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Marco Pessoa

@marcopessoa.bsky.social
285 followers 1.3K following 24 posts

Parent, husband, vinyl collector. Research Scientist at Embrapa, Brazil. Plant genomics, plant genetic resources, and breeding of tropical forages. 1st-gen DSc.

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Marco Pessoa @marcopessoa.bsky.social · 21/08/2026
Genomics of tropical forage grasses in Brazil: resources, progress, and future directions cdnsciencepub.com/doi/10.1139/...
cdnsciencepub.com
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 Megathyrsus maximus, as ...
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Marco Pessoa @marcopessoa.bsky.social · 21/08/2026
www.researchsquare.com/article/rs-1...
researchsquare.com
Chloroplast genomes of Vanilla spp. (Orchidaceae) provide new evolutionary insights into the genus
The genus Vanilla (Orchidaceae) holds significant economic value due to its production of aromatic compounds; however, numerous species are increasingly threatened by overexploitation and habitat dest...
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bioRxiv Genetics @biorxiv-genetic.bsky.social · 09/08/2026
Flywheel Genomics: Simultaneous trait discovery and genetic gain in plant breeding www.biorxiv.org/content/10.64898/20…
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Kieran Samuk @ksamuk.bsky.social · 03/08/2026
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!
Alt text: Schematic of the pixy workflow. Left, inputs: a bgzipped, tabix- or CSI-indexed VCF with callable sites supplied as an all-sites VCF or gVCF blocks, a populations file, and optional BED and sites files. Centre, core: windowing by fixed width, BED or region; statistic selection; options for Hudson's FST, multiallelic SNPs, automatic ploidy detection and multicore execution. Right, outputs: one TSV per statistic for pi, dxy, FST, Watterson's theta and Tajima's D, with raw count columns for exact aggregation. Bottom, development: GitHub fork and pull request, local checks with ruff, mypy and pytest, continuous integration across Python 3.10 to 3.14, and distribution through conda-forge. Features new since the 2021 release are badged "new".
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Mao-Jan Lin @maojanlin.bsky.social · 03/08/2026
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...
biorxiv.org
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...
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Ben Lehner @benlehner.bsky.social · 03/08/2026
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...
biorxiv.org
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...
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Marco Pessoa @marcopessoa.bsky.social · 04/08/2026
This fellow greeted me at work this morning. A tucunaçu in Portuguese, a toco toucan in English (Ramphastos toco), the largest species of toucan.
A toco toucan standing on a dead trunk of a tree. The sky is partially cloudy in the background, and branches of another tree are seen in the left side of the image.
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Katharina Hoff @katharinahoff.bsky.social · 27/07/2026
Tiberius predicts genes in eukaryotic genomes via our web service bioinf.uni-greifswald.de/tiberius/ #genomeannotation #geneprediction #eukaryotes
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Genome Journal @genomejournal.bsky.social · 08/07/2026
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 ow.ly/Ufgx50ZiwaA
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Genome Journal @genomejournal.bsky.social · 13/07/2026
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 ow.ly/C0j950Ziwcc
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Marco Pessoa @marcopessoa.bsky.social · 21/07/2026
Our latest review: Genomics of tropical forage grasses in Brazil: resources, progress, and future directions cdnsciencepub.com/doi/10.1139/... #genomics #breeding #forages
cdnsciencepub.com
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 ...
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Timothy Burke @bubbaprog.xyz · 30/06/2026
As called on TV Trece in Paraguay:
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Marco Pessoa @marcopessoa.bsky.social · 16/06/2026
www.nature.com/articles/s41...
nature.com
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...
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ERGA - European Reference Genome Atlas @ergabiodiv.bsky.social · 25/05/2026
💡 #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.com
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.
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Angie Rasmussen @angierasmussen.bsky.social · 25/05/2026
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-...
rasmussenretorts.substack.com
Why Ebola Isn't Going to "Go Airborne"
And stop sounding so excited about it
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Bethany Brookshire @beebrookshire.bsky.social · 19/05/2026
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.
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Richard Sever @richardsever.bsky.social · 19/05/2026
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...
nature.com
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.
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Andrew Roger @andrewjroger.bsky.social · 06/05/2026
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...
academic.oup.com
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
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Reposted by Marco Pessoa
Ketan Joshi @ketanjoshi.co · 04/05/2026
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...
Retraction Note: The effect of ChatGPT on students’ learning performance, learning perception, and higher-order thinking: insights from a meta-analysis
Jin Wang & Wenxiang Fan 
Humanities and Social Sciences Communications volume 13, Article number: 528 (2026) Cite this article

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The Original Article was published on 06 May 2025

Retraction Note to: Humanities and Social Sciences Communications https://doi.org/10.1057/s41599-025-04787-y, published online 06 May 2025

The Editor has decided to retract this paper owing to concerns regarding discrepancies in the meta-analysis. These issues ultimately undermine the confidence the Editor can place in the validity of the analysis and resulting conclusions. The authors have not responded to correspondence regarding this retraction.
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Marco Pessoa @marcopessoa.bsky.social · 30/04/2026
It is on their Instagram page too. So yeah, seems official.
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Marco Pessoa @marcopessoa.bsky.social · 30/04/2026
Haven't seen any news reporting on it either
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
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.
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Marco Pessoa @marcopessoa.bsky.social · 28/04/2026
Same here
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Vaughn Cooper @vscooper.micropopbio.org · 26/04/2026
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
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Melody Schreiber @melodyschreiber.com · 26/04/2026
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
cidrap.umn.edu
Butantan dengue vaccine estimated to be 81% effective against severe disease for at least 5 years
Vaccine efficacy against symptomatic dengue was 65%.
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The Associated Press @apnews.com · 26/04/2026
Sabastian Sawe of Kenya has become the first person to run a marathon in under 2 hours.
bit.ly
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.
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Marco Pessoa @marcopessoa.bsky.social · 25/04/2026
A gorgeous sunset after my afternoon run. Brasília, Brazil.
A bikeway with a cloudy sunset with orange tonesA tree and a cloudy sunset
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Kat Tenbarge @kattenbarge.bsky.social · 23/04/2026
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
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WHO @who.int · 23/04/2026
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 bit.ly/4mH2HWi
Illustration of diverse family generations celebrating vaccination with a large vaccine vial and immunization card, promoting World Immunization Week 2026.
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Katharina Hoff @katharinahoff.bsky.social · 24/04/2026
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
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Olivia Guest · Ολίβια Γκεστ @olivia.science · 21/04/2026
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.
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Theoretical and Applied Genetics @theorapplgenet.bsky.social · 20/04/2026
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.
rdcu.be
Genomic approaches to build de novo elite breeding gene pools from locally adapted landraces
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Science Magazine @science.org · 16/04/2026
Astronomers have completed the largest 3D map of the universe ever made. Learn more: scim.ag/4tTqtAF
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Michael Baym @baym.lol · 16/04/2026
Some day I’ll figure out how to work this into a talk
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Jonathan Keats, PhD 🇨🇦 @pedalheadphx.bsky.social · 12/04/2026
Sounds interesting
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Clara Jeffery @clarajeffery.bsky.social · 11/04/2026
Science is good. We should fund it.
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Rob Waterhouse @rmwaterhouse.bsky.social · 08/04/2026
#Biodiversity science laments how little is known about the planet’s biodiversity, yet routinely discards much of the taxonomic evidence generated during species description. www.nature.com/articles/s44...
nature.com
Digitally native species are a necessary shift in taxonomic practice
Nature Reviews Biodiversity - Biodiversity science laments how little is known about the planet’s biodiversity, yet routinely discards much of the taxonomic evidence generated during species...
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Marco Pessoa @marcopessoa.bsky.social · 05/04/2026
Weekend spins 4/n Marcos Valle - Jet-Samba (2005) Rocinante, Três Selos, Dubas R3-058/TSPL-098 Brasil, 2024 #vinyl #bossanova #jazz
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Marco Pessoa @marcopessoa.bsky.social · 05/04/2026
Weekend spins 3/n Mahavishnu Orchestra - Birds of Fire (1973) Columbia KC 31996 US pressing, 1973 #vinyl #fusion
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Marco Pessoa @marcopessoa.bsky.social · 05/04/2026
Weekend spins 2/n P J Harvey - Stories From the City, Stories from the Sea (2000) Island Records #0898541 Reissue, 2021 #vinyl #record
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Marco Pessoa @marcopessoa.bsky.social · 05/04/2026
Weekend spins 1/n John Abercrombie - Timeless ECM Records #2301 047 (1975) Brasil, Reissue, 1983 #vinyl #records #jazz #fusion #postbop
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Natalie Cooper @nhcooper123.bsky.social · 25/03/2026
Hi all. I am very excited that after 6 years I finally got my phylogenetic comparative methods book and online exercises online. Feel free to use and share. The book is here: nhcooper123.github.io/pcm-primer/. Note that it is not finished, we had to abandon it before the sunk costs fallacy broke us
nhcooper123.github.io
Phylogenetic Comparative Methods
Phylogenetic Comparative Methods
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Katie Mack @astrokatie.com · 03/04/2026
More context on this #Artemis II image: * This is the night side, lit by moonlight. You can see city lights in Spain & Portugal, & a sliver of day at lower right * The Sun is entirely behind Earth, which makes it a kind of solar eclipse, but w/ Earth doing the eclipsing instead of the Moon: ☀️🌍🚀🌕
A full disc image of Earth, as seen from the Orion Crew Module. The planet is a pale blue, swirling with white clouds and glowing slightly lighter blue in place from reflected light. At lower left, a large brown landmass is Africa, with Spain and Portugal with twinkling lights where the planet curves. At top right, auroras glow in a thin green glow, just barely separated from the planet's surface. Earth is set against the black of space (pic: NASA/R.Wiseman)
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Carl T. Bergstrom @carlbergstrom.com · 31/03/2026
Some first-rate science writing: For this story, @jdrakephd.bsky.social carefully read our recent paper and then we spent a very fun 90 minutes or so talking on zoom. His article that gets right to the heart of our model, explains it clearly, and then explores why it will matter in the future.
forbes.com
The System That Decides What Science Gets Published Is Breaking Down
The peer review system that validates scientific research is trapped in a self-defeating cycle. A new mathematical model shows why—and what comes next.
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Marco Pessoa @marcopessoa.bsky.social · 31/03/2026
www.nature.com/articles/s41...
nature.com
Highly accurate ab initio gene annotation with ANNEVO - Nature Methods
ANNEVO advances accurate and scalable ab initio gene annotation of evolutionarily diverse genomes using deep learning approach modeling sequence evolution and long-range dependencies and mixture of ex...
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Marco Pessoa @marcopessoa.bsky.social · 28/03/2026
acsess.onlinelibrary.wiley.com/doi/10.1002/...
acsess.onlinelibrary.wiley.com
A whole‐genome assembly of St. Augustinegrass and visualizing diversity within the species
The first chromosome-scale assemblies of both haplotypes of the Stenotaphrum secundatum genome were assembled. A total of 62,454 protein-coding genes were annotated across both haplotypes. A uniform...
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Marco Pessoa @marcopessoa.bsky.social · 26/03/2026
Damien Jurado - Brothers and Sisters of the Eternal Son Secretly Canadian, 2014 (SC295) #vinyl #vinylcollector
A hand holding the record jacket of Damien Jurado's Brothers and Sisters of the Eternal Son, front cover, a ficus lyrata to the right, and a record stand with a turntable and a receiver to the leftA hand holding the record jacket of Damien Jurado's Brothers and Sisters of the Eternal Son, back cover, a ficus lyrata to the right, and a record stand with a turntable and a receiver to the left
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Laura Helmuth @laurahelmuth.bsky.social · 22/03/2026
This is a great list of techniques for getting real information out of a Google search and avoiding AI slop and paid results. (One thing not included is that if you add "-ai" to a search, you block the AI summary) cardcatalogforlife.substack.com/p/google-has...
cardcatalogforlife.substack.com
Google Has a Secret Reference Desk. Here's How to Use It.
40 Google features to find exactly what you need, the alternative search engines that do things Google won't, and the reference desk framework underneath all of it.
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Marco Pessoa @marcopessoa.bsky.social · 19/03/2026
This came out today. Glad to be part of it. www.sciencedirect.com/science/arti...
sciencedirect.com
Operationalizing tropical plant genomics in Brazil
Tropical regions harbor most of Earth’s plant diversity but remain under-represented in genomic resources. Using Brazil as a case study, we highlight …
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Megan Dennis @mydennis.bsky.social · 17/03/2026
Excited so share our newest study using a single-library HiFi-CiFi approach to generate chromosome-scale diploid assemblies of two vole genomes, identifying putative drivers of divergent pair-bonding behavior, namely a prairie-vole-specific duplication of Avpr1a gene, led by @mabuelanin.bsky.social
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