Category Archives: Publications

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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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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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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Forensic genetics and genomics: Much more than just a human affair

A comprehensive review on the diverse disciplines of nonhuman forensic genetics, just published in PLoS Genetics. Indeed, it is a fantastic collaboration with the lab of Antonio Amorim and Angel Carracedo: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006960    

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Heterogeneous recombination among Hepatitis B virus genotypes

A very interesting paper on heterogeneous recombination in Hepatitis B virus, just published in Infection, Genetics and Evolution http://www.sciencedirect.com/science/article/pii/S1567134817302721  

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Eco-evo classification of tumors

Nice to contribute to this consensus statement in Nature Reviews Cancer about classifying tumors according to their ecological and evolutionary features: http://go.nature.com/2fopLbX   

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Multiregional tumor trees are not phylogenies

Our comment about misusing multiregional trees in cancer is out:   Alves JA, Prieto T, Posada D. 2017. Multiregional tumor trees are not phylogenies. Trends in Cancer: 0.1016/j.trecan.2017.06.004   https://t.co/HVb8dVpi6O   Here we show that multiregional tumor trees built from bulk … Continue reading

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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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