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
Check out that spindle 🤩🔥
At 63C, most eukaryotic cells would be busy exploding noisily, forget even trying to divide.
The microbial universe never ceases to astound 😍
Thanks for letting us be a tiny part of this! #ExpandThemAll
At 63C, most eukaryotic cells would be busy exploding noisily, forget even trying to divide.
The microbial universe never ceases to astound 😍
Thanks for letting us be a tiny part of this! #ExpandThemAll
While 𝘝. 𝘷𝘦𝘳𝘮𝘪𝘧𝘰𝘳𝘮𝘪𝘴 max temp is around 45°C, we found 𝘐. 𝘤𝘢𝘴𝘤𝘢𝘥𝘦𝘯𝘴𝘪𝘴 grows up to 63°C with optimal growth at 55-57°C🥵. We showed cellular replication via Ultrastructure Expansion Microscopy at 63°C. The previous limit for euks is 60°C!
November 25, 2025 at 8:30 PM
Check out that spindle 🤩🔥
At 63C, most eukaryotic cells would be busy exploding noisily, forget even trying to divide.
The microbial universe never ceases to astound 😍
Thanks for letting us be a tiny part of this! #ExpandThemAll
At 63C, most eukaryotic cells would be busy exploding noisily, forget even trying to divide.
The microbial universe never ceases to astound 😍
Thanks for letting us be a tiny part of this! #ExpandThemAll
Reposted by Rauf Salamzade
Really pleased to share the first paper to come out of the lab.
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
High frequency body site translocation of nosocomial Pseudomonas aeruginosa - Nature Communications
Here, the authors report within-host diversity and body site translocation dynamics in hospital samples of Pseudomonas aeruginosa and reveal that body site sharing was likely due to within-patient tra...
www.nature.com
November 25, 2025 at 10:40 AM
Really pleased to share the first paper to come out of the lab.
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
Reposted by Rauf Salamzade
Really happy to see the final version of this published in @isme-microbes.bsky.social. We show that production of and competition for biotin shapes S. aureus fitness in the context of nasal commensals doi.org/10.1093/isme...
Work lead by the amazing Kevser Bilici!
Work lead by the amazing Kevser Bilici!
Competitive fitness of Staphylococcus aureus against nasal commensals depends on biotin biosynthesis and acquisition
Abstract. The human nasal microbiome can serve as a reservoir for pathogens. In particular, the opportunistic pathogen Staphylococcus aureus can be a membe
doi.org
November 24, 2025 at 5:54 PM
Really happy to see the final version of this published in @isme-microbes.bsky.social. We show that production of and competition for biotin shapes S. aureus fitness in the context of nasal commensals doi.org/10.1093/isme...
Work lead by the amazing Kevser Bilici!
Work lead by the amazing Kevser Bilici!
Reposted by Rauf Salamzade
Every biologist knows the story of Fleming's chance discovery of penicillin. But is it true?
Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
The Penicillin Myth
Competing theories seek to explain inconsistencies surrounding Alexander Fleming’s famed discovery.
press.asimov.com
November 24, 2025 at 5:00 PM
Every biologist knows the story of Fleming's chance discovery of penicillin. But is it true?
Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
Reposted by Rauf Salamzade
I just keep reading this piece over and over again and...
arxiv.org/abs/1808.07717
arxiv.org/abs/1808.07717
Multiple Sequence Alignment is not a Solved Problem
Multiple sequence alignment is a basic procedure in molecular biology, and it is often treated as being essentially a solved computational problem. However, this is not so, and here I review the evide...
arxiv.org
November 23, 2025 at 6:09 PM
I just keep reading this piece over and over again and...
arxiv.org/abs/1808.07717
arxiv.org/abs/1808.07717
Reposted by Rauf Salamzade
New paper out: An archaeal genetic code with all TAG codons as pyrrolysine: www.science.org/doi/10.1126/...
An archaeal genetic code with all TAG codons as pyrrolysine
Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...
www.science.org
November 23, 2025 at 7:22 PM
New paper out: An archaeal genetic code with all TAG codons as pyrrolysine: www.science.org/doi/10.1126/...
Reposted by Rauf Salamzade
Editorial: Society journals matter—supporting science through renewed commitment
Editorial in @femsjournals.bsky.social microLife by @paulbrainey.bsky.social and colleagues
academic.oup.com/microlife/ad...
Editorial in @femsjournals.bsky.social microLife by @paulbrainey.bsky.social and colleagues
academic.oup.com/microlife/ad...
Editorial: Society journals matter—supporting science through renewed commitment
Paul B Rainey, Puri López-García, Zeynep Ceren Karahan, Paul Williams, Stipan Jonjić, Kenneth N Timmis; Editorial: Society journals matter—supporting scien
academic.oup.com
November 22, 2025 at 6:35 PM
Editorial: Society journals matter—supporting science through renewed commitment
Editorial in @femsjournals.bsky.social microLife by @paulbrainey.bsky.social and colleagues
academic.oup.com/microlife/ad...
Editorial in @femsjournals.bsky.social microLife by @paulbrainey.bsky.social and colleagues
academic.oup.com/microlife/ad...
Reposted by Rauf Salamzade
Geneticist and microbiologist Rita Rossi Colwell was born #OTD in 1934. She was the first researcher in the US to use computers to analyze bacteriological data, and the first woman to serve as director of the NSF. 🧪 👩🔬
November 23, 2025 at 6:32 PM
Geneticist and microbiologist Rita Rossi Colwell was born #OTD in 1934. She was the first researcher in the US to use computers to analyze bacteriological data, and the first woman to serve as director of the NSF. 🧪 👩🔬
Reposted by Rauf Salamzade
Understanding the relationship between #foraminifera & their #symbionts can help corals phys.org/news/2025-09...
Specific host - #algae relationship, yet flexible bacterial #microbiome, in diatom-bearing foraminifera: Elsa Girard et al. www.science.org/doi/10.1126/...
#Protists #Microbes #Diatoms
Specific host - #algae relationship, yet flexible bacterial #microbiome, in diatom-bearing foraminifera: Elsa Girard et al. www.science.org/doi/10.1126/...
#Protists #Microbes #Diatoms
November 23, 2025 at 7:02 PM
Understanding the relationship between #foraminifera & their #symbionts can help corals phys.org/news/2025-09...
Specific host - #algae relationship, yet flexible bacterial #microbiome, in diatom-bearing foraminifera: Elsa Girard et al. www.science.org/doi/10.1126/...
#Protists #Microbes #Diatoms
Specific host - #algae relationship, yet flexible bacterial #microbiome, in diatom-bearing foraminifera: Elsa Girard et al. www.science.org/doi/10.1126/...
#Protists #Microbes #Diatoms
Reposted by Rauf Salamzade
Here is one of my favorite papers, "A unifying framework reveals key properties of multilevel selection" by Shishi Luo. Luo highlights examples of multilevel selection and introduces a nested birth-death process to model evolutionary competition across scales.
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
A unifying framework reveals key properties of multilevel selection
Natural selection can act at multiple biological levels, often in opposing directions. Viral evolution is an important example, with selection occurri…
www.sciencedirect.com
November 23, 2025 at 12:40 AM
Here is one of my favorite papers, "A unifying framework reveals key properties of multilevel selection" by Shishi Luo. Luo highlights examples of multilevel selection and introduces a nested birth-death process to model evolutionary competition across scales.
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by Rauf Salamzade
For the U.S. Centers for Disease Control and Prevention (CDC) to be effective, the public needs to trust its recommendations. Confidence that policies are being guided by science—not politics—is at the heart of that trust. Our statement: asm.org/press-releas...
November 21, 2025 at 3:51 PM
For the U.S. Centers for Disease Control and Prevention (CDC) to be effective, the public needs to trust its recommendations. Confidence that policies are being guided by science—not politics—is at the heart of that trust. Our statement: asm.org/press-releas...
Reposted by Rauf Salamzade
How does linguistic bias reinforce privilege in science? #AppEnvMicro Editor in Chief @microgem.bsky.social offers insights and discusses how reviewers can identify it to support a more equitable review process. Read the article: asm.social/2Hp #COPE #PublicationIntegrity
Linguistic Bias and the Science Lost in Translation | ASM.org
Explore how linguistic bias subtly reinforces privilege in science by constraining scientific dissemination.
asm.social
November 21, 2025 at 7:48 PM
How does linguistic bias reinforce privilege in science? #AppEnvMicro Editor in Chief @microgem.bsky.social offers insights and discusses how reviewers can identify it to support a more equitable review process. Read the article: asm.social/2Hp #COPE #PublicationIntegrity
Reposted by Rauf Salamzade
Excited to share DupyliCate - our new tool for discovery and characterization of gene duplications:
"DupyliCate - mining, classifying, and characterizing gene duplications"
doi.org/10.1101/2025...
#Bioinformatics #Python #Genomics #Evolution
@puckerlab.bsky.social
"DupyliCate - mining, classifying, and characterizing gene duplications"
doi.org/10.1101/2025...
#Bioinformatics #Python #Genomics #Evolution
@puckerlab.bsky.social
DupyliCate - mining, classifying, and characterizing gene duplications
Paralogs, copies of a gene, form an important basis for novelty during evolution. Analysis of such gene duplications is important to understand the emergence of novel traits during evolution. DupyliCa...
doi.org
October 14, 2025 at 5:26 AM
Excited to share DupyliCate - our new tool for discovery and characterization of gene duplications:
"DupyliCate - mining, classifying, and characterizing gene duplications"
doi.org/10.1101/2025...
#Bioinformatics #Python #Genomics #Evolution
@puckerlab.bsky.social
"DupyliCate - mining, classifying, and characterizing gene duplications"
doi.org/10.1101/2025...
#Bioinformatics #Python #Genomics #Evolution
@puckerlab.bsky.social
Reposted by Rauf Salamzade
Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
GlobDB: a comprehensive species-dereplicated microbial genome resource
AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu
doi.org
November 21, 2025 at 4:21 PM
Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
Reposted by Rauf Salamzade
Incredible science coming out from our lab. Congrats @kivenson.bsky.social 🎉
Out today in Science Magazine — First author Veronika Kivenson and PIs Jill Banfield (The Banfield Lab) and Alanna Schepartz team up to reveal a new genetic code in #archaea, with implications for #methane and #climate, and #bioengineering! Learn more: https://ow.ly/Kuem50Xurh0
November 20, 2025 at 7:53 PM
Incredible science coming out from our lab. Congrats @kivenson.bsky.social 🎉
Reposted by Rauf Salamzade
Our new paper, which presents a novel strategy for targeting antibiotic resistance, is now available in Nature Microbiology.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Prodrug florfenicol amine is activated by intrinsic resistance to target Mycobacterium abscessus - Nature Microbiology
Florfenicol amine hijacks intrinsic resistance in Mycobacterium abscessus, highlighting that antimicrobial resistance mechanisms can be harnessed for antibiotic activation.
www.nature.com
November 13, 2025 at 9:44 PM
Our new paper, which presents a novel strategy for targeting antibiotic resistance, is now available in Nature Microbiology.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Rauf Salamzade
🚀New preprint from our lab!
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
November 20, 2025 at 6:52 PM
🚀New preprint from our lab!
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
Reposted by Rauf Salamzade
Viral "dark matter" dominates the virosphere. In this review by me & @karthik-a.bsky.social, we synthesize what's known, highlight major gaps, and outline paths forward for illuminating viral protein functions in diverse ecosystems.
Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises
Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising w...
pubs.acs.org
November 20, 2025 at 9:24 PM
Viral "dark matter" dominates the virosphere. In this review by me & @karthik-a.bsky.social, we synthesize what's known, highlight major gaps, and outline paths forward for illuminating viral protein functions in diverse ecosystems.
Reposted by Rauf Salamzade
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Rauf Salamzade
Let’s wrap things up: my commentary on the Asgard hypernucleosomes.
Congratulations to all the authors of the paper 🍾!
kwnsfk27.r.eu-west-1.awstrack.me/L0/https:%2F...
Cryo-EM reveals open and closed Asgard chromatin assemblies: Molecular Cell www.cell.com/molecular-ce...
Congratulations to all the authors of the paper 🍾!
kwnsfk27.r.eu-west-1.awstrack.me/L0/https:%2F...
Cryo-EM reveals open and closed Asgard chromatin assemblies: Molecular Cell www.cell.com/molecular-ce...
Cryo-EM reveals open and closed Asgard chromatin assemblies
Ranawat et al. show the cryo-EM structures of Asgard archaeal chromatin assemblies,
revealing that the histone HHoB assembles into both compact closed and extended open
hypernucleosomes. The closed co...
www.cell.com
November 20, 2025 at 4:23 PM
Let’s wrap things up: my commentary on the Asgard hypernucleosomes.
Congratulations to all the authors of the paper 🍾!
kwnsfk27.r.eu-west-1.awstrack.me/L0/https:%2F...
Cryo-EM reveals open and closed Asgard chromatin assemblies: Molecular Cell www.cell.com/molecular-ce...
Congratulations to all the authors of the paper 🍾!
kwnsfk27.r.eu-west-1.awstrack.me/L0/https:%2F...
Cryo-EM reveals open and closed Asgard chromatin assemblies: Molecular Cell www.cell.com/molecular-ce...
Reposted by Rauf Salamzade
Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf
Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy
Nature Communications - It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core...
rdcu.be
November 18, 2025 at 9:01 PM
Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf
Reposted by Rauf Salamzade
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes academic.oup.com/nar/advance-... #jcampubs
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes
Abstract. The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands rob
academic.oup.com
November 20, 2025 at 2:02 PM
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes academic.oup.com/nar/advance-... #jcampubs
Reposted by Rauf Salamzade
My first @umasschan.bsky.social/@impvienna.bsky.social affiliated paper is up!
tomtom-lite is a re-implementation of tomtom targeting the ML age of genomics. Fast annotations ("what is this motif?") and simple large-scale discovery of motifs.
Check it out!
academic.oup.com/bioinformati...
tomtom-lite is a re-implementation of tomtom targeting the ML age of genomics. Fast annotations ("what is this motif?") and simple large-scale discovery of motifs.
Check it out!
academic.oup.com/bioinformati...
November 20, 2025 at 2:02 PM
My first @umasschan.bsky.social/@impvienna.bsky.social affiliated paper is up!
tomtom-lite is a re-implementation of tomtom targeting the ML age of genomics. Fast annotations ("what is this motif?") and simple large-scale discovery of motifs.
Check it out!
academic.oup.com/bioinformati...
tomtom-lite is a re-implementation of tomtom targeting the ML age of genomics. Fast annotations ("what is this motif?") and simple large-scale discovery of motifs.
Check it out!
academic.oup.com/bioinformati...
Reposted by Rauf Salamzade
Registration is now open for @keystonesymposia.bsky.social "Beyond #Antibiotics: Emerging Strategies Combating #BacterialInfection." Deadline for scholarships and abstract selected short talks is Jan 7! Join us this May for an amazing meeting! keysym.us/KSBeyondAntibiotics26 #KSBeyondAntibiotics26
Beyond Antibiotics: Emerging Strategies for Combating Bacterial Infection | Keystone Symposia
Join us at the Keystone Symposia on Beyond Antibiotics: Emerging Strategies for Combating Bacterial Infection, May 2026, in Breckenridge, with field leaders!
keysym.us
November 19, 2025 at 5:37 PM
Registration is now open for @keystonesymposia.bsky.social "Beyond #Antibiotics: Emerging Strategies Combating #BacterialInfection." Deadline for scholarships and abstract selected short talks is Jan 7! Join us this May for an amazing meeting! keysym.us/KSBeyondAntibiotics26 #KSBeyondAntibiotics26
Reposted by Rauf Salamzade
Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
Bacterial immune systems as causes and consequences of microbiome structure
Bacterial immune systems have evolved in response to diverse molecular "parasites", yet their ecological roles remain poorly understood. This Essay explores how interactions between mobile genetic ele...
journals.plos.org
November 19, 2025 at 6:35 PM
Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...