The Baumbach group

The Baumbach group at the Technical University of Munich

Prof. Dr. Jan Baumbach

jan.baumbach[a.t_))wzw.tum.de

I'm chairing the Experimental Bioinformatics lab at the Technical University of Munich since January 2018. In part time, I am also leading the Computational BioMedicine group at the University of Southern Denmark (since October 2012). Since December 2018, I am also director of the IT Weihenstephan. Before, I have been head of the Computational Systems Biology group at the Max Planck Institute for Informatics and postdoctoral fellow at the University of California at Berkeley in the Algorithms group of Richard Karp. In 2008, I received a PhD degree from Bielefeld University where I worked in the Genome Informatics group of Jens Stoye and the Algorithms and Statistics for Systems Biology group of Sven Rahmann. During my studies I spent some time at the University of California at San Francisco in the lab of Tom Ferrin and at Rothamsted Research in the lab of Chris Rawlings.

Dr. Nina Kerstin Wenke

nina.wenke[a.t_))wzw.tum.de

I'm the science manager of the chair of Experimental Bioinformatics. I received my M.Sc. of Biotechnology working at the Max Planck Institute for Molecular Biomedicine in Muenster. Afterwards, I moved to Berlin to do my doctoral thesis at the German Center of Neurodegenerative Diseases (DZNE) and at the Charité University Hospital working on autoimmune encephalitis. In the Experimental Bioinformatics lab, I will be part of the FeatureCloud Project (Horizon 2020).

Léonie Corry

exbio[a.t_))wzw.tum.de

Léonie Corry is the secretary of the chair of Experimental Bioinformatics and assistant to Jan Baumbach. She deals with all the administrative tasks (financial and personnel related) and strives to make life a little easier for everyone in the lab...

Martina Rüttger

bioinformatik[a.t_))wzw.tum.de

Hand in hand with Léonie she supports our staff where needed to ensure our lab is full of happy people.

Dr. Josch Pauling

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​I'm a TUM junior research fellow and a ZD.B group leader at the Chair of Experimental Bioinformatics. My group works on computational lipidomics. We develop the platform LipiTUM and concentrate on analyzing and identifying lipid species in MS2+ spectra. Our aim is to bring the lipid metabolism on the play board of systems biomedicine and, thus, to unravel novel kinds of targets for the next generation of precision medicine. I studied bioinformatics in Bielefeld, Germany, and worked as research assistant at the Max Planck Institute for Informatics. I gained my PhD for the University of Southern Denmark, and did a postdoc at the Humboldt University of Berlin in the lab of Edda Klipp.

Dr. Markus List

markus.list[a.t_))wzw.tum.de

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.

Dr. Tim Kacprowski

tim.kacprowski[a.t_))wzw.tum.de

​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.

Dr. Amjad Ali

From September 2020, I will join the Chair of Experimental Bioinformatics at the TUM as a postdoctoral researcher funded by the Higher Education Commission (HEC) of Pakistan. I will be working on a collaborative project “Microbiome Signatures - Functional Relevance in the Digestive Tract”. I will be contributing towards handling and analysis of heterogeneous experimental and medical multi-omics microbiome data sets. I did my Ph.D. in microbial genomics, from Federal University of Manas Gerais, Brazil, under the supervision of Prof. Vasco Azevedo. During my Ph.D., I have been working on comparative microbial genomics. Currently, I am working as an Assistant Professor at the National University of Sciences & Technology (NUST), Islamabad.

Dr. David B. Blumenthal

david.blumenthal[a.t_))wzw.tum.de

In October 2019, I joined 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 PhD in Computer Science at the Free University of Bozen-Bolzano, Italy. During my PhD, I developed new techniques for exactly and heuristically computing the graph edit distance, a widely used distance measure for comparing attributed combinatorial graphs.

Dr. Evans Kataka

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Starting from October 2019, I will join the Chair of Experimental Bioinformatics at TU Munich as a postdoctoral researcher. I will be working on both the SyMBoD and LipiTUM projects which have an emphasis on systems biomedicine.

From 2015 until recently, I have been pursuing my Ph.D. in Bioinformatics at the Chair of Genome Oriented Bioinformatics (TUM). Previously, I received my Master’s degrees in Bioinformatics from The University of Nairobi (Kenya) after a brief visiting scholarship position at The Ohio State University (Columbus, Ohio) in Erich Grotewold’s Lab. Before that, I did my BSc in Biotechnology and Biochemistry at Kenyatta University (Kenya). During my PhD, I developed a novel method on how to use condition-specific protein-protein interaction networks in cancer to discover biomarkers at the multi-cancer, cancer-type, and cancer sub-type levels.

Dr. Judith Parkinson-Schwarz

I'm a Postdoc at the Chair of Experimental Bioinformatics working on applied biostatistics in systems medicine. From 2011 till 2016 I studied mathematics and economics at the University of Ulm for my Bachelors's and Masters's degree. I continued with my Ph.D. in statistics with main focus on survival analysis at the University of Salzburg. During that time, I was granted a scholarship by the Austrian Marshall Plan Foundation for a research stay at Georgia State University in Atlanta.

Dr. Olga Tsoy

olga.tsoy[a.t_))wzw.tum.de

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.

Dr. Olga Zolotareva

From May 2020, I will join the Chair of Experimental Bioinformatics at TU Munich as a postdoc. I will analyze proteomics data from Alzheimer's disease patients for the CLINSPECT-M project and will participate in the development of federated machine learning methods. Currently, I am finishing my PhD at DiDy Research Training Group, Bielefeld University under the supervision of Ralf Hofestaedt and Martin Ester (Simon Fraser University, Canada). During my PhD studies, I worked on the development of a novel network-constrained biclustering method and its application on breast cancer expression data. In 2018 I did 9-months visiting research at Simon Fraser University where I participated in the project on multi-omics data integration for drug response prediction. 

Dražen Jalšovec

drazen.jalsovec[a.t_))tum.de

Dražen is a IT System Administrator at Technical University of Munich - Weihenstephan. He works for multiple research groups, taking care of the local HPC Infrastructure. He studied Electrical Engineering at Faculty of Electrical Engineering, Computer Science and Information Technology Osijek.

Lion Müller

lion.mueller[a.t_))wzw.tum.de

I'm the head of the Bioinformatics Core at the IT department of TUM at Weihenstephan as well as a member and PhD candidate in applied bioinformatics at the Chair of Experimental Bioinformatics at TUM. I received my Bachelor's degree in biology in 2016, followed by a Master in bioinformatics and systems biology in 2018 at the Justus-Liebig-University Giessen, Germany. In 2017, I joined Prof Alexander Goesmann's group at the JLU Giessen as a HIWI for the duration of one year, working on tools for management and annotation of genomic data. My Master's thesis was about the improvement of the reference genome of the short-lived fish Nothobranchius furzeri at the Leibniz Institute on Aging (FLI) in Jena, Germany.

Amit Fenn

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

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.

Carlos Salort Sánchez

salort[a.t_))wzw.tum.de

I'm an industrial PhD student, working together in the Chair of Experimental Bioinformatics at TU Munich and in Huawei. I received my Bachelor's degree in Mathematics from Universitat de València, and my Master's degree in Modelling for Science and Engineering with Specialisation in Data Science from Universitat Autònoma de Barcelona. After some years working as a Data Scientist for a consulting firm in Barcelona, I moved to Munich to continue with my studies. My main research topics are related with Artificial Intelligence (classical Machine Learning and Deep Learning) and real time algorithms, and my current research topic is to apply these technologies into bioinformatics problems.

Chit Tong Lio

chit-tong.lio[a.t_))wzw.tum.de

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.

Doglas Parise

dparise[a.t_))wzw.tum.de

I'm a PhD student in the Experimental Bioinformatics lab at TU Munich and in the Laboratory of Cellular and Molecular Genetics (LGCM) at UFMG. I graduated in Computer Science – Teaching degree from UNIJUI (2013). In 2015, I moved to Belo Horizonte to do my Master studies in Bioinformatics at UFMG, in which I worked with assembly, annotation, and analysis of bacterial genomes. Currently, I'm working with bacterial regulatory networks.

Fabio Boniolo

fabio.boniolo[a.t_))tum.de

I'm a PhD candidate affiliated with the Institute of Translational Cancer Research and Experimental Cancer Therapy (Saur lab, TUM Klinikum rechts der Isar) and with the Chair of Experimental Bioinformatics (Baumbach lab, TUM School of Life Sciences Weihenstephan). 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), where I worked on the development of a bio-hybrid composite bone substitute for paediatric patients. Afterwards, I spent one year at ETH Zurich (Switzerland), where I investigated the development of advanced modelling techniques for Raman based spectral data as part of my Master’s Thesis 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 modelling.

Fengchong Wang

fengchong.wang[a.t_))tum.de

I'm a PhD candidate affiliated with the Institute of Translational Cancer Research and Experimental Cancer Therapy and with the Chair of Experimental Bioinformatics TUM. I got BSc in Biotechnology at Qufu Normal University, China, then I acquired MSc in Complex Systems at the University of Warwick, the UK and Chalmers University of Technology, Sweden. I am interested in multi-omics integration and application of machine learning in biological data.

Gihanna Galindez

gihanna.gaye[a.t_))wzw.tum.de

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.

Julian Matschinske

matschinske[a.t_))wzw.tum.de

I am a PhD candidate at the Chair of Experimental Bioinformatics at TU Munich. I obtained my master's degree in Computer Science from Friedrich-Alexander University Erlangen-Nürnberg (2019). During my studies, I have been working as a professional full-stack developer in my own company. At TUM, I am part of the EU Horizon2020 FeatureCloud project. My focus mainly lies on machine learning and data privacy in conjunction with federated systems.

Julian Späth

julian.spaeth[a.t_))wzw.tum.de

I'm a Ph.D. student at the Chair of Experimental Bioinformatics at TUM and part of the FeatureCloud project (Horizon2020). I received my B.Sc. in Medical Informatics and M.Sc. in Bioinformatics from the Eberhard Karls University Tübingen. In my master thesis, I implemented a Random Survival Forest (RSF) Python package to predict the survival of blood cancer patients based on molecular data. My focus lies on machine learning in biomedical applications. 

Justus Wolff

justus.wolff[a.t_))wzw.tum.de

I'm an Industrial PhD and my research focus at the chair of Experimental Bioinformatics at TUM is AI in Healthcare with a special emphasis on international growth of medical and economic impact.

Kundai Sachikonye

kundai.sachikonye[a.t_))wzw.tum.de

I am a PhD student in the Pauling Lab working on the LipiTUM project aimed at developing methods for the identification and quantification of lipid species in LC-MS/MS. I did my bachelors in Biochemistry and Cell Biology at Jacobs University Bremen and graduate studies in Pharmaceutical Biotechnology and Bioinformatics at HAW Hamburg, UKE Hamburg and Eberhard Karls Universitaet Tübingen. I have done internships in LC-MS/MS-related topics at UZ (Zimbabwe), Forschungs und Transferzentrum Bioprocess Hamburg, University of Groningen (Netherlands), UKE Hamburg, Leibniz Lungenzentrum Borstel and Fraunhofer IGB Stuttgart. 

Manuela Lautizi

lautizi[a.t_))wzw.tum.de

​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. 

Maria Wörheide

I’m a PhD student affiliated with the chair of Experimental Bioinformatics at the Technical University of Munich (TUM) and the Institute of Computational Biology (ICB) at the Helmholtz Zentrum München. I received my Bachelor’s and Master’s degree in bioinformatics from the Ludwig-Maximilians-Universität and TUM. During my studies I became increasingly interested in systems biology and metabolomics. I am very excited to pursue this interest during my PhD, where I am focusing on multi-omics data integration and network-based target prioritisation in Alzheimer’s disease.

Mariana Parise

mparise[a.t_))wzw.tum.de

I'm a PhD student affiliated with the Experimental Bioinformatics lab (TUM) and the Laboratory of Cellular and Molecular Genetics (UFMG). I graduated in Computer Science and in my master’s degree, I have studied Bioinformatics at UFMG (Brazil). In my master thesis, I have developed a Laboratory Information Management System focused on microorganisms and omics data (LabControl). Currently, I study transcriptional regulatory networks in bacteria.

Marisol Salgado Albarrán

marisol.salgado[a.t_))tum.de

I'm a PhD student affiliated with the Experimental Bioinformatics lab at TU Munich and the Cancer Epigenetics research group at National Cancer Institute in Mexico. My major research interest is cancer epigenomics, specifically the deregulation of gene expression related to the proteins BORIS and CTCF. Before, I obtained my Bachelor’s degree in Pharmaco-Biological Chemistry in 2015 at the National Autonomous University of Mexico and my Master's degree in Biological Sciences at the National Cancer Institute, Mexico. 

Melissa Klug

melissa.klug[a.t_))wzw.tum.de

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.

Mhaned Oubounyt

oubounyt[a.t_))wzw.tum.de

I am a PhD student in the Chair of Experimental Bioinformatics at TU Munich. I received my Bachelor degree in informatics and electronics engineering from the Cadi Ayyad University of Sciences and Technology in Morocco, and my Master degree from Chonbuk National University in South Korea. During my Master thesis, I  developed deep learning models for genomic data analysis such as RNA splicing quantification and  DNA promoter sequences classification. I am currently working under SFB924 project to develop an integrative platform.

Michael Lauber

michael.lauber[a.t_))wzw.tum.de

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.

Monica Matchado

monica.matchado[a.t_))wzw.tum.de

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.

Olga Lazareva

lazareva[a.t_))wzw.tum.de

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.

Reihaneh Torkzadehmahani

mahani[a.t_))wzw.tum.de

I am a Ph.D. candidate at the Experimental Bioinformatics chair at the Technical University of Munich(TUM). I am a part of the EU Horizon2020 FeatureCloud project and I am mainly focused on the development of privacy-preserving and federated Machine Learning methods for Biology applications. Prior to starting my Ph.D., I got my second M.Sc. degree in Computer Science from the University of California, Santa Cruz (2019) before which I did my first M.Sc. studies in Artificial Intelligence at Iran University of Science and Technology(2015).

Reza Nasirigerdeh

gerdeh[a.t_))wzw.tum.de

I am a Ph.D. student in the Chair of Experimental Bioinformatics at the Technical University of Munich (TUM). I hold a M.Sc. degree in Computer Science from the University of California, Santa Cruz(UCSC) and in Computer Engineering from Iran University of Science and Technology(IUST). Prior to that, I received my B.Sc. degree in Computer Engineering from K.N. Toosi University (KNTU) in Tehran. My academic background is in Distributed Systems, Computer Networks, and Machine Learning. Currently, I am a participant of the EU Horizon2020 FeatureCloud project, in which I focus on developing privacy-preserving distributed(federated) machine learning algorithms applicable to biomedical data.

Sepideh Sadegh

sadegh[a.t_))wzw.tum.de

​I'm 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.

Tim Rose

tim.rose[a.t_))wzw.tum.de

My name is Tim Rose. I'm a PhD student in the LipiTUM group. I received my Bachelor's degree in Quantitative Biology in Düsseldorf, where I did my thesis on equilibrium behavior of the Pentose Phosphate Pathway. After that, I worked on a master's project in modeling of radiation response of cancer cells to obtain a M.Sc. degree in Biophysics.
My research interests are analysis and modeling of multi-omics data, development of software tools for simulations/analysis and HPC. I think the utilization of multi-omics data is the key to infer the complexity of cells and get an understanding of how the different levels relate to each other and result in a specific phenotype. In my PhD project I work on data mining, analysis pipelines and the integration of lipidomics with other omics data.

Zakaria Louadi

zakaria.louadi[a.t_))wzw.tum.de

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.

Amir Abbasinejad

I'm a Master's student in Data Science at the Sapienza University of Rome, Italy. Since October 2019 I have joined the Experimental Bioinformatics chair of TUM as an intern and to do my master thesis. I am working on Federated Differential Gene Expression Analysis using breast cancer data as part of the Feature Cloud project.

Johannes Kersting

I started studying bioinformatics at the TUM and LMU in October 2016. In 2020 I got my Bachelor's degree and I am currently studying for my Master's degree, again in Munich. In parallel, i joined the Chair of Experimental Bioinformatics as a HiWi to get some working experience and apply my knowledge to "real-world" problems.