1986 …2019
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Research Output 1986 2019

2019

Correction to: Genome-wide analysis of the MYB-CC gene family of maize (Genetica, (2019), 147, 1, (1-9), 10.1007/s10709-018-0042-y)

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

Research output: Contribution to journalComment/debate

Zea mays
Genome
genome
corn
Genes

Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis

Caetano-Anollés, G., Aziz, M. F., Mughal, F., Gräter, F., Koç, I., Caetano-Anollés, K. & Caetano-Anollés, D., Jan 1 2019, In : Evolutionary Bioinformatics. 15

Research output: Contribution to journalReview article

Open Access
Metabolomics
Metabolic Networks and Pathways
Transcriptome
Proteins
protein

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., Caetano-Anollés, G., Yan, L., Li, R. & Bai, J., 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

MANET 3.0: Hierarchy and modularity in evolving metabolic networks

Mughal, F. & Caetano-Anollés, G., Oct 24 2019, In : PloS one. 14, 10, e0224201.

Research output: Contribution to journalArticle

Open Access
Metabolic Networks and Pathways
ancestry
Hierarchical systems
Enzymes
enzymes

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

Caetano-Anollés, D., Nasir, A., Kim, K. M. & Caetano-Anollés, 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-Anollés, G. & Raoult, D., Nov 27 2018, In : Frontiers in Microbiology. 9, NOV, 2668.

Research output: Contribution to journalArticle

Mosaicism
Archaea
Eukaryota
Bacteria
Genes

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

Staley, J. T. & Caetano-Anolles, G., Aug 2018, In : BioEssays. 40, 8, 1800036.

Research output: Contribution to journalReview article

Archaea
Bacteria
Cells
Eukaryota
Methane

Evolution of macromolecular structure: a 'double tale' of biological accretion and diversification

Caetano-Anollés, D., Caetano-Anollés, K. & Caetano-Anollés, G., Oct 1 2018, In : Science progress. 101, 4, p. 360-383 24 p.

Research output: Contribution to journalReview article

Genomics
Nucleic Acids
Growth
Proteins
Electric network analysis
Metabolites
Arabidopsis
Cold-Shock Response
Activity Cycles

Order and polarity in character state transformation models that root the tree of life

Caetano-Anollés, K., Caetano-Anollés, D., Nasir, A., Kim, K. M. & Caetano-Anolles, G., Jun 2018, In : Biochimie. 149, p. 135-136 2 p.

Research output: Contribution to journalLetter

Classifiers
Proteins
Bacterial Secretion Systems
Bacteria
Genes

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

Caetano-Anolles, G., Nasir, A., Kim, K. M. & Caetano-Anollés, D., Oct 1 2018, In : Evolutionary Bioinformatics. 14

Research output: Contribution to journalReview article

Phylogeny
rooting
phylogeny
Biological Evolution
Data storage equipment
2017

Commentary: History of the ribosome and the origin of translation

Caetano-Anollés, D. & Caetano-Anollés, G., Jan 10 2017, In : Frontiers in Molecular Biosciences. 3, JAN, 87.

Research output: Contribution to journalComment/debate

Molecular Evolution
Ribosomes

Do viruses exchange genes across superkingdoms of life?

Malik, S. S., Azem-e-Zahra, S., Kim, K. M., Caetano-Anollés, 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-Anollés, G., Mar 10 2017, In : Frontiers in Microbiology. 8, MAR, 380.

Research output: Contribution to journalArticle

Capsid
Capsid Proteins
Viruses
Metagenome
Planets

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

Nasir, A., Kim, K. M. & Caetano-Anolles, G., Aug 2017, In : BioEssays. 39, 8, 1700026.

Research output: Contribution to journalReview article

Long Term Evolution (LTE)
Viruses
Virus Latency
Symbiosis
Metagenomics

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

Colson, P., La Scola, B., Levasseur, A., Caetano-Anolles, G. & Raoult, D., Mar 13 2017, In : Nature Reviews Microbiology. 15, 4, p. 243-254 12 p.

Research output: Contribution to journalReview article

Mimiviridae
Amoeba
Viruses
Virus Internalization
Virology
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

RubisCO and the Search for Biomolecular Culprits of Planetary Change

Caetano-Anolles, G., Nov 2017, In : BioEssays. 39, 11, 1700174.

Research output: Contribution to journalComment/debate

Ribulose-Bisphosphate Carboxylase
Plant Proteins
Carbon Dioxide

The compressed vocabulary of the proteins of archaea

Caetano-Anolles, G., Minhas, B. F., Aziz, F., Mughal, F., Shahzad, K., Tal, G., Mittenthal, J. E., Caetano-Anollés, D., Koç, I., Nasir, A., Caetano-Anollés, K. & Kim, K. M., Sep 27 2017, Biocommunication of Archaea. Springer International Publishing, p. 147-174 28 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Vocabulary
Archaea
Proteins
proteins

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

Koc, I. & Caetano-Anolles, G., May 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-Anollés, 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

Arguments Reinforcing the Three-Domain View of Diversified Cellular Life

Nasir, A., Kim, K. M., Da Cunha, V. & Caetano-Anollés, G., Jan 1 2016, In : Archaea. 2016, 1851865.

Research output: Contribution to journalReview article

Eukaryota
ancestry
Phylogeny
eukaryote
domain structure
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 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

The phylogenomic roots of translation

Caetano-Anollés, D. & Caetano-Anollés, G., Jan 1 2016, Evolution of the Protein Synthesis Machinery and Its Regulation. Springer International Publishing, p. 9-30 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Transfer RNA
ribosomes
Ribosomes
translation (genetics)
Genetic Code
2015
Peptidyl Transferases
ribosomes
Ribosomes
transferases
accretion

A phylogenomic data-driven exploration of viral origins and evolution

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

Research output: Contribution to journalArticle

Viruses
Proteome
Replicon
Proteomics
Genome
Synthetic Biology
Ribosomes
Censuses
Proteins
Macromolecules

In grateful recognition of our Editorial Board

Bolhuis, J., Botelho, R., Caetano-Anolles, G., Carninci, P., Cheah, K., Dagan, T., Frye, M., Goodson, H., Gough, J., Groth, A., Huang, S., Isalan, M., Kaeberlein, M., López-García, P., Pei, D., Schierwater, B., Schumacher, B., Shen, M., Sorek, R., Thomas, D. & 4 others, Tian, X. L., Veitia, R., Whitelaw, E. & Wong, R., Dec 2015, In : BioEssays. 37, 12, p. 1254-1255 2 p.

Research output: Contribution to journalEditorial

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

Nasir, A., Kim, K. M. & Caetano-Anolles, G., Aug 1 2015, In : Trends in Microbiology. 23, 8, p. 448-450 3 p.

Research output: Contribution to journalShort survey

Eukaryota
History
Genome

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

Caetano-Anollés, D. & Caetano-Anollés, 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-Anollés, 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-Anollés, 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-Anollés, G., Jan 1 2014, In : Archaea. 2014, 706468.

Research output: Contribution to journalArticle

Gene Ontology
Archaea
Censuses
census
genome

Archaea: The first domain of diversified life

Caetano-Anollés, G., Nasir, A., Zhou, K., Caetano-Anollés, D., Mittenthal, J. E., Sun, F. J. & Kim, K. M., 2014, In : Archaea. 2014, 590214.

Research output: Contribution to journalReview article

Archaea
origin of life
phylogenetics
phylogeny
molecular models

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-Anollés, 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-Anollés, 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-Anollés, G., May 2014, In : PLoS computational biology. 10, 5, e1003642.

Research output: Contribution to journalArticle

Natural History
natural history
Fold
Enzymes
fold