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


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

Wolfgang Kopp, PhD

Bioinformatics Scientist

TBA

Previous Work Experience:
  • 2011 - 2011,TBA
  • 2010 - 2011, TBA
Education:
  • 2011 - 2014 TBA

Publications: TBA

Websites: TBA

E-mail: wolfgang.kopp [at] mdc-berlin [dot] de

Dan Munteanu

System Administrator

Dan provides technical (IT) support for BIMSB users, maintenance for BIMSB servers and scientific software installation on cluster nodes. He is also involved in cluster maintenance tasks.

Previous Work Experience:
  • 2013- , System Administrator , MDC/ BIMSB
  • 2009-2013, System Administrator, Alexandru Ioan Cuza University of Iasi, 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

Brendan Osberg, PhD

Biophysicist/Bioinformatics Scientist

Bren specializes in chromatin structure and organization using thermodynamic and statistical-mechanics-based modelling. Previous publications have focused on granular media and nucleosome positioning; current projects focus on deconvolution algorithms for cell-mixtures using general bio-marker algorithms.

Previous Work Experience:
  • 2014 - 2015, Researcher, Technical University of Munich (TUM), Physics of Complex Biosystems, Garching, Germany
Education:
  • 2009 - 2014, doctoral candidate, University of Munich (LMU), Chair of Statistical and Biological Physics, Munich, Germany

Selected Publications:

[Adsorption-Desorption Kinetics of Soft Particles], Physical Review Letters, 115, 088301 (2015)

[Replication-Guided Nucleosome Packing and Nucleosome Breathing Expedite the Formation of Dense Arrays], Nucleic Acids Research, Oxford Journals, 42, 13633 (2014)

[Toward a Unified Physical Model of Nucleosome Patterns Flanking Transcription Start Sites], Proceedings of the National Acadamy of Sciences, 110, 5719 (2013)

[Further publications available on researchgate]

Websites:

[LinkedIn]

[CV]

E-mail: Brendan.Osberg [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. He has had a balanced trainining of biological and computational sciences. He is interested in doing large-scale data analysis to understand the molecular biology of diseases. At MDC, he will develop tools and annotation pipelines related to RNA bioinformatics and NGS data analysis, which will be integrated with the Galaxy instance of the Berlin Institute of Medical Systems Biology.

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


Alexander Gosdschan

PhD student

Alexander will join with Baris Tursun (Tursun Research Group at MDC) during his PhD to analyse and model gene-regulation in c.elegans and other model organisms.

Previous Work Experience:
  • 2015 - 2016 Intern, MDC BIMSB, Berlin, Germany
Education:
  • 2016 - PhD Student, MDC BIMSB, Berlin, Germany
  • 2014 - 2016 Master Student, Freie Universtät Berlin, Germany
  • 2010 - 2014 Bachelor Student, Freie Universtät Berlin, Germany

E-mail: Alexander.Gosdschan [at] mdc-berlin [dot] de

Inga Patarcic

PhD student

Previous Work Experience:
  • 2013 - 2015 Researcher, The School of Medicine, University of Split
  • 2015 - 2015 Visiting Scientist, University of Edinburgh, The MRC Institute of Genetics and Molecular Medicine, Edinburgh
Education:
  • 2015 - PhD Student, MDC BIMSB, Berlin, Germany
  • 2010 - 2013 Master Student, University of Zagreb, Croatia
  • 2007 - 2010 Bachelor Student, University of Zagreb, Croatia

E-mail: inga.patarcic [at] mdc-berlin [dot] de

Jonathan (Yona) Ronen

PhD student

Previous Work Experience:
  • 2013 - 2015 Research Scientist, Social Media and Political Participation lab, New York University
  • 2010 - 2013 Software developer, Oslo, Brussels, Munich
Education:
  • 2015 - PhD Student, MDC BIMSB, Berlin, Germany
  • 2008 - 2009 M.Sc Electrical Engineering, University of California, Santa Barbara
  • 2005 - 2010 M.Sc Electrical Engineering, Norwegian U of Sci & Tech

E-mail: yablee [at] gmail [dot] com

Katarzyna Wreczycka

After completing a 6-month internship, Katarzyna has started working at MDC on 1st of October, 2015 as a PhD student. Her project is dealing with assessing prognostic and diagnostic features of high-dimensional genomics data for neuroblastoma.

PhD student

Previous Work Experience:
Education:

Websites: [LinkedIn] [Github]

E-mail: katarzyna.wreczycka [at] mdc-berlin [dot] de

Interns and Master’s students


Bożena Mika-Gospodorz

Research Intern

Bozena works on improving the genomation bioconductor package.

Previous Work Experience:
  • 2009 - 2014 TBA
Education:
  • 2005 - 2007 TBA

Websites: TBA

E-mail: TBA

Administration


Sabrina Deter

Administrative Assistant

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

Alumni


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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