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Fabricio Almeida-Silva

@almeidasilvaf.bsky.social
1.1K followers 491 following 58 posts

Postdoc at VIB-UGent (Van de Peer lab) working on polyploidy, network biology, regulation of gene expression, and (plant) genome evolution. Member of the Bioconductor Community Advisory Board. Proud father. Bookworm. 💻 almeidasilvaf.github.io

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Reposted by Fabricio Almeida-Silva
Bioconductor @bioconductor.bsky.social · 05/10/2026
📢 Bioconductor Africa Seminar Series: Developing & submitting Bioconductor packages — key steps from structuring and documenting R code to testing and preparing for submission. 🎤 Dr Fabricio Almeida-Silva 📅 Oct 28 2026 🕓 4 PM EAT Register: bit.ly/3VQEa7H
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Polina Novikova @pnovik.bsky.social · 16/09/2026
I am happy to present our work @liverworks.bsky.social @robinburns.bsky.social @alisondawnscott.bsky.social on centromeric repeat turnovers, of which we counted three in the Arabidopsis genus:
biorxiv.org
The Nature of Centromeric Repeat Turnovers in the genus Arabidopsis
Centromeres are critical for accurate segregation of chromosomes and are often composed of megabases of tandemly arranged satellite repeats. Yet, despite their conserved function, the DNA sequence of ...
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Sergey Ovchinnikov @sokrypton.org · 14/09/2026
Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr)
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Dan MacGuigan @dmacguig.bsky.social · 08/09/2026
New paper in Systematic Biology! We show how micro-synteny can help resolve a tricky fish #phylogenetic problem where traditional sequence-based analyses fall short. Genomes archive evolutionary history in more than just their basepairs. doi.org/10.1093/sysb... #fish #genomics #evolution
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Posit @posit.co · 31/08/2026
Announcing cuda​.ml 0.4.0: GPU-accelerated machine learning in #RStats! Bring #NVIDIA compute into tidymodels & parsnip workflows with 2 commands. • Accelerated XGBoost & LightGBM inference via nvForest • Portable model persistence Read more: opensource.posit.co/blog/2026-08...
opensource.posit.co
cuda.ml 0.4.0: GPU-accelerated machine learning from R
cuda.ml 0.4.0 simplifies installation, expands tidymodels integration and tree-ensemble inference, and adds portable persistence for supported fitted models.
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 26/08/2026
For folks interested I just posted my keynote on ARGs from #PEQG26 on youtube (with permission). Thanks again to @genetics-gsa.bsky.social and organizers for what was a wonderful conference (except for the 24hrs prior to my talk when I was too nervous to sleep or think straight) youtu.be/ntJOdZd0mwc
youtu.be
PEQG Keynote 2026
YouTube video by Jeffrey Ross-Ibarra
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Reposted by Fabricio Almeida-Silva
Rob Waterhouse @rmwaterhouse.bsky.social · 14/08/2026
Call for Papers: 𝐂𝐲𝐛𝐞𝐫𝐢𝐧𝐟𝐫𝐚𝐬𝐭𝐫𝐮𝐜𝐭𝐮𝐫𝐞 𝐚𝐧𝐝 𝐃𝐚𝐭𝐚 𝐌𝐚𝐧𝐚𝐠𝐞𝐦𝐞𝐧𝐭 𝐢𝐧 𝐄𝐜𝐨𝐥𝐨𝐠𝐲 𝐚𝐧𝐝 𝐄𝐯𝐨𝐥𝐮𝐭𝐢𝐨𝐧 onlinelibrary.wiley.com/page/journal...
onlinelibrary.wiley.com
Ecology and Evolution Call for Papers Cyberinfrastructure and Data Management in Ecology and Evolution
Ecology & Evolution is a broad open access journal welcoming research in ecology, evolution, and conservation science, and providing a forum for evidence-based views.
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Reposted by Fabricio Almeida-Silva
naturepoker @binomicalabs.org · 05/08/2026
#rustlang has an official LLM policy. Pretty sensible - everything boils down to "you can't copy paste LLM output without any work and call it a contribution". QC requirements are higher for LLM generated code, also common sense. blog.rust-lang.org/inside-rust/... Also this part cracked me up:
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Physalia-courses@ONLINE @physaliacourses.bsky.social · 03/08/2026
🧬 Last seats available! Join our online course Network Analysis in Systems Biology with R/ @bioconductor.bsky.social led by @almeidasilvaf.bsky.social 5–8 October. Learn to infer, analyze & compare biological networks, including GCNs and GRNs. www.physalia-courses.org/courses-work...
physalia-courses.org
Network Analysis in Systems Biology with R/Bioconductor
5-8 October 2026 To foster international participation, this course will be held online
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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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Michael Raissig @michaelraissig.bsky.social · 04/07/2026
🌾 Grass leaves are the photosynthetic powerhouses of human civilisation. @lbmountain.bsky.social's transcriptomic atlas of nearly 70,000 cells from shoot apex to mature leaf follows the genetic programs that form a grass leaf 🧬 paper doi.org/10.1093/plce... expression browser shiny.ips.unibe.ch
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Mary Williams @PlantTeaching @plantteaching.bsky.social · 07/06/2026
Oh this is so good, please read it. "If we want literate citizens, we will have to rebuild the conditions for literacy deliberately, against the grain of every incentive currently pointed the other way. I know the academy has the will to do that. It also has the obligation." 👏
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Fabricio Almeida-Silva @almeidasilvaf.bsky.social · 30/05/2026
Really excited to see these (solid) rewrites in Rust. Are we going to have all major bioinformatics tools in Rust soon? I, for one, would really like to see a solid HMMER rewrite, for instance.
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Reposted by Fabricio Almeida-Silva
PlantEvolution 🌱🌾 @plantevolution.bsky.social · 14/05/2026
Peer review crisis — this seems to make sense: A transparent universal credit system to incentivize peer review www.pnas.org/doi/10.1073/...
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Fabricio Almeida-Silva @almeidasilvaf.bsky.social · 08/05/2026
A fantastic scientific question requires a fantastic team! Glad to see this super cool study finally out!
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Reposted by Fabricio Almeida-Silva
Tobias Jores @tobiasjores.bsky.social · 30/04/2026
📢Out now on bioRxiv: We used Plant STARR-seq to characterize the species- and condition-specific enhancer activity of over 350,000 sequences derived from four plant species. For more, see below and read the paper at: www.biorxiv.org/content/10.6...
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Katharina Hoff @katharinahoff.bsky.social · 11/04/2026
1/ BRAKER4 hatched! The Earth BioGenome Project is on track to sequence ~1.5M eukaryotic species. Every one needs a structural annotation. No Perl monolith was going to survive that. So we rewrote BRAKER from the ground up. github.com/Gaius-August...
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Fabricio Almeida-Silva @almeidasilvaf.bsky.social · 06/04/2026
Best thing I’ve read on the use of LLM chatbots and its effects on learning. A piece that every (aspiring) professor should read. Brilliant, brilliantly written.
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Reposted by Fabricio Almeida-Silva
Joe Sondow @joesondow.bsky.social · 05/04/2026
Heads up GitHub users. You have less than a month left to opt out of "Allow GitHub to use my data for AI model training". "On April 24 we'll start using GitHub Copilot interaction data for AI model training unless you opt out." github.com/settings/cop...
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Bioconductor @bioconductor.bsky.social · 27/03/2026
📢 Bioconductor and Physalia Courses are offering 2 free seats per course, listed below, to participants based in low- or middle-income countries, with the aim of expanding access to high-quality training in bioinformatics and computational biology. Interested? Apply here👉 bit.ly/3Pyyzjj
A table titled ‘Upcoming’ listing bioinformatics courses with columns for date, title, and instructors. Entries include: 13–17 April 2026 – Epigenomics Data Analysis (Dr. Jacques Serizay); 4–7 May 2026 – Network Analysis in R (Dr. Fabricio Almeida-Silva); 18–20 May 2026 – Spatial Omics in R/Bioconductor (Dr. Stefano Mangiola); 6–10 July 2026 – Developing R/Bioconductor Packages for Genomics (Dr. Jacques Serizay); and a TBD course on Single-cell proteomics with R and Bioconductor (Prof. Laurent Gatto).
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Reposted by Fabricio Almeida-Silva
The Plant Cell @theplantcell.bsky.social · 19/03/2026
Duplicated genes find their space: Spatial transcriptomics illuminates evolutionary fates (Min-Yao Jhu , Fabian van Beveren , Bruno Guillotin) doi.org/10.1093/plce... #PlantScience @aspbofficial
doi.org
Duplicated genes find their space: Spatial transcriptomics illuminates evolutionary fates
Gene and genome duplications are fundamental forces driving plant evolution, leading to relaxed selection and expanding genetic toolkits (Van de Peer et al
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Reposted by Fabricio Almeida-Silva
Sainsbury Laboratory Cambridge University (SLCU) @slcuplants.bsky.social · 12/03/2026
Hiding in plain sight! 2.3M conserved non-coding sequences traced back 300M years across 284 plant species Ground-breaking study out in First Release @science.org from labs of @madelaineb.bsky.social, @idane.bsky.social & Zach Lippman ▶️ doi.org/10.1126/scie... ▶️ www.slcu.cam.ac.uk/news/hiding-...
Phylogeny of the 284 species of plants included in Conservatory data set. Conservatory uncovered ~2.3 million conserved non-coding DNA sequences across 284 plant species from 72 families including eudicots, monocots, gymnosperms, and algae. Illustrations by Professor Madelaine Bartlett.
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Nature Portfolio @natureportfolio.nature.com · 11/03/2026
A paper published in Nature presents Evo 2: an artificial intelligence-based biological foundation model trained on 9 trillion DNA base pairs spanning all domains of life that predicts functional properties from genomic sequences and provides a rich generative model for researchers in biology. 🧪
go.nature.com
Genome modelling and design across all domains of life with Evo 2 - Nature
Evo 2 is an artificial intelligence-based biological foundation model trained on 9 trillion DNA base pairs spanning all domains of life that predicts functional properties from genomic sequences and provides a rich generative model for researchers in biology.
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Polina Novikova @pnovik.bsky.social · 04/03/2026
I am happy to announce the launch of a new Arabidopsis genomics resource! Check out arabidopsislyrata.org Now you can easily look at the natural genetic variation across the entire species range of A. lyrata and A. arenosa.
arabidopsislyrata.org
Home | Alyrata Resource
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Anthony Mathelier @amathelier.bsky.social · 03/03/2026
👇 Still a couple of days to apply to join our amazing team as a Research Scientist / Software Developer. Apply if you want to build and maintain reproducible pipelines for large-scale genomic analysis to support our study of breast cancer cis-regulatory signatures and JASPAR, among other things.
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Fabricio Almeida-Silva @almeidasilvaf.bsky.social · 25/02/2026
Nice post, but this is an overcomplicated solution, IMO. If saving a ggplot to PNG distorts proportions, just don’t save it to PNG. I always save figs to PDF and use the {magick} package to convert all PDFs to 600-dpi PNGs. Easy peasy!
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The Arabidopsis Information Resource (TAIR) @tairnews.bsky.social · 19/02/2026
🎉📣 #TAIR12, the latest reannotation of the Arabidopsis thaliana genome, is now available under accession number PRJEB100887 on ENA and NCBI! Thank you all the volunteer researchers whose hard work has made this possible! #plantscience #plantbiology 🧪 bit.ly/3ZHtneT
bit.ly
Announcing the publication of TAIR12: Consult the fully reannotated genome on the European Nucleotide Archive - Phoenix Bioinformatics
TAIR (The Arabidopsis Information Resource), together with our nonprofit host Phoenix Bioinformatics, is pleased to announce the public release of TAIR12
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Tiago Peixoto @tiago.skewed.de · 23/02/2026
New blog post: "Higher orders need higher standards" skewed.de/lab/posts/hi... I discuss our current work disentangling misconceptions around "higher-order" networks: arxiv.org/abs/2602.16937 Explainer thread for the paper here: bsky.app/profile/tiag...
skewed.de
Higher orders need higher standards – Inverse Complexity Lab
Research group on inverse problems in complex systems and network science.
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 30/01/2026
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...
science.org
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
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Mario dos Reis @mariodosreis.bsky.social · 06/05/2025
Frustrated that MCMCtree does not have complex substitution models? The IQ-tree team has now developed IQ2MC, an interface for seamless integration of IQ-tree's substitution models with MCMCtree's fast Bayesian pipeline for clock dating. Read the preprint here: ecoevorxiv.org/repository/v...
ecoevorxiv.org
IQ2MC: A New Framework to Infer Phylogenetic Time Trees Using IQ-TREE 3 and MCMCTree with Mixture Models
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Vandepoele lab @vandepoelelab.bsky.social · 23/12/2025
We are pleased to announce the official release of PLAZA 5.1, our plant genomics platform, which comes with a major front-end redesign. This results in improved performance, enhanced visualization tools, and refined Toolboxes. Src: www.vandepoelelab.be/plaza/news#28
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Jonathan Eisen @phylogenomics.bsky.social · 22/12/2025
Back in the day, I spent a lot of effort pointing out that many claims of lateral gene transfer between taxa were better explained by other phenomena, like gene loss, duplicaiton and deletion, convergence, bad informatics, etc 1/n
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jlawlab.bsky.social @jlawlab.bsky.social · 11/12/2025
Have you ever wondered how new DNA methylation patterns are established? Paradigm shift ahead! We discovered a new mode of DNA methylation targeting in plants that relies on transcription factors and sequence motifs rather than chromatin modifications to regulate the methylome. rdcu.be/eQ6L5 1/8
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Tatsuya Nobori @tatsuyanobori.bsky.social · 29/11/2025
FX-Cell: a method for single-cell RNA sequencing on difficult-to-digest and cryopreserved plant samples www.nature.com/articles/s41...
nature.com
FX-Cell: a method for single-cell RNA sequencing on difficult-to-digest and cryopreserved plant samples - Nature Methods
This work describes FX-Cell and its derivatives to achieve single-cell RNA sequencing from challenging and cryopreserved plant tissues, expanding the scope of single-cell genomics across field-grown s...
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Guillaume Jacquemet @guijacquemet.bsky.social · 29/11/2025
Your periodic reminder that science is not done by a few selected "stars scientists". Science is done by hundred of thousands. Siloed money mean a few flashy discoveries and a lot of waste. Want to change things? Make funding accessible and stop funding calls with less than 2% success rate.
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Fabricio Almeida-Silva @almeidasilvaf.bsky.social · 23/11/2025
Thank you for highlighting our paper, @minyaojhu.bsky.social!
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The Plant Cell @theplantcell.bsky.social · 12/11/2025
Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes (Fabricio Almeida-Silva, Yves Van de Peer) doi.org/10.1093/plce... #PlantScience @aspbofficial
doi.org
Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes
After gene and genome duplications, expression divergence across cell types is not random, and it can be explained by a combination of gene age, gene funct
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Nature Biotechnology @natbiotech.nature.com · 10/11/2025
Fine-scale chromatin mapping uncovers principles of cis-regulatory element interactions. #NBThighlight www.cell.com/cell/fulltex...
cell.com
Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions
Li et al. apply base-pair resolution Micro Capture-C ultra to map chromatin contacts between individual motifs within cis-regulatory elements and reveal a unified model of biophysically mediated enhan...
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Tiago Peixoto @tiago.skewed.de · 09/11/2025
A team of 42 researchers lead by Oxford finds that bears do, in fact, defecate in the woods. www.oii.ox.ac.uk/news-events/...
oii.ox.ac.uk
OII | Study identifies weaknesses in how AI systems are evaluated
Largest systematic review of AI benchmarks highlights need for clearer definitions and stronger scientific standards.
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Fabricio Almeida-Silva @almeidasilvaf.bsky.social · 07/11/2025
This is brilliant!
Screenshot of the README file showcasing a comparison between dplyr verbs (group_by, summarize, arrange) and their genzdplyr counterparts (squad_up, no_cap, slay).
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Fabricio Almeida-Silva @almeidasilvaf.bsky.social · 02/11/2025
Please read the whole thread. Very interesting thoughts.
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Will Gervais @willgervais.com · 23/10/2025
Spoiler alert: it's better to have a good theoretical understanding and design appropriate statistical models than it is to throw zillions of superficially "okay, fine" models at a poorly specified (and often deliberately vague) target. A bit of good thinking >>> lots of poor thinking. Shocking!
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Fabricio Almeida-Silva @almeidasilvaf.bsky.social · 22/10/2025
Every few months I see a new paper with the expression "two to tango". Out of curiosity, I searched on Google Scholar how many papers have this expression in their titles. 1540 papers, and counting. Let's be creative, folks.
Screenshot of a Google Scholar search for papers that have the expression "two to tango" in their titles. 1540 results were found.
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Fabricio Almeida-Silva @almeidasilvaf.bsky.social · 16/10/2025
Our paper on the evolution (duplicated) gene expression divergence in spatially resolved plant transcriptomes is now out @theplantcell.bsky.social w/ @yvdp.bsky.social #PlantSci #Evolution academic.oup.com/plcell/advan...
academic.oup.com
Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes
After gene and genome duplications, expression divergence across cell types is not random, and it can be explained by a combination of gene age, gene funct
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Bioconductor @bioconductor.bsky.social · 01/10/2025
🌍 Applications now open for our first Bioconductor course in West Africa! 📅 17–21 Nov 2025 | 📍 Abomey-Calavi, Benin Free, in-person training on R, RStudio & RNA-seq workflows. Apply by 15 Oct 👉 forms.gle/d32F6xJJbsFa... More info 🔗 training.bioconductor.org/workshops/20... #Bioconductor #RStats
Front view of the GBioS building at the University of Abomey-Calavi, Benin, surrounded by palm trees with a sign reading “Genetics, Biotechnology and Seed Science Unit.” Banner text above reads “Apply Now for the Bioconductor Benin 2025 Course!
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Fabricio Almeida-Silva @almeidasilvaf.bsky.social · 22/09/2025
Glad to have contributed to this really cool work, brilliantly led by @dmacguig.bsky.social and @fishgenomes.bsky.social If I were not a plant scientist, I’d probably be working on fish genomes.
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Nature Plants @natplants.nature.com · 19/09/2025
New OA Article: "A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution" rdcu.be/eHce3 Chromatin accessibility in rice & related grasses: how regulatory DNA elements evolve across cell types & species; identifying potential silencers.
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Fabricio Almeida-Silva @almeidasilvaf.bsky.social · 10/09/2025
My thoughts exactly. Epigenetics is just genetics.
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Fabricio Almeida-Silva @almeidasilvaf.bsky.social · 06/09/2025
Quite disappointed that the authors didn’t play with UMAP parameters (or run it enough times) until the UMAP plot looked like a cow.
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