|
|
|
题名
|
作者
|
年代
|
出处
|
被引量
|
| 1 | 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 |
| 2 | 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 |
| 3 | Identification of Functional Genetic Variants in Cyclooxygenase-2 and Their Association With Risk of Esophageal Cancer显示文摘 | Xuemei Zhang Xiaoping Miao Wen Tan Baitang Ning Zhihua Liu Yuan Hong Wenguang Song Yongli Guo Xinyu Zhang Yan Shen Boqin Qiang Fred F. Kadlubar Dongxin Lin | 2005 | Gastroenterology2005，，2： | 1 |
| 4 | Identification of Functional Genetic Variants in Cyclooxygenase-2 and Their Association With Risk of Esophageal Cancer显示文摘 | Xuemei Zhang Xiaoping Miao Wen Tan Baitang Ning Zhihua Liu Yuan Hong Wenguang Song Yongli Guo Xinyu Zhang Yan Shen Boqin Qiang Fred F. Kadlubar Dongxin Lin | 2005 | Gastroenterology2005，，2： | 1 |
| 5 | Identification of Functional Genetic Variants in Cyclooxygenase-2 and Their Association With Risk of Esophageal Cancer显示文摘 | Xuemei Zhang Xiaoping Miao Wen Tan Baitang Ning Zhihua Liu Yuan Hong Wenguang Song Yongli Guo Xinyu Zhang Yan Shen Boqin Qiang Fred F. Kadlubar Dongxin Lin | 2005 | Gastroenterology2005，，2： | 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 | Assessment of research models for testing gene–environment interactions显示文摘 | Amy L. Inselman Deborah K. Hansen Hyung-yul Lee Noriko Nakamura Baitang Ning Jacqueline Pontes Monteiro Vijayalakshmi Varma Jim Kaput | 2011 | European Journal of Pharmacology2011，，： | 1 |
| 8 | 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 |
| 9 | QuaPra: Efficient transcript assembly and quantification using quadratic programming with Apriori algorithm显示文摘RNA sequencing(RNA-seq) has greatly facilitated the exploring of transcriptome landscape for diverse organisms.However,transcriptome reconstruction is still challenging due to various limitations of current tools and sequencing technologies.Here,we introduce an efficient tool,QuaPra(Quadratic Programming combined with Apriori),for accurate transcriptome assembly and quantification.QuaPra could detect at least 26.5% more low abundance(0.1–1 FPKM) transcripts with over 2.7% increase of sensitivity and precision on simulated data compared to other currently popular tools.Moreover,around one-quarter more known transcripts were correctly assembled by QuaPra than other assemblers on real sequencing data.QuaPra is freely available at http://gffzz964817d90372402ah996bv5cc9b656o5n.ffgz.tsg.suse.edu.cn/QuaPra/. | Xiangjun Ji Weida Tong Baitang Ning Christopher E. Mason David P. Kreil Pawel P. Labaj Geng Chen Tieliu Shi | 2019 | Science China(Life Sciences)2019，62，7： | 1 |
| 10 | ERCC6基因启动子区-6530C→G单核苷酸多态性的功能性分析显示文摘 | 林忠宁 凌文华 Baitang Ning Fred K Kadlubar | 2005 | 毒理学杂志2005，19，A03： | 0 |
| 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 |
您所在的机构暂未开通此部分的功能，请联系管理员