@luizirber.bsky.social
Reposted
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:26 PM
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
Reposted
Our PathogenSurveillance pipeline is out in bioRxiv. PathogenSurveillance is an open-source and automated Nextflow pipeline for population genomic analyses of WGS data. It is flexible, using both short and long read data, mixed samples of prokaryotes and eukaryotes.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification
Whole genome sequencing (WGS) offers a comprehensive, organism-agnostic method that effectively meets the need for efficient, reliable, and standardized responses to emerging threats from pathogens an...
www.biorxiv.org
November 3, 2025 at 6:52 PM
Our PathogenSurveillance pipeline is out in bioRxiv. PathogenSurveillance is an open-source and automated Nextflow pipeline for population genomic analyses of WGS data. It is flexible, using both short and long read data, mixed samples of prokaryotes and eukaryotes.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted
🏆 Conheça os premiados da Edição 2025 do Prêmio Dorneles Trémea / Jean Ferri ⭐
- Adorilson Bezerra
📌 Ceará-Mirim - RN / Coimbra - Portugal
• Organizador do
Projeto Software Livre - Rio Grande do Norte
• GruPy - RN
• Professor do IFRN
• Grupo de tradução da documentação
do Python para PT-BR
+
- Adorilson Bezerra
📌 Ceará-Mirim - RN / Coimbra - Portugal
• Organizador do
Projeto Software Livre - Rio Grande do Norte
• GruPy - RN
• Professor do IFRN
• Grupo de tradução da documentação
do Python para PT-BR
+
November 2, 2025 at 10:27 PM
🏆 Conheça os premiados da Edição 2025 do Prêmio Dorneles Trémea / Jean Ferri ⭐
- Adorilson Bezerra
📌 Ceará-Mirim - RN / Coimbra - Portugal
• Organizador do
Projeto Software Livre - Rio Grande do Norte
• GruPy - RN
• Professor do IFRN
• Grupo de tradução da documentação
do Python para PT-BR
+
- Adorilson Bezerra
📌 Ceará-Mirim - RN / Coimbra - Portugal
• Organizador do
Projeto Software Livre - Rio Grande do Norte
• GruPy - RN
• Professor do IFRN
• Grupo de tradução da documentação
do Python para PT-BR
+
Reposted
Reposted
Following ish's `filter` and bqtools' `grep`, Sassy now also has initial support for grep and filter!
Grep mode shows all matches, grouped per record, and is meant for human consumption.
Filter mode prints full matching (or non-matching) records to stdout or output files.
Grep mode shows all matches, grouped per record, and is meant for human consumption.
Filter mode prints full matching (or non-matching) records to stdout or output files.
October 30, 2025 at 11:46 PM
Following ish's `filter` and bqtools' `grep`, Sassy now also has initial support for grep and filter!
Grep mode shows all matches, grouped per record, and is meant for human consumption.
Filter mode prints full matching (or non-matching) records to stdout or output files.
Grep mode shows all matches, grouped per record, and is meant for human consumption.
Filter mode prints full matching (or non-matching) records to stdout or output files.
Reposted
TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share. pyfound.blogspot.com/2025/10/NSF-...
🧵
🧵
The official home of the Python Programming Language
www.python.org
October 27, 2025 at 2:47 PM
TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share. pyfound.blogspot.com/2025/10/NSF-...
🧵
🧵
Reposted
The desperate need to accumulate more and more at the cost of everyone else’s wellbeing should be classified as a mental disorder, and I will absolutely die on this hill.
Guillermo del Toro on wealth: "a wealthy man is a man who has enough, not a man that needs more. If you have enough to invite someone for a beer? You're rich. If you have a yacht, planes, islands, and you still need more? You're not rich."
October 27, 2025 at 3:22 AM
The desperate need to accumulate more and more at the cost of everyone else’s wellbeing should be classified as a mental disorder, and I will absolutely die on this hill.
Reposted
molho bechamel não é aquele negócio de duas mulheres conversando sem falar de homem
October 26, 2025 at 9:09 PM
molho bechamel não é aquele negócio de duas mulheres conversando sem falar de homem
Reposted
1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...
GitHub - mohsenzakeri/Movi: Fast, Cache-Efficient, and Scalable Queries on Pangenomes
Fast, Cache-Efficient, and Scalable Queries on Pangenomes - mohsenzakeri/Movi
github.com
October 21, 2025 at 8:00 PM
1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...
Reposted
End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon.
🌐 evedesign.bio
🌐 evedesign.bio
October 22, 2025 at 2:30 PM
End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon.
🌐 evedesign.bio
🌐 evedesign.bio
Reposted
Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy
academic.oup.com
October 22, 2025 at 2:20 PM
Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
Reposted
O pampa é um dos nossos biomas mais ameaçados. Se entendi a imagem, toda árvore aí é monocultura de eucalipto. Tão matando um bioma plantando árvore. O pampa tem nem 10% de sua área protegida. Nele tem mais de 64 de plantas por metro quadrado… mas só é grama, né? Só floresta importa, né? 😤
Agro superou área com vegetação nativa do Pampa ⬇️
Mapeamento mostra que vulnerabilidade ambiental do bioma é ampliada pela baixa proteção por unidades de conservação
Mapeamento mostra que vulnerabilidade ambiental do bioma é ampliada pela baixa proteção por unidades de conservação
Agro superou área com vegetação nativa do Pampa - ((o))eco
Mapeamento mostra que vulnerabilidade ambiental do bioma é ampliada pela baixa proteção por unidades de conservação
oeco.org.br
October 15, 2025 at 2:56 PM
O pampa é um dos nossos biomas mais ameaçados. Se entendi a imagem, toda árvore aí é monocultura de eucalipto. Tão matando um bioma plantando árvore. O pampa tem nem 10% de sua área protegida. Nele tem mais de 64 de plantas por metro quadrado… mas só é grama, né? Só floresta importa, né? 😤
Reposted
That reminds me of an interactive BWT searching visualization I made here: (change 'algorithm' to BWT first)
curiouscoding.nl/posts/alg-viz/
curiouscoding.nl/posts/alg-viz/
October 15, 2025 at 9:43 AM
That reminds me of an interactive BWT searching visualization I made here: (change 'algorithm' to BWT first)
curiouscoding.nl/posts/alg-viz/
curiouscoding.nl/posts/alg-viz/
Reposted
New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....
October 14, 2025 at 8:48 PM
New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....
Reposted
The Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...
Efficient and accurate search in petabase-scale sequence repositories - Nature
MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.
www.nature.com
October 9, 2025 at 2:40 PM
The Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...
Reposted
Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...
docs.google.com/document/d/1...
Postdoc Description.docx
Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...
docs.google.com
October 8, 2025 at 4:03 PM
Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...
docs.google.com/document/d/1...
Reposted
Another amazing opportunity at UMD in Mihai Pop's lab! Mihai is looking for a bioinformatics software engineer. Consider applying here if you're interested: umd.wd1.myworkdayjobs.com/en-US/UMCP/j...
Bioinformatics engineer
Job Description Summary Organization's Summary Statement: We are seeking to hire a bioinformatics engineer in the Pop lab within the University of Maryland Institute for Advanced Computer Studies (UMI...
umd.wd1.myworkdayjobs.com
October 8, 2025 at 5:08 PM
Another amazing opportunity at UMD in Mihai Pop's lab! Mihai is looking for a bioinformatics software engineer. Consider applying here if you're interested: umd.wd1.myworkdayjobs.com/en-US/UMCP/j...
Reposted
A new paper from the lab! Work led by
@drtamermansour.bsky.social and others not here on bsky. "We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem."
@drtamermansour.bsky.social and others not here on bsky. "We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem."
The Great Genotyper: a graph-based method for population genotyping of small and structural variants
Long-read sequencing (LRS) enables high-quality structural variant (SV) discovery. SV genotypers utilize these precise call sets to improve the recall and precision of genotyping in short-read sequenc...
pmc.ncbi.nlm.nih.gov
October 7, 2025 at 8:32 PM
A new paper from the lab! Work led by
@drtamermansour.bsky.social and others not here on bsky. "We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem."
@drtamermansour.bsky.social and others not here on bsky. "We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem."
Reposted
O trabalho morto do processamento exige trabalho vivo do cientista para ser tornado útil.
Mas ninguém está nem aí pra utilidade, isso aqui é capitalismo. O objetivo é dinheiro.
Bem, 16 anos atrás, o capitalismo inventou uma forma 'exótica' de transformar processamento em dinheiro: criptomoedas.+
Mas ninguém está nem aí pra utilidade, isso aqui é capitalismo. O objetivo é dinheiro.
Bem, 16 anos atrás, o capitalismo inventou uma forma 'exótica' de transformar processamento em dinheiro: criptomoedas.+
October 6, 2025 at 2:05 PM
O trabalho morto do processamento exige trabalho vivo do cientista para ser tornado útil.
Mas ninguém está nem aí pra utilidade, isso aqui é capitalismo. O objetivo é dinheiro.
Bem, 16 anos atrás, o capitalismo inventou uma forma 'exótica' de transformar processamento em dinheiro: criptomoedas.+
Mas ninguém está nem aí pra utilidade, isso aqui é capitalismo. O objetivo é dinheiro.
Bem, 16 anos atrás, o capitalismo inventou uma forma 'exótica' de transformar processamento em dinheiro: criptomoedas.+
Reposted
Existe uma história da escalada do processamento de dados global que é muito pouco contada.
Vai ser um fio longo, espero que interessem a vocês.
Em 1965, Gordon Moore, co-fundador da Intel, prevê que a capacidade de processamento /custo dobra a cada ano.
Ele previu que isso duraria 10 anos.+
Vai ser um fio longo, espero que interessem a vocês.
Em 1965, Gordon Moore, co-fundador da Intel, prevê que a capacidade de processamento /custo dobra a cada ano.
Ele previu que isso duraria 10 anos.+
".. OpenAI will receive warrants for up to 160 million AMD shares, roughly 10% of the chip company, at 1 cent per share, awarded in phases, if OpenAI hits certain milestones .."
@wsj.com $AMD
www.wsj.com/tech/ai/open...
@wsj.com $AMD
www.wsj.com/tech/ai/open...
OpenAI, AMD Announce Massive Computing Deal, Marking New Phase of AI Boom
Five-year agreement will challenge Nvidia’s market dominance, as OpenAI plans deployment of AMD’s new MI450 chips.
www.wsj.com
October 6, 2025 at 1:52 PM
Existe uma história da escalada do processamento de dados global que é muito pouco contada.
Vai ser um fio longo, espero que interessem a vocês.
Em 1965, Gordon Moore, co-fundador da Intel, prevê que a capacidade de processamento /custo dobra a cada ano.
Ele previu que isso duraria 10 anos.+
Vai ser um fio longo, espero que interessem a vocês.
Em 1965, Gordon Moore, co-fundador da Intel, prevê que a capacidade de processamento /custo dobra a cada ano.
Ele previu que isso duraria 10 anos.+
Reposted
E o nocivo e cretino empresariado brasileiro já se movimenta pra fuder o trabalhador por pura birra com a isenção de IR pra quem ganha até 5 mil.
Não há custo adicional algum - conforme a própria matéria destaca. É só ódio e nojo de pobre mesmo.
melhorrh.com.br/isencao-ir-5...
Não há custo adicional algum - conforme a própria matéria destaca. É só ódio e nojo de pobre mesmo.
melhorrh.com.br/isencao-ir-5...
October 3, 2025 at 11:49 AM
E o nocivo e cretino empresariado brasileiro já se movimenta pra fuder o trabalhador por pura birra com a isenção de IR pra quem ganha até 5 mil.
Não há custo adicional algum - conforme a própria matéria destaca. É só ódio e nojo de pobre mesmo.
melhorrh.com.br/isencao-ir-5...
Não há custo adicional algum - conforme a própria matéria destaca. É só ódio e nojo de pobre mesmo.
melhorrh.com.br/isencao-ir-5...
Reposted
#RECOMB2026 is now accepting submissions and we'd love to see your best work!
📌 Abstract registration: Nov 7, 2025
📌 Full paper submission: Nov 14, 2025
📜 More info: recomb.org/recomb2026/call_for_papers.html
📌 Abstract registration: Nov 7, 2025
📌 Full paper submission: Nov 14, 2025
📜 More info: recomb.org/recomb2026/call_for_papers.html
RECOMB 2026 | CALL FOR PAPERS
Call For Papers
recomb.org
October 2, 2025 at 12:00 PM
#RECOMB2026 is now accepting submissions and we'd love to see your best work!
📌 Abstract registration: Nov 7, 2025
📌 Full paper submission: Nov 14, 2025
📜 More info: recomb.org/recomb2026/call_for_papers.html
📌 Abstract registration: Nov 7, 2025
📌 Full paper submission: Nov 14, 2025
📜 More info: recomb.org/recomb2026/call_for_papers.html
Reposted
Normative framework of bigger tech
(aka, me trolling the tech audience)
(aka, me trolling the tech audience)
Come to my lightning talk
At @pydataparis.bsky.social in a few minutes
At @pydataparis.bsky.social in a few minutes
October 1, 2025 at 4:42 PM
Normative framework of bigger tech
(aka, me trolling the tech audience)
(aka, me trolling the tech audience)
Reposted
Looking for people to test the latest version of simd-sketch.
It's now 2x as fast at sketching, and supports skipping over kmers containing N and other ambiguous bases (which is only ~35% slower).
'cargo install simd-sketch' is right there under your fingertips ;)
github.com/RagnarGrootK...
It's now 2x as fast at sketching, and supports skipping over kmers containing N and other ambiguous bases (which is only ~35% slower).
'cargo install simd-sketch' is right there under your fingertips ;)
github.com/RagnarGrootK...
GitHub - RagnarGrootKoerkamp/simd-sketch: Compute bottom-s sketches and s-buckets sketches, using simd-minimizers crate.
Compute bottom-s sketches and s-buckets sketches, using simd-minimizers crate. - RagnarGrootKoerkamp/simd-sketch
github.com
October 1, 2025 at 2:38 PM
Looking for people to test the latest version of simd-sketch.
It's now 2x as fast at sketching, and supports skipping over kmers containing N and other ambiguous bases (which is only ~35% slower).
'cargo install simd-sketch' is right there under your fingertips ;)
github.com/RagnarGrootK...
It's now 2x as fast at sketching, and supports skipping over kmers containing N and other ambiguous bases (which is only ~35% slower).
'cargo install simd-sketch' is right there under your fingertips ;)
github.com/RagnarGrootK...
Reposted
