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Seminars, events & talks

Thursday, 25th May, 2023, 12:00

Human inversions, genes, phenotypic traits and evolution

PRBB Computational Genomics Seminar. Chair: Mar Albà During the last decades, there has been a growing interest to identify all genetic variants in humans and relate them to phenotypic traits and disease susceptibility. Most studies have focused in SNPs, but they have been able to explain just a small proportion of the genetic risk for complex diseases. The discovery of a large amount of structural variants (SVs), which affect bigger segments of DNA, suggested that they could account for part of this missing heritability. Nevertheless, the study of SVs has been hindered by the lack of a comprehensive catalogue of variants and the difficulty to identify them reliably in multiple individuals. Inversions are especially interesting because they affect recombination and could have negative consequences on fertility. However, they are often missed due to their balanced nature and the presence of highly-identical inverted repeats (IRs) at their breakpoints. As part of the INVFEST project, we have carried an exhaustive characterization of human inversion polymorphism at different levels. In particular, we have built the first non-redundant database of human inversions and characterized in detail more than 500 genome-wide predictions, eliminating many false ones. Thanks to the development of different methods to detect a wide-range of inversions, including those mediated by large IRs that typically escape most analysis, we have also generated the largest and most accurate population inversion dataset, totaling ~200 real inversion-like variants. This has shown that the majority of IR-mediated inversions have occurred recurrently multiple times and are not represented in typical genome-wide association studies (GWAS). Moreover, around half of the studied inversions have significant consequences on gene expression, epigenetic changes or disease association, emphasizing their important functional impact compared to other variants. Finally, several of the inversions show signals of positive or balancing selection. Therefore, this work contributes to a more complete understanding of human genetic variation and the role that inversions play in many organisms. Zoom webinar: https://us02web.zoom.us/j/84212222322?pwd=VmVIdHo3czlFcVZUSDhscnQ0RzN5Zz09

Speaker: Mario Cáceres ICREA Research Professor, Research Programme on Biomedical Informatics (GRIB), IMIM (Hospital del Mar Medical Research Institute) and Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB).

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Thursday, 18th May, 2023, 12:00

The temporal analysis of gene regulatory networks in early neurodevelopment

PRBB Computational Genomics Seminar. Chair: Gabriel Santpere Disorders of cortical development are characterized by complex genetic architectures involving many genes which function during corticogenesis. Little is known about the function of these disease-relevant genes across the early fetal development of the human telencephalon and the progression of the neural stem cells (NSCs). Here, we focused on lists of known genes associated with cortical disorders. We explored expression dynamics and regulatory networks in our previously reported transcriptomic datasets generated from human pluripotent stem cell-derived NSCs, which progress in vitro recapitulating regional organizing centers and cortical neurogenesis. We identified disease-specific phases across human telencephalic development when NSCs might be more vulnerable to gene dysfunction. We defined new putative implications of risk genes in the brain organizers' activity and NSCs. This work opens a new perspective to model the origins of cortical disorders in progressing NSCs across the very early phases of human fetal brain development. Zoom webinar: https://us02web.zoom.us/j/84212222322?pwd=VmVIdHo3czlFcVZUSDhscnQ0RzN5Zz09

Speaker: Xoel Mato Blanco Neurogenomics group (Gabriel Santpere), GRIB

Thursday, 11th May, 2023, 12:00

Automated structure-based learning to model complex protein-DNA interactions and co-operativity in cis-regulatory modules

PRBB Computational Genomics Seminar. Chair: Baldo Oliva Transcription factor (TF) binding is a key component of genomic regulation. There are numerous high-throughput experimental methods to characterize TF-DNA binding specificities. Their application, however, is both laborious and expensive, which makes profiling all TFs challenging. For instance, the binding preferences of ~25% human TFs remain unknown; they neither have been determined experimentally nor inferred computationally. Here, we introduce ModCRE, an automated structure homology-modelling approach to predict TF motifs and model higher-order TF regulatory complexes. We demonstrate the conditional advantage of using ModCRE over the state-of-the-art nearest-neighbor prediction as well as an improvement in prediction accuracy when using a rank-enrichment selection system. Starting from a TF sequence or structure, ModCRE predicts a set of binding motifs. The predicted motifs are then used to scan the DNA for occurrences of each, and the best matches are either profiled with a binding score or collected for their subsequent modeling into a higher-order regulatory complex with DNA, as well as other TFs and co-factors. Cooperativity is modelled by: i) the co-localization of TFs; and ii) the structural modeling of protein-protein interactions between TFs and with co-factors. Finally, as case examples, we apply ModCRE to model the interferon beta enhanceosome and the complex of OCT4, SOX2 and SOX11 with a nucleosome and compare these to experimentally determined structures. Zoom webinar:https://us02web.zoom.us/j/84212222322?pwd=VmVIdHo3czlFcVZUSDhscnQ0RzN5Zz09

Speaker: Patrick Gohl, Structural Bioinformatics group (Baldo Oliva group), GRIB

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Thursday, 27th April, 2023, 12:00

PSMAR multi-omics and clinical data integration: cBioPortal experience

PRBB Computational Genomics Seminar. Chair: TBC Next-generation sequencing (NGS) has revolutionized medicine as it can provide extremely detailed molecular profiles, allow for risk prediction, aid in diagnosis and guide personalized treatments. The detection of mutations and patterns of gene expression has become a common practice for many patients of the Parc de Salut Mar (PSMAR). This information is very valuable, as it helps patients get the appropriate diagnosis and treatment, but it can be as important for future reanalysis and secondary research use. Hence, guaranteeing that these data remain easily accessible and interoperable by the clinical and scientific community is of vital importance. With this idea, the PSMAR initiated a pilot project for the deployment of a private instance of the cBioPortal platform with an historical cohort (2014-2022) of lung adenocarcinoma patients diagnosed at our hospital. This cohort consists of mutation profiles integrated with the clinical data from IMASIS-2 database, which gathers and harmonizes different information sources of the PSMAR. This pilot project has allowed us to demonstrate the feasibility of this integration and its potential for the management of lung adenocarcinoma patients. In this talk I will present the development of this pilot project and I will elaborate on the critical issues and synergies with parallel initiatives on genetic data interoperability, secondary use and sharing. I will discuss potential uses of such effort and the future directions of the initiative. Zoom webinar: https://us02web.zoom.us/webinar/register/WN_BmCslCIdTBOd9l0jNiuhog

Speaker: Julia Perera, Bioinformatics Unit. GRIB. MARGenomics, IMIM

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Thursday, 16th February, 2023, 12:00

Benchmarking of long-read transcriptomics methods; results and insights from the LRGASP project

PRBB Computational Genomics Seminar. Chair: Mar Albà Long reads sequencing is the Method of the Year 2022 according to Nature Methods. Applied to transcriptome analysis Long reads allow the sequencing of full-length transcripts in one single read and facilities the study of transcript variants. However the technology is still noisy. The LRGASP project is an initiative to assess the quality of long reads methods for transcript identification and quantification. Long reads data was generated for different organisms, library preparation methods and sequencing platforms (PaBio, Nanopore and Illumina) and launched to the community for transcript models predictions. More than 130 transcriptome predictions datasets were generated by 13 different bioinformatics tools, analyzed with SQANTI and compared. In this seminar I will present the results of the LRGASP Challenges 1 and 3, which deal respectively with the identification of transcripts with and without a good genome annotation. Novel insights about transcriptome diversity will be discussed. Zoom webinar: https://us02web.zoom.us/j/84212222322?pwd=VmVIdHo3czlFcVZUSDhscnQ0RzN5Zz09

Speaker: Ana Conesa, Institute for Integrative Systems Biology (I2SysBio)

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Thursday, 9th February, 2023, 12:00

Genetic associations on major depression: curation and functional analysis

PRBB Computational Genomics Seminar. Chair: TBC Major depression (MD) is the leading cause of impairment worldwide. The lack of understanding of its biological underpinnings hampers the development of better diagnostic tools and treatments. Thanks to the advances in genetic association studies, multiple genetic variants significantly associated with MD have been identified. In this thesis, we aim to leverage this knowledge to advance in the understanding of MD and unravel its molecular mechanisms. For that, we developed curation guidelines to evaluate available genetic association data on MD of diverse nature, and created an expert-curated database of genetic variants associated with MD. Then, we leveraged these data and functional genomic tools to unravel the role of these variants in disease pathogenesis and propose mechanistic hypotheses. In light of the plethora of tools available to perform such analyses, we conducted a benchmarking analysis to evaluate their performance and compare their outcomes; highlighting the need for guidelines for method selection and evaluation. Overall, this thesis contributes to filling the gap regarding the quality assessment of genetic studies on MD, and to advance in discovering the functional role of MD-associated variants by using in silico approaches. Zoom webinar: https://us02web.zoom.us/j/84212222322?pwd=VmVIdHo3czlFcVZUSDhscnQ0RzN5Zz09

Speaker: Judith Pérez Granado, Integrative Bioinformatics group (Laura Furlong’s lab), GRIB

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Wednesday, 25th May, 2022, 18:00

Internet i salut: oportunitats i riscos. "La huella genética de las enfermedades"

El Departament de Medicina i Ciències de la Vida de la Universitat Pompeu Fabra (UPF) organitza l'activitat divulgativa "Internet i salut: oportunitats i riscos". Tindrà lloc dimarts 25 de maig a les 18 h, és oberta al públic general i gratuïta, però es requereix inscripció prèvia. Es podrà assistir presencialment a l'acte a la Sala Josep Marull del Campus Universitari Mar (C/Aiguader 80, Barcelona) o seguir-la en directe en streaming. Els ponents David Comas (UPF i IBE), Araceli Rosa i Ferran Casals (UB) parlaran sobre per què hi ha malalties que són comunes a totes les poblacions humanes, però altres només es presenten a algunes poblacions. També abordaran l'origen de malalties complexes com l'obesitat, l'esquizofrènia o la depressió i com els nostres gens en interacció amb l'ambient expliquen les seves altes prevalences a la nostra societat. Un altre dels aspectes que tractaran és com els avenços en les tecnologies d'anàlisi genètica ens han permès avançar en el diagnòstic, prevenció i coneixement de les malalties rares. La sessió estarà moderada per Robert Castelo (UPF). L'activitat és la vuitena sessió del cicle "No esperis una altra pandèmia per saber què s'està investigant en salut i biomedicina", organitzat amb la col·laboració de la Fundació Espanyola per a la Ciència i la Tecnologia (FECYT) - Ministeri de Ciència i Innovació. Si vols compartir les teves preguntes relacionades amb el tema abans de l'esdeveniment les pots enviar a biomed.comunicacio@upf.edu i els ponents les respondran a la sessió. Inscriu-te a l'enllaç per assistir presencialment a l'acte o aquí per a seguir la retransmissió en streaming.

Speaker: David Comas (UPF i IBE), Araceli Rosa i Ferran Casals (UB). Moderador: Robert Castelo (GRIB - UPF)

Tuesday, 24th May, 2022, 10:00

Machine learning physics and chemistry

OpenGRIB Seminar. I will present various aspects of machine learning in physics and chemistry which we have worked on, in particular in connection to drug discovery. Starting from learning neural network potentials for atoms to more solution oriented machine learning methods for drug-protein interactions and protein folding.  Link: https://www.gotomeet.me/GRIB/opengrib_seminars

Speaker: Prof. Gianni De Fabritiis, Icrea research professor at Universitat Pompeu Fabra. Head of Computational Science Laboratory, Research Programme on Biomedical Informatics (GRIB, IMIM/UPF)

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Tuesday, 10th May, 2022, 18:00

Internet i salut: oportunitats i riscos. "Redes Sociales y Salud"

El Departament de Medicina i Ciències de la Vida de la Universitat Pompeu Fabra (UPF) organitza l'activitat divulgativa "Internet i salut: oportunitats i riscos". Tindrà lloc dimarts 10 de maig a les 18 h, és oberta al públic general i gratuïta, però es requereix inscripció prèvia. Es podrà assistir presencialment a l'acte a la Sala Josep Marull del Campus Universitari Mar (C/Aiguader 80, Barcelona) o seguir-la en directe en streaming.

Els ponents Ferran Sanz (GRIB, UPF-IMIM), Liliana Arroyo (Fundació i2cat i ESADE) i Manuel Armayones (UOC) parlaran sobre les oportunitats i riscos de les xarxes socials, com poden afectar a la nostra salut o com poden permetre detectar malalties. La sessió estarà moderada per Gema Revuelta (UPF).

L'activitat és la setena sessió del cicle "No esperis una altra pandèmia per saber què s'està investigant en salut i biomedicina", organitzat amb la col·laboració de la Fundació Espanyola per a la Ciència i la Tecnologia (FECYT) - Ministeri de Ciència i Innovació. Si vols compartir les teves preguntes relacionades amb el tema abans de l'esdeveniment les pots enviar a biomed.comunicacio@upf.edu i els ponents les respondran a la sessió.

Speaker: Ferran Sanz (UPF-IMIM), Liliana Arroyo (Fundació i2cat i ESADE) i Manuel Armayones (UOC)

Thursday, 21th April, 2022, 12:00

Novel genes enable protein structural innovation and function in the brain

PRBB Computational Genomics Seminars, Chair: Gabriel Santpere (Head of Neurogenomics Group). How genuinely new protein-coding genes originate is a central question in biology. Long thought impossible to arise from non-coding sequence, novel genes arising de novo from genomic "junk" DNA or from long non-coding RNA were recently found in eukaryotic genomes. Novel genes are taxon-restricted and may encode structurally novel proteins with new protein domains. To understand how novel genes arise, we built a mathematical model based on gene and genome parameters and dynamic factors such as mutation. We combined phylostratigraphy and proteogenomics to identify novel genes in 25 eukaryotic genomes and evaluated their predicted biophysical properties. Compared to ancient proteins, novel proteins are shorter, more fragile, disordered and promiscuous, yet less prone to aggregate or to form toxic prions. We performed biophysical experiments comparing novel and ancient proteins, showed that novel genes function in vivo in zebrafish brains, and found novel genes are expressed in human brains at multiple ages. Genomic sequence turnover generates many novel genes encoding short proteins, of which some are maintained and encode proteins with distinct structural features and expressed in the brain. Thus, genomic variation continuously generates new protein structures and new functions. Zoom webinar: https://us02web.zoom.us/j/81073249721 / Password: 788137

Speaker: Victor Luria; Yale University, Department of Neuroscience, New Haven, USA. Harvard Medical School, Department of Systems Biology, Boston, USA.

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