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| 1 | Characterizing and annotating the genome using RNA-seq data显示文摘Bioinformatics methods for various RNA-seq data analyses are in fast evolution with the improvement of sequencing technologies. However, many challenges still exist in how to efficiently process the RNA-seq data to obtain accurate and comprehensive results. Here we reviewed the strategies for improving diverse transcriptomic studies and the annotation of genetic variants based on RNA-seq data. Mapping RNA-seq reads to the genome and transcriptome represent two distinct methods for quantifying the expression of genes/transcripts. Besides the known genes annotated in current databases, many novel genes/transcripts(especially those long noncoding RNAs) still can be identified on the reference genome using RNA-seq. Moreover, owing to the incompleteness of current reference genomes, some novel genes are missing from them. Genome-guided and de novo transcriptome reconstruction are two effective and complementary strategies for identifying those novel genes/transcripts on or beyond the reference genome. In addition, integrating the genes of distinct databases to conduct transcriptomics and genetics studies can improve the results of corresponding analyses. | Geng Chen Tieliu Shi Leming Shi | 2017 | Science China(Life Sciences)2017，60，2： | 22 |
| 2 | Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine显示文摘Realizing personalized medicine requires integrating diverse data types with bioinformatics.The most vital data are genomic information for individuals that are from advanced next-generation sequencing(NGS) technologies at present.The technologies continue to advance in terms of both decreasing cost and sequencing speed with concomitant increase in the amount and complexity of the data.The prodigious data together with the requisite computational pipelines for data analysis and interpretation are stressors to IT infrastructure and the scientists conducting the work alike.Bioinformatics is increasingly becoming the rate-limiting step with numerous challenges to be overcome for translating NGS data for personalized medicine.We review some key bioinformatics tasks,issues,and challenges in contexts of IT requirements,data quality,analysis tools and pipelines,and validation of biomarkers. | HONG HuiXiao ZHANG WenQian SHEN Jie SU ZhenQiang NING BaiTang HAN Tao PERKINS Roger SHI LeMing TONG WeiDa | 2013 | Science China(Life Sciences)2013，56，2： | 7 |
| 3 | mRNA enrichment protocols determine the quantification characteristics of external RNA spike-in controls in RNA-Seq studies显示文摘RNA-Seq promises to be used in clinical settings as a gene-expression profiling tool;however,questions about its variability and biases remain and need to be addressed.Thus,RNA controls with known concentrations and sequence identities originally developed by the External RNA Control Consortium(ERCC) for microarray and qPCR platforms have recently been proposed for RNA-Seq platforms,but only with a limited number of samples.In this study,we report our analysis of RNA-Seq data from 92 ERCC controls spiked in a diverse collection of 447 RNA samples from eight ongoing studies involving five species(human,rat,mouse,chicken,and Schistosoma japonicum) and two mRNA enrichment protocols,i.e.,poly(A) and RiboZero.The entire collection of datasets consisted of 15650143175 short sequence reads,131603796(i.e.,0.84%) of which were mapped to the 92 ERCC references.The overall ERCC mapping ratio of 0.84% is close to the expected value of 1.0% when assuming a 2.0% mRNA fraction in total RNA,but showed a difference of 2.8-fold across studies and 4.3-fold among samples from the same study with one tissue type.This level of fluctuation may prevent the ERCC controls from being used for cross-sample normalization in RNA-Seq.Furthermore,we observed striking biases of quantification between poly(A) and RiboZero which are transcript-specific.For example,ERCC-00116 showed a 7.3-fold under-enrichment in poly(A) compared to RiboZero.Extra care is needed in integrative analysis of multiple datasets and technical artifacts of protocol differences should not be taken as true biological findings. | QING Tao YU Ying DU TingTing SHI LeMing | 2013 | Science China(Life Sciences)2013，56，2： | 4 |
| 4 | Studies on abacavir-induced hypersensitivity reaction:a successful example of translation of pharmacogenetics to personalized medicine显示文摘Abacavir is an effective nucleoside analog reverse transcriptase inhibitor used to treat human immunodeficiency virus(HIV) infected patients.Its main side effect is hypersensitivity reaction(HSR).The incidence of the HSR is associated with ethnicity among patients exposed to abacavir,and retrospective and prospective studies show a significantly increased risk of abacavir-induced HSR in human leukocyte antigen(HLA)-B*57:01-carrying patients.Immunological studies indicated that abacavir interacts specifically with HLA-B*57:01 and changed the binding specificity between the HLA molecule and the HLA-presented endogenous peptide repertoire,leading to a systemic autoimmune reaction.HLA-B*57:01 screening,combined with patch testing,had clinically predictive value and cost-effective impact in reducing the incidence of abacavir-induced HSR regardless of the HLA-B*57:01 prevalence in the population.Therefore,the US Food and Drug Administration(FDA) and international HIV treatment guidelines recommend a routine HLA-B*57:01 screening prior to abacavir treatment to decrease false positive diagnosis and prevent abacavir-induced HSR.The studies of abacavir-induced HSR and the implementation of the HLA-B*57:01 screening in the clinic represent a successful example of the use of pharmacogenetics for personalized diagnosis and therapy. | GUO YongLi SHI LeMing HONG HuiXiao SU ZhenQiang FUSCOE James NING BaiTang | 2013 | Science China(Life Sciences)2013，56，2： | 3 |
| 5 | Identifying and annotating human bifunctional RNAs reveals their versatile functions显示文摘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. | Geng Chen Juan Yang Jiwei Chen Yunjie Song Ruifang Cao Tieliu Shi Leming Shi | 2016 | Science China(Life Sciences)2016，59，10： | 1 |
| 6 | Significant variations in alternative splicing patterns and expression profiles between human-mouse orthologs in early embryos显示文摘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. | Geng Chen Jiwei Chen Jianmin Yang Long Chen Xiongfei Qu Caiping Shi Baitang Ning Leming Shi Weida Tong Yongxiang Zhao Meixia Zhang Tieliu Shi | 2017 | Science China(Life Sciences)2017，60，2： | 1 |
| 7 | The effect of combination treatment with docosahexaenoic acid and 5-fluorouracil on the mRNA expression of apoptosis-related genes, including the novel gene BCL2L12, in gastric cancer cells显示文摘 | Zhuo Zhihong Zhang Leming Mu Qitian Lou Yanru Gong Zhaohui Shi Yijiu Ouyang Guifang Zhang Yi | 2009 | In Vitro Cellular & Developmental Biology . 2009 (1/2)2009，，1： | 1 |
| 8 | High performance genetic algorithm based text clustering using parts of speech and outlier elimination 显示文摘 | Shi Kansheng Li Leming | 2013 | Ap- plied Intelligence2013，38，4： | 1 |
| 9 | Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine显示文摘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 genome.This technology has led researchers to conduct an explosion of sequencing related projects in multidisciplinary fields of science.However,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 analysis.Particularly,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 toxicity.We 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. | Yaqiong Jin Geng Chen Wenming Xiao Huixiao Hong Joshua Xu Yongli Guo Wenzhong Xiao Tieliu Shi Leming Shi Weida Tong Baitang Ning | 2019 | Science China(Life Sciences)2019，62，7： | 1 |
| 10 | Next-generation sequencing in the clinic: Promises and challenges显示文摘 | Jiekun Xuan Ying Yu Tao Qing Lei Guo Leming Shi | 2012 | Cancer Letters2012，，： | 1 |
| 11 | Erratum to:Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine显示文摘 | HONG HuiXiao ZHANG WenQian SHEN Jie SU ZhenQiang NING BaiTang HAN Tao PERKINS Roger SHI LeMing TONG WeiDa | 2013 | Science China(Life Sciences)2013，56，3： | 0 |
| 12 | Erratum to:Studies on abacavir-induced hypersensitivity reaction:a successful example of translation of pharmacogenetics to personalized medicine显示文摘 | GUO YongLi SHI LeMing HONG HuiXiao SU ZhenQiang FUSCOE James NING BaiTang | 2013 | Science China(Life Sciences)2013，56，3： | 0 |
| 13 | Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency显示文摘Defects in genes involved in the DNA damage response cause homologous recombination repair deficiency(HRD).HRD is found in a subgroup of cancer patients for several tumor types,and it has a clinical relevance to cancer prevention and therapies.Accumulating evidence has identified HRD as a biomarker for assessing the therapeutic response of tumor cells to poly(ADP-ribose)polymerase inhibitors and platinum-based chemotherapies.Nevertheless,the biology of HRD is complex,and its applications and the benefits of different HRD biomarker assays are controversial.This is primarily due to inconsistencies in HRD assessments and definitions(gene-level tests,genomic scars,mutational signatures,or a combination of these methods)and difficulties in assessing the contribution of each genomic event.Therefore,we aim to review the biological rationale and clinical evidence of HRD as a biomarker.This review provides a blueprint for the standardization and harmonization of HRD assessments. | Wenbin Li Lin Gao Xin Yi Shuangfeng Shi Jie Huang Leming Shi Xiaoyan Zhou Lingying Wu Jianming Ying | 2023 | Genomics, Proteomics & Bioinformatics2023，21，5： | 0 |
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