Mouse facial structure under selective pressures:


Morphology can evolve very rapidly in populations, which can lead to novel adaptations in response to environmental changes. As a current postdoctoral fellow with Dr. Diethard Tautz at the Max Planck Institute for Evolutionary Biology, I am aiming to validate the functions of genes that are responsible for controlling skull and mandible structure during rodent development, and how those features are impacted by evolutionary pressures.


Diethard Tautz Group | Project Description (MPI) | Project Description (NSF)





Regulation of neurogenesis by zinc finger duplication:


My PhD thesis research with Dr. Lisa Stubbs at the Carl R. Woese Institute for Genomic Biology investigated the roles of ZNF286A, a Krüppel-type zinc finger transcription factor that regulates the differentiation of neural precursor cells in critical neuronal and developmental pathways as it winds around the DNA molecule. These pathways are implicated in microcephaly, schizophrenia, and other neurological disorders. While ZNF286A occurs as a unique gene in all other species, a gene duplication event in very recent primate history created a human-specific duplicate called ZNF286B, permitting this ancient mammalian gene to take on novel functions in the adult human brain.


Lisa J. Stubbs Lab | Research Description (IGB)




Molecular roots of the social brain:


During my PhD studies, I collaborated on a multi-disciplinary project investigating the neuromolecular basis of social behavior across species, utilitzing mice, stickleback fish, and bees as models. Just as there is diversity in the physical structure of animals, there is great variation in the structure of their social interactions with other members of their own species (ie. aggression, mate selection, care of young). Despite being separated by hundred of millions of years, it is clear that these behaviors are guided by deeply conserved neural biochemistry lying on the same gene networks. I focused mainly on the behavioral and molecular affects of aggression and maternal care in mice.


Lisa J. Stubbs Lab | Research Description (IGB) | Press Release (Simons Foundation)




Annotating the ancient origins of fold superfamily domain functions:


During my BA and beyond, I have worked on a number of projects in evolutionary bioinformatics with both Dr. Gustavo Caetano-Anollés and Dr. Jay Mittenthal, looking at the evolution of protein domain structure and their emergence in very early planetary history as a result of Earth's early chemistry in the ancient oceans. My BA research with Dr. Jay E. Mittenthal involved annotating the fold superfamily domain functions or known proteins using phylogenetic and protein fold architecture data available in published databases.


Research Description | GCA Lab










[In review]

Caetano-Anollés D, Kazemian AM, Zhang H, Lu X, Brinkman J, Sinha S, Stubbs L. (2016). ZNF286A and human-specific duplicate, ZNF286B, compete with REST at RE-1 target sites to drive differentiation of precursor cells. PLOS ONE.


[In review]

Saul MC, Seward CH, Troy J, Zhang H, Sloofman L, Lu X, Weisner PA, Caetano-Anollés D, Sun H, Zhao SD, Chandrasekaran S, Sinha S, Stubbs L. (2016). Transcriptional regulatory dynamics set the stage for a coordinated metabolic and neural response to social threat in mice. J Mol Evol.


Caetano-Anollés G, Caetano-Anollés D. (2015). Computing the origin and evolution of the ribosome from its structure – uncovering processes of macromolecular accretion benefiting synthetic biology. Comput Struct Biotechnol J, 13:427-447. LINK


Caetano-Anollés D, Caetano-Anollés G. (2015). Ribosomal accretion, apriorism and the phylogenetic method: A response to Petrov and Williams. Front Genet, 6:194. LINK


Rittschof C, Bukhari S, Sloofman L, Caetano-Anollés D, Cash-Ahmed A, Kent M, Lu X, Sanogo O, Weisner PA, Zhang H, Bell A, Ma J, Sinha S, Robinson G, Stubbs L. (2014). Neuromolecular responses to social challenge: Common mechanisms across mice, fish and bees. PNAS, 111(50): 17929–17934. LINK


Caetano-Anollés G, Mittenthal JE, Caetano-Anollés D, Kim KM. (2014). A calibrated chronology of biochemistry reveals a stem line of descent responsible for planetary biodiversity. Front Genet, 5:306. LINK


Caetano-Anollés G, Nasir A, Zhou K, Caetano-Anollés D, Mittenthal JE, Sun FJ, Kim KM. (2014). Archaea: The first domain of diversified life. Archaea, Volume 2014, Article ID 590214. LINK


Caetano-Anollés G, Wang M, Caetano-Anollés D. (2013). Structural phylogenomics retrodicts the origin of the genetic code and uncovers the impact of protein flexibility. PLOS One, 8(8):e72225. LINK


Mittenthal JE, Caetano-Anollés D, Caetano-Anollés G. (2012). Biphasic patterns of diversification and the emergence of modules. Front Genet, 3:147. LINK


Caetano-Anollés G, Kim KM, Caetano-Anollés D. (2012). The Phylogenomic Roots of Modern Biochemistry: Origins of Proteins, Cofactors and Protein Biosynthesis. J Mol Evol, 74(1-2):1-34. LINK


Kim KM, Qin T, Jiang YY, Xiong M, Caetano-Anollés D, Zhang HY, Caetano-Anollés G. (2011). Protein Domain Structure Uncovers the Origin of Aerobic Metabolism and the Rise of Planetary Oxygen. Structure, 20(1):67-76. LINK


Nowick K, Fields C, Gernat T, Caetano-Anollés D, Kholina N, Stubbs L. (2011). Gain, Loss and Divergence in Primate Zinc-Finger Genes: A Rich Resource for Evolution of Gene Regulatory Differences between Species. PLOS One, 6(6):e21553. LINK


Stubbs L, Sun Y, Caetano-Anollés D. (2011). Function and evolution of C2H2 zinc finger arrays. Subcellular Biochemistry, 52:75-94. LINK


Caetano-Anollés D, Kim KM, Mittenthal JE, Caetano-Anollés G. (2011). Proteome evolution and the metabolic origins of translation and cellular life. J Mol Evol, 72(1):14-33. LINK


Caetano-Anollés G, Wang M, Caetano-Anollés D, Mittenthal JE. (2009). The origin, evolution and structure of the protein world. Biochemical Journal, 417:621-637. LINK


Caetano-Anollés G, Yafremava LS, Gee H, Caetano-Anollés D, Kim HS, Mittenthal JE. (2009). The origin and evolution of modern metabolism. Int J Biochem Cell Biol, 41(2):285-297. LINK


Caetano-Anollés D, Wen Y, Yang ST, Lee LJ. (2008). Methods for decreasing hydrophobicity of polydimethylsiloxane (PDMS) using surface treatments and gel mixtures for use in parallel fluid flow cell culture studies. Minus 9 Nanotechnology Journal, 2008(1):1-12. LINK


Caetano-Anollés G, Sun FJ, Wang M, Yafremava LS, Harish A, Kim HS, Knudsen V, Caetano-Anollés D, Mittenthal JE. (2008). Origins and evolution of modern biochemistry: insights from genomes and molecular structure. Front Biosci, 13:5212-40. LINK


Wang M, Yafremava LS, Caetano-Anollés D, Mittenthal JE, Caetano-Anollés G. (2007). Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world. Genome Res, 17(11):1572-85. LINK


Caetano-Anollés G, Caetano-Anollés D. (2005). Universal sharing patterns in proteomes and evolution of protein fold architecture and life. J Mol Evol, 60(4):484-98. LINK


Caetano-Anollés G, Caetano-Anollés D. (2003). An evolutionarily structured universe of protein architecture. Genome Res, 13(7):1563-71. LINK






Caetano-Anollés D. (2016). “Annealing”. In: B Osmanaj & LE Santos (editors), Reference Module in Life Sciences. Oxford: Elsevier, Ltd. Article B978-0-12-374984-0.00066-8.



Caetano-Anollés D. (2016). “Polymerase Chain Reactions”. In: B Osmanaj & LE Santos (editors), Reference Module in Life Sciences. Oxford: Elsevier, Ltd. Article B978-0-12-374984-0.01186-4.


Caetano-Anollés D, Nasir A, Seufferheld M, Sun F. (2015). “Exploring the Archaeal Hologenome and Metagenome - Call for Papers”. Archaea. Cairo: Hindawi Publishing. LINK


Caetano-Anollés D. (2013). “Annealing”. In: S Brenner & JH Miller (editors), Brenner’s Encyclopedia of Genetics. 2nd Edition. Waltham (MA): Academic Press. Vol. 1, page 133. LINK


Caetano-Anollés D. (2013). “Polymerase Chain Reaction (PCR)”. In: S Brenner & JH Miller (editors), Brenner’s Encyclopedia of Genetics. 2nd Edition. Waltham (MA): Academic Press. Vol. 5, pages 392-395. LINK


Stubbs L, Sun Y, Caetano-Anollés D. (2011). Function and evolution of C2H2 zinc finger arrays. In: T. Hughes, A Handbook of Transcription Factors (Chapter 4). Berlin: Springer-Verlag. LINK


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