The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand

The effect of soil type on the bioremediation of petroleum contaminated soils

(2016) Ali Haghollahi et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

Comparison of differential gene expression to water stress among bacteria with relevant pollutant-degradation properties

(2016) Silvia K. Moreno-Forero et al.   Environmental Microbiology Reports

Degradation of Benzene by Pseudomonas veronii 1YdBTEX2 and 1YB2 Is Catalyzed by Enzymes Encoded in Distinct Catabolism Gene Clusters

(2015) Daiana de Lima-Morales et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Marine oil spill risk mapping for accidental pollution and its application in a coastal city

(2015) Dongdong Lan et al.   MARINE POLLUTION BULLETIN

IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis: Figure 1.

(2015) Bhavjinder K. Dhillon et al.   NUCLEIC ACIDS RESEARCH

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights

(2015) Claire Bertelli et al.   Frontiers in Microbiology

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Genome-wide analysis of Sphingomonas wittichii RW1 behaviour during inoculation and growth in contaminated sand

(2014) Silvia K Moreno-Forero et al.   ISME Journal

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

(2014) Shinjini Mukherjee et al.   ISME Journal

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Consed: a graphical editor for next-generation sequencing

(2013) David Gordon et al.   BIOINFORMATICS

The metabolic cost of flagellar motion inPseudomonas putida KT2440

(2013) Esteban Martínez-García et al.   ENVIRONMENTAL MICROBIOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

IMG 4 version of the integrated microbial genomes comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

In situ microbial metabolism of aromatic-hydrocarbon environmental pollutants

(2012) Che Ok Jeon et al.   CURRENT OPINION IN BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Cellular Variability of RpoS Expression Underlies Subpopulation Activation of an Integrative and Conjugative Element

(2012) Ryo Miyazaki et al.   PLoS Genetics

Genome-Wide Analysis of Salicylate and Dibenzofuran Metabolism in Sphingomonas Wittichii RW1

(2012) Edith Coronado et al.   Frontiers in Microbiology

Bioremediation approaches for organic pollutants: A critical perspective

(2011) Mallavarapu Megharaj et al.   ENVIRONMENT INTERNATIONAL

Engineering multiple genomic deletions in Gram-negative bacteria: analysis of the multi-resistant antibiotic profile of Pseudomonas putida KT2440

(2011) Esteban Martínez-García et al.   ENVIRONMENTAL MICROBIOLOGY

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Analyzing the Regulatory Role of the HigA Antitoxin within Mycobacterium tuberculosis

(2010) A. S. Fivian-Hughes et al.   JOURNAL OF BACTERIOLOGY

TADB: a web-based resource for Type 2 toxin–antitoxin loci in bacteria and archaea

(2010) Yucheng Shao et al.   NUCLEIC ACIDS RESEARCH

Tracking Hydrocarbon Plume Transport and Biodegradation at Deepwater Horizon

(2010) Richard Camilli et al.   SCIENCE

Global Transcriptional, Physiological, and Metabolite Analyses of the Responses of Desulfovibrio vulgaris Hildenborough to Salt Adaptation

(2009) Z. He et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

Biodegradation aspects of Polycyclic Aromatic Hydrocarbons (PAHs): A review

(2009) A.K. Haritash et al.   JOURNAL OF HAZARDOUS MATERIALS

Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds

(2009) Agnieszka Mrozik et al.   MICROBIOLOGICAL RESEARCH

DNAPlotter: circular and linear interactive genome visualization

(2008) T. Carver et al.   BIOINFORMATICS

GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis

(2008) Qi Zheng et al.   NUCLEIC ACIDS RESEARCH

Dynamics of Genome Rearrangement in Bacterial Populations

(2008) Aaron E. Darling et al.   PLoS Genetics