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.

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!
 

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.

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.

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.

@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. 

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.

@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.

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.

@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.

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. 

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.

I'm a postdoc at Cosy. Bio working on a research project related to the E-health care system for monitoring patients with neurodegeneration and chronic disease by analysing human behaviour using deep learning. I graduated from the Faculty of Engineering, Fayoum University, Egypt, and I did the MSc and PhD at the Computer Science Engineering Department at Egypt-Japan University of Science and Technology (E-JUST) in cooperation with Waseda University, Tokyo, Japan. There I studied machine learning algorithms. During my PhD, I briefly stayed at Waseda University for 8 months, and I travelled to present my publications at international conferences in Portugal, Spain, France, and Mexico, such as ICINCO, and ICMLA. In addition to attending a summer school at Halmstad University in Sweden, As a researcher, I worked at the Electronic Research Institute in Cairo on human activity recognition using deep learning by collecting data from smartwatches, and at the same time, I worked as a lecturer at Fayoum University for undergraduates, and I supervised some graduation projects.

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.

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.

 

@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.

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.

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.

@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.

I will be working as a Ph.D. candidate at the Cosy.Bio lab from April 2023 and be part of DrugSiderAI project. I earned a B.Sc. in Electrical Engineering from IAU and an M.Sc. in Biomedical Engineering from AUT. During my master’s program, I gained experience in signal processing and machine learning (ML) methods for biomedical applications. After graduation, I conducted research on applying ML techniques to transcriptomic data, with the goal of advancing personalized medicine. Moreover, I focused on network-based approaches and gained experience working with graph convolutional neural networks to capture the complex relationships in biological data. My primary research interest lies at the crossroads of applying network-based ML to the field of medicine. I am excited to continue exploring this field and contributing to cutting-edge research as part of the Cosy.Bio team.

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. 

I will start as a PhD student at Cosy Bio in April 2023. I studied my Bachelor in Biology and my Master in Bioinformatics, both at the Univeristy Hamburg. I am involved in the future cloud project and therefore generally working on federated/distributed learning and databases, looking to bring useful tools for collaborations in research. 

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.

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. 

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.

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.
 

"I have been a Ph.D. research assistant at CosyBio at the University of Hamburg since January 2023, and I am part of the PhysioAI and FeatureCloud projects. I got a M.Sc. in IT engineering from QIAU in 2021 and worked in different tech companies as a web developer. I'm interested in Deep Learning, Transfer Learning, and Federated learning."

@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.

@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.

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.

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.

 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.

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’. 

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.

@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.

I received my B.S. in computer engineering from FUM, and M.Sc. in computer science (AI) from AUT, Iran. In my master’s thesis, I proposed a method for multi-view subspace clustering by using autoencoder neural networks. My research interests include statistical machine learning, optimization, neural networks, and interdisciplinary fields of AI.  Since February 2023, I started my work as a guest researcher at CosyBio, where I am going to work on a project which aims to detect colorectal cancer at an early stage by applying federated learning methods. 

@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.

I'm a master's student at the University of Maastricht, studying Drug Development and Neurohealth. In January 2023 I will be returning to Cosy.Bio to work on my master's thesis under the supervision of Dr. Olga Tsoy and Lena Hackl. I will be looking at tissue-specific andbloodbased biomarkers in cardiomyopathies. In 2021/2022, I first joined Cosy.Bio to work on the thesis for my MSc degree in Systems Biology (Maastricht University), under the supervision of Dr. Olga Zolotareva, working towards a federated implementation of a DNA methylation microarray data analysis workflow. Before this, I obtained a BSc (Hons) degree in Forensic Science at Anglia Ruskin University.

"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. "

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.

Since March 2023, I've been a visiting researcher at CoSy.Bio lab and a PhD student at the chair of Proteomics and Bioanalytics, TUM. I'm a part of the CLINSPECT-M project and am interested in personalized medicine and biomarker discovery. I have an interdisciplinary background in pharmaceutical chemistry and computational and molecular biology. I hold a specialist degree (equivalent to an MSc) in Pharmacy and an MSc in Chemistry. I worked on terminal transferase modifications for de novo DNA synthesis at the Institute of Bioorganic Chemistry (Minsk, Belarus) and studied interaction preference in gene regulatory networks during the Bioinformatics for Biologists CPD program. 

Since April 2023, I have joined CoSy.Bio as a research associate and am actively involved in the DrugSiderAI and PoSyMed projects. My primary research interest is employing interpretable machine learning techniques to uncover new biological insights. I am currently in the final stages of completing my PhD under the guidance of Professor Mikhail Gelfand at IITP RAS (Moscow, Russia). My doctoral research focused on investigating the role of mRNA secondary structure in mRNA editing of cephalopods. Additionally, I worked as a junior researcher at the Skoltech institute in Moscow and contributed to several projects in the fields of bacterial genomics and human alternative splicing research.

Starting from May 2022 I will work as a HiWi 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.

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.

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.

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.

As a student of bioinformatics at the University of Hamburg, I focused on the intersection of data science and machine learning within the field of bioinformatics. I hold a Bachelor's degree in Molecular Life Sciences and am currently pursuing my Master's degree. My Master's thesis delves into the optimization of pipelines to identify isoforms in single-cell RNA sequencing data, a crucial aspect of understanding gene expression at the cellular level. I am excited to see the potential discoveries and advancements that my research may uncover.

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++.

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 CosyBio.

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 learningwith health record data. 

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.

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.

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.

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.