Deep learning and its applications in biomedicine

…, D Song, W Shu, W Li, Y Zhou, X Bo… - Genomics …, 2018 - academic.oup.com
Advances in biological and medical technologies have been providing us explosive volumes
of biological and physiological data, such as medical images, electroencephalography, …

[PDF][PDF] clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

…, T Feng, L Zhou, W Tang, LI Zhan, X Fu, S Liu, X Bo… - The innovation, 2021 - cell.com
Functional enrichment analysis is pivotal for interpreting high-throughput omics data in life
science. It is crucial for this type of tool to use the latest annotation databases for as many …

Machine learning methods, databases and tools for drug combination prediction

…, B Yan, Y Zhang, J Wang, S He, X Bo - Briefings in …, 2022 - academic.oup.com
Combination therapy has shown an obvious efficacy on complex diseases and can greatly
reduce the development of drug resistance. However, even with high-throughput screens, …

[HTML][HTML] PEDLA: predicting enhancers with a deep learning-based algorithmic framework

F Liu, H Li, C Ren, X Bo, W Shu - Scientific reports, 2016 - nature.com
Transcriptional enhancers are non-coding segments of DNA that play a central role in the
spatiotemporal regulation of gene expression programs. However, systematically and …

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

G Yu, F Li, Y Qin, X Bo, Y Wu, S Wang - Bioinformatics, 2010 - academic.oup.com
The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to
compute similarities between genes and gene groups, and have became important basis for …

[HTML][HTML] Deep learning-based transcriptome data classification for drug-target interaction prediction

L Xie, S He, X Song, X Bo, Z Zhang - BMC genomics, 2018 - Springer
Xiaochen BoXiaochen Bo … Zhongnan Zhang and Xiaochen Bo directed the project
and contributed to manuscript revisions. All Authors read and approved the final manuscript. …

A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data

…, H Li, S Jiang, R Li, W Li, H Chen, X Bo - Briefings in …, 2019 - academic.oup.com
The Cancer Genome Atlas (TCGA) is a publicly funded project that aims to catalog and
discover major cancer-causing genomic alterations with the goal of creating a comprehensive ‘…

[HTML][HTML] Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome

H Chen, Y Tian, W Shu, X Bo, S Wang - PloS one, 2012 - journals.plos.org
Chromatin insulators are DNA elements that regulate the level of gene expression either by
preventing gene silencing through the maintenance of heterochromatin boundaries or by …

ggtreeExtra: compact visualization of richly annotated phylogenetic data

…, L Zhan, T Wu, E Hu, Y Jiang, X Bo… - Molecular biology …, 2021 - academic.oup.com
We present the ggtreeExtra package for visualizing heterogeneous data with a phylogenetic
tree in a circular or rectangular layout ( https://www.bioconductor.org/packages/ggtreeExtra )…

[HTML][HTML] A benchmark study of deep learning-based multi-omics data fusion methods for cancer

…, Y Zhang, L Wu, J Wang, M Wang, Z Zhang, S He, X Bo - Genome biology, 2022 - Springer
Background A fused method using a combination of multi-omics data enables a comprehensive
study of complex biological processes and highlights the interrelationship of relevant …