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

Staley JT, Caetano-Anollés G.

Bioessays. 2018 Jun 26. doi: 10.1002/bies.201800036. [Epub ahead of print]


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

Caetano-Anollés K, Caetano-Anollés D, Nasir A, Kim KM, Caetano-Anollés G.

Biochimie. 2018 Jun;149:135-136. doi: 10.1016/j.biochi.2018.04.001. Epub 2018 Apr 7.


Do Viruses Exchange Genes across Superkingdoms of Life?

Malik SS, Azem-E-Zahra S, Kim KM, Caetano-Anollés G, Nasir A.

Front Microbiol. 2017 Oct 31;8:2110. doi: 10.3389/fmicb.2017.02110. eCollection 2017.


RubisCO and the Search for Biomolecular Culprits of Planetary Change.

Caetano-Anollés G.

Bioessays. 2017 Nov;39(11). doi: 10.1002/bies.201700174. Epub 2017 Oct 13. No abstract available.


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

Nasir A, Kim KM, Caetano-Anollés G.

Front Microbiol. 2017 Jun 23;8:1178. doi: 10.3389/fmicb.2017.01178. eCollection 2017.


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

Nasir A, Kim KM, Caetano-Anollés G.

Bioessays. 2017 Aug;39(8). doi: 10.1002/bies.201700026. Epub 2017 Jun 16. Review.


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

Chang HX, Yendrek CR, Caetano-Anolles G, Hartman GL.

BMC Microbiol. 2017 May 10;17(1):110. doi: 10.1186/s12866-017-1020-8. No abstract available.


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

Koç I, Caetano-Anollés G.

PLoS One. 2017 May 3;12(5):e0176129. doi: 10.1371/journal.pone.0176129. eCollection 2017.


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

Nasir A, Caetano-Anollés G.

Front Microbiol. 2017 Mar 10;8:380. doi: 10.3389/fmicb.2017.00380. eCollection 2017.


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

Colson P, La Scola B, Levasseur A, Caetano-Anollés G, Raoult D.

Nat Rev Microbiol. 2017 Apr;15(4):243-254. doi: 10.1038/nrmicro.2016.197. Epub 2017 Feb 27. Review.


Commentary: History of the ribosome and the origin of translation.

Caetano-Anollés D, Caetano-Anollés G.

Front Mol Biosci. 2017 Jan 10;3:87. doi: 10.3389/fmolb.2016.00087. eCollection 2016. No abstract available.


Arguments Reinforcing the Three-Domain View of Diversified Cellular Life.

Nasir A, Kim KM, Da Cunha V, Caetano-Anollés G.

Archaea. 2016 Dec 5;2016:1851865. doi: 10.1155/2016/1851865. eCollection 2016. Review.


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

Caetano-Anollés D, Caetano-Anollés G.

Life (Basel). 2016 Dec 2;6(4). pii: E43.


Investigating the Control of Chlorophyll Degradation by Genomic Correlation Mining.

Ghandchi FP, Caetano-Anolles G, Clough SJ, Ort DR.

PLoS One. 2016 Sep 12;11(9):e0162327. doi: 10.1371/journal.pone.0162327. eCollection 2016.


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

Chang HX, Yendrek CR, Caetano-Anolles G, Hartman GL.

BMC Microbiol. 2016 Jul 12;16(1):147. doi: 10.1186/s12866-016-0761-0. Erratum in: BMC Microbiol. 2017 May 10;17 (1):110.


A Dynamic Model for the Evolution of Protein Structure.

Tal G, Boca SM, Mittenthal J, Caetano-Anollés G.

J Mol Evol. 2016 May;82(4-5):230-43. doi: 10.1007/s00239-016-9740-1. Epub 2016 May 5.


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

Aziz MF, Caetano-Anollés K, Caetano-Anollés G.

Sci Rep. 2016 Apr 28;6:25058. doi: 10.1038/srep25058.


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

Caetano-Anollés G.

Commun Integr Biol. 2016 Jan 8;9(1):e1123356. doi: 10.1080/19420889.2015.1123356. eCollection 2016 Jan-Feb. Erratum in: Commun Integr Biol. 2016 Mar-Apr;9(2):e1178031.


A phylogenomic data-driven exploration of viral origins and evolution.

Nasir A, Caetano-Anollés G.

Sci Adv. 2015 Sep 25;1(8):e1500527. doi: 10.1126/sciadv.1500527. eCollection 2015 Sep.


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

Shahzad K, Mittenthal JE, Caetano-Anollés G.

BMC Syst Biol. 2015 Aug 11;9:44. doi: 10.1186/s12918-015-0192-9.


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

Nasir A, Kim KM, Caetano-Anollés G.

Trends Microbiol. 2015 Aug;23(8):448-50. doi: 10.1016/j.tim.2015.06.001. Epub 2015 Jun 22.


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

Caetano-Anollés D, Caetano-Anollés G.

Front Genet. 2015 Jun 2;6:194. doi: 10.3389/fgene.2015.00194. eCollection 2015.


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

Caetano-Anollés G.

J Mol Evol. 2015 Apr;80(3-4):162-5. doi: 10.1007/s00239-015-9677-9. Epub 2015 Apr 12.


Untangling the origin of viruses and their impact on cellular evolution.

Nasir A, Sun FJ, Kim KM, Caetano-Anollés G.

Ann N Y Acad Sci. 2015 Apr;1341:61-74. doi: 10.1111/nyas.12735. Epub 2015 Mar 10. Review.


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

Mercante V, Duarte CM, Sánchez CM, Zalguizuri A, Caetano-Anollés G, Lepek VC.

Front Plant Sci. 2015 Jan 30;6:12. doi: 10.3389/fpls.2015.00012. eCollection 2015.


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

Caetano-Anollés G, Caetano-Anollés D.

Comput Struct Biotechnol J. 2015 Jul 26;13:427-47. doi: 10.1016/j.csbj.2015.07.003. eCollection 2015. Review.


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

Caetano-Anollés G, Mittenthal JE, Caetano-Anollés D, Kim KM.

Front Genet. 2014 Sep 11;5:306. doi: 10.3389/fgene.2014.00306. eCollection 2014.


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

Nasir A, Kim KM, Caetano-Anollés G.

Archaea. 2014 Aug 31;2014:706468. doi: 10.1155/2014/706468. eCollection 2014.


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

Kim KM, Nasir A, Hwang K, Caetano-Anollés G.

J Mol Evol. 2014 Dec;79(5-6):240-62. doi: 10.1007/s00239-014-9637-9. Epub 2014 Aug 17.


The origin and evolution of the archaeal domain.

Caetano-Anollés G, Kim KM.

Archaea. 2014 Jun 4;2014:915828. doi: 10.1155/2014/915828. eCollection 2014. No abstract available.


Archaea: the first domain of diversified life.

Caetano-Anollés G, Nasir A, Zhou K, Caetano-Anollés D, Mittenthal JE, Sun FJ, Kim KM.

Archaea. 2014 Jun 2;2014:590214. doi: 10.1155/2014/590214. eCollection 2014. Review.


The natural history of biocatalytic mechanisms.

Nath N, Mitchell JB, Caetano-Anollés G.

PLoS Comput Biol. 2014 May 29;10(5):e1003642. doi: 10.1371/journal.pcbi.1003642. eCollection 2014 May.


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

Caetano-Anollés G, Sun FJ.

Front Genet. 2014 May 9;5:127. doi: 10.3389/fgene.2014.00127. eCollection 2014. No abstract available.


The distribution and impact of viral lineages in domains of life.

Nasir A, Forterre P, Kim KM, Caetano-Anollés G.

Front Microbiol. 2014 Apr 30;5:194. doi: 10.3389/fmicb.2014.00194. eCollection 2014. No abstract available.


Global patterns of protein domain gain and loss in superkingdoms.

Nasir A, Kim KM, Caetano-Anollés G.

PLoS Comput Biol. 2014 Jan 30;10(1):e1003452. doi: 10.1371/journal.pcbi.1003452. eCollection 2014 Jan.


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

Nasir A, Caetano-Anollés G.

Archaea. 2013 Dec 31;2013:648746. doi: 10.1155/2013/648746. eCollection 2013.


The importance of using realistic evolutionary models for retrodicting proteomes.

Kim KM, Nasir A, Caetano-Anollés G.

Biochimie. 2014 Apr;99:129-37. doi: 10.1016/j.biochi.2013.11.019. Epub 2013 Dec 4.


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

Yafremava LS, Di Giulio M, Caetano-Anollés G.

Archaea. 2013;2013:680436. doi: 10.1155/2013/680436. Epub 2013 Sep 26.


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.

PLoS One. 2013 Aug 21;8(8):e72225. doi: 10.1371/journal.pone.0072225. eCollection 2013.


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

Hwang K, Oh J, Kim TK, Kim BK, Yu DS, Hou BK, Caetano-Anollés G, Hong SG, Kim KM.

PLoS One. 2013 May 1;8(5):e62623. doi: 10.1371/journal.pone.0062623. Print 2013. Erratum in: PLoS One. 2013;8(5). doi:10.1371/annotation/bb3baaad-6b58-41a0-96cc-7bdc819de411.


Phylogenomics supports a cellularly structured urancestor.

Seufferheld MJ, Caetano-Anollés G.

J Mol Microbiol Biotechnol. 2013;23(1-2):178-91. doi: 10.1159/000346552. Epub 2013 Apr 18. Review.


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

Caetano-Anollés G, Seufferheld MJ.

J Mol Microbiol Biotechnol. 2013;23(1-2):152-77. doi: 10.1159/000346551. Epub 2013 Apr 18. Review.


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

Bukhari SA, Caetano-Anollés G.

PLoS Comput Biol. 2013;9(3):e1003009. doi: 10.1371/journal.pcbi.1003009. Epub 2013 Mar 28.


Viral evolution: Primordial cellular origins and late adaptation to parasitism.

Nasir A, Kim KM, Caetano-Anollés G.

Mob Genet Elements. 2012 Sep 1;2(5):247-252.


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

Caetano-Anollés K, Caetano-Anollés G.

PLoS One. 2013;8(3):e59300. doi: 10.1371/journal.pone.0059300. Epub 2013 Mar 13.


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

Yafremava LS, Wielgos M, Thomas S, Nasir A, Wang M, Mittenthal JE, Caetano-Anollés G.

Front Genet. 2013 Feb 25;4:16. doi: 10.3389/fgene.2013.00016. eCollection 2013.


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

Kim HS, Mittenthal JE, Caetano-Anollés G.

J Integr Bioinform. 2013 Feb 14;10(1):214. doi: 10.2390/biecoll-jib-2013-214.


Evolutionary optimization of protein folding.

Debès C, Wang M, Caetano-Anollés G, Gräter F.

PLoS Comput Biol. 2013;9(1):e1002861. doi: 10.1371/journal.pcbi.1002861. Epub 2013 Jan 17.


Benefits of using molecular structure and abundance in phylogenomic analysis.

Caetano-Anollés G, Nasir A.

Front Genet. 2012 Sep 6;3:172. doi: 10.3389/fgene.2012.00172. eCollection 2012. No abstract available.

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