Published in Bioinformatics on December 23, 2005
Semantic similarity in biomedical ontologies. PLoS Comput Biol (2009) 5.05
Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinformatics (2008) 2.87
Information theory applied to the sparse gene ontology annotation network to predict novel gene function. Bioinformatics (2007) 2.15
NanoParticle Ontology for cancer nanotechnology research. J Biomed Inform (2010) 2.07
A comparison of imputation procedures and statistical tests for the analysis of two-dimensional electrophoresis data. Proteome Sci (2010) 1.42
Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes. BMC Bioinformatics (2008) 1.39
Biological impact of missing-value imputation on downstream analyses of gene expression profiles. Bioinformatics (2010) 1.15
Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments. BMC Genomics (2010) 1.14
Integrative missing value estimation for microarray data. BMC Bioinformatics (2006) 0.97
Missing value imputation improves clustering and interpretation of gene expression microarray data. BMC Bioinformatics (2008) 0.96
A literature-based similarity metric for biological processes. BMC Bioinformatics (2006) 0.91
Incorporating Nonlinear Relationships in Microarray Missing Value Imputation. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.91
Assessment of protein set coherence using functional annotations. BMC Bioinformatics (2008) 0.88
A meta-data based method for DNA microarray imputation. BMC Bioinformatics (2007) 0.88
Robust imputation method for missing values in microarray data. BMC Bioinformatics (2007) 0.87
Integrative analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: a non-linear model to predict abundance of undetected proteins. Bioinformatics (2009) 0.87
Missing value imputation for microarray gene expression data using histone acetylation information. BMC Bioinformatics (2008) 0.85
Impact of missing value imputation on classification for DNA microarray gene expression data--a model-based study. EURASIP J Bioinform Syst Biol (2010) 0.84
A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization. BioData Min (2012) 0.81
How to improve postgenomic knowledge discovery using imputation. EURASIP J Bioinform Syst Biol (2009) 0.78
Missing value imputation for microRNA expression data by using a GO-based similarity measure. BMC Bioinformatics (2016) 0.77
An unsupervised approach to predict functional relations between genes based on expression data. Biomed Res Int (2014) 0.75
MVIAeval: a web tool for comprehensively evaluating the performance of a new missing value imputation algorithm. BMC Bioinformatics (2017) 0.75
An improved method for functional similarity analysis of genes based on Gene Ontology. BMC Syst Biol (2016) 0.75
An integrative imputation method based on multi-omics datasets. BMC Bioinformatics (2016) 0.75
A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics (2009) 2.70
GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinformatics (2006) 2.37
Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia. Cancer Discov (2013) 1.93
Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. Bioinformatics (2007) 1.54
Integrating probe-level expression changes across generations of Affymetrix arrays. Nucleic Acids Res (2005) 1.42
Genetic variants and their interactions in the prediction of increased pre-clinical carotid atherosclerosis: the cardiovascular risk in young Finns study. PLoS Genet (2010) 1.39
Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming. Immunity (2010) 1.28
Quantitative subcellular proteome and secretome profiling of influenza A virus-infected human primary macrophages. PLoS Pathog (2011) 1.22
Alignment of LC-MS images, with applications to biomarker discovery and protein identification. Proteomics (2008) 1.22
Identification of novel IL-4/Stat6-regulated genes in T lymphocytes. J Immunol (2003) 1.20
Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies. Genome Biol (2009) 1.10
Th1 response and cytotoxicity genes are down-regulated in cutaneous T-cell lymphoma. Clin Cancer Res (2006) 1.05
Identification of novel genes regulated by IL-12, IL-4, or TGF-beta during the early polarization of CD4+ lymphocytes. J Immunol (2003) 1.02
Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks. Bioinformatics (2009) 1.02
Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays. IEEE/ACM Trans Comput Biol Bioinform (2010) 1.01
A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments. Proteomics (2005) 1.00
Quality classification of tandem mass spectrometry data. Bioinformatics (2005) 1.00
Target inhibition networks: predicting selective combinations of druggable targets to block cancer survival pathways. PLoS Comput Biol (2013) 1.00
A statistical score for assessing the quality of multiple sequence alignments. BMC Bioinformatics (2006) 0.98
Missing value imputation improves clustering and interpretation of gene expression microarray data. BMC Bioinformatics (2008) 0.96
Making sense of large-scale kinase inhibitor bioactivity data sets: a comparative and integrative analysis. J Chem Inf Model (2014) 0.95
Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets. Brief Bioinform (2009) 0.95
Obatoclax, saliphenylhalamide, and gemcitabine inhibit influenza a virus infection. J Biol Chem (2012) 0.94
Reproducibility-optimized test statistic for ranking genes in microarray studies. IEEE/ACM Trans Comput Biol Bioinform (2008) 0.93
Improved statistical modeling of tumor growth and treatment effect in preclinical animal studies with highly heterogeneous responses in vivo. Clin Cancer Res (2012) 0.92
Toward more realistic drug-target interaction predictions. Brief Bioinform (2014) 0.92
Early suppression of immune response pathways characterizes children with prediabetes in genome-wide gene expression profiling. J Autoimmun (2010) 0.91
An update on clinical proteomics in Alzheimer's research. J Neurochem (2009) 0.90
Model-based prediction of sequence alignment quality. Bioinformatics (2008) 0.89
Gaussian mixture model-based segmentation of MR images taken from premature infant brains. J Neurosci Methods (2009) 0.88
Pripper: prediction of caspase cleavage sites from whole proteomes. BMC Bioinformatics (2010) 0.88
Filtering strategies for improving protein identification in high-throughput MS/MS studies. Proteomics (2009) 0.88
Quantitative maps of genetic interactions in yeast - comparative evaluation and integrative analysis. BMC Syst Biol (2011) 0.87
Quantitative proteomics analysis of the nuclear fraction of human CD4+ cells in the early phases of IL-4-induced Th2 differentiation. Mol Cell Proteomics (2010) 0.87
Predicting quantitative genetic interactions by means of sequential matrix approximation. PLoS One (2008) 0.86
Hierarchical grid transformation for image warping in the analysis of two-dimensional electrophoresis gels. Proteomics (2002) 0.85
Network pharmacology applications to map the unexplored target space and therapeutic potential of natural products. Nat Prod Rep (2015) 0.85
Predicting drug-target interactions through integrative analysis of chemogenetic assays in yeast. Mol Biosyst (2013) 0.84
Evaluation of partial volume effect correction methods for brain positron emission tomography: Quantification and reproducibility. J Med Phys (2007) 0.84
Comparison of PDQuest and Progenesis software packages in the analysis of two-dimensional electrophoresis gels. Proteomics (2003) 0.84
Genetic variants and their interactions in disease risk prediction - machine learning and network perspectives. BioData Min (2013) 0.83
Chk1 targeting reactivates PP2A tumor suppressor activity in cancer cells. Cancer Res (2013) 0.82
Biochemical and clinical approaches in evaluating the prognosis of colon cancer. Anticancer Res (2007) 0.82
Efficient estimation of emission probabilities in profile hidden Markov models. Bioinformatics (2003) 0.82
Mahalanobis distance screening of Arabidopsis mutants with chlorophyll fluorescence. Photosynth Res (2010) 0.82
Overnight variability in transcutaneous carbon dioxide predicts vascular impairment in women. Exp Physiol (2008) 0.81
Using Peptide-Level Proteomics Data for Detecting Differentially Expressed Proteins. J Proteome Res (2015) 0.81
A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization. BioData Min (2012) 0.81
Resampling reveals sample-level differential expression in clinical genome-wide studies. OMICS (2009) 0.81
Improving identification of differentially expressed genes by integrative analysis of Affymetrix and Illumina arrays. OMICS (2006) 0.81
Intra-tissue steroid profiling indicates differential progesterone and testosterone metabolism in the endometrium and endometriosis lesions. J Clin Endocrinol Metab (2014) 0.81
Sleep quality, daytime sleepiness and fasting insulin levels in women with chronic obstructive pulmonary disease. Respir Med (2005) 0.81
Exploring the transcriptomic variation caused by the Finnish founder mutation of lysinuric protein intolerance (LPI). Mol Genet Metab (2011) 0.80
Kinetics and STAT4- or STAT6-mediated regulation of genes involved in lymphocyte polarization to Th1 and Th2 cells. Eur J Immunol (2003) 0.80
Statistical methods for identifying conserved residues in multiple sequence alignment. Stat Appl Genet Mol Biol (2004) 0.79
Can carotid body perfusion act as a respiratory controller? J Theor Biol (2007) 0.78
Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations. Algorithms Mol Biol (2012) 0.78
PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use. Int J Proteomics (2011) 0.77
Optimized detection of transcription factor-binding sites in ChIP-seq experiments. Nucleic Acids Res (2011) 0.77
Compid: a new software tool to integrate and compare MS/MS based protein identification results from Mascot and Paragon. J Proteome Res (2010) 0.77
Automated pattern ranking in differential display data analysis. Methods Mol Biol (2006) 0.77
Statistical detection of quantitative protein biomarkers provides insights into signaling networks deregulated in acute myeloid leukemia. Proteomics (2014) 0.77
Effect of medroxyprogesterone on inspiratory flow shapes during sleep in postmenopausal women. Respir Physiol Neurobiol (2003) 0.77
Inspiratory flow shape clustering: an automated method to monitor upper airway performance during sleep. Comput Methods Programs Biomed (2006) 0.77
Medroxyprogesterone improves nocturnal breathing in postmenopausal women with chronic obstructive pulmonary disease. Respir Res (2005) 0.77
Ovarian endometriosis signatures established through discovery and directed mass spectrometry analysis. J Proteome Res (2014) 0.76
Genome-wide scoring of positive and negative epistasis through decomposition of quantitative genetic interaction fitness matrices. PLoS One (2010) 0.76
Pravastatin-induced improvement in coronary reactivity and circulating ATP and ADP levels in young adults with type 1 diabetes. Front Physiol (2012) 0.75
Computer-assisted identification of multitrace electrophoretic patterns in differential display experiments. Electrophoresis (2007) 0.75
Pre-processing of Orbitrap higher energy collisional dissociation tandem mass spectra to reduce erroneous iTRAQ ratios. Rapid Commun Mass Spectrom (2012) 0.75
State of vigilance, oestrogen replacement therapy, and lipid profile as modifiers of nocturnal movement-induced heart rate responses. Clin Physiol Funct Imaging (2003) 0.75
Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nat Commun (2016) 0.75
Non-invasive respiratory monitoring during wakefulness and sleep in pre- and postmenopausal women. Respir Physiol Neurobiol (2005) 0.75
Overnight features of transcutaneous carbon dioxide measurement as predictors of metabolic status. Artif Intell Med (2007) 0.75
Nocturnal transcutaneous carbon dioxide tension in postmenopausal estrogen users and non-users. Menopause Int (2009) 0.75