Genomic Analysis of γ-Hexachlorocyclohexane-Degrading Sphingopyxis lindanitolerans WS5A3p Strain in the Context of the Pangenome of Sphingopyxis

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Sphingopyxis lindanitolerans sp. nov. strain WS5A3pT enriched from a pesticide disposal site

(2018) Michal A. Kaminski et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Local applications but global implications: Can pesticides drive microorganisms to develop antimicrobial resistance?

(2018) Balasubramanian Ramakrishnan et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Genome Organization of Sphingobium indicum B90A: An Archetypal Hexachlorocyclohexane (HCH) Degrading Genotype

(2017) Helianthous Verma et al.   Genome Biology and Evolution

Genome-based reclassification of Sphingopyxis ummariensis as a later heterotypic synonym of Sphingopyxis terrae, with the descriptions of Sphingopyxis terrae subsp. terrae subsp. nov. and Sphingopyxis terrae subsp. ummariensis subsp. nov.

(2017) Guang-Da Feng et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Complete genome sequence of Novosphingobium resinovorum SA1, a versatile xenobiotic-degrading bacterium capable of utilizing sulfanilic acid

(2017) Botond Hegedűs et al.   JOURNAL OF BIOTECHNOLOGY

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

(2016) Leighton Pritchard et al.   Analytical Methods

Genomic analysis of the nitrate-respiring Sphingopyxis granuli (formerly Sphingomonas macrogoltabida) strain TFA

(2016) Inmaculada García-Romero et al.   BMC GENOMICS

Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide

(2016) Michiro Tabata et al.   DNA RESEARCH

Genome-guided insights reveal organophosphate-degrading Brevundimonas diminuta as Sphingopyxis wildii and define its versatile metabolic capabilities and environmental adaptations

(2016) Sunil Parthasarathy et al.   Genome Biology and Evolution

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Novel LinA Type 3 δ-Hexachlorocyclohexane Dehydrochlorinase

(2015) Nidhi Shrivastava et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Ten years of pan-genome analyses

(2015) George Vernikos et al.   CURRENT OPINION IN MICROBIOLOGY

Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance

(2015) Hiromi Kato et al.   DNA RESEARCH

Sphingopyxis flava sp. nov., isolated from a hexachlorocyclohexane (HCH)-contaminated soil

(2015) Helianthous Verma et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Sphingopyxis fribergensis sp. nov., a soil bacterium with the ability to degrade styrene and phenylacetic acid

(2015) Michel Oelschlägel et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets

(2015) Tungadri Bose et al.   PLoS One

Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains

(2015) S. L. Pearce et al.   G3-Genes Genomes Genetics

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways

(2014) Helianthous Verma et al.   BMC GENOMICS

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Sphingopyxis indica sp. nov., isolated from a high dose point hexachlorocyclohexane (HCH)-contaminated dumpsite

(2012) S. Jindal et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Genome Sequence of Sphingobium indicum B90A, a Hexachlorocyclohexane-Degrading Bacterium

(2012) S. Anand 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

Crystal Structure of the Hexachlorocyclohexane Dehydrochlorinase (LinA-Type2): Mutational Analysis, Thermostability and Enantioselectivity

(2012) Ankit S. Macwan et al.   PLoS One

ThelinGenes for γ-Hexachlorocyclohexane Degradation inSphingomonassp. MM-1 Proved to Be Dispersed across Multiple Plasmids

(2011) Michiro TABATA et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Lindane Toxicity: A Comprehensive Review of the Medical Literature

(2011) Katherine Nolan et al.   PEDIATRIC DERMATOLOGY

Kinetic and Sequence-Structure-Function Analysis of Known LinA Variants with Different Hexachlorocyclohexane Isomers

(2011) Pooja Sharma et al.   PLoS One

Isolation of a novel thermostable dehydrochlorinase (LinA) from a soil metagenome

(2011) Ankit S. Macwan et al.   3 Biotech

Hexachlorocyclohexane (HCH) as new Stockholm Convention POPs—a global perspective on the management of Lindane and its waste isomers

(2010) John Vijgen et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Metabolic profiles and phylogenetic diversity of microbial communities from chlorinated pesticides contaminated sites of different geographical habitats of India

(2010) N. Manickam et al.   JOURNAL OF APPLIED MICROBIOLOGY

Comparative genomics of the genus Bifidobacterium

(2010) F. Bottacini et al.   MICROBIOLOGY-SGM

Crystallization and preliminary X-ray analysis of γ-hexachlorocyclohexane dehydrochlorinase LinA fromSphingobium japonicumUT26

(2009) Masahiko Okai et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

Sphingopyxis ummariensis sp. nov., isolated from a hexachlorocyclohexane dump site

(2009) P. Sharma et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

The genomic basis of trophic strategy in marine bacteria

(2009) F. M. Lauro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pseudomonas sp. to Sphingobium indicum: a journey of microbial degradation and bioremediation of Hexachlorocyclohexane

(2008) Rup Lal et al.   INDIAN JOURNAL OF MICROBIOLOGY