📢 📢 📢 The registration for the NLSEB meeting 2024 is now open!!! Join us on April 23 at Akoesticum in Ede. There will be amazing keynote speakers, parallel presentation sessions, cultural intermezzo and much more!
Registration is open until March 5.
https://www.nlseb.nl/nlseb-meeting-2024
#Evolution #EvolutionaryBiology #NLSEB

We are looking for a colleague! Assistant/associate professor machine learning in bioinformatics at Wageningen University https://www.wur.nl/en/vacancy/assistantassociate-professor-machine-learning-in-bioinformatics.htm
#Bioinformatics #MachineLearning #WUR #AssistantProfessor #AssociateProfessor

#Bacteriophages encode anti-CRISPR proteins that inactivate bacterial #CRISPR-Cas systems, allowing successful invasion, replication & integration. This study shows that #antiCRISPR protein AcrIIA1 induces degradation of #Cas9 in human cells #PLOSBiology https://plos.io/3uUGAos

Is your tap water drinkable? Please boost if you can.. I wanna see something…

We are looking for a colleague! Assistant/associate professor machine learning in bioinformatics at Wageningen University https://www.wur.nl/en/vacancy/assistantassociate-professor-machine-learning-in-bioinformatics.htm
#Bioinformatics #MachineLearning #WUR #AssistantProfessor #AssociateProfessor

I'm very excited to share that our bacteriophage recovery tool, Phables has been accepted for publication in the OUP Bioinformatics journal.

Publication: https://doi.org/10.1093/bioinformatics/btad586
GitHub: https://github.com/Vini2/phables

A big thank you to everyone at FAME for supporting this work.
@BeardyMcJohnFace @npbhavya @griggo_grig @GB13Faithless @AbbeyHutton @Sassel1985 @linsalrob

#bioinformatics #metagenomics #bacteriophages #assembly #assemblygraph #graphtheory #flownetworks

@JacobPhD Email communication is clearly preferred over in person communication here

What could go wrong?
#genomics #bioinformatics
https://www.biorxiv.org/content/10.1101/2023.09.08.556814v1

The small variant calling benchmarking initiative of NGS-CN is published. Thanks a lot to all the contributors and @dfg_public
for the funding. Here is the paper: https://doi.org/10.12688/f1000research.140344.1
In short: we have implemented a continuous, driven benchmark of small genomic variant calling results: calls on @ZENODO_ORG
, evaluation via #snakemake inside @github
actions, reporting via #datavzrd, contribution via pull requests. (1/x)

I don't optimize my code because that just leads to disappointment.

Instead, I pessimize it.

evopython: a Python package for feature-focused, comparative genomic data exploration http://biorxiv.org/cgi/content/short/2023.09.02.556042v1?rss=1

If you are drafting figures for a scientific paper or presentation, remember that https://scidraw.io/ exists: a repository of free SVG cartoons for science.

#SciDraw is supported by the Sainsbury Wellcome Centre – @SWC_Neuro

All content on SciDraw is shared under creative commons license (CC-BY) unless stated otherwise.

#inkscape #SVG #science

That time of year......

@alexcc also I've noticed that general Google searches are often swamped with hits to Frontiers and MDPI journals, even if they are not the most relevant. It feels a bit like big mega journals broke Google.

One of the best papers of the year... you have to read this one.

Genome content predicts the carbon catabolic preferences of heterotrophic bacteria

https://www.nature.com/articles/s41564-023-01458-z

ProstT5 is a protein LLM with structure-aware embeddings. It was trained on structures (Foldseek’s 3Di) and AA sequences. It translates AA to 3Di for sensitive foldseek search and designs proteins by converting 3Di to AA.
Work by Michael Heinzinger et al. from the Rost lab.

Code: https://github.com/mheinzinger/ProstT5
📄 https://www.biorxiv.org/content/10.1101/2023.07.23.550085v1

We are looking for a bioinformatics PhD student - get in touch if you want to to apply state-of-the-art machine learning methods to gene sequences and protein structures to analyze evolutionary patterns
https://www.wur.nl/en/vacancy/phd-researcher-in-bioinformatics-investigating-protein-evolution-using-machine-learning.htm
#PhD #PhDPosition #Evolution #Genomics #ProteinStructure #MachineLearning

"I think many students, especially from countries with cultures completely different from our own, genuinely don’t know how to get in touch with potential supervisors. If you have a few seconds a day, replying to these types of emails might do quite a bit of good."

How to respond to generic emails requesting to work with you. Matthew Holden

https://mathemagicalconservation.wordpress.com/2019/10/04/how-to-respond-to-generic-emails-requesting-to-work-with-you/

What internet are you reading these days?

Here's the full list of websites and newsletters filling the "science blog" slot in my current reading list — which ones are you following, too, and which ones should I be following?

https://www.molecularecologist.com/2023/08/09/what-internet-are-you-reading-these-days/

#science #reading #blogging

Did you love (or indeed miss) #SMBE2023? Don’t despair: We’re already planning #SMBE2024. Save the date 7–11 July 2024 and see you then in Mexico! ⁦‪@SMBEmeetings‬⁩