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Biomedizinische Informatik und Mechatronik

Publikationen 2008-2014

2013/2014

Journal Papers
  • Grünerbl A, Bahle G, Hanser F, Lukowicz P. UWB indoor location for monitoring dementia patients: The challenges and perception of a real-life deployment. Int J Amb Comp Intell, 2013;5(4):45-59.
  • Handler M, Fischer G, Seger M, Kienast R, Nowak CN, Pehböck D, Hintringer F, Baumgartner C. Computer simulation of cardiac cryoablation: comparison with in-vivo data. Med Eng Phys, 2013;35(12):1754-61 PMID: 23972331
  • Kienast R, Stöger M, Handler M, Hanser F, Baumgartner C. (2014) Alterations of field potentials in isotropic cardiomyocyte cell layers induced by multiple endogenous pacemakers under normal and hypothermal conditions, Am J Physiol Heart Circ Physiol, 2014 Aug 1 [Epub ahead of print]. PMID: 25085965
  • Seger M, Hanser F, Dichtl W, Stuehlinger M, Hintringer F, Trieb T, Pfeifer B, Berger T. Non-invasive imaging of cardiac electrophysiology in a cardiac resynchronization therapy defibrillator patient with a quadripolar left ventricular lead. Europace, 2014;16(5):743-749. PMID: 2479896
Konferenzbeiträge
  • Handler M, Fischer G, Kienast R, Baumgartner C. Simulating effects of increased heat transfer surfaces between applicator tip and refrigerant in cardiac cryoablation. Ann. Meeting of the Austrian Society for Biomedical Engineering (ÖGBMT), Hall, Austria, 2014, pp. 55-56.
  • Kienast R, Stöger M, Handler M, Hanser F, Baumgartner C. Influence of variations in the angle of different excitation directions in isotropic cardiomyocyte monolayers. Ann. Meeting of the Austrian Society for Biomedical Engineering (ÖGBMT), Hall, Austria, 2014, pp. 53-54.
  • Popovscaia M, Baumgartner C (2014) A combined approach for similarity search and analysis in biochemical molecular databases. Ann. Meeting of the Austrian Society for Biomedical Engineering (ÖGBMT), Hall, Austria, 2014, pp. 65-66.
  • Rienmüller T, Handler M, Toifl M, Rienmüller R, Baumgartner C. Myocardial blood flow quantification from dynamic CT scans. Ann. Meeting of the Austrian Society for Biomedical Engineering (ÖGBMT), Hall, Austria, 2014, pp. 15-16.
  • Toifl M. Quantitative measurement of left ventricular myocardial perfusion based on dynamic CT scans. Ann. Meeting of the Austrian Society for Biomedical Engineering (ÖGBMT), Hall, Austria, 2014, pp. 33-34.
  • Kienast R, Handler M, Stöger M, Hanser F, Baumgartner C. A system for analyzing thermal induced effects of propagation direction dependent features in field potentials of cardiomyocyte monolayers using multi-electrode arrays. Proc. 40th Int. Cong. on Electrocardiology, Glasgow, 2013.
Buchkapitel
  • Breit M, Baumgartner C, Weinberger KM. Data handling and analysis in metabolomics. In: Current Applications of Chemometrics, Nova Sciences Publisher, chapter, To appear in October 2014.
  • Netzer M, Handler M, Pfeifer B, Dander A, Baumgartner C. Knowledge Discovery in Proteomic Mass Spectrometry Data. In: Knowledge discovery in proteomic mass spectrometry data. Academic Publish, to appear in October 2014.
Herausgeberschaften
  • Baumgartner C, Mayr W (Eds) Tagungsband zur Jahrestagung der Österreichischen Gesellschaft für Biomedizinische Technik In: UMIT-Lecture Notes in Biomedical Computer Science and Mechatronics, Volume 4, 2014, ISBN: 978-3-9503191-3-2.
  • Brandstötter M, Rienmüller T (Eds) Insight 2014, In: UMIT-Lecture Notes in Biomedical Computer Science and Mechatronics, Volume 3, 2014, ISBN: 978-3-9503191-2-5.
Abstracts
  • Rienmüller T, Baumgartner C, Makarenko V, Bockeria L, Ourednicek P, Rienmüller R. Effect of different reconstruction algorithms on quantitative evaluation of dynamic CT data for the estimation of myocardial blood flow. Cardiac Imaging 2014. ESCR annual scientific meeting 2014, Paris, France, 2014 (Poster und Posterpreis).
  • Binder E, Moser C, Maurer K, Kreye SK, Schwienbacher M, Schermer E, Karall T, Binder E, Meraner D, Baumgartner C, Stein JI, Hofer SE, Baumgartner D. (2014) Früherkennung von makrovaskulären Veränderungen bei Kindern und Jugendlichen mit Diabetes mellitus Typ 1 (T1DM). 52. Jahrestagung der Österreichischen Gesellschaft für Kinder – und Jugendheilkunde (ÖGKJ), Wien, 2014 (Poster und Posterpreis)

2012/2013

Journal Papers
  • Baumgartner C, Blinowska KJ, Cichocki A, Dickhaus H, Durka PJ, McClintock PVE, Pfurtscheller G, Stefanovska A, Tong S. Discussion of “Time-frequency techniques in biomedical signal analysis: A tutorial review of similarities and differences”. Methods Inf Med, 2013;52: 297-307. PMID: 23922177
  • Cerqueira FR, Ferreira RS, Oliveira AP, Gomes AP, Ramos HJO, Graber A, Baumgartner C. MUMAL: Multivariate analysis in shotgun proteomics using machine learning techniques, BMC Genomics, 2012;13(Suppl 5):S4. PMID: 23095859
  • Fang X, Netzer M, Baumgartner C, Bai C, Wang XD. Genetic network and gene set enrichment analysis to identify biomarkers related to cigarette smoking and lung cancer. Cancer Treat Rev, 2013;39:77-88. PMID: 22789435
  • Rienmüller T, Hofbaur M, Travé-Massuyès L, Bayoudh M. Mode set focused hybrid estimation. Int J Appl Math Comput Sci (AMCS), 2013; 23(1):131 144.
  • Pallua JD, Schäfer G, Seifarth C, Becker M, Schneider S, Meding s, Rauser S, Walch A, Handler M, Netzer M, Popovscaia M, Osl M, Baumgartner C, Lindner H, Kremser L, Sarb B, Bartsch G, Huck CW, Bonn GK, Klocker H. MALDI-MS Tissue Imaging Identification of Biliverdin Reductase B Overexpression in Prostate Cancer. J Proteomics, 2013, [Epub ahead of print] PMID: 23954705
  • Zeimet AG, Reimer D, Huszar M, Winterhoff B, Puistola U, Abdel Azim S, Müller-Holzner E, Ben-Arie A, van Kempen LC, Petru E, Jahn S, Geels YP, Massuger LF, Amant F, Polterauer S, Lappi-Blanco E, Bulten J, Meuter A, Tanouye S, Oppelt P, Stroh-Weigert M, Reinthaller A, Mariani A, Hackl W, Netzer M, Schirmer U, Vergote I, Altevogt P, Marth C, Fogel M. L1CAM in Early-Stage Type I Endometrial Cancer: Results of a Large Multicenter Evaluation. J Natl Cancer Inst. 2013; Jun 18. [Epub ahead of print] PMID: 23781004
Konferenzbeiträge
  • Baumgartner C. A clinical metabolomics strategy to discover new biomarkers in complex diseases: an overview. D-A-CH BMT’2013, Graz, Austria, Biomed Tech (Berl), 2013.  PMID:24043029
  • Handler M, Kienast R, Seger M, Nowak CN, Popovscaia M, Hanser F, Baumgartner C. Effects of tip-applicator positioning on recorded temperature profiles in cryoablation procedures estimated by finite element modeling. D-A-CH BMT’2013, Graz, Austria, Biomed Tech (Berl), 2013. PMID:24043048
  • Handler M*., Kienast R*., Hanser F., Fischer G., Baumgartner C. Selektive Kühlung im myokardialen Gewebe in-vitro und in-vivo: Simulation und Prototyping. International Forum Mechatronics 2012, ISBN 978-3-200-02777-0, pp. 145-157.
  • Kienast R, Stöger M, Fischer G, Hanser F, Baumgartner C. Detection of multiple pacemaker centers in cardiomyocyte cell layers for estimating wavefront propagation patterns. D-A-CH BMT’2013, Graz, Austria, Biomed Tech (Berl), 2013. PMID:24042803
  • Makarenko V, Rienmüller T, Handler M, Krestinich IM, Zhorzholiani ST, Bockeria L, Ourednicek P, Baumgartner C, Rienmüller R. Feasibility of rotational 256 row CT in measuring myocardial perfusion in anaesthetized dogs. ECR, Vienna, 2013 (poster).
  • Popovscaia M, Baumgartner C, Handler M, Klocker H. Identifying biologically meaningful groups of genes in the antrogen receptor network. D-A-CH BMT’2013, Graz, Austria, Biomed Tech (Berl), 2013. PMID:24043015
  • Rienmüller T, Handler M, Ourednicek P, Makarenko V, Bockeria L,  Krestinich IM, Zhorzholiani ST, Rienmüller R, Baumgartner C.  Contrast agent concentration of 180-210 mgJ/ml allows for quantitative estimation of myocardial perfusion in dogs. ECR, Vienna, 2013 (poster).
  • Rienmüller T, Baumgartner C, Handler M, Makarenko V, Krestinich IM, Zhorzholiani ST, Bockeria L, Ourednicek P, Rienmüller R. Quantitative estimation of left ventricular myocardial perfusion based on dynamic CT scans. D-A-CH BMT’2013, Graz, Austria, Biomed Tech (Berl), 2013. PMID:24042936
  • Schinner M. Patient individual parameterization of cardiac ventricular tachycardia termination algorithm. D-A-CH BMT’2013, Graz, Austria, Biomed Tech (Berl), 2013. PMID:24043028
Abstracts
  • Kienast, R., Fischer, G., Stöger, M., Handler, M., Hanser, F., Baumgartner, C. "A system for analysing thermal induced effects of propagation direction dependent features in field potentials of cardiomyocyte monolayers using multi-electrode arrays." Journal of Electrocardiology 2013;46(4):e32.
  • Handler M, Rienmüller T, Ourednicek P, Makarenko V, Bockeria L, Zhorzholiani S, Krestinich I, Rienmüller R, Baumgartner C. Assessment of HU-value stability in dynamic CT-scans for quantitative estimation of myocardial perfusion. ECR, Vienna, Eur Radiol, 2013 Insights Imaging 4:Suppl.1.
  • Bockeria L, Makarenko V, Rienmüller T, Handler M, Ourednicek P, Zhorzholiani ST, Krestinich IM, Baumgartner C, Rienmüller R. Multivariate analysis on cardiac determinants for estimating myocardial perfusion in an animal model using dynamic CT data. Cardiac Imaging, London, 2013.
  • Makarenko V, Bockeria L, Ourednicek P, Rienmüller T, Handler M, Zhorzholiani ST, Krestinich IM, Baumgartner C, Rienmüller R. Lowest Iodine concentration for contrast enhanced CT measurements of myocardial perfusion. Cardiac Imaging, London, 2013.

2011/2012

Journal Papers
  • Kusonmano K, Netzer M, Baumgartner C, Dehmer M, Liedl KR, Graber A. Effects of pooling samples on the performance of classifiers: A comparative study. ScientificWorldJournal, 2012: 278352. PMID: 22654582
  • Liebensteiner MC, Platzer HP, Burtscher M, Hanser F, Raschner C. The e ffect of gender on force, muscle activity, and frontal plane knee alignment during maximum eccentric leg press exercise, Knee Surg Sport Tr A, 2012; 20: 510.516. PMID: 21647657
  • Netzer M, Weinberger K, Handler M, Seger M, X Fang, Kugler K, Graber A, Baumgartner C. Profiling human response to physical exercise: A computational strategy for the identification and kinetic analysis of metabolic biomarkers. J Clin Bioinforma,  2011, 1:34 PMID: 22182709
  • Netzer M, Kugler KG, Mueller LAJ, Weinberger KM, Baumgartner C, Dehmer M. A network-based feature selection approach to identify metabolic signatures in disease. J Theor Biol, 2012, 310: 216-222. PMID: 22771628
  • Seger M, Fischer G, Handler M, Hintringer F, Klima G, Baumgartner C. Achieving elongated lesions employing cardiac cryoablation: a preclinical evaluation study, Cryobiology, 2012, 65: 145-150. PMID: 22580465
  • Zhou Z, Netzer N, Lee IH, Handler M, Manickam VA, Baumgartner C, Lushington GH, Visvanathan M. OmicsMiner: A Biological Data Mining Framework. J Data Mining in Genom Proteomics, 2012, 3:2
Konferenzbeiträge
  • Handler M, Fischer G, Seger M, Kienast R, Schuette A, Baumgartner C. Effect of insulating layers in loop applicators for cardiac cryoablation. Proc. 4th Int. Conf. on Bioinformatics, Biocomputational Systems and Biotechnologies, (Biotechno 2012), pp. 20-25.
  • Handler M, Fischer G, Seger M, Kienast R, Hintringer F, Baumgartner C. Simulation des Temperaturprofils bei kardialer Kryoablation mittels Tip-Applikator – Parameteranpassung und Validierung durch in-vivo Daten. Ann. Meeting of the Austrian Society for Biomedical Engineering (ÖGBMT), Hall, Austria, 2012, 37-38.
  • Kienast R, Handler M, Stöger M, Hintringer F, Fischer G, Baumgartner C. Measurement Of Electrophysiological Changes During Cryo Catheter Ablation In The Heart Of Domestic Pig: A Proof Of Concept Study. Proc. 8th Int. Meeting on Substrate-Integrated Microelectrode Arrays, Reutligen, Germany, 2012, pp.149-153.
  • Kienast R, Stöger M, Handler M, Hintringer F, Fischer G, Baumgartner C. Hypotermal effects on chicken cardiomyocytes in vitro: a proof of concept study. Ann. Meeting of the Austrian Society for Biomedical Engineering (ÖGBMT), Hall, Austria, 2012, pp. 11-12.
  • Netzer M, Fang X, Handler M, Baumgartner C. A coupled two step network-based approach to identify genes associated with breast cancer. Proc. 4th Int. Conf. on Bioinformatics, Biocomputational Systems and Biotechnologies, (Biotechno 2012), pp. 1-5.
  • Netzer M, Baumgartner C. Methoden für die Suche metabolischer Biomarker – ein Update. Ann. Meeting of the Austrian Society for Biomedical Engineering (ÖGBMT), Hall, Austria, 2012, pp. 51-52.
  • Rienmüller T, Rienmüller A, Baumgartner C. Bewegungsachsen des Kniegelenks in Hinblick auf die Knieendoprothetik – Ein Überblick. Ann. Meeting of the Austrian Society for Biomedical Engineering (ÖGBMT), Hall, Austria, 2012, pp. 41-42.
  • Seger M, Handler M, Fischer G, Rabl H, Hintringer F, Baumgartner C. Simulation des Temperaturfeldes und relevanter Parameter für kardiale Kryoablation mit kreisförmigem Katheter. Ann. Meeting of the Austrian Society for Biomedical Engineering (ÖGBMT), Hall, Austria, 2012, 35-36.
Letters und Buchkapitel
  • Berger T, Seger M, Pfeifer B. NICE - Noninvasive Imaging of Cardiac Electrophysiolog. In: Electrophysiology - From Plants to Heart, InTech Open Acces Publisher, ISBN 978-953-51-0006-5 , February 2012, Chapter 7, pp 157-186.
  • Fischer G, Handler M, Kienast R, Baumgartner C. Letter to the Editor with respect to the article by Tormos et al., Med Eng Phys, 2012; 34:795 PMID: 22658452
  • Osl M, Netzer M, Dreiseitl S, Baumgartner C. Applied Data Mining: From Biomarker Discovery to Decision Support Systems. In: Trajanoski Z (Eds), Computational Medicine, Springer Verlag, 2012, Chapter 10, pp. 173-184.
Editorial
  • Baumgartner C, Mayr W (Eds) Tagungsband zur Jahrestagung der Österreichischen Gesellschaft für Biomedizinische Technik In: UMIT-Lecture Notes in Biomedical Computer Science and Mechatronics, Volume 2, 2012, ISBN: 978-3-9503191-1-8
Sonstige Schriften
  • Baumgartner C, Kienast R, Handler M, Stöger M, Fischer G. Von der Grundlagenforschung bis zum High Tech Medizinprodukt: Am Beispiel des Projektes Kryotipkatheter. Tagungsband zur Wissenschaftsenquete, Landhaus Tirol, 2012

2010/2011

Journal Papers
  • Baumgartner C, Osl M, Netzer M, Baumgartner D. Bioinformatic-driven search for metabolic biomarkers in disease. J Clin Bioinforma,  2011;1:2. PMID: 21884622
  • Berger T, Pfeifer B, Hanser F, HIntringer F, Fischer F, Netzer M, Trieb T, Stuehlinger M, Dichtl W, Baumgartner C, Pachinger O, Seger M. Single-beat noninvasive imaging of ventricular endocardial and epicardial activation in patients undergoing CRT. PLoS One, 2011;6:e16255. PMID: 21298045
  • Dander A, Handler M, Netzer M, Pfeifer B, Baumgartner C. KD3: Knowledge Discovery in Database Design tool for workflow-based exploration of biomedical data sets, TLDKS IV LNCS, 2011, 6990:148:157. DOI: 10.1007/978-3-642-23740-9_7 
  • Mattes J, Chemelli A, Wick M, Soimu D, Pontow C, Lopez A, Netzer M, Chemelli-Steingruber IE. Evaluation of a new computerized analysis system developed for the processing of CT follow-up scans after EVR of infrarenal aneurysm. Eur J Radiol, 2011 Feb 5. [Epub ahead of print] PMID: 21300491
  • Mueller LAJ, Kugler KG, Netzer M, Graber A, Dehmer M. A Network-Based Approach to Classify the Three Domains of Life, Biology Direct, 2011, accepted.
  • Pallua JD, Schaefer G, Bittner LK, Pezzei C, Huck-Pezzei V, Schoenbichler SA, Becker M, Schneider S, Meding S, Rauser S, Walch A, Handler M, Netzer M, Osl M, Seger M, Pfeifer B, Baumgartner C, Lindner H, Kremser L, Sarg B, Klocker H, Bartsch G, Bonn GK, Huck CWMatrix Assisted Laser Desorption/Ionization (MALDI) Imaging Mass Spectrometry (IMS) for Direct Tissue Analysis. LC GC Eur, 2011, accpeted
  • Rantner L, Stühlinger M, Nowak C, Spuller K, Etsadashvili K, Stühlinger X, Berger T, Dichtl W, Gothe R, Fischer G, Hintringer F. Localizing the Accessory Pathway in Patients With Ventricular Preexcitation Using a Score Based Algorithm. Methods Inf Med, 2011.
Editorial
  • Baumgartner C (Editor) (2011) Proceedings of the Eighth IASTED International Conference on Biomedical Engineering, BioMed 2011, Acta Press. ISBN: 978-0-88986-866-3
Buchkapitel
  • Fischer G, Wieser L, Hintringer F. Modeling Mother Rotor Anchoring in Branching Atrial Tissue. In: Atrial Fibrillation, InTech Open Access Publisher, ISBN 978-953-307-994-3 ., To appear in: October 2011.
  • Kienast R, Baumgartner C. Data Integration on Biomedical Data Using Semantic Web Technologies. In: Bioinformatics, InTech Open Access Publisher, ISBN 978-953-307-282-1 , 2011, Chapter 3, pp. 57-82.
  • Pfeifer B. Biophysical Modeling Using Cellular Automata (Chapter 23), pp.485-528. In: Salcido A (Ed) Cellular Automata - Implicity Behind Complexity InTech Open Access Publisher. ISBN: 978-953-307-230-2 , March 2011.
Konferenzbeiträge
  • Cerqueira FR,  Ferreira RS, Oliveira AP, Ramos HJO, Baumgartner C. Machine learning approach for evaluating identications of peptides and proteins in complex mixtures, X-meeting, Florianopolis, Brazil, 2011.
  • Handler M , Pallua JD, Schäfer G, Netzer M, Osl M, Seger M, Pfeifer B, Becker M, Meding S, Rauser S, Walch A, Klocker H, Bartsch G, Huck CW, Baumgartner C, Bonn GK. A workflow for preprocessing and proteomic biomarker identification on mass-spectrometry data. Proc. 8th IASTED Int. Conf. on Biomedical Engineering, Innsbruck, Austria (Biomed’2011), 2011; 181-187.
  • Osl M, Dreiseitl S. Early diagnosis of acute myocardial infarction using kernel methods. Proc. 8th IASTED Int. Conf. on Biomedical Engineering, Innsbruck, Austria (Biomed’2011), 2011; 175-180.
  • Seger M, Handler M, Fischer G, Hintringer F, Baumgartner C. Simulation of the spatio-temporal spread of cooling flux in cardiac tissue due to catheterized cryoablation. Proc. 8th IASTED Int. Conf. on Biomedical Engineering, Innsbruck, Austria (Biomed’2011), 2011;83-88.
  • Seger M, Netzer M, Hanser F, Pfeifer B, Dichtl W, Stuehlinger M, Trieb T, Hintringer F, Pachinger O, Baumgartner C, Berger T. Assessment of cardiac resynchronization therapy by non-invasive reconstruction of cardiac activation times. Proc. 8th IASTED Int. Conf. on Biomedical Engineering, Innsbruck, Austria (Biomed’2011), 2011;283-288.

2009/2010

Journal Papers
  • Baumgartner C, Lewis GD, Netzer M, Pfeifer B, Gerszten RE. A new data mining approach for profiling and categorizing kinetic patterns of metabolic biomarkers after myocardial injury. Bioinformatics, 2010;26(14):1745-1751. PMID: 20483816
  • Cerqueira F, Graber A, Schwikowski B, Baumgartner C. MUDE: A new approach for optimizing sensitivity in the target-decoy search strategy for large-scale peptide/protein identification. J Proteome Res, 2010;9(5):2265-2277. PMID: 20199108
  • Dreiseitl S, Osl M, Baumgartner C, Vinterbo S. Evaluation of Heuristics for Rule Ranking. Artif Intell Med, 2010;50:175-180. PMID: 20466526 
  • Millonig G, Praun S, Netzer M, Baumgartner C, Mueller S, Villinger J, Vogel W. Non-invasive diagnosis of liver diseases by breath analysis using an optimized ion-molecule reaction-mass spectrometry approach: a pilot study. Biomarkers, 2010;15(4):297-306. PMID: 20151876
  • Pfeifer B, Seger M, Netzer M, Osl M, Modre R, Schreier G, Hanser F Wurz M, Baumgartner C. An epidemological modeling and data integration framework. Methods Inf Med, 2010;49(3):290-296. PMID: 20411210
Buchkapitel
  • Netzer M, Baumgartner C. Ensemble Feature Selection in Biomedical Applications. In: Plant C, Böhm C. Database Technology for Life Sciences and Medicine. World Scientific Publishing, 2010;Vol. 6 (Chap. 11): 21-239. ISBN: 978-981-4307-70-3 .
Konferenzbeiträge
  • Dreiseitl, S., Osl, M., Scheibböck, C., Binder, M. Outlier Detection with One-Class SVMs: An Application to Melanoma Prognosis. In Proceedings of the AMIA Annual Symposium, accepted.

  • Hanser F, Baumgartner C. Erkennung von Kniegelenksfehlbelastungen mittels einfacher Sensoren. 6. Int. Mechatronikforum, Winterthur, Schweiz, 2010.
  • Mueller LAJ, Kugler KG, Dander A, Baumgartner C, Graber A, Dehmer M. A Network-based Approach to Classify Disease Stages of Prostate Cancer Using Quantitative Network Measures. 11th Int. Conf. on Bioinformatics & Computational Biology (Biocomp’10),2010; 55-61.
  • Osl M, Dreiseitl S, Kim J, Patel K, Baumgartner C, Ohno-Machado L. Effect of data predictive modeling: a study using gene expression data. AMIA 2010 Annual Symposium, 2010.
  • Saboor S, Hanser F, Ammenwerth E. Einsatz von Sensoren in realen Settings - Eine Analyse von Anforderungen und Herausforderungen. In: Schmücker P, Ellsässer KH, Hayna S (Hrsg): 55. GMDS-Jahrestagung, 5. - 9. September 2010, Mannheim. pp. 626-628.
  • Visvanathan M*, Netzer M*, Rao S*, Anand V, Bousfield GR, Baumgartner C, Lushington GH. A Multi-Tier Data Mining Workfow to Analyze the Age Related Shift from Diglycosylated-to-Tetra-glycosylated-FSH Secretion by the Anterior Pituitary. ACM Int. Conf. on Bioinformatics and Computational Biology, 2010; accepted.
Patente
  • Baumgartner C, Netzer M, Pfeifer B. Identification of biomarkers. Filed on 10/2009.

2008/2009

Journal Papers
  • Cerqueira F, Morandell S, Ascher S, Mechtler K, Huber L, Pfeifer B, Graber A, Tilg B, Baumgartner C. Improving phosphopeptide/protein identification using a new data mining framework for MS/MS spectra preprocessing, J Proteomics Bioinform, 2009;2(3):150-164. ISSN: 0974–276X
  • Kühn A, Baumgartner D, Baumgartner C, Hörer J, Schreiber C, Hess J, Vogt M. Impaired elastic properties of the ascending aorta persist within the first 3 years after neonatal coarctation repair. Pediatr Cardiol, 2009;30:46-51. PMID: 18685801
  • Netzer M, Millonig G, Osl M, Pfeifer B, Praun S, Villinger J, Vogel W, Baumgartner C. A new ensemble-based algorithm for identifying breath gas marker candidates in liver disease using ion molecule reaction mass spectrometry. Bioinformatics, 2009;25:941-947. PMID: 19223453
  • Osl M, Dreiseitl S, Netzer M, Cerqueira F, Pfeifer B, Baumgartner C. Demoting redundant features to improve the discriminatory ability in cancer data, J Biomed Inform, 2009;42:721-725. PMID: 19460463 
  • Osl M, Baumgartner C, Tilg B, Dreiseitl S. On the combination of logistic regression and local probability estimates. African Journal of Information and Communication Technology. 2009;5:84-90.
  • Visvanathan M, Netzer M, Seger M, Ardagarla BS, Baumgartner C, Sittapalam S , Lushington GH. Oncogenes & pathway identification using filter based approaches between various carcinoma types in lung. Int J Comput Biol Drug Des, 2009;2:236-251. PMID: 20090162 
  • Visvanathan M, Pfeifer B, Baumgartner C, Tilg B, Lushington GH. Integrative Approach for Combining TNFalpha-NFkappaB Mathematical Model to a Protein Interaction Connectivity Map. In: M?ndoiu I, Narasimhan G, Zhang Y (Eds.): ISBRA 2009, Lect Notes Comput Sci, 2009;5542:63-74. PMID: 20191103 
Buchkapitel
  • Osl M, Baumgartner C, Dreiseitl S. Classifier Combination. In: Agbinya JI, Lal SK (Eds). Biomedical and Environmental Sensing. Chapter 14, River Publishers Denmark, Aalborg, 2009. ISBN 978-87-92329-28-8 .
Konferenzbeiträge
  • Dreiseitl S, Osl M. Pairwise Performance as Feature Selection Strategy. Proc. 12th Int. Conf. on Computer Aided Systems Theory, 2009.
  • Herbig J, Seger M, Kohl I, Mayramhof G, Titzmann T, Preinfalk A, Winkler K, Dunkl J, Pfeifer B, Baumgartner C, Hansel A. Online breath sampling with PTR-MS - A setup for large screening studies. Proc. 4th Int. Conf. on Proton Transfer Reaction Mass Spectrometry and Its Applications, Innsbruck, Austria, 2009. 
  • Kusonmano K, Netzer M, Pfeifer B, Baumgartner C, Liedl KR, Graber A. (2009) Evaluation of the impact of dataset characteristics for classification problems in biological applications. ICBB 2009, International Conference on Bioinformatics and Biomedicine, Venice, Italy.
  • Netzer M*, Seger M*, Visvanathan M*, Lushington GH, Pfeifer B, Baumgartner C. (2009) Filter  based approaches for selecting significant genes between various cancer types in lung. ICBB 2009, International Conference on Bioinformatics and Biomedicine, Venice, Italy. 
  • Netzer M, Millonig G, Pfeifer B, Kusonmano K, Praun S, Villinger J, Vogel W, Baumgartner C. Stacked Feature Selection in Liver Disease using IMR-MS analysis. Proc. Int. Workshop on Database Technology for Data Management in Life Sciences and Medicine (DBLM’09), Linz, Austria, 2009, accepted.
  • Pfeifer B, Seger M, Netzer M, Osl M, Modre-Osprian R, Schreier G, Baumgartner C. An Epidemiologic Modeling and data integration framework. eHealth 2009, Vienna, Austria, 2009.

2008

Journal Papers 
  • Baumgartner C, Rejtar T, Kullolli M, Akella LM, Karger BL. SeMoP: A New Computational Strategy for the Unrestricted Search for Modified Peptides Using LC-MS/MS Data. J Proteome Res, 2008; 7(9):4199-4208. PMID: 18686985
  • Kugler K, Tejada MM, Baumgartner C, Tilg B, Graber A, Pfeifer B. Bridging Data Management and Knowledge Discovery in the Life Sciences. The Open Bioinformatics Journal, 2008;2:28-36. ISSN: 1875-0362 
  • Lewis GD, Wei R, Liu E, Yang E, Shi X, Martinovic M, Farrell L, Asnani A, Cyrille M, Ramanathan A, Shaham O, Berriz G, Lowry PA, Palacios I, Tasan M, Roth FP, Min J, Baumgartner C, Keshishian H, Addona T, Mootha VK, Rosenzweig A, Carr SA, Fifer MA, Sabatine MS, Gerszten RE. Metabolite profiling of blood from individuals undergoing planned myocardial infarction reveals early markers of myocardial injury. J Clin Invest, 2008;118(10):3503-3512. PMID: 18769631
  • Muehlthaler H, Quatember B, Fraedrich G, Muehlthaler M, Pfeifer B, Greiner A, Schocke M. Quantification of Blood Flow Velocity in Stenosed Arteries by the use of Finite Elements: An Observer-Independent Noninvasive Method. Magn Reson Imaging. 2008,26(8):1152-9. PMID: 18687550 
  • Nowak CN, Fischer G, Wieser L, Tilg B, Neurauter A, Strohmenger HU. Spatial-temporal filter effect in a computer model study of ventricular fibrillation / Räumlicher und zeitlicher Filtereffekt in einer Computermodellstudie zum Herzkammerflimmern. Biomed Tech (Berl), 2008;53(4):163-73. PMID: 18652560 
  • Osl M, Dreiseitl S, Pfeifer B, Weinberger K, Klocker H, Bartsch G, Schäfer G, Tilg B, Graber A,  Baumgartner C. A new rule-based data mining algorithm for identifying metabolic markers in prostate cancer using tandem mass spectrometry. Bioinformatics, 2008;24(24):2908-2914. PMID: 18815183 
  • Pfeifer B, Kugler K, Tejada M, Baumgartner Ch, Seger M, Osl M, Netzer M, Handler M, Dander A, Wurz M, Graber A, Tilg B. A Cellular Automation Framework for Infectious Disease Spread Simulation. Open Med Inform J, 2008;2:70-81. PMID: 19415136
  • Pfeifer B, Hanser F, Seger M, Fischer G, Modre-Osprian R, Tilg B. Patient-Specific Volume Conductor Modeling for Non-Invasive Imaging of Cardiac Electrophysiology. Open Med Inform J, 2008;2:32-41. PMID: 19415133 
  • Visvanathan M, Breit M, Pfeifer B, Baumgartner C, Modre-Osprian R, Tilg B. DMSP-Database for modeling signaling pathways. Combining biological and mathematical modeling knowledge for pathways. Methods Inf Med, 2008;47:140-148. PMID: 18338085   
  • Wieser L, Nowak CN, Tilg B, Fischer G. Mother Rotor Anchoring in Branching Tissue With Heterogeneous Membrane Properties. Biomed Tech (Berl), 2008;53:25-35. PMID: 18251708
  • Wieser L, Richter HE, Plank G, Pfeifer B, Tilg B, Nowak CN, Fischer G: A Finite Element Formulation for Atrial Tissue Monolayer. Methods Inf Med, 2008;47:131-139. PMID: 18338084
Patente
  • Plant C, Baumgartner C, Tilg B. EP2076880. Feature Selection on Proteomic Data for Identifying Biomarker Candidates. Pub. No.: WO/2008/037479 (pending).
Konferenzbeiträge
  • Nowak CN, Fischer G, Wieser L, Strohmenger HU, Tilg B.  Frequency Distribution Effects of Anchored Mother Rotors - a Computer Model Study. 30th Annual International IEEE EMBS Conference, August 20-24, 2008, Vancouver, British Columbia, Canada.
  • Nowak CN, Fischer G, Neurauter A, Wieser L, Tilg B, Strohmenger HU. Comparison of Countershock Prediction Features Based on Autoregressive and Fourier Transformed Spectral Analysis. 35th annual Computers in Cardiology conference, September 14-17, 2008, Bologna, Italy.
  • Osl M,  Baumgartner C,  Tilg B,  Dreiseitl S. On the combination of logistic regression  and local probability estimates. Proc. 3rd Int. Conf. on Broadband Communications, Information Technology & Biomedical Applications (BroadCom' 08), 23-26 Nov. 2008, Pretoria, South Africa.
  • Osl M, Ohno-Machado L, Baumgartner C, Tilg B, Dreiseitl S. Improving Calibration of Logistic Regression Models by Local Estimates. AMIA 2008, Washington DC.
  • Pfeifer B, Kugler K, Tejada M, Baumgartner Ch, Seger M, Graber A, Tilg B. A Modeling Framework for Simulating Contagious Diseases in Populations. 4th Kuala Lumpur International Conference on Biomedical Engineering, 25-28 June 2008, Kuala Lumpur, Malaysia.
  • Pfeifer B, Tejada MM, Kugler K, Osl M, Netzer M, Seger M, Modre-Osprian R, Schreier G, Tilg B. A Biomedical Knowledge Discovery in Databases Design Tool - Turning Data into Information. eHealth 2008, Wien, 29.-30. Mai 2008.