Category Archives: Publications

species tree review in barcode isse

Diego Mallo’s review on species trees in the open access theme issue “From DNA barcodes to biomes” compiled and edited by Paul DN Hebert, Mehrdad Hajibabaei and Peter M Hollingsworth is out. Access content online at bit.ly/PTB1702. The main TOC … Continue reading

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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 … Continue reading

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Another paper on UCA

Leo 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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SimPhy paper available at SysBio!

Our paper on SimPhy, a simulator of species, locus and gene trees has been accepted in Systematic Biology and is available ahead of print at:   http://sysbio.oxfordjournals.org/content/early/2015/10/26/sysbio.syv082.abstract  

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A few thoughts on cancer molecular evolution

A random walk column has been published on JME on Cancer molecular evolution. These are a few lines with some pointers about potential uses of evolutionary approaches in cancer.     http://link.springer.com/article/10.1007%2Fs00239-015-9695-7

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Unsorted Homology within Locus and Species Trees

It is now the turn for printed versions! You can find our penultimate paper in the current version of Systematic Biology (November 2014) . Here we show how classical homology categories can fail to describe homology relationships when we consider … Continue reading

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A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

Our latest article has just been published in Systematic Biology. It describes a model for estimating the set of  species trees conforming to several tree-to-tree distances at once. We show how we can use reconciliation distances, the recently developed mulRF distance, … Continue reading

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Science paper on HIV-1 hidden history

We have participated in a Science paper published today on the early spread of HIV-1 from Kinshasa (DRC) around 1920, and the emphasize the role of transportation, social changes and public health campaigns. The early spread and epidemic ignition of … Continue reading

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New collaborative paper on fish C3 evolution

PLoS ONE just published a paper on the C3 complement gene family, in which we collaborated with other groups to characterize its evolution. Interestingly from this side, we found an old C3 duplication common to all teleost fishes. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0099673  

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paper on ABC estimation

A new paper on ABC joint estimation of recombination, substitution and dN/dS rates has just been published in Heredity. http://www.nature.com/hdy/journal/v112/n3/abs/hdy2013101a.html

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