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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 101-110 of 359 total displayed.

Past content

Computational Biology
LOMETS: A local meta-threading-server for protein structure prediction
Sitao Wu and Yang Zhang
Nucleic Acids Res. 2007; 35: 3375-3382. [Abstract] [Full text] [Print PDF] [ Supplementary Material ]  

Computational Biology
Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations
Steven Van Vooren, Bernard Thienpont, Björn Menten, Frank Speleman, Bart De Moor, Joris Vermeesch, and Yves Moreau
Nucleic Acids Res. 2007; 35: 2533-2543. [Abstract] [Full text] [Print PDF] [ Supplementary Material ]  

Computational Biology
Hierarchical classification of functionally equivalent genes in prokaryotes
Hongwei Wu, Fenglou Mao, Victor Olman, and Ying Xu
Nucleic Acids Res. 2007; 35: 2125-2140. [Abstract] [Full text] [Print PDF] [ Supplementary Material ]  

Computational Biology
Consensus sequences improve PSI-BLAST through mimicking profile–profile alignments
Dariusz Przybylski and Burkhard Rost
Nucleic Acids Res. 2007; 35: 2238-2246. [Abstract] [Full text] [Print PDF] [ Supplementary Material ]  

Computational Biology
Graph-based identification of cancer signaling pathways from published gene expression signatures using PubLiME
Giacomo Finocchiaro, Francesco Mattia Mancuso, Davide Cittaro, and Heiko Muller
Nucleic Acids Res. 2007; 35: 2343-2355. [Abstract] [Full text] [Print PDF] [ Supplementary Material ]  

Methods Online
Exploiting noise in array CGH data to improve detection of DNA copy number change
Jing Hu, Jian-Bo Gao, Yinhe Cao, Erwin Bottinger, and Weijia Zhang
Nucleic Acids Res. 2007; 35: e35. [Abstract] [Full text] [Print PDF]  

Molecular Biology
Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency of BAC/PAC recombineering techniques
S. Semprini, T.J. Troup, N. Kotelevtseva, K. King, J.R.E. Davis, L.J. Mullins, K.E. Chapman, D.R. Dunbar, and J.J. Mullins
Nucleic Acids Res. 2007; 35: 1402-1410. [Abstract] [Full text] [Print PDF]  

Computational Biology
DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces
Harianto Tjong and Huan-Xiang Zhou
Nucleic Acids Res. 2007; 35: 1465-1477. [Abstract] [Full text] [Print PDF] [ Supplementary Material ]  

Computational Biology
Energetics of protein–DNA interactions
Jason E. Donald, William W. Chen, and Eugene I. Shakhnovich
Nucleic Acids Res. 2007; 35: 1039-1047. [Abstract] [Full text] [Print PDF] [ Supplementary Material ]  

Computational Biology
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry
Trevor W. Siggers and Barry Honig
Nucleic Acids Res. 2007; 35: 1085-1097. [Abstract] [Full text] [Print PDF] [ Supplementary Material ]  

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