Universiteit Leiden

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This Week’s Discoveries | 26 September 2017

26 september 2017
Oort Building
Niels Bohrweg 2
2333 CA Leiden
De Sitterzaal

First lecture

A large role for small peptides

Vera is professor of Computational Biology at IBL. Her research group applies existing computational methods and also develops new algorithms. Depending on the biological question, they pick from an array of bioinformatic methods including genomics, proteomics, molecular phylogenies, 3D modeling, network analysis and data integration to gain more insight into biological systems.

Recently, small peptides have gained attention in molecular biology in all domains of life. We found that in bacteria many putative small peptides are actually essential and even in human cells the presence of short Open Reading Frame (sORF) encoded peptides has been shown. Where traditionally these peptides have been ignored in gene prediction, as their coding signal is submerged in the background noise of non-coding parts genomes, now with advancement of technologies we can start to identify them not only in plants and animals but also in fungi and bacteria. Using bioinformatics methods we try to uncover the role these peptides play in the cell. To achieve this, we combine comparative genomics, sequence analysis and three-dimensional modeling. We find many putative interactions between small peptides and larger proteins, suggesting they have a large role in signaling.

Second lecture

Parallelism in Depth

Alfons started as an assistant professor at LIACS in June this year. He studies parallel systems and their correctness. Alfons was awarded a VENI grant from NWO in July 2016.

Finding the fastest route through busy traffic, deciding correctness of complex digital systems and analyzing biological, social-media, or computer networks are all problems that are solved efficiently by “depth-first” search algorithms. These algorithms do not scale on modern computing hardware, which features an ever greater amount of parallelism. Based on the successful parallelization of two depth-first algorithms, we aim to parallelize many others by using a similar strategy. To ensure correctness of both algorithms and implementations, we will employ automated verification.

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