Published in Nucleic Acids Res on December 22, 2008
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Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res (2001) 7.11
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Thermodynamics of RNA-RNA binding. Bioinformatics (2006) 3.10
Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays. Nucleic Acids Res (2004) 2.91
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PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. Bioinformatics (2002) 2.65
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Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics (2004) 1.93
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Physical principles and visual-OMP software for optimal PCR design. Methods Mol Biol (2007) 1.90
Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression. Nucleic Acids Res (2004) 1.87
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Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res (2005) 1.65
YODA: selecting signature oligonucleotides. Bioinformatics (2004) 1.59
OligoDesign: Optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling. Nucleic Acids Res (2003) 1.59
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Prioritized selection of oligodeoxyribonucleotide probes for efficient hybridization to RNA transcripts. Nucleic Acids Res (2003) 1.52
Independent component analysis of microarray data in the study of endometrial cancer. Oncogene (2004) 1.48
A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets. Nucleic Acids Res (2008) 1.47
Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics (2007) 1.45
GoArrays: highly dynamic and efficient microarray probe design. Bioinformatics (2004) 1.44
A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus. BMC Genomics (2005) 1.41
Oligodb--interactive design of oligo DNA for transcription profiling of human genes. Bioinformatics (2002) 1.36
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Secondary structure in the target as a confounding factor in synthetic oligomer microarray design. BMC Genomics (2005) 1.17
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A robust method for the amplification of RNA in the sense orientation. BMC Genomics (2005) 1.07
Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region. BMC Bioinformatics (2002) 0.99
Effects of target length on the hybridization efficiency and specificity of rRNA-based oligonucleotide microarrays. Appl Environ Microbiol (2006) 0.98
Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction. Nucleic Acids Res (2008) 0.96
Fast and sensitive probe selection for DNA chips using jumps in matching statistics. Proc IEEE Comput Soc Bioinform Conf (2003) 0.95
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Importance of probe location for quantitative comparison of signal intensities among genes in microarray analysis. J Biochem Biophys Methods (2008) 0.77
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (2007) 18.59
ViennaRNA Package 2.0. Algorithms Mol Biol (2011) 9.43
The Vienna RNA websuite. Nucleic Acids Res (2008) 9.02
Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A (2005) 8.15
Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genet (2005) 5.48
Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat Biotechnol (2005) 4.68
Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol (2007) 4.28
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res (2006) 3.59
RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics (2008) 3.29
Thermodynamics of RNA-RNA binding. Bioinformatics (2006) 3.10
Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr Biol (2004) 2.88
The expansion of the metazoan microRNA repertoire. BMC Genomics (2006) 2.80
A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Nat Genet (2008) 2.74
Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol Biol (2006) 2.74
Structured RNAs in the ENCODE selected regions of the human genome. Genome Res (2007) 2.69
The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol (2008) 2.51
Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J Mol Biol (2004) 2.49
Local RNA base pairing probabilities in large sequences. Bioinformatics (2005) 2.17
Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis. Nucleic Acids Res (2008) 2.10
Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling. Bioinformatics (2011) 2.00
Variations on RNA folding and alignment: lessons from Benasque. J Math Biol (2007) 1.91
The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures. Nucleic Acids Res (2007) 1.88
RNAz 2.0: improved noncoding RNA detection. Pac Symp Biocomput (2010) 1.87
Determining a significant change in protein expression with DeCyder during a pair-wise comparison using two-dimensional difference gel electrophoresis. Proteomics (2004) 1.82
Conserved RNA secondary structures in Flaviviridae genomes. J Gen Virol (2004) 1.81
RNAplex: a fast tool for RNA-RNA interaction search. Bioinformatics (2008) 1.80
B7-H3 is a potent inhibitor of human T-cell activation: No evidence for B7-H3 and TREML2 interaction. Eur J Immunol (2009) 1.71
AREsite: a database for the comprehensive investigation of AU-rich elements. Nucleic Acids Res (2010) 1.58
SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics (2007) 1.51
LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. RNA (2012) 1.51
Evolutionary patterns of non-coding RNAs. Theory Biosci (2005) 1.49
Independent component analysis of microarray data in the study of endometrial cancer. Oncogene (2004) 1.48
Visualization of barrier tree sequences. IEEE Trans Vis Comput Graph (2006) 1.45
RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA (2011) 1.42
The transcriptome of syncytia induced by the cyst nematode Heterodera schachtii in Arabidopsis roots. Plant J (2008) 1.41
Expansins are involved in the formation of nematode-induced syncytia in roots of Arabidopsis thaliana. Plant J (2006) 1.38
RNAs everywhere: genome-wide annotation of structured RNAs. J Exp Zool B Mol Dev Evol (2007) 1.38
Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays. BMC Genomics (2008) 1.36
RNA-directed DNA methylation and plant development require an IWR1-type transcription factor. EMBO Rep (2009) 1.32
De novo prediction of structured RNAs from genomic sequences. Trends Biotechnol (2009) 1.31
RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction. Nucleic Acids Res (2012) 1.27
RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Res (2011) 1.25
Physico-chemical foundations underpinning microarray and next-generation sequencing experiments. Nucleic Acids Res (2013) 1.25
Strategies for measuring evolutionary conservation of RNA secondary structures. BMC Bioinformatics (2008) 1.21
Effects of aneuploidy on genome structure, expression, and interphase organization in Arabidopsis thaliana. PLoS Genet (2008) 1.19
Tuning the transcription rate of recombinant protein in strong Escherichia coli expression systems through repressor titration. Biotechnol Prog (2003) 1.19
RNPomics: defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles. Nucleic Acids Res (2010) 1.13
Transcriptomic characterization of two major Fusarium resistance quantitative trait loci (QTLs), Fhb1 and Qfhs.ifa-5A, identifies novel candidate genes. Mol Plant Pathol (2013) 1.12
Development of an antibiotic-free plasmid selection system based on glycine auxotrophy for recombinant protein overproduction in Escherichia coli. J Biotechnol (2008) 1.12
Multiple sequence alignments of partially coding nucleic acid sequences. BMC Bioinformatics (2005) 1.11
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. BMC Bioinformatics (2006) 1.10
A systematic comparison of spectral-domain optical coherence tomography and fundus autofluorescence in patients with geographic atrophy. Ophthalmology (2011) 1.09
N(pro) fusion technology to produce proteins with authentic N termini in E. coli. Nat Methods (2007) 1.09
Fast accessibility-based prediction of RNA-RNA interactions. Bioinformatics (2011) 1.09
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Arthropod 7SK RNA. Mol Biol Evol (2008) 1.04
RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs. Hum Mutat (2013) 1.03
A folding algorithm for extended RNA secondary structures. Bioinformatics (2011) 1.03
Robotic spotting of cDNA and oligonucleotide microarrays. Trends Biotechnol (2005) 1.02
The response to unfolded protein is involved in osmotolerance of Pichia pastoris. BMC Genomics (2010) 1.02
RNAsnoop: efficient target prediction for H/ACA snoRNAs. Bioinformatics (2009) 1.01
Prediction of consensus RNA secondary structures including pseudoknots. IEEE/ACM Trans Comput Biol Bioinform (2006) 1.01
Myo-inositol oxygenase genes are involved in the development of syncytia induced by Heterodera schachtii in Arabidopsis roots. New Phytol (2009) 1.01
Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. J Biotechnol (2011) 1.01
The RNAsnp web server: predicting SNP effects on local RNA secondary structure. Nucleic Acids Res (2013) 1.00
From structure prediction to genomic screens for novel non-coding RNAs. PLoS Comput Biol (2011) 0.99
Monitoring of transcriptome and proteome profiles to investigate the cellular response of E. coli towards recombinant protein expression under defined chemostat conditions. J Biotechnol (2008) 0.98
Evaluation of the GFP signal and its aptitude for novel on-line monitoring strategies of recombinant fermentation processes. J Biotechnol (2004) 0.96
Hybridization thermodynamics of NimbleGen microarrays. BMC Bioinformatics (2010) 0.96
Improvement of bioprocess monitoring: development of novel concepts. Microb Cell Fact (2006) 0.96
GMI1, a structural-maintenance-of-chromosomes-hinge domain-containing protein, is involved in somatic homologous recombination in Arabidopsis. Plant J (2011) 0.96
Plasmid-free T7-based Escherichia coli expression systems. Biotechnol Bioeng (2010) 0.96
How microRNAs choose their targets. Nat Genet (2007) 0.95
Bcheck: a wrapper tool for detecting RNase P RNA genes. BMC Genomics (2010) 0.95
TSSAR: TSS annotation regime for dRNA-seq data. BMC Bioinformatics (2014) 0.94
Impact of targeted vector design on Co/E1 plasmid replication. Trends Biotechnol (2002) 0.94
Soft sensors in bioprocessing: a status report and recommendations. Biotechnol J (2012) 0.94
From consensus structure prediction to RNA gene finding. Brief Funct Genomic Proteomic (2009) 0.94
Stabilizing plasmid copy number to improve recombinant protein production. Biotechnol Bioeng (2002) 0.92
Evaluation of three industrial Escherichia coli strains in fed-batch cultivations during high-level SOD protein production. Microb Cell Fact (2013) 0.92
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Invertebrate 7SK snRNAs. J Mol Evol (2008) 0.91
Comparative transcription profiling and in-depth characterization of plasmid-based and plasmid-free Escherichia coli expression systems under production conditions. Appl Environ Microbiol (2013) 0.90
Cognitive tasks for driving a brain-computer interfacing system: a pilot study. IEEE Trans Neural Syst Rehabil Eng (2004) 0.89
RNA Accessibility in cubic time. Algorithms Mol Biol (2011) 0.88
Computational design of RNAs with complex energy landscapes. Biopolymers (2013) 0.88
The impact of quantitative optimization of hybridization conditions on gene expression analysis. BMC Bioinformatics (2011) 0.87
BibGlimpse: the case for a light-weight reprint manager in distributed literature research. BMC Bioinformatics (2008) 0.86
Detection of RNA structures in porcine EST data and related mammals. BMC Genomics (2007) 0.86
Process analytical technology (PAT) for biopharmaceuticals. Biotechnol J (2011) 0.86
Overexpression of the transcription factor RAP2.6 leads to enhanced callose deposition in syncytia and enhanced resistance against the beet cyst nematode Heterodera schachtii in Arabidopsis roots. BMC Plant Biol (2013) 0.85
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