Papers 2007

Carugo O. A structural proteomics filter: prediction of the quaternary structural type of hetero-oligomeric proteins on the basis of their sequences. Journal of Applied Crystallography 40(6):986-989, 2007

Carugo O. Detailed estimation of bioinformatics prediction reliability through the Fragmented Prediction Performance Plots. BMC Bioinformatics 8(1):380, 2007

Carugo O, Djinovic-Carugo K, Gorbalenya AE, and Tucker P. Likelihood of crystallization: Experimental and computational approaches. J Appl Cryst, 40(2):392-393, 2007

Carugo O, Djinovic-Carugo K, Gorbalenya AE, and Tucker P. Preface of the special issue of Curr. Prot. Pept. Sci. Curr Prot Pept Sci, 8(2):119-120 2007

Carugo O. Identification of domains in protein crystal structures. Journal of Applied Crystallography 40(4):778-781, 2007

Carugo O. Isoelectric points of multi-domain proteins. Bioinformation, 2(3):101-104, 2007

Carugo O. Recent progress in measuring structural similarity between proteins. Curr Protein Pept Sci 8(3):219-241, 2007

Carugo O. Statistical validation of the root-mean-square-distance, a measure of protein structural proximity. Protein Eng Des Sel 20(1):33-37, 2007

Eisenhaber B and Eisenhaber F. Posttranslational modifications and subcellular localization signals: indicators of sequence regions without inherent 3D structure? Curr Protein Pept Sci 8(2):197-203, 2007

Eisenhaber B, Chumak N, Eisenhaber F, and Hauser MT. The ring between ring fingers (RBR) protein family. Genome Biology 8(3):209, 2007

ENCODE Project Consortium, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447(7146):799-816, 2007

Gruber AR, Neuböck R, Hofacker IL, and Washietl S. The RNAz web server: Prediction of thermodynamically stable and evolutionarily conserved RNA structures. 35 (Web Server issue): W335-8, 2007

Hartler J, Thallinger GG, Stocker G, Sturn A, Burkard TR, Körner E, Rader R, Schmidt A, Mechtler K, and Trajanoski Z. MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data. BMC Bioinformatics 8(1):197, 2007

Kowalska A, Bozsaky E, Ramsauer T, Rieder D, Bindea G, Lorch T, Trajanoski Z, Ambros PF. A new platform linking chromosomal and sequence information. Chromosome Res. 15(3):327-339, 2007

Kulterer B, Friedl G, Jandrositz A, Sanchez-Cabo F, Prokesch A, Paar C, Scheideler M, Windhager R, Preisegger K-H, and Trajanoski Z. Gene Expression Profiling of Human Mesenchymal Stem Cells derived from Bone Marrow during Expansion and Osteoblast Differentiation. BMC Genomics 8(1):70, 2007

Maurer-Stroh S, Koranda M, Benetka W, Schneider G, Sirota FL, and Eisenhaber F. Towards Complete Sets of Farnesylated and Geranylgeranylated Proteins. PLoS Computational Biology 3(4):e66, 2007

Müller WG, Rieder D, Karpova TS, John S, Trajanoski Z, and McNally JG. Organization of chromatin and histone modifications at a transcription site. J Cell Biol 177(6):957-967, 2007

Neuberger G, Schneider G, and Eisenhaber F. pkaPS: Prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model. Biol Direct 2(1):1, 2007

Thallinger GG, Baumgartner K, Pirklbauer M, Mehes G, Buck CR, Zatloukal K, and Trajanoski Z. TAMEE: data management and analysis for tissue microarrays. BMC Bioinformatics 8(1):81, 2007

The Athanasius F.Bompfünewerer RNA Consortium:, Backofen R, Bernhart SH, Flamm C, Fried C, Fritzsch G, Hackermuller J, Hertel J, Hofacker IL, Missal K, Mosig A, Prohaska SJ, Rose D, Stadler PF, Tanzer A, Washietl S, and Will S. RNAs everywhere: genome-wide annotation of structured RNAs. J Exp Zoolog B Mol Dev Evol 308B(1):1-25, 2007

Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermuller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigo R, Snyder M, Gerstein MB, Reymond A, Hofacker IL and Stadler PF. Structured RNAs in the ENCODE selected regions of the human genome. Genome Res 17(6):852-864, 2007

Will S, Missal K, Hofacker IL, Stadler PF, and Backofen R. Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLoS Biology 3(4):e65, 2007