iiinova — where your digital self keeps evolving

Reposted by Sergi Arredondo-Alonso

Daniel Padfield @padpadpadpad.bsky.social · 11/03/2024

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...

1199

Reposted by Sergi Arredondo-Alonso

Eduardo Rocha @epcrocha.bsky.social · 21/02/2024

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...

03132

Reposted by Sergi Arredondo-Alonso

Sam Horsfield @samuelhorsfield.bsky.social · 12/02/2024

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.

195

Reposted by Sergi Arredondo-Alonso

Marco Galardini @mgalactus.bsky.social · 09/11/2023

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...

microbiologyresearch.org

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...

12618

Reposted by Sergi Arredondo-Alonso

Ákos T Kovács @evolvedbiofilm.bsky.social · 24/11/2023

A rugged yet easily navigable fitness landscape -in Science from Andreas Wagner www.science.org/doi/10.1126/...

1114

Reposted by Sergi Arredondo-Alonso

Alan McNally @alanmcn1.bsky.social · 18/10/2023

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

58043

Sergi Arredondo-Alonso @arredondo.bsky.social · 16/10/2023

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!

14021

Reposted by Sergi Arredondo-Alonso

Zamin Iqbal @zaminiqbal.bsky.social · 04/10/2023

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!

24856

Reposted by Sergi Arredondo-Alonso

Richard Sever @richardsever.bsky.social · 28/09/2023

bioRxiv goes big on Bluesky: accounts for all subject categories now available (Please Reskeet) connect.biorxiv.org/news/2023/09...

9285308

Reposted by Sergi Arredondo-Alonso

Wolfgang Huber @wkhuber.bsky.social · 27/09/2023

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.

66014

Reposted by Sergi Arredondo-Alonso

Willem van Schaik @wvschaik.bsky.social · 26/09/2023

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

02738

Reposted by Sergi Arredondo-Alonso

Alan McNally @alanmcn1.bsky.social · 05/09/2023

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...

01429