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Seminars, events & talks

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

Friday, 23th July, 2021, 13:00

Identifying longitudinal psychiatric signatures in HD using dynamic time warping

While Huntington's disease (HD) is diagnosed by the onset of motor symptoms, psychiatric disturbances bear a greater burden on daily functioning. Such psychiatric features can present up to fifteen years prior to formal disease diagnosis, although there is great inter-individual heterogeneity in symptom expression and evolution. As such, the present study strives to discern longitudinal psychiatric signatures that inform patterns of HD progression. Forty-seven HD gene-expansion carriers (23 premanifest, 24 manifest) underwent evaluation for depression, irritability, apathy, and executive dysfunction using the short-Problem Behavior Assessment (PBA-s) for a maximum total of six longitudinal visits. Unsupervised clustering of weighted PBA-s scores was performed with an adapted Disease Trajectories analysis software based on dynamic time warping (DTW), a technique that allows the non-linear alignment of sequences that may vary in overall lengths or speed, but can conceal the same temporal characteristics. This proof-of-concept allowed the identification of clusters with shared patterns of psychiatric evolution. Next, selected clusters were assessed for group differences in diagnostic status and severity of psychiatric features. This seminar will serve as a rehearsal of my Master's defense, which I completed under the supervision of Dr. Alexia Giannoula and Dr. Laura Furlong. In this way, I hope to stimulate a discussion regarding the analytical pipeline and its applicability and interpretability in the clinical field. Link: https://www.gotomeet.me/GRIB/opengrib_seminars

Speaker: Audrey De Paepe, Master of Multidisciplinary Research (BIST), Cognition & Brain Plasticity Unit (UB) - Research Programme on Biomedical Informatics (GRIB, IMIM/UPF)

Room Online

Tuesday, 22th June, 2021, 10:00

Bioinformatics, combining facility and research

OpenGRIB Seminar. Bioinformatics is a common need in most research labs. Therefore it is important to have access to a core facility that is able to implement the standard methodology to extract knowledge from biological data, including omics data. In addition, new methods are continuously developed in the field to meet increasing data analysis demands. In this context, we will explain our experience as a service oriented facility and will also see some of the recently funded projects we are involved in, coming out of fields as disparate as COVID-19, bladder cancer or major depression disorder. Link: https://www.gotomeet.me/GRIB/opengrib_seminars

Speaker: Lara Nonell, PhD BiCoH (Human Computational Biology), MARGenomics, IMIM Scientific and Technical Services

Room Online

Thursday, 20th May, 2021, 12:00

Identifying genomic variants acting on brain specializations

PRBB Computational Genomics Seminars, Chair: Mar Albà (Head of Evolutionary Genomics Group) Humans possess a nervous system which confers very distinct cognitive abilities and very distinct cognitive disorders. The study of brain development is critical for the understanding of the evolution of these distinct features. To discern the genetic causes in evolution and disease influencing human-specific phenotypes one needs to identify the relevant variants affecting relevant genes among thousands of other variants predicted to be neutral. Among the approximately 35 million single nucleotide polymorphisms (SNPs), 5 million insertions or deletions (indels), and 90 megabases of structural variants where the human and chimpanzee genomes differ are countless variants associated with development, function or disease. However, identifying these rare variants from among the thousands of variants expected to be neutral is a herculean task, a truly "needle-in-a-haystack" scenario. Many of us have reasoned that identifying evolutionarily relevant genetic variants, as well as those implicated in disease or function, can be guided by the analysis of species differences in intermediate molecular phenotypes (e.g., transcriptomic and epigenomic signatures), which are most likely the primary effects of genomic variation. Going one step further in the strategy to identify evolutionarily relevant variants, one can interrogate divergence in the segments of the predicted regulatory elements that are directly functionally affecting gene expression: the transcription factor binding sites (TFBS). The study of the brain spatiotemporal convergence of risk for multiple neuropsychiatric traits has pointed to a reduced number of transcription factors with critical involvement in normal neurodevelopment. We aim to dissect the temporal dynamics of genome-wide transcription factor binding site occupancy for a selection of risk convergence transcription factors (TF) at different stages of neurodevelopment and with an evolutionary perspective.  But even when the connection has strong probability of causality, one still needs to demonstrate the mechanisms underlying the phenotypic change, which is an effort rarely pursued by evolutionary biologists. This project aims to deal with these two problems by i) reduce the search space for relevant variants into a tractable list, and ii) test their functional effects in a system proximal to human fetal brain development consisting in iPSC-derived neural cultures. Zoom webinar: https://us02web.zoom.us/j/81073249721  / Password: 788137

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

Room Online

Tuesday, 27th April, 2021, 10:00

Taking full advantage of Real World Data through Biomedical Informatics

OpenGRIB Seminar. Real World Data (RWD) in Medicine is data derived from different sources such as structured data from electronic medical records, clinical annotations free text, patient-reported outcomes or even social media. The use of Biomedical Informatics tools is critical to make the most of extracting, analyzing and understanding health information from RWD. In this session, we will give an overview of some applications of Biomedical Informatics used in this area of research. Link: https://www.gotomeet.me/GRIB/opengrib_seminars

Speaker: Miquel Angel Mayer, MD, Senior Researcher, Integrative Biomedical Informatics Group - Research Programme on Biomedical Informatics (GRIB, IMIM/UPF)

Room Online



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