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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.
Working for Ensembl and then for the ENCODE project at the Wellcome Trust Sanger Institute as a Bioinformatician brought me to 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), Next-Generation Sequencing applications, data integration, 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.

Available 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.
    Quite old now, but a useful example of early tools for the trade using VBA programming.
    [source code]
  • AutoPrime
    in collaboration with Gunnar Wrobel (2003-2004)
    Tool for the rapid generation of primer sequences for RealTime-PCR experiments.
    Started out of curiosity and grown to still be used by many researches around the world.
    [source code]
  • FACT
    in collaboration with Gunnar Wrobel and Nicolas Delhomme (2001-2005)
    Flexible framework for the interpretation of data from high-throughput experiments.
    Used for the explorative analysis with potential to be expanded to various data sources.
    [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.
    A world-leading source of genome annotation and an excellent API for data extraction.
    [source code and data]
  • AnnoTrack
    As part of the ENCODE project (2008-2011)
    Genome annotation tracking system based on the project management software Redmine
    Web-based tool to organise multiple annotation projects.
    [source code and data]

Documents about the work:

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
Development and validation of a next-generation sequencing-based protocol for 24-chromosome aneuploidy screening of embryos
Fiorentino F, Biricik A, Bono S, Spizzichino L, Cotroneo E, Cottone G, Kokocinski F, Michel CE
Fertil Steril  2014  101(5):1375-82   [Abstract]
GENCODE: The reference human genome annotation for The ENCODE Project
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigo R, Hubbard TJ
Genome Res.   2012  22(9):1760-74.   [Abstract]  [Full text]
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, Sustainability and Nature conservation, Museumsgesellschaft Bad Dürkheim, Kokocats Adventures travel blog

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