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Items: 1 to 50 of 133

1.

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]

PMID:
29944192
2.

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.

PMID:
29631013
3.
4.

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.

5.

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.

PMID:
29027685
6.

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.

7.

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.

PMID:
28621804
8.

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.

9.

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.

10.

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.

11.

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.

PMID:
28239153
12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

PMID:
27146880
18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

PMID:
26112912
23.

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.

24.

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.

25.

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.

PMID:
25758413
26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

PMID:
25128982
31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

PMID:
23615204
43.

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.

PMID:
23615203
44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

PMID:
23406778
49.

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.

50.

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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