Published in Bioinformatics on January 01, 2003
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
Recent evolutions of multiple sequence alignment algorithms. PLoS Comput Biol (2007) 4.88
Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics (2009) 2.64
3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment. Nucleic Acids Res (2004) 2.50
Quality measures for protein alignment benchmarks. Nucleic Acids Res (2010) 2.23
Automatic assessment of alignment quality. Nucleic Acids Res (2005) 1.97
MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Res (2006) 1.85
A statistical score for assessing the quality of multiple sequence alignments. BMC Bioinformatics (2006) 0.98
Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words. PLoS One (2011) 0.76
IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments. Evol Bioinform Online (2015) 0.75
The PROSITE database, its status in 2002. Nucleic Acids Res (2002) 14.71
Recent improvements to the PROSITE database. Nucleic Acids Res (2004) 11.89
PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform (2002) 8.77
3DCoffee: combining protein sequences and structures within multiple sequence alignments. J Mol Biol (2004) 6.01
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39
Numerous potentially functional but non-genic conserved sequences on human chromosome 21. Nature (2002) 5.38
Long-range heterogeneity at the 3' ends of human mRNAs. Genome Res (2002) 3.91
High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat Biotechnol (2002) 3.04
R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res (2008) 2.69
EPD in its twentieth year: towards complete promoter coverage of selected model organisms. Nucleic Acids Res (2006) 2.49
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. Nucleic Acids Res (2004) 2.47
KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading. PLoS Genet (2010) 2.44
Multireplicon genome architecture of Lactobacillus salivarius. Proc Natl Acad Sci U S A (2006) 2.43
The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. Nucleic Acids Res (2002) 2.30
Classification of human astrocytic gliomas on the basis of gene expression: a correlated group of genes with angiogenic activity emerges as a strong predictor of subtypes. Cancer Res (2003) 2.15
A human homolog of yeast Est1 associates with telomerase and uncaps chromosome ends when overexpressed. Curr Biol (2003) 2.14
CaspR: a web server for automated molecular replacement using homology modelling. Nucleic Acids Res (2004) 1.91
Indexing strategies for rapid searches of short words in genome sequences. PLoS One (2007) 1.85
Nineteen additional unpredicted transcripts from human chromosome 21. Genomics (2002) 1.80
ChIP-Seq data reveal nucleosome architecture of human promoters. Cell (2007) 1.74
CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature. Nucleic Acids Res (2004) 1.73
Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets. J Struct Funct Genomics (2003) 1.70
trome, trEST and trGEN: databases of predicted protein sequences. Nucleic Acids Res (2004) 1.65
Peroxisome proliferator-activated receptor structures: ligand specificity, molecular switch and interactions with regulators. Biochim Biophys Acta (2007) 1.50
Telomere maintenance in fission yeast requires an Est1 ortholog. Curr Biol (2003) 1.30
PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments. Nucleic Acids Res (2006) 1.29
Genome-wide prediction of matrix attachment regions that increase gene expression in mammalian cells. Nat Methods (2007) 1.21
UCNEbase--a database of ultraconserved non-coding elements and genomic regulatory blocks. Nucleic Acids Res (2012) 1.20
EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era. Nucleic Acids Res (2012) 1.17
ZFN-site searches genomes for zinc finger nuclease target sites and off-target sites. BMC Bioinformatics (2011) 1.16
MER41 repeat sequences contain inducible STAT1 binding sites. PLoS One (2010) 1.15
Signal search analysis server. Nucleic Acids Res (2003) 1.11
HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sites. Nucleic Acids Res (2006) 1.08
R-Coffee: a web server for accurately aligning noncoding RNA sequences. Nucleic Acids Res (2008) 1.07
Similarities and differences of polyadenylation signals in human and fly. BMC Genomics (2006) 1.06
Can survival prediction be improved by merging gene expression data sets? PLoS One (2009) 1.04
Nuclear factor I revealed as family of promoter binding transcription activators. BMC Genomics (2011) 1.04
Structural and functional interaction sites between Na,K-ATPase and FXYD proteins. J Biol Chem (2004) 1.03
Long distance control of MHC class II expression by multiple distal enhancers regulated by regulatory factor X complex and CIITA. J Immunol (2004) 1.01
Stealth proteins: in silico identification of a novel protein family rendering bacterial pathogens invisible to host immune defense. PLoS Comput Biol (2005) 1.01
BlastR--fast and accurate database searches for non-coding RNAs. Nucleic Acids Res (2011) 0.98
The transcription factor Rfx3 regulates beta-cell differentiation, function, and glucokinase expression. Diabetes (2010) 0.96
ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries. PLoS One (2012) 0.96
A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing. BMC Genomics (2011) 0.96
RNA profiling and chromatin immunoprecipitation-sequencing reveal that PTF1a stabilizes pancreas progenitor identity via the control of MNX1/HLXB9 and a network of other transcription factors. Mol Cell Biol (2012) 0.94
Identification of CIITA regulated genetic module dedicated for antigen presentation. PLoS Genet (2008) 0.91
Practicality and time complexity of a sparsified RNA folding algorithm. J Bioinform Comput Biol (2012) 0.90
Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time. BMC Genomics (2007) 0.90
Identification of evolutionarily conserved regulatory elements in the mouse Fgf8 locus. Genesis (2006) 0.89
Nucleosome eviction from MHC class II promoters controls positioning of the transcription start site. Nucleic Acids Res (2009) 0.84
Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements. Bioinformatics (2012) 0.83
CleanEx: new data extraction and merging tools based on MeSH term annotation. Nucleic Acids Res (2009) 0.81
Promoter rearrangements cause species-specific hepatic regulation of the glyoxylate reductase/hydroxypyruvate reductase gene by the peroxisome proliferator-activated receptor alpha. J Biol Chem (2005) 0.81
Nuclear Factor I genomic binding associates with chromatin boundaries. BMC Genomics (2013) 0.80
Proof of concept for microarray-based detection of DNA-binding oncogenes in cell extracts. Nucleic Acids Res (2005) 0.80
Use of ChIP-Seq data for the design of a multiple promoter-alignment method. Nucleic Acids Res (2012) 0.79
MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data. Nucleic Acids Res (2007) 0.78
Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words. PLoS One (2011) 0.76
Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge. Bioinformatics (2005) 0.75