Nicole Perna

Nicole Perna

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Nicole Perna

Nicole Perna

Publications by authors named "Nicole Perna"

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52Publications

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Tailoring a Global Iron Regulon to a Uropathogen.

mBio 2020 Mar 24;11(2). Epub 2020 Mar 24.

Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA

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http://dx.doi.org/10.1128/mBio.00351-20DOI Listing
March 2020

Complete Genome Sequence of Dickeya dianthicola ME23, a Pathogen Causing Blackleg and Soft Rot Diseases of Potato.

Microbiol Resour Announc 2019 Feb 14;8(7). Epub 2019 Feb 14.

Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA.

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http://dx.doi.org/10.1128/MRA.01526-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6376422PMC
February 2019

The Enterobacterium Trabulsiella odontotermitis Presents Novel Adaptations Related to Its Association with Fungus-Growing Termites.

Appl Environ Microbiol 2015 Oct 10;81(19):6577-88. Epub 2015 Jul 10.

Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1128/AEM.01844-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561680PMC
October 2015

Transcriptome changes associated with anaerobic growth in Yersinia intermedia (ATCC29909).

PLoS One 2013 7;8(10):e76567. Epub 2013 Oct 7.

Biotechnology Center, University of Wisconsin - Madison, Madison, Wisconsin, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0076567PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3792023PMC
August 2014

Computing the joint distribution of tree shape and tree distance for gene tree inference and recombination detection.

IEEE/ACM Trans Comput Biol Bioinform 2013 Sep-Oct;10(5):1263-74

University of Wisconsin, Madison.

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http://dx.doi.org/10.1109/TCBB.2013.109DOI Listing
August 2014

Inferring ancient metabolism using ancestral core metabolic models of enterobacteria.

BMC Syst Biol 2013 Jun 11;7:46. Epub 2013 Jun 11.

Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, USA.

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http://dx.doi.org/10.1186/1752-0509-7-46DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694032PMC
June 2013

The evolution of metabolic networks of E. coli.

BMC Syst Biol 2011 Nov 1;5:182. Epub 2011 Nov 1.

Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, USA.

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http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0
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http://dx.doi.org/10.1186/1752-0509-5-182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3229490PMC
November 2011

chipD: a web tool to design oligonucleotide probes for high-density tiling arrays.

Nucleic Acids Res 2010 Jul 6;38(Web Server issue):W321-5. Epub 2010 Jun 6.

Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA.

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http://dx.doi.org/10.1093/nar/gkq517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896189PMC
July 2010

progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement.

PLoS One 2010 Jun 25;5(6):e11147. Epub 2010 Jun 25.

Genome Center and Department of Computer Science, University of Wisconsin, Madison, Wisconsin, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0011147PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892488PMC
June 2010

Reordering contigs of draft genomes using the Mauve aligner.

Bioinformatics 2009 Aug 10;25(16):2071-3. Epub 2009 Jun 10.

Genome Evolution Laboratory, University of Wisconsin-Madison, 425G Henry Mall Suite 4400V, Madison, WI 53706, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723005PMC
August 2009

Phylogeny and virulence of naturally occurring type III secretion system-deficient Pectobacterium strains.

Appl Environ Microbiol 2009 Jul 1;75(13):4539-49. Epub 2009 May 1.

Department of Plant Pathology, University of Wisconsin-Madison, 53706, USA.

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http://dx.doi.org/10.1128/AEM.01336-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2704834PMC
July 2009

Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli.

Genome Biol 2006 31;7(5):R44. Epub 2006 May 31.

Department of Mathematics, Lincoln Drive, University of Wisconsin, Madison WI 53706, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2006-7-5-r44DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779527PMC
August 2006

Genome-wide identification of plant-upregulated genes of Erwinia chrysanthemi 3937 using a GFP-based IVET leaf array.

Mol Plant Microbe Interact 2004 Sep;17(9):999-1008

Department of Plant Pathology, University of California, Riverside 92521, USA.

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http://dx.doi.org/10.1094/MPMI.2004.17.9.999DOI Listing
September 2004

Mauve: multiple alignment of conserved genomic sequence with rearrangements.

Genome Res 2004 Jul;14(7):1394-403

Department of Computer Science, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.2289704
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http://dx.doi.org/10.1101/gr.2289704DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC442156PMC
July 2004

GRIL: genome rearrangement and inversion locator.

Bioinformatics 2004 Jan;20(1):122-4

Department of Computer Science, University of Wisconsin-Madison, 1656 Linden Dr, Madison, WI 53706, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg378DOI Listing
January 2004

Acquisition of stcE, a C1 esterase inhibitor-specific metalloprotease, during the evolution of Escherichia coli O157:H7.

J Infect Dis 2003 Jun 4;187(12):1907-14. Epub 2003 Jun 4.

Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, USA.

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http://dx.doi.org/10.1086/374719DOI Listing
June 2003

ASAP, a systematic annotation package for community analysis of genomes.

Nucleic Acids Res 2003 Jan;31(1):147-51

Animal Health and Biomedical Sciences, University of Wisconsin-Madison, 656 Linden Dr Madison, WI 53706-1581, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC165572PMC
http://dx.doi.org/10.1093/nar/gkg125DOI Listing
January 2003

Identification and characterization of lpfABCC'DE, a fimbrial operon of enterohemorrhagic Escherichia coli O157:H7.

Infect Immun 2002 Oct;70(10):5416-27

Center for Vaccine Development and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC128367PMC
http://dx.doi.org/10.1128/iai.70.10.5416-5427.2002DOI Listing
October 2002

Genomic variability of O islands encoding tellurite resistance in enterohemorrhagic Escherichia coli O157:H7 isolates.

J Bacteriol 2002 Sep;184(17):4690-8

Department of Medical Microbiology and Immunology, 1-28 Medical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC135296PMC
http://dx.doi.org/10.1128/jb.184.17.4690-4698.2002DOI Listing
September 2002

Characterization of Cah, a calcium-binding and heat-extractable autotransporter protein of enterohaemorrhagic Escherichia coli.

Mol Microbiol 2002 Aug;45(4):951-66

Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD 21201, USA.

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http://dx.doi.org/10.1046/j.1365-2958.2002.03094.xDOI Listing
August 2002

Microarray profiling of Erwinia chrysanthemi 3937 genes that are regulated during plant infection.

Mol Plant Microbe Interact 2002 Jul;15(7):619-29

Department of Plant Pathology and Center for Plant Cell Biology, University of California, Riverside 92521, USA.

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http://dx.doi.org/10.1094/MPMI.2002.15.7.619DOI Listing
July 2002

hrp genes of Erwinia chrysanthemi 3937 are important virulence factors.

Mol Plant Microbe Interact 2002 May;15(5):472-80

Department of Plant Pathology, University of California, Riverside 92521, USA.

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http://dx.doi.org/10.1094/MPMI.2002.15.5.472DOI Listing
May 2002

Strains of Escherichia coli O157:H7 differ primarily by insertions or deletions, not single-nucleotide polymorphisms.

J Bacteriol 2002 Apr;184(7):1873-9

Division of Infectious Diseases, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC134921PMC
http://dx.doi.org/10.1128/jb.184.7.1873-1879.2002DOI Listing
April 2002

Urease of enterohemorrhagic Escherichia coli: evidence for regulation by fur and a trans-acting factor.

Infect Immun 2002 Feb;70(2):1027-31

Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC127683PMC
http://dx.doi.org/10.1128/iai.70.2.1027-1031.2002DOI Listing
February 2002