The List Lab - Big Data in BioMedicine

We develop predictive models and software tools that integrate big heterogeneous (OMICS) data. Our long term vision is that our research finds application in clinical practice. Towards this goal, we also address challenges in data privacy as well as in explainability and continuity in modelling.

To learn more about our research visit our website: http://biomedical-big-data.de

Group members

Dr. Markus List

I'm a leading the research group on Big Data in Biomedicine which is part of the Chair of Experimental Bioinformatics at the TUM School of Life Sciences Weihenstephan. In 2011, I received a MSc in bioinformatics from the University of Tübingen, Germany. Next, I moved to Denmark to do a PhD in the Molecular Oncology group in the Health Faculty of the University of Southern Denmark. There, I developed a complex software pipeline reaching from RNAi drug target discovery using robotic automation systems down to systems biology evaluation.  I then moved to the Max Planck Institute for Informatics in Saarbrücken where I worked as a PostDoc on developing better methods for making epigenomics data available and on using statistical learning for unraveling miRNA sponge regulation in cancer. With my research group I want to bring together epigenenomics, microRNA regulation, network biology and machine learning to add a new perspective to systems medicine.

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Dr. David Blumenthal

In October 2019, I will join the Chair of Experimental Bioinformatics at TU Munich as a postdoctoral researcher. My main focus will be to apply techniques from combinatorial optimization and graph theory to address problems in network biology and systems medicine. From 2007 to 2015, I studied Mathematics and Philosophy at FU Berlin and TU Berlin and received Master’s degrees in both disciplines. After that, I did a Ph.D. in Computer Science at the Free University of Bozen-Bolzano, Italy. During my Ph.D., I developed new techniques for exactly and heuristically computing the graph edit distance, a widely used distance measure for comparing attributed combinatorial graphs.

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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 PhD 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.

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Chit Tong Lio

Starting April 2020 I am a Ph.D. student. Currently, I am a biology master student from LMU Munich, where I have experience in working with sequencing data analysis. In my master thesis, I work at the Chair of Experimental Bioinformatics on time course network enrichment analysis on X-irradiated human fibroblast using TiCoNE and machine learning.

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Fabio Boniolo

I'm a PhD candidate at the Tum Center for Translational Cancer Research (TranslaTum) and at the

Chair of Experimental Bioinformatics. I received both my B.Sc. (2016) and my M.Sc. (2018) in Biomedical engineering from Politecnico di Milano, Italy. During my studies, I had the chance to work as an intern at Industrie Biomediche Insubri S.A (Mezzovico-Vira, Switzerland) and to spend one year at ETH Zurich, where I worked on my Master’s Thesis project “Development of advanced modeling techniques for Raman based spectral data of bioprocesses” in the Morbidelli Group. My research interests lie at the intersection between cancer biology, systems medicine, and biostatistics. In particular, I'm interested in the development of computational tools to assess the relationship between effectors and oncogenic phenotypes through multi-omics data integration and latent variable modeling.

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Melissa Klug

My PhD project is a connection between the Molecular Cardiology lab at the Klinikum rechts der Isar Munich and the Chair of Experimental Bioinformatics. I received my B.Sc. of Biology from the University of Hohenheim, Stuttgart, in 2015 and my M.Sc. of Biology from the LMU Munich in 2019. The results of my Master thesis at the Molecular Cardiology lab laid the foundation of this joined project. I am aiming to deeply characterize the proteome and transcriptome of human blood platelets using (sc)RNA-sequencing, mass spectrometry and single-cell mass cytometry.

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Michael Lauber

In June 2019 I started my PhD at the Chair of Experimental Bioinformatics. I have received a bachelor's and master's degree in Biochemistry from TUM. During my masters, I also started to study computer science at LMU. For my master thesis, I joined the lab of Alex Marson at UC San Francisco and established a CRISPR screen to study transcriptional regulation in human regulatory T cells. After finishing my studies I continued to apply CRISPR in T cells at TUM for another year. However, I realized that bioinformatics and data analysis makes me the most excited. My main interest lies in genetic and epigenetic regulation.

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Monica Matchado

​I am a Ph.D. student at Chair of Experimental Bioinformatics at TU Munich. I will be working on the Microbiome Project. I received my Bachelor's degree in Bioinformatics from Tamil Nadu Agricultural University and my Masters from Karunya Institute of Technology and Sciences, India. My master thesis was about building a draft genome annotation of Carica cauliflora using NGS pipeline. For my part-semester project, I worked on the characterization of Alternative Splicing events in Arabidopsis thaliana using the RNA-Seq approach at MPI-MP, Germany. After my masters, I worked as Research Fellow at Ganga Hospital, India where I focused on 16S Metagenomics as well as Proteomics. I am interested in learning and applying Machine learning concepts in solving biological questions.

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Olga Lazareva

I'm a PhD student in the Chair of Experimental Bioinformatics at TU Munich. In 2015, I received a B.S. in Applied Mathematics in Moscow, and after some time in the industry, I moved to Rome to do an MSc in Data Science at La Sapienza University of Rome. I  wrote my Master's thesis in the Chair of Experimental Bioinformatics on a problem of conjoint clustering of patients, networks and omics data and then stayed for my PhD. In January 2020 I have also received Fellowship from Zentrum Digitalisierung.Bayern (ZD.B) and now I am focusing on various unsupervised methods for multi-omics data integration and analysis.

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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.

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Markus Hoffmann

I study Bioinformatics at Technical University Munich an Ludwig-Maximilians University in my Masters. I came to the ListLab as part of my master pratical course where I contributed to implementing a web application and API for SPONGE. Further, I am now working as a student programmer with Dr. Blumenthal. 

Michael Hartung

I am a Master's student in Bioinformatics at the TUM and LMU in Munich since autumn 2018. Right before, I received a Bachelor's degree in Bioinformatics from the Goethe University in Frankfurt, where I wrote my thesis in the machine learning area.
At the Chair of Experimental Bioinformatics I am working on SPONGE with the goal to detect and visualize ceRNA interactions based on miRNA expression data. 

Michaela Müller

I'm a Master's student in Bioinformatics at LMU and TUM. So far, I have been working both on bulk- and single-cell RNASeq data. Since November 2019 I am doing an internship on analyzing transcriptomics and proteomics data of blood platelet data in cardiovascular disease cases.

Veronika Stiegler

I am a Masters student in Bioinformatics at the Technical University of Munich and the Ludwig-Maximillian University and joined the ListLab to develop a web application for SPONGE as part of an advanced practical course.

Aparna Chauhan

I'm a Bachelor student in Biotechnology at Delhi Technological University, India. I joined List Lab as an intern in April 2020 and work on microbiome project involving analysis of microbial abundance in metagenomic datasets using a graph based method which also accounts for compositionality.

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.

Konstantinos Mechteridis

I am a bioinformatic bachelor student, at the TUM and LMU, since summer 2018. Also, I had the opportunity to gather experience in information systems management and knowledge management at the TUM. In April 2020 I will be joining List Lab to work amongst other things on the R package of KeyPathWayMiner and my bachelor thesis.

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.

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 ListLab for my Bachelor's thesis on quantifying SNPs in mitochondrial DNA, as for me the mitochondrion is the most interesting cell organelle there is.

Alexander Dietrich

I am studying Bioinformatics at the TUM and LMU as my master since 2019. I am joining the ListLab as a HIWI to continue the project of my group from the SystemsBiomedicine practical course, where we introduced a new shiny-application to explore the microbiome, including co-occurrence analysis and clustering by functional topics.

Christopher Rieß

I am a Bioinformatics bachelor student at the LMU and TUM since 2017 and I've come to the ListLab to write my bachelor thesis on the prediction of chromatin structure from ChIP-seq data. Since my personal focus has always gone towards machine learning technology, this thesis topic seemed like a perfect fit for me and I'm glad I was accepted for it.

Kevin Yuan

I am a Bioinformatics Bachelor student at the Ludwig Maximilian University of Munich and Technical University of Munich since October 2017. 
Currently I am working as a HiWi at the Experimental Bioinformatics chair at the Technical University to gather more practical experience.

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Quirin Manz

Since 2016 I am studying Bioinformatics at the LMU and TUM. For my bachelor thesis I joined to ListLab in 2019 and will look into histone modifications' impact on alternative splicing. Since August 2019 I'm working as a hiwi.

quirin.manz[a.t_))tum.de

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Alumni

Thibault Bechtler

During his bachelor thesis, Thibault analyzed time-series proteomics and phospho-proteomics data of Arabidopsis thaliana using network enrichment methods.

Octavia-Andreea Ciora

During her bachelor thesis, Octavia investigated the role of circular RNA in sponging and implemented a docker pipeline for analysing matched small- and total-RNA sequencing data.

Patrick Hoffmann

In his bachelor thesis, Patrick used machine learning to predict epitope-specificity from T cell receptor repertoires.

Miriam Hilger

During her bachelor thesis, Miriam worked on a systematic pancancer analysis for positive microRNA regulation.

Akshit Achara

Akshit is a Masters student in Mathematics at BITS Pilani, India. He joined the ListLab from Aug'19 to Dec'19 towork on a machine learning based strategy for benchmarking miRNA target prediction methods.

Quirin Heiß

During his Master thesis, Quirin implemented a Django-based web interface for the network-constrained biclustering method BiGAnts.

Gregor Sturm

Gregor did his Master with us in immuno-oncology. In collaboration with Pieris Pharmaceuticals in Freising and Prof. Zlatko Trajanoski's Lab in Innsbruck he aimed to better understand the functional orientation of immune cells in the tumor micro-environment. He continued as a PhD student in the Trajanoski lab in Innsbruck.

Laura Marsoner

From 2018-2019, Laura was working as a student programmer in the ListLab to improve the web version of KeyPathwayMiner. 

Anne Hartebrodt

During her Master thesis, Anne developed a probabilistic approach for KeyPathwayMiner. pKPM accepts p-values rather than discrete values as input and allows for growing subnetworks under tight FDR control, i.e. without the need for choosing parameters K and L as it is the case in the current version of KPM. Anne moved to Odense where she starts a PhD in the Röttger lab.

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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