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Anthropogenic causes of jellyfish blooms and their direct consequences for humans: a review

by Robert W Olafson, William D McCubbin, C M Kay, Ratna K Vadlamudi, Jaekyoon Shin, Rama Pal, J P N Rai, D F Ortiz, L Kreppel, D M Speiser, G Scheel, G McDonald, D W Ow, F Radtke, R Heuchel, Oleg Georgiev, M Hergersberg, M Gariglio, Z Dembic, Walter Schaffner, Vladimir N Noskov, Satoko Maki, Yasuo Kawasaki, Sun-Hee Leem, Bun-Ichiro Ono, Hiroyuki Araki, Youri Pavlov, Akio Sugino, Jun Fujita, Jim Dover, Jessica Schneider, Mary Anne Tawiah-Boateng, Adam Wood, Kimberly Dean, Mark Johnston, Ali Shilatifard, Rossana Sapiro, Igor Kostetskii, Patricia Olds-Clarke, George L Gerton, Glenn L Radice, Jerome F Strauss Iii, Lydia A Finney, Thomas V O'Halloran, N Ratkevicius, J A Correa, Alejandra Moenne, Changjiang Xu, Christina Yong-Tao Li, Ah-Ng Tony Kong, Marie W Michael C Wooten, Xiao Hu, Jeganathan Ramesh Babu, M Lamar Seibenhener, Thangiah Geetha, Michael G Paine, Marie W Michael C Wooten, Carys L Mitchelmore, E Alan Verde, Virginia M Weis, Jennifer E Purcell, Shin-ichi Uye, Wen-Tseng Lo, Nicholas H Putnam, Mansi Srivastava, Uffe Hellsten, Bill Dirks, Jarrod Chapman, Asaf Salamov, Astrid Terry, Harris Shapiro, Erika Lindquist, Vladimir V Kapitonov, Rukhsana N Hasan, Andrew I Schafer, Da Wei Huang, Brad T Sherman, Richard A Lempicki, Simon Anders, Wolfgang Huber, Wuxian Shi, Mark R Chance, Judith-Irina Pagel, Elisabeth Deindl, Chuya Shinzato, Mayuko Hamada, Eiichi Shoguchi, Takeshi Kawashima, Nori Satoh, J R Brock, G K Bielmyer, Jae-Sung Rhee, In Tag Yu, Bo-Mi Kim, Chang-Bum Jeong, Kyun-Woo Lee, Min-Jung Kim, Su-Jae Lee, Gyung Soo Park, Jae-Seong Lee, Sharon J Schultz, Andrew M Fry, C Sütterlin, Thomas Ried, Erich A Nigg, Pierre Tardent, X S Ye, Gang Xu, R T Pu, R R Fincher, S L McGuire, A H Osmani, S A Osmani, Kiyoshi Nose, Motoi Ohba, Zeng-Feng Wang, Michael L Whitfield, T C Ingledue 3rd, Zbigniew Dominski, William F Marzluff, L Canesi, A Viarengo, C Leonzio, M Filippelli, G Gallo, Stephan Clemens, Eugene J Kim, Dieter Neumann, Julian I Schroeder, Bo Zhang, Dieter Egli, Oleg Georgiev, Walter Schaffner, Joel L Rosenbaum, George B Witman, Carys L Mitchelmore, E Alan Verde, Amy H Ringwood, Virginia M Weis, K J W Van Look, D E Kime, M Lamar Seibenhener, Jeganathan Ramesh Babu, Thangiah Geetha, Hing C Wong, N Rama Krishna, Marie W Michael C Wooten, John A Darling, Adam R M Reitzel, Patrick M Burton, Maureen E Mazza, Joseph F Ryan, James C Sullivan, John R Finnerty, Hesham M Korashy, Ayman O S El-Kadi, Irfan Rahman, Aruna Kode, Saibal K Biswas, Jared V Goldstone, Arkaitz Ibarra, Etienne Schwob, Juan Méndez, Erwin Grill, Susanne Löffler, Ernst- L Winnacker, Meinhart H Zenk, C H Ric De Vos, Marjolein J Vonk, Riet Vooijs, Henk Schat, Ross Howden, Peter B Goldsbrough, Chris R Andersen, Christopher S Cobbett, A Maur, Tanja Belser, Greg Elgar, Oleg Georgiev, Walter Schaffner, Olena K Vatamaniuk, Stéphane Mari, Yu-Ping Lu, Philip A Rea, Christopher S Cobbett, Peter B Goldsbrough, Ana Conesa, Stefan Götz, Juan Miguel García-Gómez, Javier Terol, Manuel Talón, Montserrat Robles, Thomas D Schmittgen, Kenneth J Livak, Henry Jay Forman, Hongqiao Zhang, Alessandra Rinna, Christopher C Franklin, Donald S Backos, Isaac Mohar, Collin C White, Henry Jay Forman, Terrance J Kavanagh, Igor Ulitsky, Adi Maron-Katz, Seagull Shavit, Dorit Sagir, Chaim Linhart, Ran Elkon, Amos Tanay, Roded Sharan, Yosef Shiloh, Ron Shamir, Mary-Elizabeth C Miller, William M Graham, Aldo Nicosia, Teresa Maggio, Salvatore Mazzola, Fabrizio Gianguzza, Angela Cuttitta, Salvatore Costa, Ann M Tarrant, Adam R M Reitzel, Chun K Kwok, Matthew J Jenny, Owen W Griffith, Stephan Clemens, Julian I Schroeder, Thomas Degenkolb, Freya Q Schafer, Garry R Buettner, Juan Méndez, Bruce Stillman, Jared V Goldstone, A Hamdoun, B J Cole, M Howard-Ashby, D W Nebert, M Scally, M Dean, D Epel, Mark E Hahn, J J Stegeman, Douglas I Lin, Priya Aggarwal, J Alan Diehl, Adam R M Reitzel, James C Sullivan, Nikki Traylor-Knowles, John R Finnerty, Srivatsan Kidambi, Joel Yarmush, Wayne Fong, Sangeetha Kamath, Joseph SchianodiCola, Yaakov Nahmias, Shelly C Lu, Ci Ma, Jennifer L Marlowe, Alvaro Puga, Hernán Speisky, Maritza Gómez, Francesca Burgos-Bravo, Camilo López-Alarcón, Carolina Jullian, Claudio Olea-Azar, Margarita E Aliaga, Damian Szklarczyk, Andrea Franceschini, Michael Kuhn, Milan Simonovic, Alexander Roth, Pablo Minguez, Tobias Doerks, Manuel Stark, Jean Muller, Peer Bork, Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras, Andrew M Fry, Laura O'Regan, Sarah R Sabir, Richard Bayliss, Macarena Mellado, Rodrigo A Contreras, Alberto González, Geraldine Dennett, Alejandra Moenne, Alexandros Onoufriadis, Amelia Shoemark, Miriam Schmidts, Mitali Patel, Gina Jimenez, Hui Liu, Biju Thomas, Mellisa Dixon, Robert A Hirst, Andrew Rutman, Adam R M Reitzel, Yale J Passamaneck, Sibel I Karchner, Diana G Franks, Mark Q Martindale, Ann M Tarrant, Mark E Hahn, Ron Elran, Maayan Raam, Roey Kraus, Vera Brekhman, Noa Sher, Inbar Plaschkes, Vered Chalifa-Caspi, Tamar Lotan show all authors
Molecular and Cellular Biology ()
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Abstract

Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases.Results: To align our large (exceeding 80 billon reads) ENCODE Transcriptome RNA-seq dataset we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously un-described RNA-seq alignment algorithm which utilizes sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by more than a factor of 50 in mapping speed, aligning to the human genome 550 Million 2x76bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full length RNA sequences. Using Roche 454 sequencing of RT-PCR amplicons, we experimentally validated 1,960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy.Implementation and Availability: STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/Contact: dobin@cshl.edu

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