Published in BMC Genomics on July 07, 2009
The word landscape of the non-coding segments of the Arabidopsis thaliana genome. BMC Genomics (2009) 0.98
High-throughput next-generation sequencing technologies foster new cutting-edge computing techniques in bioinformatics. BMC Genomics (2009) 0.81
WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures. BMC Bioinformatics (2010) 0.77
The human genome browser at UCSC. Genome Res (2002) 168.23
Clustal W and Clustal X version 2.0. Bioinformatics (2007) 126.47
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
The generic genome browser: a building block for a model organism system database. Genome Res (2002) 42.64
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60
Reactome: a knowledgebase of biological pathways. Nucleic Acids Res (2005) 20.05
TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res (2000) 15.70
MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res (2006) 15.32
Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol (1998) 13.99
Divergent transcription from active promoters. Science (2008) 11.03
Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet (2004) 9.96
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res (2007) 8.79
TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics (2002) 8.45
Human-mouse genome comparisons to locate regulatory sites. Nat Genet (2000) 8.08
Dinucleotide relative abundance extremes: a genomic signature. Trends Genet (1995) 6.32
Identification of regulatory regions which confer muscle-specific gene expression. J Mol Biol (1998) 6.13
Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol (1997) 4.85
Comparative DNA analysis across diverse genomes. Annu Rev Genet (1998) 3.67
Bidirectional gene organization: a common architectural feature of the human genome. Cell (2002) 3.47
Comparative genomic structure of prokaryotes. Annu Rev Genet (2004) 3.34
Genomic signature: characterization and classification of species assessed by chaos game representation of sequences. Mol Biol Evol (1999) 3.33
Global dinucleotide signatures and analysis of genomic heterogeneity. Curr Opin Microbiol (1998) 3.09
Chaos game representation of gene structure. Nucleic Acids Res (1990) 2.91
P-Match: transcription factor binding site search by combining patterns and weight matrices. Nucleic Acids Res (2005) 2.87
Informatics for unveiling hidden genome signatures. Genome Res (2003) 2.60
Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics (2004) 2.51
Discovery and modeling of transcriptional regulatory regions. Curr Opin Biotechnol (2000) 2.41
Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. Proc Natl Acad Sci U S A (1999) 2.38
Genome-scale compositional comparisons in eukaryotes. Genome Res (2001) 2.32
Absent sequences: nullomers and primes. Pac Symp Biocomput (2007) 2.07
Efficient computation of absent words in genomic sequences. BMC Bioinformatics (2008) 1.91
Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes. PLoS Comput Biol (2007) 1.69
The Z curve database: a graphic representation of genome sequences. Bioinformatics (2003) 1.31
Codon bias signatures, organization of microorganisms in codon space, and lifestyle. Mol Biol Evol (2004) 1.24
Analysis of the compositional biases in Plasmodium falciparum genome and proteome using Arabidopsis thaliana as a reference. Gene (2004) 1.03
Determination of bias in the relative abundance of oligonucleotides in DNA sequences. J Comput Biol (2001) 0.95
GENSTYLE: exploration and analysis of DNA sequences with genomic signature. Nucleic Acids Res (2005) 0.93
Dinucleotide compositional analysis of Sinorhizobium meliloti using the genome signature: distinguishing chromosomes and plasmids. Funct Integr Genomics (2002) 0.92
Genome comparisons and analysis. Curr Opin Struct Biol (2003) 0.86
A novel bioinformatic strategy for unveiling hidden genome signatures of eukaryotes: self-organizing map of oligonucleotide frequency. Genome Inform (2002) 0.83
A genome signature based on markov modeling. Conf Proc IEEE Eng Med Biol Soc (2005) 0.77
Finding Occurrences of Relevant Functional Elements in Genomic Signatures. Int J Comput Sci (2008) 0.76
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Galaxy: a platform for interactive large-scale genome analysis. Genome Res (2005) 35.75
Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res (2004) 24.52
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res (2003) 11.12
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Res (2005) 7.09
MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res (2003) 4.97
Cross-species sequence comparisons: a review of methods and available resources. Genome Res (2003) 3.90
Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat. Genome Res (2004) 3.53
GALA, a database for genomic sequence alignments and annotations. Genome Res (2003) 2.56
Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners. BMC Genomics (2008) 2.50
A cognitive task analysis of information management strategies in a computerized provider order entry environment. J Am Med Inform Assoc (2006) 2.02
AGRIS: the Arabidopsis Gene Regulatory Information Server, an update. Nucleic Acids Res (2010) 1.95
Generation and comparative analysis of approximately 3.3 Mb of mouse genomic sequence orthologous to the region of human chromosome 7q11.23 implicated in Williams syndrome. Genome Res (2002) 1.80
PhenCode: connecting ENCODE data with mutations and phenotype. Hum Mutat (2007) 1.75
A bioinformatics approach to the identification, classification, and analysis of hydroxyproline-rich glycoproteins. Plant Physiol (2010) 1.64
BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features. BMC Syst Biol (2010) 1.53
A comparative study of different machine learning methods on microarray gene expression data. BMC Genomics (2008) 1.46
Genomic features defining exonic variants that modulate splicing. Genome Biol (2010) 1.46
Evaluation of graphic cardiovascular display in a high-fidelity simulator. Anesth Analg (2003) 1.36
Multispecies comparative analysis of a mammalian-specific genomic domain encoding secretory proteins. Genomics (2003) 1.29
Molecular determinants of NOTCH4 transcription in vascular endothelium. Mol Cell Biol (2005) 1.27
Epinome - a novel workbench for epidemic investigation and analysis of search strategies in public health practice. AMIA Annu Symp Proc (2010) 1.21
Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus. Genome Res (2008) 1.21
Prediction of DNA-binding residues from protein sequence information using random forests. BMC Genomics (2009) 1.16
The employment of an iterative design process to develop a pulmonary graphical display. J Am Med Inform Assoc (2003) 1.13
Comparative analyses of bidirectional promoters in vertebrates. BMC Bioinformatics (2008) 1.10
TaASR1, a transcription factor gene in wheat, confers drought stress tolerance in transgenic tobacco. Plant Cell Environ (2013) 1.09
Gene regulation mediated by microRNAs in response to green tea polyphenol EGCG in mouse lung cancer. BMC Genomics (2014) 1.08
Selecting subsets of newly extracted features from PCA and PLS in microarray data analysis. BMC Genomics (2008) 1.04
Tissue-specific and ubiquitous expression patterns from alternative promoters of human genes. PLoS One (2010) 1.04
MicroRNA and messenger RNA profiling reveals new biomarkers and mechanisms for RDX induced neurotoxicity. BMC Genomics (2014) 1.02
3D protein structure prediction with genetic tabu search algorithm. BMC Syst Biol (2010) 1.00
Comparison of feature selection and classification for MALDI-MS data. BMC Genomics (2009) 0.99
Dimension reduction with redundant gene elimination for tumor classification. BMC Bioinformatics (2008) 0.99
The word landscape of the non-coding segments of the Arabidopsis thaliana genome. BMC Genomics (2009) 0.98
Investigation of transmembrane proteins using a computational approach. BMC Genomics (2008) 0.98
The evaluation of a pulmonary display to detect adverse respiratory events using high resolution human simulator. J Am Med Inform Assoc (2006) 0.95
BLT1-dependent alveolar recruitment of CD4(+)CD25(+) Foxp3(+) regulatory T cells is important for resolution of acute lung injury. Am J Respir Crit Care Med (2012) 0.93
Analyzing adjuvant radiotherapy suggests a non monotonic radio-sensitivity over tumor volumes. BMC Genomics (2008) 0.93
Asymmetric bagging and feature selection for activities prediction of drug molecules. BMC Bioinformatics (2008) 0.91
Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts. BMC Genomics (2009) 0.91
Supervised learning-based tagSNP selection for genome-wide disease classifications. BMC Genomics (2008) 0.90
Promoting synergistic research and education in genomics and bioinformatics. BMC Genomics (2008) 0.89
Induction of innate immunity by lipid A mimetics increases survival from pneumonic plague. Microbiology (2008) 0.89
Lipid A mimetics are potent adjuvants for an intranasal pneumonic plague vaccine. Vaccine (2008) 0.89
Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors. Nucleic Acids Res (2013) 0.89
Differential analysis of ovarian and endometrial cancers identifies a methylator phenotype. PLoS One (2012) 0.88
Bidirectional promoters as important drivers for the emergence of species-specific transcripts. PLoS One (2013) 0.88
Orthology-driven mapping of bidirectional promoters in human and mouse genomes. BMC Bioinformatics (2014) 0.87
Multi-species sequence comparison reveals dynamic evolution of the elastin gene that has involved purifying selection and lineage-specific insertions/deletions. BMC Genomics (2004) 0.86
Functional analysis of synonymous substitutions predicted to affect splicing of the CFTR gene. J Cyst Fibros (2012) 0.85
Supervised learning method for the prediction of subcellular localization of proteins using amino acid and amino acid pair composition. BMC Genomics (2008) 0.84
Improving prediction accuracy of tumor classification by reusing genes discarded during gene selection. BMC Genomics (2008) 0.84
The crosstalk hypothesis: why language interferes with driving. J Exp Psychol Gen (2012) 0.84
Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research. BMC Genomics (2008) 0.83
A hybrid machine learning-based method for classifying the Cushing's Syndrome with comorbid adrenocortical lesions. BMC Genomics (2008) 0.83
Male bovine GH transgenic mice have decreased adiposity with an adipose depot-specific increase in immune cell populations. Endocrinology (2014) 0.82
Differential expression of human telomerase catalytic subunit mRNA by in situ hybridization in pheochromocytomas. Endocr Pathol (2006) 0.82
Interactive agent based modeling of public health decision-making. AMIA Annu Symp Proc (2009) 0.79
Genome-wide detection of a TFIID localization element from an initial human disease mutation. Nucleic Acids Res (2010) 0.79
Engineered epidermal growth factor mutants with faster binding on-rates correlate with enhanced receptor activation. FEBS Lett (2011) 0.79
WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures. BMC Bioinformatics (2010) 0.77
Improved diagnostic performance of a commercial Anaplasma antibody competitive enzyme-linked immunosorbent assay using recombinant major surface protein 5-glutathione S-transferase fusion protein as antigen. J Vet Diagn Invest (2013) 0.77
ILOOP--a web application for two-channel microarray interwoven loop design. BMC Genomics (2008) 0.77
Predicting protein disorder by analyzing amino acid sequence. BMC Genomics (2008) 0.77
Finding Occurrences of Relevant Functional Elements in Genomic Signatures. Int J Comput Sci (2008) 0.76
Identification of Intrinsically Unstructured Proteins using hierarchical classifier. Int J Data Min Bioinform (2008) 0.76
Functional analysis of a novel cis-acting regulatory region within the human ankyrin gene (ANK-1) promoter. Mol Cell Biol (2010) 0.76
A family with X-linked anophthalmia: exclusion of SOX3 as a candidate gene. Am J Med Genet A (2005) 0.76
Unique alterations of an ultraconserved non-coding element in the 3'UTR of ZIC2 in holoprosencephaly. PLoS One (2012) 0.75
Proteome analysis of the plant-pathogenic bacterium Xanthomonas oryzae pv. oryzae. Biochim Biophys Acta (2013) 0.75
The emerging genomics and systems biology research lead to systems genomics studies. BMC Genomics (2014) 0.75
Feature selection for the imbalanced QSAR problems by using easyensemble. Int J Comput Biol Drug Des (2008) 0.75
Fabrication of high stable metal oxide hollow nanospheres and their catalytic activity towards 4-nitrophenol reduction. ACS Appl Mater Interfaces (2017) 0.75
Improving prediction accuracy of drug activities by utilising unlabelled instances with feature selection. Int J Comput Biol Drug Des (2008) 0.75
Discovering Gene Regulatory Elements Using Coverage-based Heuristics. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.75
2009 and beyond: the decade of personalised medicine. Int J Comput Biol Drug Des (2008) 0.75
Immunotherapy of HPV infection-caused genital warts using low dose cyclophosphamide. Expert Rev Clin Immunol (2014) 0.75
Irrelevant gene elimination for partial least squares based dimension reduction by using feature probes. Int J Data Min Bioinform (2009) 0.75
The potential global market size and public health value of an HIV-1 vaccine in a complex global market. Vaccine (2010) 0.75