Simon Harris
@simonrharris.bsky.social
Senior Program Officer in the Genomic Epidemiology and Modelling team at The Bill & Melinda Gates Foundation. Pathogen genomics and bioinformatics.
Reposted by Simon Harris
Today’s poem is called ‘The Good Old Days’.
December 1, 2024 at 9:01 AM
Today’s poem is called ‘The Good Old Days’.
Reposted by Simon Harris
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....
www.nejm.org/doi/full/10....
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 ...
www.nejm.org
November 28, 2024 at 7:37 AM
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....
www.nejm.org/doi/full/10....
Reposted by Simon Harris
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 🖥️🧬🧶
📄 biorxiv.org/content/10.1...
💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶
November 27, 2024 at 9:08 AM
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 🖥️🧬🧶
📄 biorxiv.org/content/10.1...
💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶
Reposted by Simon Harris
Closing date 2 Dec, so get your applications in!
JOB CLAXON!
I am recruiting a post-doctoral researcher on a BBSRC-funded project (36 months) on the genetics and functional genomics of vancomycin resistance in enterococci.
Further details here: edzz.fa.em3.oraclecloud.com/hcmUI/Candid...
Please DM or email me if you want to discuss this post.
I am recruiting a post-doctoral researcher on a BBSRC-funded project (36 months) on the genetics and functional genomics of vancomycin resistance in enterococci.
Further details here: edzz.fa.em3.oraclecloud.com/hcmUI/Candid...
Please DM or email me if you want to discuss this post.
Research Fellow - Department of Microbes, Infections and Microbiomes - 104864 - Grade 7
This exciting BBSRC-funded project aims to mechanistically characterise the fitness costs associated with vancomycin resistance in the Gram-positive opportunistic pathogens Enterococcus faecalis and E...
edzz.fa.em3.oraclecloud.com
November 26, 2024 at 10:48 PM
Closing date 2 Dec, so get your applications in!
Reposted by Simon Harris
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
- 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
November 26, 2024 at 8:10 AM
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
- 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
Reposted by Simon Harris
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
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
November 25, 2024 at 5:25 PM
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
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
Reposted by Simon Harris
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...
www.annualreviews.org/content/jour...
November 21, 2024 at 3:27 PM
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...
www.annualreviews.org/content/jour...
Reposted by Simon Harris
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
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
https://dx.plos.org/10.1371/journa…
November 21, 2024 at 6:03 PM
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
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
Reposted by Simon Harris
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)
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)
Data | Centers for Disease Control and Prevention
Data published by CDC public health programs to help save lives and protect people from health, safety, and security threats.
data.cdc.gov
November 20, 2024 at 7:29 PM
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)
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)
Reposted by Simon Harris
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!
November 20, 2024 at 5:06 PM
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!
Reposted by Simon Harris
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)
November 4, 2024 at 11:51 AM
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)
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...
“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...
Monty Python collaborator claims Life of Brian was 'more accurate than Bible'
It was 'completely misunderstood'.
metro.co.uk
November 8, 2024 at 8:35 PM
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...
“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...
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.
November 28, 2023 at 5:12 PM
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.
Reposted by Simon Harris
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
November 6, 2023 at 2:25 PM
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...
November 13, 2023 at 7:44 PM
Illumina have announce a new access program to help support global access to genomics www.illumina.com/company/news...
Reposted by Simon Harris
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
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
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...
www.careers.luc.edu
October 21, 2023 at 3:52 PM
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
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
Reposted by Simon Harris
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...
quadram.ac.uk/vacancies/he...
October 21, 2023 at 3:52 PM
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...
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
October 21, 2023 at 8:42 AM
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
Reposted by Simon Harris
PhD opportunity with me and Mark Webber! Some microbial genomics, some molecular biology, all fun. Apply here: buff.ly/3FjzrzS
October 19, 2023 at 7:55 AM
PhD opportunity with me and Mark Webber! Some microbial genomics, some molecular biology, all fun. Apply here: buff.ly/3FjzrzS
Reposted by Simon Harris
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...
#microsky
www.findaphd.com/phds/project...
October 18, 2023 at 4:17 PM
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...
#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.
October 7, 2023 at 9:55 AM
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.
Reposted by Simon Harris
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
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
www.findaphd.com
October 6, 2023 at 4:06 PM
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
Reposted by Simon Harris
ACF opportunities in Infectious Disease at University of Birmingham
www.birmingham.ac.uk/research/act...
www.birmingham.ac.uk/research/act...
October 6, 2023 at 9:29 AM
ACF opportunities in Infectious Disease at University of Birmingham
www.birmingham.ac.uk/research/act...
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...
October 5, 2023 at 1:35 PM
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...
Reposted by Simon Harris
👩🔬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!😁
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!😁
September 29, 2023 at 11:31 AM
👩🔬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!😁
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!😁