Software
Chorus2
Design of genome-scale oligonucleotide-based probes for fluorescence in situ hybridization (FISH)
CrisprStitch
An integrated tool to fast evaluate the efficiency of CRISPR editing systems.
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](/assets/images/oligo_db.png)
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](/assets/images/plantdhs.jpg)
PlantDHS
PlantDHS: a database for DNase I hypersensitive sites (DHSs) in plants.
![CAPE](/assets/images/CAPE/cape.png)
CAPE
CAPE: An efficient CRISPR-Cas12a promoter editing system for crop improvement [JBrowse preview](https://bioinfor.yzu.edu.cn/jbrowse2/cape) ## Introduction we demonstrate a **CAPE** based promoter editing and tuning pipeline for efficient production of useful quantitative...
![CAPE](/assets/images/CAPE/cape.png)
CAPE
CAPE: An efficient CRISPR-Cas12a promoter editing system for crop improvement JBrowse preview Introduction we demonstrate a CAPE based promoter editing and tuning pipeline for efficient production of useful quantitative trait...
Lab meeting
![Role of lncRNAs in cis- and trans-regulatory responses to salt in Populus trichocarpa](/assets/images/lab_meeting/2022-05-17.png)
Role of lncRNAs in cis- and trans-regulatory responses to salt in Populus trichocarpa
Abstract: Long non-coding RNAs (lncRNAs) are emerging as versatile regulators in diverse biological processes. How- ever, little is known about their cis- and trans-regulatory contributions in gene expression under salt...
![ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation](/assets/images/lab_meeting/2022-05-11.png)
ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation
Abstract: Regulatory elements control gene expression through transcription initiation (promoters) and by enhancing transcription at distant regions (enhancers). Accurate identification of reg- ulatory elements is fundamental for annotating genomes and...
![Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation](/assets/images/lab_meeting/2022-04-26.png)
Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation
Abstract: High-altitude adaptation of Tibetans represents a remarkable case of natural selection during recent human evolution. Previous genome-wide scans found many non-coding variants under selection, suggesting a pressing need to...
![DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development](/assets/images/lab_meeting/2022-04-12.png)
DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development
Abstract: A contribution of DNA methylation to defense against invading nucleic acids and maintenance of genome integrity is uncontested; however, our understanding of the extent of involvement of this epigenetic...
![ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation](/assets/images/lab_meeting/2022-04-13.png)
ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation
Abstract: Regulatory elements control gene expression through transcription initiation (promoters) and by enhancing transcription at distant regions (enhancers). Accurate identification of regulatory elements is fundamental for annotating genomes and understanding...
![A comprehensive catalog of predicted functional upstream open reading frames in humans](/assets/images/lab_meeting/2022-04-06.png)
A comprehensive catalog of predicted functional upstream open reading frames in humans
Abstract: Upstream open reading frames (uORFs) latent in mRNA transcripts are thought to modify translation of coding sequences by altering ribosome activity. Not all uORFs are thought to be active...
![ALK, the Key Gene for Gelatinization Temperature, is a Modifier Gene for Gel Consistency in Rice](/assets/images/lab_meeting/2022-03-30.png)
ALK, the Key Gene for Gelatinization Temperature, is a Modifier Gene for Gel Consistency in Rice
Abstract: Gelatinization temperature (GT) is an important parameter in evaluating the cooking and eating quality of rice. Indeed, the phenotype, biochemistry and inheritance of GT have been widely studied in...
![Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis](/assets/images/lab_meeting/2022-03-23.png)
Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis
Abstract: Background: Chromatin provides a tunable platform for gene expression control. Besides the well-studied core nucleosome, H1 linker histones are abundant chromatin components with intrinsic potential to influence chromatin function....
![The two clock proteins CCA1 and LHY activate VIN3 transcription during vernalization through the vernalization-responsive cis-element](/assets/images/lab_meeting/2022-03-14.png)
The two clock proteins CCA1 and LHY activate VIN3 transcription during vernalization through the vernalization-responsive cis-element
Abstract: Vernalization, a long-term cold-mediated acquisition of flowering competence, is critically regulated by VERNALIZATION INSENSITIVE 3 (VIN3), a gene induced by vernalization in Arabidopsis. Although the function of VIN3 has...
![A quantitative genomics map of rice provides genetic insights and guides breeding](/assets/images/lab_meeting/2022-03-07.png)