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Works at MDC as of March 2014 as the group leader for the bioinformatics platform. He has experience in computational epigenomics, cancer genomics and regulatory genomics. He is generally interested in large-scale data-sets in biology and machine-learning applications.
- 2013-2014, Postdoctoral Fellow, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- 2012-2013, Senior Research Associate, Weill Cornell Medical College of Cornell University, New York, USA
- 2010-2012, Postdoctoral Associate, Weill Cornell Medical College of Cornell University, New York, USA
- See [LinkedIn] for more ...
- 2005-2010, PhD (Genomics & Bioinformatics), University of Bergen, Bergen, Norway
- 2001-2005, B.Sc (Bio. Sciences & Bioeng./Bioinformatics track), Sabanci University, Istanbul, Turkey
Publications: [PubMed] [GoogleScholar] [ImpactStory]
Websites: [LinkedIn] [Mendeley] [Github] [slideshare] [blog]
E-mail: altuna.akalin [at] mdc-berlin [dot] de
Alex is a trained bioinformatician. He is experienced in workflow development and analysis of sequencing data including short/long-read RNA-Seq, ChIP-Seq, ATAC-Seq and BS-Seq.
- 2021 - 2022 Researcher, University of Hamburg, Germany
- 2016 - 2022 PhD Student, MDC BIMSB, Berlin, Germany
Publications: [PubMed]
Websites: [LinkedIn] [Github]
E-mail: [email protected]
Vedran supports research projects for the platform. He has extensive experience in next-generation sequencing analysis: RNA-seq, ChIP-seq, smallRNA-seq and whole genome sequencing.
- 2011 - 2011, Researcher,Uni Research/Bergen Center for Computational Science, Bergen, Norway
- 2010 - 2011, Researcher, University of Zagreb, Croatia
- 2011 - 2014 PhD student,University of Zagreb, Croatia
Publications: [PubMed]
Websites: [LinkedIn] [Github]
E-mail: vedran.franke [at] mdc-berlin [dot] de
Artür is a trained statistician, computational scientist and bioinformatician. His main research interest is Network Science, and he aims to develop graph-based statistical learning frameworks for analyzing omics datasets towards, e.g., Spatial Biology and Biological Knowledge Graphs. He has built several software packages and tools that implement statistical learning methods for knowledge discovery, and he has extensive expertise in analyzing data from a large variety of omics technologies such as scRNA-Seq, CITE-Seq, SLAM-Seq etc..
- 2020 – 2022, Postdoctoral Research Fellow, UMass Bioinformatics Core, Worcester, USA
- 2019 – 2020, Postdoctoral Research Fellow, Broad Institute of MIT and Harvard, Boston, USA
- 2017 – 2019, Teaching Assistant Professor, Yeditepe University, Istanbul, Turkey
- 2013 – 2017, PhD, Computational Sciences, Koç University, Istanbul, Turkey
Publications: [GoogleScholar]
Websites: [Homepage] [LinkedIn] [Github]
E-mail: [email protected]
Dan's big challenge is to maintain, extend and keep safe the BIMSB's IT infrastructure consisting of application servers, virtualization systems, storage, databases and dedicated systems used to analyze the biological data. Most of these systems are based on open source technologies (inclusing the operating systems/Linux) and they are designed based on the idea that a scientist must do science and not to loose time with unfriendly IT systems - of course, this cannot be done wihout a very close relationship with the users.
- 2013- now, System Administrator/Engineer , MDC/ BIMSB
- 2009-2013, System Administrator, Alexandru Ioan Cuza University of Iasi - Faculty of Computer Science, Romania
- 2003-2009, System Administrator, Cersanit SA, Romania
- MSc, Computer Science, Alexandru Ioan Cuza University of Iasi, Romania
- BSc, Computer Science, Alexandru Ioan Cuza University of Iasi, Romania
Websites: [LinkedIn]
E-mail: dan.munteanu [at] mdc-berlin [dot] de
Bora has started working at MDC on 1st of August, 2015 as a bioinformatics scientist. His roles in the platform include research, collaborations with other labs in the institute, and supporting other researchers in the form of consultations, mentorships, workshops, and user-friendly software development. His current research is focused on development of deep learning-based multi-modal data integration tools for precision oncology.
- 2014-2015, Bridging Postdoctoral Fellow, Structural and Computational Biology Unit European Molecular Biology Laboratory, Heidelberg, Germany
- 2011-2014, PhD, Structural and Computational Biology Unit European Molecular Biology Laboratory, Heidelberg, Germany
- 2008-2010, M.Sc, CIHR/MSFHR Bioinformatics Training Program Simon Fraser University and BC Cancer Research Center Vancouver, Canada
- 2003-2008, B.Sc Biological Sciences and Bioengineering (followed a Bioinformatics curriculum), Sabanci University, Istanbul, Turkey
Publications: [PubMed] [GoogleScholar]
Websites: [LinkedIn] [Github] [ResearchGate]
E-mail: bora.uyar [at] mdc-berlin [dot] de
Ricardo provides IT support for BIMSB scientists. He has extensive experience in GNU/Linux system administration (RHCE) and programming.
Since 2014 Ricardo works on GNU Guix, a functional package manager, which allows us to build scientific software reproducibly and manage complex software environments. Ricardo is an Emacs, Scheme, and Free Software enthusiast.
- 2009 - 2014, Server, cluster and workstation administrator, Siemens Ltd. China, Shanghai
- 2008 - 2009, Developer, Siemens AG, Berlin
- 2007 - 2008, Developer, Siemens Switchgear Ltd., Shanghai
- 2005 - 2007 Siemens Technik Akademie, Berlin
Websites: [Homepage] [Code] [Github]
E-mail: ricardo.wurmus [at] mdc-berlin [dot] de
Works at MDC as of January 2024 as guest PhD Student. He has experience in RNAseq data analysis and Snakemake. He is implementing methods for porting in cloud the pipelines of the group. He is generally interested in miRNA, single cell RNAseq and stem cells.
- 2022-2022, Bioinformatics Scientist, National Councils of Researches, Bari, Italy
- 2021-2022, Biologist/Bioinformatics Scientist, National Institute for the Infectious Diseases Lazzaro Spallanzani, Rome, Italy
- 2018-2018, Post Graduate Internship, San Camillo hospital, Rome, Italy
- 2022-Now, PhD Life Sciences (Bioinformatics and Omics track), Sapienza University, Rome, Italy
- 2015-2017, M.Sc Genetics and Molecular Biology, Sapienza University, Rome, Italy
- 2008-2015, B.Sc Biological Sciences, Sapienza University, Rome, Italy
Publications: [PubMed]
Websites: [Github]
E-mail: francesco.santini [at] mdc-berlin [dot] de
Janosch joined the Bioinformatics & Omics Data Science Platform at MDC BIMSB as a PhD student in January 2024. He develops and applies machine learning methods for the discovery of new cancer drug targets and biomarkers.
- 2023 Junior Software Engineer, status C AG, Berlin, Germany
- 2019-2023 MSc Industrial Biotechnology, Technische Universität Berlin, Berlin, Germany
- 2015-2020, BSc Biotechnology, Technische Universität Berlin, Berlin, Germany
Websites: [LinkedIn] [Github]
E-mail: [email protected]
Enhancing machine learning-aided cancer biology with prior biological knowledge integration.
- 2019 - 2022 Software Developer, Ukraine.
- 2017 - 2018 Junior Software Engineer, Gliwice, Poland.
- 2016 - 2017 Intern, Enamine Ltd, Kyiv, Ukraine.
- 2013 - 2017 Research Intern, Ukrainian National Cancer Institute, Kyiv, Ukraine.
- 2022 - PhD Student, MDC BIMSB, Berlin, Germany.
- 2015 - 2017 MSc, Cytology and Histology (Biology), Taras Shevchenko National University of Kyiv, Kyiv, Ukraine.
- 2011 - 2015 BSc, Biology, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine.
Publications: [PubMed]
Websites: [LinkedIn] [Github]
E-mail: [email protected]
Nour is workin on the development of a genomic patient matching system using tumor genome profiles.
- 2021 - now , Data Scientist, Mushlabs GmbH
- 2021 - 2023, MSc Bioinformatics, Free University of Berlin, Berlin, Germany
- 2017 - 2021, BSc Bioinformatics, Lebanese American University
Websites: [LinkedIn] [Github]
E-mail: [email protected]
Jonas started in the lab in April 2022 as a HiWi student working to improve the PiGx-SARS-CoV-2 pipeline's code quality and deconvolution accurracy. As of September 2022 he is working on his Master's thesis, exploring the feasibility of improving prediction accurracy of machine learning models using cancer bulk RNA-sequencing through residuals derived from deconvolution models.
2022: Intern, MDC BIMSB, Berlin, Germany
- 2020 - now, MSc Bioinformatics, University of Potsdam, Potsdam, Germany
- 2016 - 2020, BSc Biology, University of Tuebingen, Tuebingen, Germany
Publications: [PubMed]
Websites: [Github]
E-mail: jonas.freimuth.mdc-berlin.de
Vic-Fabienne acitively participates in a range of projects focused on developing bioinformatics tools for omics science, with a specific emphasis on machine learning. Notably, she have contributed to the PiGx-Sars-Cov-2 analysis pipeline.
- 2019 - 2023, Intern (Labs: Ohler, Preibisch, Akalin, N.Rajewsky), MDC BIMSB, Berlin, Germany
- 2020 - now, MSc Bioinformatics, University of Potsdam, Potsdam, Germany
- 2016 - 2019, BSc Biochemistry, University of Tuebingen, Tuebingen, Germany
Publications: [PubMed]
Websites: [LinkedIn] [Github]
E-mail: [email protected]
Visting student in 2022, currently PhD Student at DKFZ
Websites: [LinkedIn]
Visting Researcher in 2022, currently at InstaDeep Ltd
Publications: [GoogleScholar]
Websites: [LinkedIn]
Internship from 2021-2022, currently PhD Student at F.Müller Lab at Saarland University
Publications: [PubMed]
Websites: [LinkedIn]
PhD Student and Bioinformatics Scientist for Arcas.ai from 2015-2022, currently at Inceptive
Publications: [PubMed]
Websites: [LinkedIn]
Postdoctoral Researcher from 2020 - 2022, currently at Eagle Genomics
Publications: [PubMed]
Websites: [LinkedIn]
Bioinformatics Scientist from 2020-2021, currently PhD Student at TU Hamburg
Publications: [PubMed]
Websites: [LinkedIn]
PhD Student from 2015-2021, currently at Ardigen
Publications: [PubMed]
Websites: [LinkedIn]
Bioinformatics Scientist from 2017-2021, currently at Roche Diagnostics
Publications: [PubMed]
Websites: [LinkedIn]
PhD Student from 2015-2019, currently at MDC, Data Management
Websites: [LinkedIn]
Master Thesis in 2020
Websites: [Github]
Bioinformatics Scientist from 2017-2019, currently at Max Planck Institute for Molecular Genetics, Berlin.
Publications:[publications on researchgate]
Websites: [LinkedIn]
Intern in 2017, currently at Ardigen
Websites: [LinkedIn]
Bioinformatics Scientist from 2015-2017, currently at University of Freiburg
Publications: [PubMed]
Webserver: [Web]
E-mail: dilmurat.yusuf [at] gmail [dot] com