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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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Francisca Modinger

maria.modinger.larrain[a.t_))uni-hamburg.de

I joined the CoSyBio team in September 2023. 
In terms of my education, I studied Business Administration and Management (BWL). Additionally, I hold a Master's Degree in Service and Development. 
Previously, I worked in the copper industry as a supply-chain manager.
 
As part of my current position, I provide support to the team by taking on various responsibilities such as organizing and planning tasks to ensure smooth workflow. My aim is to facilitate the Team's work so they can focus on what they do best.

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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. Together with my colleague Dr. Nina Wenke, we manage grant applications, projects and day-to-day business of the institute. 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_))uni-hamburg.de

As the Science Manager of CoSy.Bio, collaborating closely with my colleague Dr. Christina Saak to spearhead proposal writing, manage grant applications, and coordinate various projects. My journey with the CoSy.Bio team commenced in 2019 when I joined the Technical University Munich. Prior to this, I earned my M.Sc. in Biotechnology at the Max Planck Institute for Molecular Biomedicine in Muenster. Following this, I embarked on my doctoral research in Berlin, delving into autoimmune encephalitis at the German Center for Neurodegenerative Diseases (DZNE) and the Charité University Hospital.

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Dr. Olga Tsoy

olga.tsoy[a.t_))uni-hamburg.de

I’m a group leader of the Computational Genomics and Transcriptomics group (cgat-group.de). My main research interest is mechanisms of pathological conditions such as diseases with complex phenotypes and drug side effects and the role of alternative splicing. I graduated from Lomonosov Moscow State University (Moscow, Russia) and did PhD in Kharkevich Institute in Moscow in Professor Mikhail Gelfand's 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, USA), and at Okinawa Institute of Science and Technology (Okinawa, Japan) where I went on working on the regulation of bacterial metabolic pathways. As a research scientist, I worked at the Skolkovo Institute of Science and Technology (Moscow) on 3D chromatin structure analysis. In 2019, I joined the group of Professor Jan Baumbach at the Technical University of Munich, and continued working with the group at the University of Hamburg.

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Dr. Olga Zolotareva

olga.zolotareva[a.t_))uni-hamburg.de

I specialize in the analysis of biomedical multi-omics data, discovery of biomarkers, gene prioritization, and drug response prediction. Since May 2021, I am heading research group Computational and Systems Medicine at the UHH. We develop algorithms and create computational tools for exploration of disease heterogeneity and patient stratification, reconstruction of regulatory networks, and prioritization of drugs and drug targets. Since the privacy of patient-derived data is a major roadblock on the way of personalized medicine, we work on privacy-aware methods for distributed patients’ data analysis.

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Daniel Buchberger

daniel.buchberger[a.t_))uni-hamburg.de

Since October 2021, I’m one of three admins in the CoSy.bio 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. Fernando M. Delgado Chaves

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

In October 2021, I embarked on a postdoctoral researcher journey with the CoSy.Bio team at the University of Hamburg. I am a Biotechnologist by training but I soon pivoted to Bioinformatics and Computational Biologists.
My research focuses on network and precision medicine, biomarker discovery, and large language models (like ChatGPT) for biomedical tasks. I am also interested in bridging the communication gap between clinicians and informaticians, advocating for collaborative, synergistic efforts. Beyond research, I also value science communication in the digital age, mentoring, and education.

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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

maria.louise.elkjaer[a.t_))uni-hamburg.de

Since May 2022, as a postdoc at CoSy.Bio, I have been applying my neuroimmunology expertise, developed during my PhD at the University of Southern Denmark, to systems and network biology using single-cell multi-omics. Enhanced by experiences at Imperial College London, the Medical University of Vienna, and the University of Gothenburg, my research is primarily focused on multiple sclerosis. Currently, with the support of the Lundbeckfonden Postdoc Fellowship, I am dedicated to uncovering new disease mechanisms and therapeutic targets.

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Dr. Sara Ashry Sayed Mohammed

sara.ashry.sayed.mohammed[a.t_))uni-hamburg.de

Currently, I am a researcher at CoSy.Bio, focusing on a Systematic Review of Transfer Learning of Human Activities using IMU Sensors. My research involves both manual and automated approaches, with a particular emphasis on Large Language Models (LLMs) and Generative Pre-trained Transformers. In addition, I actively participate in PhysioAI meetings.
I completed my bachelor's at Fayoum University, Egypt, and pursued my MSc and PhD at Egypt-Japan University of Science and Technology in collaboration with Waseda University, Tokyo, focusing on machine learning algorithms. During my Ph.D., I spent 8 months at Waseda University, and after Ph.D., I worked as a researcher at the Electronic Research Institute in Cairo; while serving as a lecturer at Fayoum University, where I supervised graduation projects, contributing to my expertise in human activity recognition based on IMU sensors and Data Management.

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Dr. Tanja Laske

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

I am a postdoctoral researcher and junior research group leader 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 team and me develop innovative computational methods that link bioinformatics multi-omics analysis with dynamic models to improve model predictions for complex diseases and biological processes, such as bone defect healing within the SyMBoD project. Furthermore, I am developing methodologies for artificial intelligence-based research of defective interfering particles within the Vir-AI-DIP project. Using machine and deep learning techniques we analyze and optimize the antiviral potential of defective viral genomes for improved prevention and treatment of infectious diseases.

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Ahmad Taheri

ahmad.taheri(a.t_))uni-hamburg.de

I am a PhD candidate and research associate at the Institute for Computational Systems Biology at the University of Hamburg, contributing to the Microb-AI-ome project. Prior to joining the CoSy.Bio lab, I worked as a research and laboratory assistant at the Cloud and Edge Computing Research Lab at YU, Iran. My primary research interests revolve around topics such as Generative AI, Federated/Distributed Learning, Computational Intelligence, and Metaheuristic Methods.

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Andreas Maier

In May 2021, I started as a PhD student at CoSy.Bio (UHH). My current tasks include work surrounding the REPO-TRIAL drug repurposing project. I contribute in the development of network-based drug repurposing solutions but also in the research for applications of LLMs in systems medicine for knowledge generation and extraction. 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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Farzaneh Firoozbakht

I am a research associate at the CoSy.Bio lab since April 2023, working on the DrugSiderAI and PosyMed projects. 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. Following my graduation, I conducted research on applying ML techniques to transcriptomic data, with the aim of advancing personalized medicine. Additionally, 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.

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Jeanine Liebold

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

Since April 2022, I am a PhD student at CoSy.Bio and at the Chair of Genome Informatics of Prof. Stefan Kurtz, both at the University of Hamburg. My research interests are mainly in machine learning and deep learning, with a focus on the application of these methods to bioinformatics problems, in particular, the prediction of protein-protein interactions in the event of alternative splicing. I hold a master’s degree in Intelligent Adaptive Systems from the University of Hamburg, where I wrote my master’s thesis on feature recognition in audio and video data with deep learning. Before that, I received my bachelor’s degree in Electrical and Information Engineering from HAW Hamburg.

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Jens Lohmann

jens.lohmann[a.t_))uni-hamburg.de

After receiving a bachelor's degree in Biotechnology at the University of Stuttgart, I relocated to the University of Hamburg to pursue a Master's degree in Bioinformatics. During this time, I joined CoSy.Bio for my master thesis on Defective Interfering Particles (DIPs) and employed Machine Learning to reveal the mechanisms of their generation. Since July 2023 I am a PhD student to continue this research. Besides that I am also developing a neural network using federated learning to enhance the quality of live for patients dealing with prostate cancer while preserving their data privacy.

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Julian Klemm

julian.klemm[a.t_))uni-hamburg.de

I'm a Ph.D. student at CoSy.Bio since April 2023 and part of the FeatureCloud (https://featurecloud.ai/) and Microb-AI-Ome (https://microbaiome.net/home) project.
I studied by B.Sc. of Biology at University Hamburg as well as my M.Sc. of Bioinformatics also at University Hamburg. In my master thesis I focused on privacy enhancing techniques for federated learning, especially differential privacy, while in my PhD my focus is on a federated data warehouse to allow easier data sharing in a privacy preserving manner. Generally, I'm focused on bringing privacy preserving tools for almost effortless federated collaboration.

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Julian Matschinske

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

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 web developer in my own company. At TUM and later UHH, I was part of the EU Horizon2020 FeatureCloud project, doing my PhD in computer science. My focus mainly lies on machine learning and data privacy in conjunction with federated systems. Today, I am working with CosyBio on dehaze, a company aiming to bring precision medicine into clinical practice. I have a passion for difficult technical challenges requiring an analytical approach and cross-domain expertise.
 

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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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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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Kristopher Nolte

kristopher.nolte[a.t))bnitm.de

I am a PhD student at the Bernhard Nocht Institute for Tropical Medicine (BNITM) and am involved in research into mosquito biology. My focus is on the application of machine learning to analyse patterns in mosquito wings. This research aims to improve our understanding of mosquito biology and vector surveillance methods, contributing to the overall goal of mitigating the impact of mosquito-borne diseases such as malaria and dengue fever. My academic path began with a degree in biochemistry at the University of Würzburg, later switching to health sciences in Hamburg. I am particularly interested in computer vision and the extraction of biologically relevant information from images. Before my current job, I did research at DESY, where I studied X-ray diffraction patterns through the lens of machine learning and at the BNITM to investigate the usefulness of open access data for disease modelling.

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Lena Hackl

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

I’m a PhD candidate at CoSy.Bio since April 2021 after finishing my M.Sc. Computer Science at TUM. Before, I gained some experience with ligand binding site prediction using CNNs and Class Activation maps at Rostlab and with single cell analysis in human T-cell immunology at Zielinski Lab. At the Chair of Experimental Bioinformatics at TUM I worked on exon-specific differences in microRNA regulation due to alternative splicing for my Master’s thesis. Currently I'm excited to research the application of deep learning methods for extracting splice junctions from RNAseq data with low sequencing depth.

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Mahdie Rafiei

mahdie.rafiei(a.t_))uni-hamburg.de

I have been a PhD student at the Chair of Computational Systems Biology at the University of Hamburg since January 2023 and I am part of the PhysioAI project. The primary aim of PhysioAI is to assess and enhance AI-powered multimodal tools for measuring physical activity in osteoarthritis treatment. I am particularly interested in Deep Learning, Transfer Learning, and Federated Learning. I received an M.Sc. in Computer Science from QIAU in 2021. My master's thesis focused on the research of recommender systems using machine learning techniques. Throughout my studies, I worked for over 5 years in tech companies as a web developer.

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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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Marius Klages

marius[a.t_))dehaze.de

Marius graduated from WHU with a B.S. in Business Administration and from Harbour.Space University with an MBA and M.E. in Data Science. Prior to working on bringing the federated learning technology from academic usage into the market, Marius built up his own startup in preventive health, which was then sold to BEAT81.

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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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Mhaned Oubounyt

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

I am a postdoc at CoSy.Bio working on the NetMap project, where we are developing a dimensionality reduction method for single-cell molecular data based on the explanatory power of differential regulatory networks. My research interests include single-cell transcriptomics and spatial single-cell network analysis. Specifically, I focus on developing methods for inferring gene co-expression and gene regulatory networks from single-cell data and spatial single-cell data.

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Michael Hartung

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

I am a PhD student at the Institute for Computational Systems Biology at the University of Hamburg. 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 by 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 worked in different tech startups doing software development and engineering.
My research interests revolve around network-based drug repurposing as well as different approaches to in silico biomarker identification, developing tools like Drugst.One (https://drugst.one/), UnPaSt (https://apps.cosy.bio/unpast/) and the Epistasis Disease Atlas (https://epistasis-disease-atlas.com/home). 

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Mohammad Bakhtiari

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

Since May 2021, I have been actively involved as a Ph.D. research assistant at the CoSy.Bio lab at the University of Hamburg, where my work plays a crucial role in the EU Horizon 2020 FeatureCloud project. I hold a Master of Science in Artificial Intelligence from IUST, culminating in a thesis that explored hybrid recommendation systems using Bayesian networks. Currently, my research is predominantly centered around privacy-preserving Federated Learning, with a special emphasis on its applications within biomedicine, including single-cell RNA-seq and medical imaging data.

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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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Nico Kaiser

nico.kaiser[a.t_))zmnh.uni-hamburg.de>

I started as a Ph.D. student at CoSy.Bio in August 2023. My research focus is the computational analysis of spatial multi-omics image data in a collaboration with the Universitätsklinikum Hamurg-Eppendorf (UKE). I earned my Bachelor's and Master's degree in medical engineering (at RAC Remagen and FAU Erlangen), where I specialized in utilizing deep learning and computer vision methods for medical image analysis. Before starting my Ph.D. I also worked as a software engineer for a company doing medical imaging software.

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Niklas Probul

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

I've been pursuing my PhD at CoSy.Bio since October 2021. My main research focus involves examining the connection between the gut microbiome and colorectal cancer, with a particular emphasis on exploring the potential applications of federated learning in this domain. Furthermore, I'm an active member of the FeatureCloud core development team, where I'm involved in implementing a federated database and overseeing various sysops tasks. While my expertise lies in Federated Learning and Random Forests, I have a deep interest in all aspects of data science!

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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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Niloofar Mehdizadeh

niloofar.mehdizadeh[a.t_))uni-hamburg.de

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 CoSy.Bio, where I am going to work on a project which aims to detect colorectal cancer at an early stage by applying federated learning methods. 

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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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Shihab Ullah

md.ullah[a.t_))uni-hamburg.de

Since January 2024, I have been working as research associate at the Institute for Computational Systems Biology at the University of Hamburg contributing to the dAIbetes-Net project. This initiative involves developing a federated database network to connect and structure data in local repositories distributed around the globe, while respecting patient data privacy by design. Prior to my tenure at the CoSy.Bio laboratory, my professional journey included positions as a Developer and Data Analyst, culminating in the successful completion of an M.Sc. degree in Computer Science from the University of Southern Denmark in 2022. My professional interests span diverse domains with a focus on areas such as Data Science and Governance, Blockchain, Generative AI, and Federated/Distributed Learning etc.

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Silke Van Elferen

silke.van.elferen[a.t_))uni-hamburg.de

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.

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Simon Süwer

simon.suewer[a.t_))uni-hamburg.de

Since January 2024 I am a PhD student at CoSy.Bio for the projects FeatureCloud (https://featurecloud.ai/) and dAIbetes. I completed my Bachelor of Science in Applied Computer Science at the University of Applied Sciences and Arts Hannover, followed by a Master of Science in Computer Science at the University of Vienna, specialising in Data Science. In my master thesis I worked on the combination of session- and sequence-based recommender systems in a dynamic Graph Neural Network (GNN), in particular on the development of hierarchical dynamic GNNs.

 

My current research aims at developing privacy-preserving tools that make federated collaboration not only easier, but almost effortless. By merging theory and practice, my goal is to create innovative solutions to complex challenges that redefine the way we think about data collaboration and privacy.

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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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Yuliya Burankova

yuliya.burankova[a.t_))uni-hamburg.de

Since March 2023, I've joined CoSy.Bio as a visiting researcher and have started a PhD at TUM's Proteomics and Bioanalytics chair. I have an interdisciplinary background in pharmacy and computational and molecular biology, and am interested in tool development for personalized medicine and biomarker discovery. As part of the CLINSPECT-M project, my focus is on federated learning in mass-spectrometry proteomics. Currently, I am developing FedProt, a novel method for privacy-preserving federated differential protein expression analysis. Additionally, I am involved in developing UnPaSt, the unsupervised patient stratification method, and clinical RNAseq data analysis.

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Zoe Chervontseva

zoia.chervontseva[a.t_))uni-hamburg.de

Since April 2023, I have joined CoSy.Bio as a postdoc. My primary research interest is employing interpretable machine learning techniques to gain new biological insights. I did my PhD under the guidance of Professor Mikhail Gelfand at IITP RAS (Moscow, Russia). My doctoral research was focused on investigating the role of mRNA secondary structure in mRNA editing of cephalopods. Additionally, I worked as a junior researcher at the Skolkovo Institute of Science and Technology and contributed to several projects in the fields of bacterial genomics and human alternative splicing research.

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Adrian Hölzlwimmer

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I am currently enrolled in the Bioinformatics bachelor's program at TUM / LMU. I am set to join the CoSy.Bio team as a HiWi in March, where I will be working on the NeDRex project.

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Andre Bembennek

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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.

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Ann-Sofie Schäfer

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I currently serve as a science communicator and am entrusted with overseeing the social media presence at CoSy.Bio. My journey led me from Munich to Hamburg in 2021, where I started studying Biology at the University of Hamburg. Next year, I will be writing my Bachelor's thesis, possibly within the field of bioinformatics, because it truly fascinates me.

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Christian Hoffmann

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I am a bioinformatics master's student at the Technical University of Munich (TUM) and Ludwig Maximilian University of Munich (LMU). I joined the CoSy.Bio team as a HIWI in Spring 2022 to acquire hands-on experience and hone my practical skills. I am currently involved in the REPO-TRIAL drug repurposing project, where my primary task is to validate computational predictions using a range of techniques such as statistical analysis and data visualization.

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Christoph Horlebein

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I am enrolled in the M.Sc. Bioinformatics at ZBH/UHH. In August 2023, I joined CoSy.Bio as a student assistant and analyse time course data from multi-omics experiments on impaired bone healing. I previously obtained a master's degree in Nutritional Sciences at FSU Jena

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Elias Albrecht

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I am a master's student in bioinformatics at the Technical University of Munich (TUM) and Ludwig Maximilian University of Munich (LMU). For my BSc thesis I evaluated domain-domain interaction prediction methods and used the PPIDM method to infer new interactions. I will join the CoSy.Bio team from January 2024 as a HIWI and will be working to update DIGGER and NEASE, with a focus on making the tools easily available online.
 

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Fabian Neuhaus

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I am a bioinformatics master's student at the University of Hamburg
(UHH) with a background in pure chemistry.
With a strong foundation in the natural sciences, I've directed my academic focus toward the informatics side of bioinformatics during my master's studies. Presently, I am contributing as a student assistant in the CoSy.Bio group. My current focus revolves around enhancing transcription factor prediction tools by integrating structural data into the prediction process.

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Julian Poschenrieder

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I am a student in the bioinformatics master's program at TUM and LMU. I have joined the Cosy.Bio team as a HiWi (student assistant) to gain practical experience in the field of bioinformatics. Currently, I am a member of the development team working on our epistasis detection tool, "NeEDL".

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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 CoSy.Bio.

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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 CoSy.Bio 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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Prof. Dr. Harald Schmidt

hschmidt[a.t_))ppmlab.net

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

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

  • Justus Wolff, Postdoc
  • Fabio Boniolo, Postdoc at Dana-Farber Cancer Institute, Boston
  • Melisa Klug,Field Application Scientist at Standard BioTools,Munich
  • Michael Lauber,
  • Tim Rose,Postdoc at Universität Heidelberg
  • Marisol Salgado Albarrán, Postdoc at Universidad Nacional Autónoma de México
  • 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
  • Amit Fenn, Postdoc
  • Chit Tong Lio, Postdoc
  • Zakaria Louadi, Postdoc
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