Interfaculty Bioinformatics Unit

Welcome to the Interfaculty Bioinformatics Unit | IBU.

We specialize in next generation sequencing (NGS) technologies and genomics data science. We work closely with researchers from study design and conceptualisation to advanced data analysis.

We regularly contribute to large-scale interdisciplinary research projects and develop data processing pipelines and tools for data exploration and visualisation. We are equipped with state-of-the-art computational infrastructure and have access to a comprehensive software repository.

We train the next generation of bioinformaticians through our own research projects, specific courses and our Master program in Bioinformatics and Computational Biology.

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News

New OpenProject Features: simplifying collaboration with customers

The IBU collaborates on numerous projects with various partners each year, so we are committed to continuously improving our project management. Recently, we hired a software engineer to customize a plugin for OpenProject that specifically addresses our unit's unique requirements. With these improvements, our customers will benefit from a more comprehensive project overview, streamlined reporting capabilities, and a simplified project initiation process at the IBU.
More details will follow next month.

NOMIC: a hub for omics data analysis of non-model organisms

Many researchers within the university work with non-model organisms (i.e. not human or mouse). However, performing data analysis on data from such organisms poses many challenges. IBU received funding to set up a hub to encourage knowledge exchange and support such challenging but important projects. The project will start in January 2025. Already interested? Contact Geert van Geest (geert.vangeest@unibe.ch).

Bring Your Own Data - IBU joining forces with DSL

The IBU team is joining the "Bring your Own Data" events next week (on Oct. 14th and Oct. 15th only).

New projects - new MSc students at the IBU!

With their 3rd semester starting, we have three master students joining us for the research project. We look forward to be working with them!

Promotion of Young Researchers of the University of Bern

Dr. Joana Carlevaro-Fita received the funds in regards to the above stated program. Congratulations!

Teacher of the Year: 2023-2024

Stephan Peischl is awarded Teacher of the Year, 2023-2024. Congratulations!

Approved SNSF grant!

Stephan Peischl's SNSF grant got approved. Congratulations! It titles «Evolutionary
dynamics of chromosomal inversions and local adaptation».

Innovative Resource Award: Thomas Roder with OpenGenomeBrowser at the SIB Bioinformatics Award ceremony 2023

Thomas Roder's OpenGenomeBrowser Wins SIB Innovative Resource Award at [BC]² Conference!

Thomas Roder, IBU staff scientist, has been honoured with the prestigious Innovative Resource Award from the Swiss Institute of Bioinformatics at the [BC]² Conference. The award honours Thomas’s outstanding contribution to the field of comparative genomics through the development of the software OpenGenomeBrowser.
It comes with a generous cash prize of 10,000 CHF to support continued development of the software.

latest IBU publication

OpenGenomeBrowser: a versatile, dataset-independent and scalable web platform for genome data management and comparative genomics

IBU at Nacht der Forschung 2022!

IBU will be at Nacht der Forschung 2022. Come visit us at room 117 in the main building (Hochschulstrasse 4), we will be there between 4pm and midnight.
LEGO und Erdeeren? Erbgut erforschen.

Thomas Roder wins best poster award for "OpenGenomeBrowser"

At the SIB Bioinformatics Summit conference, Thomas Roder received an award for the software "OpenGenomeBrowser" poster presentation.
You can check out his website here.

Biparatopic sybodies neutralize SARS-CoV-2 variants of concern and mitigate drug resistance

Together with Philippe Plattet of Neurovirology at Vetsuisse and the Group of Markus Seeger at UZH we have published a paper on how synthetic nanobodies can help to cure COVID now and in the future.

CAIM Research Fund Award: Preventing kidney stones in a personalized way

The project “Machine learning models in the prediction of kidney stone recurrence”
was awarded to Prof. Dr. Daniel Fuster and PD Dr. Rémy Bruggmann for full funding in the CAIM Research Funding Call 2021/22.

Morganella morganii, a biogenic amine producer from cheese

Biogenic amines in cheese may pose a risk to consumers. Researchers from the University of Bern and Agroscope provide a detailed insight about the biogenic amine producing bacterium Morganella morganii.

Video

OpenGenomeBrowser

OpenGenomeBrowser is a self-hostable, open-source software that manages access to genomic databases and drastically simplifies basic comparative genomics analysis steps. It allows users to filter genomes based on metadata, create phylogenetic trees, search for annotations, align genes, compare gene loci, interactively browse biochemical pathways, study dotplots, search for orthologous genes, perform gene trait matching, execute BLAST searches, and access the raw data.

New analysis workflows

We have set up new analysis workflows for spatial transcriptomics and epigenomics.
Check out our services page for more information.

BBBHub online

The BBBHub is a data hub which centralizes and organizes raw and processed RNA-Seq data from reserch in the field of Brain Barriers. This data hub is spearheaded at the Interfaculty Bioinformatics Unit of the University of Bern and is part of the European network BtRAIN.

Special cells contribute to regenerate the heart in Zebrafish

It is already known that zebrafish can flexibly regenerate their hearts after injury. An international research group led by Prof. Nadia Mercader of the University of Bern now shows that certain heart muscle cells play a central role in this process. The insights gained could be used to initiate a similar repair process in the human heart.

Bioinformatics und new Sequencing Technologies

Collegium Generale Lecture Series: Dr. Rémy Bruggmann, head of the IBU and BCPM management board member, speaks about Bioinformatics und new Sequencing Technologies (Podcast in German).

Single cell transcriptome atlas of the Drosophila larval brain.

The latest publication of Dr. Rémy Bruggmann can be found on elifesciences.org.

One Health Website online

The Interfaculty Research Cooperation "One Health: Cascading and Microbiome-Dependent Effects on Multitrophic Health" examines causal relationships between environmental, animal and human health. We investigate how environmental chemicals such as heavy metals, pesticides and plant secondary metabolites affect microbial communities and health at the interfaces between soils, plants, animals and humans. By unraveling underlying mechanisms, our work contributes to a better understanding of integrated health and supports the development of healthy food chains.
[Text from onehealth.unibe.ch]

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Contact

University of Bern
Bioinformatics and Computational Biology

Baltzerstrasse 6
3012 Bern

Phone: +41 31 684 48 99