Category Archives: Research

NGS coverage and evolutionary inferences from single-cells

New paper just out @GenomeMedicine! We report the impact of sequencing depth (and sampling effort) towards variant detection, genotype accuracy, clonal inference and phylogenetic reconstruction from single-cell cancer data. https://rdcu.be/LJ4E

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NGSphy: phylogenomic simulation of next-generation sequencing data

NGSphy, our tool for simulating NGS reads along gene trees or genome-wide along a species tree with multiple gene families, is now published in Bioinformatics. https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty146/4925260?redirectedFrom=fulltext Source code, full documentation, and tutorials including a “Getting started” guide are available at http://github.com/merlyescalona/ngsphy

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Substitution Rates Predicted by Stability-Constrained Models of Protein Evolution Are Not Consistent with Empirical Data

Both stability-constrained and structure-constrained substitution models are required to realistically predict the effect of mutations during protein evolution. A great study with Ugo Bastolla’s lab just published in Molecular Biology and Evolution, https://academic.oup.com/mbe/article-abstract/35/3/743/4775142?redirectedFrom=fulltext

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Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish

Congratulations Iria for publishing a very nice paper describing the assembly of the genome of a beautiful angelfish! https://www.nature.com/articles/s41598-018-19430-x  

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Two open PhD positions in computational cancer evolution!

Two open Marie Curie PhD positions (CONTRA ITN)  in computational cancer evolution at our lab. Please apply!    ESR 11: Estimation of tumour growth rates from NGS data Understanding the process of tumour growth is fundamental for many aspects of cancer … Continue reading

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Jose Tubio moves to USC!

Jose Tubio is moving to the University of Santiago de Compostela with his team. Best wishes Jose!

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Our Christmas gathering

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Laura Tomás got the UVIGO academic excellence award for new PhD students!

Congratulations to our EXCELLENT Laura!

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Evaluating the Neolithic Expansion at Both Shores of the Mediterranean Sea

The Neolithic expansion at both shores of the Mediterranean Sea was not different after all. A nice study applying approximation Bayesian computation for model selection and parameters estimation. Just published in Molecular Biology and Evolution, https://academic.oup.com/mbe/article/34/12/3232/4237582  

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ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability

A new evolutionary framework for ancestral protein reconstruction accounting for structural constraints, just published in Systematic Biology https://academic.oup.com/sysbio/article-abstract/66/6/1054/2840014/ProtASR-An-Evolutionary-Framework-for-Ancestral?redirectedFrom=fulltext

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