The Kacprowski Lab - Computational Systems Medicine

Our group aims to elucidate the molecular mechanisms behind phenotypes in general and human diseases, in particular. To that end, we develop integrative bioinformatics methods leveraging network analysis, machine learning techniques, and statistical approaches. We apply own and existing approaches in close collaboration with biologists and physicians to derive insights from multi-omics data. Visit us at www.compsysmed.de

Group members

Dr. Tim Kacprowski

I'm a junior research group leader at the Chair of Experimental Bioinformatics. My group works on network biology, multi omics integration and machine learning in the context of systems medicine. In my graduate studies at the University of Greifswald in Germany, I analysed different omics data in the context of common diseases. Before I joined the Interfaculty Institute of Functional Genomics at the University Medicine Greifswald, I studied bioinformatics in Saarbrücken, focussing on network biology. During my studies I spent some time abroad at the University of Iceland. I was awarded a Honor's Degree in Bioinformatics from the Saarland University and the Max-Planck-Institute for Informatics.

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Dr. Olga Tsoy

I'm a Postdoc at the Chair of Experimental Bioinformatics working on the BMBF funded Sys_CARE project about alternative splicing in cardiac and renal diseases. I graduated from Lomonosov Moscow State University and did PhD in Kharkevich Institute in Moscow at professor Gelfand lab. There I studied the evolution of transcriptional regulatory networks in bacteria. During my PhD I shortly stayed at Stowers Institute for Medical Research, Kansas-City, where I went on working on regulation of bacterial metabolic pathways. As a research scientist, I worked in Skolkovo Institute of Science and Technology, Moscow on 3D chromatin structure analysis.

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Amit Fenn

I'm a Ph.D. candidate at the chair of Experimental Bioinformatics at TUM. My project is the study of alternative splicing in heart and kidney using machine learning to analyze multi-omics data. I studied cellular biology, specializing in the mitochondria, during my Master's at LMU. For my Master's thesis, I explored splicing within ribosomal protein genes, in the context of the biogenesis of mitochondria.

amit.fenn[a.t_))@wzw.tum.de

Chit Tong Lio

I’m a PhD candidate at the Chair of Experimental Bioinformatics starting from April 2020. I will be focusing on using machine learning methods to study the alternative splicing events in cardiac and kidney diseases. I’m particularly interested in exploring omics data in a time series manner. I got my BSc in Life Sciences in Taiwan and my MSc in Biology at LMU Munich. In my master thesis, I have been performing time course network enrichment analysis on X-irradiated human fibroblast.

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Gihanna Galindez

I’m a PhD student at the Chair of Experimental Bioinformatics at TU Munich. I obtained my bachelor’s degree in Molecular Biology and Biotechnology from the University of the Philippines. Then, I studied Life Science Informatics at the University of Bonn in Germany. In my master’s thesis, I used machine learning to identify chromatin features involved in immunity-related transcriptional reprogramming in plants. I am working under the REPO-TRIAL project to apply network analysis and machine learning for drug repurposing.

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Manuela Lautizi

I’m a PhD student in the Chair of Experimental Bioinformatics in collaboration with the Institute of Pathology, both at TUM. I’ve originally joined Prof. Baumbach’s lab to work on my master’s thesis in bioinformatics, focused to identify pathway-based subnetwork of genes most significantly associated to survival time of cancer patients. Other topics of my interest are machine learning (both supervised and unsupervised), manipulation and analysis of the data from a statistical point of view. 

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Sepideh Sadegh

I am a PhD student in the Chair of Experimental Bioinformatics at TU Munich. I received my Bachelor’s degree in Biomedical Engineering from Amirkabir University of Technology (Tehran, Iran) and my Master’s degree in Bioinformatics from Saarland University (Saarbrücken, Germany). In my master thesis I analyzed disease-specific gene regulatory networks in terms of co-regulatory network motifs. My research interests include multi-omics data and network biology. I am currently involved in REPO-TRIAL, a H2020 funded drug repurposing project.

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Zakaria Louadi

I'm a Ph.D student in the Chair of Experimental Bioinformatics involved in Sys_CARE project. I received a Bachelor's degree in Electrical Engineering from Cadi Ayyad University in Marrakesh and a MSc with a focus on AI and deep learning from Jeonbuk National University in South Korea. In my master thesis, I worked on developing Deep Splicing Code a sequence-based tool for the classification of alternative splicing events. My research interests include machine learning and its applications in computational biology.

Amrei Menzel

I am a master student of bioinformatics at TUM and LMU. I joined the Chair of Experimental Bioinformatics to write my master thesis in the field of genetic statistics, which is mainly about identifying linkage disequilibrium patterns in biological networks.

Anton Smirnov

Currently working on my MSc thesis (“Comparison of normalization and transformation methods in sequencing data analysis”), guided by Tim Kacprowski and Olga Tsoy. I hold BSc degrees in Bioinformatics (TUM and LMU), Chemistry and Biochemistry (LMU). As secondary projects, I also hack around with phage therapy and a couple of crowd-centered services.

Lena Maria Hackl

I am doing my M.SC. Computer science at the Technical University of Munich right now. I gained some experience with ligand binding site prediction in a project at Rostlab at TUM. So, in May 2020, I joined the ListLab at the Chair of Experimental Bioinformatics to work on exon-specific annotation of miRNA binding sites for my Master’s thesis.

Tim Faro

I’m in my first year towards a master’s degree in Bioinformatics at the LMU and Technical University of Munich. After finishing my bachelor’s thesis on breast cancer radiomics, I continued to work at the Chair of Experimental Bioinformatics in Weihenstephan as a student research assistant to further develop my thesis project.

Ertida Muka

I'm rounding up my Bioinformatics studies at LMU and TUM Munich with a bachelor's thesis at the Chair of Experimental Bioinformatics. In collaboration with the Institute of Pathology in Munich, my thesis studies the detection of Copy Number Variants using off target data, generated from targeted next-generation sequencing.

Evelyn Scheibling

I'm a Bachelor student in Bioinformatics at the Technical University of Munich and the Ludwig-Maximilian University. In October 2019, I joined the Chair of Experimental Bioinformatics in Weihenstephan to work on my bachelor thesis on the indentification of miRNA binding site enriched transcripts in The Cancer Genome Atlas.

Judith Bernett

I’ve been studying Bioinformatics at the Technical University of Munich and the LMU since October 2016 and joined the Chair of Experimental Bioinformatics for my bachelor’s thesis. Here, I developed a risk score for mortality prediction in patients undergoing transcatheter aortic valve implantation. Currently, I am working as a HiWi at the chair to continue my work and deepen my knowledge on the subject of computational systems medicine.

Rafaela Relota

I am a Bioinformatics bachelor student at the TUM and LMU since October 2017. In May/June 2020 I will be joining the Chair of Experimental Bioinformatics to work on my bachelor thesis about alternative splicing in tissues and blood.

Rahel Caspar

I am a Bachelor student in Bioinformatics at the TUM and LMU since October 2016. In December 2019 I joined the Chair of Experimental Bioinformatics to work on my bachelor thesis about the landscape of the alternative splicing events in a healthy population.

Thomas Eska

I’m a bioinformatics bachelor student at the TUM and the LMU. I joined the Chair of Experimental Bioinformatics for my bachelor’s thesis on drug repurposing using transcription factor and drug perturbation data.

Thomas Mauermeier

I am an undergraduate student in the bioinformatics program at the TUM and LMU. In April 2020 I joined the chair of experimental bioinformatics in order to work on my bachelor's thesis on the extension and evaluation of a further centrality measure in the NetworkPrioritizer Cytoscape app.

Valentin Hildemann

Studying Bioinformatics since 2017 at the LMU and TUM in Munich I am now working towards my Bachelor’s degree. Therefore I joined the Chair of Experimental Bioinformatics for my Bachelor’s thesis on quantifying SNPs in mitochondrial DNA, as for me the mitochondrion is the most interesting cell organelle there is.

Fanny Rößler

I’m a bioinformatics Master student at the Technical University of Munich and the LMU. I joined the Chair of Experimental Bioinformatics as a HiWi to gain more practical experience in bioinformatics during my Bachelor’s degree in October 2018, and am continuing this for my master. In March 2020 I finished my bachelor thesis on a thyrotoxicosis gene expression time series at the Chair. I will continue this and similar projects as a student research assistant.

Jonas Schäfer

I study bioinformatics at the TUM and LMU since October 2018. To apply some of my learned knowledge, I joined the chair of Experimental Bioinformatics as a Hiwi.

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Alumni

  • Lorenzo Viola, MSc

  • Nils Mehrtens, BSc

  • Niklas Probul, BSc

  • Chris Li, PREP

  • Olga Lesina, Student Research Assistant

  • Weilong Li, PhD Student

  • Andreas Stelzer, BSc

  • Christoph Kloppert, BSc

  • Pauline Nickel, BSc

 

Chair of Experimental Bioinformatics

TUM School of Life Sciences Weihenstephan

Technical University of Munich

Tel: +49-8161-71-2136

E-Mail: exbio[a.t_))wzw.tum.de

Office: OG-L06