Genomes and Genes
Gunter P Wagner
Affiliation: Yale University
- Wagner G, Zhang J. The pleiotropic structure of the genotype-phenotype map: the evolvability of complex organisms. Nat Rev Genet. 2011;12:204-13 pubmed publisher..This finding has major implications for the evolvability of complex organisms and the mapping of disease-causing mutations. ..
- Wagner G, Kin K, Lynch V. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci. 2012;131:281-5 pubmed publisher..We propose a slight modification of RPKM that eliminates this inconsistency and call it TPM for transcripts per million. TPM respects the average invariance and eliminates statistical biases inherent in the RPKM measure. ..
- Nnamani M, Ganguly S, Erkenbrack E, Lynch V, Mizoue L, Tong Y, et al. A Derived Allosteric Switch Underlies the Evolution of Conditional Cooperativity between HOXA11 and FOXO1. Cell Rep. 2016;15:2097-2108 pubmed publisher..This study shows that TF function can evolve through changes affecting the functional output of a pre-existing protein complex. ..
- Chavan A, Bhullar B, Wagner G. What was the ancestral function of decidual stromal cells? A model for the evolution of eutherian pregnancy. Placenta. 2016;40:40-51 pubmed publisher..We further propose that extended gestation evolved independently in the major eutherian clades explaining why the major lineages of eutherian mammals differ with respect to the mechanisms maintaining pregnancy. ..
- Lynch V, Roth J, Wagner G. Adaptive evolution of Hox-gene homeodomains after cluster duplications. BMC Evol Biol. 2006;6:86 pubmed..These results further suggest that adaptive evolution actively contributed to Hox-gene homeodomain functions. ..
- ..This asymmetric expression correlates with independent morphological evolutionary variation of digit 1. ..
- Wagner G, Nnamani M, Chavan A, Maziarz J, Protopapas S, Condon J, et al. Evolution of Gene Expression in the Uterine Cervix related to Steroid Signaling: Conserved features in the regulation of cervical ripening. Sci Rep. 2017;7:4439 pubmed publisher..Western-blotting on mouse cervix confirmed large scale histone de-acetylation in labor. This finding may have important implications for the control of premature cervical ripening and prevention of preterm birth in humans. ..
- Wagner G. Evolutionary genetics: the nature of hidden genetic variation unveiled. Curr Biol. 2003;13:R958-60 pubmed
- Chavan A, Griffith O, Wagner G. The inflammation paradox in the evolution of mammalian pregnancy: turning a foe into a friend. Curr Opin Genet Dev. 2017;47:24-32 pubmed publisher..We propose that this model allows us to understand the differences between 'good inflammation' and 'bad inflammation'. Further, it allows us to understand the influence of inflammation on the outcome of pregnancy and maternal health. ..
- Armstrong D, McGowen M, Weckle A, Pantham P, Caravas J, Agnew D, et al. The core transcriptome of mammalian placentas and the divergence of expression with placental shape. Placenta. 2017;57:71-78 pubmed publisher..115 genes are important for the core functions of the placenta in all eutherian species analyzed. The molecular functions and pathways enriched in the core placenta align with the evolutionarily conserved functionality of the placenta. ..
- Wagner G, Takahashi K, Lynch V, Prohaska S, Fried C, Stadler P, et al. Molecular evolution of duplicated ray finned fish HoxA clusters: increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences. J Mol Evol. 2005;60:665-76 pubmed..e., putative cis-regulatory elements. These results suggest that the 5' HoxA genes in the same cluster belong to a co-evolutionary unit in which genes have a tendency to diverge together. ..