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publications [2012/01/31 20:24]
haruo
publications [2016/06/21 03:22]
gaou
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 > This is the main article. Please cite this paper when you publish your research work using G-language System. > This is the main article. Please cite this paper when you publish your research work using G-language System.
  
-  * "​G-language System as a platform for large-scale analysis of high-throughput omics data", Arakawa K, Tomita M, //Journal of Pesticide Science//, 2006, 31(3):​282-288([[http://​www.jstage.jst.go.jp/​article/​jpestics/​31/​3/​282/​_pdf|PDF]]).+  * "​G-language System as a platform for large-scale analysis of high-throughput omics data", Arakawa K, Tomita M, //Journal of Pesticide Science//, 2006, 31(3):​282-288([[https://​www.jstage.jst.go.jp/​article/​jpestics/​31/​3/​31_3_282/​_pdf|PDF]]).
  
 > This is a review describing G-language System and related software packages. Please also cite this article. > This is a review describing G-language System and related software packages. Please also cite this article.
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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: ===
 +
 +  * "​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]])
 +
   * "​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: ===
 +
 +  * "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: ===
  
-  * "Comparative genomic analysis ​of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae", Suzuki H, Lefebure TPavinski Bitar PStanhope MJ, //BMC Genomics//, 201213(1):38(([[http://​www.ncbi.nlm.nih.gov/​pubmed/​22272658|PubMed]])+  * "Draft Genome Sequence of Caedibacter varicaedens,​ a Kappa Killer Endosymbiont Bacterium ​of the Ciliate Paramecium biaurelia", Suzuki H, Dapper ALJackson CELee H, Pejaver V, Doak TG, Lynch M, Preer JR Jr., //Genome Announc.//, 20153(6). piie01310-15. doi: 10.1128/​genomeA.01310-15.([[http://​www.ncbi.nlm.nih.gov/​pubmed/​26543129|PubMed]])
  
-  * "Functional bias of positively selected genes in Streptococcus genomes", Suzuki H, Stanhope MJ, //Infect Genet Evol.//, 2011in press (([[http://​www.ncbi.nlm.nih.gov/​pubmed/​22155358|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.//, 201420(11):​1919-32. doi: 10.1097/​MIB.0000000000000183. ​([[http://​www.ncbi.nlm.nih.gov/​pubmed/​25230163|PubMed]])
  
-  * "​Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution",​ Suzuki H, Lefebure T, Hubisz MJ, Bitar PP, Lang P, Siepel A and Stanhope MJ, //Genome Biology and Evolution//,​ 2011, 3:​168-85. ​(([[http://​www.ncbi.nlm.nih.gov/​pubmed/​21282711|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]]) 
 + 
 +  * "​Comparative functional genomics of Lactobacillus spp. reveals possible mechanisms for specialization of vaginal lactobacilli to their environment",​ Mendes-Soares H, Suzuki H, Hickey RJ, Forney LJ, //J Bacteriol.//,​ 2014, 196(7):​1458-70. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​24488312|PubMed]]) 
 + 
 +  * "​Functional bias of positively selected genes in Streptococcus genomes",​ Suzuki H, Stanhope MJ, //Infect Genet Evol.//, 2012, 12(2):​274-7. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​22155358|PubMed]]) 
 + 
 +  * "​Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae",​ Suzuki H, Lefebure T, Pavinski Bitar P, Stanhope MJ, //BMC Genomics//, 2012, 13(1):38. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​22272658|PubMed]]) 
 + 
 +  ​* "​Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution",​ Suzuki H, Lefebure T, Hubisz MJ, Bitar PP, Lang P, Siepel A and Stanhope MJ, //Genome Biology and Evolution//,​ 2011, 3:168-85. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​21282711|PubMed]])
  
   * "GPAC: Benchmarking the sensitivity of genome informatics analysis to genome annotation completeness",​ Arakawa K, Nakayama Y, Tomita M, //In Silico Biology//, 2006, 6:0006 ([[http://​www.ncbi.nlm.nih.gov/​entrez/​query.fcgi?​cmd=Retrieve&​db=PubMed&​list_uids=16789913|PubMed]])   * "GPAC: Benchmarking the sensitivity of genome informatics analysis to genome annotation completeness",​ Arakawa K, Nakayama Y, Tomita M, //In Silico Biology//, 2006, 6:0006 ([[http://​www.ncbi.nlm.nih.gov/​entrez/​query.fcgi?​cmd=Retrieve&​db=PubMed&​list_uids=16789913|PubMed]])
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   * "​Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations",​ Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, Ho PY, Kakazu Y, Sugawara K, Igarashi A, Harada A, Masuda T, Sugiyama N, Togashi T, Hasegawa M, Takai Y, Yugi K, Arakawa K, Iwata N, Toya Y, Nakayama Y, Nishioka T, Shimizu K, Mori H, Tomita M, //​Science//,​ 2007, 316(5824): 593-597. ([[http://​www.ncbi.nlm.nih.gov/​entrez/​query.fcgi?​db=pubmed&​cmd=Retrieve&​dopt=AbstractPlus&​list_uids=17379776&​query_hl=1&​itool=pubmed_docsum|PubMed]])   * "​Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations",​ Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, Ho PY, Kakazu Y, Sugawara K, Igarashi A, Harada A, Masuda T, Sugiyama N, Togashi T, Hasegawa M, Takai Y, Yugi K, Arakawa K, Iwata N, Toya Y, Nakayama Y, Nishioka T, Shimizu K, Mori H, Tomita M, //​Science//,​ 2007, 316(5824): 593-597. ([[http://​www.ncbi.nlm.nih.gov/​entrez/​query.fcgi?​db=pubmed&​cmd=Retrieve&​dopt=AbstractPlus&​list_uids=17379776&​query_hl=1&​itool=pubmed_docsum|PubMed]])
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 ===== Software developed with G-language System ===== ===== Software developed with G-language System =====
  
publications.txt · Last modified: 2016/06/21 03:22 by gaou