BioBam Bioinformatics

Missed our latest OmicsBox webinar on tracking pathway activity across time and conditions? The full recording is now on our YouTube channel. In the session, Marta (https://lnkd.in/eyb8Fr7c) walked through time-course gene expression analysis with maSigPro and pathway interpretation using transcriptomics data from a non-model Cladonia lichen. We showed how to find gene clusters with distinct expression patterns over time between conditions, and how OmicsBox pathway workflows add functional context to those dynamics. Watch the full demo whenever it suits you. https://lnkd.in/ekiM_PGr #OmicsBox #Bioinformatics #Transcriptomics #GeneExpression

Congratulations Ryuji Morizane and colleagues at Massachusetts General Hospital and Harvard Medical School on new work in Nature npj Biomedical Innovations. Morizane et.al. developed a scalable stirred-bioreactor method to mass-produce vascularized kidney organoids with human endothelial integration. Single-cell RNA sequencing and functional assays showed stronger nephron maturation, and implanted nephron sheets achieved in vivo glomerular filtration with size selectivity. OmicsBox supported the single-cell data analysis as well as the functional interpretation. https://lnkd.in/eX_-3MER #OmicsBox #Bioinformatics #Genomics #RegenerativeMedicine

Looking forward!

We are hosting a live OmicsBox webinar: Tracking Pathway Activity Across Time and Conditions. Our colleague Marta (https://lnkd.in/eyb8Fr7c) will guide a practical session on time-course gene expression and pathway interpretation with transcriptomics data from a non-model species. Using a Cladonia lichen dataset, we will show how maSigPro finds gene clusters with distinct expression patterns across time and conditions, and how pathway workflows in OmicsBox add functional context to those dynamics. The session starts with a short OmicsBox 4 introduction, then walks through the full workflow from expression changes to enriched pathways. No coding background needed. Tuesday, 23 June 2026 — two sessions: 9:30 or 18:30 CEST. Register: https://lnkd.in/ei8PNcAQ #OmicsBox #Bioinformatics #Transcriptomics #GeneExpression

Last Friday at the Innotransfer session on Bioinformatics at UPV's Ciudad Politécnica de la Innovación, our colleague Stefan presented BioBam and OmicsBox to a full room of researchers and industry people. After the talks there was time for one-to-one meetings and to catch up with colleagues and friends. Thank you to the Universitat Politècnica de València and the Innotransfer team for a very well-organised event. https://lnkd.in/esTniSXz #OmicsBox #Bioinformatics #Genomics #BioBam

Explore recent research studies that cited OmicsBox. From polar seas to coral reefs, these three publications demonstrate how OmicsBox helps researchers translate genomic data into biological insights. Liu et al. (Scientific Data, 2025) assembled a chromosome-level genome for the Arctic stout eelblenny (Anisarchus medius) and used OmicsBox for Gene Ontology assignment alongside BLAST, InterProScan, and KEGG: https://lnkd.in/eHbUz2Vk Zheng et al. (Scientific Data, 2025) published a chromosome-level genome for Phoxinus lagowskii, an Amur minnow central to cold-water aquaculture in China, with OmicsBox's Blast2GO for GO annotation: https://lnkd.in/ew34uUy4 Djamaa et al. (Frontiers in Physiology, 2026) compared coral larval proteomes across metamorphosis in Pocillopora acuta with the help of the OmicsBox Functional Analysis Module: https://lnkd.in/eTwmmEBq #Bioinformatics #OmicsBox #Blast2GO #Genomics #MarineBiology

Happy to present our new AI-Summaries! OmicsBox still runs the same trusted bioinformatics analyses you rely on for your end-to-end analysis. What is new are AI-powered result summaries: narrative reports that highlight the main findings when an analysis finishes. The core science does not change. Our team defines what matters for each analysis type, and the AI helps turn that into clear text so you can review outcomes faster and focus on what comes next. Our colleague Marta wrote about how this works on the BioBam blog, with examples from transcriptomics time courses and functional enrichment. https://lnkd.in/eACe_g-T #OmicsBox #Bioinformatics #Genomics #BioBam

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. OmicsBox 4.0 brings several new concepts, including CloudSync and AI summaries, together with many new analysis features and user experience improvements. Much of the work focuses on moving analysis and data to the cloud in a clear, transparent way. On the transcriptomics side, a highlight is gene co-expression analysis with integrated functional interpretation. The full release notes are on our blog: https://lnkd.in/ejgDNnvP #OmicsBox #Bioinformatics #Genomics #BioBam

OmicsBox in Action: Dr. Fagbohun et. al. at the Center for Agriculture and Natural Sciences, Wilmington College, recently published a multi-omics study on triple-negative breast cancer in Nature Cell Death Discovery (2026). He and his colleagues combined whole-genome sequencing, bulk RNA-seq, differential expression, functional enrichment, and variant-level interpretation on berry-derived gold nanoparticles in 4T1 cells. In a new OmicsBox in Action post on the BioBam blog, he describes how OmicsBox supported the project: DESeq2-based differential expression, interactive QC and plots, GO and pathway enrichment (including KEGG and Reactome), and variant annotation linked to transcriptomic changes. Full story here: https://lnkd.in/enM3jdSd Congratulations and a big thank you for sharing from the whole team here at BioBam! #OmicsBox #Bioinformatics #Genomics #Transcriptomics

Large FASTA or FASTQ files are normal in genomics work, but are somethimes tricky to handle. We published a short OmicsBox HowTo that walks you through splitting those files into smaller parts so you can move data, run tests on subsets and keep analyses practical. If you already use OmicsBox for routine workflows, this is a small utility guide you can keep in mind for the next oversized run. If you are newer to OmicsBox, it is also a straightforward example of how we handle these files without extra scripting. Read the guide: https://lnkd.in/eWANdcgD #OmicsBox #Bioinformatics #Genomics