UBC Annual Symposium

This year will feature our sixth edition of the yearly Utrecht Bioinformatics Center Symposium. Save the date to join a full day of interesting keynotes, local PI’s and selected talks from PhD candidates and postdocs as well as a poster session during lunch.

October 7th 2019

Geertekerk | Geertekerkhof 23 | 3511 XC | Utrecht


Send your poster Title and Abstract before September 14th

to: c.c.heuzer@uu.nl



9:00 – 10:00 Registration
10:00 Welcome by Adrien Melquiond
10:15 Keynote: Thijs Ettema, Wageningen University and Research. On the archaeal origin of eukaryotes
11:00 Coffee break
11:30 Session 1
PI Talk: Vlad Cojocaru, Hubrecht Insititute, Structural modeling and molecular simulations of protein-DNA interactions
Talk 1: Roy Straver, UMCU, Consensus calling using raw nanopore data for Cyclomics-seq
Talk 2: Laura Dijkhuizen, UU, Partners&Passengers: Endophytic microbes persistently present in the genus Azolla revealed by comparative metagenomics
12:40 – 14:30 Walking lunch and Poster Presentation
14:30 Session 2
PI talk:  Anita Schurch, UMC Utrecht, Prediction and exploration of the pan-plasmidome of medically relevant bacterial species
Talk 3: Niels Aerts, UU, Architecture and dynamics of hormone-driven gene regulatory networks in plant immunity
Talk 4: Rurika Oka, PMC, Characterizing the etiology of pediatric acute myeloid leukemia by studying mutation accumulation in normal hematopoiesis
15:40 Coffee Break
16:00 Keynote speaker: Sara Pulit, Vertix Pharmaceuticals, San Diego, Bringing genetics to drug discovery: What computational biology can (and can’t do – yet) to help find new medicines
16:45 Award Ceremony: Poster Price
17:00 Drinks and Social Event
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Sara Pulit | Bringing genetics to drug discovery: What computational biology can (and can’t do – yet) to help find new medicines

from Vertex Pharmaceuticals, San Diego: Sara has been working in Utrecht, with a strong emphasis on genetic association studies to unravel genetic predispositions for different diseases. She has recently moved to Vertex Pharmaceuticals where she continues to apply genetics and bioinformatics in an industrial setting.

Abstract: The mapping of the human genome nearly two decades ago has resulted in a tidal wave of genetic discoveries. Linkage analyses revealed the underpinnings of rare diseases, genome-wide association studies yielded insights into common diseases, and sequencing continues to uncover the genetic keys to an array of syndromes and disorders. With this veritable mountain of discoveries before us, a primary aim of genetics (and computational biology more broadly) is to discover if and how these findings can lead us to transformative medicines for serious diseases. In my talk, I will describe how genetic studies – performed even before the human genome had been mapped – paved the way to our understanding of cystic fibrosis (CF) and in turn informed existing therapeutics for the treatment of CF. I will also discuss how genetics and computational biology has transformed and continues to transform the drug discovery process.

Thijs Ettema

from Uppsala University (Sweden): Dr. Ettema’s lab is focused on characterizing microbial diversity using state-of-the-art technologies such as single-cell sequencing and metagenomics. By assessing microbial diversity, he is also attempting to gain additional insights in evolutionary differences between the main domains of life.

Vlad Cojocaru | Structural modeling and molecular simulations of protein-DNA interactions

I will present here our recent efforts in understanding the mechanisms by which transcription factors recognize DNA in different chromatin contexts. Transcription factors are proteins that regulate gene expression by binding to DNA regulatory regions to activate or repress the transcription of genomic DNA into RNA. Many transcription factors are involved in determining the identity of a cell and usually just a few of them are sufficient to convert between different cellular states. Such conversions have important applications in regenerative therapies but are often inefficient and uncontrollable. Understanding the mechanisms by which transcription factors recognize their sequence specific binding sites on DNA and especially on DNA wrapped in chromatin will provide means to optimize cell state conversions. I will demonstrate how molecular simulations can be used to decode these mechanisms.

Anita Schürch | Prediction and exploration of the pan-plasmidome of medically relevant bacterial species 

In bacteria, a considerable part of the genome can be encoded on mobile genetic elements. These mobile genetic elements disseminate important traits such as antibiotic resistance genes which can spread through different hosts and environments. However, the reconstruction of mobile genetic elements such as plasmids from short read genomic and metagenomic sequencing data is challenging. I will present novel computational strategies to reconstruct plasmids and their potential to study plasmid sequences at the bacterial species level. This allowed the  exploration of the pan-plasmidome of Enterococcus faecium, an important multi-drug resistant nosocomial pathogen. We observed that isolates from hospital patients carry more plasmid sequences than isolates from other sources. Moreover, plasmidomes rather than chromosomes are highly specific for the isolation source.