BioBam

Could not join us live for Tracking Pathway Activity Across Time and Conditions? The webinar is on our YouTube channel now.

Our colleague Marta led the session on time-course RNA-seq with maSigPro, comparing gene expression patterns between conditions, and pathway analysis for non-model organisms. We used a real Cladonia lichen dataset and ran everything in OmicsBox, from dynamic gene clusters to enriched pathways.

Grab a coffee and watch at your own pace.

https://www.youtube.com/watch?v=V2lOSOKqE7s

Congratulations to Ryuji Morizane and the team at Harvard Medical School and Massachusetts General Hospital.

Their new paper in Nature npj Biomedical Innovations describes a way to scale up vascularized kidney organoids in stirred bioreactors, with more than 50 times better production efficiency than conventional culture. The organoids mature further, vascularize with human endothelia, and can filter in living mice.

OmicsBox was used for single-cell data analysis and further functional analysis and interpretation.

Read the paper: https://www.nature.com/articles/s44385-025-00063-5

On 23 June, our colleague Marta leads a new OmicsBox webinar on time-course RNA-seq and pathway interpretation.

We will work through a real transcriptomics dataset from a Cladonia lichen: maSigPro to find gene clusters that change over time, compare patterns between conditions, and connect the results to pathway enrichment for non-model organisms. There is a short look at OmicsBox 4 first, then the practical demo from expression dynamics to biological insight.

Pick the session that fits your day: 9:30 or 18:30 CEST.

Register here: https://events.zoom.us/eo/AvwSOjeTUdUKPu_RiZSdcVvUayLFkbODlfbzAdZgx9WtMwRcl6Dm~AggLXsr32QYFjq8BlYLZ5I06Dg/events

Last Friday we joined the Innotransfer session on Bioinformatics at UPV's Ciudad Politécnica de la Innovación.

Our colleague Stefan presented BioBam and OmicsBox. Great talks and a very well organised event. After the presentations there were one-to-one meetings, and time to catch up with collegues and friends. Well done.

Muchas gracias to the UPV and the Innotransfer team for the invitation and organization.

https://innotransfer.org/evento/bioinformatica/

Three new OmicsBox cCitation about polar fish, freshwater aquaculture, reef science!!

Researchers in China mapped the Arctic stout eelblenny genome (a climate indicator in Arctic coastal waters) and annotated genes with the Blast2GO Methodology.

A group from France profiled coral larvae as they settle on the reef and used OmicsBox to sort differential proteins into immunity, sensing, and skeleton-related pathways.

Another Chinese team released a high-quality genome for the Amur minnow Phoxinus lagowskii, usign the rich Gene Ontology functionalities.

Big result tables are useful until you need to explain what they mean. OmicsBox can now turn key outcomes into AI-powered result summaries: short narrative reports when an analysis finishes.

Same trusted analyses, same control over your plots and data. The summaries are predefined for each analysis type to what counts as a main finding. The AI helps write it up so you spend less time on manual wrap-up.

Our colleague Marta walks through it on the blog, with examples from time-course RNA-seq and GO enrichment.

https://www.biobam.com/omicsai_result_summaris/

We are happy to announce OmicsBox 4.0.

This release has been a long time in the making, and we hope you feel it was worth the wait. CloudSync and AI summaries are among the new ideas, along with many analysis and UX improvements, with a clear focus on running work in the cloud without losing visibility. Gene co-expression with integrated functional analysis is a transcriptomics highlight.

Read the full release notes on our blog: https://www.biobam.com/omicsbox-4-0-release/

Subscribe Discover our subscription plans and configure your own. OmicsBox is an all-in-one, user-friendly bioinformatics software solution.

OmicsBox in Action: Oladapo Fagbohun at Wilmington College (Center for Agriculture and Natural Sciences). He and his colleagues published a triple-negative breast cancer paper in Cell Death Discovery, and he explains on the blog how OmicsBox fit the pipeline: RNA-seq from count matrices through differential expression and enrichment, plus variant annotation across genomic and transcriptomic layers.

https://www.biobam.com/omicsbox-in-action-triple-negative-breast-cancer-research

Big thank you for sharing, from the OmicsBox team!

Need to sub-sample FASTA or FASTQ files? We added a simple OmicsBox guide on splitting them into smaller pieces so uploads and test stay manageable. Read it here: https://www.biobam.com/howto-split-fasta-fastq-files/

We published a deep dive for anyone who works with polyploid RNA-seq and wondered which haplotype does what. Sounds simple but is actually tricky to do: phased genomes so reads know where they belong, long reads so assignment is more trustworthy, then careful bioinformatics so quantification stays fair between haplotypes. Nadja wrote this blog arround a sweetpotato example and shows this type of analysis end to end in a tough genome.

https://www.biobam.com/allele-specific-expression-with-long-read-rna-seq-and-phased-reference-genomes/