The Team

Altuna Akalin, PhD

Group Leader

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.

Previous Work Experience:
Education:

Publications: [PubMed] [GoogleScholar] [ImpactStory]

Websites: [LinkedIn] [Mendeley] [Github] [slideshare] [blog]

E-mail: altuna.akalin [at] mdc-berlin [dot] de

Research and IT Staff


Alexander Blume, PhD

Bioinformatics Scientist

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.

Previous Work Experience:
  • 2021 - 2022 Researcher, University of Hamburg, Germany
Education:
  • 2016 - 2022 PhD Student, MDC BIMSB, Berlin, Germany

Publications: [PubMed]

Websites: [LinkedIn] [Github]

E-mail: Alexander.Blume@mdc.berlin.de

Vedran Franke, PhD

Bioinformatics Scientist

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.

Previous Work Experience:
  • 2011 - 2011, Researcher,Uni Research/Bergen Center for Computational Science, Bergen, Norway
  • 2010 - 2011, Researcher, University of Zagreb, Croatia
Education:
  • 2011 - 2014 PhD student,University of Zagreb, Croatia

Publications: [PubMed]

Websites: [LinkedIn] [Github]

E-mail: vedran.franke [at] mdc-berlin [dot] de

Artür Manukyan, PhD

Bioinformatics Scientist

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..

Previous Work Experience:
  • 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 
Education:
  • 2013 – 2017, PhD, Computational Sciences, Koç University, Istanbul, Turkey 

Publications: [GoogleScholar]

Websites: [Homepage] [LinkedIn] [Github]

E-mail: Artuer.Manukyan@mdc.berlin.de

Dan Munteanu

System Engineer

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.

Previous Work Experience:
  • 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
Education:
  • 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 Uyar, PhD

Bioinformatics Scientist

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.

Previous Experience:

Publications: [PubMed] [GoogleScholar]

Websites: [LinkedIn] [Github] [ResearchGate]

E-mail: bora.uyar [at] mdc-berlin [dot] de

Ricardo Wurmus

System Administrator

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.

Previous Work Experience:
  • 2009 - 2014, Server, cluster and workstation administrator, Siemens Ltd. China, Shanghai
  • 2008 - 2009, Developer, Siemens AG, Berlin
  • 2007 - 2008, Developer, Siemens Switchgear Ltd., Shanghai
Education:
  • 2005 - 2007 Siemens Technik Akademie, Berlin

Websites: [Homepage] [Code] [Github]

E-mail: ricardo.wurmus [at] mdc-berlin [dot] de

PhD Students


Francesco Santini

PhD Student

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.

Previous Work Experience:
Education:

Publications: [PubMed]

Websites: [Github]

E-mail: francesco.santini [at] mdc-berlin [dot] de

Fabian Janosch Krüger

PhD Student

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.

Previous Work Experience:
  • 2023 Junior Software Engineer, status C AG, Berlin, Germany
Education:
  • 2019-2023 MSc Industrial Biotechnology, Technische Universität Berlin, Berlin, Germany
  • 2015-2020, BSc Biotechnology, Technische Universität Berlin, Berlin, Germany

Websites: [LinkedIn] [Github]

E-mail: FabianJanosch.Krueger@mdc-berlin.de

Taras Savchyn

PhD Student

Enhancing machine learning-aided cancer biology with prior biological knowledge integration.

Previous Work Experience:
  • 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.
Education:
  • 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: Taras.Savchyn@mdc.berlin.de

Interns and Master’s students


Nour Alkhoury

Master Student

Nour is workin on the development of a genomic patient matching system using tumor genome profiles.

Previous Work Experience:
  • 2021 - now , Data Scientist, Mushlabs GmbH
Education:

Websites: [LinkedIn] [Github]

E-mail: Nour.Alkhoury@mdc.berlin.de

Jonas Freimuth

Master student

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.

Previous Work Experience:

2022: Intern, MDC BIMSB, Berlin, Germany

Education:

Publications: [PubMed]

Websites: [Github]

E-mail: jonas.freimuth.mdc-berlin.de

Vic-Fabienne Schumann

Master Student

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.

Previous Work Experience:
  • 2019 - 2023, Intern (Labs: Ohler, Preibisch, Akalin, N.Rajewsky), MDC BIMSB, Berlin, Germany
Education:

Publications: [PubMed]

Websites: [LinkedIn] [Github]

E-mail: Vic-Fabienne.Schumann@mdc.berlin.de

Administration


Sabrina Deter

Administrative Assistant

E-mail: sabrina.deter [at] mdc-berlin [dot] de

Alumni


Yunhee Jeong

Visting student in 2022, currently PhD Student at DKFZ

Websites: [LinkedIn]

Miguel Arbesú, PhD

Visting Researcher in 2022, currently at InstaDeep Ltd

Publications: [GoogleScholar]

Websites: [LinkedIn]

Irem Gündüz

Internship from 2021-2022, currently PhD Student at F.Müller Lab at Saarland University

Publications: [PubMed]

Websites: [LinkedIn]

Jonathan (Yona) Ronen, PhD

PhD Student and Bioinformatics Scientist for Arcas.ai from 2015-2022, currently at Inceptive

Publications: [PubMed]

Websites: [LinkedIn]

Rafael Cuadrat, PhD

Postdoctoral Researcher from 2020 - 2022, currently at Eagle Genomics

Publications: [PubMed]

Websites: [LinkedIn]

Jan Dohmen

Bioinformatics Scientist from 2020-2021, currently PhD Student at TU Hamburg

Publications: [PubMed]

Websites: [LinkedIn]

Katarzyna Wreczycka, PhD

PhD Student from 2015-2021, currently at Ardigen

Publications: [PubMed]

Websites: [LinkedIn]

Wolfgang Kopp, PhD

Bioinformatics Scientist from 2017-2021, currently at Roche Diagnostics

Publications: [PubMed]

Websites: [LinkedIn]

Inga Patarcic, PhD

PhD Student from 2015-2019, currently at MDC, Data Management

Websites: [LinkedIn]

Veronika Severin

Master Thesis in 2020

Websites: [Github]

Brendan Osberg, PhD

Bioinformatics Scientist from 2017-2019, currently at Max Planck Institute for Molecular Genetics, Berlin.

Publications:[publications on researchgate]

Websites: [LinkedIn]

Bożena Mika-Gospodorz

Intern in 2017, currently at Ardigen

Websites: [LinkedIn]

Dilmurat Yusuf, PhD

Bioinformatics Scientist from 2015-2017, currently at University of Freiburg

Publications: [PubMed]

Webserver: [Web]

E-mail: dilmurat.yusuf [at] gmail [dot] com


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