Nick Sanderson
@nickdsandy.bsky.social
Bioinformatician interested in infection and immunity. Direct from sample sequencing for diagnostics. MMM group, NDM, Oxford University
It's 2025, why are all reference managers still crap.
October 24, 2025 at 8:19 AM
It's 2025, why are all reference managers still crap.
Reposted by Nick Sanderson
New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon
github.com/bede/deacon
Deacon: fast sequence filtering and contaminant depletion https://www.biorxiv.org/content/10.1101/2025.06.09.658732v1
June 13, 2025 at 1:25 PM
New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon
github.com/bede/deacon
Reposted by Nick Sanderson
Deacon: fast sequence filtering and contaminant depletion https://www.biorxiv.org/content/10.1101/2025.06.09.658732v1
June 13, 2025 at 1:46 AM
Deacon: fast sequence filtering and contaminant depletion https://www.biorxiv.org/content/10.1101/2025.06.09.658732v1
Reposted by Nick Sanderson
Terminal Genome Viewer (tgv), written in Rust github.com/zeqianli/tgv
May 27, 2025 at 5:37 PM
Terminal Genome Viewer (tgv), written in Rust github.com/zeqianli/tgv
@bedec.bsky.social presenting his deacon human filtering tool poster pitch at #ABPHM25
May 22, 2025 at 4:40 PM
@bedec.bsky.social presenting his deacon human filtering tool poster pitch at #ABPHM25
A new preprint from us. Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue. Where high host contamination is still a big issue. We find modest improvements in bacterial yield. But not enough to improve diagnostics
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue
Metagenomic approaches to diagnosis of prosthetic joint infections promise more accurate and more rapid diagnosis. However, the high host DNA to bacterial DNA ratio is a challenge. Nanopore adaptive s...
www.medrxiv.org
March 17, 2025 at 8:58 AM
A new preprint from us. Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue. Where high host contamination is still a big issue. We find modest improvements in bacterial yield. But not enough to improve diagnostics
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Reposted by Nick Sanderson
Come and work with us!
We are looking for a Medical Statistican.
Closing date: 4 Feb 2025
bit.ly/3E5JtaI
We are looking for a Medical Statistican.
Closing date: 4 Feb 2025
bit.ly/3E5JtaI
Job Details
bit.ly
January 20, 2025 at 11:38 AM
Come and work with us!
We are looking for a Medical Statistican.
Closing date: 4 Feb 2025
bit.ly/3E5JtaI
We are looking for a Medical Statistican.
Closing date: 4 Feb 2025
bit.ly/3E5JtaI
Reposted by Nick Sanderson
Come and work with us!
Programme Manager is a key central role that sets large strategic objectives and manages practical issues across the MMM Unit.
Grade 9, £55,636 - £64,228, deadline noon 6 Jan 25
bit.ly/4fGgnwv
Programme Manager is a key central role that sets large strategic objectives and manages practical issues across the MMM Unit.
Grade 9, £55,636 - £64,228, deadline noon 6 Jan 25
bit.ly/4fGgnwv
Job Details
bit.ly
November 26, 2024 at 9:14 AM
Come and work with us!
Programme Manager is a key central role that sets large strategic objectives and manages practical issues across the MMM Unit.
Grade 9, £55,636 - £64,228, deadline noon 6 Jan 25
bit.ly/4fGgnwv
Programme Manager is a key central role that sets large strategic objectives and manages practical issues across the MMM Unit.
Grade 9, £55,636 - £64,228, deadline noon 6 Jan 25
bit.ly/4fGgnwv
That’s it, now @nedboulting.bsky.social and @iandunt.bsky.social are here, I no longer need to look at X/twitter. This place is getting really good
November 11, 2024 at 7:28 PM
That’s it, now @nedboulting.bsky.social and @iandunt.bsky.social are here, I no longer need to look at X/twitter. This place is getting really good
Reposted by Nick Sanderson
Our latest paper now published in MGen. Long read surveillance identifying inter-species spread of a KPC plasmid in Birmingham
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
pQEB1: a hospital outbreak plasmid lineage carrying bla
KPC-2
While conducting genomic surveillance of carbapenemase-producing Enterobacteriaceae (CPE) from patient colonisation and clinical infections at Birmingham’s Queen Elizabeth Hospital (QE), we identified...
www.microbiologyresearch.org
September 2, 2024 at 3:28 PM
Our latest paper now published in MGen. Long read surveillance identifying inter-species spread of a KPC plasmid in Birmingham
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
Reposted by Nick Sanderson
Bats from the Colombian Caribbean Reveal a new subtype of Influenza A (H18N12) http://biorxiv.org/cgi/content/short/2024.08.25.609627v1
August 27, 2024 at 2:24 AM
Bats from the Colombian Caribbean Reveal a new subtype of Influenza A (H18N12) http://biorxiv.org/cgi/content/short/2024.08.25.609627v1
Our latest paper evaluating nanopore R10.4.1 sequencing for de novo assembly of bacterial pathogen genomes has been published in Microbial Genomics. We may no longer need hybrid assemblies
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing
Whole-genome reconstruction of bacterial pathogens has become an important tool for tracking transmission and antimicrobial resistance gene spread, but highly accurate and complete assemblies have lar...
www.microbiologyresearch.org
May 14, 2024 at 8:21 AM
Our latest paper evaluating nanopore R10.4.1 sequencing for de novo assembly of bacterial pathogen genomes has been published in Microbial Genomics. We may no longer need hybrid assemblies
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
Reposted by Nick Sanderson
New preprint: reprocessing 5million SARS-CoV-2 genomes to remove systematic errors (+thereby improve the phylogeny) and improve representation of genomes from the Global South. Huge amount of work esp. from Martin Hunt @angieshinrichs.bsky.social +collabs
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
May 1, 2024 at 3:20 PM
New preprint: reprocessing 5million SARS-CoV-2 genomes to remove systematic errors (+thereby improve the phylogeny) and improve representation of genomes from the Global South. Huge amount of work esp. from Martin Hunt @angieshinrichs.bsky.social +collabs
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Nick Sanderson
🌟 Dive into the fascinating world of plasmid evolution with Will Matlock's brilliant talk from our Oxford Pop Up event, now on YouTube 👉
'Gene essentiality shapes plasmid GC-content' youtu.be/snMchJCJQ5U
@wtmatlock.bsky.social
#ECR #MicrobialGenomics #MNGPopUp #Plasmids
'Gene essentiality shapes plasmid GC-content' youtu.be/snMchJCJQ5U
@wtmatlock.bsky.social
#ECR #MicrobialGenomics #MNGPopUp #Plasmids
William Matlock | Gene essentiality shapes plasmid GC-content
Plasmids are extrachromosomal replicons. When taken as a whole, plasmids are typically AT-rich compared to the host chromosome. However, the GC-content of in...
youtu.be
April 23, 2024 at 7:56 AM
🌟 Dive into the fascinating world of plasmid evolution with Will Matlock's brilliant talk from our Oxford Pop Up event, now on YouTube 👉
'Gene essentiality shapes plasmid GC-content' youtu.be/snMchJCJQ5U
@wtmatlock.bsky.social
#ECR #MicrobialGenomics #MNGPopUp #Plasmids
'Gene essentiality shapes plasmid GC-content' youtu.be/snMchJCJQ5U
@wtmatlock.bsky.social
#ECR #MicrobialGenomics #MNGPopUp #Plasmids
Reposted by Nick Sanderson
Reviewer help please- looking for someone with expertise in using bioinformatic analysis of ribosomal protein (L7/L12) structures to predict B- and T-cell antigenic epitopes as potential vaccine targets
March 19, 2024 at 3:03 PM
Reviewer help please- looking for someone with expertise in using bioinformatic analysis of ribosomal protein (L7/L12) structures to predict B- and T-cell antigenic epitopes as potential vaccine targets
Reposted by Nick Sanderson
First step in a community project to provide a uniformly assembled, annotated and searchable set of bacterial genomes, our preprint on our initial release of 1.9 million genome assemblies+taxonomic estimates. (figure compares with previous 661k dataset)
www.biorxiv.org/content/10.1...
#microsky
www.biorxiv.org/content/10.1...
#microsky
March 11, 2024 at 1:45 PM
First step in a community project to provide a uniformly assembled, annotated and searchable set of bacterial genomes, our preprint on our initial release of 1.9 million genome assemblies+taxonomic estimates. (figure compares with previous 661k dataset)
www.biorxiv.org/content/10.1...
#microsky
www.biorxiv.org/content/10.1...
#microsky
90% of slack usage is deciding when to go for lunch
February 26, 2024 at 11:53 AM
90% of slack usage is deciding when to go for lunch
Reposted by Nick Sanderson
Another preprint, this time on the accuracy of R10.4.1/kit14 using the new methylation aware basecalling model.
TL;DR we think it’s as good as hybrid assemblies now
www.biorxiv.org/content/10.1...
TL;DR we think it’s as good as hybrid assemblies now
www.biorxiv.org/content/10.1...
January 13, 2024 at 10:16 AM
Another preprint, this time on the accuracy of R10.4.1/kit14 using the new methylation aware basecalling model.
TL;DR we think it’s as good as hybrid assemblies now
www.biorxiv.org/content/10.1...
TL;DR we think it’s as good as hybrid assemblies now
www.biorxiv.org/content/10.1...
New preprint on our work using SureSelect target enrichment to sequence N. gonorrhoeae direct from sample www.medrxiv.org/content/10.1...
January 10, 2024 at 3:45 PM
New preprint on our work using SureSelect target enrichment to sequence N. gonorrhoeae direct from sample www.medrxiv.org/content/10.1...
New desk with an actual view and blueskies! Thanks for moving up in the world @scousemicrobe.bsky.social
January 10, 2024 at 3:06 PM
New desk with an actual view and blueskies! Thanks for moving up in the world @scousemicrobe.bsky.social
My new years resolution is to stop accepting review requests from for-profit journals
January 9, 2024 at 3:59 PM
My new years resolution is to stop accepting review requests from for-profit journals
Reposted by Nick Sanderson
📢 I have a funded PhD position available in Glasgow.
Functional genomics project with vaginal Lactobacillus. Please share
www.findaphd.com/phds/project...
Functional genomics project with vaginal Lactobacillus. Please share
www.findaphd.com/phds/project...
December 20, 2023 at 4:28 PM
📢 I have a funded PhD position available in Glasgow.
Functional genomics project with vaginal Lactobacillus. Please share
www.findaphd.com/phds/project...
Functional genomics project with vaginal Lactobacillus. Please share
www.findaphd.com/phds/project...
Reposted by Nick Sanderson
Come do a PhD with me at University of Glasgow.
3-year fully funded PhD for UK students.
Friend to Foe: Colonisation as an Entry Point for S. aureus Infectionhttps://www.findaphd.com/phds/project/fully-funded-friend-to-foe-colonisation-as-an-entry-point-for-staphylococcus-aureus-infection/?p166823
3-year fully funded PhD for UK students.
Friend to Foe: Colonisation as an Entry Point for S. aureus Infectionhttps://www.findaphd.com/phds/project/fully-funded-friend-to-foe-colonisation-as-an-entry-point-for-staphylococcus-aureus-infection/?p166823
December 11, 2023 at 3:13 PM
Come do a PhD with me at University of Glasgow.
3-year fully funded PhD for UK students.
Friend to Foe: Colonisation as an Entry Point for S. aureus Infectionhttps://www.findaphd.com/phds/project/fully-funded-friend-to-foe-colonisation-as-an-entry-point-for-staphylococcus-aureus-infection/?p166823
3-year fully funded PhD for UK students.
Friend to Foe: Colonisation as an Entry Point for S. aureus Infectionhttps://www.findaphd.com/phds/project/fully-funded-friend-to-foe-colonisation-as-an-entry-point-for-staphylococcus-aureus-infection/?p166823
Our work on the 2022-2023 flu season is out as preprint now www.medrxiv.org/content/10.1...
December 5, 2023 at 1:23 PM
Our work on the 2022-2023 flu season is out as preprint now www.medrxiv.org/content/10.1...