Original articles (Methodological papers)

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)

Bennett KL, Funk M, Tschernutter M, Breitwieser FP, Planyavsky M, Ubaida-Mohien C et al. Proteomic analysis of human cataract aqueous humour: Comparison of one-dimensional gel LCMS with two-dimensional LCMS of unlabelled and iTRAQ(R)-labelled specimens. J Proteomics 74(2):151-166, 2011 (3.851)

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

Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25(8):1091-1093, 2009 (5.039)

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

Carugo O. Detailed estimation of bioinformatics prediction reliability through the Fragmented Prediction Performance Plots. BMC Bioinformatics 8(1):380, 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. 2007;2(3):101-104.

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

Cerqueira FR, Morandell S, Ascher S, Mechtler K, Huber LA, Pfeifer B et al. Improving Phosphopeptide/protein Identification using a New Data Mining Framework for MS/MS Spectra Preprocessing. J Proteomics Bioinform 2(3):150-164, 2009 (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)

Cserzo M, Eisenhaber F, Eisenhaber B, and Simon I. TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter. Bioinformatics 20(1):136-137, 2004

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)

Dehmer M, Emmert-Streib F, and Gesell T. A comparative analysis of multidimensional features of objects resembling sets of graphs. Applied Mathematics and Computation 196(1):221-235, 2008

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, Eisenhaber F, Maurer-Stroh S, and Neuberger G. Prediction of sequence signals for lipid post-translational modifications: insights from case studies. Proteomics 4(6):1614-1625, 2004

Eisenhaber B, Schneider G, Wildpaner M, and Eisenhaber F. A sensitive predictor for potential GPI lipid modification sites in fungal protein sequences and its application to genome-wide studies for Aspergillus nidulans, Candida albicans, Neurospora crassa, Saccharomyces cerevisiae and Schizosaccharomyces pombe. J Mol Biol 337(2):243-253, 2004

Eisenhaber B, Wildpaner M, Schultz CJ, Borner GH, Dupree P, and Eisenhaber F. Glycosylphosphatidylinositol lipid anchoring of plant proteins. Sensitive prediction from sequence- and genome-wide studies for Arabidopsis and rice. Plant Physiol 133(4):1691-1701, 2003

Eisenhaber F, Eisenhaber B, Kubina W, Maurer-Stroh S, Neuberger G, Schneider G, and Wildpaner M. Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Pi, NMT and PTS1. Nucleic Acids Res 31(13):3631-3634, 2003

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

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)

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

Geigl JB, Obenauf AC, Waldispuehl-Geigl J, Hoffmann EM, Auer M, Hormann M et al. Identification of small gains and losses in single cells after whole genome amplification on tiling oligo arrays. Nucleic Acids Res 37(15):e105, 2009 (6.878)

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)

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. Epub 2007 Apr 22.

Hackl H, Maurer M, Mlecnik B, Hartler J, Stocker G, Miranda-Saavedra D, and Trajanoski Z. GOLD.db: genomics of lipid-associated disorders database. BMC Genomics 5(1):93, 2004

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

Hartler J, Trotzmuller M, Chitraju C, Spener F, Kofeler HC, and Thallinger GG. Lipid Data Analyzer: Unattended Identification and Quantitation of Lipids in LC-MS Data. Bioinformatics 27(4):572-577, 2011 (4.925)

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

Hofacker IL, Bernhart SH, and Stadler PF. Alignment of RNA base pairing probability matrices. Bioinformatics 20(14):2222-2227, 2004

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)

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

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

Kirillova S, Kumar S, and Carugo O. Protein Domain Boundary Predictions: A Structural Biology Perspective. Open Biochem J 3(1):1-8, 2009 (0.000)

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

Leparc GG, Tüchler T, Striedner G, Bayer K, Sykacek P, Hofacker IL et al. Model-based probe set optimization for high-performance microarrays. Nucleic Acids Res 37(3):e18, 2009 (6.954)

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

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

Maurer-Stroh S, Gouda M, Novatchkova M, Schleiffer A, Schneider G, Sirota FL, Wildpaner M, Hayashi N, and Eisenhaber F. MYRbase: analysis of genome-wide glycine myristoylation enlarges the functional spectrum of eukaryotic myristoylated proteins. Genome Biol 5(3):R21, 2004

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, 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

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

Mueller LA, Kugler KG, Dander A, Graber A, and Dehmer M. QuACN: an R package for analyzing complex biological networks quantitatively. Bioinformatics 27(1):140-141, 2011 (4.925)

Mujezinovic N, Raidl G, Hutchins JR, Peters JM, Mechtler K, and 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

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)

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

Neuberger G, Kunze M, Eisenhaber F, Berger J, Hartig A, and Brocard C. Hidden localization motifs: naturally occurring peroxisomal targeting signals in non-peroxisomal proteins. Genome Biol 5(12):R97, 2004

Neuberger G, Maurer-Stroh S, Eisenhaber B, Hartig A, and Eisenhaber F. Motif refinement of the peroxisomal targeting signal 1 and evaluation of taxon-specific differences. J Mol Biol 328(3):567-579, 2003

Neuberger G, Maurer-Stroh S, Eisenhaber B, Hartig A, and Eisenhaber F. Prediction of peroxisomal targeting signal 1 containing proteins from amino acid sequence. J Mol Biol 328(3):581-592, 2003

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

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, 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-W218, 2006

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

Ooi HS, Kwo CY, Wildpaner M, Sirota FL, Eisenhaber B, Maurer-Stroh S et al. ANNIE: integrated de novo protein sequence annotation. Nucleic Acids Res 37(Web server issue):W435-W440, 2009 (6.878)

Osl M, Dreiseitl S, Cerqueira F, Netzer M, Pfeifer B, and Baumgartner C. Demoting redundant features to improve the discriminatory ability in cancer data. J Biomed Inform 42(4):721-725, 2009 (1.924)

Pabinger S, Rader R, Agren R, Nielsen J, Trajanoski Z. MEMOSys: Bioinformatics platform for genome-scale metabolic models BMC Syst Biol. 5:20, 2011 (4.064)

Pabinger S, Thallinger GG, Snajder R, Eichhorn H, Rader R, and Trajanoski Z. QPCR: Application for real-time PCR data management and analysis. BMC Bioinformatics 10(1):268, 2009 (3.470)

Pieler R, Sanchez-Cabo F, Hackl H, Thallinger GG, and Trajanoski Z. ArrayNorm: comprehensive normalization and analysis of microarray data. Bioinformatics 20(12):1971-1973, 2004

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

Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75(23):7537-7541, 2009 (3.801)

Schneider G, Neuberger G, Wildpaner M, Tian S, Berezovsky I, and 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

Seemann SE, Richter AS, Gesell T, Backofen R, and Gorodkin J. Structural conserved RNA interactions predicted by PETcofold. Bioinformatics 27(2):211-219, 2011 (4.926)

Sikic K and Carugo O. CARON - Average RMSD of NMR structure ensembles. Bioinformation 4(3):132-133, 2009 (0.000)

Steinkellner G, Rader R, Thallinger GG, Kratky C, and Gruber K. VASCo: computation and visualization of annotated protein surface contacts. BMC Bioinformatics 10(1):32, 2009 (3.470)

Stocker G, Fischer M, Rieder D, Bindea G, Kainz S, Oberstolz M et al. iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis. BMC Bioinformatics 10(1):390, 2009 (3.781)

Stocker G, Rieder D, and Trajanoski Z. ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux cluster. Bioinformatics 20(5):805-807, 2004

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

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)

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 and Hofacker IL. Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J Mol Biol 342(1):19-30, 2004

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

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

Wolfinger MT, Svrcek-Seiler WA, Flamm C, Hofacker IL, and Stadler PF. Efficient computation of RNA folding dynamics. J Phys A: Math Gen 37(17):4731-4741, 2004

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

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

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)