Six Guest Lectures in Bioinformatics - Day 2
IBV hosts six guest lectures in Bioinformatics on Tuesday June 25th and Thursday June 27th.
PROGRAM DAY 2 (June 27th)
09.15-10.00: Modeling genomes in 3D from high-throughput sequencing data
Jonas Paulsen, Department of Molecular Medicine, University of Oslo, Norway
Abstract: Eukaryotic genomes are folded into a three-dimensional (3D) structure essential for maintaining proper gene regulation. High-throughput sequencing techniques, including ChIP-seq and Hi-C, can be utilized to probe the 3D genome. Here, I present the use of computational modeling to integrate such data into whole genome 3D models that reveal new aspects of gene regulation during stem cell differentiation.
10.15-11.00 Towards a map of transcription factor binding sites in the human genome
Anthony Mathelier, Centre for Molecular Medicine Norway (NCMM), University of Oslo, Norway
Abstract: Transcriptional regulation is essential to cell growth and differentiation and is achieved through interactions between transcription factors (TFs) and the DNA. TFs bind to the DNA in a sequence-specific manner at their binding sites (TFBSs) to regulate gene transcription. Hence, the identification of TFBSs genome-wide is a critical step towards understanding how gene expression regulation works.
I will present ChIP-eat, a uniform ChIP-seq data processing pipeline, from raw data to accurate, TF-specific TFBS prediction in the human genome. The results show that our predictions are supported by strong experimental and computational evidences for direct TF – DNA interactions. Our work culminates with the generation of a large, publicly available collection of uniformly processed ChIP-seq data sets from which we obtain accurate TFBS predictions.
11.15-12.00: Resolving genomes from metagenomes: achievements and opportunities
Christopher Quince, Warwick Medical School, University of Warwick, UK
Abstract: The direct extraction of microbial genomes from metagenomes has transformed our understanding of microbial diversity. In the first half of my talk I will explain how metagenome assembled genomes (MAGs) can be obtained through assembly and contig clustering. This will be followed by a pedagogical description of how our own algorithm CONCOCT uses both sequence composition and coverage across multiple samples to cluster contigs. I will then give a brief overview of applications of CONCOCT to a number of data sets including Tara oceans. The MAGs that result from metagenome binning are still composites of multiple strains and in the second half of my talk I will discuss how to resolve strain-level subpopulations within MAGs. I will introduce our DESMAN (De novo extraction of strains from metagenomes) pipeline and present results from tracking strains during fecal microbiome transplants. I will conclude with a description of my latest research resolving strains directly on assembly graphs and the potential of new long read technologies.