

A calibrated chronology of biochemistry reveals a stem line of descent responsible for planetary biodiversity

scientific article

A general framework of persistence strategies for biological systems helps explain domains of life

scientific article published on 25 February 2013

A phylogenomic census of molecular functions identifies modern thermophilic archaea as the most ancient form of cellular life

scientific article

A phylogenomic data-driven exploration of viral origins and evolution

scientific article

A tree of cellular life inferred from a genomic census of molecular functions

scientific article published on 17 August 2014

A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation

scientific article

Advances in Molecular Exploration of Crop Plants under Environmental Stresses from Genetic and Genomic Perspectives

scientific article published in 2023

An approach of orthology detection from homologous sequences under minimum evolution

scientific article published on August 2008

An evolutionarily structured universe of protein architecture

scientific article

Ancestral Insertions and Expansions of rRNA do not Support an Origin of the Ribosome in Its Peptidyl Transferase Center

scientific article

Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes

article by Philippe Colson et al published 2018 in Frontiers in Microbiology

Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms

scientific article (publication date: 8 November 2011)

Archaea-First and the Co-Evolutionary Diversification of Domains of Life

scientific article published on 26 June 2018

Archaea: the first domain of diversified life

scientific article

Arguments Reinforcing the Three-Domain View of Diversified Cellular Life

scientific article

Benefits of using molecular structure and abundance in phylogenomic analysis ⬇️

scientific article published on September 6, 2012

Biphasic patterns of diversification and the emergence of modules ⬇️

scientific article published on August 7, 2012

CLUSTOM: a novel method for clustering 16S rRNA next generation sequences by overlap minimization

scientific article

Commentary: History of the ribosome and the origin of translation

scientific article

Common evolutionary trends for SINE RNA structures

scientific article

Comparative analysis of barophily-related amino acid content in protein domains of Pyrococcus abyssi and Pyrococcus furiosus

scientific article published on 26 September 2013

Comparative analysis of proteomes and functionomes provides insights into origins of cellular diversification

scientific article published on 31 December 2013

Comparative genomic and phylogenetic analyses reveal the evolution of the core two-component signal transduction systems in enterobacteria

scientific article published on 5 January 2010

Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology

scientific article

Correction to: Genome-wide analysis of the MYB-CC gene family of maize

article

Correction: CLUSTOM: A Novel Method for Clustering 16S rRNA Next Generation Sequences by Overlap Minimization.

scientific article published on 6 May 2013

Creationism and intelligent design are incompatible with scientific progress: A response to Shanta and Vêdanta.

scientific article

Do Viruses Exchange Genes across Superkingdoms of Life?

scientific article published on 31 October 2017

Dual RNase and β-lactamase Activity of a Single Enzyme Encoded in Archaea

scientific article published on 14 November 2020

Emergence and evolution of modern molecular functions inferred from phylogenomic analysis of ontological data

scientific article

Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis

scientific article published on 05 September 2019

Erratum to: Genomic characterization of plant cell wall degrading enzymes and in silico analysis of xylanases and polygalacturonases of Fusarium virguliforme

scientific article published on 10 May 2017

Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome

scientific article

Evolutionary optimization of protein folding

scientific article

Evolutionary patterns in the sequence and structure of transfer RNA: a window into early translation and the genetic code

scientific article (publication date: 30 July 2008)

Evolutionary patterns in the sequence and structure of transfer RNA: early origins of archaea and viruses

scientific article

Evolved RNA secondary structure and the rooting of the universal tree of life

scientific article published on 01 March 2002

Extensive and specific responses of a eukaryote to bacterial quorum-sensing signals

scientific article

Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: are they proof of an ancient genome duplication event?

scientific article (publication date: 25 September 2007)

Genome-Wide Identification and Characterization of the Vacuolar H+-ATPase Subunit H Gene Family in Crop Plants

scientific article published on 16 October 2019

Genome-wide analysis of the MYB-CC gene family of maize

scientific article published on 21 September 2018

Genomic characterization of plant cell wall degrading enzymes and in silico analysis of xylanses and polygalacturonases of Fusarium virguliforme

scientific article

Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya

scientific article published in 2012

Global patterns of protein domain gain and loss in superkingdoms

scientific article

Grass evolution inferred from chromosomal rearrangements and geometrical and statistical features in RNA structure

scientific article published in May 2005

History of biological metal utilization inferred through phylogenomic analysis of protein structures

scientific article (publication date: 8 June 2010)

Human metallo-β-lactamase enzymes degrade penicillin

scientific article published on 21 August 2019

Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification

scientific article published on 10 March 2017

Investigating the Control of Chlorophyll Degradation by Genomic Correlation Mining

scientific article

Lokiarchaeota: eukaryote-like missing links from microbial dark matter?

scientific article published on 22 June 2015

Long-term evolution of viruses: A Janus-faced balance

scientific article

MANET 3.0: Hierarchy and modularity in evolving metabolic networks

scientific article published on 24 October 2019

MANET: tracing evolution of protein architecture in metabolic networks

scientific article

Metabolite-Centric Reporter Pathway and Tripartite Network Analysis of s Under Cold Stress

scholarly article by Ibrahim Koç et al published 2018 in Frontiers in Bioengineering and Biotechnology

Mimivirus: leading the way in the discovery of giant viruses of amoebae

scientific article published on 27 February 2017

NOBAI: a web server for character coding of geometrical and statistical features in RNA structure

scientific article published on 29 April 2008

New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release

scientific article published on 23 October 2020

Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes

scientific article

Origins and evolution of modern biochemistry: insights from genomes and molecular structure

scientific article published on May 2008

Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells

scientific article

Phylogenetic profiling, an untapped resource for the prediction of secreted proteins and its complementation with sequence-based classifiers in bacterial type III, IV and VI secretion systems.

scientific article published on 31 January 2018

Phylogenomics supports a cellularly structured urancestor

scientific article published on 18 April 2013

Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks

scientific article published on 2 December 2016

Protein Domain Structure Uncovers the Origin of Aerobic Metabolism and the Rise of Planetary Oxygen ⬇️

scientific article published on January 11, 2012

Proteome Evolution and the Metabolic Origins of Translation and Cellular Life ⬇️

scientific article published on November 17, 2010

Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world

scientific article

Reductive evolution of proteomes and protein structures ⬇️

scientific article published on July 5, 2011

Reply to Mulkidjanian and Galperin: Zn may have constrained evolution during the Proterozoic but not the Archean.

scientific article

Ribosomal History Reveals Origins of Modern Protein Synthesis ⬇️

scientific article published on March 12, 2012

Ribosomal accretion, apriorism and the phylogenetic method: a response to Petrov and Williams

scientific article

Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions

scholarly article by Gustavo Caetano-Anollés et al published 2018 in Evolutionary Bioinformatics

RubisCO and the Search for Biomolecular Culprits of Planetary Change

scientific article published on 13 October 2017

Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility

scientific article (publication date: 2013)

Structural phylogenomics reveals gradual evolutionary replacement of abiotic chemistries by protein enzymes in purine metabolism

scientific article

Structural phylogenomics uncovers the early and concurrent origins of cysteine biosynthesis and iron-sulfur proteins ⬇️

scientific article published on June 25, 2012

Testing Empirical Support for Evolutionary Models that Root the Tree of Life

The Phylogenomic Roots of Modern Biochemistry: Origins of Proteins, Cofactors and Protein Biosynthesis ⬇️

scientific article published on January 1, 2012

The absence of protein Y4yS affects negatively the abundance of T3SS Mesorhizobium loti secretin, RhcC2, in bacterial membranes

scientific article published on 30 January 2015

The ancient history of the structure of ribonuclease P and the early origins of Archaea

scientific article

The coevolutionary roots of biochemistry and cellular organization challenge the RNA world paradigm

scientific article published on 18 April 2013

The distribution and impact of viral lineages in domains of life

scientific article

The early history and emergence of molecular functions and modular scale-free network behavior

scientific article

The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms

scientific article

The evolutionary history of the structure of 5S ribosomal RNA

scientific article

The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world

scientific article

The impact of oxygen on metabolic evolution: a chemoinformatic investigation

scientific article

The importance of using realistic evolutionary models for retrodicting proteomes.

scientific article published on 04 December 2013

The natural history of biocatalytic mechanisms

scientific article (publication date: May 2014)

The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data

scientific article (publication date: 2017)

The natural history of transfer RNA and its interactions with the ribosome

scientific article (publication date: 2014)

The organization of domains in proteins obeys Menzerath-Altmann's law of language.

scientific article

The origin and evolution of modern metabolism

scientific article published on 26 August 2008

The origin and evolution of tRNA inferred from phylogenetic analysis of structure

scientific article

The origin and evolution of the archaeal domain.

scientific article published on 4 June 2014

The origin and evolution of viruses inferred from fold family structure

scientific article published on 03 August 2020

The origin of modern 5S rRNA: a case of relating models of structural history to phylogenetic data

scientific article

The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture

scientific article

The origin, evolution and structure of the protein world.

scientific article

The proteomic complexity and rise of the primordial ancestor of diversified life

scientific article

Tracing the evolution of RNA structure in ribosomes

scientific article published on June 2002

Transfer RNA and the origins of diversified life.

scientific article

Universal sharing patterns in proteomes and evolution of protein fold architecture and life.

scientific article published in April 2005

Untangling the origin of viruses and their impact on cellular evolution

scientific article

Viral evolution: Primordial cellular origins and late adaptation to parasitism

scientific article (publication date: September 2012)

Widespread Recruitment of Ancient Domain Structures in Modern Enzymes during Metabolic Evolution

scientific article

Widespread recruitment of ancient domain structures in modern enzymes during metabolic evolution

scientific article published on 14 February 2013

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