Federico Lopez

@flopezos.bsky.social

Evolutionary biology, genomics, bioinformatics, social insects.

Just had a great zoom with a very talented undergraduate student from another country I would love to recruit. I really don't love telling students not to come here, but because our funding and visa situation is so volatile I can't in good conscience recommend a PhD in the US.

Our paper is out! 📣 we find that molecular measures of genetic variation do not predict heritable genetic variation across species - important implications for the application of genomic data for conservation! www.pnas.org/doi/10.1073/...

Nucleotide diversity is a poor predictor of short-term adaptive potential | PNAS

The capacity to adapt is essential for a population to avoid extinction in a changing world and is recognized as a global conservation priority. Ad...

pnas.org

Our new genome annotation method relies almost entirely on transcriptome and alignment evidence, and as a result outperforms pretty much all other de novo pipelines. Check out the just-published paper led by Aleksey Zimin: rdcu.be/frSOg

Efficient evidence-based genome annotation with EviAnn

Nature Methods - EviAnn surpasses existing genome annotation methods by leveraging gene expression and protein sequence homology evidence to achieve higher accuracy and efficiency.

rdcu.be

A new Science study shows that bumble bees can position a ball underneath a fake “flower” to reach a reward, suggesting they can exhibit spontaneous problem-solving and challenging the notion that such advanced cognitive abilities are exclusive to large-brained vertebrates. https://scim.ag/4vs08dC

The first single-cell three-dimensional lamprey brain atlas reveals that the vertebrate common ancestor already had a highly regionalized brain, and subsequent neuronal specialization likely drove vertebrate brain diversification. Learn more this week in Science: https://scim.ag/4whLqXp

As living fossils, lampreys, such as this Far Eastern brook lamprey (Lethenteron reissneri), provide an irreplaceable model for reconstructing the ancestral vertebrate brain. The first single-cell three-dimensional lamprey brain atlas reveals that the vertebrate common ancestor (~500 million years ago) already had a highly regionalized brain, and subsequent neuronal specialization likely drove vertebrate brain diversification.

Photo: Nobuhiko Akiyama/Minden Pictures
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Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

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The heaviest Russian air attack on Kyiv in two weeks saw several people killed and the Pechersk Lavra monastery, a symbol of Ukrainian spiritual and cultural history, catch fire, authorities said.

Nineteen russian ballistic missiles, cruise missiles and Shahed drones are raining down on Kyiv right now. This is horrific. The UNESCO-listed Kyiv-Pechersk Lavra has been targeted. A thousand years of Ukrainian history, faith, and culture are once again under attempted destruction.

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