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Felix Kokocinski


About myself




Research interest:


Data management and data integration in genome research

With modern technologies it is possible to bring a high degree of automation into today's laboratories
and to conduct experiments in a high-throughput fashion. The organisation and analysis of this
process is challenging and crucial for successful research.



      Contact me


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.
By combining laboratory experiments 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)
    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 on
    metazoan genomes.
    [source code and data]
  • AnnoTrack
    As part of the ENCODE project
    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
The genome sequence of taurine cattle: a window to ruminant biology and evolution
Bovine Genome Sequencing and Analysis Consortium, Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, Câmara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, et al.
Science  2009  324(5926):522-8  [Full text]
Ensembl 2008
Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Gräf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kähäri A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Slater G, Smedley D, Spudich G, Trevanion S, Vilella AJ, Vogel J, White S, Wood M, Birney E, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJ, Kasprzyk A, Proctor G, Smith J, Ureta-Vidal A, Searle S.
Nucleic Acids Res. (Database issue)  2008     [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

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