Papers 2010

Baumgartner C, Lewis GD, Netzer M, Pfeifer B, and Gerszten RE. A new data mining approach for profiling and categorizing kinetic patterns of metabolic biomarkers after myocardial injury. Bioinformatics 26(14):1745-1751, 2010 (4.926)

Bogner-Strauss JG, Prokesch A, Sanchez-Cabo F, Rieder D, Hackl H, Duszka K et al. Reconstruction of gene association network reveals a transmembrane protein required for adipogenesis and trageted by PPAR-gamma. Cell Mol Life Sci 67(23):4049-4064, 2010 (6.090)

Boria I, Gruber AR, Tanzer A, Bernhart SH, Lorenz R, Mueller MM et al. Nematode sbRNAs: Homologs of Vertebrate Y RNAs. J Mol Evol 70(4):346-358, 2010 (2.762)

Burkard TR, Rix U, Breitwieser FP, Superti-Furga G, and Colinge J. A computational approach to analyze the mechanism of action of the kinase inhibitor bafetinib. PLoS Comput Biol 6(11):e1001001, 2010 (5.759)

Carugo O. Clustering criteria and algorithms. Methods Mol Biol 609:175-196, 2010 (0.000)

Carugo O. Clustering tendency in the protein fold space. Bioinformation 4(8):347-351, 2010 (0.000)

Carugo O and Eisenhaber F. Data Mining Techniques for the Life Sciences. Humana Press, New York, NJ, USA, 2010, ISBN 978-1-60327-240-7.

Carugo O. Proximity measures for cluster analysis. Methods Mol Biol 609:163-174, 2010 (0.000)

Cerqueira FR, Graber A, Schwikowski B, and Baumgartner C. MUDE: A New Approach for Optimizing Sensitivity in the Target-Decoy Search Strategy for Large-Scale Peptide/Protein Identification. J Proteome Res 9(5):2265-2277, 2010 (5.684)

Dreiseitl S, Osl M, Baumgartner C, and Vinterbo S. An evaluation of heuristics for rule ranking. Artif Intell Med 50(2010):175-180, 2010 (1.645)

Flamm C, Ullrich A, Ekker H, Mann M, Högerl D, Rohrschneider M et al. Evolution of metabolic networks: A computational framework. J Syst Chem 1:4, 2010 (0.000)

Giegerich R and Höner zu Siederdissen C. Semantics and Ambiguity of Stochastic RNA Family Models. IEEE/ACM Transactions on Computational Biology and Bioinformatics 8(2):499-516, 2010 (1.866)

Gruber AR, Findeiss S, Washietl S, Hofacker IL, and Stadler PF. RNAz 2.0: Improved Noncoding RNA Detection. Pac Symp Biocomput 15:69-79, 2010 (0.000)

Hackl H, Stocker G, Charoentong P, Mlecnik B, Bindea G, Galon J et al. Information technology solutions for integration of biomolecular and clinical data in the identification of new cancer biomarkers and targets for therapy. Pharmacol Ther 128(3):488-498, 2010 (8.897)

Hofacker IL, Flamm C, Heine C, Wolfinger MT, Scheuermann G, and Stadler PF. BarMap: RNA Folding Kinetics on Dynamic Energy Landscapes. RNA 16(7):1308-1316, 2010 (5.018)

Höner zu Siederdissen C and Hofacker IL. Discriminatory power of RNA family models. Bioinformatics 26(18):i453-i459, 2010 (4.926)

Kirillova S, Tosatto SC, and Carugo O. FRASS: the web-server for RNA structural comparison. BMC Bioinformatics 11(1):327, 2010 (3.428)

Laschober GT, Ruli D, Hofer E, Muck C, Carmona-Gutierrez D, Ring J et al. Identification of evolutionarily conserved genetic regulators of cellular aging. Aging Cell 9(6):1084-1097, 2010 (7.554)

Lorenz C, Gesell T, Zimmermann B, Schoeberl U, Bilusic I, Rajkowitsch L et al. Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts. Nucleic Acids Res 38(11):3794-3808, 2010 (6.878)

Marth K, Novatchkova M, Focke-Tejkl M, Jenisch S, Jager S, Kabelitz D et al. Tracing antigen signatures in the human IgE repertoire. Mol Immunol 47(14):2323-2329, 2010 (3.202)

Millonig G, Praun S, Netzer M, Baumgartner C, Müller S, Villinger J et al. Breath analysis in liver disease followed by a new statistical model for optimizing the discriminatory power - a feasibility study. Biomarkers 15(4):297-306, 2010 (1.728)

Mlecnik B, Tosolini M, Charoentong P, Kirilovsky A, Bindea G, Berger A et al. Biomolecular network reconstruction identifies T cell homing factors associated with survival in colorectal cancer. Gastroenterology 138(4):1429-1440, 2010 (12.591)

Mlecnik B, Sanchez-Cabo F, Charoentong P, Bindea G, Pages F, Berger A et al. Data integration and exploration for the identification of molecular mechanisms in tumor-immune cells interaction. BMC Genomics 11(Suppl 1):S7, 2010 (3.926)

Mueckstein U, Leparc GG, Posekany A, Hofacker I, and Kreil DP. Hybridization thermodynamics of NimbleGen Microarrays. BMC Bioinformatics 11(1):35, 2010 (3.780)

Mujezinovic N, Schneider G, Wildpaner M, Mechtler K, and Eisenhaber F. Reducing the haystack to find the needle: improved protein identification after fast elimination of non-interpretable peptide MS/MS spectra and noise reduction. BMC Genomics 11 Suppl 1:S13, 2010 (3.760)

Netzer M and Baumgartner C. Ensemble Feature Selection in Biomedical Applications. In: Database Technology for Life Sciences and Medicine. (Eds. Plant C, Böhm C) World Scientific Publishing, Singapore, 2010

Obermayr E, Sanchez-Cabo F, Tea MK, Singer CF, Krainer M, Fischer MB et al. Assessment of a six gene panel for the molecular detection of circulating tumor cells in the blood of female cancer patients. BMC Cancer 10(1):666, 2010 (2.660)

Schnorrer F, Schonbauer C, Langer CC, Dietzl G, Novatchkova M, Schernhuber K et al. Systematic genetic analysis of muscle morphogenesis and function in Drosophila. Nature 464(7286):287-291, 2010 (31.434)

Tian S and Jianhua W. Comparative study of the binding pockets of mammalian proprotein convertases and its implications for the design of specific small molecule inhibitors. Int J Biol Sci 6(1):89-95, 2010 (0.000)

Ubaida-Mohien C, Hartler J, Breitwieser FP, Rix U, Remsing-Rix L, Winter G et al. MASPECTRAS 2: An Integration and Analysis Platform for Proteomic Data. Proteomics 10(14):2719-2722, 2010 (4.586)

Washietl S and Gesell T. Graph Representations and Algorithms in Computational Biology of RNA Secondary Structure. In: Structural Analysis of Complex Networks. (Ed. Dehmer M) Birkhäuser, Boston, USA, 2010

Yusuf D, Marz M, Stadler PF, and Hofacker IL. Bcheck: a wrapper tool for detecting RNase P RNA genes. BMC Genomics 11(1):432, 2010 (3.428)

Zimmermann B, Gesell T, Chen D, Lorenz C, and Schroeder R. Monitoring Genomic Sequences During SELEX Using High-Throughput Sequencing: Neutral SELEX. PLoS ONE 5(2):e9169, 2010 (4.351)