Published in Nucleic Acids Res on May 15, 2008
PicXAA-R: efficient structural alignment of multiple RNA sequences using a greedy approach. BMC Bioinformatics (2011) 1.46
DSAP: deep-sequencing small RNA analysis pipeline. Nucleic Acids Res (2010) 1.41
Tfold: efficient in silico prediction of non-coding RNA secondary structures. Nucleic Acids Res (2010) 0.97
Characterization of a novel insect-specific flavivirus from Brazil: potential for inhibition of infection of arthropod cells with medically important flaviviruses. J Gen Virol (2014) 0.95
Gain and loss of an intron in a protein-coding gene in Archaea: the case of an archaeal RNA pseudouridine synthase gene. BMC Evol Biol (2009) 0.89
Accelerated evolution of mitochondrial but not nuclear genomes of Hymenoptera: new evidence from crabronid wasps. PLoS One (2012) 0.89
Extensive diversity of Rickettsiales bacteria in two species of ticks from China and the evolution of the Rickettsiales. BMC Evol Biol (2014) 0.87
Against expectation: a short sequence with high signal elucidates cone snail phylogeny. Mol Phylogenet Evol (2010) 0.86
Elements in the canine distemper virus M 3' UTR contribute to control of replication efficiency and virulence. PLoS One (2012) 0.84
Progress and Current Challenges in Modeling Large RNAs. J Mol Biol (2015) 0.83
Informatic resources for identifying and annotating structural RNA motifs. Mol Biotechnol (2008) 0.80
A very short, functionally constrained sequence diagnoses cone snails in several Conasprella clades. Mol Phylogenet Evol (2012) 0.79
In silico analysis of combinatorial microRNA activity reveals target genes and pathways associated with breast cancer metastasis. Cancer Inform (2011) 0.79
Solving nucleic acid structures by molecular replacement: examples from group II intron studies. Acta Crystallogr D Biol Crystallogr (2013) 0.78
IRBIS: a systematic search for conserved complementarity. RNA (2014) 0.76
All 37 Mitochondrial Genes of Aphid Aphis craccivora Obtained from Transcriptome Sequencing: Implications for the Evolution of Aphids. PLoS One (2016) 0.75
CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs. Int J Mol Sci (2013) 0.75
Application of RNA-seq for mitogenome reconstruction, and reconsideration of long-branch artifacts in Hemiptera phylogeny. Sci Rep (2016) 0.75
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol (1970) 155.96
Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res (2003) 77.89
T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol (2000) 57.88
MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res (2005) 31.64
Vienna RNA secondary structure server. Nucleic Acids Res (2003) 19.69
ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res (2005) 11.90
Secondary structure prediction for aligned RNA sequences. J Mol Biol (2002) 8.80
Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Res (2006) 6.59
Recent evolutions of multiple sequence alignment algorithms. PLoS Comput Biol (2007) 4.88
M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res (2006) 4.53
Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol (2007) 4.28
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Res (2006) 3.76
A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res (2005) 2.89
R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res (2008) 2.69
Alignment of RNA base pairing probability matrices. Bioinformatics (2004) 2.42
An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol Biol (2006) 2.35
Local RNA base pairing probabilities in large sequences. Bioinformatics (2005) 2.17
Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics (2006) 2.08
Multiple structural alignment and clustering of RNA sequences. Bioinformatics (2007) 1.98
STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time. Bioinformatics (2006) 1.46
Murlet: a practical multiple alignment tool for structural RNA sequences. Bioinformatics (2007) 1.41
RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences. Mol Phylogenet Evol (2003) 1.38
RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment. Bioinformatics (2007) 1.32
A practical guide to the art of RNA gene prediction. Brief Bioinform (2007) 1.21
Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res (2003) 38.75
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol (2011) 28.61
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics (2002) 8.11
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol (2007) 8.03
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
The UniProt-GO Annotation database in 2011. Nucleic Acids Res (2011) 5.19
Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics (2008) 5.00
APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. Bioinformatics (2003) 4.88
Toward interoperable bioscience data. Nat Genet (2012) 4.72
M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res (2006) 4.53
New and continuing developments at PROSITE. Nucleic Acids Res (2012) 4.41
Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell (2002) 4.38
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Res (2011) 4.00
ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res (2012) 3.70
Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. BMC Bioinformatics (2006) 3.31
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods (2012) 3.17
Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma. Nat Genet (2011) 3.10
A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res (2005) 2.89
Rhea--a manually curated resource of biochemical reactions. Nucleic Acids Res (2011) 2.87
Describing biological protein interactions in terms of protein states and state transitions: the LiveDIP database. Mol Cell Proteomics (2002) 2.76
The genome of the fire ant Solenopsis invicta. Proc Natl Acad Sci U S A (2011) 2.74
The Microbe browser for comparative genomics. Nucleic Acids Res (2009) 2.71
Between-group analysis of microarray data. Bioinformatics (2002) 2.71
R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res (2008) 2.69
MADE4: an R package for multivariate analysis of gene expression data. Bioinformatics (2005) 2.66
UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res (2011) 2.45
Analysis and comparison of benchmarks for multiple sequence alignment. In Silico Biol (2006) 2.33
HAMAP in 2013, new developments in the protein family classification and annotation system. Nucleic Acids Res (2012) 2.16
Sequence embedding for fast construction of guide trees for multiple sequence alignment. Algorithms Mol Biol (2010) 2.15
A method for the generation of standardized qualitative dynamical systems of regulatory networks. Theor Biol Med Model (2006) 2.14
Clustal Omega, accurate alignment of very large numbers of sequences. Methods Mol Biol (2014) 2.11
Multiple sequence alignments. Curr Opin Struct Biol (2005) 2.05
Cross-platform comparison and visualisation of gene expression data using co-inertia analysis. BMC Bioinformatics (2003) 1.93
CaspR: a web server for automated molecular replacement using homology modelling. Nucleic Acids Res (2004) 1.91
Guidelines for reporting the use of mass spectrometry in proteomics. Nat Biotechnol (2008) 1.90
Proteomic analysis of the mouse liver mitochondrial inner membrane. J Biol Chem (2003) 1.86
Synchronous versus asynchronous modeling of gene regulatory networks. Bioinformatics (2008) 1.85
The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Nucleic Acids Res (2007) 1.84
Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling. Plant J (2012) 1.84
Dynamic simulation of regulatory networks using SQUAD. BMC Bioinformatics (2007) 1.75
Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets. J Struct Funct Genomics (2003) 1.70
ViralZone: a knowledge resource to understand virus diversity. Nucleic Acids Res (2010) 1.66
FastEpistasis: a high performance computing solution for quantitative trait epistasis. Bioinformatics (2010) 1.58
Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival. PLoS One (2009) 1.55
STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time. Bioinformatics (2006) 1.46
Co-regulation of Gremlin and Notch signalling in diabetic nephropathy. Biochim Biophys Acta (2007) 1.44
A multivariate analysis approach to the integration of proteomic and gene expression data. Proteomics (2007) 1.39
Temporal change in gene expression in the rat dentate gyrus following passive avoidance learning. J Neurochem (2007) 1.37
A randomized, double-blind placebo controlled trial of balapiravir, a polymerase inhibitor, in adult dengue patients. J Infect Dis (2012) 1.37
CDK9 regulates AR promoter selectivity and cell growth through serine 81 phosphorylation. Mol Endocrinol (2010) 1.35
Altered cytoplasmic-to-nuclear ratio of survivin is a prognostic indicator in breast cancer. Clin Cancer Res (2008) 1.34
Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses. Mol Cell Proteomics (2007) 1.31
Influence of acute phytochemical intake on human urinary metabolomic profiles. Am J Clin Nutr (2007) 1.29
Structural and functional properties of genes involved in human cancer. BMC Genomics (2006) 1.29
PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments. Nucleic Acids Res (2006) 1.29
GWIPS-viz: development of a ribo-seq genome browser. Nucleic Acids Res (2013) 1.28
MIMAS 3.0 is a Multiomics Information Management and Annotation System. BMC Bioinformatics (2009) 1.24
Evolutionary trajectories of primate genes involved in HIV pathogenesis. Mol Biol Evol (2009) 1.23
OpenFluDB, a database for human and animal influenza virus. Database (Oxford) (2010) 1.20
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst Biol (2013) 1.20
CENP-F expression is associated with poor prognosis and chromosomal instability in patients with primary breast cancer. Int J Cancer (2007) 1.17
ENFIN--A European network for integrative systems biology. C R Biol (2009) 1.17
Database resources for the tuberculosis community. Tuberculosis (Edinb) (2013) 1.16
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. Brief Bioinform (2011) 1.15
Reconciliation of metabolites and biochemical reactions for metabolic networks. Brief Bioinform (2012) 1.14
Evaluation of iterative alignment algorithms for multiple alignment. Bioinformatics (2004) 1.14
The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data. Toxicon (2012) 1.12
Regulation of the hypoxic response in Candida albicans. Eukaryot Cell (2010) 1.11
Making automated multiple alignments of very large numbers of protein sequences. Bioinformatics (2013) 1.11
Integrating transcription factor binding site information with gene expression datasets. Bioinformatics (2006) 1.10
Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis. BMC Genomics (2011) 1.10
Application of DNA microarray technology in determining breast cancer prognosis and therapeutic response. Expert Opin Biol Ther (2005) 1.10
Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma. PLoS One (2011) 1.09
Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences. PLoS One (2013) 1.09
Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays. Genome Biol (2010) 1.08
The copper regulon of the human fungal pathogen Cryptococcus neoformans H99. Mol Microbiol (2011) 1.08
Identification of novel inter-genotypic recombinants of human hepatitis B viruses by large-scale phylogenetic analysis. Virology (2012) 1.08
Correlation between biofilm formation and the hypoxic response in Candida parapsilosis. Eukaryot Cell (2009) 1.06
miR-187 is an independent prognostic factor in breast cancer and confers increased invasive potential in vitro. Clin Cancer Res (2012) 1.04
Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model. Bioinformatics (2013) 1.02
Hepatitis B virus subgenotyping: history, effects of recombination, misclassifications, and corrections. Infect Genet Evol (2013) 1.01
Supervised multivariate analysis of sequence groups to identify specificity determining residues. BMC Bioinformatics (2007) 0.99
BlastR--fast and accurate database searches for non-coding RNAs. Nucleic Acids Res (2011) 0.98
Hypoxia selectively activates the CREB family of transcription factors in the in vivo lung. Am J Respir Crit Care Med (2008) 0.97
Modeling stochasticity and robustness in gene regulatory networks. Bioinformatics (2009) 0.97
TIE-2 and VEGFR kinase activities drive immunosuppressive function of TIE-2-expressing monocytes in human breast tumors. Clin Cancer Res (2013) 0.97
ViralZone: recent updates to the virus knowledge resource. Nucleic Acids Res (2012) 0.96
Clustal omega. Curr Protoc Bioinformatics (2014) 0.95
Detecting microRNA activity from gene expression data. BMC Bioinformatics (2010) 0.94
A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk. Bioinformatics (2011) 0.94
Microarray analysis of isolated human islet transcriptome in type 2 diabetes and the role of the ubiquitin-proteasome system in pancreatic beta cell dysfunction. Mol Cell Endocrinol (2012) 0.93
A complete analysis of HA and NA genes of influenza A viruses. PLoS One (2010) 0.93