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Department: Any ÅAU / Department of Information Technologies UTU / Department of Information Technology UTU / Department of Mathematics and Statistics UTU / Turku School of Economics, Institute of Information Systems Sciences

Research Unit: Any Algorithmics and Computational Intelligence Group (ACI) Biomathematics Research Unit (BIOMATH) Communication Systems (ComSys) Computational Biomodeling Laboratory (Combio Lab) Data Mining and Knowledge Management Laboratory Distributed Systems Laboratory (DS Lab) Embedded Computer and Electronic Systems (ECES) Embedded Systems Laboratory (ESLAB) FUNDIM, Fundamentals of Computing and Discrete Mathematics Institute for Advanced Management Systems Research (IAMSR) Learning and Reasoning Lab Software Construction Laboratorium Software Development Laboratory (SwDev) Software Engineering Laboratory (SE Lab) Turku BioNLP Group Turku Optimization Group (TOpGroup) UTU Information Systems Science (ISS)

Publication type: Any Monographs Edited books Edited special issues of journals Edited proceedings Articles in journals Articles in proceedings Chapters in edited books Ph.D. thesis Lic. thesis Technical reports

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Articles in journals (11):

• Heidi Vähämaa, Ville R. Koskinen, Waltteri Hosia, Robert Moulder, Olli S. Nevalainen, Riitta Lahesmaa, Tero Aittokallio, Jussi Salmi, PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use. International Journal of Proteomics Vol. 2011 , 9, 2011.
• Niina Lietzén, Lari Natri, Olli Nevalainen, Jussi Salmi, Tuula Nyman, Compid – A New Software Tool to Integrate and Compare MS/MS Based Protein Identification Results from Mascot and Paragon. Journal of Proteome Research , 2010.
• Mirva Piippo, Niina Lietzen, Olli S. Nevalainen, Jussi Salmi, Tuula A. Nyman, 233. Pripper: Prediction of Caspase Cleavage Sites from Whole Proteomes. BMC Bioinformatics DOI: 10.1186/1471-2105-11-320, 1–7, 2010.
• Jussi Salmi, Tuula A. Nyman, Olli S. Nevalainen, Tero Aittokallio, Filtering Strategies for Improving Protein Identification in High-Volume MS/MS Studies. Proteomics 9(4), 848–860, 2009.
• Jussi Salmi, Tuula A. Nyman, Olli S. Nevalainen, Tero Aittokallio, Filtering strategies for improving protein identification in high-throughput MS/MS studies. Proteomics , 2008.
• Jussi Salmi, Robert Moulder, Jan-Jonas Filén, Olli S. Nevalainen, Tuula A. Nyman, Riitta Lahesmaa, Tero Aittokallio, Quality Classification of Tandem Mass Spectrometry Data. Bioinformatics 22(4), 400–406, 2006.
• Tero Aittokallio, Jussi Salmi, Tuula A. Nyman, Olli S. Nevalainen, Geometrical Distortions in Two-Dimensional Gels: Applicable Correction Methods. Journal of Chromatography 815(1-2), 25-37, 2005.
• Robert Moulder, Jan-Jonas Filen, Jussi Salmi, Mikko Katajamaa, Olli Nevalainen, Matej Oresic, Tero Aittokallio, Riitta Lahesmaa, Tuula Nyman, A Comparative Evaluation of Software for the Analysis of Liquid Chromatography-Tandem Mass Spectrometry Data from Isotope Coded Affinity Tag Experiments. Proteomics 5(11), 2748–2760, 2005.
• Arsi Rosengren, Jussi Salmi, Tero Aittokallio, Jan Westerholm, Riitta Lahesmaa, Tuula Nyman, Olli Nevalainen, Comparison of PDQuest and Progenesis Software Packages in the Analysis of Two-Dimensional Electrophoresis Gels. PROTEOMICS 3(10), 1936–1946, 2003.
• Irina Virtanen, Tero Aittokallio, Jarno Tähtinen, Jussi Salmi, Jaakko Järvi, Päivi Polo-Kantola, Olli Polo, State of Vigilance, Oestrogen Replacement Therapy, and Lipid Profile as Modifiers of Nocturnal Movement-Induced Heart Rate Responses. Clinical Physiology and Functional Imaging 23(5), 293–299, 2003.
• Jussi Salmi, Tero Aittokallio, Jan Westerholm, Matias Griese, Arsi Rosengren, Tuula Nyman, Riitta Lahesmaa, Olli Nevalainen, Hierarchical Grid Transformation for Image Warping in the Analysis of Two-Dimensional Electrophoresis Gels. Proteomics 2(11), 1504–1515, 2002.

Articles in proceedings (1):

• Jussi Salmi, Robert Moulder, Jan-Jonas Filén, Olli S. Nevalainen, Riitta Lahesmaa, Tuula A. Nyman, Tero Aittokallio, Filtering Bad Quality Tandem Mass Spectra Prior to Protein Identification. In: GPBM-2006, 2006.

Ph.D. thesis (1):

• Jussi Salmi, Improving Data Analysis in Proteomics. TUCS Dissertations 76. Turku Centre for Computer Science, 2006.

Technical reports (2):

• Jussi Salmi, Robert Moulder, Jan-Jonas Filén, Olli S. Nevalainen, Riitta Lahesmaa, Tuula A. Nyman, Tero Aittokallio, Filtering Bad Quality Tandem Mass Spectra Prior to Protein Identification. TUCS Technical Reports 729, Turku Centre for Computer Science, 2005.
• Jussi Salmi, Tero Aittokallio, Tuula A. Nyman, Olli S. Nevalainen, Correcting Distortions in 2D Gels - A Survey. TUCS Technical Reports 653, Turku Centre for Computer Science, 2004.