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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 31-40 of 359 total displayed.
- Computational Biology
Experimentally based contact energies decode interactions responsible for protein–DNA affinity and the role of molecular waters at the binding interface
- N. Alpay Temiz and Carlos J. Camacho
Nucleic Acids Res. 2009; 37: 4076-4088.
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- Methods Online
Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes
- Shaoqiang Zhang, Minli Xu, Shan Li, and Zhengchang Su
Nucleic Acids Res. 2009; 37: e72.
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- Methods Online
ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences
- Yijun Sun, Yunpeng Cai, Li Liu, Fahong Yu, Michael L. Farrell, William McKendree, and William Farmerie
Nucleic Acids Res. 2009; 37: e76.
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- Methods Online
TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences
- Yujun Han, James M. Burnette, III, and Susan R. Wessler
Nucleic Acids Res. 2009; 37: e78.
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- Methods Online
Sim4cc: a cross-species spliced alignment program
- Leming Zhou, Mihaela Pertea, Arthur L. Delcher, and Liliana Florea
Nucleic Acids Res. 2009; 37: e80.
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- Methods Online
Tissue-specific regulatory network extractor (TS-REX): a database and software resource for the tissue and cell type-specific investigation of transcription factor-gene networks
- Federico Colecchia, Denise Kottwitz, Mandy Wagner, Cosima V. Pfenninger, Gerald Thiel, Ingo Tamm, Carsten Peterson, and Ulrike A. Nuber
Nucleic Acids Res. 2009; 37: e82.
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- Methods Online
MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming
- Srayanta Mukherjee and Yang Zhang
Nucleic Acids Res. 2009; 37: e83.
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- Computational Biology
Prediction of novel microRNA genes in cancer-associated genomic regions—a combined computational and experimental approach
- Anastasis Oulas, Alexandra Boutla, Katerina Gkirtzou, Martin Reczko, Kriton Kalantidis, and Panayiota Poirazi
Nucleic Acids Res. 2009; 37: 3276-3287.
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- Computational Biology
PROCAIN: protein profile comparison with assisting information
- Yong Wang, Ruslan I. Sadreyev, and Nick V. Grishin
Nucleic Acids Res. 2009; 37: 3522-3530.
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- Methods Online
Microarray labeling extension values: laboratory signatures for Affymetrix GeneChips
- Yun-Shien Lee, Chun-Houh Chen, Chi-Neu Tsai, Chia-Lung Tsai, Angel Chao, and Tzu-Hao Wang
Nucleic Acids Res. 2009; 37: e61.
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