Author Archives: Leonardo de Oliveira Martins

About Leonardo de Oliveira Martins

I am currently a postdoc working in David Posada's lab at the University of Vigo, Spain. I did my Ph.D. at the Universty of Tokyo, and have both an M.Sc. in Biotechnology and a B.Sc. in Molecular Sciences completed at the University of Sao Paulo, Brasil.

This blog is being put to sleep

I realized that I have too many blogs, too little time. Since I didn’t quite get the grip of wordpress (I cannot customize the way I want, I don’t have full control about the final formatting, I cannot add gadgets, … Continue reading

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Repent that you lack the figure!

This week (yes, it’s taking me the whole week ;) I am reading the article ‘Can We Avoid “SIN” in the House of “No Common Mechanism”?’ by Mike Steel, and realized that there was something missing: the figure 2, on … Continue reading

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The GPU hype and bioinformatics algorithms

I am a big fan of GPU computing (and other “alternative” hardware), but it was refreshing to read this commentary by Lars Jensen, which I could summarize by this statement: You do not see anyone publishing papers with titles like … Continue reading

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Facts are there to be used, not regurgitated

Nice editorial at BioEssays written by Andrew Moore, about an experimental examination at a biology class (excerpt): So the scientists, knowing the kind of minds they needed to emerge from the school system, teamed up with the school teachers to … Continue reading

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Distribution of recombination distances between trees – poster at SMBE2010

I just came back from SMBE2010, where I presented a poster about our recombination detection software and had the chance to see awesome research other people are doing. The poster can be downloaded here (1.MB in pdf format) and I’m … Continue reading

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New experimental and theoretical approaches towards the understanding of the emergence of viral infections

Some articles of interest, with quotes from abstracts, from the Theme Issue ‘New experimental and theoretical approaches towards the understanding of the emergence of viral infections’ compiled and edited by Santiago F. Elena and Rémy Froissart – Philosophical Transactions of … Continue reading

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fault-tolerant conversion between sequence alignments

Despite I’m very charitable when testing my own programs, I’m not so nice when asked to scrutinize other people’s work. That’s why I was happy to see the announcement about the ALTER web server being published at Nucleic Acids Research … Continue reading

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The specialization of novel genes

Recently a paper about the software MANTiS called my attention, and I’ve been trying to write about it for a while. This announcement at the EvolDir list seemed like the perfect opportunity. I must warn you though that I’ve never … Continue reading

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Using System-on-a-Chip hardware to speed up alignments

In recent years there has been an explosion of parallel algorithms for solving bioinformatics problems, namely phylogenetic reconstruction and sequence alignment. These algorithms follow the growth of new hardware solutions like  Field-Programmable Gate Arrays (integrated circuits capable of  performing simple … Continue reading

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Harold Jeffreys’ Theory of Probability Revisited (Statistical Science 2009, Vol. 24, No. 2)

There is a paper (with discussion) on Statistical Science 2009, Vol. 24, No. 2 about Harold Jeffreys’ “Theory of Probability” book, which is one the foundations of Bayesian Statistics. The Institute of Mathematical Statistics (responsible for Statistical Science) encourages the … Continue reading

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