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Felix Kokocinski


About myself


After growing up in beautiful Wachenheim (Germany) and a highschool year in St.Louis (USA) with YfU/PPP I studied molecular biology and informatics at the universities of Freiburg and Heidelberg. I obtained my diploma and PhD at the German Cancer Research Center (DKFZ) Heidelberg.
I've worked as a Bioinformatician for Ensembl and then for the ENCODE project at the Wellcome Trust Sanger Institute in Cambridge (UK). I then joined the Cambridge start-up company BlueGnome Ltd. as a senior Bioinformatician which has since become part of Illumina Inc.
 
 

Research interest:


My interest and experience are in the area of genome bioinformatics. Topics include: Genomic microarrays (aCGH), LIMS, data intergration, gene prediction and genome annotation.
 
Genome annotation and analysis.
The genetic make-up of many organisms, including human, has been deciphered.
One of the great tasks of our time is the interpretation and usage of this information.
Important steps in this process are the identification of functional elements and their interconnection using laboratory and computational methods.

Felix Kokocinski
      Contact me
 

Data management and data integration in genome research
One key to this understanding is the integration of all data available. By combining heterogeneous data
sources (databases, flat files, web services, etc.), literature, laboratory data and bioinformatic analysis
we will learn more about how life works and how to better target certain diseases.

Avaliable software projekts:

  • QuickLIMS
    in collaboration with Gunnar Wrobel (2001-2003)
    A simple MS Access database system as an example for a laboratory data
    management systems for microarray facilities
    [source code]
  • AutoPrime
    in collaboration with Gunnar Wrobel (2003-2004)
    Tool for the rapid generation of primer sequences for
    RealTime-PCR experiments
    [source code]
  • FACT
    in collaboration with Gunnar Wrobel and Nicolas Delhomme (2001-2005)
    Flexible framework for the interpretation of data from high-throughput
    experiments
    [source code]
  • EnsEMBL
    joint project between the EMBL/EBI and the Wellcome Trust Sanger Institute
    Software system which produces and maintains automatic annotation of
    metazoan genomes.
    [source code and data]
  • AnnoTrack
    As part of the ENCODE project (2008-2011)
    Genome annotation tracking system based on the project management software Redmine
    [source code and data]

Documents about the work:

Theses
Diplomarbeit: Nachweis genomischer Imbalancen mittels DNA-Microarrays mit Ziel-Sequenzen unterschiedlicher Komplexitaet
Diploma Thesis: Detection of genomic imbalances using DNA-microarrays with probe sequences of different complexity
   [Zusammenfassung]  [Gesamttext]
Dissertation: Verarbeitung und funktionelle Analyse von molekularen Profilen aus Microarray-Experimenten
PhD Thesis: Data management and functional analysis of molecular profiles from microarray experiments
   [Abstract]   [Zusammenfassung]  [Gesamttext]
Selected Publications
AnnoTrack--a tracking system for genome annotation.
Kokocinski F, Harrow J, Hubbard T.
BMC Genomics  2010  11:538   [Abstract]  [Full text]
Ensembl's 10th year
Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Gräf S, Haider S, Hammond M, Howe K, Jenkinson A, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Koscielny G, Kulesha E, Lawson D, Longden I, Massingham T, McLaren W, Megy K, Overduin B, Pritchard B, Rios D, Ruffier M, Schuster M, Slater G, Smedley D, Spudich G, Tang YA, Trevanion S, Vilella A, Vogel J, White S, Wilder SP, Zadissa A, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Smith J, Searle SM
Nucleic Acids Research  2010  38(Database issue):D557-62   [Abstract]  [Full text]
The DNA sequence and biological annotation of human chromosome 1
S. G. Gregory, K. F. Barlow, K. E. McLay, R. Kaul, D. Swarbreck, A. Dunham, C. E. Scott, K. L. Howe, K. Woodfine, C. C. A. Spencer, M. C. Jones, C. Gillson, S. Searle, Y. Zhou, F. Kokocinski, et al.
Nature  2006  441, 315-321   [Abstract]  [Full text]
FACT - a framework for the functional interpretation of high-throughput experiments
Felix Kokocinski, Nicolas Delhomme, Gunnar Wrobel, Lars Hummerich, Grischa Toedt and Peter Lichter
BMC Bioinformatics  2005  6(1):161   [Abstract | Zusammenfassung]  [Full text]
AutoPrime: Selecting Primers for Expressed Sequences
Gunnar Wrobel, Felix Kokocinski, Peter Lichter
Genome Research  2004  5:P11   [Abstract]  [Full text]
QuickLims: Facilitating the data management for DNA-microarray production.
Felix Kokocinski , Gunnar Wrobel, Meinhard Hahn, Peter Lichter
BioInformatics  2003  19 (2), 283-284   [Abstract | Zusammenfassung]  [Full text]

All Publications & Conference contributions

BBC article about the chromosom 1 project

ENCODE Encyclopaedia of DNA Elements


Other Interests:

Running, Martial Arts, Scuba diving, Rock'n'Roll & Rockabilly, Robotics and future studies, Museumsgesellschaft Bad Dürkheim

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