Vishnu Raghuram

Population diversity declines between inoculated and exposed guinea pigs. Viral titers in nasal lavage samples are indicated by the overall height of the bar. Red lines show LOD (50 PFU/mL). Colors within the bars represent unique barcodes, and the height of each color indicates barcode frequency within the sample. Plots for individual animals are paired with those of their cage mate. Representative pairs for direct contact (top half) and aerosol (bottom half) exposure are shown from three experimental replicates. Guinea pig ID numbers are shown in the upper right corner of each plot.

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

🧪🧬🖥️

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...

🦘✂️ 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...

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

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.

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, ...

(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

1. Our questjons were not about executive ordere but about ASM doing things wihtout any communication of memebrship
asm.org/press-releas...

The Kalamari Databse YouTube video by The Bioinformatics Lab

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...

Spaces are limited so if youre sure you can make it, register!

https://www.bio.cam.ac.uk/11th-microbial-bioinformatics-hackathon

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).

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...

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.

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

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.

The entire archive of CDC datasets can be found here.

HUGE shoutout to data archivists- this work is important 👏🙌🏻

archive.org/details/2025...

Trans people cannot be erased.

#WontBeErased

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!

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 ...

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....

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

Ten species comprise half of the bacteriology literature, leaving most species unstudied Microbiology research has historically focused on a few species of model organisms. Our bibliographic analysis finds extreme bias in the distribution of bacteriology research across species, with half...

www.biorxiv.org/content/10.1...

🔎 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...

Would also be great if biorxiv had a "I would like to review this paper" button

India's 'blockbuster' drugs to combat antibiotic-resistant superbugs A number of promising new drugs from India show potential to fight antibiotic-resistant bacteria.

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...

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...

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

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

Ah thanks for your input. However afaik resumes are usually submitted as a PDF so how does one tell what software was used to make it?

Quite late to the party but I finally remade my resume using #LaTeX. I can see the light. Should have done this years ago!

What do you all use?

#microsky #microbiology #bioinformatics #genomics
🖥️🦠🧬

👀 Working on a #StarterPack for early career researchers (PhD students & Postdocs) in #genomics & #bioinformatics 🧬🖥️ Please share! Happy to add those working in this area so please suggest. Seeing a lot of PIs on here but would love to see more students 🎓🚀

Hello, I would like to be added please!