Simon Harris

The Good Old Days   Pity the poor children of today, with their calendars stuffed with chocolates,   never to know the thrill of opening a small cardboard door and discovering behind it   a picture of a bell. Brian Bilston

Today’s poem is called ‘The Good Old Days’.

Effect of a Reduced PCV10 Dose Schedule on Pneumococcal Carriage in Vietnam | NEJM After pneumococcal disease and colonization have been controlled through vaccination campaigns, a reduced pneumococcal conjugate vaccine (PCV) schedule may be sufficient to sustain that control at ...

Very happy to share our new study out today in the New England Journal of Medicine, showing fewer PCV doses are non-inferior to standard schedules in maintaining control of vaccine-type carriage in Vietnam. This could make vacc programmes much more affordable for LMICs.

www.nejm.org/doi/full/10....

Promotional logo for MMseqs2 16 with the MMseqs2 Rocket mascot as a smart phone like App logo

MMseqs2 Release 16 Highlights: GPU-accelerated search📄, ORF or new 6-frame translated search modes, contig taxonomy always keeps the longest ORF, bug fixes (reduced memory and higher sensitivity) and relicensed as MIT
📄 biorxiv.org/content/10.1...
💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶

Closing date 2 Dec, so get your applications in!

Info: We updated our Bakta WEB version:

- MUCH faster annotations via optimized Kubernetes nodes and locally-attached databases
- Software-Update to v1.10.1
- Database-Update to v5.1

Publicly available at: bakta.computational.bio

NEW Publication!😄

Here, we show how #PhyKIT — a broadly applicable toolkit for #phylogenomics — can be used to construct phylogenomic data matrices (& quantify biases therein), detect anomalies in predicted orthology, calculate gene-gene coevolution, & more!

🔗: tinyurl.com/yc5ja4xz

The first review article from my lab, helmed by @celiasouque.bsky.social, "From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance" is now online and open access at Annual Reviews Microbiology:
www.annualreviews.org/content/jour...

HERE's our paper revealing phylogenomic variations in #Salmonella Agona that lead toward persistent infection

dx.plos.org/10.1371/journal.ppat.1012679

Great job to our @Emmabeansworth.bsky.social, @gemma-langridge.bsky.social, @winnielee.bsky.social & UKHSA's Marie Chattaway & Amina Ismail Ahmed

I thought it might be worthwhile to do a quick primer on CDC.gov datasets and public data resources.

1. DATA.CDC.GOV (data.cdc.gov/browse)
Datasets from across the agency, in browsable, machine readable format (Socrata system). Other/older collections are on:

2. WONDER.CDC.GOV (wonder.cdc.gov)

Say hi to everyone for me

Kaptive v3 is out! It’s much faster than the old version, with improved typeability of K and O loci from low quality draft genomes. Go see Tom’s poster at #KLEBS24!

We have a paid internship opportunity in our group at EMBL-EBI (Cambridge) starting in February 2025, working on pneumococcal serotyping using deep learning. (1/3)

Monty Python collaborator claims Life of Brian was 'more accurate than Bible' It was 'completely misunderstood'.

What’s Michael Palin done to upset the Metro?
“A Gumby was a recurring character featured throughout Monty Python’s works, usually played by Michael Palin, who was simple-minded.”

metro.co.uk/2024/11/07/m...

CPHIA opening

Tedros being awarded a lifetime achievement award by the DG of Africa CDC

A masked weaver bird hanging from its nest

A crocodile sunning itself near my feet

My first time in Zambia, attending the 3rd Conference on Public Health in Africa. Privileged to witness Tedros being awarded a lifetime achievement award. And I’ve never had lunch at a hotel with weaver birds and crocodiles next to me before.

I'm happy to announce we received BMGF support to develop amplicon sequencing for wastewater surveillance! www.birmingham.ac.uk/news/2023/1-... @pathogenomenick.bsky.social @simonrharris.bsky.social

Illumina have announce a new access program to help support global access to genomics www.illumina.com/company/news...

Excited to start working with you Josh! Congratulations on the grant.

Biology, Assistant Professor in Genetics/Genomics, Tenure-Track Loyola University Chicago (LUC), College of Arts and Sciences, Department of Biology seeks qualified candidates for an appointment as Assistant Professor, beginning Fall 2024. The Department of Biolog...

Please share widely.
The Department of Biology at Loyola University Chicago is searching for a new assistant professor in genetics, genomics, or bioinformatics. I am chairing the search and will happily answer any questions about the position.
www.careers.luc.edu/postings/26656

Head of Bioinformatics to lead and cultivate a specialised bioinformatics core support team. Salary: Competitive Contract Length: Permanent Apply by 4 December 2023

Come work with us! The Quadram is in search of a Head of Bioinformatics to lead and cultivate a specialised bioinformatics core support team. Applications Close 04 December 2023

quadram.ac.uk/vacancies/he...

A week to go until the 2023 PHA4GE conference seems like a good time to encourage all genomic epi bioinformaticians to get involved and help develop standards and methods for open source, reproducible bioinformatics for global public health. pha4ge.org

PhD opportunity with me and Mark Webber! Some microbial genomics, some molecular biology, all fun. Apply here: buff.ly/3FjzrzS

PhD studentship with myself and Ed Feil at the University of Bath looking at the evolution and epidemiology of plasmids - in particular looking at plasmid fusions/hybrids/recombinants. Lots of fun bioinformatics! Open to UK or international students.
#microsky
www.findaphd.com/phds/project...

En route to Dakar for the Grand Challenges Annual meeting. Looking forward to our sessions on integrating genomics with epidemiology and modelling in LMICs and to experience everything else that’s planned.

Funded MScR - Genomic Analysis of Antibacterial Drug Resistant Bacteria from Welsh Beef Farms at Uni... PhD Project - Funded MScR - Genomic Analysis of Antibacterial Drug Resistant Bacteria from Welsh Beef Farms at University of Bristol, listed on FindAPhD.com

Opportunity for a FULLY-FUNDED MSc by research: Genomic Analysis of Antibacterial Drug Resistant Bacteria from Welsh Beef Farms, University of Bristol. www.findaphd.com/phds/project... #MicroSky

ACF opportunities in Infectious Disease at University of Birmingham

www.birmingham.ac.uk/research/act...

This new paper from the Africa PGI discusses the future needs for pathogen genomics workforce development in Africa based on lessons learned from the last three years of the PGI www.thelancet.com/journals/lan...

👩‍🔬New **PostDoc** Opportunity!👨‍🔬

My new Epidemiology & Virus Evolution (EVE) group at SwissTPH is looking for a PostDoc in evolution & phylogenetics of respiratory viruses 🦠🌳

Interested? See here for more details & to apply!
jobs.swisstph.ch/Vacancies/92...

Please share!😁

I'm recruiting PhD students for Oct 24 start at University of Bath. Fully funded for UK students only. If interested in developing data structures/algorithms for bacterial genomics, or exploring plasmid epidemiology, or ML/AI on bacterial/phage geno/pheno data, give me a call!

Registration now open for this conference--Antimicrobial Resistance: Genomes, Big Data, and Emerging Technologies. Check out the amazing line-up of speakers, submit an abstract, and join us for an exciting meeting! coursesandconferences.wellcomeconnectingscience.org/event/antimi...

I had it last week. Symptoms started 1 1/2 days before LFT positive, and I really suffered with it this time too.