Identifying genomic islands with deep neural networks

被引:0
作者
Rida Assaf
Fangfang Xia
Rick Stevens
机构
[1] Department of Computer Science,
[2] University of Chicago,undefined
[3] Computing Environment and Life Sciences Division,undefined
[4] Argonne National Laboratory,undefined
[5] Data Science and Learning Division,undefined
[6] Argonne National Laboratory,undefined
[7] The University of Chicago Consortium for Advanced Science and Engineering,undefined
[8] University of Chicago,undefined
来源
BMC Genomics | / 22卷
关键词
Genomic island; Deep learning; Transfer learning; Computer vision; Inception V3;
D O I
暂无
中图分类号
学科分类号
摘要
引用
收藏
相关论文
共 147 条
  • [1] Langille M(2010)Detecting genomic islands using bioinformatics approaches Nat Rev Microbiol 8 373-82
  • [2] Hsiao W(1990)Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vitro and in vivo in various extraintestinal Escherichia coli isolates Microb Pathog 8 213-25
  • [3] Brinkman F(2014)Islander: a database of precisely mapped genomic islands in tRNA and tmRNA genes Nucleic Acids Res 43 D48-D53
  • [4] Hacker J(1990)A bacterial virulence determinant encoded by lysogenic coliphage lambda Nature 346 871-4
  • [5] Hudson C(2004)Genomic islands in pathogenic and environmental microorganisms Nat Rev Microbiol 2 414-24
  • [6] Lau B(2016)Computational methods for predicting genomic islands in microbial genomes Comput Struct Biotechnol J 14 200-6
  • [7] Williams K(2009)Genomic islands: tools of bacterial horizontal gene transfer and evolution FEMS Microbiol Rev 33 376-3793
  • [8] Barondess JJ(2012)PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies Nucleic Acids Res 40 e126-e126
  • [9] Beckwith J(2014)New applications for phage integrases J Mol Biol 426 2703-16
  • [10] Dobrindt U(2005)The viriosphere, diversity, and genetic exchange within phage communities Curr Opin Microbiol 8 444-50