🧬 Why are we still studying genes in isolation when biology works as a network?
🔗 multiDEGGs: Single or Multiomic Differential Network Analysis for Biomarker Discovery and Feature Engineering for Predictive Modeling. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0001
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#Bioinformatics #Multiomics #MachineLearning #PrecisionMedicine #DataScience #Biomarkers
Orchestrating podman containers is just a baseline skill in the brave new world of bio packages compiled against cutting edge glibc :-/
Maybe I should look into ansible too while I'm at this. Does anyone actually use it in #bioinformatics context out there?
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🦠 Could algorithms help us outpace evolving superbugs?
🔗 Antibacterial Drug Discovery: Deep Learning Successes and Challenges through the Structural Biology Lens. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0008
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#AntibioticResistance #DrugDiscovery #ComputationalBiology #StructuralBiology #MachineLearning #Bioinformatics
If you’re into #Rstats and/or #bioinformatics, if you care about #ReproducibleResearch, consider helping out fellow #Guix hackers!
https://codeberg.org/guix-science/guix-cran-scripts/
The scripts above are what powers the automated imports of CRAN and Bioconductor as Guix channels, and they need ❤
🎉New preprint out today! We present rastair - an ultra-fast SNP and methylation caller for TAPS or 5-Base data. Rastair takes less than 1h to process e.g. a 50x 5-Base dataset, yet SNP call accuracy is nearly identical to GATK on WGS data 🔥
https://www.biorxiv.org/content/10.64898/2026.03.19.712983v1
Cytosine methylation is a crucial epigenetic mark that impact tissue-specific chromatin conformation and gene expression. For many years, bisulfite sequencing (BS-seq), which converts all non-methylated cytosine (C) to thymine (T), remained the only approach to measure cytosine methylation at base resolution. Recently, however, several new methods that convert only methylated cytosines to thymine (mC→T) have become widely available. Here we present rastair, an integrated software toolkit for simultaneous SNP detection and methylation calling from mC→T sequencing data such as those created with Watchmaker's TAPS+ and Illumina's 5-Base chemistries. Rastair combines machine-learning-based variant detection with genotype-aware methylation estimation. Using NA12878 benchmark datasets, we show that rastair outperforms existing methylation-aware SNP callers and achieves F1 scores exceeding 0.99 for datasets above 30x depth, matching the accuracy of state-of-the-art tools run on whole-genome sequencing data. At the same time, rastair is significantly faster than other genetic variant callers, processing a 30x depth file takes less than 30 minutes given 32 CPU cores on an Intel Xeon, and half as long when a GPU is available. By integrating genotyping with methylation calling, rastair reports an additional 500,000 positions in NA12878 where a SNP turns a non-CpG reference position into a "de-novo" CpG. Vice-versa, rastair also identifies positions where a variant disrupts a CpG and corrects their reported methylation levels. Rastair produces standard-compliant outputs in vcf, bam and bed formats, facilitating integration into downstream analyses pipelines. Rastair is open-source and available via conda, Dockerhub, and as pre-compiled binaries from https://www.rastair.com. ### Competing Interest Statement Pascal Hertleif is a employee and owner of Softleif AB, a software development company. All other authors declare no competing financial interests. Ludwig Institute For Cancer Research
Dear colleagues, as a former speaker at an ISMB conference, I can only *HIGHLY RECOMMEND* to stay away from this years' installment of "ISCB's Annual Flagship Meeting".
Already regsistered? There is still time: "Last day for full refund upon cancellation (You have until 23:59 Anywhere on Earth) *no extensions* ISMB 2026 March 31, 2026"
ISCB still has the original twitter logo on their webpage to show how out of touch with reality and recent developments it is. Shameful.
Hi everyone 🖖
If you are thinkging about using #nanopore for genomic surveillance in #hospitals, but don't have the #bioinformatics nor command-line skills, don't let that put you off.
'Modernising Medical Microbiology', at @NDMOxford in #Oxford, has developed `OxBreaker': a graphical tool that can help identify budding #outbreaks by #healthcare professionals without having to upload your data to external servers and compromise patient privacy. Worth a read 👇
Real-time genomic surveillance may mitigate the spread of health-care-associated infections, but whole-genome sequencing costs and the need for specialised expertise constrain its wide implementation in public health. Here we present ‘ OxBreaker ’, an automated and species-agnostic pipeline optimised for the high-resolution analysis of bacterial and plasmid genomes sequenced via Oxford Nanopore Technologies (ONT). ‘ OxBreaker ’ streamlines the transition from raw reads to phylogenetic inference through automated reference selection and high-accuracy variant calling. It is accessible via a graphical user interface (GUI) that can be easily installed locally and operated by non-specialists. Benchmarking against technical and biological replicates of high-priority pathogens demonstrates high accuracy, with false positive variant rates reduced to 0–4 single-nucleotide polymorphisms (SNPs) for common species. We further validated the pipeline by accurately characterising previously published clonal and plasmid-mediated outbreaks, reproducing established phylogenies with improved accessibility. By providing a stable, scalable, open-source offline-compatible solution that matches the resolution of short-read platforms while maintaining the speed of long-read technology, ‘ OxBreaker ’ is designed to facilitate the adoption of local, real-time genomic surveillance for frontline infection prevention and control. ### Competing Interest Statement The authors have declared no competing interest. NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, NIHR207397 NIHR Biomedical Research Centre, Oxford, GB
RE: https://mastodon.uy/@almati/116279193867252180
«For the sake of the safety of our community and in the name of genuine unity amongst mathematical scientists across the globe, we the undersigned commit not to participate in the ICM if it is to be held in the United States.»
Which got >1300 signatures.
I wonder if anyone in the #bioinformatics / computational biology community has mounted something similar in face of #ISMB2026 in Washington, DC.
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