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Items: 29

1.

Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis.

Caetano-Anollés G, Aziz MF, Mughal F, Gräter F, Koç I, Caetano-Anollés K, Caetano-Anollés D.

Evol Bioinform Online. 2019 Sep 5;15:1176934319872980. doi: 10.1177/1176934319872980. eCollection 2019. Review.

2.

Deregulating mitochondrial metabolite and ion transport has beneficial effects in yeast and human cellular models for NARP syndrome.

Su X, Rak M, Tetaud E, Godard F, Sardin E, Bouhier M, Gombeau K, Caetano-Anollés D, Salin B, Chen H, di Rago JP, Tribouillard-Tanvier D.

Hum Mol Genet. 2019 Jul 5. pii: ddz160. doi: 10.1093/hmg/ddz160. [Epub ahead of print]

PMID:
31276579
3.

Testing Empirical Support for Evolutionary Models that Root the Tree of Life.

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

J Mol Evol. 2019 Apr;87(2-3):131-142. doi: 10.1007/s00239-019-09891-7. Epub 2019 Mar 18.

4.

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

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

Evol Bioinform Online. 2018 Oct 20;14:1176934318805101. doi: 10.1177/1176934318805101. eCollection 2018. Review.

5.

Evolution of macromolecular structure: a 'double tale' of biological accretion and diversification.

Caetano-Anollés D, Caetano-Anollés K, Caetano-Anollés G.

Sci Prog. 2018 Oct 1;101(4):360-383. doi: 10.3184/003685018X15379391431599. Epub 2018 Oct 8. Review.

PMID:
30296968
6.

Agricultural research, or a new bioweapon system?

Reeves RG, Voeneky S, Caetano-Anollés D, Beck F, Boëte C.

Science. 2018 Oct 5;362(6410):35-37. doi: 10.1126/science.aat7664. No abstract available.

PMID:
30287653
7.

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
8.

Implementing Goal-Directed Foraging Decisions of a Simpler Nervous System in Simulation.

Brown JW, Caetano-Anollés D, Catanho M, Gribkova E, Ryckman N, Tian K, Voloshin M, Gillette R.

eNeuro. 2018 Mar 1;5(1). pii: ENEURO.0400-17.2018. doi: 10.1523/ENEURO.0400-17.2018. eCollection 2018 Jan-Feb.

9.

Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice.

Saul MC, Seward CH, Troy JM, Zhang H, Sloofman LG, Lu X, Weisner PA, Caetano-Anolles D, Sun H, Zhao SD, Chandrasekaran S, Sinha S, Stubbs L.

Genome Res. 2017 Jun;27(6):959-972. doi: 10.1101/gr.214221.116. Epub 2017 Mar 29.

10.

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.

11.

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.

12.

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.

13.

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.

14.

Neuromolecular responses to social challenge: common mechanisms across mouse, stickleback fish, and honey bee.

Rittschof CC, Bukhari SA, Sloofman LG, Troy JM, Caetano-Anollés D, Cash-Ahmed A, Kent M, Lu X, Sanogo YO, Weisner PA, Zhang H, Bell AM, Ma J, Sinha S, Robinson GE, Stubbs L.

Proc Natl Acad Sci U S A. 2014 Dec 16;111(50):17929-34. doi: 10.1073/pnas.1420369111. Epub 2014 Dec 1.

15.

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.

16.

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.

17.

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.

18.

Biphasic patterns of diversification and the emergence of modules.

Mittenthal J, Caetano-Anollés D, Caetano-Anollés G.

Front Genet. 2012 Aug 7;3:147. doi: 10.3389/fgene.2012.00147. eCollection 2012.

19.

Protein domain structure uncovers the origin of aerobic metabolism and the rise of planetary oxygen.

Kim KM, Qin T, Jiang YY, Chen LL, Xiong M, Caetano-Anollés D, Zhang HY, Caetano-Anollés G.

Structure. 2012 Jan 11;20(1):67-76. doi: 10.1016/j.str.2011.11.003.

20.

The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesis.

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

J Mol Evol. 2012 Feb;74(1-2):1-34. doi: 10.1007/s00239-011-9480-1. Epub 2012 Jan 1. Erratum in: J Mol Evol. 2012 Feb;74(1-2):35-6.

PMID:
22210458
21.

Gain, loss and divergence in primate zinc-finger genes: a rich resource for evolution of gene regulatory differences between species.

Nowick K, Fields C, Gernat T, Caetano-Anolles D, Kholina N, Stubbs L.

PLoS One. 2011;6(6):e21553. doi: 10.1371/journal.pone.0021553. Epub 2011 Jun 29.

22.

Function and Evolution of C2H2 Zinc Finger Arrays.

Stubbs L, Sun Y, Caetano-Anolles D.

Subcell Biochem. 2011;52:75-94. doi: 10.1007/978-90-481-9069-0_4.

PMID:
21557079
23.

Proteome evolution and the metabolic origins of translation and cellular life.

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

J Mol Evol. 2011 Jan;72(1):14-33. doi: 10.1007/s00239-010-9400-9. Epub 2010 Nov 17.

PMID:
21082171
24.

The origin, evolution and structure of the protein world.

Caetano-Anollés G, Wang M, Caetano-Anollés D, Mittenthal JE.

Biochem J. 2009 Feb 1;417(3):621-37. doi: 10.1042/BJ20082063. Review.

PMID:
19133840
25.

The origin and evolution of modern metabolism.

Caetano-Anollés G, Yafremava LS, Gee H, Caetano-Anollés D, Kim HS, Mittenthal JE.

Int J Biochem Cell Biol. 2009 Feb;41(2):285-97. doi: 10.1016/j.biocel.2008.08.022. Epub 2008 Aug 26. Review.

PMID:
18790074
26.

Origins and evolution of modern biochemistry: insights from genomes and molecular structure.

Caetano-Anolles G, Sun FJ, Wang M, Yafremava LS, Harish A, Kim HS, Knudsen V, Caetano-Anolles D, Mittenthal JE.

Front Biosci. 2008 May 1;13:5212-40. Review.

PMID:
18508583
27.

Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world.

Wang M, Yafremava LS, Caetano-Anollés D, Mittenthal JE, Caetano-Anollés G.

Genome Res. 2007 Nov;17(11):1572-85. Epub 2007 Oct 1.

28.

Universal sharing patterns in proteomes and evolution of protein fold architecture and life.

Caetano-Anollés G, Caetano-Anollés D.

J Mol Evol. 2005 Apr;60(4):484-98.

PMID:
15883883
29.

An evolutionarily structured universe of protein architecture.

Caetano-Anollés G, Caetano-Anollés D.

Genome Res. 2003 Jul;13(7):1563-71.

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