Tag Archives: transcriptomics

The CBBL Organizes an Update Workshop on Omics Data Analysis at the UVic-UCC

Posted by 19 de December de 2025

The Computational Biochemistry and Biophysics Laboratory (CBBL), part of the Bioinformatics and Bioimaging Research Group (Bi-Squared) at the University of Vic – Central University of Catalonia (UVic-UCC), in collaboration with the Central Catalonia Institute for Health Research (IRIS-CC), organized the workshop “Update in Omics Data Analysis: genome structure, metagenomics and gene regulation”. The session provided a forum to discuss and review recent developments in omics data analysis, aimed at researchers, students, and professionals in the field.

Held shortly before Christmas at the Torre dels Frares Campus in Vic, the event brought together postdoctoral researchers who presented and discussed recent advances in key areas of bioinformatics, including genome structure, metagenomics, and gene regulation using large-scale omics datasets. The workshop concluded with a round-table discussion that encouraged dialogue on emerging challenges and future directions in biological data analysis.

The program featured presentations by:

This workshop aligns with IRIS-CC’s outreach and training initiatives and supports scientific exchange and skills development within the bioinformatics and bioimaging research community.

For more information, please visit the event webpage: Update in Omics Data Analysis: genome structure, metagenomics and gene regulation.

Roger Casals presents his doctoral research at scverse 2025

Posted by 1 de December de 2025

Last November, Roger Casals, PhD candidate at the Computational Biochemistry and Biophysics Lab (CBBL), travelled to Stanford University to take part in scverse 2025, one of the key gatherings for the single-cell and multi-omics community.

During the conference, Roger presented a poster with some of the latest results from his PhD. His project focuses on building gene regulatory networks from single-cell data to understand cell state transitions, a line of work that is becoming increasingly important as we try to make sense of complex biological systems.

Beyond the science, the conference gave Roger the chance to meet many members of the scverse community, discuss ideas in person, and learn from researchers developing cutting-edge tools. Topics like agentic AI and virtual cell models were especially exciting, forecasting us where the field is heading.

Roger’s participation was possible thanks to a travel grant from the conference, along with support from the Department of Biosciences (FCTE), the BI-Squared Group, and IRIS-CC.

 

The CBBL at the JBI2025

Posted by 24 de October de 2025

The CBBL was present in the XV Bioinformatics Symposium (JBI2025), that took place in Madrid on October 22nd-24th, hosted by the CNB/CSIC. The lab presented results on three research projects:

    • Topics Session #4 Single-Cell Omics. Talk by Roger Casals on “Mechanistic inference of cell state transitions via Boolean GRNs from single-cell data” Roger Casals Franch, Pau Badia-i-Mompel, Jordi Villà-Freixa, Julio Saez-Rodriguez, Jovan Tanevski, and Adrián López García de Lomana;

    • “A Bioinformatics Pipeline Reveals a Shared IκBα Interface for NF-κB and Histone Binding”, Martin Floor, Jordi Villà-Freixa, Joan Bertran and Lluís Espinosa; poster on the recent work published in Cell Reports; and
    • “Standard-of-Care Therapy Induces Phenotypic Reprogramming of Non-Malignant Oligodendrocytes in Glioblastoma“, Jing Yang, Jordi Villà-Freixa and Adrián López García de Lomana.

Roger Casals co-authors a Benchmarking study on Multimodal Gene Regulatory Networks

Posted by 27 de December de 2024

We are thrilled to announce the publication of a new preprint, “Comparison and evaluation of methods to infer gene regulatory networks from multimodal single-cell data”, led by Pau Badia-i-Mompel as the first author, with contributions from Roger Casals and the Saez-Lab team.

In this work, we present Gene Regulatory nETwork Analysis (GRETA), a comprehensive framework designed to infer, compare, and evaluate gene regulatory networks (GRNs). Using GRETA, we benchmarked both multimodal and unimodal GRN inference methods, setting a foundation for future advancements in the field.

GRETA graphical abstract

This preprint is an important step in understanding multiomic gene regulatory networks and reflects the collaborative efforts of the Saez-Lab, under the leadership of Julio Saez-Rodriguez.

Check out the results and tools here:

If you want to stay updated or join the discussion, check out our announcement on BlueSky.

 

 

Roger Casals presents his immunotherapy research at the SEBiBC congress

Posted by 19 de October de 2024

Roger Casals has participated in the first congress of the Spanish Society of Bioinformatics and Computational Biology (SEBiBC), presenting the poster entitled “Trajectory inference and transcriptional regulators of T cell response upon immunotherapy in non-melanoma skin cancer”. The congress, held at the Fira de Valencia from October 16 to 18, brought together prominent researchers in the field of bioinformatics and computational biology, consolidating itself as a success in its first edition.

In his presentation, Casals presented the results of a study that allows mapping the differentiation trajectories of T cells in the tumor microenvironment. Through a comprehensive functional analysis, the work identifies key transcription factors in the modulation of the immune response after immunotherapy in cases of non-melanoma skin cancer. These findings may be a basis for better understanding the mechanisms of response to immunotherapy, opening doors to future personalized therapies.

The work of Roger Casals has been possible thanks to the collaboration with Lara Nonell, expert in bioinformatics from the Vall d’Hebron Institute of Oncology (VHIO), as well as with the support of her doctoral co-tutors, Adrián López García de Lomana from the University of Iceland and Jordi Villà-Freixa.

Roger Casals, selected to present a poster for the Award of Computing in Oncology (VHIO)

Posted by 22 de February de 2024

Roger Casals, UVIC-UCC PhD student in the Bioinformatics program and member of the CBBL, was selected to present the poster “Trajectory Inference Methods Comparison in Cancer Immunotherapy” at the first edition of the Award of Computing in Oncology, organized by the Vall d’Hebron Institute of Oncology (VHIO).

The contest was held on February 21, 2024 at the Casa Convalescència in Barcelona and was a meeting to recognize the best master’s thesis in computational science at national level.

Roger works in the analysis of “single-cell” transcriptomics data, which allows analyzing gene expression at scale individual cells, revealing crucial details about biology.

This work has been supervised by Lara Nonell i Mazelon (VHIO), Jordi Villà i Freixa (UVic-UCC / IRIS-CC) and Adrián López García de Lomana (UVic-UCC, HI), and has had the support of the “Programa Investigo AGAUR” (2023 INV-200003TG1) at as a technologist at the IRIS-CC.