Published in Bioinformatics on April 01, 2002
Reovirus infection triggers inflammatory responses to dietary antigens and development of celiac disease. Science (2017) 2.70
QUBIC: a qualitative biclustering algorithm for analyses of gene expression data. Nucleic Acids Res (2009) 1.69
Discovering biological progression underlying microarray samples. PLoS Comput Biol (2011) 1.65
Analysis of time-series gene expression data: methods, challenges, and opportunities. Annu Rev Biomed Eng (2007) 1.55
Transcription factor expression dynamics of early T-lymphocyte specification and commitment. Dev Biol (2008) 1.42
Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential. Nucleic Acids Res (2005) 1.18
Density-equalizing Euclidean minimum spanning trees for the detection of all disease cluster shapes. Proc Natl Acad Sci U S A (2007) 1.12
A differentiation-based phylogeny of cancer subtypes. PLoS Comput Biol (2010) 0.98
Systematic gene function prediction from gene expression data by using a fuzzy nearest-cluster method. BMC Bioinformatics (2006) 0.94
Iterative class discovery and feature selection using Minimal Spanning Trees. BMC Bioinformatics (2004) 0.90
Comprehensive evaluation of matrix factorization methods for the analysis of DNA microarray gene expression data. BMC Bioinformatics (2011) 0.88
Local Context Finder (LCF) reveals multidimensional relationships among mRNA expression profiles of Arabidopsis responding to pathogen infection. Proc Natl Acad Sci U S A (2003) 0.88
EXCAVATOR: a computer program for efficiently mining gene expression data. Nucleic Acids Res (2003) 0.87
Clustering of High Throughput Gene Expression Data. Comput Oper Res (2012) 0.83
ESPD: a pattern detection model underlying gene expression profiles. Bioinformatics (2004) 0.80
TreeVis: a MATLAB-based tool for tree visualization. Comput Methods Programs Biomed (2012) 0.78
A temporal precedence based clustering method for gene expression microarray data. BMC Bioinformatics (2010) 0.78
Protein-protein interaction analysis for functional characterization of helicases. Methods (2016) 0.76
Analyses of crime patterns in NIBRS data based on a novel graph theory clustering method: Virginia as a case study. ScientificWorldJournal (2014) 0.75
A NEW CLUSTERING METHOD AND ITS APPLICATION TO PROTEOMIC PROFILING FOR COLON CANCER. IASTED Int Conf Comput Syst Biol (2006) (2006) 0.75
Hierarchical classification of functionally equivalent genes in prokaryotes. Nucleic Acids Res (2007) 0.75
A methodology to assess the intrinsic discriminative ability of a distance function and its interplay with clustering algorithms for microarray data analysis. BMC Bioinformatics (2013) 0.75
HAMSTER: visualizing microarray experiments as a set of minimum spanning trees. Source Code Biol Med (2009) 0.75
Genome sequence of the palaeopolyploid soybean. Nature (2010) 17.82
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
Operon prediction using both genome-specific and general genomic information. Nucleic Acids Res (2006) 4.41
Long-term monitoring shows hepatitis B virus resistance to entecavir in nucleoside-naïve patients is rare through 5 years of therapy. Hepatology (2009) 4.00
Enhanced computer vision with Microsoft Kinect sensor: a review. IEEE Trans Cybern (2013) 3.75
Slug antagonizes p53-mediated apoptosis of hematopoietic progenitors by repressing puma. Cell (2005) 3.73
DOOR: a database for prokaryotic operons. Nucleic Acids Res (2008) 3.50
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born. J Chem Theory Comput (2012) 3.40
Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res (2007) 3.40
Graph embedding and extensions: a general framework for dimensionality reduction. IEEE Trans Pattern Anal Mach Intell (2007) 3.06
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc Natl Acad Sci U S A (2003) 2.52
Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics (2006) 2.49
B lymphocyte stimulator overexpression in patients with systemic lupus erythematosus: longitudinal observations. Arthritis Rheum (2003) 2.47
An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J (2010) 2.41
Visualization of nitric oxide in living cells by a copper-based fluorescent probe. Nat Chem Biol (2006) 2.33
Local production of B lymphocyte stimulator protein and APRIL in arthritic joints of patients with inflammatory arthritis. Arthritis Rheum (2003) 2.21
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14
Prediction of functional modules based on comparative genome analysis and Gene Ontology application. Nucleic Acids Res (2005) 2.07
Understanding the unique characteristics of suicide in China: national psychological autopsy study. Biomed Environ Sci (2005) 1.90
Microarray analysis of chitin elicitation in Arabidopsis thaliana. Mol Plant Pathol (2002) 1.80
Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia. Epigenetics (2012) 1.80
Epidermal growth factor-like domain 7 protects endothelial cells from hyperoxia-induced cell death. Am J Physiol Lung Cell Mol Physiol (2007) 1.75
Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques (2004) 1.74
An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer. Nucleic Acids Res (2010) 1.73
Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res (2013) 1.72
Photoaffinity isolation and identification of proteins in cancer cell extracts that bind to platinum-modified DNA. Chembiochem (2009) 1.71
Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae. Nucleic Acids Res (2004) 1.71
Barcodes for genomes and applications. BMC Bioinformatics (2008) 1.70
Efficacy of entecavir in chronic hepatitis B patients with mildly elevated alanine aminotransferase and biopsy-proven histological damage. Hepatology (2010) 1.61
Long-term treatment with entecavir induces reversal of advanced fibrosis or cirrhosis in patients with chronic hepatitis B. Clin Gastroenterol Hepatol (2010) 1.60
Optimal mutation sites for PRE data collection and membrane protein structure prediction. Structure (2011) 1.55
Musite, a tool for global prediction of general and kinase-specific phosphorylation sites. Mol Cell Proteomics (2010) 1.55
Comparisons among two fertile and three male-sterile mitochondrial genomes of maize. Genetics (2007) 1.53
CUBIC: identification of regulatory binding sites through data clustering. J Bioinform Comput Biol (2003) 1.47
No supernovae associated with two long-duration gamma-ray bursts. Nature (2006) 1.47
catena-Poly[[bis(thiocyanato-kappa N)cadmium(II)]-di-mu-thiourea-kappa(4)S:S]. Acta Crystallogr C (2002) 1.45
SNP discovery by high-throughput sequencing in soybean. BMC Genomics (2010) 1.45
Comparative genomics analysis of NtcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis. Nucleic Acids Res (2005) 1.44
Preoperative rosuvastatin protects patients with coronary artery disease undergoing noncardiac surgery. Cardiology (2015) 1.43
Single feature polymorphism discovery in rice. PLoS One (2007) 1.42
MUFOLD: A new solution for protein 3D structure prediction. Proteins (2010) 1.42
SoyDB: a knowledge database of soybean transcription factors. BMC Plant Biol (2010) 1.40
Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations. J Am Chem Soc (2009) 1.40
Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics (2010) 1.39
PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands. Bioinformatics (2008) 1.35
Computational identification of protein methylation sites through bi-profile Bayes feature extraction. PLoS One (2009) 1.34
Mapping of orthologous genes in the context of biological pathways: An application of integer programming. Proc Natl Acad Sci U S A (2005) 1.33
BAFF overexpression and accelerated glomerular disease in mice with an incomplete genetic predisposition to systemic lupus erythematosus. Arthritis Rheum (2005) 1.33
P3DB: a plant protein phosphorylation database. Nucleic Acids Res (2008) 1.31
Legume transcription factor genes: what makes legumes so special? Plant Physiol (2009) 1.30
Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes. BMC Evol Biol (2004) 1.30
Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. BMC Genomics (2012) 1.29
Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress. J Bacteriol (2007) 1.29
Proteomic analysis of soybean root hairs after infection by Bradyrhizobium japonicum. Mol Plant Microbe Interact (2005) 1.27
Genomic and genetic evidence for the loss of umami taste in bats. Genome Biol Evol (2011) 1.27
Using Internet search engines to obtain medical information: a comparative study. J Med Internet Res (2012) 1.25
Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae. OMICS (2004) 1.25
Understanding protein dispensability through machine-learning analysis of high-throughput data. Bioinformatics (2004) 1.24
A protocol for computer-based protein structure and function prediction. J Vis Exp (2011) 1.23
Root hair systems biology. Trends Plant Sci (2010) 1.21
Genome-scale probe and primer design with PRIMEGENS. Methods Mol Biol (2007) 1.20
Mosaic: making biological sense of complex networks. Bioinformatics (2012) 1.19
A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sjögren's syndrome at 7q11.23. Nat Genet (2013) 1.19
Homolog-specific PCR primer design for profiling splice variants. Nucleic Acids Res (2011) 1.19
PROSPECT II: protein structure prediction program for genome-scale applications. Protein Eng (2003) 1.19
Visual event recognition in videos by learning from Web data. IEEE Trans Pattern Anal Mach Intell (2012) 1.18
An oligonucleotide microarray resource for transcriptional profiling of Bradyrhizobium japonicum. Mol Plant Microbe Interact (2007) 1.17
Contrast-enhanced whole-heart coronary MRA at 3.0T for the evaluation of cardiac venous anatomy. Int J Cardiovasc Imaging (2010) 1.17
Regulation of cellular oncosis by uncoupling protein 2. J Biol Chem (2002) 1.17
ProteinDBS: a real-time retrieval system for protein structure comparison. Nucleic Acids Res (2004) 1.17
Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing. Nucleic Acids Res (2011) 1.15
Identification of miRNA from Porphyra yezoensis by high-throughput sequencing and bioinformatics analysis. PLoS One (2010) 1.15
Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102. Nucleic Acids Res (2006) 1.14
Establishment of a protein reference map for soybean root hair cells. Plant Physiol (2008) 1.14
Computational prediction of Pho regulons in cyanobacteria. BMC Genomics (2007) 1.13
Automated Tongue Feature Extraction for ZHENG Classification in Traditional Chinese Medicine. Evid Based Complement Alternat Med (2012) 1.12
Improving the performance of DomainParser for structural domain partition using neural network. Nucleic Acids Res (2003) 1.12
Quantitative assessment of relationship between sequence similarity and function similarity. BMC Genomics (2007) 1.12
Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. Mol Plant Microbe Interact (2008) 1.11
Targeting oncogenic miR-335 inhibits growth and invasion of malignant astrocytoma cells. Mol Cancer (2011) 1.11
Multilinear discriminant analysis for face recognition. IEEE Trans Image Process (2007) 1.11
Clinical features and prognosis in adult-onset Still's disease: a study of 104 cases. Clin Rheumatol (2010) 1.08
Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding. Nucleic Acids Res (2013) 1.08
A computational method for assessing peptide- identification reliability in tandem mass spectrometry analysis with SEQUEST. Proteomics (2004) 1.08
Systems analysis of seed filling in Arabidopsis: using general linear modeling to assess concordance of transcript and protein expression. Plant Physiol (2010) 1.07
Computational analyses of high-throughput protein-protein interaction data. Curr Protein Pept Sci (2003) 1.07
Inhibition of MDR1 expression with altritol-modified siRNAs. Nucleic Acids Res (2007) 1.06
PDCD5 interacts with Tip60 and functions as a cooperator in acetyltransferase activity and DNA damage-induced apoptosis. Neoplasia (2009) 1.06
Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation-enriched bisulfite sequencing. PLoS One (2010) 1.06
Prediction of pathogenicity islands in enterohemorrhagic Escherichia coli O157:H7 using genomic barcodes. FEBS Lett (2010) 1.05
ThreaDom: extracting protein domain boundary information from multiple threading alignments. Bioinformatics (2013) 1.05
Identification of genes and pathways involved in kidney renal clear cell carcinoma. BMC Bioinformatics (2014) 1.05
Phylogenetic analysis using complete signature information of whole genomes and clustered Neighbour-Joining method. Int J Bioinform Res Appl (2006) 1.05
A link between SIN1 (MAPKAP1) and poly(rC) binding protein 2 (PCBP2) in counteracting environmental stress. Proc Natl Acad Sci U S A (2008) 1.04
Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea. BMC Genomics (2008) 1.04
Phosphoproteomic analysis of seed maturation in Arabidopsis, rapeseed, and soybean. Plant Physiol (2012) 1.04
Whole genome co-expression analysis of soybean cytochrome P450 genes identifies nodulation-specific P450 monooxygenases. BMC Plant Biol (2010) 1.04
Quantitative phosphoproteomic analysis of soybean root hairs inoculated with Bradyrhizobium japonicum. Mol Cell Proteomics (2012) 1.03
Domain adaptation from multiple sources: a domain-dependent regularization approach. IEEE Trans Neural Netw Learn Syst (2012) 1.03