Nearly 90% of the disease risk-associated variants identified from genome-wide association studies (GWAS) are in non-coding regions of the genome. The annotations obtained from analyzing functional genomics assays can provide additional information to pinpoint causal variants, which are often not the lead variants identified from association studies. However, the lack of available annotation tools limits the use of such data. To address the challenge, we have previously built the RegulomeDB database for prioritizing and annotating variants in non-coding regions1, which has been a highly utilized resource for the research community (Supplementary Fig. 1). RegulomeDB annotates a variant by intersecting its position with genomic intervals identified from functional genomic assays and computational approaches. It also incorporates those hits of a variant into a heuristic ranking score, representing its potential to be functional in regulatory elements. Here we present a newer version of the RegulomeDB web server, RegulomeDB v2.1 (http://regulomedb.org). We improve and boost annotation power by incorporating thousands of newly processed data from functional genomic assays in GRCh38 assembly, and now include probabilistic scores from the SURF algorithm that was the top performing non-coding variant predictor in CAGI 52. We also provide interactive charts and genome browser views to allow users an easy way to perform exploratory analyses in different tissue contexts.

Genomic and epigenomic features are captured at a genome-wide level by using high-throughput sequencing (HTS) technologies. Peak calling delineates features identified in HTS experiments, such as open chromatin regions and transcription factor binding sites, by comparing the observed read distributions to a random expectation. Since its introduction, F-Seq has been widely used and shown to be the most sensitive and accurate peak caller for DNase I hypersensitive site (DNase-seq) data. However, the first release (F-Seq1) has two key limitations: lack of support for user-input control datasets, and poor test statistic reporting. These constrain its ability to capture systematic and experimental biases inherent to the background distributions in peak prediction, and to subsequently rank predicted peaks by confidence. To address these limitations, we present F-Seq2, which combines kernel density estimation and a dynamic ‘continuous’ Poisson test to account for local biases and accurately rank candidate peaks. The output of F-Seq2 is suitable for irreproducible discovery rate analysis as test statistics are calculated for individual candidate summits, allowing direct comparison of predictions across replicates. These improvements significantly boost the performance of F-Seq2 for ATAC-seq and ChIP-seq datasets, outperforming competing peak callers used by the ENCODE Consortium in terms of precision and recall.

Three-dimensional (3D) object detection has important applications in robotics, automatic loading, automatic driving and other scenarios. With the improvement of devices, people can collect multi-sensor/multimodal data from a variety of sensors such as Lidar and cameras. In order to make full use of various information advantages and improve the performance of object detection, we proposed a Complex-Retina network, a convolution neural network for 3D object detection based on multi-sensor data fusion. Firstly, a unified architecture with two feature extraction networks was designed, and the feature extraction of point clouds and images from different sensors realized synchronously. Then, we set a series of 3D anchors and projected them to the feature maps, which were cropped into 2D anchors with the same size and fused together. Finally, the object classification and 3D bounding box regression were carried out on the multipath of fully connected layers. The proposed network is a one-stage convolution neural network, which achieves the balance between the accuracy and speed of object detection. The experiments on KITTI datasets show that the proposed network is superior to the contrast algorithms in average precision (AP) and time consumption, which shows the effectiveness of the proposed network.

No abstract

No abstract