Tag Archives: phd

Annual Conference of the Interuniversity PhD Program in Bioinformatics Held at UVic-UCC for the Second Time

Posted by 11 de February de 2026

Conference Highlights

Last Friday, February 6, UVic-UCC hosted the annual conference of the Interuniversity PhD Program in Bioinformatics. The program includes students from eight Catalan universities (UAB, UB, UOC, UPC, UdL, URV, UdG, and UVic-UCC) and is promoted by the Bioinformatics Barcelona association. This event—highly relevant within the program and previously held at our university in 2023—allows students from all participating universities to present their research in a scientific conference format. This year, close to one hundred submissions were received. Of these, eight were selected for oral presentations, while the remainder were presented as posters. The conference also featured two invited talks. Dr. Elisenda Bonet-Carne, CEO and co-founder of FetalLife, SL, presented the company’s research, which focuses on developing equipment for the care of premature infants. Dr. Eduard Ocaña, Ramón y Cajal researcher at the Universitat Oberta de Catalunya, presented results from his studies on the origin of eukaryotes.

Organization, Support, and the Role of Bioinformatics

The conference received financial support from the Doctoral Schools of UVic-UCC and UAB, as well as from IRIS-CC through its Bioinformatics and Bioimaging Research Area (ARBB). It was organized by the program’s local node, coordinated by Jordi Villà i Freixa in collaboration with the academic committee of the doctoral program and a technical secretariat formed by PhD students Roger Casals, Gabriel Ruiz, Sergi Soldevila, and Jing Yang, together with FCTE administrative staff member Yolanda Tristancho. The conference was inaugurated by the program coordinator, Dr. Margarida Julià-Sapé (UAB), alongside the Director of the UVic-UCC Doctoral School, Dr. Marta Otero, and the Dean of the FCTE and coordinator of BI-SQUARED, Dr. Malu Calle.

Bioinformatics focuses on studying living systems through the analysis of biological data and, often, through computational simulation. Research in this field has grown exponentially over recent decades as increasingly efficient techniques have been developed to generate experimental genomic, transcriptomic, proteomic, metabolomic, and other types of data. Bioinformatics sits at the intersection of mathematics, statistics, physics, chemistry, biology, medicine, and computer science, aiming to describe life quantitatively and to predict outcomes within its immense complexity.

As Dean Calle recalled at the opening of the conference, these days mark the 25th anniversary of the publication—through two articles in Science and Nature by a public consortium and a private consortium—of the first complete draft of the human genome, a milestone that opened a new era in bioinformatics research. Over the last decade, advances in machine learning and artificial intelligence applied to bioinformatics have provided exceptional momentum, enabling increasingly ambitious exploration of the life sciences and the development of biotechnology in all its dimensions.

Program Outlook and Future Challenges

This interuniversity PhD program builds on the high-level master’s degrees offered by Catalan universities, particularly the MSc in Omics Data Analysis offered by the FCTE, and positions our country as an international reference center in bioinformatics. As emphasized by Dr. Marta Otero, the program’s main future challenges include consolidating the excellence of the theses developed within it while also increasing enrollment.

This will require greater internationalization by seeking global alliances to compete for European funding to finance predoctoral contracts and by promoting mobility stays for current PhD candidates. It will also involve encouraging thesis projects aimed at addressing emerging challenges through interdisciplinary co-supervision, and boosting the development of theses with an industrial doctorate distinction to accelerate the program’s social and economic impact.

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.

 

PhD Student Nayanika Das Begins Research Visit at the University of Groningen

Posted by 10 de October de 2025

We are delighted to share that our PhD student Nayanika Das has embarked on a research visit to the laboratory of Prof. Gerard Roelfes at the University of Groningen, The Netherlands. This visit marks an exciting step forward in her doctoral work on understanding and optimizing the function of enzymes, this time for proteins containing artificial amino acids.

During her stay, Nayanika will collaborate closely with the Roelfes group to investigate the incorporation of the noncanonical amino acid para-aminophenylalanine (pAF) into the nonenzymatic protein scaffold LmrR. Remarkably, this modification transforms LmrR into a proficient and stereoselective artificial enzyme (LmrR_pAF) — an elegant example of how chemical innovation can endow proteins with entirely new catalytic functions.

Nayanika’s research will combine experimental validation in the laboratory with computational modeling efforts. Specifically, she will contribute to the development of an Empirical Valence Bond (EVB) model aimed at uncovering the molecular details of the mechanism of action of pAF in the reactions catalyzed by LmrR_pAF. By integrating theoretical and experimental approaches, her work will help elucidate how artificial amino acids expand the functional landscape of proteins and open new avenues for biocatalysis and synthetic biology.

We wish Nayanika a productive and inspiring stay in Groningen and look forward to the exciting results that will emerge from this collaboration with the Roelfes Lab.

New article on data analysis of freshwater pond’s nutrients in response to environmental variables

Posted by 11 de June de 2025

Ponds are vital freshwater ecosystems that support rich biodiversity and provide important services to people and nature. However, they are still often overlooked in studies on land use and climate change. To better understand how these small but important water bodies are affected, we have collaborated in the data analysis from 240 ponds, surveyed across eight countries—seven in Europe and one in South America (Uruguay).

The study, published in the journal Hydrobiologia (Bartrons, 2025), examined how a combination of pond-specific features, surrounding land use, livestock activity, and climate patterns influence the concentrations of key nutrients, such as nitrogen and phosphorus. Results showed that the structure of the ponds themselves plays a major role: shallow ponds and those that dry out quickly (short hydroperiods) tended to have higher levels of both nitrogen (TN) and phosphorus (TP). In contrast, deeper ponds that stratify thermally (form temperature layers) had higher nitrogen levels, likely due to internal recycling of nutrients.

The first two ordination axes of a Principal Component Analysis (PCA) based on standardized mean annual physical and chemical variables in the ponds (points). The larger symbols in the plot represent the centroids (group means) for each country, indicating the central tendency of that group in the ordination space (Bartrons, 2025).

The surrounding landscape also mattered. Ponds in agricultural areas had elevated nutrient levels, while those near forests showed lower phosphorus concentrations. Seasonal changes further shaped these patterns—phosphorus levels were typically highest in summer, while nitrogen was diluted during wetter, cooler periods, especially in semi-permanent ponds.

Overall, the study led by our collaborator Mireia Bartrons, from the Aquatic Ecology Research Group at the FCTE, and with participation of two members of the lab including PhD student Jing Yang as a co-first author, highlights how pond health is shaped by a complex interplay of physical characteristics, land use, and climate. These findings emphasize the urgent need to better protect and manage ponds within broader environmental and land-use policies.

Cite:
(Bartrons, 2025) Bartrons, M., Yang, J., Cuenca‑Cambronero, M. et al. Why ponds concentrate nutrients: the roles of internal features, land use, and climate. Hydrobiologia (2025). https://doi.org/10.1007/s10750-025-05907-0

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.

CDK6 is activated by the atypical cyclin I to promote E2F‐mediated gene expression and cancer cell proliferation

Posted by 1 de June de 2023

A paper has been just published in Molecular Oncology in a collaboration led by our colleagues Josep Clotet and Mariana P. Ribeiro (UIC Barcelona) on the interaction of CDK6 with the atypical cyclin I. The CBBL has contributed with molecular modelling analysis of the interface region. Martin Floor and Pau MArc Muñoz, past members of the CBBL, did all the computational work.

Abstract: Cyclin-dependent kinases (CDKs), together with their cyclin partners, are the master cell cycle regulators. Remarkably, the cyclin family was extended to include atypical cyclins, characterized by distinctive structural features, but their partner CDKs remain elusive. Here, we conducted a yeast two-hybrid screen to identify new atypical cyclin–CDK complexes. We identified 10 new complexes, including a complex between CDK6 and cyclin I (CCNI), which was found to be active against retinoblastoma protein. CCNI upregulation increased the proliferation of breast cancer cells in vitro and in vivo, with a magnitude similar to that seen upon cyclin D upregulation, an effect that was abrogated by CDK6 silencing or palbociclib treatment. In line with these findings, CCNI downregulation led to a decrease in cell number and a reduction in the percentage of cells reaching S phase. Finally, CCNI upregulation correlated with the high expression of E2F target genes in large panels of cancer cell lines and tissue samples from breast cancer patients. In conclusion, we unveil CCNI as a new player in the pathways that activate CDK6, enriching the wiring of cell cycle control..

Workshop of the Interuniversity PhD program in Bioinformatics

Posted by 24 de January de 2023

On February 3rd, the PhD program in Bioinformatics, a joint program of the UAB, UB, UdG, UdL, UOC, UPC, URV and UVic-UCC universities, in collaboration with the Bioinformatics Barcelona association (@BiBcn), will meet at the UVic-UCC Aula Magna to host its annual workshop. In this event, along with presentations and poster sessions by the current students of the program, we will enjoy keynote talks by Dr. Mar Albà (IMIM/ICREA) and Dr. María Ortiz (Bristol Myers Squibb).

You can find the up-to-date details of the workshop at https://mon.uvic.cat/cbbl/outreach/phdworkshop2023/

Attendance is free, but registration is needed. If you plan to attend, please, fill in the form at https://forms.gle/qjub49uRb5JHnvM56.

We hope seeing you in Vic for this good networking event, with topics on

  • Omics and molecular bioinformatics
  • Biomolecular modelling and simulation
  • Systems and synthetic biology
  • Data science in bioinformatics
  • Biostatistics and mathematical modelling in bioinformatics

#phdbioinfo2023