Genome Sequencing and Comparative Transcriptomics Provide a Holistic View of 4-Nitrophenol Degradation and Concurrent Fatty Acid Catabolism by Rhodococcus sp. Strain BUPNP1

Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

(2018) Jongsik Chun et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Genome analysis, metabolic potential and predatory capabilities of Herpetosiphon llansteffanense sp. nov.

(2018) Paul G. Livingstone et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Transcriptomics and Lipidomics of the Environmental Strain Rhodococcus ruber Point out Consumption Pathways and Potential Metabolic Bottlenecks for Polyethylene Degradation

(2017) Kévin Gravouil et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulatingRhodococcus opacusPD630

(2016) Aki Yoneda et al.   NUCLEIC ACIDS RESEARCH

Degradation of 4-nitrophenol in presence of heavy metals by a halotolerant Bacillus sp. strain BUPNP2, having plant growth promoting traits

(2015) Kriti Sengupta et al.   SYMBIOSIS

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production

(2014) John Blazeck et al.   Nature Communications

Breaking Down Lignin to High-Value Chemicals: The Conversion of Lignocellulose to Vanillin in a Gene Deletion Mutant of Rhodococcus jostii RHA1

(2013) Paul D. Sainsbury et al.   ACS Chemical Biology

Rhodococcus jostii: a home for Rhodococcus strain RHA1

(2013) Amanda L. Jones et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

P2RP: a web-based framework for the identification and analysis of regulatory proteins in prokaryotic genomes

(2013) Mohamed Barakat et al.   BMC GENOMICS

Draft Genome Sequence of the Nitrophenol-Degrading Actinomycete Rhodococcus imtechensis RKJ300

(2012) S. Vikram et al.   JOURNAL OF BACTERIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

WebMGA: a customizable web server for fast metagenomic sequence analysis

(2011) Sitao Wu et al.   BMC GENOMICS

Identification and characterization of another 4-nitrophenol degradation gene cluster, nps, in Rhodococcus sp. strain PN1

(2011) Kenta Yamamoto et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Microbial degradation of aromatic compounds — from one strategy to four

(2011) Georg Fuchs et al.   NATURE REVIEWS MICROBIOLOGY

Degradation of 4-Nitrophenol, 2-Chloro-4-nitrophenol, and 2,4-Dinitrophenol byRhodococcus imtechensisStrain RKJ300

(2010) Anuradha Ghosh et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

p-Nitrophenol Degradation via 4-Nitrocatechol inBurkholderiasp. SJ98 and Cloning of Some of the Lower Pathway Genes

(2010) Archana Chauhan et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Dual Two-Component Regulatory Systems Are Involved in Aromatic Compound Degradation in a Polychlorinated-Biphenyl Degrader, Rhodococcus jostii RHA1

(2010) H. Takeda et al.   JOURNAL OF BACTERIOLOGY

Nitroaromatic Compounds, from Synthesis to Biodegradation

(2010) K.-S. Ju et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Identification and Characterization of Catabolic para-Nitrophenol 4-Monooxygenase and para-Benzoquinone Reductase from Pseudomonas sp. Strain WBC-3

(2009) J.-J. Zhang et al.   JOURNAL OF BACTERIOLOGY

Mechanism of 4-Nitrophenol Oxidation in Rhodococcus sp. Strain PN1: Characterization of the Two-Component 4-Nitrophenol Hydroxylase and Regulation of Its Expression

(2008) M. Takeo et al.   JOURNAL OF BACTERIOLOGY