Category Archives: Research

New PhD thesis in the lab!

Posted on December 21, 2018 by dposada

Congratulations to Nuria for passing with honors her Ph.D. viva!

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New paper on germline evolution of human cancer genes by Alberto Vicens

Posted on November 30, 2018 by dposada

https://www.mdpi.com/2073-4425/9/12/582

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Comparing single-cell whole-genome amplification strategies

Posted on October 17, 2018 by dposada

We finally put it together: https://www.biorxiv.org/content/early/2018/10/16/443754

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Merly got her PhD

Posted on May 4, 2018 by dposada

Congratulations to Merly for her PhD awarded today on NGS phylogenomics! You’ve been a GREAT student. Good luck for your postdoc at UC Santa Cruz. We’ll miss you…  

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NGS coverage and evolutionary inferences from single-cells

Posted on April 17, 2018 by dposada

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

Posted on March 12, 2018 by Merly Escalona

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

Posted on March 3, 2018 by Miguel Arenas

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

Posted on February 1, 2018 by dposada

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!

Posted on January 8, 2018 by dposada

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!

Posted on January 1, 2018 by dposada

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

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