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Bioinformatics and computational biology involve the use of techniques from applied mathematics, informatics, statistics, and computer science to solve biological problems. Research in computational biology often overlaps with systems biology. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, and the modeling of evolution.

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Fast and accurate long-read alignment with Burrows–Wheeler transform  Heng Li, Richard Durbi
Speeding up whole-genome alignment by indexing frequency vectors  Tamer Kahveci, Vebjorn Ljosa, Ambuj K. Singh
Survey on index based homology search algorithm  Xianyang Jiang, Peiheng Zhang, Xinchun Liu, Stephen S.-T. Yau
A Database Index to Large Biological Sequences  Ela Hunt , Malcolm P. Atkinson , Robert W. Irving
An algorithm for searching sequence databases in time proportional to the logarithm of the database size  Eldar Giladi , Michael G. Walker , James Ze Wang , Wayne Volkmuth
Effective Indexing and Filtering for Similarity Search in Large Biosequence Databases  Ozgur Ozturk , Hakan Ferhatosmanoglu
Error Tolerant Indexing and Alignment of Short Reads with Covering Template Families  Giladi E, Healy J, Myers G, Hart C, Kapranov P, Lipson D, Roels S, Thayer E, Letovsky S.
Indexing and Retrieval for Genomic Databases  Hugh E. Williams, Justin Zobel
Pattern Matching in Computational Biology  Guy Blelloch
Rapid similarity searches of nucleic acid and protein data banks  John Wilbur, David Lipman
SST: an algorithm for finding near-exact sequence matches in time proportional to the logarithm of the database size  Eldar Giladi, Michael Walker, James Wang, Wayne Volkmuth
The ed-tree: an index for large DNA sequence databases  Zhenqiang Tan, Xia Cao, Beng Chin Ooi, Anthony K. H. Tun