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Centre for Computational Life Sciences (CCLS)

CCLS Past Events 2021

We will continue our popular seminar series online as long as the regulations concerning the Covid pandemic require this. We are planning the meetings on the 3rd Tuesday of the month at 2 pm, unless otherwise announced.

12 October 2021: Bas Goulooze

Please click for the slides of the talk (PDF).

Modelling withdrawal symptoms in critically ill children

Children admitted to the intensive care can require large amounts of sedative drugs and painkillers. This puts them at a great risk for withdrawal symptoms once treatment with these drugs is stopped. We need more knowledge to avoid withdrawal in children, but available data is limited and many research questions remain unexplored in clinical studies due to ethical constraints. In this presentation, I will present how we leveraged available literature knowledge in combination with a novel modelling technique to analyse clinical withdrawal data in children. Using the model, we simulated ‘what if’ scenarios to generate new clinical hypotheses.

21 Sept 21: Bert van Duijn - IBL

Experimental modelling in the Plant Biodynamics Laboratory: Polar and intracellular transport of the plant hormone auxin.

The Plant Biodynamics Laboratory (PBDL) favours multidisciplinary research. Depending on the problems under investigation, PBDL establishes collaborations between experts from for example molecular genetics, molecular and electro cell physiology, biochemistry, organic chemistry, analytical mathematics, mathematical statistics and computational sciences.

The plant hormone auxin (IAA) belongs to a complex system of chemical messengers which have a pivotal role in the coordination of growth and development between different parts of the plants, such as for example the shoot and root system.

We investigate the dynamics of long-distance polar auxin transport (PAT) by mathematical and computational analysis of experimental transport data. In particular, we investigate the functional role of the so-called PIN proteins which are assumed to be the polar distributed intracellular auxin-anion export carriers as postulated in the chemiosmotic theory of PAT. Our results already suggest that in spite of all the indirect evidence PINs are not solely or not at all responsible for PAT.

In addition we investigate the green algae Chara as model system for intra and inter cellular transport processes. Although it is known that Chara produces the natural auxin IAA, its transport and mechanism of action in Chara were unknown. However, over the past few years we were successful to be the first in demonstrating the presence of directional transport of IAA comparable to polar auxin transport (PAT) in terrestrial plants. Our program is now aimed at understanding the intracellular mechanism of this transport.

Seminar Bert van Duijn

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Tuesday 15 June Manix Medema; University of Wageningen

Title: Computational Omics Strategies for Natural Product Discovery 
Plants, fungi and bacteria produce a wealth of specialized metabolites, which are a great source for natural product drug discovery. Due to the accelerated accumulation of omics data, computational methods have become more and more important to identify these molecules and to assess their biological activities. Here, I will highlight the work performed in my research group on using these approaches to accelerate natural product discovery. Specifically, I will discuss the use of computational approaches to investigate biosynthetic diversity across large numbers of genomes, integrative genome/metabolome mining to link gene clusters to molecules, and computational approaches to predict biological activities of molecules based on omics data. 

Marnix Medema - Computational Omics Strategies for Natural Product Discovery

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Tuesday 18 May at 2 pm: André Leier, University of Alabama, USA

Title: Computational Approaches for the Development of Gene Therapies

Unfortunately, there is no video available for this talk as the information that was shared had not been published as yet.

Richard Allmendinger: Experimental challenges in drug design and discovery optimization

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Tuesday 20 April at 2 pmRichard Allmendinger, The University of Manchester
TitleExperimental challenges in drug design and discovery optimization
Evaluating candidate solutions by conducting an experiment, e.g. a physical, biological or chemical experiment, can be expensive, time-consuming and resource intense. Drug development is a prime example where optimization relies on experiments. This talk will provide an overview of some non-standard challenges arising due to experiments, such as non-homogeneous per-objective evaluation times in a multi-objective problem, dynamic resource constraints, and non-static drug libraries in a drug discovery problem. Some existing techniques to cope with these challenges will be introduced, and, finally, promising areas of future work discussed. 

Thursday 18 March at 4 pm: Nataša Jonoska, University of South Florida, USA
Title Detecting complexities in a scrambled genome through spacial graphs
DNA rearrangement is a process found on both developmental and evolutionary scale. The process itself and the molecular shape at the time of the rearrangement can be modeled through 4-regular graphs.  These graph models are illustrated through the rearrangement processes in a well studied ciliate species Oxytricha trifallax where DNA recombination is observed on a massive scale.  Our studies show gene segments that recombine during DNA rearrangement processes may be organized on the chromosome in a variety of ways. They can overlap, interleave or one may be a subsegment of another. We use colored directed graphs to represent contigs containing rearranged segments where edges represent recombining segment organization. Using graph properties we associate a point in a higher dimensional Euclidean space to each graph such that cluster formations and analysis can be performed with various methods. The analysis shows some emerging graph structures indicating that segments of a single gene can interleave, or even contain,  all of the segments from several other genes in between its segments.

Joost Batenburg: Tomographic Techniques for Life Sciences

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Tuesday 16 February at 2 pm: Joost Batenburg, Professor of Imaging and Visualisation, Leiden Institute for Advanced Computer Science, Leiden University 
TitleTomographic Techniques for Life Sciences
In this talk I will go over various types of tomographic imaging (CT scanning, electron tomography, optical tomography) that are used for biomedical and life science research. A key step in each of these imaging modalities is the tomographic reconstruction step, where the data acquired by the imaging instrument is turned into a 3D representation of the specimen. While this operation is usually hidden inside the instrument’s software, it can dramatically influence the resulting image quality, imaging artefacts, and as a result the ability to observe key internal processes with sufficient accuracy. 
I will discuss various recent breakthroughs in algorithms and machine learning models that enable to compute high quality images from severely undersampled data, and to do so in real-time, leading to an interactive computational imaging instrument.


Tuesday 19 January at 2 pm: Jeroen Codée, Professor of Organic Chemistry, Leiden Institute of Chemistry, Leiden University
TitleComputation chemistry to understand reactive intermediated and direct stereoselective synthesis
Chemically synthesized carbohydrates (glycans/oligosaccharides) are indispensable in biochemical and medical research. Their synthesis is challenging because of the highly reactive intermediates that play an important role in connecting different carbohydrate building blocks. We have developed computational strategies to understand how the structure of these fleeting species governs their reactivity. Rather than studying a single example, we have mapped the reactivity of a large family of related species to establish structure-reactivity rules. The body of systematic experimental data that we are currently gathering may be used in the future to computationally predict the outcome of glycosylation reactions eventually enabling the in silico design of synthetic routes to fast-forward oligosaccharide synthesis and boost glycobiological and glycomedical research. 

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