News | Scibiome

Congratulations to Dr. Lisa-Marie Bente on her successful PhD defense!

Mon, 14 Sep 2026 00:00:00 +0000

Congratulations to Dr. Lisa-Marie Bente on her successful PhD defense!

We are delighted to announce that Lisa-Marie Bente successfully defended her PhD thesis, “Three-dimensional Image Processing in Biomedicine,” on 14 September 2026, here at BRICS. Congratulations, Dr. Bente!

Her dissertation spans three projects on image analysis in biological and medical settings. The first applies state-of-the-art deep learning and explainability techniques to automate labour-intensive manual lab work. The other two projects are particularly striking: they show that the newest and most complex approach is not always the best route. Instead, smartly arranging simpler techniques can yield results that are more robust, more interpretable, and better performing than their fancier alternatives.

It is a message we find well worth sharing. In a field that tends to chase ever-increasing complexity, Lisa’s work is a thoughtful reminder to weigh that complexity against robustness and simplicity.

Lisa, it has been a pleasure to watch you grow into the researcher you are today. The whole team congratulates you and wishes you all the best for what comes next!

Day of Young Software Developers: Award for Students of the Division Data Science in Biomedicine

Tue, 23 Jul 2024 00:00:00 +0000

On July 11, students from the Technical University of Braunschweig presented the results of this year’s software development internship. The event provided a platform for aspiring developers to showcase their semester projects and compete with other talents from the fields of Computer Science, Business Informatics, and Information Systems Engineering.

Three teams were awarded for their innovative projects:

1st Place: "Virtual Reality Learning Environment for Children with ADHD"

2nd Place: "Radlritter"

3rd Place: "Mixed Reality Multiplayer without Cloud"

A team of students from the Division Data Science in Biomedicine secured second place with their innovative project “Radlritter.” The students developed an app for safe bicycle navigation based on data from the OpenBikeSensor, a system for measuring passing distances of cars to bicycles. With this app, users can plan routes along streets where cars maintain a greater distance from cyclists, thereby increasing cyclist safety.

This app offers a practical application that directly contributes to improving traffic safety and showcases the students’ ability to find technological solutions for real-world problems.

During the development of this app, the team also received valuable support from the Institutes of Computer Graphics and Machine Tools and Production Technology.

We are proud of the achievements of our students and delighted with the recognition the Division Data Science in Biomedicine has received for this valuable project. Remarkably, this marks the second consecutive year our students have secured a spot in the top three. Congratulations to all involved and many thanks for their dedication and creativity!

Successful workshop on computer modelling in biology and medicine 2024 in Dresden

Wed, 10 Jul 2024 00:00:00 +0000

On 6 and 7 June 2024, the workshop of the GMDS/IBS-DR working groups ‘Mathematical Models in Medicine and Biology’ and ‘Statistical Methods in Bioinformatics’ took place in Dresden. Researchers from systems biology, bioinformatics and biostatistics discussed the latest advances in the modelling of biological systems and the development of statistical methods in biology and medicine. Markus Wolfien (University Hospital Carl Gustav Carus, Dresden) described the workshop as a “great success”, emphasising its importance for scientific exchange and networking.

The programme covered topics such as artificial intelligence in translational medicine, integration of different types of data in models, genomics, proteomics and analysis of single- cell data. Keynote speakers were Anne-Christin Hauschild (University of Göttingen), Kathrin Thedieck (University of Innsbruck) and Carsten Marr (Helmholtz Centre Munich).

Lisa-Marie Bente presented the project “Semi-Automatic Dead-End and Gap Correction for Metabolic Models (SAMC)” by Martin Piepgras on the automatic correction of metabolic models. Viviane Steinberg shed light on “Delineating immune escape mechanisms in acute myeloid leukaemia through single-cell analyses” by investigating immune evasion in CAR-T cell therapy for AML.

The workshop was supported by GMDS and IBS-DR at the Centre for Regenerative Therapies (CRTD) in Dresden. We would like to thank all participants for an inspiring workshop.

Paper 'On the limits of 16S rRNA gene-based metagenome prediction and functional profiling' now available

Mon, 04 Mar 2024 00:00:00 +0000

The paper “On the limits of 16S rRNA gene-based metagenome prediction and functional profiling” coauthored by Tim Kacprowski has now been published in Microbial Genomcis.

The publication titled 'Inference of differential gene regulatory networks using boosted differential trees' now published in Bioinformatics Advances.

Mon, 04 Mar 2024 00:00:00 +0000

The paper “Inference of differential gene regulatory networks using boosted differential trees” coauthored by Tim Kacprowski has now been published in Bioinformatics Advances. BoostDiff is available at click hier.

P4D: Our Group is Part of the Largest German Study to Improve Treatment of Depression

Fri, 23 Dec 2022 00:00:00 +0000

Using biomarkers to find individualised diagnosis and therapy paths – what already works in oncology should also become possible in psychiatry. The project entitled “Personalisierte, prädiktive, präzise und präventive Medizin zur Verbesserung der Früherkennung, Diagnostik, Therapie und Prävention depressiver Erkrankungen“ (P4D) (Personalised, Predictive, Precise and Preventive Medicine to Improve Early Detection, Diagnosis, Therapy and Prevention of Depressive Disorders) aims to develop individualised treatment approaches with the help of biomarkers, but also magnetic resonance imaging, brain wave measurements and sleep diagnostics.

Up to now, patients with depression have all been treated according to the same scheme. Although psychotherapy and/or antidepressants lead to a considerable improvement in depression in many patients, these treatment methods are not effective or not sufficiently effective for some of those affected. This is due to the fact that different brain dysfunctions are hidden behind the clinical picture on a neurobiological level. For this reason, research is working to identify these and to develop individualised diagnosis and treatment methods for patients.

Instead of trying out different treatment methods, as has been the case up to now, it should be possible in future to determine the best therapy for the patient at the beginning of the depression treatment. In this way, more people with depression can be treated more effectively. On the other hand, those involved in the project also expect a faster improvement in the quality of life for the patients and hope to be able to avoid a chronification of the depression. “To this end, we will not only develop new risk scores, but also integrate and evaluate the molecular data using systems medicine. In this way, we expect to identify molecular mechanisms that can explain the different therapy response behaviour,” Professor Tim Kacprowski describes the sub-project of TU Braunschweig, which will start in September 2024.

About the study The study, which is funded by the Federal Ministry of Education and Research (BMBF) with 10 million euros over five years, involves seven universities (Hannover Medical School, Leibniz University Hannover, Technische Universität Braunschweig, Greifswald University Medicine, Würzburg University Clinic, Kiel University and Goethe University Frankfurt am Main) as well as the Fraunhofer Institute for Toxicology and Experimental Medicine, the Stiftung Deutsche Depressionshilfe (German Depression Aid Foundation) and the Bavarian company BioVariance.

Around 1,000 patients are recruited for P4D. The study is characterised by the fact that the test persons are examined comprehensively and very different parameters are recorded. In addition to magnetic resonance imaging, electroencephalography and sleep analyses, physical examinations, various questionnaires and blood samples are also evaluated. By collecting as much information as possible about the patient, this can be used to tailor the therapy individually to the person concerned.

Original press release of TU Braunschweig: https://magazin.tu-braunschweig.de/en/pi-post/with-individualised-medicine-against-depression/

PLRI will co-host HealthHack 2023

Mon, 19 Dec 2022 00:00:00 +0000

HealthHack 2023 - we’ll be a part of it! On March 4 and 5 it’s hack, tinker, code for the health and care of tomorro wat the TRAFO Hub in Braunschweig! As a participating institution, we are looking forward to many exciting ideas. Will we see you in Braunschweig? Register now! More information can be found here!

KI4ALL: Teaching more Artificial Intelligence in university

Thu, 25 Aug 2022 00:00:00 +0000

Artificial Intelligence (AI) is considered one of the leading technologies of the future. However, a responsible application of AI requires knowledge about its fundamentals, so called AI literacy.

Introducing the KI4ALL initiative, the universities TU Braunschweig, TU Clausthal and Ostfalia aim to teach AI topics to a wider audience, including students and employees. The universities plan to create a joint course catalog offering a variety of contents such as online lectures and practical labs.

More information: https://magazin.tu-braunschweig.de/pi-post/ki-fuer-alle/

BIOMEDAS: Lisa-Marie Bente receives Best Talk Award

Thu, 07 Jul 2022 00:00:00 +0000

During the BIOMEDAS retreat Lisa-Marie Bente has received an award for her talk on “Biomarker Mining for Neurodegenerative and -inflammatory Diseases”. The retreat forms part of the PhD program offered by BIOMEDAS. In her 3 minute flash talk, Lisa-Marie Bente has outlined her research on her two main projects concerning Alzheimer’s Disease (AD) and Multiple Sclerosis (MS): Using FDG-PET scans she trains a convolutional neural network which distinguishes between healthy brains and brains with AD. Concerning MS, she compares different types of lesions in the brain of MS patients and examines methylation patterns in the DNA.

Tim Kacprowski elected as one of the leaders of the working group Statistical Methods in Bioinformatics of the GMDS e.V.

Tue, 28 Jun 2022 00:00:00 +0000

During the Workshop on Computational Methods in Biology and Medicine 2022, Tim Kacprowski has been elected as one of three leaders of the working group Statistical Methods in Bioinformatics. The working group is part of the GMDS e.V. and focuses on statistical aprroaches for the analysis of omics data.

More Transparency in Artificial Intelligence

Fri, 27 Aug 2021 15:00:00 +0000

Here’s the press release of TU Braunschweig:

In the last decades, new technologies have made it possible to develop a wide variety of systems that can generate huge amounts of biomedical data, for example in cancer research. At the same time, completely new possibilities have developed for examining and evaluating this data using artificial intelligence methods. AI algorithms in intensive care units, e.g., can predict circulatory failure at an early stage based on large amounts of data from several monitoring systems, by processing a lot of complex information from different sources at the same time, which is far beyond human capabilities.

This great potential of AI systems leads to an unmanageable number of biomedical AI applications. Unfortunately, the corresponding reports and publications do not always adhere to best practices or provide only incomplete information about the algorithms used or the origin of the data. This makes assessment and comprehensive comparisons of AI models difficult. The decisions of AIs are not always comprehensible to humans and results are seldomly fully reproducible. This situation is untenable, especially in clinical research, where trust in AI models and transparent research reports are crucial to increase the acceptance of AI algorithms and to develop improved AI methods for basic biomedical research.

To address this problem, an international research team including the division Data Science in Biomedicine of Peter L. Reichertz Institute for Medical Informatics (PLRI) has proposed the AIMe registry for artificial intelligence in biomedical research, a community-driven registry that enables users of new biomedical AI to create easily accessible, searchable and citable reports that can be studied and reviewed by the scientific community.

The freely accessible registry is available at aime-registry.org and consists of a user-friendly web service that guides users through the AIMe-standard and enables them to generate complete and standardised reports on the AI models used. A unique AIMe identifier is automatically created, which ensures that the report remains persistent and can be specified in publications. Hence, authors don’t have to cope with the time-consuming description of all facets of the AI used in articles for scientific journals and simply refer to the report in the AIMe registry.

Since the registry is designed as a web platform maintained by the scientific community, every user can ask questions about existing reports, make comments or suggest improvements. This feedback from the community will also be included in the annual update of the AIMe standard, and interested researchers can join the AIMe Steering Committee to become more involved in the further standardisation of biomedical AI.

“In the AIMe-registry, you can not only register novel AI methods in a citable manner. You can also search for existing methods for your specific application. There’s no need to reinvent the wheel and you can be sure that the AI is properly evaluated and adheres to the AIMe standard. AI developers and users alike will profit immensely from the AIMe-registry.” says Professor Tim Kacprowski, director of the division Data Science in Biomedicine of PLRI and member of BRICS – Braunschweig Integrated Centre of Systems Biology.

Paper 'CSF proteome in multiple sclerosis subtypes related to brain lesion transcriptomes' now available

Tue, 23 Feb 2021 00:00:00 +0000

The paper “CSF proteome in multiple sclerosis subtypes related to brain lesion transcriptomes”, coauthored by Tim Kacprowski, is now available on Pubmed.

BiCoN: Paper now published in Bioinformatics

Tue, 05 Jan 2021 00:00:00 +0000

The paper “BiCoN: Network-constrained biclustering of patients and omics data” for the BiCoN tool coauthored by Tim Kacprowski has now been published in Bioinformatics.

PySCNet: Preprint released on bioRxiv

Tue, 05 Jan 2021 00:00:00 +0000

The manuscript “PySCNet: A tool for reconstructing and analyzing gene regulatory network from single-cell RNA-Seq data” coauthored by Tim Kacprowski is now available on bioRxiv.

DIGGER: Digging into alternative splicing

Sat, 03 Oct 2020 00:00:00 +0000

The paper “DIGGER: exploring the functional role of alternative splicing in protein interactions” for the DIGGER tool by Zakaria Louadi et al. is now published in Nucleic Acids Research.

New paper released: miRNA Alterations in Alzheimer's Disease Mouse Model

Wed, 26 Aug 2020 00:00:00 +0000

The paper MiRNA Alterations Elicit Pathways Involved in Memory Decline and Synaptic Function in the Hippocampus of Aged Tg4-42 Mice coauthored by Tim Kacprowski and Fanny Rößler is now available in Frontiers in Neuroscience.

sPLINK: federated GWAS approach beats meta-analysis

Mon, 08 Jun 2020 00:00:00 +0000

sPLINK (safe PLINK) allows the federated, privacy-preserving analysis of GWAS data. It works on distributed datasets without exchanging raw data and is robust against imbalanced phenotype distributions across cohorts. Federated and user-friendly analysis with sPLINK, thus, has the potential to replace meta-analysis as the gold standard for collaborative GWAS. The manuscript “sPLINK: A Federated, Privacy-Preserving Tool as a Robust Alternative to Meta-Analysis in Genome-Wide Association Studies” for the sPLINK tool is now available on bioRxiv.

Multi-Omics Analysis in a Network Context: Chapter released on Elsevier

Mon, 01 Jun 2020 00:00:00 +0000

Manuela Lautizi, Amit Fenn and Tim Kacprowski from our group contributed to a new chapter for the “Reference Module in Biomedical Sciences” about multi-omics analysis in a network context. It provides a detailed overview of 19 current network enrichment tools, including guidelines for the selection of the most suitable methods for a partcular analysis. The chapter is now available on Elsevier.

CoVex: Our contribution to the fight against the pandemic

Fri, 17 Apr 2020 00:14:00 +0000

To address the current Corona pandemic, the Chair of Experimental Bioinormatics started a two week “ExBio vs. COVID-19” hackaton in cooperation with two TUM virologists. The Computational Systems Medicine recearch group was represented by Gihanna Galindez, Tim Kacprowski and Sepideh Sadegh.

During the hackaton a first version of the tool CoVex was developed, a drug repurposing tool that integrates virus-human interaction data for SARS-CoV-2 and SARS-CoV. It is now available as online analysis platform. Current development updates and research can also be found on the Chair of Experimental Bioinormatics website.

A preprint is now available on arXiv.

EpiGEN: Paper published in Bioinformatics

Thu, 16 Apr 2020 00:00:00 +0000

The manuscript “EpiGEN: an epistasis simulation pipeline” for the EpiGEN tool is now available on Bioinformatics.

Scellnetor: Preprint released on bioRxiv

Fri, 03 Apr 2020 00:00:00 +0000

The manuscript “Comparative single-cell trajectory network enrichment identifies pseudo-temporal systems biology patterns in hematopoiesis and CD8 T-cell development” is now available on bioRxiv. It introduces the new tool Scellnator, a novel network-constrained scRNA-seq clustering application. An interactive online version is available at the Scellnetor website.

New Group Members and Alumni

Mon, 23 Mar 2020 00:00:00 +0000

Recently Zakaria Louadi joined the Computational Systems Medicine research group as a PhD student. Rahel Caspar, Amrei Menzel, Ertida Muka and Evelyn Scheibling also joined the team to work on their theses for their bioinformatics degree.

Christoph Kloppert, Pauline Nickel and Andreas Stelzer finished their Bachelor’s theses in February. Judith Bernett, Tim Faro and Fanny Rößler also completed their theses and decided to stay at the Chair as student research assistants during their Master studies. They will further develop their Bachelor projects and support the group’s current research. Chit Tong Lio finished her Master’s thesis and will continue her studies as PhD student at the Chair.

We also are happy to welcome our new Bachelor students Thomas Eska and Valentin Hildemann, as well as Anton Smirnov, who decided to join our group for his Master’s thesis.

BiCoN: Preprint released on bioRxiv

Mon, 03 Feb 2020 00:00:00 +0000

The manuscript “BiCoN: Network-constrained biclustering of patients and omics data” for the BiCoN tool is now available on bioRxiv.

Fast Log-Rank Test: New software released

Thu, 30 Jan 2020 00:00:00 +0000

The C++ based implementation of the log-rank test is now available as a Python package and R package.

More information about the tool can be found on the software page.

New paper co-authored by Tim Kacprowski

Sun, 26 Jan 2020 00:00:00 +0000

A paper co-authored by Tim Kacprowski with the title “Genetic studies of urinary metabolites illuminate mechanisms of detoxification and excretion in humans” has just been published in Nature Genetics.

Invited talk at PMBC2019

Tue, 13 Aug 2019 15:46:00 +0000

Tim Kacprowski has been invited to give a talk at the 2nd International Congress on Precision Medicine, taking place on October 14-15 at the Hilton Munich City in Munich, Germany. The talk will be about ‘‘Multi-Omics Characterization of Induced Thyrotoxicosis’’.

The group grows

Wed, 24 Apr 2019 23:01:00 +0000

Olga Tsoy will join as a Post-Doc. Amit Fenn and Gihanna Galindez join as PhD Students. Tim Faro, Judith Bernett, Andreas Stelzer, Christoph Kloppert and Fanny Rößler decided to do their Bachelor’s thesis with us.

Invited talk at IGLD2019

Wed, 30 Jan 2019 13:39:00 +0000

Tim Kacprowski has been invited to give a talk at the Jahressymposium der Interdisziplinären Gruppe für Labor und Durchflussyztometrie, taking place from March 07-08 at the Congress Center in Frankfurt. The talk will be about ‘‘Zirkulierende miRNAs als potentielle Biomarker’’.

Invited talk at GQ2019

Thu, 29 Nov 2018 00:00:00 +0000

Tim Kacprowski has been invited to give a talk at the 9th Gene Quantification Event qPCR dPCR & NGS 2019, taking place from March 18-22 at the TUM School of Life Sciences in Weihenstephan. The talk will be about ‘‘Circulating miRNAs as Potential Biomarkers’’.

PhD Student position (65% E13, 3 years) available immediately

Thu, 29 Nov 2018 00:00:00 +0000

Project description

Diseases are currently defined and diagnosed based on symptoms (e.g., hypertension, depression) or affected organs (e.g., heart failure, nephropathy). Clearly, there is a lack of mechanistic understanding of diseases that could improve disease definitions and allow for more informed selection and development of therapies. To achieve such understanding we develop integrative bioinformatics methods leveraging network analysis, machine learning techniques and statistical approaches. Your work will focus on the development of graph-based machine learning techniques to identify disease- and patient-specific dysregulated subnetworks.

You bring

Degree in bioinformatics, molecular biology, computer science, or similar
Solid understanding of molecular biology
Experience with omics data analysis, graph analysis, machine learning
Strong programming skills in Python, R, and / or Java
Familiarity with Linux and HPC environments
Fluency in English in written and spoken language
Strong commitment and motivation, ability to work collaboratively

We offer

At the Chair of Experimental Bioinformatics you will find a supportive and productive research environment with a young, dynamic team of more than 20 international researchers at different stages in their career and education. Furthermore, you will have the chance to participate in a large EU-wide project and travel to international meetings with other scientists.

Send your application including your CV, grades, publications (if any) and a reference letter to tim.kacprowski@wzw.tum.de.