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publications [2014/08/18 20:33]
haruo
publications [2016/06/21 03:22] (current)
gaou
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 > This paper describes the REST/SOAP Web services of the G-language System. > This paper describes the REST/SOAP Web services of the G-language System.
 +
 +  * "​GEMBASSY:​ an EMBOSS associated software package for comprehensive genome analyses",​ Itaya H, Oshita K, Arakawa K, Tomita M, //Source Code Biol Med//, 2013, 8(1):17. doi: 10.1186/​1751-0473-8-17. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​23987304|PubMed]]).
 +
 +> This paper describes the EMBOSS interface package for the G-language System.
  
 ===== Review papers related to G-language Project ===== ===== Review papers related to G-language Project =====
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 === Genomic Compositional Skews: === === Genomic Compositional Skews: ===
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 +  * "​Undesigned selection for replication termination of bacterial chromosomes",​ Kono N, Arakawa K, Sato M, Yoshikawa H, Tomita M, Itaya M, //J Mol Biol//, 2014, 12;​426(16):​2918-27. doi: 10.1016/​j.jmb.2014.06.005. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​24946150|PubMed]])
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   * "​Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index",​ Arakawa K, Suzuki H, Tomita M, //BMC Genomics//, 2009, 10:640. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​20042086|PubMed]])   * "​Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index",​ Arakawa K, Suzuki H, Tomita M, //BMC Genomics//, 2009, 10:640. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​20042086|PubMed]])
  
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   * "​Noise-reduction filtering for accurate detection of replication termini in bacterial genomes",​ Arakawa K, Saito R, Tomita M, //FEBS Letters//, 2007, 581(2):​253-258. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​17188685|PubMed]])   * "​Noise-reduction filtering for accurate detection of replication termini in bacterial genomes",​ Arakawa K, Saito R, Tomita M, //FEBS Letters//, 2007, 581(2):​253-258. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​17188685|PubMed]])
 +
 +=== Genomics Compositions:​ ===
 +  * "​Plasmids are vectors for redundant chromosomal genes in the Bacillus cereus group",​ Zheng J, Guan Z, Cao S, Peng D, Ruan L, Jiang D, Sun M, //BMC Genomics//, 2015, 16(1):6. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​25608745|PubMed]])
  
 === Oligonucleotides:​ === === Oligonucleotides:​ ===
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 === Codons: === === Codons: ===
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 +  * "Codon Adaptation of Plastid Genes",​ Suzuki H and Morton BR, //PLoS One//, 2016, 11(5):​e0154306. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​27196606|PubMed]])
 +
 +  * "​Analysis of amino acid and codon usage in Paramecium burs aria", Dohra H, Fujishima M, Suzuki H, //FEBS Lett.//, 2015, 589(20 Pt B):​3113-3118. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​26341535|PubMed]])
 +
 +  * "​Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo", Nakahigashi K, Takai  Y, Shiwa Y, Wada M, Honma M, Yoshikawa H, Tomita M, Kanai A, Mori H, //BMC Genomics//, 2014, 15:1115. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​25512115|PubMed]])
 +
   * "​Measure of synonymous codon usage diversity among genes in bacteria",​ Suzuki H, Saito R, Tomita M, //BMC Bioinformatics//,​ 2009, 10:167. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​19480720|PubMed]])   * "​Measure of synonymous codon usage diversity among genes in bacteria",​ Suzuki H, Saito R, Tomita M, //BMC Bioinformatics//,​ 2009, 10:167. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​19480720|PubMed]])
  
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 === Genomics: === === Genomics: ===
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 +  * "Draft Genome Sequence of Caedibacter varicaedens,​ a Kappa Killer Endosymbiont Bacterium of the Ciliate Paramecium biaurelia",​ Suzuki H, Dapper AL, Jackson CE, Lee H, Pejaver V, Doak TG, Lynch M, Preer JR Jr., //Genome Announc.//, 2015, 3(6). pii: e01310-15. doi: 10.1128/​genomeA.01310-15.([[http://​www.ncbi.nlm.nih.gov/​pubmed/​26543129|PubMed]])
 +
 +  * "​Comparative genomic and phenomic analysis of Clostridium difficile and Clostridium sordellii, two related pathogens with differing host tissue preference",​ Scaria J, Suzuki H, Ptak CP, Chen JW, Zhu YZ, Guo XK, Chang YF, //BMC Genomics//, 2015, 16:448. doi:​10.1186/​s12864-015-1663-5. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​26059449|PubMed]])
 + 
 +  * "​Inflammation-associated Adherent-invasive Escherichia coli Are Enriched in Pathways for Use of Propanediol and Iron and M-cell Translocation",​ Dogan B, Suzuki H, Herlekar D, Sartor RB, Campbell BJ, Roberts CL, Stewart K, Scherl EJ, Araz Y, Bitar PP, Lefébure T, Chandler B, Schukken YH, Stanhope MJ, Simpson KW, //Inflamm Bowel Dis.//, 2014, 20(11):​1919-32. doi: 10.1097/​MIB.0000000000000183. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​25230163|PubMed]])
  
   * "Draft genome sequences of three Holospora species (Holospora obtusa, Holospora undulata, and Holospora elegans), endonuclear symbiotic bacteria of the ciliate Paramecium caudatum",​ Dohra H, Tanaka K, Suzuki T, Fujishima M, Suzuki H, //FEMS Microbiol Lett.//, 2014, doi: 10.1111/​1574-6968.12577. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​25115770|PubMed]])   * "Draft genome sequences of three Holospora species (Holospora obtusa, Holospora undulata, and Holospora elegans), endonuclear symbiotic bacteria of the ciliate Paramecium caudatum",​ Dohra H, Tanaka K, Suzuki T, Fujishima M, Suzuki H, //FEMS Microbiol Lett.//, 2014, doi: 10.1111/​1574-6968.12577. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​25115770|PubMed]])
publications.1408393999.txt.gz · Last modified: 2014/08/18 20:33 by haruo