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by Djebali, Sarah and Davis, Carrie A and Merkel, Angelika and Dobin, Alex and Lassmann, Timo and Mortazavi, Ali and Tanzer, Andrea and Lagarde, Julien and Lin, Wei and Schlesinger, Felix and Xue, Chenghai and Marinov, Georgi K and Khatun, Jainab and Williams, Brian A and Zaleski, Chris and Rozowsky, Joel and Röder, Maik and Kokocinski, Felix and Abdelhamid, Rehab F and Alioto, Tyler and Antoshechkin, Igor and Baer, Michael T and Bar, Nadav S and Batut, Philippe and Bell, Kimberly and Bell, Ian and Chakrabortty, Sudipto and Chen, Xian and Chrast, Jacqueline and Curado, Joao and Derrien, Thomas and Drenkow, Jorg and Dumais, Erica and Dumais, Jacqueline and Duttagupta, Radha and Falconnet, Emilie and Fastuca, Meagan and Fejes-Toth, Kata and Ferreira, Pedro and Foissac, Sylvain and Fullwood, Melissa J and Gao, Hui and Gonzalez, David and Gordon, Assaf and Gunawardena, Harsha and Howald, Cedric and Jha, Sonali and Johnson, Rory and Kapranov, Philipp and King, Brandon and Kingswood, Colin and Luo, Oscar J and Park, Eddie and Persaud, Kimberly and Preall, Jonathan B and Ribeca, Paolo and Risk, Brian and Robyr, Daniel and Sammeth, Michael and Schaffer, Lorian and See, Lei-Hoon and Shahab, Atif and Skancke, Jorgen and Suzuki, Ana Maria and Takahashi, Hazuki and Tilgner, Hagen and Trout, Diane and Walters, Nathalie and Wang, Huaien and Wrobel, John and Yu, Yanbao and Ruan, Xiaoan and Hayashizaki, Yoshihide and Harrow, Jennifer and Gerstein, Mark and Hubbard, Tim and Reymond, Alexandre and Antonarakis, Stylianos E and Hannon, Gregory and Giddings, Morgan C and Ruan, Yijun and Wold, Barbara and Carninci, Piero and Guig, Roderic and Gingeras, Thomas R
Nature, ISSN 0028-0836, 09/2012, Volume 489, Issue 7414, pp. 101 - 108
Journal Article
by Yue, Feng and Cheng, Yong and Breschi, Alessandra and Vierstra, Jeff and Wu, Weisheng and Ryba, Tyrone and Sandstrom, Richard and Ma, Zhihai and Davis, Carrie and Pope, Benjamin D and Shen, Yin and Pervouchine, Dmitri D and Djebali, Sarah and Thurman, Robert E and Kaul, Rajinder and Rynes, Eric and Kirilusha, Anthony and Marinov, Georgi K and Williams, Brian A and Trout, Diane and Amrhein, Henry and Fisher-Aylor, Katherine and Antoshechkin, Igor and DeSalvo, Gilberto and See, Lei-Hoon and Fastuca, Meagan and Drenkow, Jorg and Zaleski, Chris and Dobin, Alex and Prieto, Pablo and Lagarde, Julien and Bussotti, Giovanni and Tanzer, Andrea and Denas, Olgert and Li, Kanwei and Bender, M.A and Zhang, Miaohua and Byron, Rachel and Groudine, Mark T and McCleary, David and Pham, Long and Ye, Zhen and Kuan, Samantha and Edsall, Lee and Wu, Yi-Chieh and Rasmussen, Matthew D and Bansal, Mukul S and Kellis, Manolis and Keller, Cheryl A and Morrissey, Christapher S and Mishra, Tejaswini and Jain, Deepti and Dogan, Nergiz and Harris, Robert S and Cayting, Philip and Kawli, Trupti and Boyle, Alan P and Euskirchen, Ghia and Kundaje, Anshul and Lin, Shin and Lin, Yiing and Jansen, Camden and Malladi, Venkat S and Cline, Melissa S and Erickson, Drew T and Kirkup, Vanessa M and Learned, Katrina and Sloan, Cricket A and Rosenbloom, Kate R and De Sousa, Beatriz Lacerda and Beal, Kathryn and Pignatelli, Miguel and Flicek, Paul and Lian, Jin and Kahveci, Tamer and Lee, Dongwon and Kent, W. James and Santos, Miguel Ramalho and Herrero, Javier and Notredame, Cedric and Johnson, Audra and Vong, Shinny and Lee, Kristen and Bates, Daniel and Neri, Fidencio and Diegel, Morgan and Canfield, Theresa and Sabo, Peter J and Wilken, Matthew S and Reh, Thomas A and Giste, Erika and Shafer, Anthony and Kutyavin, Tanya and Haugen, Eric and Dunn, Douglas and Reynolds, Alex P and Neph, Shane and Humbert, Richard and Hansen, R. Scott and De Bruijn, Marella and ... and Mouse ENCODE Consortium and The Mouse ENCODE Consortium
Nature, ISSN 0028-0836, 11/2014, Volume 515, Issue 7527, pp. 355 - 364
Journal Article
Bioinformatics, ISSN 1367-4803, 01/2013, Volume 29, Issue 1, pp. 15 - 21
Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure,... 
SPLICE JUNCTIONS | ALIGNMENT | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | SEQUENCE | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | ALGORITHMS | ENCODE | Sequence Analysis, RNA - methods | Sequence Alignment - methods | RNA Splicing | Algorithms | Humans | Gene Expression Profiling | Software | Genome, Human | Cluster Analysis | Original Papers
Journal Article
Science, ISSN 0036-8075, 5/2005, Volume 308, Issue 5725, pp. 1149 - 1154
Journal Article
by Gerstein, Mark B and Rozowsky, Joel and Yan, Koon-Kiu and Wang, Daifeng and Cheng, Chao and Brown, James B and Davis, Carrie A and Hillier, Ladeana and Sisu, Cristina and Li, Jingyi Jessica and Pei, Baikang and Harmanci, Arif O and Duff, Michael O and Djebali, Sarah and Alexander, Roger P and Alver, Burak H and Auerbach, Raymond and Bell, Kimberly and Bickel, Peter J and Boeck, Max E and Boley, Nathan P and Booth, Benjamin W and Cherbas, Lucy and Cherbas, Peter and Di, Chao and Dobin, Alex and Drenkow, Jorg and Ewing, Brent and Fang, Gang and Fastuca, Megan and Feingold, Elise A and Frankish, Adam and Gao, Guanjun and Good, Peter J and Guigó, Roderic and Hammonds, Ann and Harrow, Jen and Hoskins, Roger A and Howald, Cédric and Hu, Long and Huang, Haiyan and Hubbard, Tim J. P and Huynh, Chau and Jha, Sonali and Kasper, Dionna and Kato, Masaomi and Kaufman, Thomas C and Kitchen, Robert R and Ladewig, Erik and Lagarde, Julien and Lai, Eric and Leng, Jing and Lu, Zhi and MacCoss, Michael and May, Gemma and McWhirter, Rebecca and Merrihew, Gennifer and Miller, David M and Mortazavi, Ali and Murad, Rabi and Oliver, Brian and Olson, Sara and Park, Peter J and Pazin, Michael J and Perrimon, Norbert and Pervouchine, Dmitri and Reinke, Valerie and Reymond, Alexandre and Robinson, Garrett and Samsonova, Anastasia and Saunders, Gary I and Schlesinger, Felix and Sethi, Anurag and Slack, Frank J and Spencer, William C and Stoiber, Marcus H and Strasbourger, Pnina and Tanzer, Andrea and Thompson, Owen A and Wan, Kenneth H and Wang, Guilin and Wang, Huaien and Watkins, Kathie L and Wen, Jiayu and Wen, Kejia and Xue, Chenghai and Yang, Li and Yip, Kevin and Zaleski, Chris and Zhang, Yan and Zheng, Henry and Brenner, Steven E and Graveley, Brenton R and Celniker, Susan E and Gingeras, Thomas R and Waterston, Robert
Nature, ISSN 0028-0836, 08/2014, Volume 512, Issue 7515, pp. 445 - 448
Journal Article
by Birney, Ewan and Stamatoyannopoulos, John A and Dutta, Anindya and Guigó, Roderic and Gingeras, Thomas R and Margulies, Elliott H and Weng, Zhiping and Snyder, Michael and Dermitzakis, Emmanouil T and Thurman, Robert E and Kuehn, Michael S and Taylor, Christopher M and Neph, Shane and Koch, Christoph M and Asthana, Saurabh and Malhotra, Ankit and Adzhubei, Ivan and Greenbaum, Jason A and Andrews, Robert M and Flicek, Paul and Boyle, Patrick J and Cao, Hua and Carter, Nigel P and Clelland, Gayle K and Davis, Sean and Day, Nathan and Dhami, Pawandeep and Dillon, Shane C and Dorschner, Michael O and Fiegler, Heike and Giresi, Paul G and Goldy, Jeff and Hawrylycz, Michael and Haydock, Andrew and Humbert, Richard and James, Keith D and Johnson, Brett E and Johnson, Ericka M and Frum, Tristan T and Rosenzweig, Elizabeth R and Karnani, Neerja and Lee, Kirsten and Lefebvre, Gregory C and Navas, Patrick A and Neri, Fidencio and Parker, Stephen C. J and Sabo, Peter J and Sandstrom, Richard and Shafer, Anthony and Vetrie, David and Weaver, Molly and Wilcox, Sarah and Yu, Man and Collins, Francis S and Dekker, Job and Lieb, Jason D and Tullius, Thomas D and Crawford, Gregory E and Sunyaev, Shamil and Noble, William S and Dunham, Ian and Denoeud, France and Reymond, Alexandre and Kapranov, Philipp and Rozowsky, Joel and Zheng, Deyou and Castelo, Robert and Frankish, Adam and Harrow, Jennifer and Ghosh, Srinka and Sandelin, Albin and Hofacker, Ivo L and Baertsch, Robert and Keefe, Damian and Dike, Sujit and Cheng, Jill and Hirsch, Heather A and Sekinger, Edward A and Lagarde, Julien and Abril, Josep F and Shahab, Atif and