A novel convolutional layer with adaptive kernels for effective mining complex patterns in omics data.

On July 6th, 2021, Gao Lab from Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG) published a research article named “Identifying complex motifs in massive omics data with a variable-convolutional layer in deep neural network” on Briefings in Bioinformatics, proposing a novel convolutional layer for deep neural networks.   Deep Read more about A novel convolutional layer with adaptive kernels for effective mining complex patterns in omics data.[…]

Cell BLAST for China’s top ten bioinformatics advances of 2020

The Cell BLAST study (Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST) was recently awarded by Genomics, Proteomics and Bioinformatics (GPB) as China’s top ten bioinformatics advances of 2020. As a powerful tool for studying cellular heterogeneity, single-cell transcriptomic sequencing has seen rapid development in recent years, with large amounts of data Read more about Cell BLAST for China’s top ten bioinformatics advances of 2020[…]

Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST

scRNA-seq has seen rapid development over the recent years, providing powerful technological support for studying important biological problems including cellular functions and gene regulatory networks. In a typical scRNA-seq study, cell annotation regarding cell types and cell differentiation progress is usually the first step. However, the standard annotation process is rather tedious, and cannot guarantee Read more about Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST[…]

AnnoLnc2: the one-stop portal to systematically annotate novel lncRNAs for human and mouse

Long noncoding RNAs (lncRNAs) have been demonstrated to play many important regulatory roles via various mechanisms (1), and many characteristics have been used to infer their functions. For example, analyzing the natural selection pressures on lncRNAs can reveal whether they are functional (2), and their subcellular localization indicates where they perform functions (3). Functional enrichment Read more about AnnoLnc2: the one-stop portal to systematically annotate novel lncRNAs for human and mouse[…]

RefLnc for China’s top ten bioinformatics database of 2019

By analyzing the largest compendium of 14,166 samples from normal and tumor tissues, Ge Gao’s team significantly expand the landscape of human long noncoding RNA with a high-quality atlas: RefLnc (Reference catalog of LncRNA, http://reflnc.gao-lab.org/). Considered the influence RefLnc has made in human lncRNA field,RefLnc has being awarded as China’s top ten bioinformatics database of Read more about RefLnc for China’s top ten bioinformatics database of 2019[…]

Expectation Pooling: a novel pooling layer with explicit probabilistic interpretation

Convolutional neural network (CNN) has been widely used in sequence classification and mechanism mining of omic datasets since the publication of the two pilot studies, DeepBind (1) and DeepSEA (2). The intrinsic operation of CNN itself, however, has long been taken as a ‘black-box’. Recently some studies have attempted to tackle this problem; for example, Read more about Expectation Pooling: a novel pooling layer with explicit probabilistic interpretation[…]

PlantRegMap: charting functional regulatory maps in plants

On November 8, 2019, the research group of Gao Ge, a researcher at the State Key Laboratory of Protein and Plant Gene Research at Peking University, published a research paper entitled “PlantRegMap: charting functional regulatory maps in plants” in the journal Nucleic Acids Research (https://doi.org/10.1093/nar/gkz1020). The study mapped the functional transcriptional regulation map of 63 Read more about PlantRegMap: charting functional regulatory maps in plants[…]