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Seminars, events & talks

Thursday, 2nd February, 2017, 12:00

Evolutionary Genomics

"Comparative Transcriptomics and RiboSeq: Looking at De Novo Gene Emergence in Saccharomycotina"

In de novo gene emergence, a segment of non-coding DNA undergoes a series of changes which enables transcription of the segment, potentially leading to a new protein with a novel function. What makes de novo genes different from other genes? Due to their unique origins, young de novo genes have no homology with other genes and may not initially be under the same selective constraints. While dozens of de novo genes have been observed in many species, the mechanisms driving their appearance are not yet well understood. To study this phenomena, we have performed deep RNA-seq and ribosome profiling (RP) on 11 species of yeast from the phylum of Ascomycota in both rich media and oxidative stress conditions. These data have been used to classify the conservation of genes at different depths in the yeast phylogeny. Hundreds of genes in each species were novel (non-annotated), and many were identified as putative de novo genes; these can then be tested for signals of translation using our RP data. We show that putative de novo genes have different properties when compared to phylogenetically conserved genes. Understanding the mechanisms behind de novo gene emergence in a 'simple' eukaryote like S. cerevisiae may help to explain some of the unique adaptations seen in more complex organisms.

Speaker: Will Blevins (Evolutionary Genomics group of GRIB)

Room Aula room 473.10 (4th floor PRBB)

Friday, 20th January, 2017, 13.00 - 14.00

Computational Biophysics

Protein dynamics and molecular design: computational approaches with an eye to chemical biology

Speaker: Giorgio Colombo, Instituto di Chimica del Riconoscimento Molecolare, CNR, Italia​,

Room ​ Xipre Room (Seminar ​173.06-183.01), PRBB Building

Thursday, 19th January, 2017, 12:00

Evolutionary Genomics

"Evolution by innovation: Is the de novo emergence of coding genes a myth or a mystery - or both?"

In this lecture I will review the basics behind what makes proteins the most basic elements on which selection acts, how they mediate evolvability of organisms and why it seems so unlikely that a protein emergence de novo, i.e. by creation of a new ORF from previously untranscribed DNA. Since such emergence has, however, been observed we -- and many other groups around the world -- are desperately trying to resolve this mysterious puzzle which puts two fundamental schools of thought -- biophysics and genetics -- at odds.

Speaker: Erich Bornberg-Bauer Molecular Evolution and Bioinformatics. Institute for Evolution and Biodiversity. Universität Münster. Germany.

Room Aula room 473.10 (4th floor)

Thursday, 15th December, 2016, 12:00

Computational RNA Biology

"Intratumoral evolution of breast cancer in response to therapy"

Population heterogeneity within tumors is essential to the development of drug resistance. However, precise quantification of cellularity levels of subpopulations, and in particular how they evolve in response to treatment, has been challenging. Here we describe the high precision characterization of subclonal evolution within triple-negative breast cancer patient-derived xenografts (PDXs) generated from three patients in response to multiple chemotherapies, covering >100 total samples and allowing for extensive intratumoral comparisons. Computational mutation and copy number analysis from post-treatment sequencing indicated sample-specific differences in tumor populations both in response to treatment and due to genetic drift. I will describe the evolutionary behaviors we have observed, which include selective sweeps, spatial diffusion, and symbiosis.

Speaker: Jeffrey Chuang, Ph.D, The Jackson Laboratory for Genomic Medicine; University of Connecticut Health Center Dept. of Genetics and Genome Sciences; Host: Eduardo Eyras

Room Aula room 473.10 (4th floor)

Thursday, 15th September, 2016, 12.30 - 13.30

Computational Biophysics

Redesigning Drug Design of kinase inhibitors

Drug design lags far behind other engineering disciplines in lacking predictive, quantitative models that allow small-molecule therapeutics to be designed, rather than fortuitously discovered. While many challenges exist to building these models, our laboratory uses cycles of computational predictions coupled to experimental measurements to rapidly generate data that can be used to improve rigorous, quantitative approaches to small molecule design based on alchemical free energy calculations.  In this talk, we describe how this process can be done cheaply in an automated manner by inverting the drug discovery problem, and describe our first few steps toward this goal in the design of selective kinase inhibitors.
 

Speaker: John Chodera, Assistant Faculty Member, Computational Biology Memorial Sloan-Kettering Cancer Center, NYC, USA

Room Xipre Room (173.06-183.01), PRBB Building

Sunday, 4th September, 2016, 13:30 - 17:00 (half day tutorial)

Integrative Biomedical Informatics

Tutorial at ECCB 2016 - DisGeNET: a discovery platform to support translational research on human diseases

Recent technological breakthroughs have produced an unprecedented increase in the amount of data on the genetic determinants of diseases. To unveil the molecular mechanisms that underlie diseases and to support drug discovery projects, it is necessary to place these data in the context of the current biomedical knowledge. Despite the large volume of information available, its analysis and interpretation are hindered because it is annotated using different criteria and vocabularies and fragmented across different resources. Furthermore, a large fraction of data on diseases is only available as free text in biomedical publications. To overcome these difficulties we have developed DisGeNET (Piñero et al, 2015), a discovery platform that contains information on human diseases and their genes. In this tutorial we will provide an overview of the main features of DisGeNET, and then introduce the suite of tools that the platform offers to support translational research.  The tutorial includes a hands-on session organized around case studies that will illustrate how to use these tools. Materials will be made available via the DisGeNET website. Target audience: the tutorial is aimed at a variety of audiences: bioinformaticians, systems biology users, biologists, and healthcare practitioners.

Speaker: Laura I. Furlong and Janet Piñero - IBI group of GRIB (IMIM-UPF)

Room 15th European Conference on Computational Biology - The Hague, Netherlands - World Forum Convention Center

Monday, 30th May, 2016, 12:00

Integrative Biomedical Informatics

Making big sense from big data in toxicology

Scientific Sessions PRBB Organizer: PRBB_CRG Conferences. Hosts: Esther Barreiro & Ferran Sanz 

Speaker: Prof. Thomas Hartung, Center for Alternatives to Animal Testing, Doerenkamp-Zbinden Foundation. Evidence-based Toxicology, Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health. Baltimore, USA.

Room Marie Curie Room (Charles Darwin Sq.) PRBB.

Thursday, 12th May, 2016, 12:00

Functional Genomics

A population-level analysis of mutations affecting 5'ss splicing

Wild-type processing of RNA transcripts by the splicing machinery is a fundamental step in the gene expression pathway. Mutations affecting this step can produce aberrant splicing with deleterious effects that ultimately lead to disease. Mutation databases curating the scientific literature store an increasing number of single nucleotide variants (SNVs) inducing aberrant splicing involved in disease. Yet, this increase is far below the current growth rate of genetically profiled diseased individuals. This results in many SNVs of unknown effect. In this context, understanding the deleterious effects of SNVs on 5'ss splicing becomes extremely important to attempt a sensible prioritization of such SNVs. Population-level allele frequencies constitute a valuable resource to gather understanding of mutation processes. We have used the last release of the 1000 Genomes and the ExAC catalogs of human variation to characterize mutations that affect 5'ss splicing and attempt a sensible prioritization of such SNVs.

Speaker: Pau Puigdaval - Functional Genomics Group, GRIB (UPF-IMIM)

Room Aula room 473.10 (4th floor)

Wednesday, 4th May, 2016, 14:00

GPCR drug discovery

Tumour genomes shed light into mutational processes and cancer vulnerabilities

Speaker: Núria López-Bigas - Head of the Computational Genomics group of GRIB (IMIM-UPF)

Room Sala Marie Curie - Ground floor - PRBB

Friday, 29th April, 2016, 11.00 - 12.00

Computational Biophysics

Incremental Unsupervised Training of Deep Architectures

After a brief introduction to deep architectures and their typical supervised and unsupervised training approaches, the talk focuses on incremental strategies (at the base of natural learning). We will present our experience on incremental training of both CNN (Convolutional Neural Networks) and HTM (Hierarchical Temporal Memory). In particular a recently proposed semi-supervised tuning strategy (exploiting time coherence) proved to be very effective in conjunction with HTM, sometimes approaching supervised training accuracy.

Speaker: Davide Maltoni, University of Bologna (Dept. of Computer Science and Engineering - DISI)

Room Xipre Seminar (173.06)



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