Published in Bioinformatics on January 15, 2007
BALL--biochemical algorithms library 1.3. BMC Bioinformatics (2010) 1.12
Biochemical and biophysical analysis of five disease-associated human adenylosuccinate lyase mutants. Biochemistry (2009) 0.87
Assessing the performance of implicit solvation models at a nucleic acid surface. Phys Chem Chem Phys (2008) 0.81
Minimizing frustration by folding in an aqueous environment. Arch Biochem Biophys (2007) 0.80
Electrostatic potential of human immunodeficiency virus type 2 and rhesus macaque simian immunodeficiency virus capsid proteins. Front Microbiol (2012) 0.80
Gradient Models in Molecular Biophysics: Progress, Challenges, Opportunities. J Mech Behav Mater (2013) 0.79
A new approach to the selectivity of ion channels: nonlocal electrostatic consideration. Dokl Biochem Biophys (2008) 0.76
Nonlocal Electrostatics in Spherical Geometries Using Eigenfunction Expansions of Boundary-Integral Operators. Mol Based Math Biol (2015) 0.75
Experimental charge density from electron microscopic maps. Protein Sci (2017) 0.75
Linking epigenetic function to electrostatics: The DNMT2 structural model example. PLoS One (2017) 0.75
Charge density distributions derived from smoothed electrostatic potential functions: design of protein reduced point charge models. J Comput Aided Mol Des (2011) 0.75
Charting a dynamic DNA methylation landscape of the human genome. Nature (2013) 5.80
GeneTrail--advanced gene set enrichment analysis. Nucleic Acids Res (2007) 5.10
Visualization of omics data for systems biology. Nat Methods (2010) 4.59
OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics (2008) 4.41
Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs). Nucleic Acids Res (2005) 4.15
NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity. Nucleic Acids Res (2011) 3.19
The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Proteomics (2012) 2.82
Simultaneous alignment of short reads against multiple genomes. Genome Biol (2009) 2.79
BNDB - the Biochemical Network Database. BMC Bioinformatics (2007) 2.75
Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell (2013) 2.64
MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition. Bioinformatics (2006) 2.40
KIRMES: kernel-based identification of regulatory modules in euchromatic sequences. Bioinformatics (2009) 2.35
Multiple sclerosis: microRNA expression profiles accurately differentiate patients with relapsing-remitting disease from healthy controls. PLoS One (2009) 2.14
Toward the blood-borne miRNome of human diseases. Nat Methods (2011) 2.14
High-accuracy peak picking of proteomics data using wavelet techniques. Pac Symp Biocomput (2006) 1.77
GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments. BMC Bioinformatics (2008) 1.77
SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data. Bioinformatics (2007) 1.61
miRNAs in lung cancer - studying complex fingerprints in patient's blood cells by microarray experiments. BMC Cancer (2009) 1.61
GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences. Nucleic Acids Res (2005) 1.57
Complex humoral immune response against a benign tumor: frequent antibody response against specific antigens as diagnostic targets. Proc Natl Acad Sci U S A (2005) 1.56
A dictionary on microRNAs and their putative target pathways. Nucleic Acids Res (2010) 1.54
YLoc--an interpretable web server for predicting subcellular localization. Nucleic Acids Res (2010) 1.43
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. BMC Bioinformatics (2009) 1.41
Computation of significance scores of unweighted Gene Set Enrichment Analyses. BMC Bioinformatics (2007) 1.41
An automated pipeline for high-throughput label-free quantitative proteomics. J Proteome Res (2013) 1.39
Specific peripheral miRNA profiles for distinguishing lung cancer from COPD. Lung Cancer (2011) 1.38
SVMHC: a server for prediction of MHC-binding peptides. Nucleic Acids Res (2006) 1.33
High-throughput miRNA profiling of human melanoma blood samples. BMC Cancer (2010) 1.32
Going from where to why--interpretable prediction of protein subcellular localization. Bioinformatics (2010) 1.32
A combinatorial approach to protein docking with flexible side chains. J Comput Biol (2002) 1.29
The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Mol Cell Proteomics (2013) 1.28
Tools for label-free peptide quantification. Mol Cell Proteomics (2012) 1.27
Integrated modeling of the major events in the MHC class I antigen processing pathway. Protein Sci (2005) 1.23
MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization. Bioinformatics (2008) 1.20
Combining structure and sequence information allows automated prediction of substrate specificities within enzyme families. PLoS Comput Biol (2010) 1.19
Machine learning competition in immunology - Prediction of HLA class I binding peptides. J Immunol Methods (2011) 1.18
SherLoc2: a high-accuracy hybrid method for predicting subcellular localization of proteins. J Proteome Res (2009) 1.17
A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis. Bioinformatics (2009) 1.17
Stable serum miRNA profiles as potential tool for non-invasive lung cancer diagnosis. RNA Biol (2011) 1.16
Complex dewetting scenarios captured by thin-film models. Nat Mater (2003) 1.16
LC-MSsim--a simulation software for liquid chromatography mass spectrometry data. BMC Bioinformatics (2008) 1.14
BALL--biochemical algorithms library 1.3. BMC Bioinformatics (2010) 1.12
Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks. J Comput Biol (2008) 1.12
OpenMS and TOPP: open source software for LC-MS data analysis. Methods Mol Biol (2011) 1.12
Prediction of dual protein targeting to plant organelles. New Phytol (2009) 1.10
OptiTope--a web server for the selection of an optimal set of peptides for epitope-based vaccines. Nucleic Acids Res (2009) 1.10
Frequent overexpression of the genes FXR1, CLAPM1 and EIF4G located on amplicon 3q26-27 in squamous cell carcinoma of the lung. Int J Cancer (2007) 1.09
Absolute myoglobin quantitation in serum by combining two-dimensional liquid chromatography-electrospray ionization mass spectrometry and novel data analysis algorithms. J Proteome Res (2006) 1.07
BALLView: a tool for research and education in molecular modeling. Bioinformatics (2005) 1.07
Transcriptome analysis by GeneTrail revealed regulation of functional categories in response to alterations of iron homeostasis in Arabidopsis thaliana. BMC Plant Biol (2011) 1.06
A mathematical framework for the selection of an optimal set of peptides for epitope-based vaccines. PLoS Comput Biol (2008) 1.06
Staphylococcus aureus ClpC ATPase is a late growth phase effector of metabolism and persistence. Proteomics (2009) 1.05
Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics. BMC Bioinformatics (2007) 1.05
A minimally invasive multiple marker approach allows highly efficient detection of meningioma tumors. BMC Bioinformatics (2006) 1.05
POPISK: T-cell reactivity prediction using support vector machines and string kernels. BMC Bioinformatics (2011) 1.03
Probabilistic consensus scoring improves tandem mass spectrometry peptide identification. J Proteome Res (2011) 1.03
Novel autoantigens immunogenic in COPD patients. Respir Res (2009) 1.01
Amplicons on chromosome 12q13-21 in glioblastoma recurrences. Int J Cancer (2010) 1.01
miRTrail--a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases. BMC Bioinformatics (2012) 1.01
Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays. Nucleic Acids Res (2013) 1.00
Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. BMC Syst Biol (2009) 0.99
Comparative immunopeptidomics of humans and their pathogens. Proc Natl Acad Sci U S A (2004) 0.99
Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics. J Proteome Res (2010) 0.99
Automated label-free quantification of metabolites from liquid chromatography-mass spectrometry data. Mol Cell Proteomics (2013) 0.98
Immunogenicity of autoantigens. BMC Genomics (2011) 0.97
Genome wide expression profiling identifies specific deregulated pathways in meningioma. Int J Cancer (2009) 0.96
Evidence for the mode of action of the highly cytotoxic Streptomyces polyketide kendomycin. Chembiochem (2007) 0.95
The role of phosphorylatable serine residues in the DNA-binding domain of Arabidopsis bZIP transcription factors. Eur J Cell Biol (2010) 0.95
De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation. Electrophoresis (2009) 0.95
Preparation of superhydrophobic silicon oxide nanowire surfaces. Langmuir (2007) 0.95
Universal peptide vaccines - optimal peptide vaccine design based on viral sequence conservation. Vaccine (2011) 0.95
TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data. J Proteome Res (2012) 0.94
TOPPView: an open-source viewer for mass spectrometry data. J Proteome Res (2009) 0.94
A different view on DNA amplifications indicates frequent, highly complex, and stable amplicons on 12q13-21 in glioma. Mol Cancer Res (2008) 0.94
An integer linear programming approach for finding deregulated subgraphs in regulatory networks. Nucleic Acids Res (2011) 0.94
Exploiting physico-chemical properties in string kernels. BMC Bioinformatics (2010) 0.93
Peak intensity prediction in MALDI-TOF mass spectrometry: a machine learning study to support quantitative proteomics. BMC Bioinformatics (2008) 0.93
From sequence to structure and back again: approaches for predicting protein-DNA binding. Proteome Sci (2004) 0.93
A new Lamarckian genetic algorithm for flexible ligand-receptor docking. J Comput Chem (2010) 0.93
BALLDock/SLICK: a new method for protein-carbohydrate docking. J Chem Inf Model (2008) 0.92
Toward an early diagnosis of lung cancer: an autoantibody signature for squamous cell lung carcinoma. Int J Cancer (2008) 0.92
Novel immunogenic antigens increase classification accuracy in meningioma to 93.84%. Int J Cancer (2011) 0.92
EpiToolKit--a web server for computational immunomics. Nucleic Acids Res (2008) 0.91
Improving peptide identification in proteome analysis by a two-dimensional retention time filtering approach. J Proteome Res (2009) 0.91
Identification of lung cancer with high sensitivity and specificity by blood testing. Respir Res (2010) 0.91
Towards in silico design of epitope-based vaccines. Expert Opin Drug Discov (2009) 0.90
SNEP: SNP-derived epitope prediction program for minor H antigens. Immunogenetics (2005) 0.90
Automated bond order assignment as an optimization problem. Bioinformatics (2011) 0.90
Compositionality, stochasticity, and cooperativity in dynamic models of gene regulation. HFSP J (2007) 0.89
Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report. J Proteomics (2013) 0.89
Epitope prediction algorithms for peptide-based vaccine design. Proc IEEE Comput Soc Bioinform Conf (2003) 0.89
Pattern of serum autoantibodies allows accurate distinction between a tumor and pathologies of the same organ. Clin Cancer Res (2008) 0.88
Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry. Proteomics (2015) 0.87
Universality of protein reentrant condensation in solution induced by multivalent metal ions. Proteins (2010) 0.87