Marco Pessoa
@marcopessoa.bsky.social
Parent, husband, vinyl collector. Research Scientist at Embrapa, Brazil. Plant genomics, plant genetic resources, and breeding of tropical forages. 1st-gen DSc.
Just posted: a group paper describing major updates to my software pixy, for population genetic summary statistics. www.biorxiv.org/content/10.6... New since 2021: arbitrary ploidy, multiallelic sites, missingness-aware Watterson's θ and Tajima's D, Hudson's FST, multicore execution!
1/ Excited to share our preprint ImpuT2T: a pangenome-based assembly patching tool ImpuT2T scaffolds draft human assemblies with a pangenome (HPRC2) and patches gaps by leveraging linkage disequilibrium and sequence identity between contigs and reference haplotypes Code: github.com/maojanlin/Im...
ImpuT2T: Pangenome-Based Patching for Human Genome Assemblies
With improvements in sequencing and assembly have come many high-quality telomere-to-telomere assemblies and reference pangenomes. However, the long-read sequencing recipes needed for high quality ass...
biorxiv.org
1st genome sequenced (Sanger 1977), 1st genome synthesised (Venter 2003), 1st genome + proteome fully mutated (Huijin Xiangua 2026!) @crg.eu @sangerinstitute.bsky.social Complete Mutagenesis of the Genome and Proteome of ΦX174 www.biorxiv.org/content/10.6...
Complete Mutagenesis of the Genome and Proteome of ΦX174
The bacteriophage ΦX174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the ΦX174 ge...
biorxiv.org
This fellow greeted me at work this morning. A tucunaçu in Portuguese, a toco toucan in English (Ramphastos toco), the largest species of toucan.
Tiberius predicts genes in eukaryotic genomes via our web service bioinf.uni-greifswald.de/tiberius/ #genomeannotation #geneprediction #eukaryotes
Hybrid assembly (#Nanopore + #Illumina) reveals a complex plant mitochondrial #genome in Caryocar brasiliense 🧬 Two circular #chromosomes, extensive repeat content, and gene transfers from chloroplast and nuclear genomes shape mitochondrial #evolution https://ow.ly/Ufgx50ZiwaA
What gives #açaí its colour and #nutrient packed punch? 🫐🌿 New study presents the first genome of Euterpe oleracea and uses #RNA-seq to uncover the #genes driving fruit ripening and anthocyanin production in purple vs white varieties https://ow.ly/C0j950Ziwcc
Our latest review: Genomics of tropical forage grasses in Brazil: resources, progress, and future directions cdnsciencepub.com/doi/10.1139/... #genomics #breeding #forages
Genomics of tropical forage grasses in Brazil: resources, progress, and future directions
Brazil is the global leader in the production and export of tropical forage seeds. The livestock sector primarily relies on tropical grasses, including species of Urochloa and Megathirsus maximus, as ...
cdnsciencepub.com
www.nature.com/articles/s41...
A k-mer-based genome-wide association study approach empowering gene mining in polyploids - Nature Genetics
KMERIA, a k-mer-based genome-wide association study approach, specifically designed for polyploids, enhances statistical power and efficiency in agronomic variant discovery when applied to high-ploidy...
nature.com
💡 #KnowledgeHighlight | Tutorials: Learning Bioinformatics At Home by Harvard informatics 🧬 🖥️ github.com/harvardinfor... Explore open-access training materials in the ERGA #KnowledgeHub ➡️ knowledge.erga-biodiversity.eu #tutorials #genomics #bioinformatics #unix #Python #rnaseq
GitHub - harvardinformatics/learning-bioinformatics-at-home: resources for learning bioinformatics
resources for learning bioinformatics. Contribute to harvardinformatics/learning-bioinformatics-at-home development by creating an account on GitHub.
github.com
For the last time (it's not the last time, I fear), Ebola virus is not going to mutate to go airborne and I've got receipts. rasmussenretorts.substack.com/p/why-ebola-...
Why Ebola Isn't Going to "Go Airborne"
And stop sounding so excited about it
rasmussenretorts.substack.com
I realize I sound like old man yelling at clouds but... ...in my day WE READ ALL THE CITATIONS BEFORE WE CITED THEM. That's how you GAIN THE KNOWLEDGE TO CITE THEM IN THE FIRST PLACE. Signed: Someone who literally read two whole books on the color blue just to write a single 1000 word article.
Dr. Holly Walters@manigarm.bsky.social · 3mo agoI'm sorry, what? In writing my first monograph, I spent six weeks trying to track down a citation in TWO languages I didn't know. And good thing too, because the citation was wrong. That's scholarship. That's research. You know, the thing we're trained to do?!?
Cohen: "any paper we accept will be scraped up and fed to the next generation of LLMs, and we don’t want to contribute to a death spiral of nonsense and hallucination" @philipncohen.com www.nature.com/articles/d41...
Researchers who use hallucinated references to face arXiv ban
The preprint server is the latest to impose stiff penalties on authors who contribute to AI ‘slop’ — but not everyone is convinced it’s the right approach.
nature.com
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih
academic.oup.com
A big study that was cited as evidence that text generators are good for students has been retracted: www.linkedin.com/posts/ben-wi... www.nature.com/articles/s41...
Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.
The truly stunning part of this marathon WR is his final full 5K split from 35-40K. 13:42 🤯 That wins most major 5K races
Here's more info: www.cidrap.umn.edu/dengue/butan... Brazil recently began production of the vaccine, which could be a major step in limiting dengue -- also known as "bone-break fever" for reasons you can probably imagine
Butantan dengue vaccine estimated to be 81% effective against severe disease for at least 5 years
Vaccine efficacy against symptomatic dengue was 65%.
cidrap.umn.edu
Eileen Clancy 🧿@clancyny.bsky.social · 3mo agoHuge achievement! The first single-dose vaccine to combat all four types of dengue virus. An estimated 5.6 billion people are at risk of dengue, with an estimated 100–400 million infections occurring every year, mostly in tropical and sub-tropical climates. [Google Translate ⤵️]
Sabastian Sawe of Kenya has become the first person to run a marathon in under 2 hours.
Sabastian Sawe of Kenya wins London Marathon in world-record time, first to finish under two hours
Sabastian Sawe of Kenya has become the first person to run a marathon in under 2 hours. Sawe smashed the men’s world record by winning the London Marathon in 1 hour, 59 minutes and 30 seconds on Sunday.
bit.ly
A gorgeous sunset after my afternoon run. Brasília, Brazil.
When the president is a heinous abuser, when many of the most popular celebrities are heinous abusers, when the richest people in the world are heinous abusers, when the people developing new technology are heinous abusers, well that’s how you get a culture that incentivizes abuse
It's #WorldImmunizationWeek Vaccines have saved more than 150 million lives since 1974 — not by accident, but because ordinary people made the decision to protect themselves, their children and one another. That’s 6 lives every minute, every day, for more than 5 decades https://bit.ly/4mH2HWi
Tiberius 2.0.0 is out 🎉 Now supports 7 eukaryotic clades, covering ~92% of NCBI assemblies. Modular rewrite + ~30% faster runtime. Benchmarks included, more soon. Thanks to Lars Gabriel, Richard Krieg & Felix Becker 🙌 github.com/Gaius-August... #bioinformatics #genomics #genomeannotation
It's nobody's fault of course but sometimes it feels even academics forget that papers from writing to publication usually take prob more than a year. And that's part of the whole point. Slower than frenetic news and slower than blog posts is good actually because it is required for the process.
Many nascent breeding programs cross locally‑elite lines but lack structured gene‑pool design. This study compares genomic approaches to infer elite gene pools, showing that QTL‑based inference plus iso‑elite crosses boosts genetic gain in simulated forward‑breeding programs.
Genomic approaches to build de novo elite breeding gene pools from locally adapted landraces
rdcu.be
Astronomers have completed the largest 3D map of the universe ever made. Learn more: https://scim.ag/4tTqtAF
