Publications

===== Book about G-language System =====

• "Learning Bioinformatics with Open Source Software", (in Japanese), Japan Open Bioinformatics Research Group, //Tokyo Denki University Press//, 2008, (ISBN4501622601) http://www.amazon.co.jp/exec/obidos/ASIN/4501622601/gaounet-22/ref=nosim/. ===== Publication about G-language System =====
• "G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining", Arakawa K, Mori K, Ikeda K, Matsuzaki T, Kobayashi Y, Tomita M, //Bioinformatics//, 2003, 19(2):305-306 (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12538262&query_hl=1&itool=pubmed_docsum).

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(https://www.jstage.jst.go.jp/article/jpestics/31/3/31_3_282/_pdf).

This is a review describing G-language System and related software packages. Please also cite this article.

• "Computational Genome Analysis Using The G-language System", Arakawa K, Suzuki H, Tomita M, //Genes, Genomes and Genomics//, 2008, 2(1): 1-13 (http://www.g-language.org/data/gaou/doc/GGG-1-2008proof.pdf).

This review describes the algorithms implemented in G-language System, especially focusing on the identification of binding sites, analysis of genomic compositional skews, and codons.

• "G-language genome analysis environment with REST and SOAP web service interfaces", Arakawa K, Kido N, Oshita K, Tomita M, //Nucleic Acids Res.//, 2010, 38 Suppl:W700-705 (http://www.ncbi.nlm.nih.gov/pubmed/20439313).

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).

This paper describes the EMBOSS interface package for the G-language System.

===== Review papers related to G-language Project =====

• "Visualizing Complex Omics Information - Scientific Visualization for Genomics and Systems Biology", Arakawa K, Yachie N, Tomita M, //BIOforum Europe//, 2008, 6:27-29 (http://www.g-language.org/data/gaou/doc/BIOforumEurope-2008.pdf).

• "Large-scale Modeling for Systems Biology", Arakawa K, Tomita M, //BIOforum Europe//, 2006, 10:54-55 (http://www.g-language.org/data/gaou/doc/BIOforumEurope-54-55.pdf). ===== Researches using G-language System =====

=== 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)

• "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)

• "In silico prediction of the origin of replication among bacteria: a case study of bacteroides thetaiotaomicron.", Pallejà A, Guzman E, Garcia-Vallvé S, Romeu A, //OMICS//, 2008, 12(3):201-210. (http://www.ncbi.nlm.nih.gov/pubmed/18582175)

• "Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes", Arakawa K, Tomita M, //Evolutionary Bioinformatics//, 2007, 3:279-286. (http://la-press.com/journals.php?pa=abstract&content_id=393)

• "The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection", Arakawa K, Tomita M, //Evolutionary Bioinformatics//, 2007, 3:145-154. (http://la-press.com/journals.php?pa=abstract&content_id=349)

• "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)

=== 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)

=== Oligonucleotides: ===

• "Predicting Plasmid Promiscuity Based on Genomic Signature", Suzuki H, Yano H, Brown CJ, Top EM, //Journal of Bacteriology//, 2010, 192(22):6045-6055. (http://pubmed.org/20851899)

• "A web server for interactive and zoomable Chaos Game Representation images", Arakawa K, Oshita K, Tomita M, //Source Code for Biology and Medicine//, 2009, 4:6. (http://www.ncbi.nlm.nih.gov/pubmed/19761591)

• "Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes.", Suzuki H, Sota M, Brown CJ, Top EM, //Nucleic Acids Res//, 2008, doi:10.1093/nar/gkn753. (http://www.ncbi.nlm.nih.gov/pubmed/18953039)

• "Significance of the genomic properties of Chi sites validated from the distribution of all octamers in Escherichia coli", Arakawa K, Uno R, Nakayama Y, Tomita M, //Gene//, 2007, 392(1-2):239-246. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17270364&query_hl=1&itool=pubmed_docsum)

• "Over-representation of Chi sequences caused by di-codon increase in Escherichia coli K-12", Uno R, Nakayama Y, Tomita M, //GENE//, 2006, 380(1): 30-37. (http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16854534)

• "The orientation bias of Chi sequences is a general tendency of G-rich oligomers", Uno R, Nakayama Y, Arakawa K, Tomita M, //Gene//, 2000, 259(1-2):207-215 (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11163978&query_hl=1&itool=pubmed_docsum)

=== 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)

• "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)

• "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)

• "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)

• "Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria.", Suzuki H, Brown CJ, Forney LJ, Top EM, //DNA Res//, 2008, doi:10.1093/dnares/dsn028. (http://www.ncbi.nlm.nih.gov/pubmed/18940873)

• "Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria.", Suzuki H, Saito R, Tomita M, //EURASIP J Bioinform Syst Biol//, 2007, 61374. (http://www.ncbi.nlm.nih.gov/pubmed/18350114)

• "A problem in multivariate analysis of codon usage data and a possible solution.", Suzuki H, Saito R, Tomita M, //FEBS Lett//, 2005, 579(28):6499-6504. (http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16289058)

• "The 'weighted sum of relative entropy': a new index for synonymous codon usage bias.", Suzuki H, Saito R, Tomita M, //Gene//, 2004, 335:19-23. (http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=15194186)

=== Gene structures: ===

• "On the Interplay of Gene Positioning and the Role of Rho- Independent Terminators in Escherichia coli", Yachie N, Arakawa K, Tomita M, //FEBS Letters//, 2006, 580(30):6909-6914.(http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17156778&query_hl=1&itool=pubmed_docsum)
• "On dynamics of overlapping genes in bacterial genomes.", Fukuda Y, Nakayama Y, Tomita M, //Gene//, 2003, 323:181-187. (http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=14659892)

=== Genomics: ===

• "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)

• "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)

• "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)

• "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)

• "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)

• "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)

• "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)

• "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)

• "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)

• "Sequencing and analysis of the large virulence plasmid pLVPK of Klebsiella pneumoniae CG43.", Chen YT, Chang HY, Lai YC, Pan CC, Tsai SF, Peng HL, //Gene//, 2004, 337:189-98. (http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=15276215)

• "The Applications of Systematic In-Frame, Single-Gene Knockout Mutant Collection of Escherichia coli K-12.", Baba T, Huan HC, Datsenko K, Wanner BL, Mori H, //Methods Mol Biol//, 2008, 416:183-194 (http://www.ncbi.nlm.nih.gov/pubmed/18392968)

=== RNA: ===

• "Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes.", Kochiwa H, Tomita M, Kanai A, //BMC Evol Biol.//, 2007, 7:128. (http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17663799&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum)
• "In Silico Screening of Archaeal tRNA-encoding Genes Having Multiple Introns with Bulge-Helix-Bulge Splicing Motifs", Sugahara J, Yachie N, Arakawa K*, Tomita M, //RNA//, 2007, 13(5): 671-681. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17369313&query_hl=1&itool=pubmed_docsum)
• "Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model.", Yachie N, Numata K, Saito R, Kanai A, Tomita M, //Gene//, 2006, 372:171-181. (http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16564143)

=== Systems Biology: ===

• "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) ===== Software developed with G-language System =====

• "Pathway Projector: Web-based Zoomable Pathway Browser using KEGG Atlas and Google Maps API", Kono N, Arakawa K, Ogawa R, Kido N, Oshita K, Ikegami K, Tamaki S, Tomita M, PLoS One, 2009, 4(11):e7710. (http://www.ncbi.nlm.nih.gov/pubmed/19907644)

• "Genome Projector: zoomable genome map with multiple views", Arakawa K, Tamaki S, Kono N, Kido N, Ikegami K, Ogawa R and Tomita M, //BMC Bioinformatics//, 2009, 10:31. (http://www.ncbi.nlm.nih.gov/pubmed/19166610)

• "Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics", Tamaki S, Arakawa K, Kono N, Tomita M, //Genomics Proteomics Bioinformatics//, 2007, 5(1): 53-58. (http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17572364)

• "MEGU: Pathway mapping web-service based on KEGG and SVG", Kono N, Arakawa K, Tomita M, //In Silico Biology//, 2006, 6(6):621-655. (http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17518769)

• "GEM System: Automatic prototyping of cell-wide metabolic pathway models from genomes", Arakawa K, Yamada Y, Shinoda K, Nakayama Y, Tomita M, //BMC Bioinformatics//, 2006, 7:168 (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16553966&query_hl=6&itool=pubmed_docsum)

• "Comprehensive software suite for bioinformatics analysis of cDNAs", Arakawa K, Suzuki H, Fujishima K, Fujimoto K, Ueda S, Matsui M, Tomita M, //Genomics Proteomics Bioinformatics//, 2005, 3(3):179-188 (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16487083&query_hl=4&itool=pubmed_docsum)

• "KEGG-based pathway visualization tool for complex omics data", Arakawa K, Kono N, Yamada Y, Mori H, and Tomita M, //In Silico Biology//, 2005, 5:0039 (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16268787&query_hl=1&itool=pubmed_docsum)

• "Computational analysis of stop codon readthrough in D.melanogaster.", Sato M, Umeki H, Saito R, Kanai A, Tomita M, //Bioinformatics//, 2003, 19(11):1371-1380. (http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=15276215)