This application requests support for our continuing research activities in evolutionary theory, and in the analysis of molecular sequence data. The emphasis is on developing mathematical, statistical, and computing concepts and methods to help assess and interpret molecular sequence features and determinants of evolutionary processes. Our research program will concentrate in four main areas. 1) Studies of the evolution of social traits with emphasis on altruistic and cooperative behaviors; 2) studies in evolutionary theory and processes including sex allocation and sex conversion dynamics and the evolution of modifier genes under differential fertility regimes; (3) human population genetics with the development and interpretation of gene frequently maps and modeling of the evolution of traits subject to genetic and cultural influences; (4) studies of molecular sequence data including investigations on the nature of codon and amino acid preferences with respect to different classifications of genes and an extensive analysis of charge and hydropathy configurations over different categories of genes in many species and possible interpretations for function and structure. The interplay between theoretical analysis, data analysis, computer algorithms, and interaction with biologists and medical faculty at Stanford has been a key factor in our program. The unique collaboration between our groups and members of the biology and medical departments provides an ideal framework for achieving the research objectives defined in this grant.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Genetics Study Section (GEN)
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Stanford University
Schools of Arts and Sciences
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Hao, Bingtao; Naik, Abani Kanta; Watanabe, Akiko et al. (2015) An anti-silencer- and SATB1-dependent chromatin hub regulates Rag1 and Rag2 gene expression during thymocyte development. J Exp Med 212:809-24
Macario, Alberto J L; Brocchieri, Luciano; Shenoy, Avinash R et al. (2006) Evolution of a protein-folding machine: genomic and evolutionary analyses reveal three lineages of the archaeal hsp70(dnaK) gene. J Mol Evol 63:74-86
Karlin, Samuel; Brocchieri, Luciano; Campbell, Allan et al. (2005) Genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes. Proc Natl Acad Sci U S A 102:7309-14
Brocchieri, Luciano; Karlin, Samuel (2005) Protein length in eukaryotic and prokaryotic proteomes. Nucleic Acids Res 33:3390-400
Brocchieri, Luciano; Kledal, Thomas N; Karlin, Samuel et al. (2005) Predicting coding potential from genome sequence: application to betaherpesviruses infecting rats and mice. J Virol 79:7570-96
Karlin, Samuel; Mrazek, Jan; Ma, Jiong et al. (2005) Predicted highly expressed genes in archaeal genomes. Proc Natl Acad Sci U S A 102:7303-8
Karlin, Samuel; Theriot, Julie; Mrazek, Jan (2004) Comparative analysis of gene expression among low G+C gram-positive genomes. Proc Natl Acad Sci U S A 101:6182-7
Karlin, Samuel; Barnett, Melanie J; Campbell, Allan M et al. (2003) Predicting gene expression levels from codon biases in alpha-proteobacterial genomes. Proc Natl Acad Sci U S A 100:7313-8
Campbell, Allan (2003) Prophage insertion sites. Res Microbiol 154:277-82
Ma, Jiong; Campbell, Allan; Karlin, Samuel (2002) Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures. J Bacteriol 184:5733-45

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