|
|
|
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 | Diagnosis and Numerical Modeling of an Explosive Cyclone over the Northwestern Pacific显示文摘An explosive cyclone that took place over the Northwestern Pacific from 12 UTC 18 to 18 UTC 21 November 2007 was investigated.The synoptic situations and structure of this cyclone were documented by using the 1°×1°final analysis data of the National Center for Environmental Prediction.This cyclone developed explosively around 18 UTC 19 and reached its maximum deepening rate(MDR,1.3 Bergeron)around 06 UTC 20 November 2007.At its MDR moment,the surface cyclone center was located in the downstream of the upper-level trough and northern entrance zone of the upper-level jet.The diagnosis using Zwack-Okossi equation suggested that cyclonic-vorticity advection and warm air advection acted to deepen this cyclone,while adiabatic cooling suppressed its development.In an investigation of this cyclone development,numerical sensitivity results obtained by using the Weather and Research Forecasting model showed that the latent heat release in the lower level had less contribution,whereas the surface sensible and latent fluxes played important roles.With a warmer ocean surface,the cyclone tended to intensify.Two topography tests were designed to examine the mountain influences on the development of this cyclone:removing a mountain and doubling the height of a mountain.Results show that the Changbai Mountains suppressed the development of the cyclone by preventing the southern moisture air from invading the inland.Without the moisture air,no latent heat release occurs when this cyclone passes over the Changbai Mountains. | SUN Baitang LI Pengyuan ZHANG Shuqin GUO Jingtian FU Gang | 2021 | Journal of Ocean University of China2021，20，4： | 1 |
| 7 | 干扰COX-2基因表达对人肺腺癌A2细胞体外恶性增殖的影响(英文)显示文摘Objective:We explored the interfering effect of COX-2 gene expression and the influence on the malignant proliferation of A2 cells by RNAi after quenching COX-2 in vitro. Methods:COX-2 was selected as the subject. Three COX-2 siRNA expression vectors with human U6 promoter were constructed and three vectors and the vacant vector (pEGFP) were transfected into A2 cells with lipofectamine respectively. The cell strains transfected were constructed. The change of COX-2 expression levels was examined by Western blot and RT-PCR. The effects on the proliferation of A2 cells after silencing COX-2 were studied by cell growth curve and clonogenic assay in vitro. Results: The three siRNA and U6 promoter cloned into pEGFP plasmid were validated by PCR, restriction endonucleases identification, DNA sequencing and BLAST alignment. The cell strains transfected were named as A2-3, A2-7, A2-10 and A2-p respectively. Green fluorescence was seen in A2-p cells and not in A2-3, A2-7 and A2-10 cells in 24, 48 and 72 h after transfected. The results of RT-PCR and Western blot showed the three siRNA expression vectors produced effects and the expression of COX-2 was inhibited in different extent. In contrast to A2 cells, the levels of COX-2 mRNA of A2-3, A2-7 and A2-10 cells reduced 15.6%, 20.4% and 64.2% respectively; the levels of COX-2 protein of A2-3, A2-7 and A2-10 cells reduced 23.7%, 36.7% and 60.2% respectively. The results of cell growth curve and clonogenic assay showed the growth of A2-10 cell slowed and the colonial formation rate reduced but the growth of A2-3 and A2-7 cells had not obvious changes in contrast to the controls (A2 and A2-p). Conclusion: Silencing the COX-2 gene in vitro by RNAi technique can significantly inhibit the malignant proliferation of A2 cells. | Weiying Li Hui Wang Baitang Lai Xuehui Yang Chunyan Zhang | 2009 | The Chinese-German Journal of Clinical Oncology2009，8，9： | 1 |
| 8 | 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 |
| 9 | Enhanced stability of Fe-modified CuO-ZnO-ZrO_(2)-Al_(2)O_(3)/HZSM-5 bifunctional catalysts for dimethyl ether synthesis from CO_(2)hydrogenation显示文摘A series of iron(Fe)modified CuO-ZnO-ZrO_(2)-Al_(2)O_(3)(CZZA)catalysts,with various Fe loadings,were prepared using a co-precipitation method.A bifunctional catalyst,consisting of Fe-modified CZZA and HZSM-5,was studied for dimethyl ether(DME)synthesis via CO_(2)hydrogenation.The effects of Fe loading,reaction temperature,reaction pressure,space velocity,and concentrations of precursor for the synthesis of the Fe-modified CZZA catalyst on the catalytic activity of DME synthesis were investigated.Long-term stability tests showed that Fe modification of the CZZA catalyst improved the catalyst stability for DME synthesis via CO_(2)hydrogenation.The activity loss,in terms of DME yield,was significantly reduced from 4.2%to 1.4%in a 100 h run of reaction,when the Fe loading amount was 0.5(molar ratio of Fe to Cu).An analysis of hydrogen temperature programmed reduction revealed that the introduction of Fe improved the reducibility of the catalysts,due to assisted adsorption of H2 on iron oxide.The good stability of Femodified CZZA catalysts in the DME formation was most likely attributed to oxygen spillover that was introduced by the addition of iron oxide.This could have inhibited the oxidation of the Cu surface and enhanced the thermal stability of copper during long-term reactions. | Xiao Fan Shoujie Ren Baitang Jin Shiguang Li Miao Yu Xinhua Liang | 2021 | Chinese Journal of Chemical Engineering2021，34，10： | 1 |
| 10 | 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 |
| 11 | 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 |
| 12 | 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://gffzz964817d90372402ah5u0xq0p0kovk69p9.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 |
| 13 | Diagnostic Analyses and Numerical Modeling of Explosive Cyclone over Northwestern Pacific on January 11-13,2012显示文摘In this paper,we use FNL grid data obtained from the National Centers for Environmental Prediction(NCEP)to analyze an explosive cyclone(EC)that occurred over the northwestern Pacific Ocean from January 11 to 13,2012.To simulate the EC,we used the Weather Research and Forecasting model(WRFV3.5).The cyclone outbreak occurred east of Japan from January 11 to 12 and weakened near the Kamchatka Peninsula on January 13.The analysis results show a distinct frontal structure,in which the high potential vorticity(PV)of the upper troposphere extends downward to the surface,which can facilitate EC development.A low-level jet stream develops with the EC,which can lead to more distinct convergence.The results of sea surface temperature(SST)sensitivity tests suggest that changes in the SST can affect cyclone intensity,but have little effect on its path.When small changes are made to the SST,the air pressure at the cyclonic center responds more distinctly to an increased SST than a decreased SST.The results of our latent heat release test suggest that diabatic heating processes lead to maximum PV values in the lower troposphere.Latent heat is also one of the important factors influencing EC development. | WANG Guanlan SUN Baitang SUN Yawen LI Pengyuan | 2022 | Journal of Ocean University of China2022，21，4： | 0 |
| 14 | 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 |
| 15 | 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 |
| 16 | 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 |
| 17 | HZSM-5 zeolites undergoing the high-temperature process for boosting the bimolecular reaction in n-heptane catalytic cracking显示文摘High-temperature treatment is key to the preparation of zeolite catalysts.Herein,the effects of hightemperature treatment on the property and performance of HZSM-5 zeolites were studied in this work.X-Ray diffraction,N2physisorption,27Al magic angle spinning nuclear magnetic resonance(MAS NMR),and temperature-programmed desorption of ammonia results indicated that the hightemperature treatment at 650℃ hardly affected the inherent crystal and texture of HZSM-5zeolites but facilitated the conversion of framework Al to extra-framework Al,reducing the acid site and enhancing the acid strength.Moreover,the high-temperature treatment improved the performance of HZSM-5 zeolites in n-heptane catalytic cracking,promoting the conversion and light olefins yield while inhibiting coke formation.Based on the kinetic and mechanism analysis,the improvement of HZSM-5 performance caused by high-temperature treatment has been attributed to the formation of extra-framework Al,which enhanced the acid strength,facilitated the bimolecular reaction,and promoted the entropy change to overcome a higher energy barrier in n-heptane catalytic cracking. | Chenggong Song Zhenzhou Ma Xu Hou Hao Zhou Huimin Qiao Changchang Tian Li Yin Baitang Jin Enxian Yuan | 2024 | Chinese Journal of Chemical Engineering2024，66，2： | 0 |
| 18 | 同一靶点对不同Cyclooxygenase-2蛋白表达水平肺癌细胞恶性增殖的影响(英文)显示文摘Objective: The aim of the study was to explore the effects of the same target (si-10) on lung cancer cells with different expression levels of cyclooxygenase-2 (COX-2) protein by RNAi and malignant proliferation of these cells. Methods: COX-2 was selected as the target and one siRNA expression vector with the best effect was selected and thought as the subject from three COX-2 siRNA expression vectors with human U6 promoter. The siRNA expression vector (psi-10) and the vacant vector (pEGFP) were transfected into these cells with different COX-2 expression states (801D, A549 and LTEP-A2) with lipofectamine respectively and the transfected cell strains were constructed. The change of COX-2 expression levels was examined by Western blot and RT-PCR. The effects on the proliferation of lung cancer cells were studied by cell growth curve and clonogenic assay. Results: The siRNA and U6 promoter were validated by PCR, restriction endonucleases identification and DNA sequencing and BLAST alignment and cloned into the pEGFP vector. The cell strains transfected that 801D was used as maternal line were named as 801D-p and 801D-10 respectively. The cell strains transfected that A549 was used as maternal line were named as A549-p and A549-10 respectively. The cell strains transfected that LTEP-A2 was used as maternal line were named as LTEP-A2-p and LTEP-A2-10 respectively. These cells transfected pEGFP (801D-p, A549-p and LTEP-A2-p) had the expression of GFP and 801D-10, A549-10 and LTEP-A2-10 cells had not in 24, 48 and 72 hours after transfected. The results of RT-PCR and Western blot showed the siRNA expression vector produced marked effects in two cells (A549 and LTEP-A2) expressing COX-2 and the expression of COX-2 was inhibited. But the inhibited effects were differ- ent and the expression of COX-2 was more inhibited obviously in LTEP-A2 cells than in A549 cells though the expression of COX-2 was also inhibited obviously in A549 cells. In contract to their maternal line, the levels of COX-2 mRNA of LTEP-A2-10 and A549-10 cells reduced 64.2% and 61.2% respectively; the levels of COX-2 protein reduced 60.2% and 56.2% respectively. But the levels of COX-2 mRNA and protein had not change in 801D cells not expressing COX-2. The results of cell growth curve and clonogenic assay showed the growth of LTEP-A2-10 cells slowed and the clonal formation rate reduced and the size of the colonies became small; the growth of A549-10 cells showed slow and more obviously in the cell growth curve especially. But the growth of 801D-10 cells had not obvious change. Conclusion: The si-10 target of COX-2 has different inhibition effects on lung cancer cells with different COX-2 expression levels and the different inhibition effects have different effects on cells malignant proliferation. | Weiying Li Hui Wang Baitang Lai Xuehui Yang Chunyan Zhang | 2010 | The Chinese-German Journal of Clinical Oncology2010，9，3： | 0 |
您所在的机构暂未开通此部分的功能，请联系管理员