The following list of publications are written by GeneBio staff and/or GeneBio partners.
Please contact us for further information.

Small Molecule Screening

  • Mylonas R, Mauron Y, Masselot A, Binz PA, Budin N, Fathi M, Viette V, Hochstrasser DF, Lisacek F. "X-Rank: a robust algorithm for small molecule identification using tandem mass spectrometry." Anal Chem. 2009 Sep 15;81(18):7604-10.

Protein Identification & Characterization

  • Yohann Couté, Yannick Brunner, Domitille Schvartz, Céline Hernandez, Alexandre Masselot, Frédérique Lisacek, Claes B. Wollheim, Jean-Charles Sanchez. "Early activation of the fatty acid metabolism pathway by chronic high glucose exposure in rat insulin secretory β-cells." Proteomics 2010 Volume 10 Issue 1.
  • Andreas Quandt, Alexandre Masselot, Patricia Hernandez, Céline Hernandez, Sergio Maffioletti, Ron D. Appel, Frederique Lisacek. "SwissPIT: An workflow-based platform for analyzing tandem-MS spectra using the Grid" PROTEOMICS Volume 9, Issue 10, Date: No. 10 May 2009.
  • Erik Ahrné, Alexandre Masselot, Pierre-Alain Binz, Markus Müller, Frederique Lisacek. "A simple workflow to increase MS2 identification rate by subsequent spectral library search" Proteomics 9(6):1731-6, 2009 Mar.
  • Colinge J, Cusin I, Reffas S, Mahé E, Niknejad A, Rey PA, Mattou H, Moniatte M, Bougueleret L. "Experiments in searching small proteins in unannotated large eukaryotic genomes." J Proteome Res. 2005 Jan-Feb;4(1):167-74.
  • Colinge J, Chiappe D, Lagache S, Moniatte M, Bougueleret L. "Differential Proteomics via probabilistic peptide identification scores." Anal Chem. 2005 Jan 15;77(2): 596-606.
  • Colinge J, Masselot A, Cusin I, Mahé E, Niknejad A, Argoud-Puy G, Reffas S, Bederr N, Gleizes A, Rey P-A, Bougueleret L. "High performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics," Proteomics. 2004 Jul;4(7):1977-84.
  • Colinge J, Masselot A. "Mass spectrometry has married statistics: uncle is functionality, children are selectivity and sensitivity," DDT: TARGETS, Vol. 3, No. 2 (Suppl.), 2004, pp. 50-55.
  • Colinge J, Magnin J, Masselot A. A systematic statistical analysis of ion trap tandem mass spectra in view of peptide scoring. In: Proceeding of the Workshop on Algorithms in Bioinformatics (WABI), R. Page and G. Benson (Eds), Budapest, September 2003, LNBI 2812, Springer, 25-38, 2003.
  • Colinge J, Masselot A, Giron M, Dessingy T, Magnin J. "OLAV: towards high-throughput tandem mass spectrometry data identification," Proteomics, Vol. 3, No. 8, August 2003, pp. 1454-1463.
  • Colinge J, Magnin J, Dessingy T, Giron M and Masselot A. Improved peptide charge state assignment. Proteomics, 3:1434-1440, 2003.  
Proteome Imaging
  • Voordijk, S., Walther, D., Bouchet, G., Appel, R.D. Image Analysis Tools in Proteomics. Encyclopedia of the human genome. Macmillan Publishers Ltd., Nature Publishing Group; 2003: 404-410. 
  • Appel R.D., Hochstrasser D.F. Computer Analysis of 2-D Images. In: 2-D Proteome Analysis Protocols, A.J. Link (Ed.), Humana Press, Totowa NJ,1998, pp 363­381
  • Appel R.D., Palagi P., Walther D., Vargas J.R., Sanchez J.C., Pasquali C., Ravier F., Hochstrasser D.F. Melanie II: a third generation software package for analysis of two-dimensional electrophoresis images - I. Features and user interface Electrophoresis 18, 1997, 2724-2734.
  • Appel R.D., Palagi P., Vargas J.R., Hochstrasser D.F. Melanie II: a third generation software package for analysis of two-dimensional electrophoresis images - II. Algorithms Electrophoresis 18, 1997, 2735-2748.
  • Hochstrasser D.F., Appel R.D., Vargas R., Perrier R., Ravier F., Funk M., Pellegrini Ch., Muller A.F., Scherrer J-R. Clinical molecular scanner : the Melanie project. MD-Computing, 8, 85-91, 1991.
Data Integration & Knowledge Discovery
  • Koh J.L.Y, Lisacek F., Gopalakrishnan K, Lee M.L, Brusic V. (2005) Cleaning data artefacts for mining sequence data, submitted to Bioinformatics.
  • Tbahriti, I, Chichester, C., Lisacek, F., Ruch, P.(2005) Using argumentation to retrieve articles with similar citations: an inquiry into improving related articles search in the MEDLINE digital library. Int. J. Med Inform. In the press
  • Ruch P, Baud R, Chichester C, Geissbuhler A, Lisacek F, Marty J, Rebholz-Schuhmann D, Tbahriti I, Veuthey AL. (2005) Extracting key sentences with latent argumentative structuring. Stud Health Technol Inform.116:835-40.
  • Lisacek F., Chichester C., Kaplan A., Sandor A. (2005) Discovering Paradigm Shift Patterns in Biomedical Abstracts: Application to Neurodegenerative Diseases. Proceedings of the First International Symposium on Semantic Mining in Biomedicine (SMBM), April 2005, European Bioinformatics Institute, Hinxton, UK.
  • Coute Y., Burgess J.A., Diaz J.J., Chichester C., Lisacek F., Greco A., Sanchez J.C. (2005) Deciphering the human nucleolar proteome. Mass Spectrometry Rev. In the press.
  • Nikitin F., Rance B., Itoh M., Kanehisa M., Lisacek F. (2004) Using Protein Motif Combinations to Update KEGG Pathway Maps and Orthologue Tables. Genome Inform Ser Workshop Genome Inform. 15(2) :266-75.
  • Tbahriti I., Chichester C., Lisacek F., Ruch P. (2004) Using Argumentation to Retrieve Articles with Similar Citations from MEDLINE. Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications pp8-14, COLING 2004, Geneva, Switzerland, August 2004.
  • Lisacek F., Chichester C., Gonnet P., Jaillet O., Kappus S., Nikitin F., Roland P., Rossier G., Truong L., Appel R.D. (2004) Shaping Biological Knowledge: applications in proteomics. Comp. Funct. Genom. 5: 190-195
  • Gonnet P., Rudd K., Lisacek F. (2004) Fine-tuning the prediction of sequences cleaved by signal peptidase II: a curated set of proven and predicted lipoproteins of E. coli K-12 Proteomics 4: 1597-1613.
  • Lisacek F. (2004) Methods of computational genomics: an overview. Chapter 8 of The Compact Handbook of Computational Biology, eds. A.K. Konopka, J.C. Crabbe, Marcel Dekker, New-York (ISBN: 0-8247-0982-9). 
  • Nikitin F., Lisacek F. Investigating protein domain combinations in complete proteomes. (2003) Computational Biology and Chemistry 27(4-5) : 481-95 
  • Lisacek F. (2003) Shaping Biological Knowledge Pharmacogenomics 4(1):5-8
  • Nikitin F., Lisacek F. (2003) Computer-aided strategies for characterising protein isoforms, pp259-268, Handbook of Proteomics Methods, edited by P. Michael Conn, Humana Press, Totowa, NJ, USA.
  • Chichester C., Nikitin F., Ravarini J-C., Lisacek F. (2003) Consistency checks for characterizing protein forms. Computational Biology and Chemistry 27: 29-35.
  • Gonnet P., Lisacek F. (2002) Probabilistic alignment of motifs with sequences. Bioinformatics 18: 1091-1101.
  • Lisacek F. (2002) Pattern searches, Proteomics section of the Encyclopaedia of the Human Genome, Nature Publishing Group,
  • Lisacek F., Traini M., Sexton D., Harry J., Wilkins M. (2001) Strategies for protein isoform identification from EST sequences and its application to peptide mass fingerprinting. Proteomics 1: 186-193.
Proteomics Databases
  • Falquet L., Pagni M., Bucher P., Hulo N., Sigrist C.J, Hofmann K., Bairoch A. (2002) The PROSITE database, its status in 2002. Nucleic Acids Res. 30:235-238
  • Gasteiger E., Jung E., Bairoch A. (2001) SWISS-PROT: Connecting biological knowledge via a protein database. Curr. Issues Mol. Biol. 3:47-55
  • Hoogland C., Sanchez J.-C., Tonella L., Binz P.-A., Bairoch A., Hochstrasser D.F., Appel R.D. (2000) The 1999 SWISS-2DPAGE database update. Nucleic Acids Res. 28: 286-288
  • Apweiler R., Gateau A., Contrino S., Martin M.J., Junker V., O'Donovan C., Lang F., Mitaritonna N., Kappus S., Bairoch A.(1997). Protein Sequence Annotation in the Genome Era: The Annotation Concept of SWISS-PROT + TREMBL In: Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology (ISMB), Gaasterland T., Karp P., Karplus K., Ouzounis C., Sander C., Valencia A., eds., Halkidiki, Greece
Books & Special Journal Issues
  • Methods in Molecular Biology (1999) volume112
  • Proteome Research: new frontiers in functional genomics edited by  Wilkins M.R, Williams K.L , Appel R.D. , Hochstrasser D.F , 1997, Springer.