Simon Roux
@simrouxvirus.bsky.social
Virus-obsessed bioinformatician, DOE JGI Scientist, Enjoy exploring the viral world with #metagenomics and other cool #omics toys. He/him. Opinions my own.
Reposted by Simon Roux
Teaching experimental design again tomorrow and once more reminded of this awesome distillation of why we need to teach it.
www.youtube.com/watch?v=PbOD...
www.youtube.com/watch?v=PbOD...
Biostatistics vs. Lab Research
YouTube video by JavaMama926
www.youtube.com
November 23, 2025 at 5:25 PM
Teaching experimental design again tomorrow and once more reminded of this awesome distillation of why we need to teach it.
www.youtube.com/watch?v=PbOD...
www.youtube.com/watch?v=PbOD...
Reposted by Simon Roux
The malwarebytes Google opting-your-emails-into-ai-training thing is not true. The post is based on one bad tweet.
I know anti-tech lamenting is a Bluesky core principle, but please use the same judgement you would for any other clickbait.
www.theverge.com/news/826902/...
I know anti-tech lamenting is a Bluesky core principle, but please use the same judgement you would for any other clickbait.
www.theverge.com/news/826902/...
Google denies ‘misleading’ reports of Gmail using your emails to train AI
Google says “we do not use your Gmail content for training our Gemini AI model.”
www.theverge.com
November 22, 2025 at 8:58 AM
The malwarebytes Google opting-your-emails-into-ai-training thing is not true. The post is based on one bad tweet.
I know anti-tech lamenting is a Bluesky core principle, but please use the same judgement you would for any other clickbait.
www.theverge.com/news/826902/...
I know anti-tech lamenting is a Bluesky core principle, but please use the same judgement you would for any other clickbait.
www.theverge.com/news/826902/...
Reposted by Simon Roux
Tonight on #FridayNightZillow: A trio of cheap, fab Victorians in Wichita, recently named America's most affordable major city, starting at just $190K! Also showing a blank check mansion with its own race track (!) and a lot more, so stick around!🧵
November 22, 2025 at 2:19 AM
Tonight on #FridayNightZillow: A trio of cheap, fab Victorians in Wichita, recently named America's most affordable major city, starting at just $190K! Also showing a blank check mansion with its own race track (!) and a lot more, so stick around!🧵
Reposted by Simon Roux
Today is Duodi the 2nd of Frimaire in the year 234.
Frimaire is the month of frost.
Today we celebrate cattle turnips.#JacobinDay
More information on cattle turnips
Frimaire is the month of frost.
Today we celebrate cattle turnips.#JacobinDay
More information on cattle turnips
November 21, 2025 at 11:00 PM
Today is Duodi the 2nd of Frimaire in the year 234.
Frimaire is the month of frost.
Today we celebrate cattle turnips.#JacobinDay
More information on cattle turnips
Frimaire is the month of frost.
Today we celebrate cattle turnips.#JacobinDay
More information on cattle turnips
Reposted by Simon Roux
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
The missing heritability question is now (mostly) answered
Not with a bang but with a whimper
theinfinitesimal.substack.com
November 21, 2025 at 10:34 PM
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
Reposted by Simon Roux
Another great post from Sasha demonstrating what will ring true to many of us-- our environments include our siblings, making it unlikely that siblings have identical environments.
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
The missing heritability question is now (mostly) answered
Not with a bang but with a whimper
theinfinitesimal.substack.com
November 21, 2025 at 10:55 PM
Another great post from Sasha demonstrating what will ring true to many of us-- our environments include our siblings, making it unlikely that siblings have identical environments.
Reposted by Simon Roux
Our latest T7SS study is now out in Science Advances!
We solved the cryoEM structure of the T7SSb core unit (T7bCU) composed of YukB, YukC, and YukD from Bacillus subtilis, revealing how these components assemble within the secretion machinery.
www.science.org/doi/10.1126/...
We solved the cryoEM structure of the T7SSb core unit (T7bCU) composed of YukB, YukC, and YukD from Bacillus subtilis, revealing how these components assemble within the secretion machinery.
www.science.org/doi/10.1126/...
A ubiquitin-like protein controls assembly of a bacterial type VIIb secretion system
Cryo-EM structure reveals how a ubiquitin-like protein orchestrates assembly of a bacterial weapon system.
www.science.org
November 21, 2025 at 7:05 PM
Our latest T7SS study is now out in Science Advances!
We solved the cryoEM structure of the T7SSb core unit (T7bCU) composed of YukB, YukC, and YukD from Bacillus subtilis, revealing how these components assemble within the secretion machinery.
www.science.org/doi/10.1126/...
We solved the cryoEM structure of the T7SSb core unit (T7bCU) composed of YukB, YukC, and YukD from Bacillus subtilis, revealing how these components assemble within the secretion machinery.
www.science.org/doi/10.1126/...
Reposted by Simon Roux
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 Simon Roux
Quick heads up - there will soon be a job posting for a Staff Scientist / Senior Staff Scientist in our lab in Copenhagen to support all our mass spec proteomics adventures!
Great colleagues, lots of cool projects… and you’ll get to work with me 😅
Please DM if you’re interested!
Great colleagues, lots of cool projects… and you’ll get to work with me 😅
Please DM if you’re interested!
November 20, 2025 at 5:09 PM
Quick heads up - there will soon be a job posting for a Staff Scientist / Senior Staff Scientist in our lab in Copenhagen to support all our mass spec proteomics adventures!
Great colleagues, lots of cool projects… and you’ll get to work with me 😅
Please DM if you’re interested!
Great colleagues, lots of cool projects… and you’ll get to work with me 😅
Please DM if you’re interested!
Reposted by Simon Roux
Team fish - we need your help! We are trying to build a database of all the fish chromosome-scale genomes where sex chromosomes have been identified. Have you build one or some? Do you know someone who has? Can you post the link in the comments? Please spread the word and repost! Thank you!
November 20, 2025 at 4:44 PM
Team fish - we need your help! We are trying to build a database of all the fish chromosome-scale genomes where sex chromosomes have been identified. Have you build one or some? Do you know someone who has? Can you post the link in the comments? Please spread the word and repost! Thank you!
Reposted by Simon Roux
Brand new preprint from my lab, showing that TnpB, the ancestor of Cas12, acts as a gene drive in plasmids! And it turns out in conjugative plasmids that it acts as a primitive anti-self defense system, providing a potential link between its transposon effect and becoming CRISPR!
What is the best strategy to win any contest?
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
November 20, 2025 at 10:17 PM
Brand new preprint from my lab, showing that TnpB, the ancestor of Cas12, acts as a gene drive in plasmids! And it turns out in conjugative plasmids that it acts as a primitive anti-self defense system, providing a potential link between its transposon effect and becoming CRISPR!
Reposted by Simon Roux
Excited to share our new review article on Viral Dark Matter led by PhD student @kosmopoulos.bsky.social. We talk about what is known and unknown in the world of viruses (specifically phage), and highlight future opportunities for research and biotechnology. pubs.acs.org/doi/10.1021/...
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 9:04 PM
Excited to share our new review article on Viral Dark Matter led by PhD student @kosmopoulos.bsky.social. We talk about what is known and unknown in the world of viruses (specifically phage), and highlight future opportunities for research and biotechnology. pubs.acs.org/doi/10.1021/...
Reposted by Simon Roux
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/...
Reposted by Simon Roux
🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.
Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.
A thread 1/8
Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.
A thread 1/8
November 20, 2025 at 8:40 PM
🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.
Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.
A thread 1/8
Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.
A thread 1/8
Reposted by Simon Roux
We have a date for the free-to-attend #anvio workshop and ECR Symposium for 2026, and we look forward to meeting you at the @hifmb.de in Oldenburg, Germany!
Please find more information on the venue, program, and the application form here, and spread the word 😇
anvio.org/workshops/20...
Please find more information on the venue, program, and the application form here, and spread the word 😇
anvio.org/workshops/20...
November 20, 2025 at 6:42 PM
We have a date for the free-to-attend #anvio workshop and ECR Symposium for 2026, and we look forward to meeting you at the @hifmb.de in Oldenburg, Germany!
Please find more information on the venue, program, and the application form here, and spread the word 😇
anvio.org/workshops/20...
Please find more information on the venue, program, and the application form here, and spread the word 😇
anvio.org/workshops/20...
Reposted by Simon Roux
We're headed to ASMCUE in San Antonio, TX this weekend! Educators, stop by our workshop with KBase tomorrow and our Microbrew Talk on Sunday to learn more about leveraging the NMDC's resources for microbiome workforce development and undergraduate education🧪 @ASM.org @kbase.us
November 20, 2025 at 8:14 PM
Reposted by Simon Roux
Wisconsin Evolution is accepting applications for our Seminar Series' Early Career Scientist Award. Come share your evolution research and visit UW-Madison's evolution community. Open to grad students and postdocs (<5 yrs post PhD) from outside UW-Madison.
Apply by Dec 15th here: shorturl.at/4a4O6
Apply by Dec 15th here: shorturl.at/4a4O6
Early Career Scientist Awards 2026
Application to the UW-Madison Evolution Seminar Series - Early Career Scientist Awards.
urldefense.com
November 19, 2025 at 8:55 PM
Wisconsin Evolution is accepting applications for our Seminar Series' Early Career Scientist Award. Come share your evolution research and visit UW-Madison's evolution community. Open to grad students and postdocs (<5 yrs post PhD) from outside UW-Madison.
Apply by Dec 15th here: shorturl.at/4a4O6
Apply by Dec 15th here: shorturl.at/4a4O6
Reposted by Simon Roux
Faculty search at UAlbany targeting folks broadly applying AI/ML to infectious disease research!! Please RT 🙏
albany.interviewexchange.com/jobofferdeta...
albany.interviewexchange.com/jobofferdeta...
November 18, 2025 at 11:15 PM
Faculty search at UAlbany targeting folks broadly applying AI/ML to infectious disease research!! Please RT 🙏
albany.interviewexchange.com/jobofferdeta...
albany.interviewexchange.com/jobofferdeta...
Reposted by Simon Roux
New lunch spot in downtown Berkeley: Aburaya Japanese-style fried chicken, every weekday, inside Spats!
November 18, 2025 at 8:47 PM
New lunch spot in downtown Berkeley: Aburaya Japanese-style fried chicken, every weekday, inside Spats!
Reposted by Simon Roux
Microbial science moves forward when we do. Submit your early abstract for #ASMicrobe 2026 and join thousands of scientists advancing discovery, collaboration and innovation.
Deadline: Dec. 2, 2 p.m. ET.
Share your science → asm.social/2Gv
Deadline: Dec. 2, 2 p.m. ET.
Share your science → asm.social/2Gv
November 13, 2025 at 12:32 PM
Microbial science moves forward when we do. Submit your early abstract for #ASMicrobe 2026 and join thousands of scientists advancing discovery, collaboration and innovation.
Deadline: Dec. 2, 2 p.m. ET.
Share your science → asm.social/2Gv
Deadline: Dec. 2, 2 p.m. ET.
Share your science → asm.social/2Gv
Reposted by Simon Roux
OK, #bioinformatics folk. We have some (many many) reads from a metagenome. They have been binned into a bacterial genome. They have no matches to any known genome in any database. They code for "bacterial" genes. What are good triple-checks to do to argue that they are not, in fact, euk sequence?
November 18, 2025 at 5:29 PM
OK, #bioinformatics folk. We have some (many many) reads from a metagenome. They have been binned into a bacterial genome. They have no matches to any known genome in any database. They code for "bacterial" genes. What are good triple-checks to do to argue that they are not, in fact, euk sequence?
Reposted by Simon Roux
We're hiring! My dept. is looking for a candidate with a research program focusing on plant systems. All areas of molecular and cellular biology research will be considered. Not sure if you'd fit? Reach out to me. Please share! #microsky
November 17, 2025 at 6:18 PM
We're hiring! My dept. is looking for a candidate with a research program focusing on plant systems. All areas of molecular and cellular biology research will be considered. Not sure if you'd fit? Reach out to me. Please share! #microsky
Reposted by Simon Roux
SingleM v0.20.2 - ONT/PacBio input reads now supported (if somewhat inefficiently), plus improved Lyrebird database for phage profiling.
Microbial fraction is now prokaryotic fraction, easier to specify input genomes.
Microbial fraction is now prokaryotic fraction, easier to specify input genomes.
November 17, 2025 at 4:49 AM
SingleM v0.20.2 - ONT/PacBio input reads now supported (if somewhat inefficiently), plus improved Lyrebird database for phage profiling.
Microbial fraction is now prokaryotic fraction, easier to specify input genomes.
Microbial fraction is now prokaryotic fraction, easier to specify input genomes.
Reposted by Simon Roux
Diving through the purple sulfur bacteria layer of Fayetteville Green Lake with our ROV last month. This is the most intense density of PSB that I've seen in many years!
November 8, 2025 at 6:30 PM
Diving through the purple sulfur bacteria layer of Fayetteville Green Lake with our ROV last month. This is the most intense density of PSB that I've seen in many years!