Papers 2006

Benetka W, Koranda M, and Eisenhaber F. Protein Prenylation: An (Almost) Comprehensive Overview on Discovery History, Enzymology, and Significance in Physiology and Disease. Monatshefte fr Chemie / Chemical Monthly 137(10):1241-1281, 2006

Benetka W, Koranda M, Maurer-Stroh S, Pittner F, Eisenhaber F. Farnesylation or geranylgeranylation? Efficient assays for testing protein prenylation in vitro and in vivo. BMC Biochem. 7:6, 2006

Bernhart SH, Hofacker IL, and Stadler PF. Local RNA base pairing probabilities in large sequences. Bioinformatics 22(5):614-615, 2006

Bernhart SH, Tafer H, Muckstein U, Flamm C, Stadler PF, and Hofacker IL. Partition function and base pairing probabilities of RNA heterodimers. Algorithms for Molecular Biology 1(1):3, 2006

Eisenhaber F. Introduction Bioinformatics: Mystery, Astrology or Service Technology? In: Discovering Biomolecular Mechanisms with Computational Biology. (Ed. Eisenhaber F), 1-10. Springer - New York, Landes Biosciences - Georgetown, 2006

Eisenhaber F. Prediction of Protein Function: Two Basic Concepts and One Practical Recipe. In: Discovering Biomolecular Mechanisms with Computational Biology. (Ed. Eisenhaber F), 39-54. Springer - New York, Landes Biosciences - Georgetown, 2006

Forst CV, Flamm C, Hofacker IL, and Stadler PF. Algebraic comparison of metabolic networks, phylogenetic inference and metabolic innovation. BMC Bioinformatics 7(1):67, 2006

Galon J, Costes A, Sanchez-Cabo F, Kirilovsky A, Mlecnik B, Lagorce-Pages C, Tosolini M, Camus M, Berger A, Wind P, Zinzindohoue F, Bruneval P, Cugnenc PH, Trajanoski Z, Fridman WH, Pages F. Type, density, and location of immune cells within human colorectal tumors predict clinical outcome. Science 313(5795):1960-1964, 2006

Hertel J, Lindemeyer M, Missal K, Fried C, Tanzer A, Flamm C, Hofacker IL, and Stadler PF. The Expansion of the Metazoan MicroRNA Repertoire. BMC Genomics 7(1):25, 2006

Mückstein U, Tafer H, Hackermuller J, Bernhart SH, Stadler PF, and Hofacker IL. Thermodynamics of RNA-RNA Binding. Bioinformatics 22(10):1177-1182, 2006

Mujezinovic N, Raidl G, Hutchins JR, Peters JM, Mechtler K, Eisenhaber F. Cleaning of raw peptide MS/MS spectra: Improved protein identification following deconvolution of multiply charged peaks, isotope clusters, and removal of background noise. Proteomics 6(19):5117-5131, 2006

Novatchkova M, Schneider G, Fritz R, Eisenhaber F, Schleiffer A. DOUTfinder--identification of distant domain outliers using subsignificant sequence similarity. Nucleic Acids Research 34(Web Server issue):W214-218, 2006

Rainer J, Sanchez-Cabo F, Stocker G, Sturn A, and Trajanoski Z. CARMAweb: comprehensive R- and BioConductor-based web service for microarray data analysis. Nucleic Acids Research 34(Web Server issue):W498-503, 2006

Schmidt S, Rainer J, Riml S, Ploner C, Jesacher S, Achmuller C, Presul E, Skvortsov S, Crazzolara R, Fiegl M, Raivio T, Janne OA, Geley S, Meister B, and Kofler R. Identification of glucocorticoid-response genes in children with acute lymphoblastic leukemia. Blood 107(5):2061-2069, 2006

Schneider G, Neuberger G, Wildpaner M, Tian S, Berezovsky I, Eisenhaber F. Application of a sensitive collection heuristic for very large protein families: evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases. BMC Bioinformatics 7:164, 2006

Tschernatsch MMO, Mlecnik B, Trajanoski Z, Zechner R, and Zimmermann R. LPL-mediated lipolysis of VLDL induces an upregulation of AU-rich mRNAs and an activation of HuR in endothelial cells. Atherosclerosis, 2006

Watrin E, Schleiffer A, Tanaka K, Eisenhaber F, Nasmyth K, Peters JM. Human Scc4 is required for cohesin binding to chromatin, sister-chromatid cohesion, and mitotic progression. Curr Biology 16(9):863-874, 2006

Wolfinger MT, Will S, Hofacker IL, Backofen R, and Stadler PF. Exploring the lower part of discrete polymer model energy landscapes. Europhysics Letters 74(4):726-732, 2006