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Reference-free analysis of long-read RNA sequencing for non-model species

  With improvements in accuracy and steadily decreasing costs, long-read sequencing technologies, such as the platforms provided by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), have revolutionized the field of transcriptomics in recent years. Compared to short-read sequencing, which requires RNA fragmentation, long-read sequencing technologies can sequence RNA molecules in their entirety. This allows researchers to study the transcriptome

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OmicsBox in a New Scientific Publication on Sorghum Stress Responses

  At BioBam we are proud to see OmicsBox supporting scientific research. It is always rewarding to witness our users making significant advances in their respective fields and publishing their findings in esteemed journals such as Nature Scientific Data. These publications reinforce OmicsBox’s role as a valuable tool in bioinformatics, helping researchers analyze complex datasets with precision and efficiency. A

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LongTREC Secondments at BioBam: Advancing Long-Read Transcriptomics Through Collaboration

The LongTREC Marie Skłodowska-Curie Actions Doctoral Networks is an innovative European initiative that advances transcriptomics through Long-Read RNA Sequencing (lrRNA-seq). PhD candidates participating in LongTREC benefit from collaborative opportunities with public and industry partners, gaining invaluable expertise while developing advanced tools and workflows.  As part of the LongTREC network, BioBam hosts secondments and offers an unique environment where academia meets

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Cell Type Prediction with CellKb

Single-cell transcriptomics has revolutionized the way we understand complex biological systems. By enabling researchers to study gene expression at the resolution of individual cells, it uncovers cellular heterogeneity, reveals intricate developmental pathways, and provides insights into disease mechanisms. However, as powerful as single-cell RNA sequencing (scRNA-Seq) is, translating its immense data into meaningful biological insights remains a great challenge. One

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OmicsBox 3.4: CellKb’s Advanced Cell-Type Annotation

Improved Metagenomics Classification, and Enhanced Long-Read Transcriptomics Pipelines We proudly present the OmicsBox Version 3.4 release that introduces a range of enhancements designed to address the evolving needs of modern genomics and transcriptomics research. A key highlight of OmicsBox 3.4 is the integration of CellKb, a robust cell-type prediction tool for single-cell RNA sequencing (scRNA-Seq) analysis. CellKb streamlines scRNA-Seq annotation

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BioBam Joins BIOVALSA: Innovative Valorization of Plant Biomass Waste in Valencia for Functional Bioplastic Production

We are proud to contribute to BIOVALSA, an initiative supported by the Instituto Valenciano de Competitividad e Innovación (IVACE+i). This collaboration unites leading Valencian organizations such as AIMPLAS, VIROMII, Prime Biopolymers, UPV, and BioBam. The project focuses on transforming agricultural residues—such as rice straw and citrus prunings—into high-value bioplastics like polylactic acid (PLA) and polybutylene succinate (PBS), used across various

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BioBam at LongTREC meeting in Sweden

Our Teammate and PhD student Fabian Jetzinger, part of the LongTREC MSCA doctoral network, recently spent two months in Stockholm to collaborate with the developers of the isONpipeline tools. This pipeline, part of the OmicsBox Transcriptomics module, facilitates reference-free transcriptome reconstruction from Oxford Nanopore or PacBio long-read RNA sequencing data. Learning from their expertise and bringing in his own set

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OmicsBox in SEBiBC First Congress: End-to-end Single Cell Data Analysis Poster

  At BioBam we were thrilled to attend and sponsor the First Congress of Sociedad Española de Bioinformática i Biología Computacional (SEBiBC) in Valencia, a gathering of experts and researchers in bioinformatics and computational biology. Thanks to our colleague Marta Benegas, we had the opportunity to showcase our work advancing single-cell RNA sequencing (scRNA-Seq) analysis this year. Single-cell RNA sequencing

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Genome Completeness Assessment with BUSCO

Constructing a high-quality genome assembly is a complex and challenging process. De novo assemblies often suffer from fragmentation, gaps, and various types of assembly errors, which can compromise downstream analyses. Ensuring the completeness and accuracy of these assemblies is essential for robust biological insights. This is where BUSCO (Benchmarking Universal Single-Copy Orthologs) comes into play. BUSCO is a widely used

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