Papers 2005

Bompfünewerer AF, Flamm C, Fried C, Fritzsch G, Hofacker IL, Lehmann J, Missal K, Mosig A, Müller B, Prohaska SJ, Stadler BMR, Stadler PF, Tanzer A, Washietl S, and Witwer C. Evolutionary Patterns of Non-Coding RNAs. Theor Biosci 123(4):301-369, 2005

Di Camillo B, Sanchez-Cabo F, Toffolo G, Nair SK, Trajanoski Z, and Cobelli C. A quantization method based on threshold optimization for microarray short time series. BMC Bioinformatics 6(Suppl 4):S11, 2005

Eisenhaber B and Eisenhaber F. Sequence complexity of proteins and its significance in annotation. In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. (Ed. Subramaniam S) Wiley Interscience, New York, 2005

Gardner PP, Wilm A, and Washietl S. A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res 33(8):2433-2439, 2005

Hackl H, Burkard TR, Sturn A, Rubio R, Schleiffer A, Tian S, Quackenbush J, Eisenhaber F, and Trajanoski Z. Molecular processes during fat cell development revealed by gene expression profiling and functional annotation. Genome Biol 6(13):R108, 2005

Hofacker IL and Stadler PF. Memory efficient folding algorithms for circular RNA secondary structures. Proc.German Conf.on Bioinformatics (GCB '05): 15-25, 2005

Kals M, Natter K, Thallinger GG, Trajanoski Z, and Kohlwein SD. YPL.db2: the Yeast Protein Localization database, version 2.0. Yeast 22(3):213-218, 2005

Maurer M, Molidor R, Sturn A, Hartler J, Hackl H, Stocker G, Prokesch A, Scheideler M, and Trajanoski Z. MARS: microarray analysis, retrieval, and storage system. BMC Bioinformatics 6(1):101, 2005

Mückstein U, Tafer H, Hackermüller J, Bernhart SH, Stadler PF, and Hofacker IL. Thermodynamics of RNA-RNA Binding. Proc.German Conf.on Bioinformatics (GCB '05): 3-13, 2005

Mlecnik B, Scheideler M, Hackl H, Hartler J, and Trajanoski Z. PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways. Nucleic Acids Res 33(Web Server issue):W633-W637, 2005

Novatchkova M, Bachmair A, Eisenhaber B, and Eisenhaber F. Proteins with two SUMO-like domains in chromatin-associated complexes: the RENi (Rad60-Esc2-NIP45) family. BMC Bioinformatics 6(1):22, 2005

Novatchkova M, Wildpaner M, Schweizer D, and Eisenhaber F. PhyloDome--visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets. Nucleic Acids Res 33(Web Server issue):W121-W125, 2005

Pages F, Berger A, Camus F, Sanchez-Cabo F, Costes A, Molidor R, Mlecnik B, Kirilovsky A, Nilsson M, Damotte D, Meatchi T, Bruneval P, Cugnenenc PH, Trajanoski Z, Fridman WH, and Galon J. Effector memory T cells, early metastasis, and survival in colorectal cancer. N Engl J Med 353(25):2654-2666, 2005

Parson W, Kirchebner R, Mühlmann R, Renner K, Kofler A, Schmidt S, and Kofler R. Cancer cell line identification by short tandem repeat profiling: power and limitations. FASEB J 19(3):434-436, 2005

Ploner C, Schmidt S, Presul E, Renner K, Schröcksnadel K, Rainer J, Riml S, and Kofler R. Glucocorticoid-induced apoptosis and glucocorticoid resistance in acute lymphoblastic leukemia. J Steroid Biochem Mol Biol 93(2-5):153-160, 2005

Sturn A, Maurer M, Molidor R, and Trajanoski Z. Systems for the management of pharmacogenomic information. In: Pharmacogenomics: Methods and Applications. (Ed. Innocenti F), 193-208. Humana Press, Totowa, 2005

Vogl C, Sanchez-Cabo F, Stocker G, Hubbard SJ, Wolkenhauer O, and Trajanoski Z. A fully Bayesian model to cluster gene expression profiles. Bioinformatics 21(Suppl 2):ii130-ii136, 2005

Washietl S, Hofacker IL, and Stadler PF. Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci USA 102(7):2454-2459, 2005

Washietl S, Hofacker IL, Lukasser M, Hüttenhofer A, and Stadler PF. Genome-wide mapping of conserved RNA Secondary Structures predicts Thousands of functional Non-Coding RNAs in Human. Nat Biotechnol 23(11):1383-1390, 2005

Yu JS, Ongarello S, Fiedler R, Chen XW, Toffolo G, Cobelli C, and Trajanoski Z. Ovarian cancer identification based on dimensionality reduction for high-throughput mass spectrometry data. Bioinformatics 21(10):2200-2209, 2005