The human gut microbiome plays a central role in host physiology, contributing to digestion, metabolism, and immune regulation. It is increasingly recognized as a promising therapeutic target, with interventions ranging from dietary modulation and probiotics to fecal microbiota transplantation and live biotherapeutics.

Despite substantial progress, the traditional ecological framework used to associate microbiome composition with host phenotypes is reaching its limits. While marker gene (16S rRNA) sequencing has long served as a cost-effective and informative standard, the field is undergoing a transition toward shotgun metagenomics, which provides comprehensive access to the microbial gene repertoire along with functional insights and strain-level resolution.

In this work, we leverage advances in shotgun metagenomics together with modern machine learning to develop predictive and interpretable models of the gut microbiome. We explore function prediction using deepFRI, highlighting the advantages of homology-independent approaches that incorporate structural information and enable broad coverage of microbial genes. Building on this, we introduce GUT-FORMer, a foundation model framework that integrates taxonomic and functional signals into a unified representation of the microbiome.

Together, these approaches demonstrate the potential of combining large-scale metagenomic data with representation learning to improve microbiome-based inference. I will present recent results illustrating how such models can support robust diagnostic strategies and provide new insights into host-microbiome interactions, with implications for personalized interventions.

Dr. Tomasz Kościółek is the Head of the Structural and Functional Genomics research team at the Sano Centre for Computational Medicine in Kraków; Assistant Professor at the Faculty of Computer Science of the AGH University of Kraków; co-founder and Chief Scientific Officer of onebiome Sp. z o.o.; member of the Polish Academy of Sciences’ Young Academy (term 2024–2029); and Board Member of the Polish Bioinformatics Society for the 2026–2028 term.

He obtained an M.Sc. in Chemistry from the Jagiellonian University and a Ph.D. in Biological Sciences from University College London (UK). He completed a postdoctoral fellowship in Rob Knight’s group at the University of California San Diego (USA). From 2019 to 2023, he led a bioinformatics group at the Małopolska Centre of Biotechnology, Jagiellonian University in Kraków, and from 2023 to 2024 he was a university professor in the Department of Data Engineering and Exploratory Data Analysis at the Silesian University of Technology in Gliwice. He has received grants from NAWA, NCN, FNP and NCBR. He is the author of over 30 peer-reviewed scientific publications, including in Nature, Nature Biotechnology, and Nature Communications, among others, and is a co-inventor on three patent applications.

He works on developing and applying computational methods to better understand the function and dynamics of the human gut microbiome. He contributed to the development of widely used microbiome analysis tools – QIIME 2 and Qiita – and also works on state-of-the-art machine learning and statistical methods for protein function prediction (deepFRI) and for modeling dysbiosis and microbiome dynamics. The goal of his group is to build a multi-level understanding of the microbiome – from genes, through structures, to functions and therapies.

The transition toward a more sustainable and ethical food system demands innovative approaches to protein production. Cultivated meat and seafood have emerged as a compelling solution, yet significant scientific and technological barriers remain between laboratory-scale cell culture and commercially viable manufacturing. The Cellular Agriculture team within the Bioprocess Engineering group at Wageningen University & Research (WUR) is addressing these challenges through an integrated research program spanning the full production pipeline, from cell line development and bioprocess scale-up to final product formulation.

Active projects include the scale-up of cultivated fish fat processes, the development of octopus muscle cell lines as a novel model organism, and the engineering of sustainable, animal-free culture media using microalgae hydrolysates as amino acid sources. The team is also advancing plant-based microcarrier technology to support anchorage-dependent cell growth at scale. Underpinning all experimental work is an integrated bioprocess design framework that combines cell and bioreactor modelling with techno-economic and environmental assessments, enabling systematic evaluation of process innovations before costly scale-up.

Alongside research, WUR is pioneering cultivated meat education in Europe, offering the first dedicated master-level course on cultivated meat and seafood production.

Dr. Joao Marques Garcia is a biomedical engineer and holds a PhD on tissue engineering and regenerative medicine. Between 2022 and 2024, Joao joined the Directorate of Human and Robotic Exploration at the European Space Agency as a research fellow. Here, he explored the feasibility of using cultivated meat to feed astronauts in long-term space missions. As of March 2024, Joao was appointed Assistant Professor at the Wageningen University, where he is involved in research on cellular agriculture, and cultivated meat and seafood. In particular, Joao is interested in the development of robust cell lines, optimization of culture media formulations, and scaffold development. In addition, Joao is the coordinator of the master course on Cultivated Meat and Seafood, the first of its kind in Europe.

I am a junior PI at CBMSO-CSIC funded by the Ramón y Cajal program with former experience as research scientist and instructor at Boston University (School of Medicine) and Massachusetts General Hospital-Harvard Medical School. My research experience span transcription regulation, RNA biology and cell cycle, all aimed to elucidate the molecular mechanisms underlying gene expression reprogramming during development and in response to stress. I am devoted to understanding mitotic-associated gene expression rewiring to drive innovation in developmental-related disease and improve public health.

As a principal investigator at the CBM, I am currently developing a research line aimed to decipher the molecular mechanisms behind gene expression changes required to build a complex organism. My immediate goal is to investigate the transmission of the transcriptional machinery across mitosis and the contribution of this process to cell differentiation. The outcome from our research will help to elucidate the molecular basis of developmental-related syndromes and to improve the diagnosis and therapies to palliate its dramatic consequences.

During my last position as a Research Scientist at Boston University, I investigated the role of cohesin in the transcriptional repression associated to mitosis. This study constituted a new frame of Cornelia de Lange Syndrome (CdLS) etiology, a cohesinopathy affecting the development and intellectual capabilities of 1:10000 newborns (Perea-Resa* et al., 2021, Trends in Cell Biology).

In a previous stage as Research Fellow at Massachusetts General Hospital-Harvard Medical School, I had a strong interest on the genome re-organization and transcriptional rewiring that occurs across the cell cycle, especially in mitosis. Using Xenopus and human cells, I deciphered that cohesin, a master regulator of chromosome topology, underlies the transcriptional shut down of mitotic chromosomes and holds a potential role in transcription restart after mitosis (Perea-Resa and Blower, 2017, Developmental Cell; Perea-Resa et al., 2020, Molecular Cell; Sharp et al., 2020, Journal of Cell Biology). During this stay I also enjoyed the opportunity to collaborate with outstanding groups in the field (I Cheeseman, MIT; BE Black, UPENN; RB Kingston, MGH-HMS).

During my PhD stage in the laboratory of Professor Julio Salinas (CIB-CSIC), I investigated the molecular mechanisms allowing plants to face environmental challenges. Using Arabidopsis as a model, I discovered the LSMs in plants, a total of 11 proteins associated in ring-shaped complexes that regulate key aspects of RNA biology as mRNA splicing and decay. My work revealed the critical role of LSMs in gene expression rewiring required for correct plant development (Perea-Resa et al., 2012, The Plant Cell), and accurate response to different abiotic stresses (Perea-Resa et al., 2016, The Plant Cell). In parallel, I revealed the first nuclear function of prefoldins in plants that, in response to stress, migrate to the nucleus to mediate the degradation of TFs (Perea-Resa et al., 2017, Molecular Plant). During this stage, I also established national and international collaborations and participated in highly diverse projects.

Along all these stages, I have shown an efficient adaptation to a variety of scientific fields, as well as a high performance supported by the number and impact of the published studies. The use of different, very-diverse model organisms as mammalian cells, Xenopus and Arabidopsis provides me with a unique view and training in molecular and cellular biology. I have maximized my training and research outcomes by pursuing opportunities that allowed me an extension of my skills, knowledge base, and research expertise. I built a solid foundation in cellular and molecular biology, especially in gene expression, RNA biology, cell cycle, proteomics, and genomics. I have also established a strong network of national and international collaborations. I am now committed to develop my independent research at the CBM to transfer my expertise into the Spanish Research System.

Ancient DNA has revolutionized our understanding of extinct and extant organisms, enabling the reconstruction of lost ecosystems and their long-gone inhabitants. However, our knowledge of ancient biology has been largely constrained to information derived from short DNA fragments or low-resolution protein sequences. While these have yielded remarkable insights, DNA primarily captures the static genetic code, and proteins merely provide a partial view of the coding fraction of the genome.

Trapped in between lies RNA, a molecular intermediate long dismissed as too transient
and unstable to survive far beyond cell death. Recent breakthroughs in isolating,
sequencing, and characterizing historical and ancient transcriptomes have challenged
this assumption, revealing that RNA preservation may be more common than previously recognized.

This keynote will trace the troubled lifetime of ancient RNA as a research field, present
recent advances enabling transcriptome recovery from historical and archaeological
specimens of iconic extinct species such as the Tasmanian tiger and the woolly
mammoth, and describe how ancient RNA is transforming our understanding of gene
regulation, developmental biology, and infectious disease through time. Looking
forward, I will discuss ongoing projects, future directions, and the unrealized potential of RNA and other biomolecules toward a multi-omics framework aimed at decoding the functional and structural biology of the past.

Dr. Emilio Mármol Sánchez is a research fellow in the Center for Evolutionary
Hologenomics at the University of Copenhagen. Trained as a veterinarian and
bioinformatician, he began his research career in Barcelona by studying gene regulatory networks and RNA biology in domestic animals. After completing his PhD in 2020, he transitioned into the emerging field of ancient transcriptomics, where during his postdoctoral work in Stockholm he developed novel laboratory and computational approaches for the isolation, sequencing, and computational analysis of ancient and historical RNA from extinct species.

Now based in Copenhagen, his research is focused on a multi-omics approach to develop novel methods applied to historical and ancient animal specimens, spanning short- and long-read DNA sequencing, RNA profiling, chromatin reconstruction, epigenetic inference, and spatial deconvolution. Through such integrative framework, his work aims to reconstruct the functional biology of the past using molecular technologies of the present.

Advanced polymer nanomaterials are playing an increasingly important role in modern regenerative medicine, drug delivery, and light-activated therapies. These materials combine biodegradable polymers, nanofibers, hydrogels, and functional nanoparticles to create smart biomedical systems capable of interacting with biological tissues at the cellular level. Polymeric nanostructures can be engineered to deliver drugs in a controlled manner, support tissue regeneration, and respond to external stimuli such as light or temperature.

Electrospun polymer nanofibers are particularly important because they mimic the structure of the natural extracellular matrix, making them suitable for tissue engineering and regenerative medicine applications. Hydrogels and crosslinked polymer networks can provide a moist, biocompatible environment for cell growth and drug delivery. The incorporation of nanoparticles, especially metallic nanoparticles such as gold nanostructures, enables photothermal effects, allowing light-activated therapy and controlled drug release.

Light-responsive nanomaterials are a promising approach for minimally invasive therapies, enabling on-demand drug release via near-infrared light. Such systems may improve treatment efficiency while reducing side effects. Overall, advanced polymer nanomaterials represent a rapidly developing field that combines materials science, nanotechnology, and medicine, offering new possibilities for regenerative therapies, targeted drug delivery, and smart biomedical devices.

Dr. Zuzanna Krysiak obtained her PhD in 2022 from AGH University of Science and Technology in Kraków, Poland, where she investigated electrospun fiber-based skin patches for atopic skin. She is an Assistant Professor in the Division of Functional Polymer Nanomaterials, led by Filippo Pierini, at the Institute of Fundamental Technological Research, Polish Academy of Sciences. She has several years of experience in the design and manufacture of biomaterials for atopic skin treatment, wound healing and scaffolds, gained in domestic and international research centers. Experience in research projects based on electrospun fibers, hydrogels, and intelligent structures combining these two types of materials, confirmed by numerous publications and two patents. Knowledge of techniques for isolating human and animal cells, as well as culturing primary cell lines. Currently, she is focused on a light-responsive platform for miRNA delivery for wound healing.