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Computational methods
Computational Methods include useful new routines and algorithms with applications to Bioinformatics such as new sequence manipulation and analysis methods. Also included are new methods of computational analysis of biological data that facilitate data interpretation.
Citations 1-10 of 359 total displayed.
- Methods Online
A generalized conformational energy function of DNA derived from molecular dynamics simulations
- Satoshi Yamasaki, Tohru Terada, Kentaro Shimizu, Hidetoshi Kono, and Akinori Sarai
Nucleic Acids Res. 2009; 37: e135.
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- Methods Online
A high throughput experimental approach to identify miRNA targets in human cells
- Lu Ping Tan, Erwin Seinen, Gerben Duns, Debora de Jong, Ody C. M. Sibon, Sibrand Poppema, Bart-Jan Kroesen, Klaas Kok, and Anke van den Berg
Nucleic Acids Res. 2009; 37: e137.
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- Computational Biology
FIGfams: yet another set of protein families
- Folker Meyer, Ross Overbeek, and Alex Rodriguez
Nucleic Acids Res. 2009; 37: 6643-6654.
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- Genomics
Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage
- Yang Huang, Eugene V. Koonin, David J. Lipman, and Teresa M. Przytycka
Nucleic Acids Res. 2009; 37: 6799-6810.
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- Methods Online
VENN, a tool for titrating sequence conservation onto protein structures
- Jay Vyas, Michael R. Gryk, and Martin R. Schiller
Nucleic Acids Res. 2009; 37: e124.
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- Methods Online
SubpathwayMiner: a software package for flexible identification of pathways
- Chunquan Li, Xia Li, Yingbo Miao, Qianghu Wang, Wei Jiang, Chun Xu, Jing Li, Junwei Han, Fan Zhang, Binsheng Gong, and Liangde Xu
Nucleic Acids Res. 2009; 37: e131.
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- Computational Biology
Detecting species-site dependencies in large multiple sequence alignments
- Roland Schwarz, Philipp N. Seibel, Sven Rahmann, Christoph Schoen, Mirja Huenerberg, Clemens Müller-Reible, Thomas Dandekar, Rachel Karchin, Jörg Schultz, and Tobias Müller
Nucleic Acids Res. 2009; 37: 5959-5968.
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- Computational Biology
Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms
- Kang Tu, Hui Yu, You-Jia Hua, Yuan-Yuan Li, Lei Liu, Lu Xie, and Yi-Xue Li
Nucleic Acids Res. 2009; 37: 5969-5980.
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- Structural Biology
Sequence variant (CTAGGG)n in the human telomere favors a G-quadruplex structure containing a G·C·G·C tetrad
- Kah Wai Lim, Patrizia Alberti, Aurore Guédin, Laurent Lacroix, Jean-François Riou, Nicola J. Royle, Jean-Louis Mergny, and Anh Tuân Phan
Nucleic Acids Res. 2009; 37: 6239-6248.
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- Computational Biology
Multiplex primer prediction software for divergent targets
- Shea N. Gardner, Amy L. Hiddessen, Peter L. Williams, Christine Hara, Mark C. Wagner, and Bill W. Colston, Jr
Nucleic Acids Res. 2009; 37: 6291-6304.
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