Every time I submit files to ENA I forget how I did it the previous time. So I have written up a guide to my future myself of how I normally approach it. Maybe it might be useful for someone else. padpadpadpad.netlify.app/posts/ena_fi...
Sergi Arredondo-Alonso
@arredondo.bsky.social
Postdoc, Scientia Fellow at Jukka Corander's group (University of Oslo). Microbial and plasmid genomics! Main interests in bioinformatics, data science and everything in the middle.
Our latest paper is out. The brainchild of @drrebeccajhall.bsky.social We had shown how different E. coli strains respond to the same MDR plasmid. Here we show how one strain responds to different MDR plasmids journals.asm.org/doi/10.1128/...
Multidrug resistance plasmids commonly reprogram the expression of metabolic genes in Escherichia coli | mSystems
The increase in infections that are resistant to multiple classes of antibiotics, including those isolates that carry carbapenamases, beta-lactamases, and colistin resistance genes, is of global conce...
journals.asm.org
Our latest on phage-plasmids(PP) is out! Two main findings. PP recombine more with (other) plasmids and phages than the latter, thereby connecting them. PP can become just phages or plasmids, which may then transition to be conjugative. All the world’s an MGE! www.nature.com/articles/s41...
Check out our latest preprint! We explore the application of Nanopore Adaptive Sampling (NAS) for serotyping Streptococcus pneumoniae, and develop a new graph-based tool, GNASTy (pronounced ‘nasty’), to increase NAS sensitivity for detecting novel unobserved serotypes.
bioRxiv Genomics@biorxiv-genomic.bsky.social · 2y agoGraph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples https://www.biorxiv.org/content/10.1101/2024.02.11.579857v1
We have published a manuscript describing a software tool to reduce ambiguity and improve interpretability in microbial GWAS, called panfeed. Here's a quick explainer: www.microbial-pangenomes-lab.org/2023/11/09/M... And here's the link to the paper: www.microbiologyresearch.org/content/jour...
Reduced ambiguity and improved interpretability of bacterial genome-wide associations using gene-clu...
The wide adoption of bacterial genome sequencing and encoding both core and accessory genome variation using k-mers has allowed bacterial genome-wide association studies (GWAS) to identify genetic var...
microbiologyresearch.org
A rugged yet easily navigable fitness landscape -in Science from Andreas Wagner www.science.org/doi/10.1126/...
Our latest paper is out now. The brilliant Chris Connor’s entire PhD in one paper. And I hope a new avenue of research opened in MDR E. coli journals.plos.org/plosbiology/... 1/n
Have you wondered if some E. clones are so successful because of their plasmids? www.biorxiv.org/content/10.1... A combination of bioinf and lab work showed that some plasmids have coexisted for centuries, and that a specific colicin gene is able to kill other clones paving their way for success!
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!
bioRxiv goes big on Bluesky: accounts for all subject categories now available (Please Reskeet) connect.biorxiv.org/news/2023/09...
We should treat methods in computational biology more like the wet lab, with positive and negative controls, and 'replication' with different inputs and parameters. Many methods rely on heuristics and even if not, objectives are typically so nuanced that provable correctness/optimality do not help.
We have two Prof-level posts open at IMI Birmingham: Microbial Genomics www.jobs.ac.uk/job/DBJ457/c... Respiratory Infection Biology www.jobs.ac.uk/job/DBJ427/c... Deadline is 30 Sept! Email @alanmcn1.bsky.social or me with questions
skANI looks like an impressive drop-in replacement for FastANI: www.nature.com/articles/s41... github.com/bluenote-157...
Fast and robust metagenomic sequence comparison through sparse chaining with skani - Nature Methods
skani achieves fast calculation of average nucleotide identity (ANI) between metagenome-assembled genomes (MAGs), with improved robustness against incomplete and fragmented MAGs.
nature.com
A reminder we have two completely open search prof posts going the IMI at Birmingham Microbial Genomics: www.jobs.ac.uk/job/DBJ457/c... Infection Biology: www.jobs.ac.uk/job/DBJ427/c...
