CEDAS, the Center for Data Science at the University of Bergen, and NORBIS, the Norwegian Research School in Bioinformatics, Biostatistics, and Systems Biology, invite both starting and experienced data scientists to an exciting joint summer school on data science and its biomedical applications from 7-11 August 2023.

The summer school will be held in Bergen at Hotel Zander K. It is mainly intended for PhD candidates, but also Postdocs and other researchers interested in learning more about data science are welcome to attend. As data science is relevant across a wide range of disciplines, we hope that we will be able to attract a diverse group of participants.

The summer school will feature keynotes, theoretical and practical sessions on Machine Learning, Statistics, and Visual Data Science, as well as a social program.

For more information, please visit the official summer school website: Joint CEDAS-NORBIS Summer School 2023

A Modelling-Based Investigation Of The Dynamic Behavior Of Reproductive Hormones In Girls And Wom

On May 5th Sophie Fischer-Holzhausen successfully defended her PhD thesis titled: A matter of timing – A modelling-based investigation of the dynamic behavior of reproductive hormones in girls and women. Female health is an important but often understudied field of human health. Consequently, a considerable number of individuals of reproductive age experience one or more menstrual disorders in ways that effects their abilities to work and contribute (https://news.mit.edu/2022/events-illuminate-critical-need-menstruation-science-1003). Understanding the endocrine control of the female reproductive system is one element that will help us to improve this situation. Hereby, mathematical models provide us with concepts to integrate the knowledge we have about the endocrine control of menstrual cycle in a systematic way, help to understand complex regulation processes and predict – with some uncertainty – the effect of treatments. In her thesis Sophie presents mechanistic models describing the endocrine regulation of the female reproductive system with focus on the hypothalamic-pituitary-gonadal axis (HPG axis). Her scientific work is presented in three research articles. The first two publications present a mechanistic model of the mature HPG axis and its interactions with the process of follicle maturation (folliculogenesis). The model parameters are investigated and the application of the model to predict the effects of hormonal medication is demonstrated. In a third scientific publication, Sophie proposes a Bayesian updating workflow that allows the incorporation of cross-sectional data in the model calibration routine.

Bioinformatics in Bergen 2023 Conference took place on 24-25 May at the Solstrand Hotel thanks to the financial support from the Trond Mohn Foundation.

The aim of the event was to create opportunities for networking and collaboration among all locally situated researchers that use bioinformatics in their work.

It was a privilege to have the key note speakers Marcus Weber (Zuse Institute Berlin), Selina Våge (Department of Biological Sciences, UiB) and Lukas Käll (KTH and SciLifeLab, Stockholm).

There were 27 speed talks, poster session and 3 hours workshop along with the discussions during the coffee breaks and the dinner.

We are pleased to announce that Lorensha Naidoo and Kira Höffler won the best poster and the best speed talk awards at BiB2023.

CBU leaders’ workshop took place at the Scandic City Bergen, May 15th. The focus was on grant application proposals, discussing computing resources for CBU, communication and visibility, and discussions in groups.

Alexey Nesterenko is our new Postdoctoral Fellow who has joined the CBU to contribute in simulating lipid membranes and carbohydrates, and to do biomacromolecular force field validation, under supervision of Markus Miettinen.

Alexey got his PhD in a field between computational chemistry and electrochemistry in 2014 at the Frumkin Institute of Physical Chemistry and Electrochemistry (IPCE) under supervision of prof. Yu. Ermakov. After his PhD, Alexey had positions at Belozersky Institute of Physico-Chemical Biology in Moscow State University, in Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, and finally in Federal Center of Brain Research and Neurotechnologies (all in Moscow).

During his PhD and after it, Alexey worked in a tight collaboration with the Laboratory of Bioelectrochemistry (Frumkin IPCE) where lipid membranes are studied with experimental, theoretical and computational methods. His PhD was focused on investigating the structure of electrical double layer at the lipid–water interface, which was done by assembling results of MD simulation and experimental results of cation adsorption measurements. He demonstrated how to compute accurately an adsorption constant and binding site density from MD simulation. Further he continued working with this lab analyzing lipid monolayer molecular structure and polycation adsorption on anionic lipid membranes.

In 2014–2022, Alexey worked in Laboratory of Molecular Basis of Embryogenesis (Shemyakin-Ovichinnikov IBCh) under supervision of prof. A. Zaraisky, where they studied and simulated pattern formation in early amphibian embryo using mathematical modeling with partial differential equations. He demonstrated there both experimentally and theoretically how difference in adsorption of growth factors onto heparin extracellular matrix could play role in pattern formation. At 2020–2023, he worked in mass-spectrometry data analysis in Institute of Fundamental Neuroscience (FCBRN) under guidance of prof. V. Belousov, where they obtain and analyze metabolomics and proteomics data in different experiments with rodent stroke and oxidative stress in eukaryotic

This week we received word that Eivind Valen has been awarded an ERC Consolidator Grant. Eivind has been leading the Valen group at the Computational Biology Unit at the University of Bergen for 9 years, where they are working towards solving questions surrounding regulation of gene expression. We are hugely proud of Eivind, and thrilled that he has received this well deserved grant!

Lennart is a guest researcher joining Reuter’s group who will work with us at CBU for 6 months. The goal of the project is to evaluate the ability of molecular mechanics force fields to model, through molecular simulations, the properties of peptide-bilayer systems observed from solid state NMR. The bulk of the work will be atomistic molecular dynamics simulations of 2 or 3 peptides and POPC lipid bilayers.

Tobias Ziolkowski, a guest researcher joining Michoel’s group who will work with us at CBU for 3 months.

Tobias started his PhD in January 2022 after two years of research experience at the Christian-Albrechts-University in Kiel. His working group “Magmatic and Hydrothermal Systems” at GEOMAR focuses on the topics oceanic volcanism, petrology, marine mineral resources and seafloor modelling.
Especially in the field of seafloor modelling, data sets from the deep sea are regularly used to map the oceans and to identify interesting underwater structures. Seafloor mapping depends strongly on the data quality of the recorded data.
During his PhD time so far, Tobias has dealt intensively with the identification of outlier in multibeam echo-sounder data and has already been able to automatically identify them with density- and distance-based methods and machine learning.
During the research stay Tobias hopes to enhance his skills in causal structure learning algorithms and causal inference to further optimize my approach.

We are glad to host Meije Mathe, a MSc Bioinformatics student at the University of Rouen Normandie, in France. Along with her master’s degree, Meije worked for 2 years as an apprentice at the Institute Pasteur of Paris.
The aim of her apprenticeship project was to decipher the informational content of epigenome mediated regulation in the switch from a healthy to a cancerous cell state.
She learned a lot about epigenetics, cancer development in humans, and developed a new method for epigenomics data integration.
Meije is very enthusiastic to start her M2 internship at the CBU, under the supervision of Håkon Dahle.
This will be a great opportunity to explore new research fields in a different cultural environment, as well as gaining professional experience before enrolling in a PhD program.
Meije’s work here will focus on investigating the phylogeny of dominating metagenomics assembled genomes from various hydrothermal systems along the Arctic Mid Ocean Ridge.

Postdoc Anna-Simone Frank from the Computational Biology Unit (CBU), Department of Informatics, Faculty of Mathematics and Natural Sciences, has been selected as one of 15 delegates into UIB’s flagship development program – Momentum.

The Momentum program is for early-stage researchers (postdocs, researchers, or associate professors), who wish to pursue an academic career at a research university.

As part of the program, Anna-Simone will attend 5 seminars in 2023, which are structured around career development and external funding. To further support her career development, she receives a stipend of 100 000 NOK that can be spent on mentoring, travel, networking, research stays, conferences, workshops, and other activities.

Anna-Simone Frank is very grateful to the Faculty of Mathematics and Natural Sciences for having the opportunity to be part of this excellent program, which comes just at the right point in her career!

For more information about the Momentum Program visit its website