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 . . .