Vishnu Raghuram
@vishnu-raghuram.bsky.social
Interested in studying evolution and transmission of pathogens using genomics and bioinformatics. Postdoc @ Umea University
MIMS | SciLifeLab | IceLab
🧬🖥️🦠
https://scholar.google.com/citations?user=THTeHfgAAAAJ&hl=en
MIMS | SciLifeLab | IceLab
🧬🖥️🦠
https://scholar.google.com/citations?user=THTeHfgAAAAJ&hl=en
Pinned
Genomic surveillance of Salmonella enterica serotype Minnesota strains from Brazilian poultry products imported into South Africa https://www.medrxiv.org/content/10.1101/2025.04.16.25325939v1
New preprint from the CompMicroLab @ Umeå University! We looked at Salmonella from imported poultry meat in South Africa. Some of them had an unusual (for Salmonella) beta-lactam resistance allele that we think is from E. Coli!
@scilifelab.se #microsky #genomics #phylogenetics #microbiology
🧪🧬🖥️
@scilifelab.se #microsky #genomics #phylogenetics #microbiology
🧪🧬🖥️
Reposted by Vishnu Raghuram
What causes viral transmission bottlenecks? This study uses barcoded virions to show that in the case of #influenza A #virus, early within-host replication dynamics (rather than a reduced inoculum population) drive loss of diversity during transmission @plosbiology.org 🧪 plos.io/4ngicDK
September 3, 2025 at 7:52 AM
What causes viral transmission bottlenecks? This study uses barcoded virions to show that in the case of #influenza A #virus, early within-host replication dynamics (rather than a reduced inoculum population) drive loss of diversity during transmission @plosbiology.org 🧪 plos.io/4ngicDK
New preprint from the CompMicroLab @ Umeå University! We looked at Salmonella from imported poultry meat in South Africa. Some of them had an unusual (for Salmonella) beta-lactam resistance allele that we think is from E. Coli!
@scilifelab.se #microsky #genomics #phylogenetics #microbiology
🧪🧬🖥️
@scilifelab.se #microsky #genomics #phylogenetics #microbiology
🧪🧬🖥️
Genomic surveillance of Salmonella enterica serotype Minnesota strains from Brazilian poultry products imported into South Africa https://www.medrxiv.org/content/10.1101/2025.04.16.25325939v1
April 18, 2025 at 12:10 PM
New preprint from the CompMicroLab @ Umeå University! We looked at Salmonella from imported poultry meat in South Africa. Some of them had an unusual (for Salmonella) beta-lactam resistance allele that we think is from E. Coli!
@scilifelab.se #microsky #genomics #phylogenetics #microbiology
🧪🧬🖥️
@scilifelab.se #microsky #genomics #phylogenetics #microbiology
🧪🧬🖥️
Reposted by Vishnu Raghuram
🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again!
forms.gle/YJP6WQjsk8KK...
forms.gle/YJP6WQjsk8KK...
Snippy: Microbial Variant Calling Community Survey
Help us drive the next wave of innovation in Single-Nucleotide Polymorphism (SNP) discovery and genome analysis by sharing your valuable experiences and insights. This in-depth survey aims at understa...
forms.gle
March 4, 2025 at 9:04 AM
🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again!
forms.gle/YJP6WQjsk8KK...
forms.gle/YJP6WQjsk8KK...
Reposted by Vishnu Raghuram
So - it happened. I was so excited to have found what was supposed to be my amazing long-term position and promising career pivot from bench to communications at the NIH. Unfortunately, I got the letter that so many others did. Several days of introspection, however, have yielded an idea: 1/n
February 19, 2025 at 3:46 PM
So - it happened. I was so excited to have found what was supposed to be my amazing long-term position and promising career pivot from bench to communications at the NIH. Unfortunately, I got the letter that so many others did. Several days of introspection, however, have yielded an idea: 1/n
Reposted by Vishnu Raghuram
So one of the things that I think is lost on AI proponents is what I call the card catalog effect, a thing I shouldn’t call it because a lot of people probably have no experience with a card catalog.
February 18, 2025 at 1:42 AM
So one of the things that I think is lost on AI proponents is what I call the card catalog effect, a thing I shouldn’t call it because a lot of people probably have no experience with a card catalog.
Reposted by Vishnu Raghuram
(1/3) Have you started your application for the SciLifeLab PULSE Fellows Program yet? This 36-month #PostDoc program is designed to empower diversity in science and equip researchers with the skills, network, and experience to thrive in academia or industry. ⬇️🧪🌍🖥️🧬⚒️
www.scilifelab.se/research/pulse
www.scilifelab.se/research/pulse
PULSE
SciLifeLab PULSE: Program for Future Leaders in Life Science SciLifeLab PULSE is a comprehensive postdoctoral program, that will train 48 future leaders in life sciences. PULSE focuses on innovative, ...
www.scilifelab.se
February 18, 2025 at 9:07 AM
(1/3) Have you started your application for the SciLifeLab PULSE Fellows Program yet? This 36-month #PostDoc program is designed to empower diversity in science and equip researchers with the skills, network, and experience to thrive in academia or industry. ⬇️🧪🌍🖥️🧬⚒️
www.scilifelab.se/research/pulse
www.scilifelab.se/research/pulse
Reposted by Vishnu Raghuram
1. Our questjons were not about executive ordere but about ASM doing things wihtout any communication of memebrship
asm.org/press-releas...
asm.org/press-releas...
ASM Responds to Member Questions About Executive Orders
Our modified pages are back up or in the process of being restored. ASM has not retracted or altered any research articles, scientific papers or peer reviewed articles on our website.
asm.org
February 3, 2025 at 9:12 PM
1. Our questjons were not about executive ordere but about ASM doing things wihtout any communication of memebrship
asm.org/press-releas...
asm.org/press-releas...
Reposted by Vishnu Raghuram
Huge shout out to @lskatz.bsky.social et al on the recent Micro Resource Announcement for Kalamari!
@andrewjpage.bsky.social and I highlight Kalamari's utility in pathogen genomics: www.youtube.com/watch?v=KDzY...
Paper here: journals.asm.org/doi/epub/10....
& Github: github.com/lskatz/Kalam...
@andrewjpage.bsky.social and I highlight Kalamari's utility in pathogen genomics: www.youtube.com/watch?v=KDzY...
Paper here: journals.asm.org/doi/epub/10....
& Github: github.com/lskatz/Kalam...
The Kalamari Databse
YouTube video by The Bioinformatics Lab
www.youtube.com
February 4, 2025 at 3:32 PM
Huge shout out to @lskatz.bsky.social et al on the recent Micro Resource Announcement for Kalamari!
@andrewjpage.bsky.social and I highlight Kalamari's utility in pathogen genomics: www.youtube.com/watch?v=KDzY...
Paper here: journals.asm.org/doi/epub/10....
& Github: github.com/lskatz/Kalam...
@andrewjpage.bsky.social and I highlight Kalamari's utility in pathogen genomics: www.youtube.com/watch?v=KDzY...
Paper here: journals.asm.org/doi/epub/10....
& Github: github.com/lskatz/Kalam...
Reposted by Vishnu Raghuram
Spaces are limited so if youre sure you can make it, register!
https://www.bio.cam.ac.uk/11th-microbial-bioinformatics-hackathon
https://www.bio.cam.ac.uk/11th-microbial-bioinformatics-hackathon
February 4, 2025 at 3:06 PM
Spaces are limited so if youre sure you can make it, register!
https://www.bio.cam.ac.uk/11th-microbial-bioinformatics-hackathon
https://www.bio.cam.ac.uk/11th-microbial-bioinformatics-hackathon
Reposted by Vishnu Raghuram
Happy Black History Month! I’m not sure if ASM is celebrating this year, so I’ll share some links to ASM resources I had previously collated on black women in microbiology that are now deleted (or at risk of being deleted). Deleted content can be viewed via the internet archive (links provided).
February 3, 2025 at 2:26 PM
Happy Black History Month! I’m not sure if ASM is celebrating this year, so I’ll share some links to ASM resources I had previously collated on black women in microbiology that are now deleted (or at risk of being deleted). Deleted content can be viewed via the internet archive (links provided).
Reposted by Vishnu Raghuram
Caring about funding and then turning around and disappearing pages highlighting minoritized scientists shows everyone where your true values lie @asm.org
bsky.app/profile/napa...
bsky.app/profile/napa...
Kudos to @asm.org I have never in my nearly 25yrs as a member been sent an "ASM Action Alert" asking me to contact my members of Congress. Make those calls. Write those emails.
There are extraordinary times and we must make ourselves heard
There are extraordinary times and we must make ourselves heard
February 3, 2025 at 12:16 PM
Caring about funding and then turning around and disappearing pages highlighting minoritized scientists shows everyone where your true values lie @asm.org
bsky.app/profile/napa...
bsky.app/profile/napa...
Reposted by Vishnu Raghuram
Well the award for most cowardly, boot-lickingest academic society has squarely gone to the American Society of Microbiology, who has taken down features of various non-white scientists. Absolutely pathetic behavior. Those articles are now coming up as “under review”. Truly sickening cowardice here.
February 3, 2025 at 4:39 AM
Well the award for most cowardly, boot-lickingest academic society has squarely gone to the American Society of Microbiology, who has taken down features of various non-white scientists. Absolutely pathetic behavior. Those articles are now coming up as “under review”. Truly sickening cowardice here.
Reposted by Vishnu Raghuram
Make the government make you take down articles @asm.org
Don’t do it in advance as a precaution because of loss if funding or whatever. Hell, I would’ve paid way higher membership dues if I knew it would help you take a stand and if you gave us that choice vs whatever this is. Now, not so much
Don’t do it in advance as a precaution because of loss if funding or whatever. Hell, I would’ve paid way higher membership dues if I knew it would help you take a stand and if you gave us that choice vs whatever this is. Now, not so much
February 3, 2025 at 12:56 PM
Make the government make you take down articles @asm.org
Don’t do it in advance as a precaution because of loss if funding or whatever. Hell, I would’ve paid way higher membership dues if I knew it would help you take a stand and if you gave us that choice vs whatever this is. Now, not so much
Don’t do it in advance as a precaution because of loss if funding or whatever. Hell, I would’ve paid way higher membership dues if I knew it would help you take a stand and if you gave us that choice vs whatever this is. Now, not so much
Reposted by Vishnu Raghuram
Ok this is not ok. ASM actively sought out BMA and its members for Juneteenth and Black History month content for the last 4 years. Actively asked for black labor and then takes it down?! @asm.org this is unacceptable. You should be standing up for marginalized microbiologists not erasing them.
Checked on the article I wrote about Juneteenth in 2023…
”under review”
”under review”
February 3, 2025 at 3:07 AM
Ok this is not ok. ASM actively sought out BMA and its members for Juneteenth and Black History month content for the last 4 years. Actively asked for black labor and then takes it down?! @asm.org this is unacceptable. You should be standing up for marginalized microbiologists not erasing them.
Reposted by Vishnu Raghuram
The entire archive of CDC datasets can be found here.
HUGE shoutout to data archivists- this work is important 👏🙌🏻
archive.org/details/2025...
HUGE shoutout to data archivists- this work is important 👏🙌🏻
archive.org/details/2025...
February 1, 2025 at 6:33 PM
The entire archive of CDC datasets can be found here.
HUGE shoutout to data archivists- this work is important 👏🙌🏻
archive.org/details/2025...
HUGE shoutout to data archivists- this work is important 👏🙌🏻
archive.org/details/2025...
Reposted by Vishnu Raghuram
February 2, 2025 at 9:27 PM
Reposted by Vishnu Raghuram
Great to see @umeaplantscicentre.bsky.social joining Bluesky! We have several research projects that connect IceLab and UPSC. UPSC is a fantastic collaborative research center conducting important and fascinating research in #plantscience. Give them a follow!
January 27, 2025 at 2:24 PM
Great to see @umeaplantscicentre.bsky.social joining Bluesky! We have several research projects that connect IceLab and UPSC. UPSC is a fantastic collaborative research center conducting important and fascinating research in #plantscience. Give them a follow!
Reposted by Vishnu Raghuram
And it’s been a while since I dipped my toe into the questions of what ‘species’ might mean for bacteria, and how they relate to ecology. But still interests me! genomebiology.biomedcentral.com/articles/10....
Relating ecological diversity to genetic discontinuity across bacterial species - Genome Biology
Background Genetic discontinuity represents abrupt breaks in genomic identity among species. Advances in genome sequencing have enhanced our ability to track and characterize genetic discontinuity in ...
genomebiology.biomedcentral.com
January 13, 2025 at 3:43 PM
And it’s been a while since I dipped my toe into the questions of what ‘species’ might mean for bacteria, and how they relate to ecology. But still interests me! genomebiology.biomedcentral.com/articles/10....
Reposted by Vishnu Raghuram
I'm putting together a Microbial Bioinformatics starter pack to help get everyone connected in our community. Let me know if there are any bluesky users to be added and share so that twitter refugees can tune back in to the fantastic world microbes go.bsky.app/3ezLo7e
January 10, 2025 at 9:38 AM
I'm putting together a Microbial Bioinformatics starter pack to help get everyone connected in our community. Let me know if there are any bluesky users to be added and share so that twitter refugees can tune back in to the fantastic world microbes go.bsky.app/3ezLo7e
Reposted by Vishnu Raghuram
Reposted by Vishnu Raghuram
🔎 for a #PhD in #computational science applied to living systems, with a #complexity angle? Do you want to work in a fun, supportive and academically stimulating environment in a city that experiences real winter and is close to nature? 5 #fundedphd available in IceLab! icelab.se/opportunitie...
December 19, 2024 at 1:56 PM
🔎 for a #PhD in #computational science applied to living systems, with a #complexity angle? Do you want to work in a fun, supportive and academically stimulating environment in a city that experiences real winter and is close to nature? 5 #fundedphd available in IceLab! icelab.se/opportunitie...
Reposted by Vishnu Raghuram
very impressed by so many of India’s doctors and scientists stepping up to organize, innovate, and strategically confront the challenge of AMR that threatens their populous country and the world beyond
🇮🇳 🧫 🦠 💊 🇮🇳
www.bbc.com/news/article...
🇮🇳 🧫 🦠 💊 🇮🇳
www.bbc.com/news/article...
India's 'blockbuster' drugs to combat antibiotic-resistant superbugs
A number of promising new drugs from India show potential to fight antibiotic-resistant bacteria.
www.bbc.com
December 5, 2024 at 2:55 PM
very impressed by so many of India’s doctors and scientists stepping up to organize, innovate, and strategically confront the challenge of AMR that threatens their populous country and the world beyond
🇮🇳 🧫 🦠 💊 🇮🇳
www.bbc.com/news/article...
🇮🇳 🧫 🦠 💊 🇮🇳
www.bbc.com/news/article...
Reposted by Vishnu Raghuram
I study bacterial genome evolution and how this affects phenotype. Also interested in using metagenome data to investigate community context of pathogens. I often work on Staphylococcus aureus (MRSA) and Chlamydia trachomatis.
Average nucleotide identity-based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome | mSystems
We analyzed the genomic diversity of Staphylococcus aureus, a globally prevalent bacterial species that causes serious infections in humans.
Our goal was to build a genetic picture of the different st...
doi.org
December 2, 2024 at 1:29 PM
I study bacterial genome evolution and how this affects phenotype. Also interested in using metagenome data to investigate community context of pathogens. I often work on Staphylococcus aureus (MRSA) and Chlamydia trachomatis.
The CompMicroLab at Umeå University is hiring a postdoc! Interested in bacterial single-cell sequencing and the oral microbiome? Click here for more details: www.microbe.dev/jobs/
#microbiology #bioinformatics #microbiome #microsky #postdoc #job
@scilifelab.se
#microbiology #bioinformatics #microbiome #microsky #postdoc #job
@scilifelab.se
jobs | The CompMicroLab <span>@</span> UmU
All open and upcoming CompMicroLab positions <span>💼</span>
www.microbe.dev
November 29, 2024 at 1:29 PM
The CompMicroLab at Umeå University is hiring a postdoc! Interested in bacterial single-cell sequencing and the oral microbiome? Click here for more details: www.microbe.dev/jobs/
#microbiology #bioinformatics #microbiome #microsky #postdoc #job
@scilifelab.se
#microbiology #bioinformatics #microbiome #microsky #postdoc #job
@scilifelab.se
Reposted by Vishnu Raghuram
IceLab counts as members 50+ researchers. Most sit in IceLab's open environment while about a third are affiliated researchers in Umeå. The research they carry out is varied and interesting. Here is a starter pack featuring those researchers! We will add more as they join.
go.bsky.app/7SYvJr4
go.bsky.app/7SYvJr4
November 25, 2024 at 8:22 AM
IceLab counts as members 50+ researchers. Most sit in IceLab's open environment while about a third are affiliated researchers in Umeå. The research they carry out is varied and interesting. Here is a starter pack featuring those researchers! We will add more as they join.
go.bsky.app/7SYvJr4
go.bsky.app/7SYvJr4