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Seminars, events & talks

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

Room Online

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)

Room Online

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.

Room Online

Tuesday, 29th March, 2022, 10:00

Illuminating the chemical space of therapeutical relevance

OpenGRIB Seminar. (Hybrid Session) Systems pharmacology is the discipline that studies the so-called 'pharmacological space' with a holistic and network-based perspective. Its challenge is to shed light on the astonishingly sophisticated biological processes that characterize living cells, and the effect that exogenous chemical entities with therapeutic purposes have when entering them. From this perspective, a series of novel computationally-developed methodologies are presented in this seminar. They aim from the exploration of the pharmacologically-relevant chemical space claimed in patents, to the unveiling of pharmacological opportunities to drug yet untargeted proteins. Link: https://www.gotomeet.me/GRIB/opengrib_seminars

Speaker: Maria José Falaguera, Systems Pharmacology Group - Research Programme on Biomedical Informatics (GRIB, IMIM/UPF)

Room Xipre 173.06 (PRBB, 1st floor) & online (GoToMeeting)

Thursday, 17th February, 2022, 12:00

Analysis of transposable elements in R and Bioconductor with atena

PRBB Computational Genomics Seminar. Chair: Robert Castelo (Head of Functional Genomics Group). Transposable elements (TEs) are DNA sequences that can mobilize within the genome either through a DNA intermediate, known as class II TEs or DNA transposons, or through an RNA intermediate, known as class I TEs or retrotransposons, as in the case of endogenous retroviruses (ERVs). Their insertions have resulted in a complex distribution of repeated elements occupying approximately half of the human genome and even higher proportions in other organisms such as plants. These elements have been described to be involved in physiological processes and human disease. TEs may exert their function through transcription, hence RNA sequencing can be used to detect their expression. However, due to their repetitive nature, reads sequenced from TE RNA transcripts usually map to multiple genomic loci and are consequently discarded in standard RNA sequencing data processing pipelines. For this reason we have developed atena, an open source software package for the analysis of TE expression in R, available at Bioconductor. The atena package re-implements in R three existing methods for TE expression quantification (TEtranscripts, ERVmap and Telescope), enabling the integration of TE expression analysis with a wide range of differential expression and functional analyses pipelines available in Bioconductor. Zoom webinar: https://us02web.zoom.us/j/81073249721 / Password: 788137

Speaker: Beatriz Calvo, Functional Genomics Group - Research Programme on Biomedical Informatics (GRIB, IMIM/UPF).

Room Online

Thursday, 27th January, 2022, 12:00

New genes and alternative isoforms detected with Oxford Nanopore direct RNA

PRBB Computational Genomics Seminar. Chair: Mar Albà (Head of Evolutionary Genomics Group). Oxford Nanopore Technologies (ONT) direct RNA (dRNA) sequencing offers several important advantages over previous RNA-Seq approaches: each long sequencing read corresponds to a single mRNA molecule, it is possible to estimate poly(A) tail length, and one can obtain information on RNA modifications. In the present work, we use dRNA to obtain a more comprehensive transcriptome of the model yeast species , S. pombe, which, in contrast to S. cerevisiae, is intron-rich. By using dRNA we uncover many high abundant transcript isoforms, some of which are likely to be translated into proteins. We also observe that lowly expressed transcripts, and a subset of the intron retention isoforms, have abnormally long poly(A) tails, suggesting that poly(A) tail can modulate gene expression. We also use dRNA in combination with Ribo-Seq to identify novel genes in the species. Zoom webinar: https://us02web.zoom.us/j/81073249721 / Password: 788137

Speaker: José Carlos Montañés, Evolutionary Genomics Group - Research Programme on Biomedical Informatics (GRIB, IMIM/UPF).

Room Online

Wednesday, 12th January, 2022, 12:00

Bioinformatics for Neuroscience Research: omics, statistics and data analysis

Speaker: Dr. Júlia Perera, Bioinformatics Unit, MARGenomics & Research Programme on Biomedical Informatics (GRIB)

Room Online

Tuesday, 5th October, 2021, 10:00

Studying neurodevelopmental molecular events in evolution and disease

OpenGRIB Seminar. Link: https://www.gotomeet.me/GRIB/opengrib_seminars

Speaker: Gabriel Santpere, Head of Neurogenomics Group - Research Programme on Biomedical Informatics (GRIB, IMIM/UPF)

Room Online



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