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Publications

These publications contain information about different algorithms and analysis methods which are part of MedicWave products.

Publications concerning OpenMS

• "OpenMS – An open-source software framework for mass spectrometry", Sturm M., Bertsch A., Gröpl C., Hildebrandt A., Hussong R., Lange E., Pfeifer N., Schulz-Trieglaff O., Zerck A., Reinert K. and Kohlbacher O., BMC BIOINFORMATICS 9 (163): 2008

Publications concerning Pathway Analysis

• "Identification of dominant signaling pathways from proteomics expression data", Roman A. Zubarev, Michael L. Nielsen, Eva M. Fung, Mikhail M. Savitski, Olga Kel-Margoulis, Edgar Wingender, Alexander Kel, JOURNAL OF PROTEOMICS 71 (2008) 89–96

Publications concerning GS4FTMS, DeNoS, PhosTShunter and ModifiComb

• "Improving protein identification using complementary fragmentation techniques in Fourier transform mass spectrometry", Nielsen ML, Savitski MM, Zubarev RA, MOLECULAR & CELLULAR PROTEOMICS 4 (6): 835-845 JUN 2005
• "Proteomics-grade de novo sequencing approach", Savitski MM, Nielsen ML, Kjeldsen F, Zubarev RA, JOURNAL OF PROTEOME RESEARCH 4 (6): 2348-2354 NOV-DEC 2005
• "PhosTShunter: A fast and reliable tool to detect phosphorylated peptides in liquid chromatography Fourier transform tandem mass spectrometry data sets", Kocher T, Savitski MM, Nielsen ML, Zubarev RA, JOURNAL OF PROTEOME RESEARCH 5 (3): 659-668 MAR 2006
• "ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures", Savitski MM, Nielsen ML, Zubarev RA, MOLECULAR & CELLULAR PROTEOMICS 5 (5): 935-948 MAY 2006
• "Extent of modifications in human proteome samples and their effect on dynamic range of analysis in shotgun proteomics", Savitski MM, Nielsen ML, Zubarev RA, MOLECULAR & CELLULAR PROTEOMICS 5 (12): 2384-2391 JUN 2007

Publications concerning ProSpect

• "ProSpect: An R Package for Analyzing SELDI Measurements Identifying Protein Biomarkers", Andreas Quandt, Alexander Ploner, Chuen Seng Tan, Janne Lehtiö, and Yudi Pawitan, COMPLIFE 2005, LNBI 3695, 140–150, 2005.
• "Finding regions of significance in SELDI measurements for identifying protein biomarkers", Chuen Seng Tan, Alexander Ploner, Andreas Quandt, Janne Lehtiö, and Yudi Pawitan, BIOINFORMATICS 22 (12): 1515–1523, 2006
• "Annotated regions of significance of SELDI-TOF-MS spectra for detecting protein biomarkers", Chuen Seng Tan, Alexander Ploner, Andreas Quandt, Janne Lehtiö, Maria Pernemalm, Rolf Lewensohn, and Yudi Pawitan, PROTEOMICS 6: 6124–6133, 2006

Publications concerning Q5

• "Probabilistic disease classification of expression-dependent proteomic data from mass spectrometry of human serum", Lilien, R.H., Farid, H., Donald, B.R., JOURNAL OF COMPUTATIONAL BIOLOGY 10 (6): 2003

Open for collaboration

MedicWave develops state-of-the-art algorithms for data mining and machine learning in collaboration with renowned researcher from around the world. These algorithms are implemented into our bioinformatics products and used for differential proteomics studies, quantification and validation of regulated proteins, and the discovery of biomarkers.

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