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 a unique environment where academia meets industry. Two doctoral students, Yalan Bi, and Juan Francisco Cervilla, have recently collaborated with the BioBam team.
Meet the candidates: Yalan Bi and Juan Franciso Cervilla
Yalan Bi, a PhD student at the Max Planck Institute for Molecular Genetics, used her time at BioBam to explore the integration of long-read transcriptomics tools with OmicsBox. During her secondment, she analyzed datasets generated by PacBio and Oxford Nanopore sequencing technologies. She worked with tools such as minimap2, IsoQuant, FLAIR, and SQANTI3 for transcriptome identification and quality control, as well as OmicsBox’s functional annotation modules like Blast2GO and InterProScan.
“For the last two months, I have been on secondment to Biobam Bioinformatics, the host institution of another LongTREC Fellow, Fabian. It’s a great pleasure to have the opportunity to learn how a bioinformatics company works and how it supports scientific research by providing user-friendly end-to-end data analysis software, OmicsBox. Various lrRNA-seq analysis tools are integrated and well implemented in OmicsBox, which is easy and simple to use through the wizard. The team’s collaborative spirit and support have made my experience here valuable.”
Juan Francisco Cervilla, a PhD student at the Earlham Institute, focused his time at BioBam on improving the evaluation of cell clustering in single-cell RNA sequencing data. He explored various publicly available tools and metrics, including the silhouette score, ROGUE score, and the recently developed Poem R package. His work highlighted the need for a multi-metric approach to accurately define the number of cell types in complex datasets.
“For two months, I had the pleasure of working with Marta at BioBam to dive deeper into the question of how to assess how many cell types are present inside a sample using quantitative metrics. It has been a great experience to be part of BioBam for a brief time. Experiencing the daily routine inside a software company and interacting with BioBam members has been a helpful and enjoyable experience for me and will have a positive impact on my future.”
BioBam’s Commitment to training the next generation of computational biologists
At BioBam, we are dedicated to simplifying bioinformatics for researchers worldwide. Our role in LongTREC is in line with this mission by bringing cutting-edge lrRNA-seq analysis to the community in an accessible, user-friendly way. As a proud partner in the LongTREC network, BioBam is committed to supporting the next generation of scientists and fostering innovation in transcriptomics.
We look forward to future collaborations that will drive progress in this transformative field.
