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1

Escherichia Coli || The Genomes of Escherichia coli K-12 and Pathogenic E. coli

Perna, Nicole T.

Year:

2002

File:

PDF, 435 KB

2002

2

Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens

Sam Zaremba, Mila Ramos-Santacruz, Thomas Hampton, Panna Shetty, Joel Fedorko, Jon Whitmore, John M Greene, Nicole T Perna, Jeremy D Glasner, Guy Plunkett, Matthew Shaker, David Pot

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 1.10 MB

english, 2009

3

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

Alfredo G. Torres, Nicole T. Perna, Valerie Burland, Abdul Ruknudin, Fred R. Blattner, James B. Kaper

Journal:

Molecular Microbiology

Year:

2002

Language:

english

File:

PDF, 483 KB

english, 2002

4

The evolution of metabolic networks ofE. coli

David J Baumler, Roman G Peplinski, Jennifer L Reed, Jeremy D Glasner, Nicole T Perna

Journal:

BMC Systems Biology

Year:

2011

Language:

english

File:

PDF, 464 KB

english, 2011

5

Analysis of theLactobacillus caseisupragenome and its influence in species evolution and lifestyle adaptation

Broadbent, Jeff R, Neeno-Eckwall, Eric C, Stahl, Buffy, Tandee, Kanokwan, Cai, Hui, Morovic, Wesley, Horvath, Philippe, Heidenreich, Jessie, Perna, Nicole T, Barrangou, Rodolphe, Steele, James L

Journal:

Year:

2012

Language:

english

File:

PDF, 1.67 MB

english, 2012

6

Genome-Wide Identification of Plant-Upregulated Genes of Erwinia chrysanthemi 3937 Using a GFP-Based IVET Leaf Array

Yang, Shihui, Perna, Nicole T., Cooksey, Donald A., Okinaka, Yasushi, Lindow, Steven E., Ibekwe, A. Mark, Keen, Noel T., Yang, Ching-Hong

Journal:

Molecular Plant-Microbe Interactions

Year:

2004

Language:

english

File:

PDF, 594 KB

english, 2004

7

CGHScan: finding variable regions using high-density microarray comparative genomic hybridization data

Bradley D Anderson, Michael C Gilson, Abigail A Scott, Bryan S Biehl, Jeremy D Glasner, Gireesh Rajashekara, Gary A Splitter, Nicole T Perna

Journal:

Year:

2006

Language:

english

File:

PDF, 549 KB

english, 2006

8

Host Range and Molecular Phylogenies of the Soft Rot Enterobacterial Genera Pectobacterium and Dickeya

Ma, Bing, Hibbing, Michael E., Kim, Hye-Sook, Reedy, Ralph M., Yedidia, Iris, Breuer, Jane, Breuer, Jeffrey, Glasner, Jeremy D., Perna, Nicole T., Kelman, Arthur, Charkowski, Amy O.

Journal:

Year:

2007

Language:

english

File:

PDF, 625 KB

english, 2007

9

hrp Genes of Erwinia chrysanthemi 3937 Are Important Virulence Factors

Yang, Ching-Hong, Gavilanes-Ruiz, Marina, Okinaka, Yasushi, Vedel, Regine, Berthuy, Isabelle, Boccara, Martine, Chen, Jason Wei-Ta, Perna, Nicole T., Keen, Noel T.

Journal:

Molecular Plant-Microbe Interactions

Year:

2002

Language:

english

File:

PDF, 476 KB

english, 2002

10

Evolutionary genomics of niche-specific adaptation to the cystic fibrosis lung in Pseudomonas aeruginosa

Dettman, Jeremy R, Kassen, Rees, Perna, Nicole

Journal:

Molecular Biology and Evolution

Year:

2020

File:

PDF, 3.14 MB

2020

11

Transcriptome Changes Associated with Anaerobic Growth in Yersinia intermedia (ATCC29909)

Babujee, Lavanya, Balakrishnan, Venkatesh, Kiley, Patricia J., Glasner, Jeremy D., Perna, Nicole T., Pereira, Inês A. Cardoso

Journal:

Year:

2013

Language:

english

File:

PDF, 614 KB

english, 2013

12

Paralogization and New Protein Architectures in Planctomycetes Bacteria with Complex Cell Structures

Mahajan, Mayank, Yee, Benjamin, Hägglund, Emil, Guy, Lionel, Fuerst, John A, Andersson, Siv G E, Perna, Nicole

Journal:

Molecular Biology and Evolution

Year:

2019

Language:

english

File:

PDF, 3.03 MB

english, 2019

13

Anxiety sensitivity and modulation of the serotonergic system in patients with PD

Pietra Romano, Nicole van Beek, Michele Cucchi, Sara Biffi, Giampaolo Perna

Journal:

Journal of Anxiety Disorders

Year:

2004

Language:

english

File:

PDF, 96 KB

english, 2004

14

Evolution of the metabolic and regulatory networks associated with oxygen availability in two phytopathogenic enterobacteria

Babujee, Lavanya, Apodaca, Jennifer, Balakrishnan, Venkatesh, Liss, Paul, Kiley, Patricia J, Charkowski, Amy O, Glasner, Jeremy D, Perna, Nicole T

Journal:

Year:

2012

Language:

english

File:

PDF, 600 KB

english, 2012

15

Tailoring a Global Iron Regulon to a Uropathogen

Banerjee, Rajdeep, Weisenhorn, Erin, Schwartz, Kevin J., Myers, Kevin S., Glasner, Jeremy D., Perna, Nicole T., Coon, Joshua J., Welch, Rodney A., Kiley, Patricia J., Gottesman, Susan

Journal:

Year:

2020

File:

PDF, 2.90 MB

2020

16

Computing the Joint Distribution of Tree Shape and Tree Distance for Gene Tree Inference and Recombination Detection

Chung, Yujin, Perna, Nicole T., Ane, Cecile

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2013

Language:

english

File:

PDF, 710 KB

english, 2013

17

Host range and genetic plasticity explain the co-existence of integrative and extrachromosomal mobile genetic elements

Cury, Jean, Oliveira, Pedro H, de la Cruz, Fernando, Rocha, Eduardo P C, Perna, Nicole

Journal:

Molecular Biology and Evolution

Year:

2018

Language:

english

File:

PDF, 6.98 MB

english, 2018

18

More Arrows in the Ancient DNA Quiver: Use of Paleoepigenomes and Paleomicrobiomes to Investigate Animal Adaptation to Environment

Liu, Yichen, Weyrich, Laura S, Llamas, Bastien, Perna, Nicole

Journal:

Molecular Biology and Evolution

Year:

2019

File:

PDF, 710 KB

2019

19

Identification of potential virulence genes inErwinia chrysanthemi3937: transposon insertion into plant-upregulated genes

Yasushi Okinaka, Nicole T. Perna, Shihui Yang, Noel T. Keen, Ching-Hong Yang

Journal:

Journal of General Plant Pathology

Year:

2006

Language:

english

File:

PDF, 291 KB

english, 2006

20

10.1038/35065664

Perna, Nicole T., Plunkett, Guy, Burland, Valerie, Mau, Bob, Glasner, Jeremy D., Rose, Debra J., Mayhew, George F., Evans, Peter S., Gregor, Jason, Kirkpatrick, Heather A., Pósfai, György, Hackett, Je

Journal:

Year:

2001

Language:

english

File:

PDF, 1.21 MB

english, 2001

21

Mitochondrial DNA: Molecular fossils in the nucleus

Nicole T Perna, Thomas D Kocher

Journal:

Current Biology

Year:

1996

Language:

english

File:

PDF, 191 KB

english, 1996

22

Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes

Nicole T. Perna, Thomas D. Kocher

Journal:

Journal of Molecular Evolution

Year:

1995

Language:

english

File:

PDF, 598 KB

english, 1995

23

10.1038/35065666

Perna, Nicole T., Plunkett, Guy, Burland, Valerie, Mau, Bob, Glasner, Jeremy D., Rose, Debra J., Mayhew, George F., Evans, Peter S., Gregor, Jason, Kirkpatrick, Heather A., Pósfai, György, Hackett, Je

Journal:

Year:

2001

Language:

english

File:

PDF, 237 KB

english, 2001

24

Genomic analysis of Picochlorum species reveals how microalgae may adapt to variable environments

Foflonker, Fatima, Mollegard, Devin, Ong, Meichin, Yoon, Hwan Su, Bhattacharya, Debashish, Perna, Nicole

Journal:

Molecular Biology and Evolution

Year:

2018

Language:

english

File:

PDF, 659 KB

english, 2018

25

Genome sequence of enterohaemorrhagic Escherichia coli O157:H7

Perna, Nicole T., Plunkett, Guy, Burland, Valerie, Mau, Bob, Glasner, Jeremy D., Rose, Debra J., Mayhew, George F., Evans, Peter S., Gregor, Jason, Kirkpatrick, Heather A.

Journal:

Year:

2001

Language:

english

File:

PDF, 922 KB

english, 2001

26

10.1038/35065672

Perna, Nicole T., Plunkett, Guy, Burland, Valerie, Mau, Bob, Glasner, Jeremy D., Rose, Debra J., Mayhew, George F., Evans, Peter S., Gregor, Jason, Kirkpatrick, Heather A., Pósfai, György, Hackett, Je

Journal:

Year:

2001

Language:

english

File:

PDF, 207 KB

english, 2001

27

Inferring ancient metabolism using ancestral core metabolic models of enterobacteria

David J Baumler, Bing Ma, Jennifer L Reed, Nicole T Perna

Journal:

BMC Systems Biology

Year:

2013

Language:

english

File:

PDF, 575 KB

english, 2013

28

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

Bob Mau, Jeremy D Glasner, Aaron E Darling, Nicole T Perna

Journal:

Year:

2006

Language:

english

File:

PDF, 890 KB

english, 2006

29

Peptide lineup against Gram-negative bacterial infection – first-in-class peptide inhibitor of H. pylori HtrA

Perna, Anna M, Schmidt, Thomas, Fugmann, Tim, Tegtmeyer, Nicole, Backert, Steffen, Wessler, Silja, Schneider, G

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 74 KB

english, 2014

30

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

Sapountzis, Panagiotis, Gruntjes, Thijs, Otani, Saria, Estevez, James, da Costa, Rafael R., Plunkett, Guy, Perna, Nicole T., Poulsen, Michael, Lovell, C. R.

Journal:

Applied and Environmental Microbiology

Year:

2015

Language:

english

File:

PDF, 2.09 MB

english, 2015

31

Vulnerability to 35% CO2 of panic disorder patients with a history of respiratory disorders

Nicole van Beek, Giampaolo Perna, Koen Schruers, Kees Verburg, Michele Cucchi, Laura Bellodi, Eric Griez

Journal:

Psychiatry Research

Year:

2003

Language:

english

File:

PDF, 95 KB

english, 2003

32

Microarray Profiling of Erwinia chrysanthemi 3937 Genes That are Regulated During Plant Infection

Okinaka, Yasushi, Yang, Ching-Hong, Perna, Nicole T., Keen, Noel. T.

Journal:

Molecular Plant-Microbe Interactions

Year:

2002

Language:

english

File:

PDF, 410 KB

english, 2002

33

Identification of E-cadherin signature motifs functioning as cleavage sites for Helicobacter pylori HtrA

Schmidt, Thomas P., Perna, Anna M., Fugmann, Tim, Böhm, Manja, Jan Hiss,, Haller, Sarah, Götz, Camilla, Tegtmeyer, Nicole, Hoy, Benjamin, Rau, Tilman T., Neri, Dario, Backert, Steffen, Schneider, Gis

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 1.50 MB

english, 2016

34

Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes

Nicole T. Perna, Thomas D. Kocher

Journal:

Journal of Molecular Evolution

Year:

1995

Language:

english

File:

PDF, 598 KB

english, 1995

35

Escherichia Coli || The Genomes of Escherichia coli K-12 and Pathogenic E. coli

Perna, Nicole T.

Year:

2002

Language:

english

File:

PDF, 435 KB

english, 2002

36

Gene Ontology annotation highlights shared and divergent pathogenic strategies of type III effector proteins deployed by the plant pathogenPseudomonas syringaepvtomatoDC3000 and animal pathogenicEscherichia colistrains

Magdalen Lindeberg, Bryan S Biehl, Jeremy D Glasner, Nicole T Perna, Alan Collmer, Candace W Collmer

Journal:

BMC Microbiology

Year:

2009

Language:

english

File:

PDF, 274 KB

english, 2009

37

Alu Insertion Polymorphism: A New Type of Marker for Human Population Studies

NICOLE T. PERNA, MARK A. BATZER, PRESCOTT L. DEININGER and MARK STONEKING

Journal:

Year:

1992

Language:

english

File:

PDF, 715 KB

english, 1992

38

Acquisition of stcE, a C1 Esterase Inhibitor–Specific Metalloprotease, during the Evolution of Escherichia coli O157:H7

Lathem, Wyndham W., Bergsbaken, Tessa, Witowski, Sarah E., Perna, Nicole T., Welch, Rodney A.

Journal:

The Journal of Infectious Diseases

Year:

2003

Language:

english

File:

PDF, 231 KB

english, 2003

39

Secreted bacterial adenosine deaminase is an evolutionary precursor of adenosine deaminase growth factor

Skaldin, Maksym, Tuittila, Minna, Zavialov, Andrey V, Zavialov, Anton V, Perna, Nicole

Journal:

Molecular Biology and Evolution

Year:

2018

Language:

english

File:

PDF, 2.51 MB

english, 2018

40

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

Ma, Xing, Perna, Nicole T., Glasner, Jeremy D., Hao, Jianjun, Johnson, Steven, Nasaruddin, Afnan Shazwan, Charkowski, Amy O., Wu, Shan, Fei, Zhangjun, Perry, Keith L., Stodghill, Paul, Swingle, Bryan,

Journal:

Microbiology Resource Announcements

Year:

2019

Language:

english

File:

PDF, 131 KB

english, 2019

41

Identification of host-microbe interaction factors in the genomes of soft rot-associated pathogensDickeya dadantii3937 andPectobacterium carotovorumWPP14 with supervised machine learning

Bing Ma,Amy O Charkowski,Jeremy D Glasner,Nicole T Perna

Journal:

Year:

2014

Language:

english

File:

PDF, 746 KB

english, 2014

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