1986 …2019
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Research Output 1986 2019

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2019

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

Bai, J., Sun, F., Wang, M., Su, L., Li, R. & Caetano-Anolles, G., Feb 15 2019, In : Genetica. 147, 1

Research output: Contribution to journalArticle

Zea mays
Genome
genome
corn
Genes

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

Kang, C., Sun, F., Yan, L., Li, R., Bai, J. & Caetano-Anolles, G., Oct 16 2019, In : International Journal of Molecular Sciences. 20, 20, 5125.

Research output: Contribution to journalArticle

Open Access
Vacuolar Proton-Translocating ATPases
genome
crops
genes
Crops

Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation

Jeong, H., Arif, B., Caetano-Anolles, G., Kim, K. M. & Nasir, A., Dec 1 2019, In : Scientific Reports. 9, 1, 5953.

Research output: Contribution to journalArticle

Open Access
Horizontal Gene Transfer
Microbiota
Human Body
Human Genome
Genes

Human metallo-β-lactamase enzymes degrade penicillin

Diene, S. M., Pinault, L., Keshri, V., Armstrong, N., Khelaifia, S., Chabrière, E., Caetano-Anolles, G., Colson, P., La Scola, B., Rolain, J. M., Pontarotti, P. & Raoult, D., Dec 1 2019, In : Scientific Reports. 9, 1, 12173.

Research output: Contribution to journalArticle

Open Access
Lactams
Penicillins
Sulbactam
Enzymes
Anti-Bacterial Agents

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

Caetano-Anollés, D., Nasir, A., Kim, K. M. & Caetano-Anolles, G., Apr 15 2019, In : Journal of Molecular Evolution. 87, 2-3, p. 131-142 12 p.

Research output: Contribution to journalArticle

Open Access
Proteome
proteome
testing
Censuses
Natural History
2018

Ancestrality and mosaicism of giant viruses supporting the definition of the fourth TRUC of microbes

Colson, P., Levasseur, A., Scola, B. L., Sharma, V., Nasir, A., Pontarotti, P., Caetano-Anolles, G. & Raoult, D., Nov 27 2018, In : Frontiers in Microbiology. 9, NOV, 2668.

Research output: Contribution to journalArticle

Mosaicism
Archaea
Eukaryota
Bacteria
Genes
Electric network analysis
Metabolites
Arabidopsis
Cold-Shock Response
Activity Cycles
2017

Do viruses exchange genes across superkingdoms of life?

Malik, S. S., Azem-e-Zahra, S., Kim, K. M., Caetano-Anolles, G. & Nasir, A., Oct 31 2017, In : Frontiers in Microbiology. 8, OCT, 2110.

Research output: Contribution to journalArticle

Viruses
Genes
Proteome
Eukaryota
Protein Structural Homology

Identification of capsid/coat related protein folds and their utility for virus classification

Nasir, A. & Caetano-Anolles, G., Mar 10 2017, In : Frontiers in Microbiology. 8, MAR, 380.

Research output: Contribution to journalArticle

Capsid
Capsid Proteins
Viruses
Metagenome
Planets
Proteome
Viruses
Vocabulary
Genome Size
Protein Domains

Phylotype and sequevar variability of Ralstonia solanacearum in Brazil, an ancient centre of diversity of the pathogen

Santiago, T. R., Lopes, C. A., Caetano-Anolles, G. & Mizubuti, E. S. G., Apr 1 2017, In : Plant Pathology. 66, 3, p. 383-392 10 p.

Research output: Contribution to journalArticle

Ralstonia solanacearum
center of diversity
Piper
Ecotype
Brazil

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

Koc, I. & Caetano-Anolles, G., May 1 2017, In : PloS one. 12, 5, e0176129.

Research output: Contribution to journalArticle

Gene Ontology
Phylogeny
Natural History
natural history
Ontology
2016

A Dynamic Model for the Evolution of Protein Structure

Tal, G., Boca, S. M., Mittenthal, J. & Caetano-Anolles, G., May 1 2016, In : Journal of Molecular Evolution. 82, 4-5, p. 230-243 14 p.

Research output: Contribution to journalArticle

protein structure
dynamic models
fold
protein
Proteins
Religious Philosophies
consciousness
Consciousness
Research
leaves
Polygalacturonase
Fusarium
Plant Cells
Computer Simulation
Cell Wall

Investigating the Control of Chlorophyll Degradation by Genomic Correlation Mining

Ghandchi, F. P., Caetano-Anolles, G., Clough, S. J. & Ort, D. R., Sep 1 2016, In : PloS one. 11, 9, e0162327.

Research output: Contribution to journalArticle

Oxygenases
Chlorophyll
oxygenases
genomics
chlorophyll

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

Caetano-Anollés, D. & Caetano-Anollés, G., 2016, In : Life. 6, 4, 24 p.

Research output: Contribution to journalArticle

Open Access
genetic code
ribosomes
Genetic Code
genome
Transfer RNA

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

Aziz, M. F., Caetano-Anollés, K. & Caetano-Anolles, G., Apr 28 2016, In : Scientific Reports. 6, 25058.

Research output: Contribution to journalArticle

Amino Acid Motifs
Metabolic Networks and Pathways
Amino Acid Sequence
History
Protein Domains
2015

A phylogenomic data-driven exploration of viral origins and evolution

Nasir, A. & Caetano-Anolles, G., Jan 1 2015, In : Science Advances. 1, 8, 1500527.

Research output: Contribution to journalArticle

Viruses
Proteome
Replicon
Proteomics
Genome

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

Caetano-Anollés, D. & Caetano-Anolles, G., Jan 1 2015, In : Frontiers in Genetics. 6, JUN, 194.

Research output: Contribution to journalArticle

Large Ribosome Subunits
Ribosomal RNA
Structural Models
Protein Biosynthesis
Growth

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

Mercante, V., Duarte, C. M., Sánchez, C. M., Zalguizuri, A., Caetano-Anolles, G. & Lepek, V. C., Jan 1 2015, In : Frontiers in Plant Science. 6, JAN, p. 1-12 12 p., 12.

Research output: Contribution to journalArticle

Mesorhizobium loti
secretin
type III secretion system
proteins
Lotus glaber

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

Shahzad, K., Mittenthal, J. E. & Caetano-Anolles, G., Aug 11 2015, In : BMC Systems Biology. 9, 1, 44.

Research output: Contribution to journalArticle

Proteome
Language
Organizations
Proteins
Protein

Untangling the origin of viruses and their impact on cellular evolution

Nasir, A., Sun, F. J., Kim, K. M. & Caetano-Anolles, G., Apr 1 2015, In : Annals of the New York Academy of Sciences. 1341, 1, p. 61-74 14 p.

Research output: Contribution to journalArticle

Viruses
Replicon
Virion
Virus
RNA Viruses
2014

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

Caetano-Anolles, G., Mittenthal, J. E., Caetano-Anollés, D. & Kim, K. M., Jan 1 2014, In : Frontiers in Genetics. 5, AUG, article 306.

Research output: Contribution to journalArticle

Chronology
Biodiversity
Biochemistry

A Phylogenomic Census of Molecular Functions Identifies Modern Thermophilic Archaea as the Most Ancient Form of Cellular Life

Nasir, A., Kim, K. M. & Caetano-Anolles, G., Jan 1 2014, In : Archaea. 2014, 706468.

Research output: Contribution to journalArticle

Gene Ontology
Archaea
Censuses
census
genome

A Tree of Cellular Life Inferred from a Genomic Census of Molecular Functions

Kim, K. M., Nasir, A., Hwang, K. & Caetano-Anolles, G., Nov 29 2014, In : Journal of Molecular Evolution. 79, 5-6, p. 240-262 23 p.

Research output: Contribution to journalArticle

Censuses
census
genomics
Phylogeny
Animalia

Global Patterns of Protein Domain Gain and Loss in Superkingdoms

Nasir, A., Kim, K. M. & Caetano-Anolles, G., Jan 1 2014, In : PLoS computational biology. 10, 1, e1003452.

Research output: Contribution to journalArticle

Archaea
proteome
Eukaryota
Proteome
Proteins

The distribution and impact of viral lineages in domains of life

Nasir, A., Forterre, P., Kim, K. M. & Caetano-Anolles, G., Jan 1 2014, In : Frontiers in Microbiology. 5, APR, 194.

Research output: Contribution to journalArticle

Replicon
Capsid
Viruses

The importance of using realistic evolutionary models for retrodicting proteomes

Kim, K. M., Nasir, A. & Caetano-Anolles, G., Apr 1 2014, In : Biochimie. 99, 1, p. 129-137 9 p.

Research output: Contribution to journalArticle

Planetary Evolution
Proteome
Molecular Models
Molecular Evolution
Phylogeny

The Natural History of Biocatalytic Mechanisms

Nath, N., Mitchell, J. B. O. & Caetano-Anolles, G., Jan 1 2014, In : PLoS computational biology. 10, 5, e1003642.

Research output: Contribution to journalArticle

Natural History
natural history
Fold
Enzymes
fold

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

Caetano-Anolles, G. & Sun, F. J., Jan 1 2014, In : Frontiers in Genetics. 5, MAY, 127.

Research output: Contribution to journalArticle

Transfer RNA
Natural History
Ribosomes
Protein Biosynthesis
Genetic Code
2013

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

Mainzer, L. S., Wielgos, M., Thomas, S., Nasir, A., Wang, M., Mittenthal, J. E. & Caetano-Anolles, G., Apr 19 2013, In : Frontiers in Genetics. 4, FEB, Article 16.

Research output: Contribution to journalArticle

Archaea
Optic Disk
Eukaryota
Automatic Data Processing
Reproduction

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

Hwang, K., Oh, J., Kim, T. K., Kim, B. K., Yu, D. S., Hou, B. K., Caetano-Anolles, G., Hong, S. G. & Kim, K. M., May 1 2013, In : PloS one. 8, 5, e62623.

Research output: Contribution to journalArticle

16S Ribosomal RNA
Cluster Analysis
Genes
ribosomal RNA
nucleotide sequences
Pyrococcus abyssi
Pyrococcus
Pyrococcus furiosus
amino acid
protein content

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

Nasir, A. & Caetano-Anolles, G., Jan 1 2013, In : Archaea. 2013, 648746.

Research output: Contribution to journalArticle

Proteome
proteome
History
Bacteria
history

Evolutionary Optimization of Protein Folding

Debès, C., Wang, M., Caetano-Anolles, G. & Gräter, F., Jan 1 2013, In : PLoS computational biology. 9, 1, e1002861.

Research output: Contribution to journalArticle

Protein folding
Protein Folding
protein folding
Evolutionary Optimization
Folding
domain structure
Proteome
Phylogeny
proteome
Fold

Phylogenomics supports a cellularly structured urancestor

Seufferheld, M. J. & Caetano-Anolles, G., Apr 1 2013, In : Journal of Molecular Microbiology and Biotechnology. 23, 1-2, p. 178-191 14 p.

Research output: Contribution to journalArticle

Organelles
Polyphosphates
Periplasm
Capsid
Cellular Structures

Structural Phylogenomics Retrodicts the Origin of the Genetic Code and Uncovers the Evolutionary Impact of Protein Flexibility

Caetano-Anolles, G., Wang, M. & Caetano-Anollés, D., Aug 21 2013, In : PloS one. 8, 8, e72225.

Research output: Contribution to journalArticle

aminoacyl tRNA ligases
Genetic Code
genetic code
Transfer RNA
Amino Acyl-tRNA Synthetases

Structural Phylogenomics Reveals Gradual Evolutionary Replacement of Abiotic Chemistries by Protein Enzymes in Purine Metabolism

Caetano-Anollés, K. & Caetano-Anolles, G., Mar 13 2013, In : PloS one. 8, 3, e59300.

Research output: Contribution to journalArticle

Biosynthesis
purines
Metabolism
chemistry
Nucleotides

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

Caetano-Anolles, G. & Seufferheld, M. J., Jan 1 2013, In : Journal of Molecular Microbiology and Biotechnology. 23, 1-2, p. 152-177 26 p.

Research output: Contribution to journalArticle

Cellular Structures
Biochemistry
RNA
Molecular Structure
Nucleic Acids

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

Kim, H. S., Mittenthal, J. E. & Caetano-Anolles, G., Jan 1 2013, In : Unknown Journal. 10, 1, 1 p.

Research output: Contribution to journalArticle

Enzymes
Archaea
Metabolic Networks and Pathways
Eukaryota
Vitamins
2012

Benefits of using molecular structure and abundance in phylogenomic analysis

Caetano-Anolles, G. & Nasir, A., Dec 1 2012, In : Frontiers in Genetics. 3, SEP, Article 172.

Research output: Contribution to journalArticle

Molecular Structure

Biphasic patterns of diversification and the emergence of modules

Mittenthal, J., Caetano-Anollés, D. & Caetano-Anolles, G., Dec 1 2012, In : Frontiers in Genetics. 3, AUG, Article 147.

Research output: Contribution to journalArticle

Cellular Structures
Molecular Structure
Embryonic Structures
RNA
Proteins
Archaea
ancestry
virus
proteome
viruses

Protein domain structure uncovers the origin of aerobic metabolism and the rise of planetary oxygen

Kim, K. M., Qin, T., Jiang, Y. Y., Chen, L. L., Xiong, M., Caetano-Anollés, D., Zhang, H. Y. & Caetano-Anolles, G., Jan 11 2012, In : Structure. 20, 1, p. 67-76 10 p.

Research output: Contribution to journalArticle

Oxygen
Biochemistry
Pyridoxal
Pyridoxal Phosphate
Censuses

Ribosomal history reveals origins of modern protein synthesis

Harish, A. & Caetano-Anolles, G., Mar 12 2012, In : PloS one. 7, 3, e32776.

Research output: Contribution to journalArticle

ribosomes
Ribosomes
protein synthesis
History
history

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

Zhang, H. Y., Qin, T., Jiang, Y. Y. & Caetano-Anolles, G., Sep 6 2012, In : Journal of Biomolecular Structure and Dynamics. 30, 5, p. 542-545 4 p.

Research output: Contribution to journalArticle

Iron-Sulfur Proteins
Cysteine
Biosynthetic Pathways
Transfer RNA
Sulfur
proteome
ancestry
fold
history
protein

The impact of oxygen on metabolic evolution: A chemoinformatic investigation

Jiang, Y. Y., Kong, D. X., Qin, T., Li, X., Caetano-Anolles, G. & Zhang, H. Y., Mar 1 2012, In : PLoS computational biology. 8, 3, e1002426.

Research output: Contribution to journalArticle

Metabolites
Oxygen
metabolite
metabolites
oxygen