The Baumbach group

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The Baumbach group at Cosy.Bio

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Prof. Dr. Jan Baumbach

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

I'm director of the Cosy.Bio institute 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.

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Eda Seibitz

eda.seibitz[a.t_))uni-hamburg.de

Since December 2021, I am part of Cosy.Bio Institute`s dynamic young team,

as assistant of Prof. Dr. Jan Baumbach.

Before I started working at Hamburg University, I have been working on major international

event projects as a Event Planner.  

Now, I am looking forward to support our international team and organize their daily administrative life, so they can fully enjoy researching!

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Dr. Christina Saak

christina.caroline.saak[a.t_))uni-hamburg.de

I have been a science manager for Cosy.Bio since December 2021. I did my PhD at Harvard University, where I studied how Proteus mirabilis utilizes a type VI secretion system to engage in bacterial social interactions. For my postdoctoral studies, I moved to the University of California - San Diego. Here, I used multi-platform metagenomics to study horizontal gene transfer in cheese rind microbiomes.

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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.

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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.

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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. 

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Daniel Buchberger

Since October 2021, I’m one of three admins in the Cosybio networks Team.Before I joined Hamburg University, I had a chance to get 2 years experience in a software development company as well as 1,5 years of experience at a social media agency.

What's my journey here? Well, try to offer my technical knowledge and experience in an easy way to everyone who needs a solution. For our future I wish for awesome projects with nice features (and for the fun some bugs) and great new things to see and learn. 
 

My main interest is to stay curios can be an easy way to grow with the challenge.

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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.

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Dr. Karen Manalastas-Cantos

karen.manalastas-cantos[a.t_))cssb-hamburg.de

@CSSB, co-supervised together with Maya Topf

 

I studied molecular biology and computer science in the University of the Philippines Diliman, before specializing in computational structural biology during my PhD in EMBL Hamburg, where I helped develop tools for modeling protein and nucleic acid structures using a combination of low and high resolution information. Currently, my interests lie in combining structural and sequence information, possibly through deep learning, to elucidate new biological insights.

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Dr. Khalique Newaz

khalique.newaz[a.t_))uni-hamburg.de

I am a Postdoc at Cosy.Bio. Additionally, I am part of the Computational Systems Biology (CDL3) group at the Center for Data Science and Computing. My research interests lie in developing data (network) science approaches to explore and understand biological systems. Currently, I study the effect of alternative splicing (a phenomenon through which a single gene gives rise to multiple proteins) on the interactions between proteins.
I did my Ph.D. in Computer Science from the University of Notre Dame, USA, where I developed network-based computational methods to compare protein 3D structures. 

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Dr. Maria Elkjaer

I am an affiliated postdoc at Cosy.Bio working on the Lundbeck Foundation Postdoc 2021 granted project: “A brain reparatory network defined by integrative single-cell omics: FoxF2 signaling in astrocytes” in collaboration with Prof. Zsolt Illes Odense University Hospital (OUH) and Prof. Richard Röttger at University of Southern Denmark (SDU).

I did my PhD in the lab. of Prof. Zsolt Illes, Department of Neurology, OUH/SDU. Using a systems biology approach, I studied the evolution of different lesion types in micro dissected human brain areas from patients with multiple sclerosis. During my education, I have stayed in the lab. of Prof. Romana Höftberger, Institute of Neurology, Medical University of Vienna (MUV) and several times in the lab. of Prof. Richard Reynolds Lab., Division of Brain Sciences, Faculty of Medicine, Imperial College London.

My main research interest is to examine the pathogenesis of brain damages vs repair by using novel strategies and technologies.

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Dr. Tanja Laske

tanja.laske[a.t_))uni-hamburg.de

Since May 2021, I am a postdoctoral researcher at the Cosy.Bio lab at the University of Hamburg. I studied Biosystems Engineering at the Otto von Guericke University Magdeburg and obtained the Master’s degree for my experimental studies on adenoviral vector production in animal cell cultures, which I performed at IBET/ITQB-UNL in Lisbon, Portugal. During my PhD, I continued infection research in the dry lab and built mathematical models of virus replication dynamics to support the optimization of influenza vaccine production at the Bioprocess Engineering department at the Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg. At Cosy.Bio, my overall goal is to address challenges in systems medicine by linking multi-omics data analysis with mechanistic models and machine learning techniques.

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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.

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Andreas Maier

In May 2021, I start as a PhD student at Cosy.Bio at the UHH. My current tasks include work surrounding the REPO-TRIAL drug repurposing project. In August 2020, I joined the Chair of Experimental Bioinformatics at TUM for the thesis of my Bioinformatics master's degree.There, I focused on the development of a web application for the analysis and exploration of heterogeneous molecular disease networks.

 

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Arvid Hutzfeldt

a.hutzfeldt[a.t_))uke.de

@UKE, PhD

I’m a PhD candidate at the Cosy.Bio institute, working in close collaboration with Markus Rinschen at the UKE. Here, I use different Proteomics approaches to research inflammatory glomerular diseases in mice as well as in human tissue samples and kidney organoids. Before, I absolved my Master in Biomedicine at the MHH in Hannover and my Bachelor in Molecular Life Sciences in Lübeck. During my Master thesis, I focussed on the characterization of regulatory proteins involved in the P. aeruginosa Type III secretion system.

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Aylin del Moral

aylin.del.moral.morales[a.t_))uni-hamburg.de

I'm a Ph.D. student from the Cancer Epigenetics research group at Universidad Autónoma Metropolitana in Mexico. I received a Bachelor's degree in Pharmaceutical Chemistry and a Master's degree in Biochemistry from Universidad Nacional Autónoma de México. My research project is co-supervised by Prof. Dr. Jan Baumbach and Prof. Dr. Maya Topf and is focused on studying the role of BORIS in ovarian cancer through transcriptomic analysis and molecular modeling.

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Chit Tong Lio

chit.tong.lio[a.t_))uni-hamburg.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.

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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.

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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.

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Fabio Patroni

I'm a PhD student at the Genetics and Molecular Biology Program (IB-UNICAMP) in the Bioinformatics area, since March 2020, under supervision of Prof. Dr. Marcelo Mendes Brandão in the Integrative and Systemic Biology Laboratory (LaBIS). I received my B.Sc. in Biomedical Sciences from IBB-UNESP and my M.Sc. in Animal Genetics and Evolution fromIB-UNICAMP. Currently, I'm a visiting researcher at Cosy.Bio working on Acute Myeloid Leukemia patient stratification using clinical, omic data and machine learning algorithms.

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Fernando M. Delgado Chaves

fernando.miguel.delgado-chaves[a.t_))uni-hamburg.de

I joined the CoSy.Bio team at the University of Hamburg in October 2021.  I am a biotechnologist by training, although I soon diverted my path to Bioinformatics.  In recent years, I have specialized in Health Biotechnology and Computational Biology, which has allowed me to collaborate with leading researchers bridging the gap between life scientists and computer scientists. My main interests are personalized medicine, biomarker discovery, integration of various medicines, science communication, mentoring and education.

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Jeanine Liebold

jeanine.liebold[a.t_))uni-hamburg.de

Starting April 2022, I am a PhD candidate at the Chair of Genome Informatics in collaboration with Cosy.Bio, both at Uni Hamburg. I hold a master’s degree in Intelligent Adaptive Systems from Uni Hamburg where I wrote my master’s thesis about feature recognition in audio and video data with deep learning. Before, I received my bachelor’s degree in Electrical and Information Engineering from HAW Hamburg. My research interests are mainly machine and deep learning and my research is about applying these methods to bioinformatic problems. 

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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.

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Julian Späth

julian.alexander.spaeth[a.t_))uni-hamburg.de

I'm a Ph.D. student at Cosy.Bio and part of the FeatureCloud/REPO-TRIAL 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. 

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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.

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Klaudia Adamowicz

klaudia.adamowicz(a.t_))uni-hamburg.de

From May 2021, I will start as a PhD candidate at Cosy.Bio at the University of Hamburg. After joining the Institute of Computational Biology (ICB) at Helmholtz Zentrum München, where I worked on single cell RNA seq analysis during my master internship, I extended my collaboration to work on a machine learning project with tensorflow 2. My interest in machine learning led me to the Chair of Experimental Bioinformatics at the Technical University of Munich for my master thesis, where I worked on node centrality measures for disease module identification to create new algorithms for use in drug repurposing.

In the future I will work on the development of a platform for integration of research and clinical data and interlink them with bioinformatics, machine learning and simulation models.

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Lena Hackl

lena.hackl(a.t_))uni-hamburg.de

I’m a PhD candidate at Cosy.Bio since April 2021. I studied Computer Science at TUM and gained some experience with ligand binding site prediction in a project at Rostlab and as a research assistant on Human T-cell Immunology at Zielinski Lab. I joined the Chair of Experimental Bioinformatics at TUM to work on exon-specific differences in microRNA regulation due to alternative splicing for my Master’s thesis. Currently I'm interested in the study of alternative splicing in transcription factors.
 

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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. 

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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. 

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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.

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Markus Hoffmann

@TUM

In March 2019, I joined the group as part of my master’s degree internship. During this time, I contributed to implementing SPONGEdb: A pan-cancer resource for competing endogenous RNA interactions. After my internship, I extended my work at the group as a HIWI working for Dr. David Blumenthal on C++ programming tasks, which helped to implement a framework for modeling epistatic interaction. As the framework results were promising, I chose to intensify my work in this field as part of my Master’s Thesis. I finished my Master’s Thesis - GenEpiSeeker: a tool for generic epistasis detection via local search – in September 2020. In October 2020, I decided to continue my work as a Ph.D. student. As a Ph.D. student, I will focus on computational methods to unravel gene-regulatory combinatorics of putative super-enhancers in cooperation with Prof. Dr. Lothar Hennighausen and the National Institute of Health (NIH), Maryland, USA.

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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.

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Mhaned Oubounyt

mhaned.oubounyt[a.t_))uni-hamburg.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.

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Mohammad Bakhtiari

mohammad.bakhtiari[a.t_))uni-hamburg.de

 From May 2021, I joined as a Ph.D. research assistant in Cosy.Bio lab at the University of Hamburg and be a part of the EU Horizon2020 FeatureCloud project. I am graduated from IUST with M.Sc. in Artificial Intelligence, where my master thesis was about hybrid recommendation systems using Bayesian networks. My current research is mainly focused on Federated Learning; I am also interested in AutoML, Multi-task Learning, and Meta-Learning.

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Mohammad Mahdi Kazemi

mohammad.kazemi.majdabadi[a.t_))uni-hamburg.de

I am a Ph.D. candidate at Cosy.Bio since January 2022. I am graduated from IUST with BS in Computer Engineering and M.Sc. in Artificial Intelligence. I have worked for more than 5 years in tech companies (such as Snapp! , TSCTMC, etc.) as a Data Scientist. At UHH I am part of the EU Horizon2020 FeatureCloud project. Currently, I am working on federated learning and Medical Image Analysis using Deep Learning. Also, I am interested in Blockchains and ‘AI, Philosophy, and Science’. 

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Michael Hartung

michael.hartung[a.t_))uni-hamburg.de

I am a PhD student at the Chair of Computational Systems Biology at the University of Hamburg. My research interests revolve around regulatory interaction networks. I received a Bachelor's degree in Bioinformatics at the Goethe University in 2018 in Frankfurt, followed by a Master's degree in Bioinformatics at the TUM and LMU in Munich in 2021. I finished my Master's thesis creating CADDIE, a web application for drug-repurposing in cancer. In 2019/20, I spent one year at the University of Helsinki. During my studies, I was working in different tech startups doing software development and software engineering.

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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.

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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.

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Niklas Probul

niklas.probul[a.t_))uni-hamburg.de

I started as a PhD candidate at Cosy.Bio in October 2021. I am part of the FeatureCloud team and will be focussing on the development of a federated Database for the FeMAI project. I obtained my Bachelor and Master at Ludwig-Maximilan University Munich and the Technical University of Munich. In my Master's Thesis at the University of Southern Denmark I researched the possible inclusion of biological networks into the structure of autoencoders.

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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.

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Sepideh Sadegh

sepideh.sadegh[a.t_))uni-hamburg.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.

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Supratim Das

supratim.das[a.t_))uni-hamburg.de

"Starting in September 2022, I am joining Cosy.Bio as a doctoral student. I received my BS and MS from the Indian Institute of Science Education and Research (IISER) – Pune. My background is in Life Sciences and Data Sciences. During my MS thesis, I worked on Genomic Data Enhancement using Deep Learning with Dr. Xinghua Shi (Temple University, PA). My research interest encompasses the interdisciplinary areas of Biology and Machine Learning. "

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Tianran Zhang

tianran.zhang[a.t_))zmnh.uni-hamburg.de

I am a PhD student co-supervised with Prof. Stefan Bonn, working in Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf. I have my bachelor and master’s degrees in Statistics. For my PhD research, I mainly work on analysis and machine learning application of multi-omics data across different tissues.

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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.

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Zakaria Louadi

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

I am a Ph.D. student at The University of Hamburg and Technical University of Munich. I developed the software DIGGER, NEASE, and Deep Splicing Code. My work mainly focuses on transcriptomics data analysis, with emphasis on the role of alternative splicing.

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Andre Bembennek

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Starting from May 2022 I will work as a HiWi on the SyMBoD-project at Cosy.Bio. Right now I am in the bioinformatics master programm of UHH. Before that, I graduated from the University of Bayreuth with a bachelor's degree in biology with specialization in molecular biology and gene technology.

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Christian Hoffmann

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I am in the bioinformatics master's program at TUM and LMU in Munich. In Spring 2022 I started as a HIWI in the Cosy.Bio team to gain more experience and develop practical skills. I’m currently part of the exon-exon interaction team. We are trying to use deep learning approaches to predict interactions between exons only using sequences.

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Fabian Neuhaus

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I am a master student at the University Hamburg (UHH) in the field of bioinformatics. Due to my bachelor of science in chemistry, I started my master with a lot of previous knowledge in natural sciences and focused my studies on the informatics part of bioinformatics. I am currently working as a student assistant in the CosyBio group. My subject is the denoising of single-cell RNA-Sequencing with deep count autoencoder networks, based on a previous master project.

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Jens Lohmann

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Starting from July 2022 I work as a HiWi on the Vir-AI-DIP project at Cosy.Bio. Since Oktober 2019 I am a masters student in Bioinformatics at the University of Hamburg. Beforehand, I did a bachelor's degree in Technical Biology at the University of Stuttgart. Currently, I am working on the mechanisms behind DI RNA de novo generation in Influenza A viruses.

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Julian Poschenrieder

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I am student in the bioinformatics bachelor program at TUM and LMU and joined the Cosy.Bio team as HiWi to gain further practical experience in the fields of Bioinformatics. Currently, I help with the development and benchmarking of an epistasis detection tool called GenEpiSeeker in c++.

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Juliane Röscheisen

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In 2022, I obtained my Bachelor's degree in informatics at the University of Hamburg. In my thesis supervised by Dr. Olga Tsoy from the CGAT group, I evaluated tools used for the detection of differential splicing in RNA-Seq data. Currently, I am enrolled in the informatics master's program at the University of Hamburg. Starting from October 2022, I will be working at Cosy.Bio as a HiWi.

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Lisi Arend

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I’m a masters student in Bioinformatics at the Technical University of Munich and Ludwig-Maximilians-Universität München since October 2020. I developed a federated Cox proportional hazard model app for the FeatureCloud platform for my bachelor thesis. Recently, I have worked with cytometry data and built CYANUS - CYtometry ANalysis Using Shiny - a user-friendly R Shiny App allowing the user to analyze cytometry data. Currently, I am working as a HiWi at the chair and work within the SyMBoD project.

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Marieca Burghardt

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In 2021 I obtained my Bachelor's degree in biotechnology. 

Since then I am an bioinformatic master student at the university in Hamburg. 

In cooperation with the UKE and Cosybio I work as a student assistant in the

field of atrificial intelligence physio therapy. So I am interested in transfer learning

with health record data. 

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Mia Le

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 I am currently writing my master thesis about defective interfering particles supervised by Tanja Laske. I started at CosyBio when I was working on my masters project in the winter semester of 2021/22 where my team and I developed a tool for consensus active module identification (CAMI) together with Andreas Maier as our supervisor. I study Bioinformatics in the masters course of the UHH. Before that I graduated with a bachelor‘s degree in Biotechnology from the TU Brunswick.

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Paula Kammer

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In 2021, I obtained a Bachelor's degree in Bioinformatics at the Friedrich-Schiller-Universität Jena. Since then, I am in the bioinformatics master program at the University of Hamburg. Starting from October 2022, I will work as a HiWi on the FeatureCloud and FeMAI project at Cosy.Bio.

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Tilman Immisch

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I’m an HCI Bachelors Student in the Research Group Knowledge Technology at UHH, developing and researching Semantic Memory for use with popular Reinforcement Learning Algorithms. I’m also currently working as a HiWi at Cosy.Bio, helping develop the DiNiro Tool for De novo reconstruction of transcriptional gene regulatory network modules.

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Prof. Dr. Harald Schmidt

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Prof. Schmidt, MD PhD PharmD, is a visiting Professor of Pharmacology and Personalised Medicine working in Systems Medicine and drug repurposing from Maastricht University, Netherlands, and a collaborator in the H2020 projects REPO-TRIAL and FeatureCloud.

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Prof. Dr. Vasco Azevedo

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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 Professor at University of Marburg
  • David B. Blumenthal, Assistant Professor at University of Erlangen
  • Josch Pauling, Group leader at Technical University of Munich
  • Markus List, Group leader at Technical University of Munich
  • Olga Lazareva, Postdoc at DKFZ Heidelberg
  • Afsaneh Mohammadnejad, Assistant Professor at University of Southern Denmark
  • Richa Batra, Postdoc at Helmholtz Center Munich
  • Nicolas Alcaraz, Postdoc at Copenhagen University
  • Eudes Barbosa, Postdoc at Helmholtz Center Munich
  • Douglas Parise, Postdoc at Laboratory of Cellular and Molecular Genetics (UFMG), Brazil
  • Mariana Parise, Postdoc  at Laboratory of Cellular and Molecular Genetics (UFMG), Brazil
  • 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