Sophie Belman
@sophiebelman.bsky.social
Schmidt Science Fellow @ Barcelona Supercomputing Center. I model infectious disease dynamics and climate leveraging pathogen genomes. Pneumococcal enthusiast. https://sophbel.github.io/website/
Previously Sanger Institute and University of Cambridge.
Previously Sanger Institute and University of Cambridge.
Reposted by Sophie Belman
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...
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
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...
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...
Reposted by Sophie Belman
Very pleased to share this newly published work with Aishani Aatresh, part of her exceptional Harvard undergrad thesis. journals.asm.org/doi/10.1128/... .
What is the relationship between viral prospecting in animals and medical countermeasure development? | mBio
Sampling in animal populations to detect novel viruses before they infect humans has
been a major activity justified by several considerations, notably by the idea that
finding such viruses will stimu...
journals.asm.org
August 25, 2025 at 7:43 PM
Very pleased to share this newly published work with Aishani Aatresh, part of her exceptional Harvard undergrad thesis. journals.asm.org/doi/10.1128/... .
Reposted by Sophie Belman
The Department of Health and Human Services has a process for making and updating recommendations like this, using expert scientists and clinicians. RFK is deliberately putting Americans' health at risk and sidestepping good science for political reasons.
#Breaking: RFK Jr. rolls back Covid vaccine recommendations for healthy children, pregnant people buff.ly/1jKJGHi
RFK Jr. rolls back Covid vaccine recommendations for healthy children, pregnant people
HHS Secretary Robert F. Kennedy Jr. announced that he has unilaterally struck the recommendation that healthy children and healthy pregnant people get Covid booster shots.
www.statnews.com
May 27, 2025 at 3:52 PM
The Department of Health and Human Services has a process for making and updating recommendations like this, using expert scientists and clinicians. RFK is deliberately putting Americans' health at risk and sidestepping good science for political reasons.
Reposted by Sophie Belman
New preprint: we used k-mer matching with suffix match length information to create an assembly-to-assembly alignment algorithm + software, kbo.
We wanted to create a reference-based aligner and variant caller that scales to at least 10-100k bacterial queries.
www.biorxiv.org/content/10.1...
We wanted to create a reference-based aligner and variant caller that scales to at least 10-100k bacterial queries.
www.biorxiv.org/content/10.1...
Sequence alignment with k-bounded matching statistics
Finding high-quality local alignments between a query sequence and sequences contained in a large genomic database is a fundamental problem in computational genomics, at the core of thousands of biolo...
www.biorxiv.org
May 26, 2025 at 8:00 AM
New preprint: we used k-mer matching with suffix match length information to create an assembly-to-assembly alignment algorithm + software, kbo.
We wanted to create a reference-based aligner and variant caller that scales to at least 10-100k bacterial queries.
www.biorxiv.org/content/10.1...
We wanted to create a reference-based aligner and variant caller that scales to at least 10-100k bacterial queries.
www.biorxiv.org/content/10.1...
Reposted by Sophie Belman
New paper: long-term trends in antibiotic resistance show signs of stabilisation (thread). journals.plos.org/plospathogen...
The evolution of antibiotic resistance in Europe, 1998–2019
Author summary Antibiotic resistance is an important public health threat: resistant infections are currently associated with 5 million deaths per year globally. This burden may increase further in th...
journals.plos.org
April 7, 2025 at 8:36 AM
New paper: long-term trends in antibiotic resistance show signs of stabilisation (thread). journals.plos.org/plospathogen...
Reposted by Sophie Belman
We are excited to announce our 2025 Schmidt Science Fellows! 32 early career researchers, nominated by the world’s leading research universities, who will take an interdisciplinary approach to advancing discovery schmidtsciencefellows.org/news/2025-fe...
April 2, 2025 at 1:48 PM
We are excited to announce our 2025 Schmidt Science Fellows! 32 early career researchers, nominated by the world’s leading research universities, who will take an interdisciplinary approach to advancing discovery schmidtsciencefellows.org/news/2025-fe...
Reposted by Sophie Belman
Very interesting opportunity for a female African microbiologist.
@tuliodna.bsky.social @ckyobutungi.bsky.social
Please promote
@tuliodna.bsky.social @ckyobutungi.bsky.social
Please promote
1/ Last call for the EMBL-UNESCO Residency Programme! ⏳
If you’re a female African scientist working in infection biology, this is your opportunity to develop scientific skills while fostering collaboration across borders.
🙌 Apply until 31 March 2025.
www.embl.org/about/info/s...
If you’re a female African scientist working in infection biology, this is your opportunity to develop scientific skills while fostering collaboration across borders.
🙌 Apply until 31 March 2025.
www.embl.org/about/info/s...
March 25, 2025 at 9:25 AM
Very interesting opportunity for a female African microbiologist.
@tuliodna.bsky.social @ckyobutungi.bsky.social
Please promote
@tuliodna.bsky.social @ckyobutungi.bsky.social
Please promote
Reposted by Sophie Belman
Interested in pursing a PhD in infectious disease dynamics, artificial intelligence, and behavioural science?
Come and join myself and Professor Stefan Flasche at the Charité Center for Global Health in Berlin:
karriere.charite.de/en/job-vacan...
Come and join myself and Professor Stefan Flasche at the Charité Center for Global Health in Berlin:
karriere.charite.de/en/job-vacan...
karriere.charite.de
March 7, 2025 at 9:41 AM
Interested in pursing a PhD in infectious disease dynamics, artificial intelligence, and behavioural science?
Come and join myself and Professor Stefan Flasche at the Charité Center for Global Health in Berlin:
karriere.charite.de/en/job-vacan...
Come and join myself and Professor Stefan Flasche at the Charité Center for Global Health in Berlin:
karriere.charite.de/en/job-vacan...
A must read opinion piece.
10 years ago, when I began teaching global health, my courses were mostly the 'blue pill' version
Slowly but surely, it has become reddish
Every year brings more improvement & reflection
@shashikalb.bsky.social & @ananyatb.bsky.social have been great co-teachers
journals.plos.org/globalpublic...
Slowly but surely, it has become reddish
Every year brings more improvement & reflection
@shashikalb.bsky.social & @ananyatb.bsky.social have been great co-teachers
journals.plos.org/globalpublic...
February 27, 2025 at 8:19 AM
A must read opinion piece.
Reposted by Sophie Belman
This is a gut-wrenching, beautifully written essay. A doctor must watch helplessly as children die because USAID's freeze on aid has limited access to nutritional supplements. time.com/7258248/us-f...
What Gutting USAID Means for My Young Patients in Burundi
“To my patients and their mothers, I offered apologies from the American people,” writes Dr. Jennifer Furin.
time.com
February 25, 2025 at 12:56 PM
This is a gut-wrenching, beautifully written essay. A doctor must watch helplessly as children die because USAID's freeze on aid has limited access to nutritional supplements. time.com/7258248/us-f...
Reposted by Sophie Belman
Goodnight friends. We end today with this quote for ourselves and for our new secretary of HHS.
February 14, 2025 at 4:46 AM
Goodnight friends. We end today with this quote for ourselves and for our new secretary of HHS.
I’m racing a Half Ironman triathlon this June. 2km swim, 90km cycle, 20km run and raising money for the Meningitis Research Foundation.
Meningitis has ~2.5 million cases and 250,000 deaths annually predominantly among children. Any donation would be great!
gofund.me/a958252f
Meningitis has ~2.5 million cases and 250,000 deaths annually predominantly among children. Any donation would be great!
gofund.me/a958252f
Donate to Half Iron(wo)man for Meningitis Research, organized by Sophie Belman
I will be racing my first Half Ironman triathlon in Zurich this June. It includ… Sophie Belman needs your support for Half Iron(wo)man for Meningitis Research
gofund.me
February 9, 2025 at 7:29 PM
I’m racing a Half Ironman triathlon this June. 2km swim, 90km cycle, 20km run and raising money for the Meningitis Research Foundation.
Meningitis has ~2.5 million cases and 250,000 deaths annually predominantly among children. Any donation would be great!
gofund.me/a958252f
Meningitis has ~2.5 million cases and 250,000 deaths annually predominantly among children. Any donation would be great!
gofund.me/a958252f
Reposted by Sophie Belman
Our mSCAPE project has been formally announced to the world by @smhopkins.bsky.social at #FOG2025 today: www.gov.uk/government/n... - a really exciting academic-public health collaboration to build a surveillance platform leveraging NHS metagenomic diagnostic data. @meerac.bsky.social
UKHSA launches new metagenomic surveillance for health security
The UK launches mSCAPE, a world-first metagenomics initiative by UKHSA to enhance health security through rapid pathogen detection and surveillance.
www.gov.uk
January 30, 2025 at 4:54 PM
Our mSCAPE project has been formally announced to the world by @smhopkins.bsky.social at #FOG2025 today: www.gov.uk/government/n... - a really exciting academic-public health collaboration to build a surveillance platform leveraging NHS metagenomic diagnostic data. @meerac.bsky.social
Reposted by Sophie Belman
Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉
https://buff.ly/4gyYCzx
We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.
🧵 A thread... 1/n
#IDSky #IDModelling
https://buff.ly/4gyYCzx
We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.
🧵 A thread... 1/n
#IDSky #IDModelling
Learning the fitness dynamics of pathogens from phylogenies - Nature
Phylowave, an innovative phylogenetic approach, can identify the main circulating pathogen lineages with increased fitness and the associated genetic changes, enabling the timely identification of…
buff.ly
January 2, 2025 at 8:03 AM
Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉
https://buff.ly/4gyYCzx
We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.
🧵 A thread... 1/n
#IDSky #IDModelling
https://buff.ly/4gyYCzx
We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.
🧵 A thread... 1/n
#IDSky #IDModelling
Reposted by Sophie Belman
New MRC-funded postdoc with me on comparative bacterial genomics/phylodynamics @roslininstitute.bsky.social university of Edinburgh. Great multidisciplinary team and collaboration with partners at Shanghai Jao Tong University.
elxw.fa.em3.oraclecloud.com/hcmUI/Candid...
elxw.fa.em3.oraclecloud.com/hcmUI/Candid...
PDRA in Bacterial Genomics
We are looking for a Post-Doctoral Research Associate in Bacterial Genomics at the Laboratory for Bacterial Evolution and Pathogenesis (www.ed.ac.uk/roslin/research/divisions/bacteriology/lbep) at The...
elxw.fa.em3.oraclecloud.com
December 4, 2024 at 9:56 AM
New MRC-funded postdoc with me on comparative bacterial genomics/phylodynamics @roslininstitute.bsky.social university of Edinburgh. Great multidisciplinary team and collaboration with partners at Shanghai Jao Tong University.
elxw.fa.em3.oraclecloud.com/hcmUI/Candid...
elxw.fa.em3.oraclecloud.com/hcmUI/Candid...
Had a great whirlwind of a trip to Tokyo for #SMBE workshop on pangenomics with an inspiring community of people. Fun to present preliminary results on the environment and the pneumococcus! Thanks to #isppd and #schmidtsciencefellows for my funding and the organizers for my registration bursary.
December 5, 2024 at 11:26 AM
Had a great whirlwind of a trip to Tokyo for #SMBE workshop on pangenomics with an inspiring community of people. Fun to present preliminary results on the environment and the pneumococcus! Thanks to #isppd and #schmidtsciencefellows for my funding and the organizers for my registration bursary.
Reposted by Sophie Belman
A Portable and Scalable Genomic Analysis Pipeline for Streptococcus pneumoniae Surveillance: GPS Pipeline https://www.biorxiv.org/content/10.1101/2024.11.27.625679v1
A Portable and Scalable Genomic Analysis Pipeline for Streptococcus pneumoniae Surveillance: GPS Pipeline https://www.biorxiv.org/content/10.1101/2024.11.27.625679v1
Ever increasing global sequencing capacity provides an unprecedented opportunity in utilising genomi
www.biorxiv.org
November 30, 2024 at 3:33 AM
A Portable and Scalable Genomic Analysis Pipeline for Streptococcus pneumoniae Surveillance: GPS Pipeline https://www.biorxiv.org/content/10.1101/2024.11.27.625679v1
Reposted by Sophie Belman
There are four (that's right four!) academic posts open at the School of Biological sciences at Cambridge University. Check them out here: www.jobs.cam.ac.uk/job/?categor... Gr10/11 (AssocProf/Reader; now Prof) Closing 26/1/25. Looking for excellent, collaborative people. Spread the word!
Job Opportunities - University of Cambridge
Current Academic jobs at the University of Cambridge.
www.jobs.cam.ac.uk
November 29, 2024 at 8:22 PM
There are four (that's right four!) academic posts open at the School of Biological sciences at Cambridge University. Check them out here: www.jobs.cam.ac.uk/job/?categor... Gr10/11 (AssocProf/Reader; now Prof) Closing 26/1/25. Looking for excellent, collaborative people. Spread the word!
Reposted by Sophie Belman
How invasive are different E .coli capsules and how many are there? Find out here and use the group 2 and 3 database to type your own!
medrxiv.org/cgi/content/...
medrxiv.org/cgi/content/...
Group 2 and 3 ABC-transporter dependant capsular K-loci contribute significantly to variation in the invasive potential of Escherichia coli
The major opportunistic pathogen Escherichia coli is the largest cause of antimicrobial resistance (AMR) associated infections and deaths globally. Considerable antigenic diversity has been documented...
medrxiv.org
November 27, 2024 at 2:44 AM
How invasive are different E .coli capsules and how many are there? Find out here and use the group 2 and 3 database to type your own!
medrxiv.org/cgi/content/...
medrxiv.org/cgi/content/...
Reposted by Sophie Belman
🚨In our new Lancet Planetary Health 📰 #COP29 we discuss the climate-health-gender nexus by
🔎 reviewing gendered health impacts of #climatechange
⌛️ summarising gender & health in UNFCCC processes
📉 assessing the gender gap in delegations at COP1-28
Full ➡️ 👀 www.thelancet.com/journals/lan...
🔎 reviewing gendered health impacts of #climatechange
⌛️ summarising gender & health in UNFCCC processes
📉 assessing the gender gap in delegations at COP1-28
Full ➡️ 👀 www.thelancet.com/journals/lan...
November 18, 2024 at 11:21 AM
🚨In our new Lancet Planetary Health 📰 #COP29 we discuss the climate-health-gender nexus by
🔎 reviewing gendered health impacts of #climatechange
⌛️ summarising gender & health in UNFCCC processes
📉 assessing the gender gap in delegations at COP1-28
Full ➡️ 👀 www.thelancet.com/journals/lan...
🔎 reviewing gendered health impacts of #climatechange
⌛️ summarising gender & health in UNFCCC processes
📉 assessing the gender gap in delegations at COP1-28
Full ➡️ 👀 www.thelancet.com/journals/lan...