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Results: 1 to 20 of 104

1.

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.

PMID:
25309572
[PubMed]
Free PMC Article
2.

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.

PMID:
25249790
[PubMed - in process]
Free PMC Article
3.

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 Aug 17. [Epub ahead of print]

PMID:
25128982
[PubMed - as supplied by publisher]
4.

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.

PMID:
24991191
[PubMed - in process]
Free PMC Article
5.

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.

PMID:
24987307
[PubMed - in process]
Free PMC Article
6.

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.

PMID:
24874434
[PubMed - in process]
Free PMC Article
7.

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.

PMID:
24847358
[PubMed]
Free PMC Article
8.

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.

PMID:
24817866
[PubMed]
Free PMC Article
9.

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.

PMID:
24499935
[PubMed - in process]
Free PMC Article
10.

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.

PMID:
24492748
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
24316279
[PubMed - indexed for MEDLINE]
Free Article
12.

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.

PMID:
24187517
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
23991065
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
23650520
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
[PubMed - indexed for MEDLINE]
16.

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
[PubMed - indexed for MEDLINE]
17.

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.

PMID:
23555236
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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.

PMID:
23550145
[PubMed]
Free PMC Article
19.

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.

PMID:
23516625
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
23443991
[PubMed]
Free PMC Article

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