Rauf Salamzade
@raufs.bsky.social
Interested in microbial ecology & evolution. Views are only my own. (he/him)
🎓: https://scholar.google.com/citations?hl=en&user=OBPpZq4AAAAJ&view_op=list_works&sortby=pubdate
👨💻: https://github.com/raufs
🎓: https://scholar.google.com/citations?hl=en&user=OBPpZq4AAAAJ&view_op=list_works&sortby=pubdate
👨💻: https://github.com/raufs
Reposted by Rauf Salamzade
Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
November 12, 2025 at 7:05 PM
Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
Reposted by Rauf Salamzade
Bioinformatics x cybersecurity: Christina Boucher and her colleague Sara Rampazzi uncovered a basic yet critical vulnerability in MinIONs through the MinKNOW software bioengineer.org/portable-gen...
Portable Genetic Sequencer Security Vulnerabilities Could Endanger Personal
Portable genetic sequencers, particularly those manufactured by Oxford Nanopore Technologies, have revolutionized the field of genomics, making DNA sequencing more accessible and practical across the
bioengineer.org
November 12, 2025 at 7:44 AM
Bioinformatics x cybersecurity: Christina Boucher and her colleague Sara Rampazzi uncovered a basic yet critical vulnerability in MinIONs through the MinKNOW software bioengineer.org/portable-gen...
Reposted by Rauf Salamzade
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 11, 2025 at 5:15 PM
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Rauf Salamzade
Heterogeneity in responses to ribosome-targeting antibiotics mediated by bacterial RNA repair | Nature Communications https://www.nature.com/articles/s41467-025-64759-3
Heterogeneity in responses to ribosome-targeting antibiotics mediated by bacterial RNA repair - Nature Communications
RNA repair helps bacteria survive antibiotic stress. Here, authors show that Rtc-driven repair causes cell-to-cell variation in resistance levels, revealing a potential form of heteroresistance, and identify key Rtc targets to enhance antibiotic effectiveness.
www.nature.com
November 12, 2025 at 2:39 AM
Heterogeneity in responses to ribosome-targeting antibiotics mediated by bacterial RNA repair | Nature Communications https://www.nature.com/articles/s41467-025-64759-3
Reposted by Rauf Salamzade
New paper from our group - megaphages, compact CRISPR-Cas effectors, and more from landfill phage, led by the talented Dr. Nikhil George (not on bsky). rdcu.be/ePo8o
Discarded diversity: novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills
link.springer.com
November 11, 2025 at 6:38 PM
New paper from our group - megaphages, compact CRISPR-Cas effectors, and more from landfill phage, led by the talented Dr. Nikhil George (not on bsky). rdcu.be/ePo8o
Reposted by Rauf Salamzade
A big thank you to @amydwillis.bsky.social and @titus.idyll.org for all your hard work and leadership. It is incredible the education, resources, network, and memories the STAMPS course has provided. There is nothing else like it and it will be missed.
Team villagers >> team werewolves 💗🐺
Team villagers >> team werewolves 💗🐺
November 12, 2025 at 2:53 AM
A big thank you to @amydwillis.bsky.social and @titus.idyll.org for all your hard work and leadership. It is incredible the education, resources, network, and memories the STAMPS course has provided. There is nothing else like it and it will be missed.
Team villagers >> team werewolves 💗🐺
Team villagers >> team werewolves 💗🐺
Reposted by Rauf Salamzade
Can we leverage bacterial competition for targeted replacement of harmful strains? Maybe! Our recent piece in @natmicrobiol.nature.com provides a theoretical framework and a set of experiments to show what it might take: www.nature.com/articles/s41...
Strain displacement in microbiomes via ecological competition - Nature Microbiology
Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.
www.nature.com
November 7, 2025 at 10:34 PM
Can we leverage bacterial competition for targeted replacement of harmful strains? Maybe! Our recent piece in @natmicrobiol.nature.com provides a theoretical framework and a set of experiments to show what it might take: www.nature.com/articles/s41...
Reposted by Rauf Salamzade
PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks www.nature.com/articles/s41... #jcampubs
PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks - Nature Communications
Prokaryotic pan-genome analysis is crucial for understanding microbial diversity, however current analytical methods often struggle to balance accuracy and computational efficiency. Here the authors p...
www.nature.com
November 10, 2025 at 3:45 PM
PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks www.nature.com/articles/s41... #jcampubs
Reposted by Rauf Salamzade
#MicrobiologyMonday: Bacteria swarm, but DYK they also "swash"? This flagella-independent movement is tied to fermentation: as cells ferment sugars, they create local osmolarity gradients, which generate a wave of fluid driving expansion. #JBacteriology: asm.social/2Gh
November 10, 2025 at 5:03 PM
#MicrobiologyMonday: Bacteria swarm, but DYK they also "swash"? This flagella-independent movement is tied to fermentation: as cells ferment sugars, they create local osmolarity gradients, which generate a wave of fluid driving expansion. #JBacteriology: asm.social/2Gh
Reposted by Rauf Salamzade
First preprint as a professor and it’s… not wastewater but bees?!?!??
Lovely collab with my colleague Dr. Jennifer VanWyk. the middle authors are all the undergrads who took my bioinformatics course last spring and analyzed novel data www.biorxiv.org/content/10.1...
Lovely collab with my colleague Dr. Jennifer VanWyk. the middle authors are all the undergrads who took my bioinformatics course last spring and analyzed novel data www.biorxiv.org/content/10.1...
Hot and Bothered, Bees’ Gut Microbiome Shifts Under Thermal Stress and Pathogen Infection.
Understanding bumble bee gut health is imperative as these vital pollinators are subjected to pathogenic infections and thermal stress from climate change. The gut microbiome serves as an indicator fo...
www.biorxiv.org
November 9, 2025 at 4:32 PM
First preprint as a professor and it’s… not wastewater but bees?!?!??
Lovely collab with my colleague Dr. Jennifer VanWyk. the middle authors are all the undergrads who took my bioinformatics course last spring and analyzed novel data www.biorxiv.org/content/10.1...
Lovely collab with my colleague Dr. Jennifer VanWyk. the middle authors are all the undergrads who took my bioinformatics course last spring and analyzed novel data www.biorxiv.org/content/10.1...
Reposted by Rauf Salamzade
Delighted that our review on resistance to last-resort antibiotics in Enterococci has been published in FEMS Microbiology Reviews
academic.oup.com/femsre/advan... (accepted manuscript version)
TL;DR: the Enterococci are really good at evolving resistance to antibiotics in new and creative ways.
academic.oup.com/femsre/advan... (accepted manuscript version)
TL;DR: the Enterococci are really good at evolving resistance to antibiotics in new and creative ways.
Resistance to last-resort antibiotics in enterococci
Abstract. The genus Enterococcus comprises a diverse group of species, many of which are commensal members of the gut microbiota of humans and animals. The
academic.oup.com
November 8, 2025 at 5:41 PM
Delighted that our review on resistance to last-resort antibiotics in Enterococci has been published in FEMS Microbiology Reviews
academic.oup.com/femsre/advan... (accepted manuscript version)
TL;DR: the Enterococci are really good at evolving resistance to antibiotics in new and creative ways.
academic.oup.com/femsre/advan... (accepted manuscript version)
TL;DR: the Enterococci are really good at evolving resistance to antibiotics in new and creative ways.
Reposted by Rauf Salamzade
Hungary 1956
'Well over a 100k people fled the country seeking asylum. Among them was a young geneticist named George Rédei, who headed for the Austrian border with a small vial of seeds tucked in his pocket.
The seeds belonged to a spindly weed in the mustard family called Arabidopsis thaliana.'
'Well over a 100k people fled the country seeking asylum. Among them was a young geneticist named George Rédei, who headed for the Austrian border with a small vial of seeds tucked in his pocket.
The seeds belonged to a spindly weed in the mustard family called Arabidopsis thaliana.'
How a humble weed became a superstar of biology
Arabidopsis thaliana was always an unlikely candidate for the limelight. But 25 years ago, the diminutive thale cress launched the botanical world into the molecular era.
knowablemagazine.org
November 6, 2025 at 8:47 AM
Hungary 1956
'Well over a 100k people fled the country seeking asylum. Among them was a young geneticist named George Rédei, who headed for the Austrian border with a small vial of seeds tucked in his pocket.
The seeds belonged to a spindly weed in the mustard family called Arabidopsis thaliana.'
'Well over a 100k people fled the country seeking asylum. Among them was a young geneticist named George Rédei, who headed for the Austrian border with a small vial of seeds tucked in his pocket.
The seeds belonged to a spindly weed in the mustard family called Arabidopsis thaliana.'
Reposted by Rauf Salamzade
Reposted by Rauf Salamzade
onetipperday.blogspot.com/2014/09/tran...
Found something easy, put it here for the search:
Install datamash:
sudo apt install datamash
And then:
cat file.tsv | datamash transpose > transposed_file.tsv
Nice and quick!
Found something easy, put it here for the search:
Install datamash:
sudo apt install datamash
And then:
cat file.tsv | datamash transpose > transposed_file.tsv
Nice and quick!
transpose a tab-delimited file in command line
A blog about Tips and Tricks for Unix, Perl, R, HTML, Javascript, Google API and mostly Bioinformatics
onetipperday.blogspot.com
November 7, 2025 at 11:59 PM
onetipperday.blogspot.com/2014/09/tran...
Found something easy, put it here for the search:
Install datamash:
sudo apt install datamash
And then:
cat file.tsv | datamash transpose > transposed_file.tsv
Nice and quick!
Found something easy, put it here for the search:
Install datamash:
sudo apt install datamash
And then:
cat file.tsv | datamash transpose > transposed_file.tsv
Nice and quick!
Reposted by Rauf Salamzade
It's International Women in Science Day ♀️, and I want to talk briefly about Rosalind Franklin.
A conventional choice for unconventional reasons: Dr. Franklin was one of the FIRST STRUCTURAL VIROLOGISTS. Let's talk about her work outside of the Crick & Watson debacle.
A conventional choice for unconventional reasons: Dr. Franklin was one of the FIRST STRUCTURAL VIROLOGISTS. Let's talk about her work outside of the Crick & Watson debacle.
February 11, 2024 at 2:31 PM
It's International Women in Science Day ♀️, and I want to talk briefly about Rosalind Franklin.
A conventional choice for unconventional reasons: Dr. Franklin was one of the FIRST STRUCTURAL VIROLOGISTS. Let's talk about her work outside of the Crick & Watson debacle.
A conventional choice for unconventional reasons: Dr. Franklin was one of the FIRST STRUCTURAL VIROLOGISTS. Let's talk about her work outside of the Crick & Watson debacle.
Reposted by Rauf Salamzade
A massive JAMA Internal Medicine study of 1.8M Americans found last season’s COVID booster still packs a punch—especially against severe illness and death.
The data are clear:
📉 Infection risk ↓ 45% at 4 weeks, 36% at 10 weeks,
#BlueSky #MedSky #SciSky #IDSky #NurseSky #EMSky
The data are clear:
📉 Infection risk ↓ 45% at 4 weeks, 36% at 10 weeks,
#BlueSky #MedSky #SciSky #IDSky #NurseSky #EMSky
Opinion | How long does covid booster protection last? A new study offers answers.
More evidence highlighting the benefit, and limitations, of covid-19 vaccines
shorturl.at
November 8, 2025 at 12:48 AM
Reposted by Rauf Salamzade
Shout out to people routinely working in their 2nd or 3rd language.
Yesterday I gave a 1-hour research seminar in French. Afterwards, my brain was pretty much done for the day.
Respect to the loads of scientists who do this daily (and usually a lot more effectively than me!)
Yesterday I gave a 1-hour research seminar in French. Afterwards, my brain was pretty much done for the day.
Respect to the loads of scientists who do this daily (and usually a lot more effectively than me!)
November 7, 2025 at 10:25 PM
Shout out to people routinely working in their 2nd or 3rd language.
Yesterday I gave a 1-hour research seminar in French. Afterwards, my brain was pretty much done for the day.
Respect to the loads of scientists who do this daily (and usually a lot more effectively than me!)
Yesterday I gave a 1-hour research seminar in French. Afterwards, my brain was pretty much done for the day.
Respect to the loads of scientists who do this daily (and usually a lot more effectively than me!)
Reposted by Rauf Salamzade
An Asgard archaeon with internal membrane compartments
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
November 7, 2025 at 10:16 PM
Reposted by Rauf Salamzade
Worried about identification of human samples from microbial sequencing? We were too- this is what we've done about it! www.sciencedirect.com/science/arti...
Benchmarking of human read removal strategies for viral and microbial metagenomics
Human reads are a key contaminant in microbial metagenomics and enrichment-based studies, requiring removal for computational efficiency, biological a…
www.sciencedirect.com
November 6, 2025 at 4:19 PM
Worried about identification of human samples from microbial sequencing? We were too- this is what we've done about it! www.sciencedirect.com/science/arti...
Reposted by Rauf Salamzade
Our method for genome size estimation from long-read overlaps is now published 🥳
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Genome size estimation from long read overlaps
AbstractMotivation. Accurate genome size estimation is an important component of genomic analyses such as assembly and coverage calculation, though existin
academic.oup.com
November 7, 2025 at 3:19 AM
Our method for genome size estimation from long-read overlaps is now published 🥳
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Reposted by Rauf Salamzade
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Reposted by Rauf Salamzade
A very nice review on my favorite archaea. The Thermococcales as a model system: historical perspectives and emerging tools | Journal of Bacteriology journals.asm.org/doi/10.1128/...
The Thermococcales as a model system: historical perspectives and emerging tools | Journal of Bacteriology
The exploration of life in extreme environments gained prominence with Thomas Brock’s
“Life at High Temperatures” (1), and his subsequent isolation of Thermus aquaticus with Hudson Freeze in 1969 (2) ...
journals.asm.org
November 6, 2025 at 9:39 AM
A very nice review on my favorite archaea. The Thermococcales as a model system: historical perspectives and emerging tools | Journal of Bacteriology journals.asm.org/doi/10.1128/...
Reposted by Rauf Salamzade
🚨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 by Rauf Salamzade
Read the investigation:
How Moderna, the company that helped save the world, unraveled
www.statnews.com/2025/10/30/m...
How Moderna, the company that helped save the world, unraveled
www.statnews.com/2025/10/30/m...
How Moderna, the company that helped save the world, unraveled
Exclusive: The inside story of why Moderna now faces a crisis unlike any in its 15-year-history.
www.statnews.com
November 6, 2025 at 5:26 PM
Read the investigation:
How Moderna, the company that helped save the world, unraveled
www.statnews.com/2025/10/30/m...
How Moderna, the company that helped save the world, unraveled
www.statnews.com/2025/10/30/m...
Reposted by Rauf Salamzade
Preprint: Bacteria sense virus-induced genome degradation via methylated mononucleotides
tinyurl.com/ch3damp
We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity
Revealed by the amazing Ilya Osterman. See his thread below👇
tinyurl.com/ch3damp
We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity
Revealed by the amazing Ilya Osterman. See his thread below👇
November 6, 2025 at 10:39 AM
Preprint: Bacteria sense virus-induced genome degradation via methylated mononucleotides
tinyurl.com/ch3damp
We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity
Revealed by the amazing Ilya Osterman. See his thread below👇
tinyurl.com/ch3damp
We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity
Revealed by the amazing Ilya Osterman. See his thread below👇