Marco Pessoa

An issue we're seeing at all levels of university is that many students are simply refusing to do *anything*. They aren't reading the syllabus, aren't following assignment guidelines, aren't engaging with material, ignoring deadlines. And this might seem like old news, but it truly has ramped up.

¿Hiciste tu doctorado en México? ¿Quieres hacer un postdoc en California? ¿Te interesa la genética evolutiva? ¡Checa esta beca y mándame un mensaje! alianzamx.universityofcalifornia.edu/research-and...

Confused writing is usually a symptom of confused thinking. As we struggle to clarify writing, we clarify our thoughts. AI writing aids rob us of that struggle, leaving clean-looking text and thoughts still confused for lack of inspection. Writing is not just a product; it is a diagnostic tool.

Text from an FAQ in Okbay et al 20222: https://www.nature.com/articles/s41588-022-01016-z a similar same statement is made in an FAQ in 2025: https://www.biorxiv.org/content/10.1101/2025.05.14.653986v1.supplementary-material Text reads: "The results of SSGAC studies have sometimes been used by online platforms, including some companies, to predict individual outcomes. We recognize that returning individual genomic “results” can be a fun way to engage people in research and other projects and to feed or stoke their interest in genomics. But it is important that participants/users understand that these individual results are not meaningful predictions and should be regarded essentially as entertainment. Failure to make this point clear risks sowing confusion and undermining trust in genetics research"

It is depressing, but all too predictable, how swiftly we’ve gone from the Social Science Genetic Association Consortium offering reassurances about the uses of behavioural polygenic scores to one of their lead authors marketing embryo selection for IQ

Asking for a friend: Colleague was shipping purified RNA samples from Brazil to Macrogen Korea. She had a FedEx prepaid shipping label provided by Macrogen. FeDex returned shipment because this was a biological sample. Anyone else had an issue like this?

Asking for a friend: Colleague was shipping purified RNA samples from Brazil to Macrogen Korea. She had a FedEx prepaid shipping label provided by Macrogen. FeDex returned shipment because this was a biological sample. Anyone else had an issue like this?

FastGA: Fast Genome Alignment www.biorxiv.org/content/10.1... 🧬🖥️🧪 www.github.com/thegenemyers...

It may be true (I don't know enough neuroscience to say) that LLMs & human brains use similar techniques to make connections between concepts & learn. But most humans don't speak confidently & coherently about something unless they actually know it. The ones who do... well, we have words for them.

I expect that consumer-facing AI programs will continue to improve and they may become much more useful tools for everyday life in the future.

But I think it was a disastrous mistake that today’s models were taught to be convincing before they were taught to be right.

I suspect that fact that the vast majority of LLM users don’t seem to have received this (really very simple!) message is because the AI companies have a vested interest in us not understanding it. “ChatGPT is smart, it just makes mistakes sometimes” is much more marketable than the truth.

When a chatbot gets something wrong, it’s not because it made an error. It’s because on that roll of the dice, it happened to string together a group of words that, when read by a human, represents something false. But it was working entirely as designed. It was supposed to make a sentence & it did.

Chatbots — LLMs — do not know facts and are not designed to be able to accurately answer factual questions. They are designed to find and mimic patterns of words, probabilistically. When they’re “right” it’s because correct things are often written down, so those patterns are frequent. That’s all.

Congrats to @dantipov.bsky.social et al. on the publication of Verkko2! The team put a ton of work into this making it the first assembler that deals with the complexity of human acrocentric chromosomes. Lots of interesting discoveries to come! genome.cshlp.org/content/earl...

Special Issue: Advancing species conservation and management through omics tools: Molecular Ecology Resources: Vol 25, No 5 Molecular Ecology Resources is a broad journal publishing computer programs, statistical & molecular advances & more for studies in evolution, ecology & conservation.

A great collection of papers here ... onlinelibrary.wiley.com/toc/17550998... Special Issue: Advancing species conservation and management through omics tools

A blueprint for the batmobile.

Your genome is not a blueprint. A thread about misleading metaphors in science communication. 🧬🧪 1/n

Fast3VmrMLM: A fast algorithm that integrates genome-wide scanning with machine learning to accelerate gene mining and breeding by design for polygenic traits in large-scale GWAS datasets #resource #PlantCommunications cell.com/plant-commun...

We're excited to share PlantCAD browser tracks: a new, unpublished dataset integrating AI techniques for plant genome analysis. Explore it here: github.com/andorfc/Plan...
We welcome the community's feedback and innovative use cases for this data!

"EviAnn consistently outperforms current state-of-the-art packages including BRAKER3, MAKER2, and FINDER... Annotation of a mammalian genome can be completed in less than an hour on a single multi-core server." www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/alekseyzimin...

Tiberius: End-to-End Deep Learning with an HMM for Gene Prediction bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Inspired by Helixer (by @AlisandraDenton ), we explore the potential of deep learning for genome annotation. We introduce Tiberius for highly accurate ab initio prediction of protein coding genes in mammals. Tiberius beats Augustus, BRAKER3, and Galba. doi.org/10.1101/2024...

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

The 'Oscar' of food prizes goes to a Brazilian who harnessed the power of bacteria This year's $500,000 World Food Prize, for advances in agriculture and nutrition, goes to a Brazilian who boosted the country's farming revolution, turning it into a soybean superpower.

The 'Oscar' of food prizes goes to a Brazilian who harnessed the power of bacteria

Mariangela Hungria found microbes that were good at capturing nitrogen from the air and turning it into fertilizer for crops.

www.npr.org/2025/05/14/n...

Genome-wide family prediction unveils molecular mechanisms underlying the regulation of agronomic traits in Urochloa ruziziensis https://www.biorxiv.org/content/10.1101/2023.09.25.559305v1 Tropical forage grasses, especially species of the genus Urochloa, play an important role in cattle

Genome-wide family prediction unveils molecular mechanisms underlying the regulation of agronomic traits in Urochloa ruziziensis https://www.biorxiv.org/content/10.1101/2023.09.25.559305v1

Advances in genomic characterization of Urochloa humidicola: exploring polyploid inheritance and apomixis https://www.biorxiv.org/content/10.1101/2023.08.31.555743v1 Tropical forage grasses are an important food source for animal feeding, with Urochloa humidicola, a

Advances in genomic characterization of Urochloa humidicola: exploring polyploid inheritance and apomixis https://www.biorxiv.org/content/10.1101/2023.08.31.555743v1

I'm not aware of any single pipeline for the whole process, but if you have CCS HiFi reads, hifiasm would be my assembler of choice.

Genomic and genetic insights into Mendel’s pea genes - Nature Characterization of the genetic architecture underlying the 7 pairs of contrasting traits studied by Mendel and the over 70 additional agronomic traits in pea (Pisum sativum) reveals their m...

The rest of Mendel's alleles characterized! So, out of 7 traits, 3 caused by TE insertions!!! (though apparently there are two different green alleles, one cause by a TE insertion, but another a promoter deletion allele)

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

The Idiot's Guide to Effective Population Size This is a reference manual for the elegant, yet hideously complex concept of effective population size (Ne), inspired by a classic, self-published manual of automotive repair ‘for the compleat idiot’...

Robin Waples' reference manual for the elegant, yet hideously complex concept of effective population size (Ne) #biodiversity #genomics #conservation #evolution onlinelibrary.wiley.com/doi/10.1111/...

Thrilled to see this paper out! 🎉

We analyzed 470 (!) angiosperm genomes and identified and dated 132 whole-genome duplication events. Importantly, we observed that WGD occurrence dates are not randomly distributed, but clustered at times of major environmental upheaval.

Accelerating whole-genome alignment in the age of complete genome assemblies Recent advancements in long-read sequencing and assembly methods have ushered in an era of high-quality genome assemblies. Modern assemblies commonly feature megabase-long sequences frequently spannin...

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

🌱 "Introducing GWAStic: A user-friendly, cross-platform solution for genome-wide association studies and genomic prediction" integrates AI and traditional statistical methods to simplify complex genomic analyses. doi.org/10.1093/bioa... #Genomics #GWAS @snowformatics.bsky.social

🧬🖥

"new science of biological computing" #bioinformatics #classics from

Aldhous P. 1993. Managing the Genome Data Deluge: Molecular biologists are turning to computer technology to help them manage the growing flood of sequencing and mapping data their field is producing. Science 262:502–503.