Theodore Alexandrov Head of Life Science group at the Center for Industrial Mathematics, and the head of MALDI Imaging Lab at Departments of Mathematics and Biochemistry University of Bremen Germany

Towards Spatial Systems Biology using Imaging Mass Spectrometry

Imaging mass spectrometry (imaging MS) has emerged in the last decade as a label-free, spatially-resolved, and multi-purpose bioanalytical technique for direct analysis of biological samples from animal tissue, plant tissue, biofilms, and polymer films.

After a decade of collective efforts, imaging MS became an analytical technique of choice to be a cornerstone for creating the spatial systems biology at the levels of cell populations, organ, and organism.

In this talk, I will present our first steps on the way to creating spatial systems biology using imaging MS. I will outline possible applications, highlight the challenges, and present recent research results. I will demonstrate how imaging MS can be used to understand molecular composition of mammalian organs and how data mining can be performed extracting and interpreting molecular signals for regions of pathological interest.

Rolf Apweiler Joint Associate Director and Senior Scientist The EMBL-European Bioinformatics Institute Cambridge United Kingdom

EMBL-EBI: Bioinformatics Infrastructure Enabling Life Science Research

Dr. Apweiler is Joint Associate Director of EMBL-EBI, and together with Ewan Birney has strategic oversight of all EMBL-EBI services. Prior to taking on this position he led protein resources, including the team responsible for EMBL-EBI's contribution to the UniProt Consortium. Dr. Apweiler has made a major contribution to methods for the automatic annotation of proteins, making it possible to add relevant information to proteome sets for entire organisms. Dr. Apweiler has spearheaded the development of standards for proteomics data, and his teams have maintained major collections of protein identifications from proteomics experiments (PRIDE) and molecular interactions (IntAct). He also leads EMBL-EBI’s contribution to the Gene Ontology. Rolf received his PhD from the University of Heidelberg in 1994, and has been at EMBL since 1987. His major contribution to the field of proteomics was recognised by his election to President of the Human Proteomics Organisation.

Ellen Baake Professor for Biomathematics and Theoretical Bioinformatics Faculty of Technology Bielefeld University Germany

Probabilistic Structures in Population Genetics

Evolution is a complex phenomenon driven by various processes, such as mutation and recombination of genetic material, reproduction of individuals, and selection of favourable types. These mechanisms have intrinsically random elements. The underlying stochastic processes are currently receiving increased world-wide attention, not least because they have shaped the genetic structure of present-day populations.

Population genetics (the theory of evolution at the level of individual genotypes within populations) today relies crucially on concepts such as ancestral lineages and random genealogies. The talk will provide an overview of modern lines of research and discuss how they blend into bioinformatics. Examples will include ancestral lines under selection, and ancestral recombination processes.

Cenk Sahinalp Professor and Canada Research Chair, School of Computing Science Simon Fraser University, Canada Professor, School of Informatics and Computing Indiana University, US

High Throughput Algorithms for Big Data Genomics

Sequencing projects involving hundreds of thousands of individual genomes are underway and the need for algorithmic speed is bigger than ever. We will go through some of the algorithmic developments introduced by the Lab for Computational Biology at SFU to address big data genomics, primarily involving one or more techniques in compression, streaming, memory hierarchy awareness and parallelization. Application areas for these algorithms will range from mapping to variant calling, novel isoform and fusion gene identification to clonality inference.

Peter Stadler Professor for Bioinformatics Institute of Computer Science Leipzig University Germany

Challenges in RNA Bioinformatics

With the advent of high throughput sequencing methods a wide range of new - and often nontrivial - research questions have arisen. One set pertains to the transcripts themselves. Circularized and trans-spliced RNAs, for example, have prompted the development of more sophisticated mapping tools. At the same time, discrepancies between transcript and reference genome hint at chemical modifications and editing, requiring general purpose variant calling algorithms. RNA-seq has become the preferred readout of elaborate experimental protocols to probe RNA structure and to infer RNA-protein interactions. These data in turn provide direct experimental evidence on RNA structure and call for systematic inclusion in RNA folding algorithm. In this presentation I will attempt to give an overview of recent developments in this area, with an emphasis on my group's research.

Tanja Woyke Staff Scientist and Microbial Genomics Program Lead DOE Joint Genome Institute Walnut Creek California

Title: Genomics of Uncultivated Microorganisms

Metagenomics and more recently single-cell genomics are powerful tools to explore phylogenetic and functional diversity of uncultivated microorganisms. The research presented here will focus on the exploration of metabolic potential and phylogeny of candidate phyla representatives by single-cell sequencing.