Biological Databases »
miRTarBase
A database curates experimentally validated microRNA-target interactions. (Nucl Acids Res, 2011) more . . .
dbPTM
An informative resource for investigating substrate site specificity and functional association of protein post-translational modifications (Nucl Acids Res, 2013) more . . .
RegPhos
A system to explore the protein kinase-substrate phosphorylation network in humans. (Nucl Acids Res, 2011) more . . .
pseudoMap
An innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes. (Database (Oxford). 2013) more . . .
Tools for Next Gen. Sequencing »
miRExpress
Analyzing high-throughput sequencing data for profiling microRNA expression. (BMC Bioinformatics, 2009) more . . .
miRTarCLIP
A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. (BMC Genomics, 2013) more . . .
MicroRNAs and small RNAs »
miRTarBase
A database curates experimentally validated microRNA-target interactions. (Nucl Acids Res, 2011) more . . .
miRTar
An integrated web server for identifying miRNA-target interactions. (BMC Bioinformatics, 2011) more . . .
miRStart
A database of human miRNA promoters. (Nucl Acids Res, 2011) more . . .
miRExpress
Analyzing high-throughput sequencing data for profiling microRNA expression. (BMC Bioinformatics, 2009) more . . .
miRTarCLIP
A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. (BMC Genomics, 2013) more . . .
RNALogo
A new approach to display structural RNA alignment. (Nucl Acids Res, 2008) more . . .
sRNAMap
A database of small noncoding regulatory RNA in microbial genomes. (Nucl Acids Res, 2009) more . . .
RegRNA
An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. (Nucl Acids Res, 2006, BMC bioinformatics, 2013) more . . .
RiboSW
Computational identification of riboswitches based on RNA conserved functional sequences and conformations. (RNA, 2009) more . . .
ViTa
A database of host microRNA targets on viruses. (Nucl Acids Res, 2007) more . . .
miRNAMap
Genomic maps of microRNAs in metazoan genomes. (Nucl Acids Res, 2006, Nucl Acids Res, 2008) more . . .
RNAMST
Efficient and flexible approach for identifying RNA structural homologs. (Nucl Acids Res, 2006) more . . .
Protein Post-translational Modifications »
dbPTM
An informative resource for investigating substrate site specificity and functional association of protein post-translational modifications (Nucl Acids Res, 2013) more . . .
RegPhos
A system to explore the protein kinase-substrate phosphorylation network in humans. (Nucl Acids Res, 2011) more . . .
KinasePhos
A web tool for identifying protein kinase-specific phosphorylation site. (Nucl Acids Res, 2005, J. Comp. Chem. 2005) more . . .
KinasePhos (ver. 2)
A web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. (Nucl Acids Res, 2007) more . . .
Sulfosite
Incorporating support vector machine for identifying protein tyrosine sulfation sites. (J Comput Chem. 2009) more . . .
MASA
Incorporating structural characteristics for identification of protein methylation sites. (J Comput Chem. 2009) more . . .
N-ACE
Using solvent accessibility and physicochemical properties to identify protein N-acetylation sites. (J Comput Chem. 2010) more . . .
dbSNO
A database of cysteine S-Nitrosylation. (Bioinformatics. 2012) more . . .
SNOSite
Exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity. (PLoS One. 2011) more . . .
Gene Regulation and Post-transcriptional Regulation »
PlantPAN
Plant Promoter Analysis Navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene group. (BMC Genomics, 2009) more . . .
SpliceInfo
An information repository for the modes of mRNA alternative splicing in human genome. (Nucl Acids Res, 2005) more . . .
ProSplicer
An alternative splicing database based on protein, mRNA, and EST sequences. (Genome Biology, 2003) more . . .
Resources for Synthetic Biology and Systems Biology »
FMM
A web server for metabolic pathway reconstruction and comparative analysis. (Nucl Acids Res, 2009) more . . .
RegPhos
A system to explore the protein kinase-substrate phosphorylation network in humans. (Nucl Acids Res, 2011) more . . .
sRNAMap
A database of small noncoding regulatory RNA in microbial genomes. (Nucl Acids Res, 2009) more . . .
ProKware
An integrated software for presenting protein structural properties in protein tertiary structures. (Nucl Acids Res, 2006) more . . .