ARTICLES
68 Article(s)
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Document(s)
Title
 
:  A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
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.;Caimet, 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, Jinhui;Wang, Jun;Wieben, Eric D.;Willey, James C.;Wu, Po-Yen;Xuan, Jiekun;Yang, Yong;Ye, Zhan;Yin, Ye;Yu, Ying;Yuan, Yate-Ching;Zhang, John;Zhang, Ke K.;Zhang, Wenqian;Zhang, Wenwei;Zhang, Yanyan;Zhao, Chen;Zheng, Yuanting;Zhou, Yiming;Zumbo, Paul;Tong, Weida;Kreil, David P.;Mason, Christopher E.;Shi, Leming
 
:  Conservation and Losses of Non-Coding RNAs in Avian Genomes
Gardner, Paul P. (School of Biological Sciences, University of Canterbury);Fasold, Mario (Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig);Burge, Sarah W. (European Molecular Biology Laboratory, European Bioinformatics Institute);Ninova, Maria (Faculty of Life Sciences, University of Manchester);Hertel, Jana (Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig);Kehr, Stephanie (Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig);Steeves, Tammy E. (School of Biological Sciences, University of Canterbury);Griffiths-Jones, Sam (Faculty of Life Sciences, University of Manchester);Stadler, Peter F. (Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna)
Here we present the results of a large-scale bioinformatics annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avia...
 
:  plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants
Patra, Deblina (Institut für Informatik, Martin-Luther-Universität Halle-Wittenberg);Fasold, Mario (Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University Leipzig);Langenberger, David (Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University Leipzig);Steger, Gerhard (Institut für Pysikalische Biologie, Heinrich-Heine-Universität Düsseldorf);Grosse, Ivo (Institut für Informatik, Martin-Luther-Universität Halle-Wittenberg);Stadler, Peter F. (Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna)
High-throughput sequencing techniques have made it possible to assay an organism's entire repertoire of small non-coding RNAs (ncRNAs) in an efficient and cost-effective manner. The moderate size of small RNA-seq datasets makes it feasible to provide...
 
:  G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration
Fasold, Mario (Universität Leipzig);Stadler, Peter (Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna);Binder, Hans (Universität Leipzig)
BACKGROUND: The brightness of the probe spots on expression microarrays intends to measure the abundance of specific mRNA targets. Probes with runs of at least three guanines (G) in their sequence show abnormal high intensities which reflect rather p...
 
:  DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments
Fasold, Mario (Universität Leipzig);Langenberger, David (Universität Leipzig);Binder, Hans (Universität Leipzig);Stadler, Peter (Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna);Hoffmann, Steve (Universität Leipzig)
Small non-coding RNAs (ncRNAs) such as microRNAs, snoRNAs and tRNAs are a diverse collection of molecules with several important biological functions. Current methods for high-throughput sequencing for the first time offer the opportunity to investig...
 
:  A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
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.;Caimet, 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, Jinhui;Wang, Jun;Wieben, Eric D.;Willey, James C.;Wu, Po-Yen;Xuan, Jiekun;Yang, Yong;Ye, Zhan;Yin, Ye;Yu, Ying;Yuan, Yate-Ching;Zhang, John;Zhang, Ke K.;Zhang, Wenqian;Zhang, Wenwei;Zhang, Yanyan;Zhao, Chen;Zheng, Yuanting;Zhou, Yiming;Zumbo, Paul;Tong, Weida;Kreil, David P.;Mason, Christopher E.;Shi, Leming
 
:  Third Report on Chicken Genes and Chromosomes 2015:
Schmid, Michael;Smith, Jacqueline;Burt, David W.;Aken, Bronwen L.;Antin, Parker B.;Archibald, Alan L.;Ashwell, Chris;Blackshear, Perry J.;Boschiero, Clarissa;Brown, C. Titus;Burgess, Shane C.;Cheng, Hans H.;Chow, William;Coble, Derrick J.;Cooksey, Amanda;Crooijmans, Richard P.M.A.;Damas, Joana;Davis, Richard V.N.;De Koning, Dirk-Jan;Delany, Mary E.;Derrien, Thomas;Desta, Takele T.;Dunn, Ian C.;Dunn, Matthew;Ellegren, Hans;Eöry, Lél;Erb, Ionas;Farré, Marta;Fasold, Mario;Fleming, Damarius;Flicek, Paul
 
:  A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
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.;Caimet, 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, Jinhui;Wang, Jun;Wieben, Eric D.;Willey, James C.;Wu, Po-Yen;Xuan, Jiekun;Yang, Yong;Ye, Zhan;Yin, Ye;Yu, Ying;Yuan, Yate-Ching;Zhang, John;Zhang, Ke K.;Zhang, Wenqian;Zhang, Wenwei;Zhang, Yanyan;Zhao, Chen;Zheng, Yuanting;Zhou, Yiming;Zumbo, Paul;Tong, Weida;Kreil, David P.;Mason, Christopher E.;Shi, Leming
 
:  A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
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, Jinhui;Wang, Jun;Wieben, Eric D.;Willey, James C.;Wu, Po-Yen;Xuan, Jiekun;Yang, Yong;Ye, Zhan;Yin, Ye;Yu, Ying;Yuan, Yate-Ching;Zhang, John;Zhang, Ke K.;Zhang, Wenqian;Zhang, Wenwei;Zhang, Yanyan;Zhao, Chen;Zheng, Yuanting;Zhou, Yiming;Zumbo, Paul;Tong, Weida;Kreil, David P.;Mason, Christopher E.;Shi, Leming