TY - JOUR AU - Rimmer, A. AU - Phan, H. AU - Mathieson, I. AU - Iqbal, Z. AU - Twigg, S. R. F. AU - Wilkie, A. O. M. PY - 2014 DA - 2014// TI - Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications JO - Nat Genet VL - 46 UR - https://doi.org/10.1038/ng.3036 DO - 10.1038/ng.3036 ID - Rimmer2014 ER - TY - JOUR AU - McKenna, A. AU - Hanna, M. AU - Banks, E. AU - Sivachenko, A. AU - Cibulskis, K. AU - Kernytsky, A. PY - 2010 DA - 2010// TI - The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.107524.110 DO - 10.1101/gr.107524.110 ID - McKenna2010 ER - TY - JOUR AU - Yang, Z. AU - Rannala, B. PY - 2012 DA - 2012// TI - Molecular phylogenetics: principles and practice JO - Nat. Rev. Genet. VL - 13 UR - https://doi.org/10.1038/nrg3186 DO - 10.1038/nrg3186 ID - Yang2012 ER - TY - STD TI - Zhou Z, McCann A, Litrup E, Murphy R, Cormican M, Fanning S, et al. Neutral genomic microevolution of a recently emerged pathogen, salmonella enterica Serovar Agona. Casadesús J, editor. PLoS Genet 2013;9:e1003471. ID - ref4 ER - TY - STD TI - Didelot X, Wilson DJ. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. Prlic A, editor. PLoS Comput Biol 2015;11:e1004041. ID - ref5 ER - TY - STD TI - Lees JA, Bentley SD, Bacterial GWAS. Not just gilding the lily. Nat Rev Microbiol. 2016;14:406–6. ID - ref6 ER - TY - JOUR AU - Andersen, J. B. AU - Sternberg, C. AU - Poulsen, L. K. AU - Bjorn, S. P. AU - Givskov, M. AU - Molin, S. PY - 1998 DA - 1998// TI - New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria JO - Appl Environ Microbiol VL - 64 ID - Andersen1998 ER - TY - JOUR AU - Amato, S. M. AU - Fazen, C. H. AU - Henry, T. C. AU - Mok, W. W. K. AU - Orman, M. A. AU - Sandvik, E. L. PY - 2014 DA - 2014// TI - The role of metabolism in bacterial persistence JO - Front Microbiol VL - 5 UR - https://doi.org/10.3389/fmicb.2014.00070 DO - 10.3389/fmicb.2014.00070 ID - Amato2014 ER - TY - JOUR AU - Read, T. D. AU - Massey, R. C. PY - 2014 DA - 2014// TI - Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology JO - Genome Med VL - 6 UR - https://doi.org/10.1186/s13073-014-0109-z DO - 10.1186/s13073-014-0109-z ID - Read2014 ER - TY - JOUR AU - Huang, D. W. AU - Sherman, B. T. AU - Lempicki, R. A. PY - 2009 DA - 2009// TI - Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn923 DO - 10.1093/nar/gkn923 ID - Huang2009 ER - TY - STD TI - Fruzangohar M, Ebrahimie E, Ogunniyi AD, Mahdi LK, Paton JC, Adelson DL. Comparative GO: A Web Application For comparative gene ontology and gene ontology-based gene selection in bacteria. Patterson RL, editor. PLoS One 2013;8:e58759. ID - ref11 ER - TY - JOUR AU - Lee, I. -. H. AU - Lee, K. AU - Hsing, M. AU - Choe, Y. AU - Park, J. -. H. AU - Kim, S. H. PY - 2014 DA - 2014// TI - Prioritizing disease-linked variants, genes, and pathways with an interactive whole-genome analysis pipeline JO - Hum Mutat VL - 35 UR - https://doi.org/10.1002/humu.22520 DO - 10.1002/humu.22520 ID - Lee2014 ER - TY - JOUR AU - Dennis, G. AU - Sherman, B. T. AU - Hosack, D. A. AU - Yang, J. AU - Gao, W. AU - Lane, H. C. PY - 2003 DA - 2003// TI - DAVID: database for annotation, visualization, and integrated discovery JO - Genome Biol VL - 4 UR - https://doi.org/10.1186/gb-2003-4-5-p3 DO - 10.1186/gb-2003-4-5-p3 ID - Dennis2003 ER - TY - JOUR AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Botstein, D. AU - Butler, H. AU - Cherry, J. M. PY - 2000 DA - 2000// TI - Gene ontology: tool for the unification of biology JO - Nat Genet VL - 25 UR - https://doi.org/10.1038/75556 DO - 10.1038/75556 ID - Ashburner2000 ER - TY - JOUR AU - Grossmann, S. AU - Bauer, S. AU - Robinson, P. N. AU - Vingron, M. PY - 2007 DA - 2007// TI - Improved detection of overrepresentation of gene-ontology annotations with parent child analysis JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm440 DO - 10.1093/bioinformatics/btm440 ID - Grossmann2007 ER - TY - JOUR AU - Majowicz, S. E. AU - Musto, J. AU - Scallan, E. AU - Angulo, F. J. AU - Kirk, M. AU - O’Brien, S. J. PY - 2010 DA - 2010// TI - The global burden of Nontyphoidal Salmonella gastroenteritis JO - Clin Infect Dis VL - 50 UR - https://doi.org/10.1086/650733 DO - 10.1086/650733 ID - Majowicz2010 ER - TY - JOUR AU - Bäumler, A. J. AU - Tsolis, R. M. AU - Ficht, T. A. AU - Adams, L. G. PY - 1998 DA - 1998// TI - Evolution of host adaptation in salmonella enterica JO - Infect Immun VL - 66 ID - Bäumler1998 ER - TY - JOUR AU - Foley, S. L. AU - Johnson, T. J. AU - Ricke, S. C. AU - Nayak, R. AU - Danzeisen, J. PY - 2013 DA - 2013// TI - Salmonella pathogenicity and host adaptation in chicken-associated Serovars JO - Microbiol Mol Biol Rev VL - 77 UR - https://doi.org/10.1128/MMBR.00015-13 DO - 10.1128/MMBR.00015-13 ID - Foley2013 ER - TY - JOUR AU - Porwollik, S. AU - Santiviago, C. A. AU - Cheng, P. AU - Florea, L. AU - Jackson, S. AU - McClelland, M. PY - 2005 DA - 2005// TI - Differences in gene content between salmonella enterica serovar Enteritidis isolates and comparison to closely related serovars Gallinarum and Dublin JO - J Bacteriol VL - 187 UR - https://doi.org/10.1128/JB.187.18.6545-6555.2005 DO - 10.1128/JB.187.18.6545-6555.2005 ID - Porwollik2005 ER - TY - JOUR AU - Fricke, W. F. AU - Mammel, M. K. AU - McDermott, P. F. AU - Tartera, C. AU - White, D. G. AU - LeClerc, J. E. PY - 2011 DA - 2011// TI - Comparative genomics of 28 salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution JO - J Bacteriol VL - 193 UR - https://doi.org/10.1128/JB.00297-11 DO - 10.1128/JB.00297-11 ID - Fricke2011 ER - TY - JOUR AU - Chu, C. AU - Feng, Y. AU - Chien, A. -. C. AU - Hu, S. AU - Chu, C. -. H. AU - Chiu, C. -. H. PY - 2008 DA - 2008// TI - Evolution of genes on the salmonella virulence plasmid phylogeny revealed from sequencing of the virulence plasmids of S. Enterica serotype Dublin and comparative analysis JO - Genomics VL - 92 UR - https://doi.org/10.1016/j.ygeno.2008.07.010 DO - 10.1016/j.ygeno.2008.07.010 ID - Chu2008 ER - TY - JOUR AU - Langridge, G. C. AU - Fookes, M. AU - Connor, T. R. AU - Feltwell, T. AU - Feasey, N. AU - Parsons, B. N. PY - 2015 DA - 2015// TI - Patterns of genome evolution that have accompanied host adaptation in Salmonella JO - Proc Natl Acad Sci VL - 112 UR - https://doi.org/10.1073/pnas.1416707112 DO - 10.1073/pnas.1416707112 ID - Langridge2015 ER - TY - JOUR AU - Rabsch, W. AU - Andrews, H. L. AU - Kingsley, R. A. AU - Prager, R. AU - Tschäpe, H. AU - Adams, L. G. PY - 2002 DA - 2002// TI - Salmonella enterica serotype typhimurium and its host-adapted variants JO - Infect Immun VL - 70 UR - https://doi.org/10.1128/IAI.70.5.2249-2255.2002 DO - 10.1128/IAI.70.5.2249-2255.2002 ID - Rabsch2002 ER - TY - JOUR AU - Pang, S. AU - Octavia, S. AU - Feng, L. AU - Liu, B. AU - Reeves, P. R. AU - Lan, R. PY - 2013 DA - 2013// TI - Genomic diversity and adaptation of salmonella enterica serovar typhimurium from analysis of six genomes of different phage types JO - BMC Genomics VL - 14 UR - https://doi.org/10.1186/1471-2164-14-718 DO - 10.1186/1471-2164-14-718 ID - Pang2013 ER - TY - JOUR AU - Thomson, N. R. AU - Clayton, D. J. AU - Windhorst, D. AU - Vernikos, G. AU - Davidson, S. AU - Churcher, C. PY - 2008 DA - 2008// TI - Comparative genome analysis of salmonella Enteritidis PT4 and salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.077404.108 DO - 10.1101/gr.077404.108 ID - Thomson2008 ER - TY - JOUR AU - Soucy, S. M. AU - Huang, J. AU - Gogarten, J. P. PY - 2015 DA - 2015// TI - Horizontal gene transfer: building the web of life JO - Nat Rev Genet VL - 16 UR - https://doi.org/10.1038/nrg3962 DO - 10.1038/nrg3962 ID - Soucy2015 ER - TY - JOUR AU - McClelland, M. AU - Sanderson, K. E. AU - Spieth, J. AU - Clifton, S. W. AU - Latreille, P. AU - Courtney, L. PY - 2001 DA - 2001// TI - Complete genome sequence of salmonella enterica serovar typhimurium LT2 JO - Nature VL - 413 UR - https://doi.org/10.1038/35101614 DO - 10.1038/35101614 ID - McClelland2001 ER - TY - JOUR AU - Rotger, R. AU - Casadesús, J. PY - 1999 DA - 1999// TI - The virulence plasmids of salmonella JO - Int Microbiol Off J Span Soc Microbiol VL - 2 ID - Rotger1999 ER - TY - JOUR AU - Libby, S. J. AU - Lesnick, M. AU - Hasegawa, P. AU - Weidenhammer, E. AU - Guiney, D. G. PY - 2000 DA - 2000// TI - The salmonella virulence plasmid spv genes are required for cytopathology in human monocyte-derived macrophages JO - Cell Microbiol VL - 2 UR - https://doi.org/10.1046/j.1462-5822.2000.00030.x DO - 10.1046/j.1462-5822.2000.00030.x ID - Libby2000 ER - TY - JOUR AU - Nielsen, L. R. PY - 2013 DA - 2013// TI - Review of pathogenesis and diagnostic methods of immediate relevance for epidemiology and control of salmonella Dublin in cattle JO - Vet Microbiol VL - 162 UR - https://doi.org/10.1016/j.vetmic.2012.08.003 DO - 10.1016/j.vetmic.2012.08.003 ID - Nielsen2013 ER - TY - STD TI - Blondel CJ, Yang H-J, Castro B, Chiang S, Toro CS, Zaldívar M, et al. Contribution of the type VI secretion system encoded in SPI-19 to chicken colonization by salmonella enterica serotypes Gallinarum and Enteritidis. Otto M, editor. PLoS One 2010;5:e11724. ID - ref31 ER - TY - JOUR AU - Neuman, J. A. AU - Isakov, O. AU - Shomron, N. PY - 2013 DA - 2013// TI - Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection JO - Brief Bioinform VL - 14 UR - https://doi.org/10.1093/bib/bbs013 DO - 10.1093/bib/bbs013 ID - Neuman2013 ER - TY - STD TI - Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, del Angel G, Levy-Moonshine A, et al. From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline: The Genome Analysis Toolkit Best Practices Pipeline. In: Bateman A, Pearson WR, Stein LD, Stormo GD, Yates JR, editors. Curr. Protoc. Bioinforma. Hoboken, NJ, USA: John Wiley & Sons, Inc.; 2013. p. 1–33. ID - ref33 ER - TY - JOUR AU - Albers, C. A. AU - Lunter, G. AU - MacArthur, D. G. AU - McVean, G. AU - Ouwehand, W. H. AU - Durbin, R. PY - 2011 DA - 2011// TI - Dindel: accurate indel calls from short-read data JO - Genome Res VL - 21 UR - https://doi.org/10.1101/gr.112326.110 DO - 10.1101/gr.112326.110 ID - Albers2011 ER - TY - JOUR AU - Fridjonsson, O. AU - Olafsson, K. AU - Tompsett, S. AU - Bjornsdottir, S. AU - Consuegra, S. AU - Knox, D. PY - 2011 DA - 2011// TI - Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing JO - BMC Genomics VL - 12 UR - https://doi.org/10.1186/1471-2164-12-179 DO - 10.1186/1471-2164-12-179 ID - Fridjonsson2011 ER - TY - JOUR AU - Beres, S. B. AU - Carroll, R. K. AU - Shea, P. R. AU - Sitkiewicz, I. AU - Martinez-Gutierrez, J. C. AU - Low, D. E. PY - 2010 DA - 2010// TI - Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics JO - Proc Natl Acad Sci VL - 107 UR - https://doi.org/10.1073/pnas.0911295107 DO - 10.1073/pnas.0911295107 ID - Beres2010 ER - TY - JOUR AU - Mansueto, L. AU - Fuentes, R. R. AU - Borja, F. N. AU - Detras, J. AU - Abriol-Santos, J. M. AU - Chebotarov, D. PY - 2017 DA - 2017// TI - Rice SNP-seek database update: new SNPs, indels, and queries JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkw1135 DO - 10.1093/nar/gkw1135 ID - Mansueto2017 ER - TY - JOUR AU - Mullaney, J. M. AU - Mills, R. E. AU - Pittard, W. S. AU - Devine, S. E. PY - 2010 DA - 2010// TI - Small insertions and deletions (INDELs) in human genomes JO - Hum Mol Genet VL - 19 UR - https://doi.org/10.1093/hmg/ddq400 DO - 10.1093/hmg/ddq400 ID - Mullaney2010 ER - TY - JOUR AU - Pattengale, N. D. AU - Alipour, M. AU - Bininda-Emonds, O. R. P. AU - Moret, B. M. E. AU - Stamatakis, A. PY - 2010 DA - 2010// TI - How many bootstrap replicates are necessary? JO - J Comput Biol VL - 17 UR - https://doi.org/10.1089/cmb.2009.0179 DO - 10.1089/cmb.2009.0179 ID - Pattengale2010 ER - TY - JOUR AU - Aberer, A. J. AU - Pattengale, N. D. AU - Stamatakis, A. PY - 2010 DA - 2010// TI - Parallelized phylogenetic post-analysis on multi-core architectures JO - J Comput Sci VL - 1 UR - https://doi.org/10.1016/j.jocs.2010.03.006 DO - 10.1016/j.jocs.2010.03.006 ID - Aberer2010 ER - TY - JOUR AU - Corander, J. AU - Marttinen, P. AU - Sirén, J. AU - Tang, J. PY - 2008 DA - 2008// TI - Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-539 DO - 10.1186/1471-2105-9-539 ID - Corander2008 ER - TY - JOUR AU - Barrow, P. A. AU - Neto, O. C. F. PY - 2011 DA - 2011// TI - Pullorum disease and fowl typhoid—new thoughts on old diseases: a review JO - Avian Pathol VL - 40 UR - https://doi.org/10.1080/03079457.2010.542575 DO - 10.1080/03079457.2010.542575 ID - Barrow2011 ER - TY - JOUR AU - Crichton, P. B. AU - Old, D. C. PY - 1990 DA - 1990// TI - Salmonellae of serotypes Gallinarum and Pullorum grouped by biotyping and Fimbrial-gene probing JO - J Med Microbiol VL - 32 UR - https://doi.org/10.1099/00222615-32-3-145 DO - 10.1099/00222615-32-3-145 ID - Crichton1990 ER - TY - JOUR AU - Joyce, E. A. AU - Chan, K. AU - Salama, N. R. AU - Falkow, S. PY - 2002 DA - 2002// TI - Redefining bacterial populations: a post-genomic reformation JO - Nat Rev Genet VL - 3 ID - Joyce2002 ER - TY - JOUR AU - Craig, M. AU - Sadik, A. Y. AU - Golubeva, Y. A. AU - Tidhar, A. AU - Slauch, J. M. PY - 2013 DA - 2013// TI - Twin-arginine translocation system ( tat ) mutants of Salmonella are attenuated due to envelope defects, not respiratory defects: role of tat in Salmonella virulence JO - Mol Microbiol VL - 89 UR - https://doi.org/10.1111/mmi.12318 DO - 10.1111/mmi.12318 ID - Craig2013 ER - TY - JOUR AU - Juhas, M. AU - van der Meer, J. R. AU - Gaillard, M. AU - Harding, R. M. AU - Hood, D. W. AU - Crook, D. W. PY - 2009 DA - 2009// TI - Genomic islands: tools of bacterial horizontal gene transfer and evolution JO - FEMS Microbiol Rev VL - 33 UR - https://doi.org/10.1111/j.1574-6976.2008.00136.x DO - 10.1111/j.1574-6976.2008.00136.x ID - Juhas2009 ER - TY - JOUR AU - Kanehisa, M. AU - Sato, Y. AU - Kawashima, M. AU - Furumichi, M. AU - Tanabe, M. K. E. G. G. PY - 2016 DA - 2016// TI - As a reference resource for gene and protein annotation JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1070 DO - 10.1093/nar/gkv1070 ID - Kanehisa2016 ER - TY - JOUR AU - Bankevich, A. AU - Nurk, S. AU - Antipov, D. AU - Gurevich, A. A. AU - Dvorkin, M. AU - Kulikov, A. S. PY - 2012 DA - 2012// TI - SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing JO - J Comput Biol VL - 19 UR - https://doi.org/10.1089/cmb.2012.0021 DO - 10.1089/cmb.2012.0021 ID - Bankevich2012 ER - TY - JOUR AU - Ondov, B. D. AU - Treangen, T. J. AU - Melsted, P. AU - Mallonee, A. B. AU - Bergman, N. H. AU - Koren, S. PY - 2016 DA - 2016// TI - Mash: fast genome and metagenome distance estimation using MinHash JO - Genome Biol VL - 17 UR - https://doi.org/10.1186/s13059-016-0997-x DO - 10.1186/s13059-016-0997-x ID - Ondov2016 ER - TY - JOUR AU - Hedge, J. AU - Wilson, D. J. PY - 2014 DA - 2014// TI - Bacterial phylogenetic reconstruction from whole genomes is robust to recombination but demographic inference is not JO - MBio VL - 5 UR - https://doi.org/10.1128/mBio.02158-14 DO - 10.1128/mBio.02158-14 ID - Hedge2014 ER - TY - JOUR AU - Makendi, C. AU - Page, A. J. AU - Wren, B. W. AU - Le Thi Phuong, T. AU - Clare, S. AU - Hale, C. PY - 2016 DA - 2016// TI - A phylogenetic and phenotypic analysis of salmonella enterica Serovar Weltevreden, an emerging agent of diarrheal disease in tropical regions. Ryan ET JO - PLoS Negl Trop Dis VL - 10 UR - https://doi.org/10.1371/journal.pntd.0004446 DO - 10.1371/journal.pntd.0004446 ID - Makendi2016 ER - TY - JOUR AU - Shabalina, S. A. AU - Spiridonov, N. A. AU - Kashina, A. PY - 2013 DA - 2013// TI - Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gks1205 DO - 10.1093/nar/gks1205 ID - Shabalina2013 ER - TY - JOUR AU - Radomski, N. AU - Thibault, V. C. AU - Karoui, C. AU - de Cruz, K. AU - Cochard, T. AU - Gutiérrez, C. PY - 2010 DA - 2010// TI - Genotypic diversity of Mycobacterium Avium subspecies from human and animal origins, studied by MIRU-VNTR and IS1311 RFLP typing methods JO - J Clin Microbiol VL - 48 UR - https://doi.org/10.1128/JCM.01869-09 DO - 10.1128/JCM.01869-09 ID - Radomski2010 ER - TY - JOUR AU - Wernegreen, J. J. PY - 2002 DA - 2002// TI - Genome evolution in bacterial endosymbionts of insects JO - Nat Rev Genet VL - 3 UR - https://doi.org/10.1038/nrg931 DO - 10.1038/nrg931 ID - Wernegreen2002 ER - TY - JOUR AU - Wiedemann, A. AU - Virlogeux-Payant, I. AU - Chaussé, A. -. M. AU - Schikora, A. AU - Velge, P. PY - 2015 DA - 2015// TI - Interactions of salmonella with animals and plants JO - Front Microbiol VL - 5 UR - https://doi.org/10.3389/fmicb.2014.00791 DO - 10.3389/fmicb.2014.00791 ID - Wiedemann2015 ER - TY - JOUR AU - Dhanani, A. S. AU - Block, G. AU - Dewar, K. AU - Forgetta, V. AU - Topp, E. AU - Beiko, R. G. PY - 2015 DA - 2015// TI - Genomic comparison of non-Typhoidal salmonella enterica Serovars typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky isolates from broiler chickens JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0128773 DO - 10.1371/journal.pone.0128773 ID - Dhanani2015 ER - TY - JOUR AU - Dhanani, A. S. AU - Block, G. AU - Dewar, K. AU - Forgetta, V. AU - Topp, E. AU - Beiko, R. G. PY - 2015 DA - 2015// TI - Correction: genomic comparison of non-Typhoidal salmonella enterica Serovars typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky isolates from broiler chickens JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0137697 DO - 10.1371/journal.pone.0137697 ID - Dhanani2015 ER - TY - JOUR AU - Weening, E. H. AU - Barker, J. D. AU - Laarakker, M. C. AU - Humphries, A. D. AU - Tsolis, R. M. AU - Bäumler, A. J. PY - 2005 DA - 2005// TI - The salmonella enterica serotype typhimurium lpf, bcf, stb, stc, std, and sth fimbrial operons are required for intestinal persistence in mice JO - Infect Immun VL - 73 UR - https://doi.org/10.1128/IAI.73.6.3358-3366.2005 DO - 10.1128/IAI.73.6.3358-3366.2005 ID - Weening2005 ER - TY - STD TI - Jelsbak L, Hartman H, Schroll C, Rosenkrantz JT, Lemire S, Wallrodt I, et al. Identification of metabolic pathways essential for fitness of salmonella typhimurium in vivo. Cloeckaert A, editor. PLoS One 2014;9:e101869. ID - ref59 ER - TY - JOUR AU - Charlier, D. AU - Glansdorff, N. PY - 2004 DA - 2004// TI - Biosynthesis of arginine and polyamines JO - EcoSal Plus VL - 1 UR - https://doi.org/10.1128/ecosalplus.3.6.1.10 DO - 10.1128/ecosalplus.3.6.1.10 ID - Charlier2004 ER - TY - JOUR AU - Tocilj, A. AU - Schrag, J. D. AU - Li, Y. AU - Schneider, B. L. AU - Reitzer, L. AU - Matte, A. PY - 2005 DA - 2005// TI - Crystal structure of N-Succinylarginine Dihydrolase AstB, bound to substrate and product, an enzyme from the arginine catabolic pathway of Escherichia Coli JO - J Biol Chem VL - 280 UR - https://doi.org/10.1074/jbc.M413833200 DO - 10.1074/jbc.M413833200 ID - Tocilj2005 ER - TY - JOUR AU - Botsford, J. L. AU - Alvarez, M. AU - Hernandez, R. AU - Nichols, R. PY - 1994 DA - 1994// TI - Accumulation of glutamate by salmonella typhimurium in response to osmotic stress JO - Appl Environ Microbiol VL - 60 ID - Botsford1994 ER - TY - JOUR AU - Csonka, L. N. AU - Ikeda, T. P. AU - Fletcher, S. A. AU - Kustu, S. PY - 1994 DA - 1994// TI - The accumulation of glutamate is necessary for optimal growth of salmonella typhimurium in media of high osmolality but not induction of the proU operon JO - J Bacteriol VL - 176 UR - https://doi.org/10.1128/jb.176.20.6324-6333.1994 DO - 10.1128/jb.176.20.6324-6333.1994 ID - Csonka1994 ER - TY - JOUR AU - Claus, S. P. AU - Guillou, H. AU - Ellero-Simatos, S. PY - 2016 DA - 2016// TI - The gut microbiota: a major player in the toxicity of environmental pollutants? JO - Npj Biofilms Microbiomes VL - 2 UR - https://doi.org/10.1038/npjbiofilms.2016.3 DO - 10.1038/npjbiofilms.2016.3 ID - Claus2016 ER - TY - JOUR AU - Lee, E. -. J. AU - Choi, J. AU - Groisman, E. A. PY - 2014 DA - 2014// TI - Control of a salmonella virulence operon by proline-charged tRNAPro JO - Proc Natl Acad Sci VL - 111 UR - https://doi.org/10.1073/pnas.1316209111 DO - 10.1073/pnas.1316209111 ID - Lee2014 ER - TY - JOUR AU - Allen, S. W. AU - Senti-Willis, A. AU - Maloy, S. R. D. N. A. PY - 1993 DA - 1993// TI - Sequence of the putA gene from salmonella typhimurium: a bifunctional membrane-associated dehydrogenase that binds DNA JO - Nucleic Acids Res VL - 11 UR - https://doi.org/10.1093/nar/21.7.1676 DO - 10.1093/nar/21.7.1676 ID - Allen1993 ER - TY - JOUR AU - Esaki, N. AU - Walsh, C. T. PY - 1986 DA - 1986// TI - Biosynthetic alanine racemase of salmonella typhimurium: purification and characterization of the enzyme encoded by the alr gene JO - Biochemistry (Mosc) VL - 25 UR - https://doi.org/10.1021/bi00359a027 DO - 10.1021/bi00359a027 ID - Esaki1986 ER - TY - JOUR AU - Yuan, C. AU - Li, J. M. AU - Ding, Y. AU - He, Q. AU - Yan, H. X. AU - JJ, L. PY - 2015 DA - 2015// TI - Estimation of L-arginine requirement for Xinyang black laying hens from 33 to 45 weeks of age JO - J Appl Poult Res VL - 24 ID - Yuan2015 ER - TY - CHAP AU - H. Karasov, W. AU - Douglas, A. E. ED - Terjung, R. PY - 2013 DA - 2013// BT - Comparative Digestive Physiology PB - Sons, Inc CY - Hoboken, NJ, USA UR - https://doi.org/10.1002/cphy.c110054 DO - 10.1002/cphy.c110054 ID - H. Karasov2013 ER - TY - JOUR AU - Gilbert, E. R. AU - Li, H. AU - Emmerson, D. A. AU - Webb, K. E. AU - Wong, E. A. PY - 2007 DA - 2007// TI - Developmental regulation of nutrient transporter and enzyme mRNA abundance in the small intestine of broilers JO - Poult Sci VL - 86 UR - https://doi.org/10.1093/ps/86.8.1739 DO - 10.1093/ps/86.8.1739 ID - Gilbert2007 ER - TY - JOUR AU - Kieboom, J. AU - Abee, T. PY - 2006 DA - 2006// TI - Arginine-dependent acid resistance in salmonella enterica Serovar typhimurium JO - J Bacteriol VL - 188 UR - https://doi.org/10.1128/JB.00323-06 DO - 10.1128/JB.00323-06 ID - Kieboom2006 ER - TY - JOUR AU - Brenneman, K. E. AU - Willingham, C. AU - Kong, W. AU - Curtiss, R. AU - Roland, K. L. PY - 2013 DA - 2013// TI - Low-pH Rescue of Acid-Sensitive Salmonella enterica Serovar Typhi strains by a Rhamnose-regulated arginine decarboxylase system JO - J Bacteriol VL - 195 UR - https://doi.org/10.1128/JB.00104-13 DO - 10.1128/JB.00104-13 ID - Brenneman2013 ER - TY - JOUR AU - Paulander, W. AU - Andersson, D. I. PY - 2010 DA - 2010// TI - Amplification of the gene for Isoleucyl-tRNA Synthetase facilitates adaptation to the fitness cost of mupirocin resistance in salmonella enterica JO - Genetics VL - 185 UR - https://doi.org/10.1534/genetics.109.113514 DO - 10.1534/genetics.109.113514 ID - Paulander2010 ER - TY - JOUR AU - Han, J. AU - Lynne, A. M. AU - David, D. E. AU - Tang, H. AU - Xu, J. AU - Nayak, R. PY - 2012 DA - 2012// TI - DNA sequence analysis of plasmids from multidrug resistant salmonella enterica serotype Heidelberg isolates. Webber MA JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0051160 DO - 10.1371/journal.pone.0051160 ID - Han2012 ER - TY - JOUR AU - Bolger, A. M. AU - Lohse, M. AU - Usadel, B. PY - 2014 DA - 2014// TI - Trimmomatic: a flexible trimmer for Illumina sequence data JO - Bioinforma Oxf Engl VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu170 DO - 10.1093/bioinformatics/btu170 ID - Bolger2014 ER - TY - JOUR AU - Li, H. AU - Durbin, R. PY - 2009 DA - 2009// TI - Fast and accurate short read alignment with burrows-wheeler transform JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp324 DO - 10.1093/bioinformatics/btp324 ID - Li2009 ER - TY - JOUR AU - Li, H. AU - Handsaker, B. AU - Wysoker, A. AU - Fennell, T. AU - Ruan, J. AU - Homer, N. PY - 2009 DA - 2009// TI - The sequence alignment/map format and SAMtools JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp352 DO - 10.1093/bioinformatics/btp352 ID - Li2009 ER - TY - JOUR AU - DePristo, M. A. AU - Banks, E. AU - Poplin, R. AU - Garimella, K. V. AU - Maguire, J. R. AU - Hartl, C. PY - 2011 DA - 2011// TI - A framework for variation discovery and genotyping using next-generation DNA sequencing data JO - Nat Genet VL - 43 UR - https://doi.org/10.1038/ng.806 DO - 10.1038/ng.806 ID - DePristo2011 ER - TY - JOUR AU - Cingolani, P. AU - Patel, V. M. AU - Coon, M. AU - Nguyen, T. AU - Land, S. J. AU - Ruden, D. M. PY - 2012 DA - 2012// TI - Using Drosophila Melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift JO - Front Genet VL - 3 UR - https://doi.org/10.3389/fgene.2012.00035 DO - 10.3389/fgene.2012.00035 ID - Cingolani2012 ER - TY - JOUR AU - Cingolani, P. AU - Platts, A. AU - Wang, L. L. AU - Coon, M. AU - Nguyen, T. AU - Wang, L. PY - 2012 DA - 2012// TI - A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila Melanogaster strain w1118; iso-2; iso-3 JO - Landes Biosci VL - 6 ID - Cingolani2012 ER - TY - JOUR AU - Danecek, P. AU - Auton, A. AU - Abecasis, G. AU - Albers, C. A. AU - Banks, E. AU - DePristo, M. A. PY - 2011 DA - 2011// TI - The variant call format and VCFtools JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr330 DO - 10.1093/bioinformatics/btr330 ID - Danecek2011 ER - TY - JOUR AU - Lescai, F. AU - Marasco, E. AU - Bacchelli, C. AU - Stanier, P. AU - Mantovani, V. AU - Beales, P. PY - 2014 DA - 2014// TI - Identification and validation of loss of function variants in clinical contexts. Mol. Genet JO - Genomic Med VL - 2 ID - Lescai2014 ER - TY - JOUR AU - Stamatakis, A. PY - 2014 DA - 2014// TI - RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu033 DO - 10.1093/bioinformatics/btu033 ID - Stamatakis2014 ER - TY - JOUR AU - Letunic, I. AU - Bork, P. PY - 2016 DA - 2016// TI - Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkw290 DO - 10.1093/nar/gkw290 ID - Letunic2016 ER - TY - JOUR AU - Revell, L. J. PY - 2012 DA - 2012// TI - Phytools: an R package for phylogenetic comparative biology (and other things): phytools: R package JO - Methods Ecol Evol VL - 3 UR - https://doi.org/10.1111/j.2041-210X.2011.00169.x DO - 10.1111/j.2041-210X.2011.00169.x ID - Revell2012 ER - TY - JOUR AU - Armstrong, R. A. PY - 2014 DA - 2014// TI - When to use the Bonferroni correction JO - Ophthalmic Physiol Opt VL - 34 UR - https://doi.org/10.1111/opo.12131 DO - 10.1111/opo.12131 ID - Armstrong2014 ER - TY - BOOK AU - Development Core Team, R. PY - 2015 DA - 2015// TI - R: a language and environment for statistical computing PB - R Foundation for Statistical Computing CY - Vienna, Austria ID - Development Core Team2015 ER - TY - JOUR AU - Yoon, S. H. AU - Park, Y. -. K. AU - Lee, S. AU - Choi, D. AU - TK, O. AU - Hur, C. -. G. PY - 2007 DA - 2007// TI - Towards pathogenomics: a web-based resource for pathogenicity islands JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkl790 DO - 10.1093/nar/gkl790 ID - Yoon2007 ER -