Gene network reconstruction reveals cell cycle and antiviral genes as major drivers of cervical cancer.

Although human papillomavirus was identified as an aetiological factor in cervical cancer, the key human gene drivers of this disease remain unknown. Here we apply an unbiased approach integrating gene expression and chromosomal aberration data. In an independent group of patients, we reconstruct and validate a gene regulatory meta-network, and identify cell cycle and antiviral genes that constitute two major subnetworks upregulated in tumour samples.

Fungi evolution revisited: application of the penalized likelihood method to a Bayesian fungal phylogeny provides a new perspective on phylogenetic relationships and divergence dates of Ascomycota groups.

The depiction of evolutionary relationships within phylum Ascomycota is still controversial because of unresolved branching orders in the radiation of major taxa. Here we generated a dataset of 166 small subunit (18S) rDNA sequences, representative of all groups of Fungi and used as input in a Bayesian phylogenetic analysis. This phylogeny suggests that Discomycetes are a basal group of filamentous Ascomycetes and probably maintain ancestor characters since their representatives are intermingled among other filamentous fungi.

Experimental phylogeny of neutrally evolving DNA sequences generated by a bifurcate series of nested polymerase chain reactions.

A known phylogeny was generated using a four-step serial bifurcate PCR method. The ancestor sequence (SSU rDNA) evolved in vitro for 280 nested PCR cycles, and the resulting 15 ancestor and 16 terminal sequences (2,238 bp each) were determined. Parsimony, distance, and maximum likelihood analysis of the terminal sequences reconstructed the topology of the real phylogeny and branch lengths accurately.