X-Meeting 2015 - 11th International Conference of th AB3C + Brazilian Symposium of Bioinformatics

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ACCEPTED  SPEAKERS


John Mattick

RNA is the computational engine of human development and cognition

High throughput sequencing and advanced imaging techniques have revealed that the vast majority of the genomes of mammals and other complex organisms is dynamically transcribed during development to produce tens if not hundreds of thousands of short and long non-protein-coding RNAs that show highly specific expression patterns and subcellular locations. Increasing numbers of these RNAs are being shown to have functions at many different levels of gene expression, including translational control and the guidance of epigenetic processes that underpin development, physiological adaptation, cognition and transgenerational communication, augmented by the superimposition of plasticity by RNA editing, RNA modification and retrotransposon mobilization. This in turn requires reassessment of the nature, scaling and hierarchies of the regulatory systems and processes that control the 4-dimensional assembly and cognitive capacities of complex organisms.

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Executive Director of the Garvan Institute of Medical Research,
Sydney-AU

Opening Lecture: 
“The extraordinary complexity of the human coding and noncoding transcriptome” 

Dr. Guilherme Oliveira
Instituto Tecnológico Vale
Belém - BR

Patrícia Palagi

Training strategies in the old continent: Swiss and European perspectives

The computational biology skills gap is still an issue worldwide and filling it is one of the main concerns of SIB Swiss Institute of Bioinformatics and its ELIXIR partners. The SIB training programme is designed in one hand to ensure that life scientists benefit fully from bioinformatics and effectively apply it to their research projects, and in the other hand to train the next generation of competent bioinformaticians. SIB is the Swiss node of ELIXIR, the European life-sciences Infrastructure for biological Information. Together, we are defining a strategic training programme to upskill European researchers to enable effective exploitation of the data, tools, standards and compute infrastructure provided by ELIXIR partners. In this talk, I will give an overview of our common training strategies and the partnerships with the international community through GOBLET.

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Swiss Institute of Bioinformatics
Geneva - CH

Robert Kuhn (course)

Genome Browser Workshop

This workshop is aimed at the biologist who is interested in exploring genomes using the University of California Santa Cruz (UCSC) Genome Browser. It is geared towards those who have little or no experience using the UCSC Genome Browser and for more advanced users who are not familiar with many of the gene-oriented browser features. Using real examples the user is guided through a step-by-step process for analyzing genes in the context of the human genome and a wide variety of genomic data. The user is shown how to use the UCSC Genome Browser for simple and more complex tasks. Tutorials, exercises and/or other informational material on using the UCSC Genome Browser will be provided.

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Associate Director of the UCSC Genome Browser
Santa Cruz - USA

Jan Baumbach

Computational Breath Analysis - Non-invasive detection of biomarkers in exhaled air and bacterial vapor

Volatile organic compounds are emitted by all living cells and tissues. We seek to non-invasively 'sniff' biomarker molecules that are predictive for the biomedical fate of individual patients or cell cultures. This promises great hope to move the therapeutic windows to earlier stages of disease progression. While portable devices for exhaled volatile metabolite measurement exist, we face the traditional biomarker research barrier: A lack of robustness hinders translation to the world outside laboratories. To move from biomarker discovery to validation, from separability to predictability, we have developed several bioinformatics methods for computational breath analysis, which have the potential to redefine non-invasive biomedical decision making by rapid and cheap matching of decisive medical patterns in exhaled air. We aim to provide a supplementary diagnostic tool complementing classic urine, blood and tissue samples. In the presentation, we will review the state of the art, study some clinical application examples, highlight existing challenges, and introduce new data mining methods for identifying exhaled biomarkers.

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University of Southern Denmark
Odense M DK

Régis Pomes

The Liquid State of Proteins

Although it was long thought that proteins must adopt a well-defined three-dimensional structure to perform their biological function, it has recently emerged that many proteins are at least partly disordered in their functional state. Even more remarkably, certain disordered proteins such as elastin have the capacity to self-assemble and separate into a liquid phase. In the assembled state, elastin fulfills a vital role by imparting extensibility, elastic recoil, and resilience to diverse tissues including arterial walls, skin, lung alveoli, and the uterus. Despite the biological importance of elastin and over eighty years of study, there is still no consensus model for its structure. We used high-performance computing to elucidate the microscopic structure of elastin. Molecular dynamics simulations exceeding 0.2 ms characterize the structural ensemble of elastin-like peptides. Results demonstrate that the hydrophobic domains of elastin are structurally disordered even when assembled together, like a bag of snakes or a plate of spaghetti. Consistent with the entropic nature of elastic recoil, the aggregated state is stabilized both by the hydrophobic effect and by an increase in conformational entropy upon self-assembly. These findings defy conventional wisdom regarding protein folding and disorder: (i) although the peptide side-chains are hydrophobic, they do not form a hydrophobic core; (ii) although the structure of elastin aggregates is maximally disordered, it is not random; and (iii) although the polypeptide backbone forms hydrogen-bonded turns, it remains significantly hydrated. This highly-disordered state underlies the two remarkable properties of elastin, its capacity to separate into a liquid phase and to undergo elastic recoil. As such, the unified picture obtained from this work resolves a long-standing controversy regarding the structure of elastin. The fact that polypeptide chains can aggregate yet retain functionally-essential conformational entropy is of broad relevance to the study of both protein disorder and protein phase separation. The structural ensemble of the elastin-like aggregate obtained here provides the first atomistic view into what may be called the liquid state of proteins.

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Hospital for Sick Children
Toronto - CA

Boris Guennewig (course)

Current methodologies in transcriptome analysis

Next generation RNA-Sequencing (RNA-Seq) is nowadays applied ubiquitously in biological and medical research. The most common application is the detection of differentially expressed genes (DEGs) facilitated through abundance estimation of the complete transcriptome at a given time-point in a sample. These abundance estimations are generated from various tools, counting or estimating the amount of reads associated with an interval of the genome or transcriptome described through an annotation. The resulting abundance matrix is barely representing the underlying complexity of the process from i) experimental design (library depth & replication), ii) adapter and quality trimming, iii) alignment of reads, iv) abundance estimation and v) differential expression analysis. Each of these steps contains a multitude of variables affecting the outcome of the final abundance matrix and subsequently the results of the DEG analysis, with its up-following ontology, co-expression and pathway analysis. In this workshop I provide an overview of the current methodologies in transcriptome analysis. This workshop is aimed at the biologist or computational biologist who is interested in exploring high throughput transcriptome data. Topics covered will be experimental design, quality control, alignments and quantification (day 1); current annotations, differential expression analysis and batch effect control (day 2); de novo assembly, alternative splicing, editing and circRNAs (day 3).

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Garvan Institute of Medical Research
 Sydney - AU

Martin Smith

The modular transcriptome: unraveling a network of functional, structured non-coding RNA domains

The majority (>80%) of our genome is dynamically transcribed into RNA in a developmentally coordinated and tissue-specific manner, producing an astounding diversity of processed non-coding transcripts. Identifying the precise molecular mechanisms implicating lncRNAs is crucial to the advancement of genomics and personalised medicine, as exemplified by the fact that most reported genetic variants associated to complex diseases occur in non-coding regions of the genome with no evidence of evolutionary sequence conservation. However, genome-wide functional annotation of lncRNAs has been limited by insufficient measures of purifying selection as well as unreliable structural predictions. We have recently exposed how over 20% of mammalian genomes present the hallmarks of purifying natural selection at the level of RNA secondary structure via comparative genomics [1]. Here, we expand these findings by revealing how a majority of these conserved RNA structure motifs present structural homologs throughout the human genome, and so with limited sequence similarity. Under the hypothesis that the structural diversity of lncRNAs serves as a modular scaffold for the recruitment and targeting of epigenetic effector complexes, amongst others, we propose that these RNA structure motifs form a network of functional domains for the recruitment of specific RNA-binding proteins. We are assigning specific functions to these motifs two-fold: (i) through the association of RNA structure motif-harbouring transcripts enriched in RNA immuno-precipitation data (RIPseq) targeting epigenetic regulatory proteins; and (ii) through a novel program for the identification of common RNA structures within a subset of sequences. The latter identifies novel and statistically significant clusters of common RNA structure motifs in RIPseq data, despite the lack of substantial sequence conservation. As more targeted sequencing data become available, these techniques will provide a tangible means of assigning biological function the complex and pervasive noncoding transcriptome.

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Garvan Institute of Medical Research
 Sydney - AU

Dr. Augusto Schrank
Universidade Federal do Rio Grande do Sul
Porto Alegre - BR

Dr. Helder Nakaya
Universidade de São Paulo
São Paulo - BR

Michelle Brazas

Supporting Trainers to Improve Bioinformatics Education Globally

A needs assessment isn’t necessary to realize that across the globe, there is a high demand for quality bioinformatics training in all domains of life science. Delivering on this demand however is not trivial. In addition to computational infrastructure and software tools, quality bioinformatics training depends upon excellent trainers and training resources. With a focus on the trainer in the learning equation, the Global Organization for Bioinformatics Learning, Education and Training (GOBLET) aims to facilitate the advancement of bioinformatics education globally by training and supporting a network of bioinformatics trainers. Activities include coordinating training efforts, sharing data sets and teaching materials, discussing best practices and building up teaching standards and teaching recognition. Examples to improve your bioinformatics training programs will be provided. Through support and development of trainer excellence, GOBLET is working to improve the global landscape in bioinformatics education.

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Ontario Institute for Cancer Research
Toronto - CA

Pedro Galante

Retrocopies in Primate Genomes

Gene duplication is a key factor contributing to phenotype diversity across and within species. Nowadays, the availability of complete genomes has led to the extensive study of genomic duplications. In this work, we performed a systematic analysis of mRNA retrocopies in seven fully sequenced primates, including human. Specifically, we catalogued their entire retrocopy repertoires and explored the origin, orthology, expression and polymorphism of these retrocopies.

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Hospital Sírio-Libanês
São Paulo - SP

Stephen Turner

The most comprehensive view of genomes, epigenomes and transcriptomes

Pacific Biosciences’ Single Molecule Real-Time (SMRT™) sequencing is nearing its 5th year of commercial deployment, since its introduction the readlength and throughput of the technology have approximately doubled every year. Today, with an average readlength over 10,000 bases and significant numbers of reads over 30,000 bases in length, the technology has changed the face of genomics. Because of its unrivaled consensus accuracy and ability to provide microbial epigenomic information SMRT sequencing is now accepted as the gold standard in microbial genomics. The genomics of more complex organisms has been similarly transformed, with SMRT sequencing providing contig N50 values up to 500 times better than have been achievable with other short read technologies. Long read sequencing data also plays an important role in elucidating the full scope of cancer genome complexity as we move into the personalized medicine era. In a targeted mode, extraction of the salient features of key regions such as MHC, KIR and microsatellite regions has been enabled by its long reads and invulnerability to sequencing content bias. In a similar manner, the long reads have precipitated a revolution in understanding of RNA transcript structure through the IsoSEQ™ system. It has shown us that half or more of proteins lacked amino acid sequences in any database prior to the infusion of data from IsoSEQ™. These and other applications of SMRT sequencing have made it into an indispensable tool in genomics and will be highlighted during my talk.

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Pacific Biosciences
Menlo Park - USA

Martin Kuiper

Networks for Knowledge

Volatile organic compounds are emitted by all living cells and tissues. We seek to non-invasively 'sniff' biomarker molecules that are predictive for the biomedical fate of individual patients or cell cultures. This promises great hope to move the therapeutic windows to earlier stages of disease progression. While portable devices for exhaled volatile metabolite measurement exist, we face the traditional biomarker research barrier: A lack of robustness hinders translation to the world outside laboratories. To move from biomarker discovery to validation, from separability to predictability, we have developed several bioinformatics methods for computational breath analysis, which have the potential to redefine non-invasive biomedical decision making by rapid and cheap matching of decisive medical patterns in exhaled air. We aim to provide a supplementary diagnostic tool complementing classic urine, blood and tissue samples. In the presentation, we will review the state of the art, study some clinical application examples, highlight existing challenges, and introduce new data mining methods for identifying exhaled biomarkers. Biological networks are exploited in many ways for gaining new knowledge about biological systems. Graph analysis of networks may provide useful characteristics about the design principles and mechanisms of pathways and regulation processes. Building networks as an object of scientific study, however, may prove to be a painstaking task, calling for elaborate database and literature surveying in order to get a comprehensive network representation in a topological correct format. We have used such elaborate approaches for instance for building logical models with predictive power for anti-cancer drug efficacy. Alternatively, the Semantic Web brings promises of enhanced sharing and use of biological knowledge. Semantic Systems Biology (SSB) aims to utilise semantic web resources as an additional toolkit for integrative and modeling approaches aiming to analyse and understand biological systems. The SSB group at the Norwegian University of Science and Technology works towards ways to reach out to end-users/biologists in order to create some user-pull to direct further implementations of semantic web resources. One of our efforts resulted in the construction of a resource for gene expression regulation analysis: the Gene eXpression Knowledge Base GeXKB. GeXKB provides a resource for finding novel network candidates potentially involved in gene expression regulation. The construction of GeXKB prompted us to start efforts in the direction of ‘semantifying’ data from the source: the curation of Transcription Factor information from scientific literature. This resulted in the TFcheckpoint database (www.tfcheckpoint.org), and the publication of a set of curation guidelines for other volunteer curators to join in this effort. This work inspired us to see if we could bring together the global community interested in the domain of transcription regulation research, and we are in the process of initiating GRECO: the Gene Regulation Consortium. GRECO aims to facilitate communication between resource and technology providers, paving the way to develop one virtual integrated high quality knowledge resource that could be used for instance in the field of regulatory network building and analysis.

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Norwegian University of Science and Technology
Trondheim - NO

Education & Training
   

 

SPONSORS


 
 
     

CONTACT


For general questions: presidente@ab3c.org.br

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