Our paper on comparison of next-generation sequencing simulators is out

Our review paper about next-generation sequencing simulators is out on Nature Reviews Genetics (advance online publication).

 

Escalona M, Rocha S, Posada D (2016). A comparison of tools for the simulation of genomic next-generation sequencing data. Nature Reviews Genetics doi:10.1038/nrg.2016.57

 

Online access: http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg.2016.57.html

Also, the full paper can be read through ReadCube:  http://rdcu.be/iW5c

We have an extended version of the tables here: http://darwin.uvigo.es/ngs-simulators

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Bernardo Rodríguez got his Galician PhD fellowship!

Congrats Bernardo!

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Bayesian species tree estimation with Guenomu

Finally our paper on Bayesian species tree estimation is published in Systematic Biology, although it has been available (advance access) there since 2014. This is a very nice method implemented by Leo Martins in the software Guenomu, in which a species tree can be build from multiple gene-family alignments. It is based on a Bayesian hierarchical statistical model of the incongruence between gene trees and species trees that ignores the evolutionary process responsible for it, inspired by Steel and Rodrigo (2008) ML supertree approach. This method does not require the identification of orthologs and can use information from multiple individuals from the same species.

guenomu.fig2

 

This paper is part of a special issue based on the  Systematic Biology symposium that I organized in 2013 Evolution meetings at Snowbird. The introduction to this symposium is also available here.

 



Martins LO, Mallo D, Posada D. 2016. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction. Systematic Biology 65: 397-416.

Posada D. 2016. Phylogenomics for Systematic Biology. Systematic Biology 65: 353-356.


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Another paper on UCA

13062_2016_120_Fig2_HTMLLeo and I have published another paper on the UCA test, maybe the last one of a series of papers showing why and how Theobald’s UCA test is biased, and proposing proper ways of doing this

 

https://biologydirect.biomedcentral.com/articles/10.1186/s13062-016-0120-y

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First draft of the mussel genome

Our first draft of the mussel genome has been published in PLoS ONE.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0151561

journal.pone.0151561.g001

We are working on a much more polished genome with more depth and long reads. Hopefully it will be ready very soon. D

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Diego Darriba got his PhD!

Diego Darriba defended today with success (“Sobresaliente cum laude“) his Ph.D thesis entitled “Selection of models of genomic evolution in HPC environments” supervised by Guillermo López (UDC),  Ramón Doallo (UDC) and David Posada (UVIGO). The thesis was carried out jointly carried out at the University of Coruña (UDC) and the University of Vigo (UVIGO), and defended  today at the School of Computer Science in A Coruña.

Congratulations Diego!!

Diego is now going to start a postdoc with Alexis Stamatakis at Heidelberg Institute for Theoretical Science (HITS) in Germany.

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Welcome to Bernardo Rodríguez (PhD student)!

Bernardo Rodríguez just joined our lab to do a PhD with Jose Tubio and David Posada on transposable element evolution in cancer.

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Jose Tubío joined the lab as RyC!

Jose Tubío just joined our group as a Ramon and Cajal fellow, coming from the University of Cambridge and the Wellcome Trust Sanger Institute (UK). Jose is focused on the study of transposable elements mobilized somatically in cancer genomes, and the analysis of their impact on cancer genome structure and function, using next-generation sequencing data. He is a member of the PanCancer Initiative, an international effort for the analysis of molecular aberrations in thousands of cancer samples.
More of his research at http://www.researchgate.net/profile/Jose_Tubio.

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Paper in PNAS by Iria about mites and human ancestry

A paper coauthored by Iria Fernández-Silva has just appeared in PNAS Early Edition

http://www.pnas.org/content/early/2015/12/09/1512609112

See comments on:

http://news.sciencemag.org/evolution/2015/12/what-mites-your-face-say-about-where-you-came

http://www.wired.com/2015/12/your-face-is-covered-in-mites-with-secrets-to-tell/

F2.medium

Congratulations Iria!

 

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New piece of opinion (in Galician) about science appreciation

Here I discuss (in Galician) why reaching the general public ends up being quite important for science and for the society in general:

http://www.gciencia.com/tribuna/o-aprecio-pola-ciencia

 

 

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