Software
Chorus2
Design of genome-scale oligonucleotide-based probes for fluorescence in situ hybridization (FISH)
CRISPR-BETS
A gRNA design software for base editing knockout using stop codon.
Popera
A software specially designed for DHS identification. Github Introduction DNase I hypersensitive sites (DHSs) are regions of chromatin that are sensitive to cleavage by the...
Latest
Chorus2 oligo datasets
Oligo datasets which host oligo sequences for Oligo-FISH. Details Introduction The oligo datasets currently host oligo sequences of nine species, including Arabidopsis, rice, maize, potato, barley, soybean, human, mouse and...
PlantDHS
PlantDHS: a database for DNase I hypersensitive sites (DHSs) in plants.
Lab meeting
Report: Analysis of gene network bifurcation during optic cup morphogenesis in zebrafish
Abstract: Sight depends on the tight cooperation between photoreceptors and pigmented cells, which derive from common progenitors through the bifurcation of a single gene regulatory network into the neural retina...
Report: RGN1 controls grain number and shapes panicle architecture in rice
Abstract: Yield in rice is determined mainly by panicle architecture. Using map-based cloning we identified an R2R3 MYB transcription factor REGULATOR OF GRAIN NUMBER1 (RGN1) affecting grain number and panicle...
Report: Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
Abstract: Thousands of species will be sequenced in the next few years; however, understanding how their genomes work, without an unlimited budget, requires both molecular and novel evolutionary approaches. We...
Report: PAM-less plant genome editing using a CRISPR–SpRY toolbox
Abstract: The rapid development of the CRISPR–Cas9, –Cas12a and – Cas12b genome editing systems has greatly fuelled basic and translational plant research1–6. DNA targeting by these Cas nucleases is restricted...
Report: The key role of terminators on the expression and post- transcriptional gene silencing of transgenes
Abstract: Transgenes have become essential to modern biology, being an important tool in functional genomic studies and also in the development of biotechnological products. One of the major challenges in...
Report: KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis
Abstract: Gene set enrichment (GSE) analysis plays an essen- tial role in extracting biological insight from genome- scale experiments. ORA (overrepresentation analy- sis), FCS (functional class scoring), and PT (path-...
Report: Integrated global analysis reveals a vitamin E- vitamin K1 sub-network, downstream of COLD1, underlying rice chilling tolerance divergence
Abstract: Rice, a staple food with tropical/subtropical origination, is susceptible to cold stress, one of the major con- straints on its yield and distribution. Asian cultivated rice consists of two...
Report: The Taxus genome provides insights into paclitaxel biosynthesis
Abstract: The ancient gymnosperm genus Taxus is the exclusive source of the anticancer drug paclitaxel, yet no reference genome sequences are available for comprehensively elucidating the paclitaxel biosynthesis pathway. We...
Report: In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants
Abstract: Background: mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites, such as splice and polyadenylation sites,...
