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Research Output

2020

Bacterial Origin and Reductive Evolution of the CPR Group

Bokhari, R. H., Amirjan, N., Jeong, H., Kim, K. M., Caetano-Anollés, G., Nasir, A. & Bapteste, E., Mar 17 2020, In : Genome biology and evolution. 12, 3, p. 103-121 19 p.

Research output: Contribution to journalArticle

Open Access

Genetic Structure of Ralstonia solanacearum and Ralstonia pseudosolanacearum in Brazil

Santiago, T. R., Lopes, C. A., Caetano-Anollés, G. & Mizubuti, E. S. G., 2020, In : Plant disease. 104, 4, p. 1019-1025 7 p.

Research output: Contribution to journalArticle

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

Tomaszewski, T., DeVries, R. S., Dong, M., Bhatia, G., Norsworthy, M. D., Zheng, X. & Caetano-Anolles, G., 2020, (In preparation) Cold Spring Harbor Laboratory Press, 36 p. (bioRxiv).

Research output: Working paper

The origin and evolution of viruses inferred from fold family structure

Mughal, F., Nasir, A. & Caetano-Anollés, G., Oct 2020, In : Archives of Virology. 165, 10, p. 2177-2191 15 p.

Research output: Contribution to journalReview article

2019

Editorial: Viruses, Genetic Exchange, and the Tree of Life

Nasir, A., Caetano-Anollés, G. & Claverie, J. M., Nov 29 2019, In : Frontiers in Microbiology. 10, 2782.

Research output: Contribution to journalEditorial

Open Access

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., 2019, In : Evolutionary Bioinformatics. 15

Research output: Contribution to journalReview article

Open Access

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

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

Research output: Contribution to journalArticle

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

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

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

Research output: Contribution to journalArticle

Open Access

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

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

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
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

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

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

Research output: Contribution to journalReview article

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

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-Anollés, G., Jun 2018, In : Biochimie. 149, p. 135-136 2 p.

Research output: Contribution to journalArticle

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

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

Research output: Contribution to journalReview article

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

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

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

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

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

Research output: Contribution to journalReview article

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

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

Research output: Contribution to journalReview article

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

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

Research output: Contribution to journalArticle

RubisCO and the Search for Biomolecular Culprits of Planetary Change

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

Research output: Contribution to journalComment/debate

The compressed vocabulary of the proteins of archaea

Caetano-Anollés, 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

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

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

Arguments Reinforcing the Three-Domain View of Diversified Cellular Life

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

Research output: Contribution to journalReview article

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

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

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

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

Research output: Contribution to journalArticle

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

2015

A phylogenomic data-driven exploration of viral origins and evolution

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

Research output: Contribution to journalArticle

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-Anollés, G., Aug 1 2015, In : Trends in Microbiology. 23, 8, p. 448-450 3 p.

Research output: Contribution to journalShort survey

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

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-Anollés, G. & Lepek, V. C., 2015, In : Frontiers in Plant Science. 6, JAN, p. 1-12 12 p., 12.

Research output: Contribution to journalArticle

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

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

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., 2014, In : Frontiers in Genetics. 5, AUG, article 306.

Research output: Contribution to journalArticle

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., 2014, In : Archaea. 2014, 706468.

Research output: Contribution to journalArticle

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

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

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

Research output: Contribution to journalArticle