Profiled support vector machines for antisense oligonucleotide efficacy prediction.

More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature. Nucleic Acids Res (2006) 1.18

Identification of sequence motifs significantly associated with antisense activity. BMC Bioinformatics (2007) 0.86

Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design. Nucleic Acids Res (2008) 0.86

Selection of antisense oligonucleotides based on multiple predicted target mRNA structures. BMC Bioinformatics (2006) 0.82

AOBase: a database for antisense oligonucleotides selection and design. Nucleic Acids Res (2006) 0.81

Prediction of antisense oligonucleotides using structural and thermodynamic motifs. Bioinformation (2012) 0.75

Survival Prediction and Feature Selection in Patients with Breast Cancer Using Support Vector Regression. Comput Math Methods Med (2016) 0.75

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol (1999) 41.48

Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci U S A (1994) 8.06

Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry (1995) 6.40

Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res (1996) 5.16

Asymptotic behaviors of support vector machines with Gaussian kernel. Neural Comput (2003) 3.40

Using mutual information for selecting features in supervised neural net learning. IEEE Trans Neural Netw (1994) 3.31

Selecting effective antisense reagents on combinatorial oligonucleotide arrays. Nat Biotechnol (1997) 2.80

Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. Nucleic Acids Res (2001) 2.09

Mapping of RNA accessible sites for antisense experiments with oligonucleotide libraries. Nat Biotechnol (1998) 1.93

Effects of RNA secondary structure on cellular antisense activity. Nucleic Acids Res (2000) 1.60

Antisense therapeutics. Curr Opin Chem Biol (1998) 1.54

Thermodynamic criteria for high hit rate antisense oligonucleotide design. Nucleic Acids Res (2003) 1.52

Potent antisense oligonucleotides to the human multidrug resistance-1 mRNA are rationally selected by mapping RNA-accessible sites with oligonucleotide libraries. Nucleic Acids Res (1996) 1.47

Secondary structure prediction and in vitro accessibility of mRNA as tools in the selection of target sites for ribozymes. Nucleic Acids Res (2000) 1.44

Antisense oligonucleotide strategies in neuropharmacology. Trends Pharmacol Sci (1994) 1.41

RNA accessibility prediction: a theoretical approach is consistent with experimental studies in cell extracts. Nucleic Acids Res (2000) 1.27

Feature selection and transduction for prediction of molecular bioactivity for drug design. Bioinformatics (2003) 1.24

Identification of sequence motifs in oligonucleotides whose presence is correlated with antisense activity. Nucleic Acids Res (2000) 1.22

Progress in antisense technology: the end of the beginning. Methods Enzymol (2000) 1.19

Prediction of antisense oligonucleotide binding affinity to a structured RNA target. Biotechnol Bioeng (1999) 1.16

Dosage individualization of erythropoietin using a profile-dependent support vector regression. IEEE Trans Biomed Eng (2003) 1.07

ODNBase--a web database for antisense oligonucleotide effectiveness studies. Oligodeoxynucleotides. Bioinformatics (2000) 1.03

Theoretical and experimental approaches to design effective antisense oligonucleotides. Front Biosci (2000) 1.00

Artificial neural network prediction of antisense oligodeoxynucleotide activity. Nucleic Acids Res (2002) 0.95

Computational antisense oligo prediction with a neural network model. Bioinformatics (2002) 0.92

Application of antisense oligonucleotides for gene functionalization and target validation. Curr Opin Mol Ther (1999) 0.91

Sensible use of antisense: how to use oligonucleotides as research tools. Trends Pharmacol Sci (2000) 0.90

mRNA accessible site tagging (MAST): a novel high throughput method for selecting effective antisense oligonucleotides. Nucleic Acids Res (2003) 0.90

SVM-based feature selection for characterization of focused compound collections. J Chem Inf Comput Sci (2004) 0.86

Application of secondary structure prediction in antisense drug design targeting protein kinase C-alpha mRNA and QSAR analysis. Acta Pharmacol Sin (2000) 0.80

Influence of mRNA self-structure on hybridization: computational tools for antisense sequence selection. Methods (2000) 0.79

The Pfam protein families database. Nucleic Acids Res (2004) 56.46

The Pfam protein families database. Nucleic Acids Res (2002) 51.34

The Pfam protein families database. Nucleic Acids Res (2009) 37.98

Pfam: clans, web tools and services. Nucleic Acids Res (2006) 34.83

The Pfam protein families database. Nucleic Acids Res (2011) 33.46

The Pfam protein families database. Nucleic Acids Res (2007) 30.53

Pfam: the protein families database. Nucleic Acids Res (2013) 22.48

A combined transmembrane topology and signal peptide prediction method. J Mol Biol (2004) 15.77

Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res (2005) 9.90

Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet (2002) 7.25

Kalign--an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics (2005) 7.01

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res (2009) 5.90

Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Res (2007) 5.29

InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res (2007) 4.15

Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics (2006) 3.98

Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics (2002) 3.79

Quality assessment of multiple alignment programs. FEBS Lett (2002) 3.28

A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics (2008) 3.19

An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics (2005) 3.05

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. Nucleic Acids Res (2008) 2.97

Genomic gene clustering analysis of pathways in eukaryotes. Genome Res (2003) 2.89

OrthoDisease: a database of human disease orthologs. Hum Mutat (2004) 2.52

jSquid: a Java applet for graphical on-line network exploration. Bioinformatics (2008) 2.46

Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Res (2009) 2.43

Automatic assessment of alignment quality. Nucleic Acids Res (2005) 1.97

PfamAlyzer: domain-centric homology search. Bioinformatics (2007) 1.90

Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. Nucleic Acids Res (2006) 1.89

ChromoWheel: a new spin on eukaryotic chromosome visualization. Bioinformatics (2004) 1.78

A general model of G protein-coupled receptor sequences and its application to detect remote homologs. Protein Sci (2006) 1.67

Improved and automated prediction of effective siRNA. Biochem Biophys Res Commun (2004) 1.58

Disease-specific, neurosphere-derived cells as models for brain disorders. Dis Model Mech (2010) 1.57

FunCoup 3.0: database of genome-wide functional coupling networks. Nucleic Acids Res (2013) 1.56

Predicting protein function from domain content. Bioinformatics (2008) 1.47

Domain tree-based analysis of protein architecture evolution. Mol Biol Evol (2007) 1.46

A novel transmembrane topology of presenilin based on reconciling experimental and computational evidence. FEBS J (2005) 1.42

Comprehensive analysis of orthologous protein domains using the HOPS database. Genome Res (2003) 1.39

Toward community standards in the quest for orthologs. Bioinformatics (2012) 1.36

Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. BMC Bioinformatics (2005) 1.33

Reliability of transmembrane predictions in whole-genome data. FEBS Lett (2002) 1.31

Comparative interactomics with Funcoup 2.0. Nucleic Acids Res (2011) 1.29

Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction. Mol Biol Evol (2005) 1.28

Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information. Brief Bioinform (2011) 1.20

A cross-study transcriptional analysis of Parkinson's disease. PLoS One (2009) 1.19

Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases. Genome Biol (2006) 1.13

FunShift: a database of function shift analysis on protein subfamilies. Nucleic Acids Res (2005) 1.12

Network-based Identification of novel cancer genes. Mol Cell Proteomics (2009) 1.12

OrthoGUI: graphical presentation of Orthostrapper results. Bioinformatics (2002) 1.10

Alternate transcription of the Toll-like receptor signaling cascade. Genome Biol (2006) 1.08

Domain architecture conservation in orthologs. BMC Bioinformatics (2011) 1.06

Hieranoid: hierarchical orthology inference. J Mol Biol (2013) 1.05

Improving profile HMM discrimination by adapting transition probabilities. J Mol Biol (2004) 1.04

Benchmarking homology detection procedures with low complexity filters. Bioinformatics (2009) 1.01

Modeling distinct osteosarcoma subtypes in vivo using Cre:lox and lineage-restricted transgenic shRNA. Bone (2013) 1.01

DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System. Bioinformatics (2009) 0.98

Orthology confers intron position conservation. BMC Genomics (2010) 0.97

Evolution of protein domain architectures. Methods Mol Biol (2012) 0.96

Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity. PLoS One (2010) 0.96

Statistical assessment of crosstalk enrichment between gene groups in biological networks. PLoS One (2013) 0.94

Comparative analysis and unification of domain-domain interaction networks. Bioinformatics (2009) 0.92

Computational antisense oligo prediction with a neural network model. Bioinformatics (2002) 0.92

Prognostic significance in breast cancer of a gene signature capturing stromal PDGF signaling. Am J Pathol (2013) 0.92

Large-scale prediction of function shift in protein families with a focus on enzymatic function. Proteins (2005) 0.92

siRNAdb: a database of siRNA sequences. Nucleic Acids Res (2005) 0.91

MetaTM - a consensus method for transmembrane protein topology prediction. BMC Bioinformatics (2009) 0.87

siRNA specificity searching incorporating mismatch tolerance data. Bioinformatics (2008) 0.86

RNAi screen indicates widespread biological function for human natural antisense transcripts. PLoS One (2010) 0.86

The SKI proto-oncogene enhances the in vivo repopulation of hematopoietic stem cells and causes myeloproliferative disease. Haematologica (2014) 0.84

Prediction of function divergence in protein families using the substitution rate variation parameter alpha. Mol Biol Evol (2006) 0.83

transition priors for protein hidden Markov models: an empirical study towards maximum discrimination. J Comput Biol (2004) 0.83

Focusing on RISC assembly in mammalian cells. Biochem Biophys Res Commun (2008) 0.83

Chromosomal clustering of nuclear genes encoding mitochondrial and chloroplast proteins in Arabidopsis. Trends Genet (2006) 0.82

The Rothmund-Thomson syndrome helicase RECQL4 is essential for hematopoiesis. J Clin Invest (2014) 0.81

OrthoDisease: tracking disease gene orthologs across 100 species. Brief Bioinform (2011) 0.81

Quality criteria for finding genes with high mRNA-protein expression correlation and coexpression correlation. Gene (2012) 0.80

Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs. BMC Genomics (2004) 0.78

NovelFam3000--uncharacterized human protein domains conserved across model organisms. BMC Genomics (2006) 0.78

Differential regulation of osteoadherin (OSAD) by TGF-beta1 and BMP-2. Biochem Biophys Res Commun (2006) 0.77

MGclus: network clustering employing shared neighbors. Mol Biosyst (2013) 0.77

Avoiding pitfalls in L1-regularised inference of gene networks. Mol Biosyst (2014) 0.76

Network analysis of functional genomics data: application to avian sex-biased gene expression. ScientificWorldJournal (2012) 0.76

Optimal sparsity criteria for network inference. J Comput Biol (2013) 0.76

Exploring the foundation of genomics: a northern blot reference set for the comparative analysis of transcript profiling technologies. Comp Funct Genomics (2004) 0.75

Sfixem--graphical sequence feature display in Java. Bioinformatics (2004) 0.75

GeneSPIDER - gene regulatory network inference benchmarking with controlled network and data properties. Mol Biosyst (2017) 0.75