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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

2019

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

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

2017

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

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

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

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

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

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

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

Global Patterns of Protein Domain Gain and Loss in Superkingdoms

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

Research output: Contribution to journalArticle

The distribution and impact of viral lineages in domains of life

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

Research output: Contribution to journalArticle

The importance of using realistic evolutionary models for retrodicting proteomes

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

Research output: Contribution to journalArticle

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

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

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

Research output: Contribution to journalArticle

2013

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

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

Research output: Contribution to journalArticle

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-Anollés, G., Hong, S. G. & Kim, K. M., May 1 2013, In : PloS one. 8, 5, e62623.

Research output: Contribution to journalArticle

Evolutionary Optimization of Protein Folding

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

Research output: Contribution to journalArticle

Phylogenomics supports a cellularly structured urancestor

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

Research output: Contribution to journalArticle

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

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

Research output: Contribution to journalArticle

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

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

Research output: Contribution to journalArticle

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

Caetano-Anollés, 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

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

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

Research output: Contribution to journalArticle

Open Access
2012

Benefits of using molecular structure and abundance in phylogenomic analysis

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

Research output: Contribution to journalArticle

Biphasic patterns of diversification and the emergence of modules

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

Research output: Contribution to journalArticle