DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference.

PubWeight™: 0.80‹?›

🔗 View Article (PMC 4464606)

Published in BMC Syst Biol on June 01, 2015

Authors

Salvatore Alaimo, Vincenzo Bonnici, Damiano Cancemi, Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti

Articles cited by this

The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science (2006) 25.99

DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res (2006) 15.19

DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res (2007) 13.94

DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res (2010) 13.68

PID: the Pathway Interaction Database. Nucleic Acids Res (2008) 12.92

Drug-target network. Nat Biotechnol (2007) 11.15

Biological robustness. Nat Rev Genet (2004) 9.98

The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19

Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res (2010) 9.18

The Reactome pathway knowledgebase. Nucleic Acids Res (2013) 8.56

Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol (2008) 8.51

Targeted cancer therapy. Nature (2004) 7.81

Drug repositioning: identifying and developing new uses for existing drugs. Nat Rev Drug Discov (2004) 7.57

New uses for old drugs. Nature (2007) 5.86

Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med (2011) 5.77

Survivin, cancer networks and pathway-directed drug discovery. Nat Rev Cancer (2008) 5.65

Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Sci Transl Med (2011) 5.30

STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res (2007) 4.88

The Connectivity Map: a new tool for biomedical research. Nat Rev Cancer (2007) 4.40

Discovery of drug mode of action and drug repositioning from transcriptional responses. Proc Natl Acad Sci U S A (2010) 4.35

Blocking oncogenic Ras signaling for cancer therapy. J Natl Cancer Inst (2001) 4.25

Multi-target therapeutics: when the whole is greater than the sum of the parts. Drug Discov Today (2006) 4.24

Tackling antibiotic resistance. Nat Rev Microbiol (2011) 3.95

Bipartite network projection and personal recommendation. Phys Rev E Stat Nonlin Soft Matter Phys (2007) 3.80

Mechanisms of drug combinations: interaction and network perspectives. Nat Rev Drug Discov (2009) 3.20

STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Res (2009) 3.06

Drug discovery. Repurposing with a difference. Science (2009) 2.97

Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. Bioinformatics (2008) 2.96

Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther (2013) 2.64

Prediction of drug-target interactions and drug repositioning via network-based inference. PLoS Comput Biol (2012) 2.63

Exploiting drug-disease relationships for computational drug repositioning. Brief Bioinform (2011) 2.52

A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors. Cancer Discov (2013) 2.46

STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Res (2013) 2.32

Unveiling the role of network and systems biology in drug discovery. Trends Pharmacol Sci (2010) 2.06

STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Res (2011) 2.05

Emergent behavior of growing knowledge about molecular interactions. Nat Biotechnol (2005) 1.95

Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Genome Res (2004) 1.92

Gaussian interaction profile kernels for predicting drug-target interaction. Bioinformatics (2011) 1.88

Mapping of the benzodiazepine recognition site on GABA(A) receptors. Curr Top Med Chem (2002) 1.61

Complexity in the signaling network: insights from the use of targeted inhibitors in cancer therapy. Genes Dev (2012) 1.60

Network context and selection in the evolution to enzyme specificity. Science (2012) 1.59

Predicting metabolic biomarkers of human inborn errors of metabolism. Mol Syst Biol (2009) 1.59

SIGMA: a set-cover-based inexact graph matching algorithm. J Bioinform Comput Biol (2010) 1.53

A pathway-based view of human diseases and disease relationships. PLoS One (2009) 1.52

Innovation: Rescuing drug discovery: in vivo systems pathology and systems pharmacology. Nat Rev Drug Discov (2005) 1.52

Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery. Mol Syst Biol (2011) 1.50

Drug-target interaction prediction by learning from local information and neighbors. Bioinformatics (2012) 1.44

Stable isotope-resolved metabolomics and applications for drug development. Pharmacol Ther (2011) 1.29

Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines. Drug Discov Today (2013) 1.24

DCDB: drug combination database. Bioinformatics (2009) 1.21

GraphFind: enhancing graph searching by low support data mining techniques. BMC Bioinformatics (2008) 1.20

Interaction of propofol and sevoflurane on loss of consciousness and movement to skin incision during general anesthesia. Anesthesiology (2006) 1.15

A New Method for Computational Drug Repositioning Using Drug Pairwise Similarity. Proceedings (IEEE Int Conf Bioinformatics Biomed) (2012) 1.05

Pathway-based drug repositioning using causal inference. BMC Bioinformatics (2013) 1.04

Estimating novel potential drug targets of Plasmodium falciparum by analysing the metabolic network of knock-out strains in silico. Infect Genet Evol (2008) 1.04

Principal network analysis: identification of subnetworks representing major dynamics using gene expression data. Bioinformatics (2010) 1.03

Human metabolic network reconstruction and its impact on drug discovery and development. Drug Discov Today (2008) 1.03

Superessential reactions in metabolic networks. Proc Natl Acad Sci U S A (2012) 1.02

Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE. Mol Biosyst (2009) 1.02

Drug-target interaction prediction through domain-tuned network-based inference. Bioinformatics (2013) 0.99

Identification of common biological pathways and drug targets across multiple respiratory viruses based on human host gene expression analysis. PLoS One (2012) 0.98

GASOLINE: a Greedy And Stochastic algorithm for optimal Local multiple alignment of Interaction NEtworks. PLoS One (2014) 0.97

SING: subgraph search in non-homogeneous graphs. BMC Bioinformatics (2010) 0.93

'Pathway drug cocktail': targeting Ras signaling based on structural pathways. Trends Mol Med (2013) 0.89

Choke point analysis of metabolic pathways in E.histolytica: a computational approach for drug target identification. Bioinformation (2007) 0.88

A subgraph isomorphism algorithm and its application to biochemical data. BMC Bioinformatics (2013) 0.86

A systems pharmacology analysis of major chemotherapy combination regimens used in gastric cancer treatment: predicting potential new protein targets and drugs. Curr Cancer Drug Targets (2011) 0.85

Shift in the equilibrium between on and off states of the allosteric switch in Ras-GppNHp affected by small molecules and bulk solvent composition. Biochemistry (2012) 0.82

A novel multi-modal drug repurposing approach for identification of potent ACK1 inhibitors. Pac Symp Biocomput (2013) 0.81

Pathway analysis for drug repositioning based on public database mining. J Chem Inf Model (2014) 0.80

The proteomics big challenge for biomarkers and new drug-targets discovery. Int J Mol Sci (2012) 0.79

SAR monitoring of evolving compound data sets using activity landscapes. J Chem Inf Model (2011) 0.78

GRAPES: a software for parallel searching on biological graphs targeting multi-core architectures. PLoS One (2013) 0.78

Metabolic network analysis revealed distinct routes of deletion effects between essential and non-essential genes. Mol Biosyst (2012) 0.77

A Comparative Study of Metabolic Network Topology between a Pathogenic and a Non-Pathogenic Bacterium for Potential Drug Target Identification. Summit on Translat Bioinforma (2009) 0.76

Articles by these authors

Introduction of gluten, HLA status, and the risk of celiac disease in children. N Engl J Med (2014) 4.64

SIGMA: a set-cover-based inexact graph matching algorithm. J Bioinform Comput Biol (2010) 1.53

Tools and collaborative environments for bioinformatics research. Brief Bioinform (2011) 1.49

Integrated microRNA and mRNA signatures associated with survival in triple negative breast cancer. PLoS One (2013) 1.43

miRandola: extracellular circulating microRNAs database. PLoS One (2012) 1.43

GraphFind: enhancing graph searching by low support data mining techniques. BMC Bioinformatics (2008) 1.20

The neurology of coeliac disease in childhood: what is the evidence? A systematic review and meta-analysis. Dev Med Child Neurol (2010) 1.12

Drug-target interaction prediction through domain-tuned network-based inference. Bioinformatics (2013) 0.99

SING: subgraph search in non-homogeneous graphs. BMC Bioinformatics (2010) 0.93

Variability in the incidence of miRNAs and genes in fragile sites and the role of repeats and CpG islands in the distribution of genetic material. PLoS One (2010) 0.93

Prediction of human targets for viral-encoded microRNAs by thermodynamics and empirical constraints. J RNAi Gene Silencing (2010) 0.90

miR-EdiTar: a database of predicted A-to-I edited miRNA target sites. Bioinformatics (2012) 0.89

A subgraph isomorphism algorithm and its application to biochemical data. BMC Bioinformatics (2013) 0.86

VIRGO: visualization of A-to-I RNA editing sites in genomic sequences. BMC Bioinformatics (2013) 0.85

Prevalence and natural history of potential celiac disease in at-family-risk infants prospectively investigated from birth. J Pediatr (2012) 0.85

A knowledge base for the discovery of function, diagnostic potential and drug effects on cellular and extracellular miRNAs. BMC Genomics (2014) 0.84

MIDClass: microarray data classification by association rules and gene expression intervals. PLoS One (2013) 0.84

A knowledge base for Vitis vinifera functional analysis. BMC Syst Biol (2015) 0.83

A pilot study on neurological manifestations and antibodies against antigens in children with hematological and other cancers. Eur J Paediatr Neurol (2012) 0.79

Treatment with the fusion inhibitor enfuvirtide influences the appearance of mutations in the human immunodeficiency virus type 1 regulatory protein rev. Antimicrob Agents Chemother (2009) 0.79

In vitro and in silico cloning of Xenopus laevis SOD2 cDNA and its phylogenetic analysis. DNA Cell Biol (2005) 0.79

Genomics, evolution, and expression of TBPL2, a member of the TBP family. DNA Cell Biol (2007) 0.78

Bioinformatics in Italy: BITS 2012, the ninth annual meeting of the Italian Society of Bioinformatics. BMC Bioinformatics (2013) 0.78

New approaches in hepatitis B vaccination for celiac disease. Immunotherapy (2014) 0.78

Extracellular circulating viral microRNAs: current knowledge and perspectives. Front Genet (2013) 0.78

Sequence similarity is more relevant than species specificity in probabilistic backtranslation. BMC Bioinformatics (2007) 0.78

GRAPES: a software for parallel searching on biological graphs targeting multi-core architectures. PLoS One (2013) 0.78

A novel computational method for inferring competing endogenous interactions. Brief Bioinform (2016) 0.77

Diathermy of leaking sclerotomies after 23-gauge transconjunctival pars plana vitrectomy: a prospective study. Retina (2013) 0.77

Involvement of GTA protein NC2beta in neuroblastoma pathogenesis suggests that it physiologically participates in the regulation of cell proliferation. Mol Cancer (2008) 0.77

Elucidating the role of microRNAs in cancer through data mining techniques. Adv Exp Med Biol (2013) 0.76

Computational design of artificial RNA molecules for gene regulation. Methods Mol Biol (2015) 0.75

On the variable ordering in subgraph isomorphism algorithms. IEEE/ACM Trans Comput Biol Bioinform (2016) 0.75

The NETTAB 2009 workshop. Brief Bioinform (2011) 0.75