@olgabiobio.bsky.social
Pinned
GitHub - olgatsiouri1996/sanger_analysis_pipeline: x86-64 Pipeline used to trim and combine sanger raw data to retrieve a consesus read and other results
x86-64 Pipeline used to trim and combine sanger raw data to retrieve a consesus read and other results - olgatsiouri1996/sanger_analysis_pipeline
github.com
hello #wetlab #bioinformatics fellas!
Do you want to use software like sangeranalyseR to analyze #sanger data? Is learning #R and installing dependences a headache? use github.com/olgatsiouri1.... This pipeline uses #docker containers to create a consesus read in fasta format and other results
Do you want to use software like sangeranalyseR to analyze #sanger data? Is learning #R and installing dependences a headache? use github.com/olgatsiouri1.... This pipeline uses #docker containers to create a consesus read in fasta format and other results
Reposted
Fascinating preprint. I've always been curious about genome stability of phages.
🧫🦠
🧫🦠
Phages evolve fast, or do they?
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
Ecological constraints foster both extreme viral-host lineage stability and mobile element diversity in a marine community
Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...
www.biorxiv.org
October 13, 2025 at 7:23 AM
Fascinating preprint. I've always been curious about genome stability of phages.
🧫🦠
🧫🦠
Reposted
Bioinformaticists need a set of Greek theater masks. 🧪 🧬 🖥️
October 6, 2025 at 8:16 PM
Bioinformaticists need a set of Greek theater masks. 🧪 🧬 🖥️
Reposted
September 25, 2025 at 9:50 PM
🧬🖥️here's how a beneficial fusarium solani interacts with Nicotiana benthamiana:
onlinelibrary.wiley.com/doi/10.1111/...
If you also want to calculate the number/length of siRNAs use:
github.com/olgatsiouri1... build with docker for minimal dependences
onlinelibrary.wiley.com/doi/10.1111/...
If you also want to calculate the number/length of siRNAs use:
github.com/olgatsiouri1... build with docker for minimal dependences
Cross‐kingdom RNAi induced by a beneficial endophytic fungus to its host requires transitivity and amplification of silencing signals
Cross-kingdom endophyte-induced silencing to host plant, requires RDR6-mediated transitivity to amplify the initial sRNA signal.
onlinelibrary.wiley.com
August 23, 2025 at 3:40 PM
🧬🖥️here's how a beneficial fusarium solani interacts with Nicotiana benthamiana:
onlinelibrary.wiley.com/doi/10.1111/...
If you also want to calculate the number/length of siRNAs use:
github.com/olgatsiouri1... build with docker for minimal dependences
onlinelibrary.wiley.com/doi/10.1111/...
If you also want to calculate the number/length of siRNAs use:
github.com/olgatsiouri1... build with docker for minimal dependences
Reposted
A diverse and distinct microbiome inside living trees. #Microbiome #LivingTrees #WoodMicrobiome #Genomics @nature.com 🧬
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A diverse and distinct microbiome inside living trees - Nature
Microbiome analyses of living trees show that a single tree can host approximately one trillion bacteria, with microbial communities distinctly partitioned between heartwood and sapwood and with…
www.nature.com
August 8, 2025 at 8:31 AM
A diverse and distinct microbiome inside living trees. #Microbiome #LivingTrees #WoodMicrobiome #Genomics @nature.com 🧬
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted
Do plasmids evolve faster 🐇, slower 🐢, or just like chromosomes 🧬?
In our new paper, we tackled this question using theory, simulations, bioinformatics, and experiments!
👇 Check out all the details in Paula’s thread!
Hint: 🐇 (most of the time)
In our new paper, we tackled this question using theory, simulations, bioinformatics, and experiments!
👇 Check out all the details in Paula’s thread!
Hint: 🐇 (most of the time)
July 22, 2025 at 3:05 PM
Do plasmids evolve faster 🐇, slower 🐢, or just like chromosomes 🧬?
In our new paper, we tackled this question using theory, simulations, bioinformatics, and experiments!
👇 Check out all the details in Paula’s thread!
Hint: 🐇 (most of the time)
In our new paper, we tackled this question using theory, simulations, bioinformatics, and experiments!
👇 Check out all the details in Paula’s thread!
Hint: 🐇 (most of the time)
Reposted
I need something halfway between markdown and rtf
July 27, 2025 at 6:29 PM
I need something halfway between markdown and rtf
you cannot be mad that people not close to israel/palestine didn't knew anything, sorry we were lied by the media what do you want me to do cry? go convince other people who have no idea. Self rigtheous winning leads to nowhere
i didnt. the bombing campaign in 2019 was also part of a genocide.
just because you're an ignorant asshole doesn't mean everyone else is!
just because you're an ignorant asshole doesn't mean everyone else is!
July 5, 2025 at 8:52 PM
you cannot be mad that people not close to israel/palestine didn't knew anything, sorry we were lied by the media what do you want me to do cry? go convince other people who have no idea. Self rigtheous winning leads to nowhere
Reposted
New blog post: Weekly Recap (June 2025, part 1). PhyloSketch for drawing phylogenies, Uncalled4 for DNA/RNA modifications, Severus for long read SV calling, CREsted for synthetic enhancer modeling, a review on genome language models, ... 🧬🖥️🧪 #Rstats blog.stephenturner.us/p/weekly-rec...
June 11, 2025 at 1:04 PM
New blog post: Weekly Recap (June 2025, part 1). PhyloSketch for drawing phylogenies, Uncalled4 for DNA/RNA modifications, Severus for long read SV calling, CREsted for synthetic enhancer modeling, a review on genome language models, ... 🧬🖥️🧪 #Rstats blog.stephenturner.us/p/weekly-rec...
Reposted
Thread: Introducing GCUA v2.0 (General Codon Usage Analysis) - a Python tool for analysing codon usage patterns in DNA sequences! Originally developed in 1998, now completely rewritten with modern features. Let me walk you through what I like about this version (PLS RT) github.com/mol-evol/gcu...
github.com
June 1, 2025 at 7:28 PM
Thread: Introducing GCUA v2.0 (General Codon Usage Analysis) - a Python tool for analysing codon usage patterns in DNA sequences! Originally developed in 1998, now completely rewritten with modern features. Let me walk you through what I like about this version (PLS RT) github.com/mol-evol/gcu...
Reposted
June 23 - 26, 2025 > The Galaxy #Bioconductor Community Conference (GBCC) | Abstract Deadline: 2025-04-08 (oops); Registration/Poster Abstract Deadline: 2025-05-09 | #OpenScience #OpenSource #UseGalaxy #RStats #GBCC2025 🧬 🖥️ 🧪
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meetings.cshl.edu/images/gbcc2...
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meetings.cshl.edu/images/gbcc2...
https://meetings.cshl.edu/images/gbcc25_logo.png)](https://gbcc2025.netlify.app/
April 9, 2025 at 7:28 PM
June 23 - 26, 2025 > The Galaxy #Bioconductor Community Conference (GBCC) | Abstract Deadline: 2025-04-08 (oops); Registration/Poster Abstract Deadline: 2025-05-09 | #OpenScience #OpenSource #UseGalaxy #RStats #GBCC2025 🧬 🖥️ 🧪
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meetings.cshl.edu/images/gbcc2...
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meetings.cshl.edu/images/gbcc2...
Reposted
If this dipshit knew anything at all about history he’d know the February Revolution was basically accomplished by libs marching in the street and the October Revolution only occurred because the Bolsheviks, never a large faction, did a coup against a liberal government that shot itself in the foot
if you thought those marches were revolutionary i don’t know what to tell you
April 7, 2025 at 1:21 AM
If this dipshit knew anything at all about history he’d know the February Revolution was basically accomplished by libs marching in the street and the October Revolution only occurred because the Bolsheviks, never a large faction, did a coup against a liberal government that shot itself in the foot
Reposted
📜 Expression of a modified Avr3a gene under the control of a synthetic pathogen-inducible promoter leads to Phytophthora infestans resistance in potato
🧑🔬 Friedrich Kauder, Dietmar J. Stahl, et al.
📔 Plant Biotechnology Journal
#️⃣ #PlantScience #PlantImmunity #SyntheticBiology #SynBio #Agriculture
🧑🔬 Friedrich Kauder, Dietmar J. Stahl, et al.
📔 Plant Biotechnology Journal
#️⃣ #PlantScience #PlantImmunity #SyntheticBiology #SynBio #Agriculture
Expression of a modified Avr3a gene under the control of a synthetic pathogen‐inducible promoter leads to Phytophthora infestans resistance in potato
Late blight resistance of potato was improved by the co-expression of the potato resistance gene R3a and the pathogen-inducible avirulence gene Avr3a of Phytopthora infestans. The synthetic pathogen-...
onlinelibrary.wiley.com
March 11, 2025 at 8:03 AM
📜 Expression of a modified Avr3a gene under the control of a synthetic pathogen-inducible promoter leads to Phytophthora infestans resistance in potato
🧑🔬 Friedrich Kauder, Dietmar J. Stahl, et al.
📔 Plant Biotechnology Journal
#️⃣ #PlantScience #PlantImmunity #SyntheticBiology #SynBio #Agriculture
🧑🔬 Friedrich Kauder, Dietmar J. Stahl, et al.
📔 Plant Biotechnology Journal
#️⃣ #PlantScience #PlantImmunity #SyntheticBiology #SynBio #Agriculture
Reposted
New in @naturecomms.bsky.social – IGI's
@doudna-lab.bsky.social + Jordan lab in
@ucberkeleyofficial.bsky.social's Dept. of Electrical Engineering & Comp Sci unveil a new #AI-based method to quickly narrow down large datasets of proteins to prioritize what to study: ow.ly/nxxn50V80fo 🧪🧬🖥️
@doudna-lab.bsky.social + Jordan lab in
@ucberkeleyofficial.bsky.social's Dept. of Electrical Engineering & Comp Sci unveil a new #AI-based method to quickly narrow down large datasets of proteins to prioritize what to study: ow.ly/nxxn50V80fo 🧪🧬🖥️
Breakthrough Method Enables Rapid Discovery of New Useful Proteins
Breakthrough Method Enables Rapid Discovery of New Useful Proteins - Innovative Genomics Institute (IGI) A new AI machine learning approach developed at the IGI lets scientists quickly search massive ...
ow.ly
February 28, 2025 at 5:44 PM
New in @naturecomms.bsky.social – IGI's
@doudna-lab.bsky.social + Jordan lab in
@ucberkeleyofficial.bsky.social's Dept. of Electrical Engineering & Comp Sci unveil a new #AI-based method to quickly narrow down large datasets of proteins to prioritize what to study: ow.ly/nxxn50V80fo 🧪🧬🖥️
@doudna-lab.bsky.social + Jordan lab in
@ucberkeleyofficial.bsky.social's Dept. of Electrical Engineering & Comp Sci unveil a new #AI-based method to quickly narrow down large datasets of proteins to prioritize what to study: ow.ly/nxxn50V80fo 🧪🧬🖥️
Reposted
Pancreatic cancer killed my mom back in 2010. This rules.
Goosebump producing news this week out of Oregon Health and Science University in the diagnosis of pancreatic CA.
They developed a groundbreaking blood test, called PAC-MANN. This new test can find pancreatic cancer in just 45 minutes, even in its earliest stages.
They developed a groundbreaking blood test, called PAC-MANN. This new test can find pancreatic cancer in just 45 minutes, even in its earliest stages.
New blood test identifies hard-to-detect pancreatic cancer with 85% accuracy
A new blood test could help doctors detect pancreatic cancer earlier, potentially improving survival rates for one of the deadliest cancers.
www.eurekalert.org
February 22, 2025 at 5:39 PM
Pancreatic cancer killed my mom back in 2010. This rules.
Reposted
Hey, if you're interested in how my team and I sequence all the human and animal viruses in community wastewater, come register for the webinar I'm delivering next week! 🦠🖥️🧬
February 6, 2025 at 4:54 PM
Hey, if you're interested in how my team and I sequence all the human and animal viruses in community wastewater, come register for the webinar I'm delivering next week! 🦠🖥️🧬
Reposted
Pannagram: unbiased pangenome alignment and the Mobilome calling https://www.biorxiv.org/content/10.1101/2025.02.07.637071v1 🧬🖥️🧪 #Rstats https://github.com/iganna/pannagram
February 9, 2025 at 12:27 PM
Pannagram: unbiased pangenome alignment and the Mobilome calling https://www.biorxiv.org/content/10.1101/2025.02.07.637071v1 🧬🖥️🧪 #Rstats https://github.com/iganna/pannagram
Reposted
Meta illegaly downloaded 80+ terabytes of books from LibGen, Anna's Archive, and Z-library to train their AI models.
In 2010, Aaron Swartz downloaded only 70 GBs of articles from JSTOR (0.0875% of Meta). Faced $1 million in fine and 35 years in jail. Took his own life in 2013.
In 2010, Aaron Swartz downloaded only 70 GBs of articles from JSTOR (0.0875% of Meta). Faced $1 million in fine and 35 years in jail. Took his own life in 2013.
February 7, 2025 at 4:45 PM
Meta illegaly downloaded 80+ terabytes of books from LibGen, Anna's Archive, and Z-library to train their AI models.
In 2010, Aaron Swartz downloaded only 70 GBs of articles from JSTOR (0.0875% of Meta). Faced $1 million in fine and 35 years in jail. Took his own life in 2013.
In 2010, Aaron Swartz downloaded only 70 GBs of articles from JSTOR (0.0875% of Meta). Faced $1 million in fine and 35 years in jail. Took his own life in 2013.
Reposted
"The cure for a fallacious argument is a better argument, not the suppression of ideas."
-Carl Sagan
-Carl Sagan
February 8, 2025 at 6:57 PM
"The cure for a fallacious argument is a better argument, not the suppression of ideas."
-Carl Sagan
-Carl Sagan
Reposted
Banana slug genome clocks in at 2.3GB.
🧪🌎🧬🖥️ #EvoSky #Genomics #Bioinformatics
phys.org/news/2025-02...
🧪🌎🧬🖥️ #EvoSky #Genomics #Bioinformatics
phys.org/news/2025-02...
Scientists produce first complete genome of a banana slug
Scientists at UC Santa Cruz have completed the first end-to-end genome of the iconic Pacific banana slug, a species synonymous with California's coastal redwood forests and the university's beloved ma...
phys.org
February 8, 2025 at 7:09 AM
Banana slug genome clocks in at 2.3GB.
🧪🌎🧬🖥️ #EvoSky #Genomics #Bioinformatics
phys.org/news/2025-02...
🧪🌎🧬🖥️ #EvoSky #Genomics #Bioinformatics
phys.org/news/2025-02...
hello #wsl2 users!! if you wanna open and use sublime text withought having to open the windows subsystem for linux terminal and you wanna make sure your file won't contain windows or mac line endings this repository is for you: github.com/BioGUIwslLab...
GitHub - BioGUIwslLab/sublime_gui: A windows x86_64 lightweight GUI app to navigate via the windows filesystem, open and run files using sublime-text in windows subsystem for linux
A windows x86_64 lightweight GUI app to navigate via the windows filesystem, open and run files using sublime-text in windows subsystem for linux - BioGUIwslLab/sublime_gui
github.com
February 5, 2025 at 4:53 PM
hello #wsl2 users!! if you wanna open and use sublime text withought having to open the windows subsystem for linux terminal and you wanna make sure your file won't contain windows or mac line endings this repository is for you: github.com/BioGUIwslLab...
Reposted
This is a cool repository of 3D printer files. Everything from specific molecules to test tube racks and all sorts of small hardware pieces.
Did you know the NIH hosts a 3D printed lab hardware repository? Looking forward to uploading stuff there too. Go check it out!
3d.nih.gov
3d.nih.gov
NIH 3D
3d.nih.gov
January 29, 2025 at 6:06 PM
This is a cool repository of 3D printer files. Everything from specific molecules to test tube racks and all sorts of small hardware pieces.
Reposted
Fight fire with fire. Open source is the only way forward. Tools got us out of ice ages and into agriculture. Tools will get us past this barrier of greed. The genie may be out of the bottle, but that goes for all players on the field.
The reveal of a new artificial intelligence assistant, DeepSeek, looks poised to wipe almost a trillion pounds in value off some of the world’s most expensive technology companies.
DeepSeek AI launch sees $1tn wiped off world’s biggest tech companies
Nvidia is the hardest-hit among American big tech related to artificial intelligence, while Samsung in Europe is down more than 20 per cent
www.independent.co.uk
January 27, 2025 at 1:35 PM
Fight fire with fire. Open source is the only way forward. Tools got us out of ice ages and into agriculture. Tools will get us past this barrier of greed. The genie may be out of the bottle, but that goes for all players on the field.