Methods & Resources
Subgenomic RNA profiling suggests novel mechanism in coronavirus gene regulation and host adaptionCORONATATOR, developed to analyze the subgenomic RNA of coronavirus, was applied on large number of sequencing data sets from coronaviruses, and shed light on viral gene regulation.
LuminoCell: a versatile and affordable platform for real-time monitoring of luciferase-based reportersDescription of affordable ($40) open-source platform for real-time in-cell monitoring of luciferase activity.
Evaluation of the correctable decoding sequencing as a new powerful strategy for DNA sequencingThis article proposed the correctable decoding sequencing technology with conservative theoretical error rate of 0.0009%, and evaluated its robustness by simulation. This technology can provide a powerful new protocol for NGS platforms, enabling accurate identification of rare mutations in medicine.
Tracking connectivity maps in human stem cell–derived neuronal networks by holographic optogeneticsHolographic optogenetic stimulation of human iPSC–derived neuronal networks was exploited to map precise functional connectivity motifs and their long-term dynamics during network development.
Sensitive visualization of SARS-CoV-2 RNA with CoronaFISHWe design an RNA-FISH method to target the plus and minus strands of SARS-CoV-2 RNA, and apply it to image the virus in cell lines, lung tissue, and nasal swabs, by fluorescence and electron microscopy.
SnRNA sequencing defines signaling by RBC-derived extracellular vesicles in the murine heartIn a unique model of fluorescent based mapping of EV recipient cells, RBC-EVs were found to signal to cardiac cells and regulate gene expression in a model of ischemic heart failure.
An extended DNA-free intranuclear compartment organizes centrosome microtubules in malaria parasitesMalaria arises during the proliferation of Plasmodium spp. in human blood, whereas the underlying atypical cell division mechanisms remain poorly understood. This study uses advanced imaging to dissect dynamics and organization of the centrosome, a key division regulator.
Statistical guidelines for quality control of next-generation sequencing techniquesCondition-specific statistical guidelines and accurate classification trees for quality control of functional genomics NGS files (RNA-seq, ChIP-seq and DNase-seq) have been generated using thousands of reference files from the ENCODE project and made available to the community.
Dissection-independent production of Plasmodium sporozoites from whole mosquitoesOvercoming limitations of traditional dissection-dependent methods for malarial sporozoite isolation from mosquitoes, a new dissection-free method is presented that yields pure, infective sporozoites.
CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq dataA systematic comparison of batch effect metrics for single cell data is performed. The new cell-specific mixing score from the R/Bioconductor CellMixS package performs well across various tasks.