@epiblue.bsky.social
A love of genomics, public health and open datasets.
Reposted
Now out in NEJM. Kudos to @dhelekal.bsky.social and @tatumdmortimer.bsky.social : www.nejm.org/doi/10.1056/...
July 10, 2025 at 11:09 AM
Now out in NEJM. Kudos to @dhelekal.bsky.social and @tatumdmortimer.bsky.social : www.nejm.org/doi/10.1056/...
Reposted
Congratulations to Matthijs Berends and team for the release of the AMR for R package version 3!
I've been using this package to produce the AGAR Kids reports and can highly recommend.
amr-for-r.org
#Rstats #AMR #IDEpi #MedSky
I've been using this package to produce the AGAR Kids reports and can highly recommend.
amr-for-r.org
#Rstats #AMR #IDEpi #MedSky
June 8, 2025 at 1:43 AM
Congratulations to Matthijs Berends and team for the release of the AMR for R package version 3!
I've been using this package to produce the AGAR Kids reports and can highly recommend.
amr-for-r.org
#Rstats #AMR #IDEpi #MedSky
I've been using this package to produce the AGAR Kids reports and can highly recommend.
amr-for-r.org
#Rstats #AMR #IDEpi #MedSky
Reposted
Excited to share our new mSphere paper describing ssRNA viruses associated with Karenia brevis harmful algal blooms in southwest Florida in mSphere led by Jean Lim - a 🧵(1/10) 🧪🦠🌊 #MicroSky #ProtistsOnSky #USFCMS @asm.org @cmarinescience.bsky.social journals.asm.org/doi/full/10....
April 20, 2025 at 3:52 PM
Excited to share our new mSphere paper describing ssRNA viruses associated with Karenia brevis harmful algal blooms in southwest Florida in mSphere led by Jean Lim - a 🧵(1/10) 🧪🦠🌊 #MicroSky #ProtistsOnSky #USFCMS @asm.org @cmarinescience.bsky.social journals.asm.org/doi/full/10....
Reposted
From @plos.org #Computational #Biology | Combining flipped-classroom and spaced-repetition learning in a master-level #bioinformatics course | #Education #OpenScience 🧬 🖥️ 🧪 🔓 CC/ @ppalagi.bsky.social
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journals.plos.org/ploscompbiol...
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journals.plos.org/ploscompbiol...
Combining flipped-classroom and spaced-repetition learning in a master-level bioinformatics course
Author summary A challenge of teaching Bioinformatics is that it is an interdisciplinary field which develops students’ skills in both Biology and Computer Science. We faced the additional challenge o...
journals.plos.org
April 16, 2025 at 11:30 AM
From @plos.org #Computational #Biology | Combining flipped-classroom and spaced-repetition learning in a master-level #bioinformatics course | #Education #OpenScience 🧬 🖥️ 🧪 🔓 CC/ @ppalagi.bsky.social
⬇️
journals.plos.org/ploscompbiol...
⬇️
journals.plos.org/ploscompbiol...
Reposted
New preprint with nice detective work by PhD student Khadija Hanga: gain of pOXA MDR plasmid is facilitated by chromosomal mutations affecting OmpF which act synergistically with the plasmid’s carbapenamase to give high level resistance. Led by @mbottery.bsky.social www.biorxiv.org/content/10.1...
Chromosomal resistance mutations facilitate acquisition of multidrug-resistance plasmids in Escherichia coli
Bacteria can gain multiple resistance mechanisms in a single step by the acquisition of multidrug-resistance (MDR) plasmids, but it is unclear how antibiotic selection during the acquisition of MDR pl...
www.biorxiv.org
April 16, 2025 at 9:58 AM
New preprint with nice detective work by PhD student Khadija Hanga: gain of pOXA MDR plasmid is facilitated by chromosomal mutations affecting OmpF which act synergistically with the plasmid’s carbapenamase to give high level resistance. Led by @mbottery.bsky.social www.biorxiv.org/content/10.1...
Reposted
Plant-Based Diets & Climate Change, A Perspective for Infectious Disease Providers
“This review advocates for the adoption of plant-based diets as a dual strategy to combat climate change & improve health outcomes, particularly in the context of infectious diseases”
academic.oup.com/ofid/advance...
“This review advocates for the adoption of plant-based diets as a dual strategy to combat climate change & improve health outcomes, particularly in the context of infectious diseases”
academic.oup.com/ofid/advance...
April 10, 2025 at 8:20 PM
Plant-Based Diets & Climate Change, A Perspective for Infectious Disease Providers
“This review advocates for the adoption of plant-based diets as a dual strategy to combat climate change & improve health outcomes, particularly in the context of infectious diseases”
academic.oup.com/ofid/advance...
“This review advocates for the adoption of plant-based diets as a dual strategy to combat climate change & improve health outcomes, particularly in the context of infectious diseases”
academic.oup.com/ofid/advance...
Reposted
We've got a new pre-print (spearheaded by @dchodge.bsky.social) on how to reconstruct unobserved antibody kinetics and infections - and use these to estimate correlates of protection: www.medrxiv.org/content/10.1...
And here's the accompanying {serojump} R package: seroanalytics.org/serojump/
And here's the accompanying {serojump} R package: seroanalytics.org/serojump/
April 9, 2025 at 8:30 AM
We've got a new pre-print (spearheaded by @dchodge.bsky.social) on how to reconstruct unobserved antibody kinetics and infections - and use these to estimate correlates of protection: www.medrxiv.org/content/10.1...
And here's the accompanying {serojump} R package: seroanalytics.org/serojump/
And here's the accompanying {serojump} R package: seroanalytics.org/serojump/
Reposted
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
Interested in bacterial genomes?
Hundreds of thousands, even millions?
All annotated, taxonomically classified, integrated with metadata.
Easily searchable, viewable, downloadable, in sync with #AllTheBacteria.
Then BakRep is for you! Poster P-CM-102 @vaam-microbes.bsky.social #VAAM25
Hundreds of thousands, even millions?
All annotated, taxonomically classified, integrated with metadata.
Easily searchable, viewable, downloadable, in sync with #AllTheBacteria.
Then BakRep is for you! Poster P-CM-102 @vaam-microbes.bsky.social #VAAM25
March 25, 2025 at 9:45 AM
Interested in bacterial genomes?
Hundreds of thousands, even millions?
All annotated, taxonomically classified, integrated with metadata.
Easily searchable, viewable, downloadable, in sync with #AllTheBacteria.
Then BakRep is for you! Poster P-CM-102 @vaam-microbes.bsky.social #VAAM25
Hundreds of thousands, even millions?
All annotated, taxonomically classified, integrated with metadata.
Easily searchable, viewable, downloadable, in sync with #AllTheBacteria.
Then BakRep is for you! Poster P-CM-102 @vaam-microbes.bsky.social #VAAM25
Reposted
“Nothing is so privileged as thinking that history belongs to the past”
-John Green, Everything is Tuberculosis
-John Green, Everything is Tuberculosis
March 22, 2025 at 10:36 AM
“Nothing is so privileged as thinking that history belongs to the past”
-John Green, Everything is Tuberculosis
-John Green, Everything is Tuberculosis
Reposted
www.nature.com/articles/s41...
In collaboration with Andrew Lang and Alison Buchan, we just published a review on the complex and sometimes convoluted interactions and evolutionary relationships among bacterial mobile genetic elements.
#phage #plasmid #evolution #bacteria #plasmidbiology #MGE
In collaboration with Andrew Lang and Alison Buchan, we just published a review on the complex and sometimes convoluted interactions and evolutionary relationships among bacterial mobile genetic elements.
#phage #plasmid #evolution #bacteria #plasmidbiology #MGE
Interactions and evolutionary relationships among bacterial mobile genetic elements - Nature Reviews Microbiology
In this Review, Lang and colleagues present an overview of the current knowledge landscape regarding mobile genetic elements in bacteria, with a focus on their evolutionary relationships and interacti...
www.nature.com
March 11, 2025 at 1:12 PM
www.nature.com/articles/s41...
In collaboration with Andrew Lang and Alison Buchan, we just published a review on the complex and sometimes convoluted interactions and evolutionary relationships among bacterial mobile genetic elements.
#phage #plasmid #evolution #bacteria #plasmidbiology #MGE
In collaboration with Andrew Lang and Alison Buchan, we just published a review on the complex and sometimes convoluted interactions and evolutionary relationships among bacterial mobile genetic elements.
#phage #plasmid #evolution #bacteria #plasmidbiology #MGE
Reposted
A study in Nature Food assesses the future climatic suitability of global croplands for 30 major food crop types, quantifying the changes in potential food crop diversity given climate conditions across four global warming levels. https://go.nature.com/3Dp5LEk #foodstudies 🧪
March 9, 2025 at 7:36 PM
A study in Nature Food assesses the future climatic suitability of global croplands for 30 major food crop types, quantifying the changes in potential food crop diversity given climate conditions across four global warming levels. https://go.nature.com/3Dp5LEk #foodstudies 🧪
Reposted
ICYMI: Black Death did not clearly select on immune genes.
1) enrichment in immune genes disappears w/ randomization test
2) 0/4 loci pass filtering thresholds
3) No evidence of significant change in frequency of the ERAP2 variant
www.nature.com/articles/s41...
1) enrichment in immune genes disappears w/ randomization test
2) 0/4 loci pass filtering thresholds
3) No evidence of significant change in frequency of the ERAP2 variant
www.nature.com/articles/s41...
Insufficient evidence for natural selection associated with the Black Death - Nature
Nature - Insufficient evidence for natural selection associated with the Black Death
www.nature.com
March 9, 2025 at 9:15 PM
ICYMI: Black Death did not clearly select on immune genes.
1) enrichment in immune genes disappears w/ randomization test
2) 0/4 loci pass filtering thresholds
3) No evidence of significant change in frequency of the ERAP2 variant
www.nature.com/articles/s41...
1) enrichment in immune genes disappears w/ randomization test
2) 0/4 loci pass filtering thresholds
3) No evidence of significant change in frequency of the ERAP2 variant
www.nature.com/articles/s41...
Reposted
The epidemiology and evolution of H3N2 canine influenza virus in dogs over 20 years. Lead by @brianrwasik.bsky.social shows that spread is determined by the dog population structure. The virus has not become better at transmitting in dogs after 1000s of transfers. pubmed.ncbi.nlm.nih.gov/40040347/
March 7, 2025 at 8:07 PM
The epidemiology and evolution of H3N2 canine influenza virus in dogs over 20 years. Lead by @brianrwasik.bsky.social shows that spread is determined by the dog population structure. The virus has not become better at transmitting in dogs after 1000s of transfers. pubmed.ncbi.nlm.nih.gov/40040347/
Reposted
Our analysis of the second incursion of H5N1 viruses (genotype D1.1) into dairy cattle in the US is now posted to virological virological.org/t/timing-and...
Timing and molecular characterisation of the transmission to cattle of H5N1 influenza A virus genotype D1.1, clade 2.3.4.4b
Jonathan E. Pekar, Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK Thomas P. Peacock, The Pirbright Institute, Woking, UK, GU24 0NF; Department of Infectious Disease, Imper...
virological.org
February 24, 2025 at 1:25 PM
Our analysis of the second incursion of H5N1 viruses (genotype D1.1) into dairy cattle in the US is now posted to virological virological.org/t/timing-and...
Reposted
Reposted
📌The need for speed: ultra-rapid high-resolution outbreak analysis in a front-line hospital microbiology laboratory |@medrxivpreprint
See how hospital labs can analyse outbreaks fast - no on-site #Bioinformatics needed, cutting delays
doi.org/10.1101/2025...
🖥️🧬💻
#AcademicSky
#MicroSky
🧪🧫🦠
See how hospital labs can analyse outbreaks fast - no on-site #Bioinformatics needed, cutting delays
doi.org/10.1101/2025...
🖥️🧬💻
#AcademicSky
#MicroSky
🧪🧫🦠
The need for speed: ultra-rapid high-resolution outbreak analysis in a front-line hospital microbiology laboratory
Many hospital laboratories have technical capacity to perform whole-genome sequencing but lack bioinformatic expertise to analyse sequence data. Sending isolates to reference laboratories creates dela...
doi.org
February 13, 2025 at 9:30 PM
📌The need for speed: ultra-rapid high-resolution outbreak analysis in a front-line hospital microbiology laboratory |@medrxivpreprint
See how hospital labs can analyse outbreaks fast - no on-site #Bioinformatics needed, cutting delays
doi.org/10.1101/2025...
🖥️🧬💻
#AcademicSky
#MicroSky
🧪🧫🦠
See how hospital labs can analyse outbreaks fast - no on-site #Bioinformatics needed, cutting delays
doi.org/10.1101/2025...
🖥️🧬💻
#AcademicSky
#MicroSky
🧪🧫🦠
Reposted
From @plos.org #Computational #Biology | #BLAST from the past: a 14 yo paper from @plosbiology.org that is still relevant 2day but should be in PLOS Computational Biology | Using BLAST to Teach "E-value-tionary" Concepts | #Bioinformatics #Education | 🧬 🖥️ 🧪
➡️ journals.plos.org/plosbiology/...
➡️ journals.plos.org/plosbiology/...
Using BLAST to Teach “E-value-tionary” Concepts
journals.plos.org
February 6, 2025 at 9:02 PM
From @plos.org #Computational #Biology | #BLAST from the past: a 14 yo paper from @plosbiology.org that is still relevant 2day but should be in PLOS Computational Biology | Using BLAST to Teach "E-value-tionary" Concepts | #Bioinformatics #Education | 🧬 🖥️ 🧪
➡️ journals.plos.org/plosbiology/...
➡️ journals.plos.org/plosbiology/...
Reposted
xOmicsShiny: an R shiny application for cross-omics data analysis and pathway mapping https://www.biorxiv.org/content/10.1101/2025.01.30.635740v1 #Rstats 🧬🖥️🧪 https://github.com/interactivereport/xOmicsShiny
February 7, 2025 at 7:30 PM
xOmicsShiny: an R shiny application for cross-omics data analysis and pathway mapping https://www.biorxiv.org/content/10.1101/2025.01.30.635740v1 #Rstats 🧬🖥️🧪 https://github.com/interactivereport/xOmicsShiny
Reposted
🌍 The @who.int has released its Global Research Agenda on AMR in Human Health, identifying 40 research priorities.
These priorities span prevention, diagnosis, and treatment to bridge knowledge gaps and inform global health policy.
💡 Read the full paper here:
bit.ly/4jG5fCd
#AMR #GlobalHealth
These priorities span prevention, diagnosis, and treatment to bridge knowledge gaps and inform global health policy.
💡 Read the full paper here:
bit.ly/4jG5fCd
#AMR #GlobalHealth
WHO global research priorities for antimicrobial resistance in human health
The WHO research agenda for antimicrobial resistance (AMR) in human health has identified 40 research priorities to be addressed by the year 2030. The…
bit.ly
February 6, 2025 at 9:06 PM
🌍 The @who.int has released its Global Research Agenda on AMR in Human Health, identifying 40 research priorities.
These priorities span prevention, diagnosis, and treatment to bridge knowledge gaps and inform global health policy.
💡 Read the full paper here:
bit.ly/4jG5fCd
#AMR #GlobalHealth
These priorities span prevention, diagnosis, and treatment to bridge knowledge gaps and inform global health policy.
💡 Read the full paper here:
bit.ly/4jG5fCd
#AMR #GlobalHealth
Reposted
A Lancet study finds AMR gonorrhea in the US is prevalent in densely populated cities. It is associated with high HIV rates. Findings highligh the need for expanded surveillance beyond the GISP, to identify at-risk areas and improve treatment strategies.
www.thelancet.com/journals/lan...
www.thelancet.com/journals/lan...
Association between city-level sociodemographic and health factors and the prevalence of antimicrobial-resistant gonorrhea in the US, 2000–2019: a spatial–temporal modeling study
Geographic location and certain population-level characteristics including population
density and HIV prevalence could provide insight about the population-level risk of
AMR gonorrhea at a county-leve...
www.thelancet.com
February 7, 2025 at 11:22 AM
A Lancet study finds AMR gonorrhea in the US is prevalent in densely populated cities. It is associated with high HIV rates. Findings highligh the need for expanded surveillance beyond the GISP, to identify at-risk areas and improve treatment strategies.
www.thelancet.com/journals/lan...
www.thelancet.com/journals/lan...
Reposted
How do changes in antibiotic use, various pathways to resistance, multiple drug resistance, and more come together to shape the success and failure of bacterial lineages in a real-world epidemic? #AMR #microsky
A preprint: www.biorxiv.org/content/10.1...
(1/15)
A preprint: www.biorxiv.org/content/10.1...
(1/15)
Quantifying the impact of antibiotic use and genetic determinants of resistance on bacterial lineage dynamics
The dynamics of antimicrobial resistance in bacteria are informed by the fitness advantages conferred by genetic determinants of resistance in the presence of antibiotic pressure and the potential fit...
www.biorxiv.org
February 7, 2025 at 9:58 PM
How do changes in antibiotic use, various pathways to resistance, multiple drug resistance, and more come together to shape the success and failure of bacterial lineages in a real-world epidemic? #AMR #microsky
A preprint: www.biorxiv.org/content/10.1...
(1/15)
A preprint: www.biorxiv.org/content/10.1...
(1/15)
Reposted
Metagenomic Profiling of Drinking Water Microbiomes: Insights into Microbial Diversity and Antimicrobial Resistance https://www.biorxiv.org/content/10.1101/2025.02.03.636216v1
February 7, 2025 at 11:47 PM
Metagenomic Profiling of Drinking Water Microbiomes: Insights into Microbial Diversity and Antimicrobial Resistance https://www.biorxiv.org/content/10.1101/2025.02.03.636216v1
Reposted
The overview of AMR that you always wanted (someone else to write) - amazing!
Truly brilliant paper with great figures! @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
Truly brilliant paper with great figures! @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
Antimicrobial resistance: a concise update
Antimicrobial resistance (AMR) is a serious threat to global public health, with approximately
5 million deaths associated with bacterial AMR in 2019. Tackling AMR requires a multifaceted
and cohesive...
www.thelancet.com
February 5, 2025 at 10:02 AM
The overview of AMR that you always wanted (someone else to write) - amazing!
Truly brilliant paper with great figures! @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
Truly brilliant paper with great figures! @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
Reposted
We will never win a war against microbes No gorilla-cillin will ever come along to save us
from emergence of AMR Resistance is inevitable
Our article published
🆕🔥 @bradspellberg.bsky.social
Sustainable Solutions to Continuous Threat of Antimicrobial Resistance
academic.oup.com/healthaffair...
from emergence of AMR Resistance is inevitable
Our article published
🆕🔥 @bradspellberg.bsky.social
Sustainable Solutions to Continuous Threat of Antimicrobial Resistance
academic.oup.com/healthaffair...
January 24, 2025 at 12:16 PM
We will never win a war against microbes No gorilla-cillin will ever come along to save us
from emergence of AMR Resistance is inevitable
Our article published
🆕🔥 @bradspellberg.bsky.social
Sustainable Solutions to Continuous Threat of Antimicrobial Resistance
academic.oup.com/healthaffair...
from emergence of AMR Resistance is inevitable
Our article published
🆕🔥 @bradspellberg.bsky.social
Sustainable Solutions to Continuous Threat of Antimicrobial Resistance
academic.oup.com/healthaffair...