Comparative genome analysis ofPseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds

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Complete Genome Sequence of the Cystic Fibrosis Pathogen Achromobacter xylosoxidans NH44784-1996 Complies with Important Pathogenic Phenotypes

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(2012) Magdalen Lindeberg et al.   TRENDS IN MICROBIOLOGY

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(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

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(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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(2011)   NUCLEIC ACIDS RESEARCH

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(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

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(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Pseudomonas syringae pv. actinidiae Draft Genomes Comparison Reveal Strain-Specific Features Involved in Adaptation and Virulence to Actinidia Species

(2011) Simone Marcelletti et al.   PLoS One

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Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Transcriptome analysis of the mobile genome ICEclc in Pseudomonas knackmussii B13

(2010) Muriel Gaillard et al.   BMC MICROBIOLOGY

A dual functional origin of transfer in the ICEclc genomic island of Pseudomonas knackmussii B13

(2010) Ryo Miyazaki et al.   MOLECULAR MICROBIOLOGY

Primer-initiated sequence synthesis to detect and assemble structural variants

(2010) Andreas Massouras et al.   NATURE METHODS

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Bacterial phenylalanine and phenylacetate catabolic pathway revealed

(2010) R. Teufel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Intracellular excision and reintegration dynamics of the ICEclcgenomic island ofPseudomonas knackmussiisp. strain B13

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DNAPlotter: circular and linear interactive genome visualization

(2008) T. Carver et al.   BIOINFORMATICS

GenomeMatcher: A graphical user interface for DNA sequence comparison

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The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae

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Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Hybrid Pathogenicity Island PAGI-5 Contributes to the Highly Virulent Phenotype of a Pseudomonas aeruginosa Isolate in Mammals

(2008) S. E. Battle et al.   JOURNAL OF BACTERIOLOGY

Stochasticity and bistability in horizontal transfer control of a genomic island in Pseudomonas

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Dynamics of Pseudomonas aeruginosa genome evolution

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