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26th Annual Computational Neuroscience Meeting (CNS*2017) of the Organization for Computational Neuroscience Antwerp, Belgium, July 15-20, 2017

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BMC NEUrOSCIENCE 2017年第SUPPL 1期18卷 59-59页

作者： [Anonymous] Indiana University Purdue University Indianapolis Indianapolis IN 46032 USA Stark Neurosciences Research Institute Indiana University School of Medicine Indianapolis IN 46032 USA Department of Mathematics East Carolina University Greenville NC 27858 USA Jülich Supercomputing Centre Forschungszentrum Jülich 52425 Jülich Germany Future Systems Swiss National Supercomputing Centre 8092 Zurich Switzerland User Engagement and Support Swiss National Supercomputing Centre 6900 Lugano Switzerland Institut de Neurosciences des Systèmes Aix Marseille Univ 13005 Marseille France Simulation Lab Neuroscience Forschungszentrum Jülich Jülich Germany Department of Experimental Psychology Ghent University 9000 Ghent Belgium Donders Center for Cognitive Neuroimaging Radboud University 6525HR Nijmegen The Netherlands Department of Electrical Computer and Energy Engineering University of Colorado Boulder CO 80309 USA Department of Neurosurgery Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Neurology Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Otolaryngology Johns Hopkins School of Medicine Baltimore MD 21287 USA INSERM U968 Paris France Sorbonne Universités UPMC University Paris 06 UMR_S 968 Institut de la Vision Paris France CNRS UMR_7210 Paris France Department of Computer Architecture and Technology University of Granada (CITIC) Granada Spain Sorbonne Universités UPMC Univ Paris 06 INSERM CNRS Institut de la Vision Paris France Department of Adaptive Machine Systems Osaka University Osaka Japan Department of Computer Science University of Cergy-Pontoise Cergy-Pontoise France Department of Physics and Astronomy College of Charleston Charleston SC 29424 USA School of Physics Faculty of Science University of Sydney Sydney NSW 2006 Australia Center of Excellence for Integrative Brain Function Australian Research Council Sydney Australia Max Planck Institute for Human Cognitive and Brain Sciences Saxony Lei

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Evaluation of the inhibitory effect of various drugs / active ingredients on the activity of human diamine oxidasein vitro

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Clinical and Translational Allergy 2014年第S3期4卷 P23-P23页

作者： roland Leitner Eva Zoernpfenning Albert Missbichler Scientific Association for Research and Education in the field of food-intolerances Austria University of Applied Sciences FH Campus Wien Molecular Biotechnology Program Austria SCIOTEC Diagnostic Technologies GmbH R&D Austria

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Comparison of rNA-seq and microarray-based models for clinical endpoint prediction

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GENOME BIOLOGY 2015年第1期16卷 133-133页

作者： Zhang, Wenqian Yu, Ying Hertwig, Falk Thierry-Mieg, Jean Zhang, Wenwei Thierry-Mieg, danielle Wang, Jian Furlanello, Cesare devanarayan, Viswanath Cheng, Jie deng, Youping Hero, Barbara Hong, Huixiao Jia, Meiwen Li, Li Lin, Simon M. Nikolsky, Yuri Oberthuer, Andre Qing, Tao Su, Zhenqiang Volland, ruth Wang, Charles Wang, May d. Ai, Junmei Albanese, davide Asgharzadeh, Shahab Avigad, Smadar Bao, Wenjun Bessarabova, Marina Brilliant, Murray H. Brors, Benedikt Chierici, Marco Chu, Tzu-Ming Zhang, Jibin Grundy, richard G. He, Min Max Hebbring, Scott Kaufman, Howard L. Lababidi, Samir Lancashire, Lee J. Li, Yan Lu, Xin X. Luo, Heng Ma, Xiwen Ning, Baitang Noguera, rosa Peifer, Martin Phan, John H. roels, Frederik rosswog, Carolina Shao, Susan Shen, Jie Theissen, Jessica Tonini, Gian Paolo Vandesompele, Jo Wu, Po-Yen Xiao, Wenzhong Xu, Joshua Xu, Weihong Xuan, Jiekun Yang, Yong Ye, Zhan dong, Zirui Zhang, Ke K. Yin, Ye Zhao, Chen Zheng, Yuanting Wolfinger, russell d. Shi, Tieliu Malkas, Linda H. Berthold, Frank Wang, Jun Tong, Weida Shi, Leming Peng, Zhiyu Fischer, Matthias BGI Shenzhen Shenzhen 518083 Guangdong Peoples R China Fudan Univ Sch Life Sci Collaborat Innovat Ctr Genet & Dev State Key Lab Genet Engn Shanghai 201203 Peoples R China Fudan Univ Sch Life Sci MOE Key Lab Contemporary Anthropol Shanghai 201203 Peoples R China Fudan Univ Sch Pharm Shanghai 201203 Peoples R China Univ Childrens Hosp Cologne Dept Pediat Oncol & Hematol D-50924 Cologne Germany Univ Cologne Fac Med Ctr Mol Med CMMC D-50924 Cologne Germany NIH NCBI Bethesda MD 20894 USA Eli Lilly & Co Res Informat Lilly Corp Ctr Indianapolis IN 46285 USA FBK I-38123 Trento Povo TN Italy AbbVie Inc Global Pharmaceut R&D Souderton PA 18964 USA GlaxoSmithKline Discovery Analyt Collegeville PA 19426 USA Rush Univ Ctr Canc Dept Internal Med Chicago IL 60612 USA US FDA Natl Ctr Toxicol Res Jefferson AR 72079 USA SAS Inst Inc Cary NC 27513 USA Marshfield Clin Res Fdn Biomed Informat Res Ctr Marshfield WI 54449 USA Thomson Reuters IP & Sci Carlsbad CA 92008 USA Loma Linda Univ Ctr Genom Loma Linda CA 92350 USA Loma Linda Univ Sch Med Div Microbiol & Mol Genet Loma Linda CA 92350 USA GeorgiaTech Dept Biomed Engn Atlanta GA 30332 USA Emory Univ Atlanta GA 30332 USA CRI CBC Fdn Edmund Mach San Michele All Adige TN Italy Childrens Hosp Los Angeles Los Angeles CA 90027 USA Schneider Childrens Med Ctr Israel Felsenstein Med Res Ctr Dept Pediat Hematol Oncol Mol Oncol IL-49202 Petah Tiqwa Israel Marshfield Clin Res Fdn Ctr Human Genet Marshfield WI 54449 USA German Canc Res Ctr Dept Theoret Bioinformat D-69120 Heidelberg Germany Univ Nottingham Queens Med Ctr Childrens Brain Tumour Res Ctr Nottingham NG7 2UH England US FDA Ctr Biol Evaluat & Res Rockville MD 20852 USA AbbVie Inc Global Pharmaceut Res & Dev Abbott Pk IL 60064 USA Univ Arkansas UALR UAMS Joint Bioinformat Grad Program Little Rock AR 72204 USA Eli Lilly & Co Lilly Corp Ctr Discovery Stat Indianapolis IN 46285 USA Univ Valencia Sch Med Dept Pathol Valencia 46010 Spain Un

Background: Gene expression profiling is being widely applied in cancer research to identify biomarkers for clinical endpoint prediction. Since rNA-seq provides a powerful tool for transcriptome-based applications beyond the limitations of microarrays, we sought to systematically evaluate the performance of rNA-seq-based and microarray-based classifiers in this MAQC-III/SEQC study for clinical endpoint prediction using neuroblastoma as a model. results: We generate gene expression profiles from 498 primary neuroblastomas using both rNA-seq and 44 k microarrays. Characterization of the neuroblastoma transcriptome by rNA-seq reveals that more than 48,000 genes and 200,000 transcripts are being expressed in this malignancy. We also find that rNA-seq provides much more detailed information on specific transcript expression patterns in clinico-genetic neuroblastoma subgroups than microarrays. To systematically compare the power of rNA-seq and microarray-based models in predicting clinical endpoints, we divide the cohort randomly into training and validation sets and develop 360 predictive models on six clinical endpoints of varying predictability. Evaluation of factors potentially affecting model performances reveals that prediction accuracies are most strongly influenced by the nature of the clinical endpoint, whereas technological platforms (rNA-seq vs. microarrays), rNA-seq data analysis pipelines, and feature levels (gene vs. transcript vs. exon-junction level) do not significantly affect performances of the models. Conclusions: We demonstrate that rNA-seq outperforms microarrays in determining the transcriptomic characteristics of cancer, while rNA-seq and microarray-based models perform similarly in clinical endpoint prediction. Our findings may be valuable to guide future studies on the development of gene expression-based predictive models and their implementation in clinical practice.

关键词： Overall Survival Neuroblastoma Prediction Performance Clinical Endpoint Gene Expression Model

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Aerodynamic simulation of evacuated tube maglev trains with different streamlined designs

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Journal of Modern Transportation 2013年第2期20卷 115-120页

作者： Chen, Xuyong Zhao, Lifeng Ma, Jiaqing Liu, Yuansen Key Laboratory of Magnetic Levitation Technologies and Maglev Trains (Ministry of Education of China) Superconductivity and New Energy R&D Center Southwest Jiaotong University Chengdu China

Based on the Navier-Stokes (N-S) equations of incompressible viscous fluids and the standard k-ε turbulence model with assumptions of steady state and two dimensional conditions, a simulation of the aerodynamic drag on a maglev train in an evacuated tube was made with ANSYS/FLOTrAN software under different vacuum pressures, blockage ratios, and shapes of train head and tail. The pressure flow fields of the evacuated tube maglev train under different vacuum pressures were analyzed, and then compared under the same blockage ratio condition. The results show that the environmental pressure of 1 000 Pa in the tube is the best to achieve the effect of aerodynamic drag reduction, and there are no obvious differences in the aerodynamic drag reduction among different streamline head shapes. Overall, the blunt-shape tail and the blockage ratio of 0.25 are more efficient for drag reduction of the train at the tube pressure of 1 000 Pa.

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AN UPWINd EULErIAN-EULErIAN MOdEL FOr NON-EQUILIBrIUM CONdENSATION IN STEAM TUrBINES

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ASME Turbo Expo: Turbine Technical Conference and Exposition

作者： Zhu, Xiaofeng Yuan, Xin Lin, Zhirong Shibukawa, Naoki Tsukuda, Tomohiko Niizeki, Yoshiki Tanuma, Tadashi Tsinghua Univ Key Lab Thermal Sci & Power Engn Minist Educ Beijing 100084 Peoples R China Toshiba Corp Power Syst Co R&D Ctr Power & Ind Syst Yokohama Kanagawa 2300045 Japan Teikyo Univ Joint Program Ctr Appl Fluid Dynam & Energy Machinery Syst Tokyo 1738605 Japan

ISBN: (纸本)9780791855201

The present paper proposes an Eulerian-Eulerian two-phase model for non-equilibrium condensing flow in steam turbines. This model is especially suitable for upwind finite volume scheme. An approximate roe type flux using real water/vapor property is constructed to calculate the upwind wet-steam flux. This flux fully couples the wetness fraction with other conservative variables in the Jacobian Matrix whose eigen-vector and eigen-value are analitically derived. A novel treatment of real wet-steam property is developed by constructing a 3-dOFs TTSE table according to IAPWS97 formulas. The table is actually a cubic and uses the mixture's density, the mixture's internal energy and wetness as independent variables. Besides homogeneous condensation, heterogeneous condensing is also integrated into the model, which facilitates simulating the effect of salt *** above methods are validated through two nozzle and one turbine cascade calculations and finally applied to a model LP steam turbine stage. results show that the current model is very robust and is able to correctly capture the non-equilibrium condensation phenomena.

关键词： Flow (dynamics) Cascades (Fluid dynamics) Steam turbines Turbines Internal energy (Physics) Nozzles Steam Water vapor Condensation Equilibrium (Physics) Jacobian matrices density Eigenvalues

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Nanocasting Technique to Prepare Lotus-leaf-like Superhydrophobic Electroactive Polyimide as Advanced Anticorrosive Coatings

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ACS APPLIEd MATErIALS & INTErFACES 2013年第4期5卷 1460-1467页

作者： Chang, Kung-Chin Lu, Hsin-I Peng, Chih-Wei Lai, Mei-Chun Hsu, Sheng-Chieh Hsu, Min-Hsiang Tsai, Yuan-Kai Chang, Chi-Hao Hung, Wei-I Wei, Yen Yeh, Jui-Ming Chung Yuan Christian Univ Dept Chem Chungli 32023 Taiwan Chung Yuan Christian Univ Ctr Nanotechnol Chungli 32023 Taiwan Chung Yuan Christian Univ R&D Ctr Membrane Technol Chungli 32023 Taiwan Chung Yuan Christian Univ Master Program Nanotechnol Chungli 32023 Taiwan Acad Sinica Inst Chem Taipei 115 Taiwan Tsinghua Univ Dept Chem Minist Educ Beijing 100084 Peoples R China Tsinghua Univ Minist Educ Key Lab Organ Optoelect & Mol Engn Beijing 100084 Peoples R China

Nanocasting technique was used to obtain a biomimetic superhydrophobic electroactive polyimide (SEPI) surface structure from a natural Xanthosoma sagittifolium leaf. An electroactive polyimide (EPI) was first synthesized through thermal imidization. An impression of the superhydrophobic Xanthosoma sagittifolium leaf was then nanocasted onto the surface of the EPI so that the resulting EPI was superhydrophobic and would prevent corrosion. Polydimethylsiloxane (PdMS) was then used as a negative template to transfer the impression of the superhydrophobic surface of the biomimetic EPI onto a cold-rolled steel (CrS) electrode. The superhydrophobic electroactive material could be used as advanced coatings that protect metals against corrosion. The morphology of the surface of the as-synthesized SEPI coating was investigated using scanning electron microscopy (SEM). The surface showed numerous micromastoids, each decorated with many nanowrinkles. The water contact angle (CA) for the SEPI coating was 155 degrees, which was significantly larger than that for the EPI coating (i.e., CA = 87 degrees). The significant increase in the contact angle indicated that the biomimetic morphology effectively repelled water. Potentiodynamic and electrochemical impedance spectroscopic measurements indicated that the SEPI coating offered better protection against corrosion than the EPI coating did.

关键词： superhydrophobic electroactive polyimide anticorrosion nanocasting

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Exome-wide association study of plasma lipids in >300,000 individuals

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NATUrE GENETICS 2017年第12期49卷 1758-+页

作者： Liu, dajiang J. Peloso, Gina M. Yu, Haojie Butterworth, Adam S. Wang, Xiao Mahajan, Anubha Saleheen, danish Emdin, Connor Alam, dewan Alves, Alexessander Couto Amouyel, Philippe di Angelantonio, Emanuele Arveiler, dominique Assimes, Themistocles L. Auer, Paul L. Baber, Usman Ballantyne, Christie M. Bang, Lia E. Benn, Marianne Bis, Joshua C. Boehnke, Michael Boerwinkle, Eric Bork-Jensen, Jette Bottinger, Erwin P. Brandslund, Ivan Brown, Morris Busonero, Fabio Caulfield, Mark J. Chambers, John C. Chasman, daniel I. Chen, Y. Eugene Chen, Yii-der Ida Chowdhury, rajiv Christensen, Cramer Chu, Audrey Y. Connell, John M. Cucca, Francesco Cupples, L. Adrienne damrauer, Scott M. davies, Gail deary, Ian J. dedoussis, George denny, Joshua C. dominiczak, Anna dube, Marie-Pierre Ebeling, Tapani Eiriksdottir, Gudny Esko, Tonu Farmaki, Aliki-Eleni Feitosa, Mary F. Ferrario, Marco Ferrieres, Jean Ford, Ian Fornage, Myriam Franks, Paul W. Frayling, Timothy M. Frikke-Schmidt, ruth Fritsche, Lars G. Frossard, Philippe Fuster, Valentin Ganesh, Santhi K. Gao, Wei Garcia, Melissa E. Gieger, Christian Giulianini, Franco Goodarzi, Mark O. Grallert, Harald Grarup, Niels Groop, Leif Grove, Megan L. Gudnason, Vilmundur Hansen, Torben Harris, Tamara B. Hayward, Caroline Hirschhorn, Joel N. Holmen, Oddgeir L. Huffman, Jennifer Huo, Yong Hveem, Kristian Jabeen, Sehrish Jackson, Anne U. Jakobsdottir, Johanna Jarvelin, Marjo-riitta Jensen, Gorm B. Jorgensen, Marit E. Jukema, J. Wouter Justesen, Johanne M. Kamstrup, Pia r. Kanoni, Stavroula Karpe, Fredrik Kee, Frank Khera, Amit V. Klarin, derek Koistinen, Heikki A. Kooner, Jaspal S. Kooperberg, Charles Kuulasmaa, Kari Kuusisto, Johanna Laakso, Markku Lakka, Timo Langenberg, Claudia Langsted, Anne Launer, Lenore J. Lauritzen, Torsten Liewald, david C. M. Lin, Li An Linneberg, Allan Loos, ruth J. F. Lu, Yingchang Lu, Xiangfeng Magi, reedik Malarstig, Anders Manichaikul, Ani Manning, Alisa K. Mantyselka, Pekka Marouli, Eirini Masca, Nicholas G. d. Maschio, Andrea Meigs, James B. Melander, Olle Mets Penn State Coll Med Inst Personalized Med Dept Publ Hlth Sci Hershey PA USA Boston Univ Sch Publ Hlth Dept Biostat Boston MA USA Broad Inst Program Med & Populat Genet Cambridge MA 02142 USA Harvard Univ Harvard Stem Cell Inst Dept Stem Cell & Regenerat Biol Cambridge MA 02138 USA Univ Cambridge Dept Publ Hlth & Primary Care MRC BHF Cardiovasc Epidemiol Unit Cambridge England Univ Cambridge Natl Inst Hlth Res Blood & Transplant Res Unit NI Donor Hlth & Genom Cambridge England Univ Penn Perelman Sch Med Cardiovasc Inst Philadelphia PA 19104 USA Univ Oxford Wellcome Trust Ctr Human Genet Oxford England Univ Penn Dept Biostat & Epidemiol Perelman Sch Med Philadelphia PA 19104 USA Ctr Noncommunicable Dis Karachi Pakistan Massachusetts Gen Hosp Ctr Genom Med Boston MA 02114 USA ICDDR B Dhaka Bangladesh Imperial Coll London London England Univ Lille INSERM CHU Lille Inst Pasteur LilleRisk Factors & Mol Determinant Lille France Univ Strasbourg Dept Epidemiol & Publ Hlth EA 3430 Strasbourg France VA Palo Alto Hlth Care Syst Palo Alto CA USA Stanford Univ Sch Med Dept Med Stanford CA USA Univ Wisconsin Milwaukee Zilber Sch Publ Hlth Milwaukee WI USA Mt Sinai Med Ctr Icahn Sch Med Mt Sinai Cardiovasc Inst New York NY 10029 USA Baylor Coll Med Dept Med Houston TX 77030 USA Copenhagen Univ Hosp Dept Cardiol Rigshosp Copenhagen Denmark Rigshosp Dept Clin Biochem Copenhagen Denmark Univ Copenhagen Fac Hlth & Med Sci Copenhagen Denmark Univ Washington Dept Med Cardiovasc Hlth Res Unit Seattle WA USA Univ Michigan Sch Publ Hlth Dept Biostat Ctr Stat Genet Ann Arbor MI 48109 USA Univ Texas Hlth Sci Ctr Houston Sch Publ Hlth Dept Epidemiol Human Genet & Environm Sci Ctr Human Genet Houston TX 77030 USA Baylor Coll Med Human Genome Sequencing Ctr Houston TX 77030 USA Univ Copenhagen Fac Hlth & Med Sci Novo Nordisk Fdn Ctr Basic Metab Res Copenhagen Denmark Ichan Sch Med Mt Sinai Charles Bronfman Inst Personalized Med New York NY U

We screened variants on an exome-focused genotyping array in >300,000 participants (replication in >280,000 participants) and identified 444 independent variants in 250 loci significantly associated with total cholesterol (TC), high-density-lipoprotein cholesterol (HdL-C), low-densitylipoprotein cholesterol (LdL-C), and/or triglycerides (TG). At two loci (JAK2 and A1CF), experimental analysis in mice showed lipid changes consistent with the human data. We also found that: (i) beta-thalassemia trait carriers displayed lower TC and were protected from coronary artery disease (CAd);(ii) excluding the CETP locus, there was not a predictable relationship between plasma HdL-C and risk for age-related macular degeneration;(iii) only some mechanisms of lowering LdL-C appeared to increase risk for type 2 diabetes (T2d);and (iv) TG-lowering alleles involved in hepatic production of TG-rich lipoproteins (TM6SF2 and PNPLA3) tracked with higher liver fat, higher risk for T2d, and lower risk for CAd, whereas TG-lowering alleles involved in peripheral lipolysis (LPL and ANGPTL4) had no effect on liver fat but decreased risks for both T2d and CAd.

关键词： Cardiovascular diseases Genome-wide association studies

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In situ preparation of nickel/carbon core–shell structure by chemical vapor deposition

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Applied Surface Science 2013年 283卷 958-962页

作者： Fuyang Cao Qi Jiang Yuan Fang Shengguang Ban Shisheng Ou Hongxia Qian Yong Zhao Key Laboratory of Advanced Technologies of Materials Ministry of Education of China Superconductivity and New Energy R&D Center Southwest Jiaotong University Chengdu 610031 China School of Materials Science and Engineering University of New South Wales Sydney 2052 NSW Australia

Nickel/carbon core–shell structure with uniform diameter has been synthesized by galvanostatic electrodeposition nickel on its surface followed by chemical vapor deposition. We proposed the growth mechanism of the core–shell structure that the precipitation of carbon from metal catalysts during the high temperature growth period lifts up metal particles leading to the formation of core–shell structure or carbon nanotubes with respect to the diameter of catalyst particles. The substrate with deposited nickel was characterized by optical microscope. The elements and features of the substrate were studied by energy dispersive X-ray spectroscopy and X-ray diffraction respectively. The morphology of the resulting material was examined by field emitting scanning electron microscopy. In addition, the electrochemical performance of the core–shell structure modified electrodes was also investigated. The result shows that electrodes modified with core structure have better electrochemical property than the bare electrodes in the [Fe(CN) 6 ] 3− /[Fe(CN) 6 ] 4− solution at a scan rate of 20 mV s −1 .

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Preparation of Nb3Al by high-energy ball milling and superconductivity

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Journal of Physics: Conference Series 2014年第1期507卷

作者： Yongliang Chen Zhao Liu Pingyuan Li Xiaolan Zhang Suhua Yang dawei Yang Lupeng du Yajing Cui Xifeng Pan Guo Yan Yong Zhao Key Laboratory of Magnetic Levitation Technologies and Maglev Trains Ministry of Education of China and Superconductivity and New Energy R&D Center Southwest Jiaotong University Chengdu 610031 China Western Superconducting Technoligies Co. Ltd. Xi'an 710018 China School of Materials Science and Engineering University of New South Wales Sydney 2052 NSW Australia

The A15 phase superconductor Nb3Al has been considered as an alternative to Nb3Sn for high field and large scale applications. However, to prepare a stoichiometric Nb3Al with fine grain structures is very difficult. High-energy ball milling is a solid state powder processing technique and is a very useful for preparing Nb-Al alloys (Nb3Al). The effects of ball milling time and annealing temperature on the formation of Nb3Al superconducting phase have been studied. Pure Nb and Al powders with stoichiometric ratio of Nb3Al were mixed and milled, and the charging and milling were performed in an inert atmosphere. Phase formation and structural evolution during high-energy ball milling have been examined by X-ray diffraction. Al disappeared and Nb peaks broadened after about one hour of milling. With increasing milling time, the peaks of Nb became considerably broader and intensities decreased, the Nb-Al solid solution phase was extensive when milled about 3 hours. In order to obtain Nb3Al superconducting phase, a subsequent anneal was required. We have annealed the as-milled powders at 800-900°C for different times to prepared Nb3Al superconducting alloy. The results indicated that Nb3Al with small amount of impurity phase can be obtained on annealing the Nb-Al solid solution phase and the superconducting transition temperature was about 15K, but it is difficult to obtain a homogeneous Nb3Al phase by annealing the amorphous powder.

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A comprehensive assessment of rNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

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NATUrE BIOTECHNOLOGY 2014年第9期32卷 903-914页

作者： Su, Zhenqiang Labaj, Pawel P. Li, Sheng Thierry-Mieg, Jean Thierry-Mieg, danielle Shi, Wei Wang, Charles Schroth, Gary P. Setterquist, robert A. Thompson, John F. Jones, Wendell d. Xiao, Wenzhong Xu, Weihong Jensen, roderick V. Kelly, reagan Xu, Joshua Conesa, Ana Furlanello, Cesare Gao, Hanlin Hong, Huixiao Jafari, Nadereh Letovsky, Stan Liao, Yang Lu, Fei Oakeley, Edward J. Peng, Zhiyu Praul, Craig A. Santoyo-Lopez, Javier Scherer, Andreas Shi, Tieliu Smyth, Gordon K. Staedtler, Frank Sykacek, Peter Tan, Xin-Xing Thompson, E. Aubrey Vandesompele, Jo Wang, May d. Wang, Jian Wolfinger, russell d. Zavadil, Jiri Auerbach, Scott S. Bao, Wenjun Binder, Hans Blomquist, Thomas Brilliant, Murray H. Bushel, Pierre r. Cain, Weimin Catalano, Jennifer G. Chang, Ching-Wei Chen, Tao Chen, Geng Chen, rong Chierici, Marco Chu, Tzu-Ming Clevert, djork-Arne deng, Youping derti, Adnan devanarayan, Viswanath dong, Zirui dopazo, Joaquin du, Tingting Fang, Hong Fang, Yongxiang Fasold, Mario Fernandez, Anita Fischer, Matthias Furio-Tari, Pedro Fuscoe, James C. Caiment, Florian Gaj, Stan Gandara, Jorge Gao, Huan Ge, Weigong Gondo, Yoichi Gong, Binsheng Gong, Meihua Gong, Zhuolin Green, Bridgett Guo, Chao Guo, Lei Guo, Li-Wu Hadfield, James Hellemans, Jan Hochreiter, Sepp Jia, Meiwen Jian, Min Johnson, Charles d. Kay, Suzanne Kleinjans, Jos Lababidi, Samir Levy, Shawn Li, Quan-Zhen Li, Li Li, Li Li, Peng Li, Yan Li, Haiqing Li, Jianying Li, Shiyong Lin, Simon M. Lopez, Francisco J. Lu, Xin Luo, Heng Ma, Xiwen Meehan, Joseph Megherbi, dalila B. Mei, Nan Mu, Bing Ning, Baitang Pandey, Akhilesh Perez-Florido, Javier Perkins, roger G. Peters, ryan Phan, John H. Pirooznia, Mehdi Qian, Feng Qing, Tao rainbow, Lucille rocca-Serra, Philippe Sambourg, Laure Sansone, Susanna-Assunta Schwartz, Scott Shah, ruchir Shen, Jie Smith, Todd M. Stegle, Oliver Stralis-Pavese, Nancy Stupka, Elia Suzuki, Yutaka Szkotnicki, Lee T. Tinning, Matthew Tu, Bimeng van deft, Joost Vela-Boza, Alicia Venturini, Elisa Walker, Stephen J. Wan, Liqing Wang, Wei Wang, Jinh US FDA Natl Ctr Toxicol Res Jefferson AR 72079 USA Boku Univ Vienna Chair Bioinformat Res Grp Vienna Austria Weill Cornell Med Coll Dept Physiol & Biophys New York NY USA Weill Cornell Med Coll HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsau New York NY USA NCBI NIH Bethesda MD USA Walter & Eliza Hall Inst Med Res Bioinformat Div Parkville Vic Australia Univ Melbourne Dept Comp & Informat Syst Parkville Vic 3052 Australia Loma Linda Univ Ctr Genom Sch Med Loma Linda CA 92350 USA Loma Linda Univ Div Microbiol & Mol Genet Sch Med Loma Linda CA 92350 USA Illumina Inc Hayward CA USA Life Technol Corp Austin TX USA Claritas Genom Cambridge MA USA Express Anal Inc Durham NC USA Harvard Univ Massachusetts Gen Hosp Sch Med Boston MA USA Stanford Genome Technol Ctr Palo Alto CA USA Virginia Tech Dept Biol Sci Blacksburg VA USA Ctr Invest Principe Felipe Computat Genom Program Valencia Spain Fdn Bruno Kessler Trento Trento Italy City Hope Natl Med Ctr DNA Sequencing Solexa Core Beckman Res Inst City Hope Comprehens Canc Ctr Duarte CA 91010 USA Northwestern Univ Ctr Genet Med Feinberg Sch Med Chicago IL 60611 USA SynapDx Corp Lexington MA USA Univ Melbourne Dept Med Biol Parkville Vic 3052 Australia GE Healthcare SeqWright Genom Serv Houston TX USA Novartis Inst Biomed Res Basel Switzerland BGI Shenzhen Bei Shan Ind Zone Shenzhen Guangdong Peoples R China Penn State Univ University Pk PA 16802 USA Genom & Bioinformat Platform Andalusia Med Genome Project Seville Spain Univ Edinburgh Edinburgh Genom Edinburgh Midlothian Scotland Australian Genome Res Facil Ltd Walter & Eliza Hall Inst Med Res Parkville Vic Australia Spheromics Kontiolahti Finland E China Normal Univ Inst Biomed Sci Ctr Bioinformat & Computat Biol Shanghai Key Lab Regulatory Biol Shanghai 200062 Peoples R China E China Normal Univ Sch Life Sci Shanghai 200062 Peoples R China Univ Melbourne Dept Math & Stat Parkville Vic 3052 Australia Mayo Clin Jacksonvil

We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the US Food and drug Administration. Examining Illumina HiSeq, Life technologies SOLid and roche 454 platforms at multiple laboratory sites using reference rNA samples with built-in controls, we assess rNA sequencing (rNA-seq) performance for junction discovery and differential expression profiling and compare it to microarray and quantitative PCr (qPCr) data using complementary metrics. At all sequencing depths, we discover unannotated exon-exon junctions, with >80% validated by qPCr. We find that measurements of relative expression are accurate and reproducible across sites and platforms if specific-filters are used. In contrast, rNA-seq and microarrays do not provide accurate absolute measurements, and gene-specific biases are observed for all examined platforms, including qPCr. Measurement performance depends on the platform and data analysis pipeline, and variation is large for transcript-level profiling. The complete SEQC data sets, comprising >100 billion reads (10Tb), provide unique resources for evaluating rNA-seq analyses for clinical and regulatory settings.

关键词： Microarray analysis rNA sequencing Life Sciences general Biotechnology Biomedicine Agriculture Biomedical Engineering/Biotechnology Bioinformatics

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