Oral presentations can range in length from 5 to 25 minutes.

Based on the submitted abstract, the respective session chairs of each session will decide on the presentation length and inform the author(s).

Dedicated poster sessions will take place on Tuesday and Wednesday.

See previous descriptions. Authors selected for an oral presentation in this category are highly encouraged to present a poster too.

Software demonstrations will take place in parallel with the poster sessions.

Title: Data-driven efforts in understanding health and disease

Chairs: Katja Baerenfaller & Konstantin Popadin

Description: Differences between individuals determine the susceptibility to infections, the response to treatments, and the risk of developing various diseases. In addition, diseases are influenced by complex interactions with the environment including the microbiome. On the other hand, similar disease phenotypes can be caused by distinct pathobiological mechanisms termed disease endotypes. Efforts in understanding health and disease therefore involve genomics with genome-wide association studies to identify variants associated with a specific trait, transcriptomics and proteomics to identify differences in gene expression patterns between healthy and disease populations, the assessment of risk factors in environmental interactions, of features to distinguish disease endotypes and of factors to predict treatment outcomes, and modern computational approaches to integrate the different datasets including patient information. In this session we welcome contributions of data-driven efforts that aim at gaining a deeper understanding of health and disease.

Topics include but are not limited to: genetic risks, GWAS, risk factors, mutational burden, ‘omics technologies, machine learning, complex traits, precision medicine

Title: Genes and genomes in the age of next generation sequencing

Chairs: Olivier Delaneau & Natasha Glover

Description: Next generation sequencing has become commonplace, and we are now entering an age where whole genome sequences are “a dime a dozen”. Thousands of different eukaryotic species’ genomes have been sequenced to date, with certain species such as humans sequenced hundreds of thousands of times over. But this is just the tip of the iceberg. The Earth BioGenome Project aims to sequence all 1.5 million known eukaryotic species in 10 years. With all this data comes a wealth a potential biological knowledge. Additionally, there must be efficient and smart ways to make sense of all these genes and genomes. The ‘-omics’ data presents layers of complexity in the form of gene expression, regulation, network interaction, epigenetics, structural, functional, and comparative genomics and more. In this session, we invite talks from SIB members which tackle these topics.

Topics include but are not limited to: bioinformatics tools for analysing genes and genomes; gene network analysis; gene regulation genomics; genome assembly, annotation and comparison; structural variant identification; gene function prediction and analysis; genomic interactions; analysis of genome-scale data; chromatin biology; epigenetics and transcriptional regulation; gene and genome evolution.

Title: Structural bioinformatics: innovative tools to address bio-macromolecular structure

Chairs: Vincent Zoete & Chan Cao

Description: The extensive use of sequencing technologies is causing a renewed interest in structural biology and bioinformatics. Three-dimensional structures of bio-macromolecules constitute an invaluable source of information to understand and predict the consequences of polymorphisms and somatic mutations, while they remain the cornerstone of structure-based drug design and protein engineering. Technical progress is providing an ever-increasing amount of high-quality experimental data, which requires computational approaches to process. These data are also being integrated with information regarding for instance biology and function, existing variants, and binding partners such as proteins or drug-like molecules. Moreover, theoretical prediction of bio-macromolecule tertiary and quaternary structures remains crucial to cover experimentally unexplored regions of the structural space. This session is dedicated to projects related to the collection, prediction, dissemination and use of bio-macromolecular structures.

Topics include but are not limited to: databases of bio-macromolecular structures; theoretical prediction and experimental characterization of tertiary and quaternary bio-macromolecular structures, including X-ray crystallography, NMR spectroscopy, electron microscopy and small angle X-ray scattering; molecular simulation and modelling; drug design; protein engineering; personalised medicine.

Title: Ecosystems bioinformatics in ecology and agriculture

Chairs: Maria Anisimova & Théo Gaboriau

Description: The living world presents numerous intricate complexities that we strive to understand by combining data analysis approaches with observation and experiments. Ecosystems vary greatly in size and diversity, for example from whole oceans, to the human gut microbiome, to simplified model systems that we use to understand interactions between organisms. Development of new bioinformatics tools and computational approaches enable us to infer complex evolutionary histories and adaptive changes and relate these to changing ecosystems. These methods help us understand the dynamics and equilibria ruling the living world in a changing environment, and offer real applications from biotechnology to biomedical research as well as in conservation biology, ecology, and agriculture. Sequencing data provide a large and varied source of information that require tools and models to investigate patterns of micro- and macro-evolutionary processes within and between species. This session aims to showcase the research of SIB groups working on unravelling the dynamics and mechanisms underlying interactions at many levels, often with applications to ecology and agriculture.

Topics include but are not limited to: speciation biology; microbiomes of all shapes and sizes; eukaryotic and prokaryotic diversity; research applications in biotechnology, agriculture, or ecosystems management; quantitative models; morphology; host-microbe interactions; ecological and evolutionary factors in communities.

Title: Evolutionary modelling with trees and traits

Chairs: Anna-Sapfo Malaspinas (reviewer), Manuel Gil (reviewer), Tim Vaughan (reviewer and session chair) & Gwénaëlle Bontonou (session chair)

Description: Comparative genomic analyses amongst diverse species and within a species can illuminate the evolutionary forces driving how species have evolved and are evolving. Phylogenetics forms a cornerstone of such analyses as it provides the evolutionary framework of the relationships between species or individuals upon which many inferences are based. The development of models and software to better understand the evolution of organisms aims to take advantage of the growing amounts of genetic and genomic data that catalogues life on our planet. This often involves taking into account the interplay of population structure, trait architecture, and selection to disentangle causes and consequences. Also critical are robust comparative methods from sequence alignment to phylogeny inference, as well as for inferring complex evolutionary histories. Delineating these histories also helps us understand the functional relationships between genes, genomes and species. Such approaches have important applications in epidemiology, public health and medicine, as well as in ecology and evolution.

Topics include but are not limited to: bioinformatics sequence analysis tools and models; statistical tools in population genetics; likelihood, Bayesian, and other methods; phylogenetics and phylogenomics; biostatistics; comparative genomics.

Title: Systems biology: solving puzzles with missing pieces

Chairs: Robert Ivanek & Anastasiya Börsch

Description: Biological systems ranging from individual cells to entire organisms have a complex structure and produce a variety of responses to changes in intrinsic as well as extrinsic environments. Biological mechanisms underlying these responses are also intricate based on the interplay between numerous components on different levels. Data types in systems biology are often extremely varied, from genetic and genomic, to clinical phenotypes, images and 3D structures, as well as proteomics and metabolomics data. Bioinformatics develops algorithms to carry out computational and mathematical analysis and modelling of complex biological systems, that together can illuminate mechanisms driving such systems and even address their evolution in time. The aim is to better understand and/or predict various phenomena in biology. This session covers all studies aiming to uncover interactions between components of biological systems and understand systems behaviour in healthy as well as disease conditions.

Topics include but are not limited to: multi-omics data integration; single-cell data integration; precision medicine; synthetic biology; modelling complex dynamics; multi-cellular systems

Title: Proteins and proteomes, from data to knowledge

Chairs: Lydie Lane & Julien Racle

Description: Proteins are key for nearly every task performed by a living organism, from shaping cells to defending them against pathogens. Recent technological advances allow their characterisation at a larger scale, but there remains a crucial need for further integrating the data generated in order to improve our understanding of the proteomes and find novel biomarkers or drug targets, for example. In this session, we are interested in everything relating to proteins such as measuring and analysing their expression levels, their modifications, their interactions and their biological roles.

Topics include but are not limited to: development of novel mass spectrometry tools and workflows for proteomics, immunoproteomics and metaproteomics; annotation and prediction of protein function; prediction and characterization of protein-protein interactions, as well as interactions with small molecules, DNA or RNA; analysis and annotation of proteoforms and post-translational modifications; discovery of biomarkers for health and disease; protein production and bioengineering; antibody-based studies.

Title: Mathematical and computational approaches to solve biological problems

Chairs: Luciano Cascione (reviewer and session chair), Emilie Pasche (reviewer) & Franziska Singer (reviewer and session chair)

Description: The quantity of data generated by the life sciences has grown exponentially over the years, the best way to handle and analyse the massive data generated is still a major challenge. It is also necessary to explore them with a systematic approach to reveal the behaviour of the system as a whole rather than as the sum of its parts. Hence, this session of SIB Days 2020 brings together researchers to discuss statistical and algorithmic approaches to improve data management, analysis, curation and interpretation.

Topics include but are not limited to: text mining, machine learning, language models and pattern recognition; Bayesian approaches; read mapping for second and third generation sequencing technologies; analysis of high-throughput biological data (transcriptomics, proteomics, metabolomics, fluxomics); techniques for managing (e.g., data compression) and visualizing massive amount of sequencing data; methods for analysis of RNA sequencing (RNA-seq) data, including RNA expression, novel transcript assembly and splicing; methods for novel sequencing technologies such as single-cell sequencing, linked-read sequencing and Hi-C; epigenetics and gene regulation, including ChIP-seq analysis, methylation profiling, and histone modification; curation support tools; personalized health.