Rodrigo Bacigalupe
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rbacigalupe.bsky.social
Rodrigo Bacigalupe
@rbacigalupe.bsky.social
microbes & data | biotech & pharma
Reposted by Rodrigo Bacigalupe
Three major respiratory viruses COVID-19, RSV & flu still drive hospitalizations yearly. A new review of 511 studies shows current vaccines work. COVID-19 mRNA shots targeting XBB.1.5 cut hospitalizations by ~46–50%; newer KP.2-adapted vaccines reached 68% effectiveness.
www.nejm.org/doi/full/10....
Updated Evidence for Covid-19, RSV, and Influenza Vaccines for 2025–2026 | NEJM
Changes in the vaccine advisory process in the United States have disrupted immunization guidance, which reinforces the need for independent evidence review to inform decisions regarding immunizati...
www.nejm.org
October 30, 2025 at 12:14 PM
Reposted by Rodrigo Bacigalupe
Phage therapy uses bacteriophages to target bacteria and treat infections. A Primer in Nature Reviews Methods Primers discusses the practical aspects of phage therapy. go.nature.com/3JXfVPv 🔒
September 16, 2025 at 7:06 PM
Reposted by Rodrigo Bacigalupe
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology
LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.
www.nature.com
September 10, 2025 at 9:12 AM
Reposted by Rodrigo Bacigalupe
E. coli engineered to display cytokines destroy hard-to-treat tumors by boosting the activity of local native and adoptive immune effector cells #NBTNV go.nature.com/3XRyVSv
rdcu.be/dWuJ3
Bacteria displaying cytokines heat up the tumor microenvironment - Nature Biotechnology
Escherichia coli engineered to display cytokines destroy hard-to-treat tumors by boosting the activity of local native and adoptive immune effector cells.
go.nature.com
September 9, 2025 at 3:31 AM
Reposted by Rodrigo Bacigalupe
Now out as preprint: versions 2.0 of both BiG-SCAPE and BiG-SLiCE have been released! With significant speed and accuracy increases, as well as new interactive functionalities. www.biorxiv.org/content/10.1...
BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters
Microbial metabolic gene clusters encode the biosynthesis or catabolism of metabolites that facilitate ecological specialization, mediate microbiome interactions and constitute a major source of medic...
www.biorxiv.org
September 1, 2025 at 10:35 PM
Reposted by Rodrigo Bacigalupe
🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...
September 3, 2025 at 8:39 AM
Reposted by Rodrigo Bacigalupe
Preprint: De-novo design of proteins that inhibit bacterial defenses

Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications

Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection
Bacterial defense systems present considerable barriers to both phage infection and plasmid transformation. These systems target mobile genetic elements, limiting the efficacy of bacteriophage-based t...
www.biorxiv.org
September 2, 2025 at 10:48 AM
Reposted by Rodrigo Bacigalupe
New preprint reveals bacteria can't just collect all resistance genes like Pokemon cards.
We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...
Genomic constraints shape the evolution of alternative routes to drug resistance in prokaryotes
Background Variation within the prokaryotic pangenome is not random, and natural selection that favours particular combinations of genes appears to dominate over random drift. What is less clear is wh...
www.biorxiv.org
August 29, 2025 at 2:05 PM
Reposted by Rodrigo Bacigalupe
The 5: COVID-19, influenza, respiratory syncytial virus (RSV), pneumonia, and herpes zoster (shingles). www.cidrap.umn.edu/adult-non-fl...
New ACC guidance urges uptake of 5 vaccines for heart patients
www.cidrap.umn.edu
August 26, 2025 at 9:20 PM
Reposted by Rodrigo Bacigalupe
Preventive cancer vaccines could harness a less-compromised immune system in vaccine recipients before their immune responses become affected by the advanced status of the disease itself. Here's a recent review of the field
www.nature.com/articles/s41...
rdcu.be/eAqSL
Vaccines for cancer prevention: exploring opportunities and navigating challenges - Nature Reviews Drug Discovery
Cancer-preventive vaccines can reduce cancer occurrence by inducing a specific immune response against tumours before they can fully develop. This Review discusses results from pioneering clinical stu...
www.nature.com
August 12, 2025 at 2:46 PM
Reposted by Rodrigo Bacigalupe
How can we engineer B cells to treat diseases? Read about the latest developments of this exciting field in this new Review out now in @natbiotech.nature.com www.nature.com/articles/s41...
Engineering B cells to treat and study human disease - Nature Biotechnology
Recent developments in B cell engineering expand our ability to study human disease and drive progress toward new B cell therapies, balancing challenges in clinical implementation with emerging opport...
www.nature.com
August 6, 2025 at 7:55 AM
Reposted by Rodrigo Bacigalupe
🧬 A new AI tool from @utaustin.bsky.social & Sanofi could speed the development of mRNA-based therapies for viruses, cancers and genetic disorders. RiboNN predicts which mRNA sequences will be most efficiently translated into proteins. cns.utexas.edu/news/researc... @taccutexas.bsky.social
New AI Tool Accelerates mRNA-Based Treatments for Viruses, Cancers, Genetic Disorders
UT Austin and Sanofi partner to build tool that predicts translation efficiency of mRNA sequences.
cns.utexas.edu
July 25, 2025 at 4:03 PM
Reposted by Rodrigo Bacigalupe
#Review

A reflection on the major challenges in bacterial mRNA vaccine design, providing strategies for tailoring mRNA construct design to promote humoral or cellular immunity, and providing an overview of the translational landscape for mRNA vaccines.

#MicroSky 🦠

www.nature.com/articles/s41...
Challenges and opportunities in mRNA vaccine development against bacteria - Nature Microbiology
This Review reflects on the major challenges in bacterial mRNA vaccine design, provides strategies for tailoring mRNA construct design to promote humoral or cellular immunity, and provides an overview...
www.nature.com
July 30, 2025 at 3:38 PM
Reposted by Rodrigo Bacigalupe
#Review

A discussion on the processes driving bacterial evolution and emergence of pathogenesis within hosts, the importance of understanding within-host genetic diversity, and the implications for transmission analysis and infectious disease control.

#MicroSky 🦠

www.nature.com/articles/s41...
Within-host bacterial evolution and the emergence of pathogenicity - Nature Microbiology
In this Review, Tonkin-Hill et al. discuss the processes driving bacterial evolution and emergence of pathogenesis within hosts, the importance of understanding within-host genetic diversity, and the ...
www.nature.com
July 30, 2025 at 3:40 PM
Reposted by Rodrigo Bacigalupe
Global Childhood Vaccination Progress Has Stalled in Recent Decades: it increased compared to the 1980s, but progress stalled and even reversed in past decades. jamanetwork.com/journals/jam...
Global Childhood Vaccination Progress Has Stalled in Recent Decades
Following the creation of the Essential Programme on Immunization in 1974, coverage for childhood vaccines against diphtheria, tetanus, pertussis, measles, polio, and tuberculosis nearly doubled from ...
jamanetwork.com
July 23, 2025 at 5:32 PM
Reposted by Rodrigo Bacigalupe
"The increase in measles cases among young people in the UK, which has already led to one death in Liverpool, is worrying and tragic ...Vaccines alone don’t save lives, vaccination does."
www.theguardian.com/society/2025...
Measles surge shows why vaccinations are crucial | Letters
Letters: We need to address vaccine misinformation and hesitancy in communities to save lives, says Simon Brassel. Plus letters from Dr Munjed Farid Al Qutob and Matthew K Belmonte
www.theguardian.com
July 23, 2025 at 5:38 PM
Reposted by Rodrigo Bacigalupe
A new impact framework for investors in life sciences bridges financial returns and patient outcomes go.nature.com/3TV0pFr
A new impact framework for investors in life sciences bridges financial returns and patient outcomes - Nature Biotechnology
A new model for quantifying the impact of capital investments in life science interventions could help investors, policymakers and healthcare stakeholders to assess, monitor and optimize the societal ...
go.nature.com
July 22, 2025 at 3:51 PM
Reposted by Rodrigo Bacigalupe
New paper alert! 🚨

Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate.

We combine theory, simulations, experimental evolution, and bioinformatics to demonstrate that mutation rates scale with plasmid copy number.

Let's dive in! 🧵👇
Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate
Plasmids are autonomously replicating DNA molecules that stably coexist with chromosomes in bacterial cells. These genetic elements drive horizontal gene transfer and play a fundamental role in bacter...
www.biorxiv.org
July 22, 2025 at 9:38 AM
Reposted by Rodrigo Bacigalupe
A contextualised protein language model reveals the functional syntax of bacterial evolution https://www.biorxiv.org/content/10.1101/2025.07.20.665723v1
July 21, 2025 at 5:17 AM
Reposted by Rodrigo Bacigalupe
New pre-print from my group - project led by PhD student Michael Hoffert. We set out on a daunting mission to generate a 'periodic table' of bacterial diversity (1/6) www.biorxiv.org/content/10.1...
A periodic table of bacteria?: Mapping bacterial diversity in trait space
Bacterial diversity can be overwhelming. There is an ever-expanding number of bacterial taxa being discovered, but many of these taxa remain uncharacterized with unknown traits and environmental prefe...
www.biorxiv.org
July 18, 2025 at 4:44 PM