The Baumbach group

The Baumbach group at the Technical University of Munich

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Prof. Dr. Jan Baumbach

jan.baumbach[a.t_))uni-hamburg.de

I'm chairing the Cosy.Bio lab at the University of Hamburg since January 2021. In part time, I am also leading the Computational BioMedicine group at the University of Southern Denmark (since October 2012). Before, I have been chair of Experimental Bioinformatics at the Technical University of Munich, Junior Research group leader 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 doctoral 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 Cosy.Bio. 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.

Dr. Amjad Ali

amjad.ali[a.t_))asab.nust.edu.pk

@TUM

In September 2020, I joined (virtually; because of the COVID19 pandemic) the Chair of Experimental Bioinformatics at the TUM as a postdoctoral researcher funded by the Higher Education Commission (HEC) of Pakistan. I am working on a collaborative project “Microbiome Signatures - Functional Relevance in the Digestive Tract”. I contribute 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

@TUM, co-supervised together with Markus List

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. Olga Tsoy

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

I'm a Postdoc at Cosy.Bio 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

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

@TUM

 

From May 2020, joined the Chair of Experimental Bioinformatics at TU Munich as a postdoc. I analyze proteomics data from Alzheimer's disease patients for the CLINSPECT-M project and 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. 

Lion Müller

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

@TUM, co-supervised together with Markus List

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 Cosy.Bio. 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

@TUM, industrial PhD

I'm an industrial PhD student, working 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

Since April 2020 I am a Ph.D. student at CoSy.Bio within the Sys_Care project. Before, I have been 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 an exchange PhD student in the Cosy.Bio lab 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

@TUM, co-supervised together with Markus List

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

@TUM

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.

Julian Matschinske

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

I am a PhD candidate at Cosy.Bio. 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 Cosy.Bio 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

@TUM, co-supervised together with Josch Pauling​

 

I'm an Industrial PhD and my research focus at Cosy.Bio is AI in Healthcare with a special emphasis on international growth of medical and economic impact.

Manuela Lautizi

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

@TUM, co-supervised together with Markus List and Tim Kacprowski

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

maria.woerheide[a.t_))helmholtz-muenchen.de

@TUM, co-supervised together with Josch Pauling

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 Cosy.Bio lab 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

@TUM

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

@TUM, co-supervised together with Markus List

 

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 Cosy.Bio. 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

@TUM, co-supervised together with Markus List

 

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

@TUM, co-supervised together with Markus List

 

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 Cosy.Bio and 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 at Cosy.Bio and 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

@TUM, co-supervised together with Tim Kacprowski

​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

@TUM, co-supervised together with Josch Pauling

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.

​Afsaneh Mohammadnejad

amohammadnejad[a.t_))health.sdu.dk

@SDU, co-supervised together with Qihua Tan and Richard Röttger

I am a PhD student at research unit of Epidemiology, Biostatistics and Biodemography at the University of Southern Denmark and a member of the Computational Biology group since March 2018. Currently, I am involved in developing methods for multivariate analysis of OMICS data. I hold a MSc degree in Applied Mathematics from SDU and I did my master thesis on GWAS.

Dominika Hozakowska-Roszkowska

roszkowska[a.t_))imada.sdu.dk

@SDU, co-supervised together with Richard Röttger

I am a PhD student since December 2018. I hold a uniform MSc degree in Medical Laboratory Science from Medical University of Warsaw (Poland) and MSc degree in Computational Biomedicine from University of Southern Denmark. Currently, I am working on a large-scale analysis and machine learning of the distribution of genetic traits in populations.

Nikolai Köhler

nikolai.koehler[a.t_))tum.de

@TUM, co-supervised together with Josch Pauling​

 

I'm a PhD student at LipiTUM where I develop a scoring method for spectrum matches for the LipiTUM platform. before I have been a MSc student in Molecular Biotechnology at TUM with a special interest in bioinformatics and biochemical analytics. Through an internship at the University of Melbourne/Metabolomics Australia I gained practical experience in MS-based lipidomics analysis and the current computational and analytical challenges.

Zakaria Louadi

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

I'm a Ph.D student Cosy.Bio 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.

Johannes Kersting

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@TUM, co-supervised together with Markus List

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 as a HiWi to get some working experience and apply my knowledge to "real-world" problems.

Alexander Dietrich

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@TUM, co-supervised together with Markus List

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.

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@TUM, co-supervised together with Markus List

I’m a bioinformatics master’s student at TUM and LMU and joined the Chair 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.

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@TUM, co-supervised together with Markus List

I am a Bioinformatics Master student at the TUM and LMU. I joined the group in 2019, when I did my bachelor thesis on the role of circular RNA in sponging and implemented a docker pipeline for analyzing matched small- and total-RNA sequencing data. Since September 2020, I am working on extending the circRNA analysis and implementing an nextflow pipeline as part of my advanced practical course. In October 2020, I started working as a student assistant.

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@TUM, co-supervised together with Markus List

I’m a bioinformatics Master student at the Technical University of Munich and the LMU. I joined 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.

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@TUM, co-supervised together with Markus List

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

Evelyn Scheibling

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@TUM, co-supervised together with Markus List

I’m a Master student in Bioinformatics at the Technical University of Munich and the Ludwig-Maximilian University. In October 2019, I joined to work on my bachelor thesis on the indentification of miRNA binding site enriched transcripts in The Cancer Genome Atlas. From October 2020, I work as a student assistant for the group.

Prof. Dr. Vasco Azevedo

vasco[a.t_))icb.ufmg.br

Prof. Vasco Azevedo, DVM, M.Sc, PhD, FESC is a visiting professor in our laboratory. He holds a full professorship position at the Federal University of Minas Gerais in Belo Horizonte, Brazil. Prof. Azevedo is a pioneer of genetics of lactic acid bacteria and corynebacterium pseudotuberculosis in Brazil. He published >240 papers in bacterial genetics, functional genomics, the development of new vaccines against and diagnostics for infectious diseases, as well as on the bioinformatics analyses of transcriptomics and proteomics data sets. He is associate editor of Genetics and Molecular Research, and member of the editorial boards of the Open Veterinary Science Journal and the International Journal of Microbiology.

Alumni

  • Tim Kacprowski, Professor at Technical University of Brunswik
  • Richard Röttger, Professor at University of Southern Denmark
  • Anne-Christin Hauschild, Assistant Prof. at University of Marburg
  • Josch Pauling, Group leader at Technical University of Munich
  • Markus List, Group leader at Technical University of Munich
  • Richa Batra, Postdoc at Helmholtz Center Munich
  • Nicolas Alcaraz, Postdoc at Copenhagen University
  • Eudes Barbosa, Postdoc at Helmholtz Center Munich
  • Alexander Groenning, Postdoc at Copenhagen University
  • Jesper Lund, Postdoc at Hasso-Plattner-Institute Potsdam
  • Evans Kataka, Data Scientist at Procter & Gamble
  • Diogo Marinho, Postdoc at Roskilde University Hospital
  • Lucas Ferreira, Postdoc at Imperial College London
  • Pen Sun, Senior Bioinformatician at Bayer AG Berlin
  • Rashid Ibragimov, Data Scientist at IBM Deutschland GmbH
  • Tobias Wittkop, Senior Data Scientist at Adaptive Biotechnologies Lmtd
  • Christian Wiwie, Bioinformatician at Qiagen Aarhus
  • Anna Hartebrodt, PhD student at University of Southern Denmark
  • Gregor Sturm, PhD student at Innsbruck Medical Center
  • Paulo Vinicius Carvalho, Postdoc at University of Southern Denmark
  • Simon Larsen, Senior Data Scientists at Energienet, Denmark
  • Weilong Li, Postdoc at University of Helsinki, Finland
  • Maria Elkjaer, Postdoc at Odense University Hospital
1200px-UHH_Universität_Hamburg_Logo_mit

 

Chair of Computational Systems Biology

University of Hamburg

Notkestrasse 9

22607 Hamburg, Germany

Tel: +49-40-42838-7313

E-Mail: cosyb@zbh.uni-hamburg.de