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by Lindblad-Toh, Kerstin and Garber, Manuel and Zuk, Or and Lin, Michael F and Parker, Brian J and Washietl, Stefan and Kheradpour, Pouya and Ernst, Jason and Jordan, Gregory and Mauceli, Evan and Ward, Lucas D and Lowe, Craig B and Holloway, Alisha K and Clamp, Michele and Gnerre, Sante and Alföldi, Jessica and Beal, Kathryn and Chang, Jean and Clawson, Hiram and Cuff, James and Di Palma, Federica and Fitzgerald, Stephen and Flicek, Paul and Guttman, Mitchell and Hubisz, Melissa J and Jaffe, David B and Jungreis, Irwin and Kent, W. James and Kostka, Dennis and Lara, Marcia and Martins, Andre L and Massingham, Tim and Moltke, Ida and Raney, Brian J and Rasmussen, Matthew D and Robinson, Jim and Stark, Alexander and Vilella, Albert J and Wen, Jiayu and Xie, Xiaohui and Zody, Michael C and Worley, Kim C and Kovar, Christie L and Muzny, Donna M and Gibbs, Richard A and Warren, Wesley C and Mardis, Elaine R and Weinstock, George M and Wilson, Richard K and Birney, Ewan and Margulies, Elliott H and Herrero, Javier and Green, Eric D and Haussler, David and Siepel, Adam and Goldman, Nick and Pollard, Katherine S and Pedersen, Jakob S and Lander, Eric S and Kellis, Manolis and Baldwin, Jen and Bloom, Toby and Chin, Chee Whye and Heiman, Dave and Nicol, Robert and Nusbaum, Chad and Young, Sarah and Wilkinson, Jane and Cree, Andrew and Dihn, Huyen H and Fowler, Gerald and Jhangiani, Shalili and Joshi, Vandita and Lee, Sandra and Lewis, Lora R and Nazareth, Lynne V and Okwuonu, Geoffrey and Santibanez, Jireh and Delehaunty, Kim and Dooling, David and Fronik, Catrina and Fulton, Lucinda and Fulton, Bob and Graves, Tina and Minx, Patrick and Sodergren, Erica and Broad Inst and Washington Univ and Baylor Coll Med and Genome Institute at Washington University and Broad Institute Sequencing Platform and Whole Genome Assembly Team and Baylor College of Medicine Human Genome Sequencing Center Sequencing Team and Medicinska fakulteten and Science for Life Laboratory, SciLifeLab and Medicinska och farmaceutiska vetenskapsområdet and Institutionen för medicinsk biokemi och mikrobiologi and Uppsala universitet
Nature, ISSN 0028-0836, 10/2011, Volume 478, Issue 7370, pp. 476 - 482
Journal Article
Genome Research, ISSN 1088-9051, 2014, Volume 24, Issue 4, pp. 616 - 628
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 05/2012, Volume 40, Issue 10, pp. 4261 - 4272
Thermodynamic folding algorithms and structure probing experiments are commonly used to determine the secondary structure of RNAs. Here we propose a formal... 
BINDING | BIOCHEMISTRY & MOLECULAR BIOLOGY | GENOME | SEQUENCE | ALGORITHM | PAIR | RNA Folding | Thermodynamics | Algorithms | Base Sequence | RNA-Binding Proteins - chemistry | RNA - chemistry | RNA, Transfer - chemistry | Nucleotides - chemistry | Energy | RNA | Protein folding | Data processing | Nucleotides | Secondary structure | Protein structure | Computational Biology
Journal Article
Nature Biotechnology, ISSN 1087-0156, 11/2005, Volume 23, Issue 11, pp. 1383 - 1390
Journal Article
Methods in molecular biology (Clifton, N.J.), ISSN 1064-3745, 2010, Volume 609, pp. 285 - 306
Noncoding RNAs (ncRNAs) are increasingly recognized as important functional molecules in the cell. Here we give a short overview of fundamental computational... 
Humans | Computational Biology | Databases, Genetic | Molecular Sequence Data | Data Mining | Sequence Homology, Nucleic Acid | Sequence Alignment | Algorithms | Animals | Sequence Analysis, RNA | Base Sequence | RNA, Untranslated - chemistry | Software | Nucleic Acid Conformation
Journal Article
by Sushmita Roy and Jason Ernst and Peter V. Kharchenko and Pouya Kheradpour and Nicolas Negre and Matthew L. Eaton and Jane M. Landolin and Christopher A. Bristow and Lijia Ma and Michael F. Lin and Stefan Washietl and Bradley I. Arshinoff and Ferhat Ay and Patrick E. Meyer and Nicolas Robine and Nicole L. Washington and Luisa Di Stefano and Eugene Berezikov and Christopher D. Brown and Rogerio Candeias and Joseph W. Carlson and Adrian Carr and Irwin Jungreis and Daniel Marbach and Rachel Sealfon and Michael Y. Tolstorukov and Sebastian Will and Artyom A. Alekseyenko and Carlo Artieri and Benjamin W. Booth and Angela N. Brooks and Qi Dai and Carrie A. Davis and Michael O. Duff and Xin Feng and Andrey A. Gorchakov and Tingting Gu and Jorja G. Henikoff and Philipp Kapranov and Renhua Li and Heather K. MacAlpine and John Malone and Aki Minoda and Jared Nordman and Katsutomo Okamura and Marc Perry and Sara K. Powell and Nicole C. Riddle and Akiko Sakai and Anastasia Samsonova and Jeremy E. Sandler and Yuri B. Schwartz and Noa Sher and Rebecca Spokony and David Sturgill and Marijke van Baren and Kenneth H. Wan and Li Yang and Charles Yu and Elise Feingold and Peter Good and Mark Guyer and Rebecca Lowdon and Kami Ahmad and Justen Andrews and Bonnie Berger and Steven E. Brenner and Michael R. Brent and Lucy Cherbas and Sarah C. R. Elgin and Thomas R. Gingeras and Robert Grossman and Roger A. Hoskins and Thomas C. Kaufman and William Kent and Mitzi I. Kuroda and Terry Orr-Weaver and Norbert Perrimon and Vincenzo Pirrotta and James W. Posakony and Bing Ren and Steven Russell and Peter Cherbas and Brenton R. Graveley and Suzanna Lewis and Gos Micklem and Brian Oliver and Peter J. Park and Susan E. Celniker and Steven Henikoff and Gary H. Karpen and Eric C. Lai and David M. MacAlpine and Lincoln D. Stein and Kevin P. White and Manolis Kellis and modENCODE Consortium and The modENCODE Consortium
Science, ISSN 0036-8075, 12/2010, Volume 330, Issue 6012, pp. 1787 - 1797
Journal Article
Methods in Molecular Biology, ISSN 1064-3745, 01/2007, Volume 395, pp. 503 - 525
The function of many noncoding RNAs (ncRNAs) depend on a defined secondary structure. RNAz detects evolutionarily conserved and thermodynamically stable RNA... 
RNA structure prediction | Noncoding RNA | Conserved RNA secondary structure | Gene finding | Thermodynamics | RNA, Untranslated - chemistry | Nucleic Acid Conformation | Sequence Homology, Nucleic Acid | Base Sequence
Conference Proceeding
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 Flamm, Christoph and Fried, Claudia and Hackermüller, Jörg and Hertel, Jana and Lindemeyer, Manja and Missal, Kristin and Tanzer, Andrea and Washietl, Stefan and Korbel, Jan and Emanuelsson, Olof and Pedersen, Jakob S and Holroyd, Nancy and Taylor, Ruth and Swarbreck, David and Matthews, Nicholas and Dickson, Mark C and Thomas, Daryl J and Weirauch, Matthew T and Gilbert, James and ... and ENCODE Project Consortium and Baylor College of Medicine Human Genome Sequencing Center and Washington University Genome Sequencing Center and Children's Hospital Oakland Research Institute and NISC Comparative Sequencing Program and Broad Institute and The ENCODE Project Consortium
Nature, ISSN 0028-0836, 06/2007, Volume 447, Issue 7146, pp. 799 - 816
Journal Article