BUSCO v6.0.0 has been released. busco.ezlab.org

Efficient and robust search of microbial genomes via phylogenetic compression Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.

Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:

rdcu.be/eg4OA

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Genome duplication in a long-term multicellularity evolution experiment - Nature In the Multicellularity Long Term Evolution Experiment, diploid yeast evolve to be tetraploid under selection for larger multicellular size, revealing how whole-genome duplication can arise due to its...

1/46 Hey folks, we have a new paper out on the MuLTEE. Strap in and I’ll tell you the story of how this “little paper on polyploidy” turned into the most data rich paper our lab has produced, largely thanks to the leadership and work ethic of @kaitong25.bsky.social.

www.nature.com/articles/s41...

Infectious diseases killed Victorian children at alarming rates — their novels highlight the fragility of public health today Between 40% and 50% of children didn’t live past 5 in the US during the 19th century. Popular authors like Charles Dickens documented the common but no less gutting grief of losing a child.

Science affords us the luxury of forgetting the impact of infectious diseases
- In the 1st half of the 19th century 40-50% of children in US did not make it past the age of 5
- TB killed 1 in 7 people in US and Europe
- smallpox killed 80% of infected children
theconversation.com/infectious-d...

devider: long-read reconstruction of many diverse haplotypes Reconstructing haplotypes is important when sequencing a mixture of similar sequences. Long-read sequencing can connect distant alleles to disentangle similar haplotypes, but handling se-quencing erro...

We built a new tool for disentangling local haplotypes from long-read sequencing: check out devider! github.com/bluenote-157...

www.biorxiv.org/content/10.1...

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(1/5) Traditionally, antibiotic discovery has centered on bacteria and fungi—until now.

For the first time, we present a systematic exploration of Archaea—a major yet underexplored branch of the tree of life—as a source of novel antimicrobial compounds. www.biorxiv.org/content/10.1...

Hybrid adaptation is hampered by Haldane’s sieve - Nature Communications Hybrids have complex genomes that influence their adaptive potential. This study reveals that yeast hybrids adapt slower than their parental species in a new environment, primarily due to a reduced ra...

For her PhD work, Carla Bautista in our group discovered that yeast hybrids adapted slower to stressful conditions, and she figured out why. See what she found here. #evolution www.nature.com/articles/s41...

What did the Last Eukaryotic Common Ancestor (#LECA) look like? Consensus View in #PLOSBiology; massive authorship including @AncestralState, @lauraeme.bsky.social, John Archbald, @andrewjroger.bsky.social, @dackslabecb.bsky.social, Jeremy Wideman. plos.io/4g0alq4

Co-supervisors of my work will be Prof. Iñaki Comas at @ibv-csic.bsky.social, and Prof. Maha Fahrat at Harward Medical School. Hopefully, we will set up methodologies that can translate into an improvement for precision epidemiology and personalized medicine.

In my case, I will build my own training path to acquire skills that allow the exploitation of M. tuberculosis genome datasets to identify genetic determinants of complex traits such as pathogen transmission.

During the next 4 years, researchers will focus on learning and applying those to their field of interest, with great emphasis on pursuing training programs such as master degrees or shorter, highly specialized courses, as well as conferences and internships in other laboratories.

Very happy to enroll Momentum program at tgu.ibv.csic.es @ibv-csic.bsky.social. Spanish Research council @csic.es created such program to build and attract capacities in edge technologies for digitization such as AI.

Bacteria found on asteroid was actually Earthly contamination, scientists report A new study of samples from Ryugu found that microorganisms can avoid even stringent contamination controls

And today in, well, no shit:

Bacteria found on asteroid was actually Earthly contamination, scientists report www.salon.com/2024/11/24/b...

That depends on your sample and your goal, but I generally would go for Kraken

reads: The Ways AI Decides How Low-Income People Work, Live, Learn, and Survive The use of artificial intelligence, or AI, by governments, landlords, employers, and other powerful private interests restricts the opportunities of low-income people in every basic aspect of life: at home, at work, in school, at government offices, and within families. AI technologies derive from a lineage of automation and algorithms that have been in use for decades with established patterns of harm to low-income communities. As such, now is a critical moment to take stock and correct course before AI of any level of technical sophistication becomes entrenched as a legitimate way to make key decisions about the people society marginalizes. Employing a broad definition of AI, this report represents the first known effort to comprehensively explain and quantify the reach of AI-based decision-making among low-income people in the United States. It establishes that essentially all 92 million low-income people in the U.S. states—everyone whose income is less than 200 percent of the federal poverty line—have some basic aspect of their lives decided by AI.

"92 million low-income people in the U.S. states—everyone whose income is less than 200 percent of the federal poverty line—have some basic aspect of their lives decided by AI"

www.techtonicjustice.org/reports/ines...

this is a damning report

Overview of the Saccharomyces cerevisiae population structure through the lens of 3,034 genomes Abstract. With the rise of high-throughput sequencing technologies, a holistic view of genetic variation within populations—through population genomics stu

A valuable and well done community resource following #OpenScience principles academic.oup.com/g3journal/ad...

Who should you nominate as reviewers for your manuscript? After a long chat with a post-grad it appears that there's a lot of misguided advice out there. Thread 👇

El Gobierno multa con 179 millones de euros a las aerolíneas de bajo coste por cobrar el equipaje de mano y la impresión de billetes Ryanair tendrá que asumir el 60% de la cuantía de esta multa, que ha adelantado la Cadena SER, con la que el Ministerio de Consumo busca disuadir a las 'low cost' de que sigan cobrando como ...

Cuando llegamos al Gobierno en 2020 no se podía multar a las grandes empresas. Nos costó 3 años -y mucho sufrimiento- aprobar la ley para poder hacerlo. Hoy el brillante @pbustinduy.bsky.social culmina ese trabajo con noticias como esta. ¡Enhorabuena! cadenaser.com/nacional/202...

I also wonder what should be the editor's response to that though...

Bluesky is emerging as the new platform for science - Mike Young Academy Scientific Twitter is about to find its true successor. And it is not X. This, our latest release, shows that the Bluesky network of scientists is growing — and growing.

Bluesky is emerging as the new platform for science

mikeyoungacademy.dk/bluesky-is-e...

Para entender por qué el PNV quiere hacer un regalo fiscal a las empresas más contaminantes de España justo después de la DANA de Valencia y por qué Aitor Esteban dispara agresivamente contra Podemos por oponerse, lo mejor es buscar a Josu Jon Imaz en Wikipedia.

El futuro de España pivotaba sobre el empobrecimiento de Andalucía*

Cómo se cuidan los señore

AllTheBacteria - all bacterial genomes assembled, available and searchable The bacterial sequence data publicly available at the global DNA archives is a vast source of information on the evolution of bacteria and their mobile elements. However, most of it is either unassemb...

Latest data from AllTheBacteria described in our updated preprint. All illumina WGS bacterial+archaeal sequence data to Aug 2024 consistently assembled, QC, and now AMR profiling. That's 2.4 million genomes. Gene annotations almost done , coming next. Please use!

www.biorxiv.org/content/10.1...

Protocolos, redes sociales, democracia I. La red precursora de internet nace en Estados Unidos a finales de la década de 1960 con el objetivo de facilitar la comunicación y el uso compartido de recursos informáticos escasos entre centros d...

En verano escribí un texto sobre la historia de internet y la tensión entre protocolos abiertos y plataformas cerrados, en el que entro un poco en cómo funciona Bluesky/atproto: amalgama.ghost.io/protocolos-r...

Cuando alguien publique "para cuándo la opción de editar el tweet?", sabremos que esto también se estará yendo a la mierda.

Hola Facu, tienes ya algún seguidor científico?

Me han dicho que esto está a prueba de naziolos...