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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[…]
Congratulations to Lan Ke for her Ph.D.!
Well done, Dr. Ke! From a seed to a sapling, and a tree in one day! Wish you more success and prosperity in days to come!
Congratulations to Feng Tian for his Ph.D.!
Well done, Dr. Tian! Stick to your way, step by step and you will arrive your destination finally. Wish you more success and prosperity in days to come!
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[…]
Congratulations to Shuai Jiang for her Ph.D.!
Well done, Dr. Jiang! We had a happy time also with some meaningful challenges in past few years. Wish you more success and prosperity in days to come!
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[…]