Seminars, events & talks

Friday, 24th April, 2020, 10.30 - 11.30

Soft-matter materials modeling in the data-driven era

Advanced statistical methods are rapidly impregnating many scientific fields, offering new perspectives on long-standing problems. In materials science, data-driven methods are already bearing fruit in various disciplines, such as hard condensed matter or inorganic chemistry, while comparatively little has happened in soft matter. I will describe how we use data-driven methods to leverage molecular simulations in soft matter. We aim at establishing structure-property relationships for complex thermodynamic processes across the chemical space of small molecules. Akin to screening experiments, we devise a high-throughput coarse-grained simulation framework. Coarse-graining is an appealing screening strategy for two main reasons: it significantly reduces the size of chemical space and it can suggest a low-dimensional representation of the structure-property relationship.

I will illustrate these aspects through the passive translocation of small molecules across a phospholipid bilayer, identifying interpretable structure-property relations, as well as recent results on the screening of small molecules to drive phase transitions in lipid mixtures. Further applications of recent machine learning architectures to molecular simulations will be described: representation learning of a free-energy landscape using Gaussian-mixture variational autoencoders, and the systematic backmapping of coarse-grained configurations to an atomistic level using conditional generative adversarial networks.

Speaker: Tristan Bereau, Van 't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam, The Netherlands

Room Charles Darwin, PRBB Innner square

Thursday, 16th January, 2020, 12:00 - 13.00

Unravelling the mystery of orphan genes to understand the origins of genetic novelty

What explains the presence of a gene only in the genome of one species and not in any other? Species-specific protein-coding genes, also known as orphans, can arise "from scratch" from previously non-genic loci, through a process known as de novo gene emergence. How exactly the evolutionary transition from non-gene to functional gene unfolds is unclear. Can such de novo emerging genes increase an organism's fitness, and if so how? Orphan genes can also result from extensive sequence divergence of ancestral genes, which can eventually erase all similarity of a gene to its homologues in other species, a process even less well understood than de novo emergence.  I will present novel findings which advance our understanding of both these evolutionary mechanisms and bring us a small step closer to a complete picture of the origins of genetic novelty.

Speaker: Nikos Vakirlis, Benaki Phytopathological Institute, Athens, Greece

Room Aula room 473.10 (4th floor)

Thursday, 9th January, 2020, 12:00

Multi-Omics Factor Analysis: a principled framework for the integration of large-scale multi-omics data

Abstract: Methods for analysing large-scale multi-omics studies are statistically challenging and currently lacking. I will present MOFA, a statistical framework for the comprehensive and scalable integration of multi-omics data. MOFA builds upon a Bayesian Factor Analysis framework combined with fast GPU-accelerated stochastic variational inference. The model allows for interpreting variation in both bulk and single-cell datasets by pooling information across cells and features to reconstruct a low-dimensional representation of the data. Uniquely, the model supports flexible sparsity constraints that allow joint modelling across multiple groups (conditions or experiments) and views (modalities or assays). To demonstrate the use of MOFA, I will present analysis from data sets of different scales and designs, including personalised medicine applications from patient cohorts and signal extraction from complex single-cell data.

Speaker: Ricard Argelaguet, European Bioinformatics Institute - EBI (Stegle/Marioni groups)

Room Aula room 473.10 (4th floor)

Thursday, 28th November, 2019, All day

Advances in Computational Biology Conference 2019

The first Advances in Computational Biology conference will bring together researchers working on systems biology, omics technologies, artificial intelligence and high-performance computing with applications to biology from both the public and private sectors. One of the main purposes of the conference is to visualize and promote the research done by women scientists and for this reason, all presenters will be women, although the conference is open to everyone. We want to create a space to foster collaborations between scientists, providing an excellent opportunity to share ideas and build research networks.  Mar Albà, head of the Evolutionary genomics group of GRIB is member of the organizing committee and Laura I. Furlong, head of the Integrative Bioinformatics group of GRIB is member of the scientific committee of the event.

Room La Pedrera Building, Barcelona, Spain

Thursday, 24th October, 2019, 12.00 - 13.00

Detecting Signs of Depression in Tweets in Spanish: Behavioral and Linguistic Analysis

Abstract: Mental disorders have become a major concern in public health, and they are one of the main causes of the overall disease burden worldwide. On the other hand, Social Media platforms allow us to observe thoughts and feelings of people's daily lives, including those of patients suffering from mental disorders. In this presentation we will discuss the usefulness of identifying the linguistic features of tweets in Spanish and the behavioral patterns of Twitter users who generate them, which could suggest signs of depression. Twitter users who are potentially suffering from depression modify the general characteristics of their language and the way they interact on social media. On the basis of these changes, these users can be monitored and supported, thus introducing new opportunities for studying depression and providing additional health care services to people with this disorder.

Speaker: Angela Leis, Integrative Biomedical Informatics, GRIB (IMIM/UPF)

Room Aula room 473.10 (4th floor)

Monday, 14th October, 2019, 10:00 - 11:00

Interaction of Membrane Cholesterol with G Protein-Coupled Receptors: Novel Insights in Health and Disease

 G protein-coupled receptors (GPCRs) are the largest class of molecules involved in signal transduction across membranes, and represent major drug targets in all clinical areas.  The overall focus of our work is on the role of membrane cholesterol in GPCR organization (oligomerization), dynamics and function with implications in health and disease.  The GPCR of choice is the serotonin1A receptor, an important neurotransmitter receptor implicated in the generation and modulation of cognitive, behavioral and developmental functions, and an important drug target.  We demonstrated that membrane cholesterol is necessary for ligand binding, and G-protein coupling and signaling of serotonin1A receptors.   Interestingly, high-resolution crystal structures of GPCRs exhibit bound cholesterol.  In this context, we reported the presence of cholesterol recognition/interaction amino acid consensus (CRAC) motifs in the serotonin1A receptor.  Recent results employing mutations in the CRAC motifs show the importance of Lys101 in transmembrane helix II in conferring cholesterol-sensitivity to signaling by the receptor.  In addition, using a combination of experimental and MD simulation approaches, we demonstrated that the receptor is more stable and compact in the presence of membrane cholesterol.  Further, our results provide important insights in cholesterol-dependent oligomerization of the receptor using a variety of approaches such as photobleaching homo-FRET, photobleaching image correlation spectroscopy, and coarse grain MD simulations.  We ension that progress in deciphering molecular details of the nature of GPCR-cholesterol interaction in the membrane would lead to better insight into our overall understanding of GPCR function in health and disease.

Speaker: Prof. Amitabha Chattopadhyay, Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India

Room Marie Curie, PRBB Inner square

Thursday, 6th June, 2019

De novo proteins in evolution and disease

Speaker: Mar Albà, Evolutionary Genomics, GRIB (IMIM)

Room Institut d'Estudis Catalans, Carrer del Carme, 47, Barcelona

Wednesday, 29th May, 2019, 09:30

III Retreat de l'IMIM

El dimecres 29 de maig tindrà lloc a l'Auditori del PRBB el III Retreat de l'IMIM. Amb aquesta iniciativa es vol donar visibilitat als projectes més rellevants que s'estan desenvolupant a cada Programa de Recerca, tot esperant que això sigui font de noves sinèrgies i d'intercanvi científic entre els diferents grups per a millorar la nostra competitivitat científica. És per aquest motiu que agrairíem us reservéssiu tota la jornada per assistir-hi, i així poder conèixer en què estan treballant els diferents grups de l'IMIM, fora del programa de recerca del que formeu part.el III Retreat de l'IMIM. Amb aquesta iniciativa es vol donar visibilitat als projectes més rellevants que s'estan desenvolupant a cada Programa de Recerca, tot esperant que això sigui font de noves sinèrgies i d'intercanvi científic entre els diferents grups per a millorar la nostra competitivitat científica. És per aquest motiu que agrairíem us reservéssiu tota la jornada per assistir-hi, i així poder conèixer en què estan treballant els diferents grups de l'IMIM, fora del programa de recerca del que formeu part.

Room Auditori del PRBB

Thursday, 9th May, 2019, 12.00 - 13.00

ResMarkerDB: a database of biomarkers of response to antibody therapy in breast and colorectal cancer

The clinical efficacy of therapeutic monoclonal antibodies for breast and colorectal cancer has greatly contributed to the improvement of patients' outcomes by individualizing their treatments. However, primary or acquired resistance may occur. Although several databases characterize biomarkers of drug response, there is a need of resources that offer this information to the user in a harmonized manner to support research and development of new alternative treatments. ResMarkerDB was developed as a comprehensive resource of biomarkers of drug response in breast and colorectal cancer. It integrates these data from existing repositories, and new data extracted and curated from the literature (referred as ResCur). It provides a user-friendly web interface ( to facilitate the exploration of current knowledge of biomarkers of response in breast and colorectal cancer. The database contains more than 500 biomarker-drug-tumour associations. ResMarkerDB aims to enhance translational research efforts in identifying actionable biomarkers of drug response in cancer.

Speaker: Judith Pérez, Integrative Biomedical Informatics, GRIB (IMIM/UPF)

Room Aula 473.10 (PRBB, 4th floor)

Tuesday, 7th May, 2019, 12:00 - 13.00

Presentation of the Human Computational Biology Group

Speaker: ​Lara Nonell, IMIM

Room Charles Darwin, PRBB Innner square

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