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Science China(Life Sciences) 2013年第2期56卷 143-155页

作者： LU BingXin ZENG ZhenBing shi tieliu Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal University Software Engineering Institute School of Software EngineeringEast China Normal University

Transcriptome reconstruction is an important application of RNA-Seq,providing critical information for further analysis of *** RNA-Seq offers the potential to identify the whole picture of transcriptome,it still presents special *** handle these difficulties and reconstruct transcriptome as completely as possible,current computational approaches mainly employ two strategies:de novo assembly and genome-guided *** order to find the similarities and differences between them,we firstly chose five representative assemblers belonging to the two classes respectively,and then investigated and compared their algorithm features in theory and real performances in *** found that all the methods can be reduced to graph reduction problems,yet they have different conceptual and practical implementations,thus each assembly method has its specific advantages and disadvantages,performing worse than others in certain aspects while outperforming others in anther aspects at the same *** we merged assemblies of the five assemblers and obtained a much better *** we evaluated an assembler using genome-guided de novo assembly approach,and achieved good *** on these results,we suggest that to obtain a comprehensive set of recovered transcripts,it is better to use a combination of de novo assembly and genome-guided assembly.

关键词： transcriptome reconstruction RNA-Seq de novo assembly genome-guided assembly

Analysis and application of large-scale protein-protein interaction data sets

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Chinese Science Bulletin 2005年第20期50卷 2267-2272页

作者： SUN Jingchun XU Jinlin LI Yixue shi tieliu School of Life Sciences & Technology Shanghai Jiaotong University Shanghai 200240 China Bioinformation Center Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China

Protein-protein interactions play key roles in cells. Lots of experimental approaches and in silico methods have been developed to identify and predict large-scale pro- tein-protein interactions. However, compared with the tradi- tionally experimental results, the high-throughput pro- tein-protein interaction data often contain the false positives in high probability. In order to fully utilize the large-scale data, it is necessary to develop bioinformatic methods for systematically evaluating those data in order to further im- prove the data reliability and mine biological information. This review summarizes the methodologies of analysis and application of high-throughput protein-protein interaction data, including the evaluation methods, the relationship be- tween protein-protein interaction data and other protein biological information, and their applications in biological study. In addition, this paper also suggests some interesting topics on mining high-throughput protein-protein interaction data.

关键词：蛋白质交互作用生物学功能预测生物途径

Lack of correlation between aristolochic acid exposure and hepatocellular carcinoma

维普期刊数据库评论

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维普期刊数据库

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Science China(Life Sciences) 2018年第6期61卷 727-728页

作者： Xiangjun Ji Guoshuang Feng Geng Chen tieliu shi The Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biology the Institute of Biomedical Sciences and School of Life Sciences East China Normal University Center for Clinical Epidemiology & Evidence-based Medicine Beijing Children's Hospital Capital Medical UniversityNational Center for Children's Health

Besides upper tract urothelial cell carcinoma(UTUCs),a recent study published in Science Translational Medicine has indicated that liver cancer may be associated with the exposure of aristolochic acids and similar derivatives(collectively,AA).However,according to our research,this study needs more number of samples for further verification which should be sampled from a wider range of people.

关键词： Lack of correlation between aristolochic acid exposure and hepatocellular carcinoma

De novo transcriptome assembly of RNA-Seq reads with different strategies

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Science China(Life Sciences) 2011年第12期54卷 1129-1133页

作者： CHEN Geng YIN KangPing WANG Charles shi tieliu Center for Bioinformatics and Computational Biology Institute of Biomedical Sciences School of Life Science East China Normal University Shanghai 200241 China Functional Genomics Core Beckman Research Institute City of Hope Comprehensive Cancer Center Duarte CA 91010 USA

De novo transcriptome assembly is an important approach in RNA-Seq data analysis and it can help us to reconstruct the transcriptome and investigate gene expression profiles without reference genome *** carried out transcriptome assemblies with two RNA-Seq datasets generated from human brain and cell line,*** then determined an efficient way to yield an optimal overall assembly using three different *** first assembled brain and cell line transcriptome using a single k-mer *** we tested a range of values of k-mer length and coverage cutoff in ***,we combined the assembled contigs from a range of k values to generate a final *** comparing these assembly results,we found that using only one k-mer value for assembly is not enough to generate good assembly results,but combining the contigs from different k-mer values could yield longer contigs and greatly improve the overall assembly.

关键词： RNA-Seq de novo transcriptome assembly next generation sequencing

Identifying and annotating human bifunctional RNAs reveals their versatile functions

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Science China(Life Sciences) 2016年第10期59卷 981-992页

作者： Geng Chen Juan Yang Jiwei Chen Yunjie Song Ruifang Cao tieliu shi Leming shi Center for Pharmacogenomics School of Pharmacy and School of Life SciencesFudan UniversityShanghai 201203China The Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology School of Life SciencesFudan UniversityShanghai 201203China Fudan-Zhangjiang Center for Clinical Genomics Shanghai 201203China Zhanjiang Center for Translational Medicine Shanghai 201203China

Bifunctional RNAs that possess both protein-coding and noncoding functional properties were less explored and poorly understood. Here we systematically explored the characteristics and functions of such human bifunctional RNAs by integrating tandem mass spectrometry and RNA-seq data. We first constructed a pipeline to identify and annotate bifunctional RNAs,leading to the characterization of 132 high-confidence bifunctional RNAs. Our analyses indicate that bifunctional RNAs may be involved in human embryonic development and can be functional in diverse tissues. Moreover, bifunctional RNAs could interact with multiple miRNAs and RNA-binding proteins to exert their corresponding roles. Bifunctional RNAs may also function as competing endogenous RNAs to regulate the expression of many genes by competing for common targeting miRNAs. Finally,somatic mutations of diverse carcinomas may generate harmful effect on corresponding bifunctional RNAs. Collectively,our study not only provides the pipeline for identifying and annotating bifunctional RNAs but also reveals their important gene-regulatory functions.

关键词： bifunctional RNA noncoding RNA RNA-seq tandem mass spectrometry

Biological data processing based on bio-processor unit(BPU), a new concept for next generation computational biology

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Science China(Life Sciences) 2018年第5期61卷 597-598页

作者： Di Liu Dongbo Bu tieliu shi Jianxiao Quan Depeng Wang Yongyong shi Xiao-Chen Bo Wenbao Han Computational Virology Group Wuhan Institute of Virology Chinese Academy of Sciences Wuhan 430071 China Key Laboratory of InteUigent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing 100190 China Center for Bioinformatics and Computational Biology and the Institute of Biomedical Sciences School of Life Sciences East China Normal University Shanghai 200214 China State Key Laboratory of Mathematical Engineering and Advanced Computation Wuxi 214122 China Jiangsu Variable Supercomputer Tech Co Ltd. Wuxi 214125 China NextOmics Blosctences Wuhan 430074 China Bio-X Institutes Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) Shanghai Jiao Tong University Shanghai 200030 China Beijing Institute of Radiation Medicine Beifing 100850 China

The revolution of biotechnology has pushed forward life sciences into the Big Data ***,high-throughput bio-techniques have greatly accelerated the integration of biology,computing and informatics,and hence substantially pushed forward the development of bioinformatics and computational *** to the latest report of data deposition within National Centre for Biotechnology Information（NCBI）,the genome sequencing projects have increased 49.94%.

关键词：计算生物学简历处理器数据基信息科学生物信息学生命科学 NCBI

Significant variations in alternative splicing patterns and expression profiles between human-mouse orthologs in early embryos

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Science China(Life Sciences) 2017年第2期60卷 178-188页

作者： Geng Chen Jiwei Chen Jianmin Yang Long Chen Xiongfei Qu Caiping shi Baitang Ning Leming shi Weida Tong Yongxiang Zhao Meixia Zhang tieliu shi The Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biology the Institute of Biomedical Sciences and School of Life Sciences East China Normal University Center for Pharmacogenomics School of Pharmacy Fudan University National Center for Toxicological Research US Food and Drug Administration Biological Targeting Diagnosis and Therapy Research Center Guangxi Medical University Department of Ophthalmology West China Hospital Sichuan University

Human and mouse orthologs are expected to have similar biological functions; however, many discrepancies have also been reported. We systematically compared human and mouse orthologs in terms of alternative splicing patterns and expression profiles. Human-mouse orthologs are divergent in alternative splicing, as human orthologs could generally encode more isoforms than their mouse orthologs. In early embryos, exon skipping is far more common with human orthologs, whereas constitutive exons are more prevalent with mouse orthologs. This may correlate with divergence in expression of splicing regulators. Orthologous expression similarities are different in distinct embryonic stages, with the highest in morula. Expression differences for orthologous transcription factor genes could play an important role in orthologous expression discordance. We further detected largely orthologous divergence in differential expression between distinct embryonic stages. Collectively, our study uncovers significant orthologous divergence from multiple aspects, which may result in functional differences and dynamics between human-mouse orthologs during embryonic development.

关键词： ortholog alternative splicing RNA-seq early embryo gene expression

Single-cell transcriptomic analysis reveals dynamic alternative splicing and gene regulatory networks among pancreatic islets

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Science China(Life Sciences) 2021年第1期64卷 174-176页

作者： Yunjin Li Jiwei Chen Qiyue Xu Zebei Han Fei Tan tieliu shi Geng Chen Center for Bioinformatics and Computational Biology and Shanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical SciencesSchool of Life SciencesEast China Normal UniversityShanghai200241China Shanghai Skin Disease Hospital Anhui Medical UniversityShanghai200443China

Dear Editor,An increasing number of single-cell RNA-seq(scRNA-seq)studies gained deep insights into the gene expression heterogeneity among individual cells by cell type/state identification(Chen et al.,2019).Alternative splicing(AS)enables genes to generate multiple isoforms through the combination of disparate exons to increase the diversity of transcriptome(Lee and Rio,2015).

关键词： al. gained among

Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine

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Science China(Life Sciences) 2019年第7期62卷 895-904页

作者： Yaqiong Jin Geng Chen Wenming Xiao Huixiao Hong Joshua Xu Yongli Guo Wenzhong Xiao tieliu shi Leming shi Weida Tong Baitang Ning Beijing Key Laboratory for Pediatric Diseases of Otolaryngology Head and Neck SurgeryBeijing Pediatric Research InstituteBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijing 100045China Center for Bioinformatics and Computational Biology and the Institute of Biomedical SciencesShanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China National Center for Toxicological Research U.S. Food and Drug AdministrationJefferson AR 72079USA Department of Surgery Massachusetts General HospitalHarvard Medical SchoolBoston MA 02114USA State Key Laboratory of Genetic Engineering School of Life Sciences and Cancer CenterCollaborative Innovation Center for Genetics and DevelopmentFudan UniversityShanghai 200433China

High-throughput next generation sequencing (NGS) is a shotgun approach applied in a parallel fashion by which the genome is fragmented and sequenced through small pieces and then analyzed either by aligning to a known reference genome or by de novo assembly without reference *** technology has led researchers to conduct an explosion of sequencing related projects in multidisciplinary fields of ***,due to the limitations of sequencing-based chemistry,length of sequencing reads and the complexity of genes,it is difficult to determine the sequences of some portions of the human genome,leaving gaps in genomic data that frustrate further ***,some complex genes are difficult to be accurately sequenced or mapped because they contain high GC-content and/or low complexity regions,and complicated pseudogenes,such as the genes encoding xenobiotic metabolizing enzymes and transporters (XMETs).The genetic variants in XMET genes are critical to predicate interindividual variability in drug efficacy,drug safety and susceptibility to environmental *** summarized and discussed challenges,wet-lab methods,and bioinformatics algorithms in sequencing "complex" XMET genes,which may provide insightful information in the application of NGS technology for implementation in toxicogenomics and pharmacogenomics.

关键词： next generation sequencing precision medicine xenobiotic metabolizing enzymes and transporters toxicogenomics pharmacogenomics

Prediction and systematic study of protein-protein interaction networks of Leptospira interrogans

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Chinese Science Bulletin 2006年第11期51卷 1296-1305页

作者： SUN Jingchun XU Jinlin CAO Jianping LIU Qi GUO Xiaokui shi tieliu LI Yixue School of Life Sciences and Technology Shanghai Jiaotong University Shanghai 200240 China Biomedical Engineering School of Life Science & Technology University of Electronic Science and Technology of China Chengdu 610054 China Department of Microbiology and Parasitology Shanghai Jiao Tong University School of Medicine Shanghai 200025 China Bioinformation Center Shanghai Institute for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China

Leptospira interrogans serovar Lai is a pathogenic bacterium that causes a spirochetal zoonosis in humans and some animals. With its complete genome sequence available, it is possible to analyze protein-protein interactions from a whole- genome standpoint. Here we combine four recently developed computational approaches (gene fusion method, gene neighbor method, phylogenetic profiles method, and operon method) to predict protein-pro- tein interaction networks of Leptospira interrogans strain Lai. Through comprehensive analysis on in- teractions among proteins of motility and chemotaxis system, signal transduction, lipopolysaccaride bio- synthesis and a series of proteins related to adhesion and invasion, we provided information for further studying on its pathogenic mechanism. In addition, we also assigned 203 previously uncharacterized proteins with possible functions based on the known functions of its interacting partners. This work is helpful for further investigating L. interrogans strain Lai.

关键词：蛋白质-蛋白质交互作用网络基因融合基因序列系统发育操纵子