(Q30666548)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

title

Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

8

Jack A Gilbert

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

author name string

Helianthous Verma

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

Roshan Kumar

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

Vivek Negi

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

Simon Lax

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

Paramjit Khurana

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

Jitendra P Khurana

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

Rup Lal

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

language of work or name

1 reference

12 September 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

volume

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

issue

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

page(s)

398-408

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 3.0 Unported

21 February 2020

copyright license

start time

12 September 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

MUMmer

object named as

MUMmer

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Comparative metagenomics of toxic freshwater cyanobacteria bloom communities on two continents

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Soil bacterial diversity screening using single 16S rRNA gene V regions coupled with multi-million read generating sequencing technologies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Genome sequence of Sphingobium indicum B90A, a hexachlorocyclohexane-degrading bacterium.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Complete genome sequence of Sphingobium sp. strain SYK-6, a degrader of lignin-derived biaryls and monoaryls

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

The whole genome sequence of Sphingobium chlorophenolicum L-1: insights into the evolution of the pentachlorophenol degradation pathway

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Bacterial species may exist, metagenomics reveal

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Bambus 2: scaffolding metagenomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Murasaki: a fast, parallelizable algorithm to find anchors from multiple genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Complete genome sequence of the representative γ-hexachlorocyclohexane-degrading bacterium Sphingobium japonicum UT26.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Transposases are the most abundant, most ubiquitous genes in nature.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Biochemistry of microbial degradation of hexachlorocyclohexane and prospects for bioremediation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

The Sequence Alignment/Map format and SAMtools

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

ABySS: a parallel assembler for short read sequence data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

PAML 4: phylogenetic analysis by maximum likelihood

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Minimus: a fast, lightweight genome assembler

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

MEGAN analysis of metagenomic data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Identifying bacterial genes and endosymbiont DNA with Glimmer

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Haloalkane dehalogenase LinB is responsible for beta- and delta-hexachlorocyclohexane transformation in Sphingobium indicum B90A.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

ISfinder: the reference centre for bacterial insertion sequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. no

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Genome Streamlining in a Cosmopolitan Oceanic Bacterium

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Genomic insights that advance the species definition for prokaryotes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Dynamics of multiple lin gene expression in Sphingomonas paucimobilis B90A in response to different hexachlorocyclohexane isomers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Organization of lin genes and IS6100 among different strains of hexachlorocyclohexane-degrading Sphingomonas paucimobilis: evidence for horizontal gene transfer

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Community structure and metabolism through reconstruction of microbial genomes from the environment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Versatile and open software for comparing large genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Low dose induction of micronuclei by lindane

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

The KEGG resource for deciphering the genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

The Pfam protein families database

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

TM4: a free, open-source system for microarray data management and analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Genome rearrangements in mammalian evolution: lessons from human and mouse genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Cloning and characterization of lin genes responsible for the degradation of Hexachlorocyclohexane isomers by Sphingomonas paucimobilis strain B90.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

The COG database: new developments in phylogenetic classification of proteins from complete genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

A greedy algorithm for aligning DNA sequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

CAP3: A DNA sequence assembly program

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Basic local alignment search tool

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Accurate identification of orthologous segments among multiple genomes.

20 June 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.153

Evaluation of hexachlorocyclohexane contamination from the last lindane production plant operating in India

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.153

INTEGRALL: a database and search engine for integrons, integrases and gene cassettes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.153

Genomic organization and genomic structural rearrangements of Sphingobium japonicum UT26, an archetypal γ-hexachlorocyclohexane-degrading bacterium.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.153

Prediction of effective genome size in metagenomic samples

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.153

The lin genes for γ-hexachlorocyclohexane degradation in Sphingomonas sp. MM-1 proved to be dispersed across multiple plasmids.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.153

Accidental organochlorine pesticide contamination of soil in Porrino, Spain.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.153

Degradation of Alpha-, Beta-, and Gamma-Hexachlorocyclohexane by a Soil Bacterium under Aerobic Conditions.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3906814

Theade4Package: Implementing the Duality Diagram for Ecologists

25 November 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.153

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/ISMEJ.2013.153

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

21 February 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24030592%20AND%20SRC:MED&resulttype=core&format=json