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Seminars, events & talks

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

Wednesday, 8th September, 2021, 13:00

Machine Learning Coarse Grained Models with Graph Neural Networks

Adrià Pérez will teach how to prepare, train and simulate coarse-grained models with graph neural networks using TorchMD, a deep learning framework for molecular simulations. We will build a coarse-grained model of the fast-folding protein chignolin in order to simulate it and reproduce its folding process. Atomistic or ab initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time-and length-scales accessible with such computationally expensive simulations is the definition of coarse-grained molecular models. Recent advances in machine learning allow us to design optimal coarse-grained models for reproducing the equilibrium thermodynamics of a macromolecule. Adria  Pérez is a Research Fellow at the Computational Science group, GRIB, UPF. He holds a Biochemistry degree from Universitat Pompeu Fabra (UPF). The computational science research group, led by Gianni de Fabritiis, is dedicated to computational science in biomedicine and machine learning. The group research interested are rooted in application of computation to solve real world problems. Specifically, they develop new methods and algorithms and apply them to computational chemistry, drug design, protein folding, etc. The group and the spin-off company Acellera, founded in 2006, has collaborated with major industries worldwide like Sony NVIDIA, HTC mobile, UCB and Pfizer. Registration: https://register.gotowebinar.com/register/5159085993874550798

Speaker: Adrià Pérez, Computational Science Group - Research Programme on Biomedical Informatics (GRIB, IMIM/UPF)

Room Online



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