Literature DB >> 23222169

Naturally selecting solutions: the use of genetic algorithms in bioinformatics.

Timmy Manning1, Roy D Sleator, Paul Walsh.   

Abstract

For decades, computer scientists have looked to nature for biologically inspired solutions to computational problems; ranging from robotic control to scheduling optimization. Paradoxically, as we move deeper into the post-genomics era, the reverse is occurring, as biologists and bioinformaticians look to computational techniques, to solve a variety of biological problems. One of the most common biologically inspired techniques are genetic algorithms (GAs), which take the Darwinian concept of natural selection as the driving force behind systems for solving real world problems, including those in the bioinformatics domain. Herein, we provide an overview of genetic algorithms and survey some of the most recent applications of this approach to bioinformatics based problems.

Entities:  

Keywords:  genetic algorithm; multiple sequence alignment; optimization; protein structure prediction

Mesh:

Year:  2012        PMID: 23222169      PMCID: PMC3813526          DOI: 10.4161/bioe.23041

Source DB:  PubMed          Journal:  Bioengineered        ISSN: 2165-5979            Impact factor:   3.269


  29 in total

1.  T-Coffee: A novel method for fast and accurate multiple sequence alignment.

Authors:  C Notredame; D G Higgins; J Heringa
Journal:  J Mol Biol       Date:  2000-09-08       Impact factor: 5.469

2.  Abandoning objectives: evolution through the search for novelty alone.

Authors:  Joel Lehman; Kenneth O Stanley
Journal:  Evol Comput       Date:  2011-02-14       Impact factor: 3.277

Review 3.  Multiple sequence alignment: in pursuit of homologous DNA positions.

Authors:  Sudhir Kumar; Alan Filipski
Journal:  Genome Res       Date:  2007-02       Impact factor: 9.043

4.  The protein folding network indicates that the ultrafast folding mutant of villin headpiece subdomain has a deeper folding funnel.

Authors:  Hongxing Lei; Changjun Chen; Yi Xiao; Yong Duan
Journal:  J Chem Phys       Date:  2011-05-28       Impact factor: 3.488

5.  Parallel Niche Pareto AlineaGA--an evolutionary multiobjective approach on multiple sequence alignment.

Authors:  Fernando José Mateus da Silva; Juan Manuel Sánchez Pérez; Juan Antonio Gómez Pulido; Miguel A Vega Rodríguez
Journal:  J Integr Bioinform       Date:  2011-09-15

6.  Predicting protein structures with a multiplayer online game.

Authors:  Seth Cooper; Firas Khatib; Adrien Treuille; Janos Barbero; Jeehyung Lee; Michael Beenen; Andrew Leaver-Fay; David Baker; Zoran Popović; Foldit Players
Journal:  Nature       Date:  2010-08-05       Impact factor: 49.962

7.  Optimization of auto-induction medium for G-CSF production by Escherichia coli using artificial neural networks coupled with genetic algorithm.

Authors:  H Tian; C Liu; X D Gao; W B Yao
Journal:  World J Microbiol Biotechnol       Date:  2012-11-07       Impact factor: 3.312

8.  Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli.

Authors:  Melody K Morris; Julio Saez-Rodriguez; David C Clarke; Peter K Sorger; Douglas A Lauffenburger
Journal:  PLoS Comput Biol       Date:  2011-03-03       Impact factor: 4.475

9.  Modeling disordered regions in proteins using Rosetta.

Authors:  Ray Yu-Ruei Wang; Yan Han; Kristina Krassovsky; William Sheffler; Michael Tyka; David Baker
Journal:  PLoS One       Date:  2011-07-29       Impact factor: 3.240

10.  Protein alignment algorithms with an efficient backtracking routine on multiple GPUs.

Authors:  Jacek Blazewicz; Wojciech Frohmberg; Michal Kierzynka; Erwin Pesch; Pawel Wojciechowski
Journal:  BMC Bioinformatics       Date:  2011-05-20       Impact factor: 3.307

View more
  5 in total

Review 1.  Under the microscope: From pathogens to probiotics and back.

Authors:  Roy D Sleator
Journal:  Bioengineered       Date:  2015       Impact factor: 3.269

Review 2.  A beginner's guide to phylogenetics.

Authors:  Roy D Sleator
Journal:  Microb Ecol       Date:  2013-04-28       Impact factor: 4.552

Review 3.  Biologically inspired intelligent decision making: a commentary on the use of artificial neural networks in bioinformatics.

Authors:  Timmy Manning; Roy D Sleator; Paul Walsh
Journal:  Bioengineered       Date:  2013-12-16       Impact factor: 3.269

4.  A transcriptomic study for identifying cardia- and non-cardia-specific gastric cancer prognostic factors using genetic algorithm-based methods.

Authors:  Junyi Xin; Yanling Wu; Xiaowei Wang; Shuwei Li; Haiyan Chu; Meilin Wang; Mulong Du; Zhengdong Zhang
Journal:  J Cell Mol Med       Date:  2020-07-10       Impact factor: 5.310

5.  The superior fault tolerance of artificial neural network training with a fault/noise injection-based genetic algorithm.

Authors:  Feng Su; Peijiang Yuan; Yangzhen Wang; Chen Zhang
Journal:  Protein Cell       Date:  2016-08-09       Impact factor: 14.870

  5 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.