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| 1 | clusterProfiler 4.0:A universal enrichment tool for interpreting omics data显示文摘Functional enrichment analysis is pivotal for interpreting highthroughput omics data in life science.It is crucial for this type of tool to use the latest annotation databases for as many organisms as possible.To meet these requirements,we present here an updated version of our popular Bioconductor package,clusterProfiler 4.0.This package has been enhanced considerably compared with its original version published 9 years ago.The new version provides a universal interface for functional enrichment analysis in thousands of organisms based on internally supported ontologies and pathways as well as annotation data provided by users or derived from online databases.It also extends the dplyr and ggplot2 packages to offer tidy interfaces for data operation and visualization.Other new features include gene set enrichment analysis and comparison of enrichment results from multiple gene lists.We anticipate that clusterProfiler 4.0 will be applied to a wide range of scenarios across diverse organisms. | Tianzhi Wu Erqiang Hu Shuangbin Xu Meijun Chen Pingfan Guo Zehan Dai Tingze Feng Lang Zhou Wenli Tang Li Zhan Xiaocong Fu Shanshan Liu Xiaochen Bo Guangchuang Yu | 2021 | The Innovation2021，2，3： | 40 |
| 2 | Deep Learning and Its Applications in Biomedicine显示文摘Advances in biological and medical technologies have been providing us explosive volumes of biological and physiological data,such as medical images,electroencephalography,genomic and protein sequences.Learning from these data facilitates the understanding of human health and disease.Developed from arti?cial neural networks,deep learning-based algorithms show great promise in extracting features and learning patterns from complex data.The aim of this paper is to provide an overview of deep learning techniques and some of the state-of-the-art applications in the biomedical?eld.We?rst introduce the development of arti?cial neural network and deep learning.We then describe two main components of deep learning,i.e.,deep learning architectures and model optimization.Subsequently,some examples are demonstrated for deep learningapplications,including medical image classi?cation,genomic sequence analysis,as well as protein structure classi?cation and prediction.Finally,we offer our perspectives for the future directions in the?eld of deep learning. | Chensi Cao Feng Liu Hai Tan Deshou Song Wenjie Shu Weizhong Li Yiming Zhou Xiaochen Bo Zhi Xie | 2018 | Genomics, Proteomics & Bioinformatics2018，16，1： | 22 |
| 3 | Magnetic resonance imaging with three-dimensional fast imaging employing steady-state acquisition with phase-cycled and short T1 inversion recovery pulse sequence for evaluating brachial plexus injury显示文摘There is a large amount of fat in the postganglionic segment of the brachial plexus nerve.The use of short T1 inversion recovery pulse sequence may improve signal strength of the brachial plexus postganglionic segment.The present study revealed that the combination of three-dimensional fast imaging employing steady-state acquisition with phase-cycled and short T1 inversion recovery pulse sequence clearly displayed the anatomical morphology and structure of the brachial plexus nerve,together with maximum intensity projection,volume rendering and other three-dimensional reconstruction techniques.Our results suggested that this method is also suitable for providing accurate assessment and diagnosis of the site,severity and scope of brachial plexus injury. | Dianxiu Ning Meiyu Sun Bo Sun Li Zhao Weisheng Zhang Lijun Wang Shaowu Wang Ailian Liu Jianlin Wu Zhijin Lang Di Ning Guanfu Liu Xiaochen Ji Xiufeng Wang | 2011 | Neural Regeneration Research2011，6，14： | 7 |
| 4 | s-HBEGF/SIRT1 circuit-dictated crosstalk between vascular endothelial cells and keratinocytes mediates sorafenib-induced hand-foot skin reaction that can be reversed by nicotinamide显示文摘Hand-foot skin reaction(HFSR),among the most significant adverse effects of sorafenib,has been limiting the clinical benefits of this frontline drug in treating various malignant tumors.The mechanism underlying such toxicity remains poorly understood,hence the absence of effective intervention strategies.In the present study,we show that vascular endothelial cells are the primary cellular target of sorafenib-induced HFSR wherein soluble heparin-binding epidermal growth factor(s-HBEGF)mediates the crosstalk between vascular endothelial cells and keratinocytes.Mechanistically,s-HBEGF released from vascular endothelial cells activates the epidermal growth factor receptor(EGFR)on keratinocytes and promotes the phosphorylation of c-Jun N-terminal kinase 2(JNK2),which stabilizes sirtuin 1(SIRT1),an essential keratinization inducer,and ultimately gives rise to HFSR.The administration of s-HBEGF in vivo could sufficiently induce hyper-keratinization without sorafenib treatment.Furthermore,we report that HBEGF neutralization antibody,Sirtl knockdown,and a classic SIRTI inhibitor nicotinamide could all significantly reduce the sorafenib-induced HFSR in the mouse model.It is noteworthy that nicotinic acid,a prodrug of nicotinamide,could substantially reverse the sorafenib-induced HFSR in ten patients in a preliminary clinical study.Collectively,our findings reveal the mechanism of vascular endothelial cell-promoted keratinization in keratinocytes and provide a potentially promising therapeutic strategy for the treatment of sorafenib-induced HFSR. | Peihua Luo Hao Yan Xueqin Chen Ying Zhang Ziying Zhao Ji Cao Yi Zhu Jiangxia Du Zhifei Xu Xiaochen Zhang Su Zeng Bo Yang Shenglin Ma Qiaojun He | 2020 | Cell Research2020，30，9： | 5 |
| 5 | Experimental investigations on cavity-actuated under-expanded supersonic oscillating jet显示文摘As one type of potential flow control actuators, cavity-actuated supersonic jet oscillators,which consist of a 2-D convergent nozzle and two face to face cavities, need to be investigated deeply to get the knowledge of their oscillating feature and underlying mechanism. Wind tunnel testing are conducted under different back pressures in a vacuum-type wind tunnel for two supersonic jet oscillators, to obtain their characteristics and the conditions for jet oscillating. The experimental results show that the continuous, nearly symmetric or asymmetric flipping between the two cavities appears over certain nozzle pressure ratio(NPR) range for both oscillators according to schlieren visualizations. Compared to the free jet, the oscillating jet with large exit achieves larger mixing; the oscillating jet with small exit has less mixing, based on the analysis of jet axial peak velocity and the entrainment. The cross-junction mode for estimating the resonance frequency in a pipe with two closed side branches is modified and obtained comparable estimations of the frequency of jet flipping with experimental data, but further investigations are needed to discover the underlying mechanism for the jet flipping. | Sun Bo Luo Xiaochen Feng Feng Wu Xiaosong | 2015 | Chinese Journal of Aeronautics2015，28，5： | 4 |
| 6 | Comprehensive analysis of miRNA-gene regulatory network with clinical significance in human cancers显示文摘microRNAs(miRNAs),particularly the exosomal miRNAs have been widely used as biomarkers and promising therapeutic targets in cancer.However,a comprehensive analysis of miRNA-gene regulatory network with clinical significance remains scarce.The emergence of high-throughput multi-omics data over large,well-characterized patient cohorts provides an unprecedented opportunity to address this problem.Herein,we performed a clinic-centered analysis to identify cancer-associated miRNAs,miRNA-target axis.We first calculated the correlation among miRNA,mRNA and 75 unique clinico-pathological characteristics(CPCs)in 26 cancer types,and established an online resource(4CR).Interestingly,we found that the high expression of several DNA methylation-related enzymes was associated with adverse outcomes of cancer patients,and these genes were regulated by a cluster of miRNAs.Furthermore,by integrating exosomal miRNA and m RNA databases,we identified exosomal miRNA biomarkers for non-invasive cancer surveillance and therapy monitoring.Finally,we explored the role of CPC-related miRNAs for therapeutic effect prediction of drugs based on their shared targets.Our analysis pipeline illustrated the significance of clinic-centered analysis in miRNA-gene pair identification and provided helpful clues for future cancer studies. | Xiuliang Cui Yang Liu Wen Sun Jin Ding Xiaochen Bo Hongyang Wang | 2020 | Science China(Life Sciences)2020，63，8： | 2 |
| 7 | Petrography and Geochemistry of the Upper Triassic Sandstones from the Western Ordos Basin, NW China: Provenance and Tectonic Implications显示文摘Petrographic and geochemical characteristics of the Upper Triassic sandstones in the western Ordos Basin were studied to provide insight into weathering characteristics,provenance,and tectonic implications.Petrographic features show that the sandstones are characterized by low-medium compositional maturity and textural maturity.The CIA and CIW values reveal weak and moderate weathering history in the source area.The geochemical characteristics together with palaeocurrent data show that the northwestern sediments were mainly derived from the Alxa Block with a typical recycled nature,while the provenance of the western and southwestern sediments were mainly from the Qinling-Qilian Orogenic Belt.The tectonic setting discrimination diagrams signify that the parent rocks of sandstones in the western and southern Ordos Basin were mainly developed from continental island arc,which is closely related to the evolution of the QinlingQilian Orogenic Belt.However,the sandstones in the northwestern Ordos Basin show complex features,which may be resulted from a typical recycling process.Overall evidence from petrography,geochemistry and sedimentology,together with previous researches suggest the Kongtongshan and Helanshan areas were the southwestern and northwestern boundary of the Ordos Basin,respectively,and there was no clear boundary between the Hexi Corridor Belt and Ordos Basin,where a large,uniform sediment dispersal system developed during the Late Triassic. | ZHAO Xiaochen LIU Chiyang XIAO Bo ZHAO Yan CHEN Yingtao | 2019 | Acta Geologica Sinica(English Edition)2019，93，6： | 2 |
| 8 | Experimental investigation on a cavity-step-actuated supersonic oscillating jet显示文摘Wind tunnel testing is conducted at different back pressures in a vacuum-type wind tunnel for a novel supersonic fluidic oscillator which consists of a two-dimensional Laval nozzle, a rectangular cavity and a backward step, to obtain its characteristics and the conditions for jet oscillating. The experimental results show that periodic asymmetrical flipping of the supersonic jet appears over certain nozzle pressure ratio(NPR) range according to schlieren visualization and pressure fluctuations. The jet flipping appears only when the jet is over expanded. The normalized average amplitude of the lateral pressure difference acting on the roofs of the cavity and the step varies around 0.2 while the periodic flipping appears. The supersonic jet periodic flipping frequencies obtained from the experiments agree well with those from the modified Rossiter mode for cavity-step acoustic resonance, but further investigations are needed to discover the underlying mechanism for the jet flipping. | Luo Xiaochen Sun Bo Wang Xiang'ang | 2017 | Chinese Journal of Aeronautics2017，30，1： | 2 |
| 9 | High-throughput sequencing reveals the disruption of methylation of imprinted gene in induced pluripotent stem cells显示文摘在导致的 pluripotent 干细胞(iPSCs ) 积累的反常 epigenetic 修正是否能最终影响 iPSC pluripotency,仍然保持争论。为了探查这个问题,有一样的基因背景的 iPSC 线和 proviral 集成地点,被建立,并且每根 iPSC 线的 pluripotency 状态用 tetraploid (4N ) 被描绘互补试金。随后,基因表示和 “ 的全球 epigenetic 修正; 4N-ON ”并且相应 “ 4N-OFF ”iPSC 线通过深定序 mRNA 表示,小 RNA 侧面, histone 修正(H3K27me3, H3K4me3,和 H3K4me2 ) ,和 DNA methylation 的分析被比较。我们发现了印的基因的那 methylation, Zrsr1,一致地与减少的 pluripotency 在 iPSC 线被破坏。而且,破坏 methylation 不能被改进文化条件或 iPSCs 的 subcloning 救。而且,在 iPSCs 的 Zrsr1 和 pluripotency 状态的 hypomethylation 之间的关系进一步在线从另外的 reprogramming 系统导出的独立 iPSC 被验证。 | Gang Chang Shuai Gao Xinfeng Hou Zijian Xu Yanfeng Liu Lan Kang Yu Tao Wenqiang Liu Bo Huang Xiaochen Kou Jiayu Chen Lei An Kai Miao Keqian Di Zhilong Wang Kun Tan Tao Cheng Tao Cai Shaorong Gao Jianhui Tian | 2014 | Cell Research2014，24，3： | 2 |
| 10 | A Yeast BiFC-seq Method for Genome-wide Interactome Mapping显示文摘Genome-wide physical protein±protein interaction(PPI)mapping remains a major challenge for current technologies.Here,we reported a high-efficiency BiFC-seq method,yeastenhanced green fluorescent protein-based bimolecular fluorescence complementation(y EGFPBiFC)coupled with next-generation DNA sequencing,for interactome mapping.We first applied y EGFP-BiFC method to systematically investigate an intraviral network of the Ebola virus.Two-thirds(9/14)of known interactions of EBOV were recaptured,and five novel interactions were discovered.Next,we used the BiFC-seq method to map the interactome of the tumor protein p53.We identified 97 interactors of p53,more than three-quarters of which were novel.Furthermore,in a more complex background,we screened potential interactors by pooling two BiFC libraries together and revealed a network of 229 interactions among 205 proteins.These results show that BiFC-seq is a highly sensitive,rapid,and economical method for genome-wide interactome mapping. | Limin Shang Yuehui Zhang Yuchen Liu Chaozhi Jin Yanzhi Yuan Chunyan Tian Ming Ni Xiaochen Bo Li Zhang Dong Li Fuchu He Jian Wang | 2022 | Genomics, Proteomics & Bioinformatics2022，20，4： | 1 |
| 11 | Replacement of Oct4 by Tet1 during iPSC Induction Reveals an Important Role of DNA Methylation/Hydroxymethylation in Reprogramming显示文摘 | Yawei Gao Jiayu Chen Ke Li Tong Wu Bo Huang Wenqiang Liu Xiaochen Kou Yu Zhang Hua Huang Yonghua Jiang Chao Yao Xiaolei Liu Zhiwei Lu Zijian Xu Lan Kang Jun Chen Hailin Wang Tao Cai Shaorong Gao | 2013 | Cell Stem Cell2013，，： | 1 |
| 12 | PIMD:An Integrative Approach for Drug Repositioning Using Multiple Characterization Fusion显示文摘The accumulation of various types of drug informatics data and computational approaches for drug repositioning can accelerate pharmaceutical research and development.However,the integration of multi-dimensional drug data for precision repositioning remains a pressing challenge.Here,we propose a systematic framework named PIMD to predict drug therapeutic properties by integrating multi-dimensional data for drug repositioning.In PIMD,drug similarity networks(DSNs)based on chemical,pharmacological,and clinical data are fused into an integrated DSN(iDSN)composed of many clusters.Rather than simple fusion,PIMD offers a systematic way to annotate clusters.Unexpected drugs within clusters and drug pairs with a high iDSN similarity score are therefore identified to predict novel therapeutic uses.PIMD provides new insights into the universality,individuality,and complementarity of different drug properties by evaluating the contribution of each property data.To test the performance of PIMD,we use chemical,pharmacological,and clinical properties to generate an iDSN.Analyses of the contributions of each drug property indicate that this iDSN was driven by all data types and performs better than other DSNs.Within the top 20 recommended drug pairs,7 drugs have been reported to be repurposed.The source code for PIMD is available at http://gffzz188fe103f8f1460as96cfv5qxuonw600f.ffgz.tsg.suse.edu.cn/Sepstar/PIMD/. | Song He Yuqi Wen Xiaoxi Yang Zhen Liu Xinyu Song Xin Huang Xiaochen Bo | 2020 | Genomics, Proteomics & Bioinformatics2020，18，5： | 1 |
| 13 | A small molecular electron acceptor based on asymmetric hexacyclic core of thieno[1,2-b]indaceno[5,6-b']thienothiophene for efficient fullerene-free polymer solar cells显示文摘A novel A-D-A(acceptor-donor-acceptor)type non-fullerene small molecule,A201,consisting of an asymmetric thieno[1,2-b]indaceno[5,6-b^0]thienothiophene(TITT)unit as middle D part and 2-(3-oxo-2,3-dihydroinden-1-ylidene)malononitrile(IC)groups as end-capped A parts was designed and synthesized.The asymmetric TITT building block showed a higher dipole moment of 0.85 Debye(1 Debye=3.33564?10^(à30)cm)compared with the symmetric analogues of indacenodithiophene(IDT)and indacenodithieno[3,2-b]thiophene(IDTT)of 0.098 and 0.13 Debye,respectively.The solution-processed bulk heterojunction solar cells using a benzotriazole(BTA)-based polymer of J71 as donor and A201 as acceptor,showed a power conversion efficiency(PCE)of 9.36%with an open-circuit voltage(V_(oc))of0.88 V,a short-circuit current(J_(sc))of 13.15 m A cm^(à2),and a fill factor(FF)of 0.67,under the illumination of AM 1.5G at 100 m W cm^(à2).The high PCE of this material combination could be attributed to its broad absorption spectrum and the high hole mobility(l_h)and electron mobility(l_e)of 9.56?10^(à4)and 5.17?10^(à4)cm^2V^(à1)s^(à1),respectively.These results indicate that the asymmetric electron-donating segments are promising to construct A-D-A type small molecular acceptors,which could largely enhance the diversity of building blocks to design photovoltaic materials. | Wenchao Zhai Ailing Tang Bo Xiao Xiaochen Wang Fan Chen Erjun Zhou | 2018 | Science Bulletin2018，63，13： | 1 |
| 14 | Replacement of Oct4 by Tet1 during iPSC Induction Reveals an Important Role of DNA Methylation/Hydroxymethylation in Reprogramming显示文摘 | Yawei Gao Jiayu Chen Ke Li Tong Wu Bo Huang Wenqiang Liu Xiaochen Kou Yu Zhang Hua Huang Yonghua Jiang Chao Yao Xiaolei Liu Zhiwei Lu Zijian Xu Lan Kang Jun Chen Hailin Wang Tao Cai Shaorong Gao | 2013 | Cell Stem Cell2013，，： | 1 |
| 15 | 3D genomic organization in cancers显示文摘Background:The hierarchical three-dimensional(3D)architectures of chromatin play an important role in fundamental biological processes,such as cell differentiation,cellular senescence,and transcriptional regulation.Aberrant chromatin 3D structural alterations often present in human diseases and even cancers,but their underlying mechanisms remain unclear.Results:3D chromatin structures(chromatin compartment A/B,topologically associated domains,and enhancerpromoter interactions)play key roles in cancer development,metastasis,and drug resistance.Bioinformatics techniques based on machine learning and deep learning have shown great potential in the study of 3D cancer genome.Conclusion:Current advances in the study of the 3D cancer genome have expanded our understanding of the mechanisms underlying tumorigenesis and development.It will provide new insights into precise diagnosis and personalized treatment for cancers. | Junting Wang Huan Tao Hao Li Xiaochen Bo Hebing Chen | 2023 | Quantitative Biology2023，11，2： | 0 |
| 16 | A Large Acute Gastroenteritis Outbreak Associated with Both Campylobacter coli and Human Sapovirus—Beijing Municipality,China,2021显示文摘Summary What is already known about this topic?Campylobacter is a significant foodborne pathogen that leads to global outbreaks of acute gastroenteritis(AGE)usually affecting less than 30 individuals.Human sapovirus(HuSaV)is an enteric virus responsible for sporadic cases and outbreaks of AGE worldwide.In a study conducted in Beijing,HuSaV detection ranked second after norovirus.What is added by this report?We present a discussion of the first large-scale outbreak of AGE caused by both Campylobacter coli(C.coli)and HuSaV.The outbreak involved a total of 996 patients and exhibited two distinct peaks over a period of 17 days.Through case-control studies,we identified exposure to raw water from a secondary water supply system as a significant risk factor.Among 83 patients,49 samples tested positive for C.coli,39 samples tested positive for HuSaV,and 27 samples tested positive for both pathogens using real-time polymerase chain reaction detection.Furthermore,whole-genome sequencing of 17 C.coli isolates obtained from 17 patients revealed that all isolates belonged to a highly clonal strain of C.coli.What are the implications for public health practice?Outbreaks of AGE resulting from multiple pathogen infections warrant increased attention.This report emphasizes the significance of ensuring the safety of drinking water,particularly in secondary supply systems. | Lin Zou Ying Li Guilan Zhou Zhenzhou Huang Changyan Ju Chunyan Zhao Xiang Gao Bojun Zhen Ping Zhang Xiaochen Guo Jing Zhang Yang Zhang Bo Liu Shaolei Zhou Aixia Yan Ying Kang Yanchun Wang Hongmei Ma Xiaohui Li Maojun Zhang | 2023 | China CDC weekly2023，5，52： | 0 |
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