(Q33617186)

English

Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia

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scholarly article

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Europe PubMed Central

PubMed publication ID

28 July 2017

Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia (English)

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

0 references

Clostridium autoethanogenum

object named as

Clostridium autoethanogenum

1 reference

based on heuristic

inferred from title

7

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

object named as

Sagar Utturkar

3

0 references

object named as

Michael Köpke

9

0 references

object named as

Steven D Brown

1

0 references

author name string

Shilpa Nagaraju

2

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Sashini De Tissera

4

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Simón Segovia

5

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Wayne Mitchell

6

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Asela Dassanayake

8

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

publication date

21 March 2014

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Biotechnology for Biofuels

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

7

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

40

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Complete Genome Sequence of the Solvent Producer Clostridium saccharobutylicum NCP262 (DSM 13864).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Efficient and accurate whole genome assembly and methylome profiling of E. coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Reducing assembly complexity of microbial genomes with single-molecule sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Genome Sequence of the Autotrophic Acetogen Clostridium autoethanogenum JA1-1 Strain DSM 10061, a Producer of Ethanol from Carbon Monoxide

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Draft genome sequences for three mercury-methylating, sulfate-reducing bacteria.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

De Novo Assembly of the Streptomyces sp. Strain Mg1 Genome Using PacBio Single-Molecule Sequencing.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

NADP-specific electron-bifurcating [FeFe]-hydrogenase in a functional complex with formate dehydrogenase in Clostridium autoethanogenum grown on CO.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

The advantages of SMRT sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Draft Genome Sequence for Caulobacter sp. Strain OR37, a Bacterium Tolerant to Heavy Metals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Draft Genome Sequence for Ralstonia sp. Strain OR214, a Bacterium with Potential for Bioremediation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

REAPR: a universal tool for genome assembly evaluation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

GAGE-B: an evaluation of genome assemblers for bacterial organisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Clostridium difficile is an autotrophic bacterial pathogen.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Genome Sequence of the Butanol Hyperproducer Clostridium saccharoperbutylacetonicum N1-4.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

QUAST: quality assessment tool for genome assemblies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

CGAL: computing genome assembly likelihoods

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Sequence assembly demystified

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Draft genome sequences for two metal-reducing Pelosinus fermentans strains isolated from a Cr(VI)-contaminated site and for type strain R7

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Hybrid error correction and de novo assembly of single-molecule sequencing reads

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

A hybrid approach for the automated finishing of bacterial genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Draft genome sequences for Clostridium thermocellum wild-type strain YS and derived cellulose adhesion-defective mutant strain AD2.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Draft genome sequence of Rhizobium sp. strain PDO1-076, a bacterium isolated from Populus deltoides.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Feature-by-feature--evaluating de novo sequence assembly

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

GAGE: A critical evaluation of genome assemblies and assembly algorithms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Repetitive DNA and next-generation sequencing: computational challenges and solutions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Clostridia: the importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Complete genome sequence of Clostridium acetobutylicum DSM 1731, a solvent-producing strain with multireplicon genome architecture.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

2,3-butanediol production by acetogenic bacteria, an alternative route to chemical synthesis, using industrial waste gas.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

PHAST: a fast phage search tool

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

CRISPR inhibition of prophage acquisition in Streptococcus pyogenes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Evolution and classification of the CRISPR-Cas systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Complete genome sequence of the cellulolytic thermophile Clostridium thermocellum DSM1313.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Genome sequence of the mercury-methylating strain Desulfovibrio desulfuricans ND132

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Complete genome sequence of the cellulolytic thermophile Caldicellulosiruptor obsidiansis OB47T.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Genome sequence of the solvent-producing bacterium Clostridium carboxidivorans strain P7T

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Transcription, processing and function of CRISPR cassettes in Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Clostridium ljungdahlii represents a microbial production platform based on syngas

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Production of biofuels from synthesis gas using microbial catalysts

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Prodigal: prokaryotic gene recognition and translation initiation site identification

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Biomass-derived syngas fermentation into biofuels: Opportunities and challenges

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Genome sequence of the cellulosome-producing mesophilic organism Clostridium cellulovorans 743B.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Genomics. Genome project standards in a new era of sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Circos: an information aesthetic for comparative genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Genesis, effects and fates of repeats in prokaryotic genomes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

ABySS: a parallel assembler for short read sequence data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Real-time DNA sequencing from single polymerase molecules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Small CRISPR RNAs guide antiviral defense in prokaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Next-generation DNA sequencing methods

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Microbiology in the post-genomic era.

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21 June 2018

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

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

PILER-CR: fast and accurate identification of CRISPR repeats

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

A putative viral defence mechanism in archaeal cells

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21 June 2018

OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups

1 reference

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21 June 2018

A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes

1 reference

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21 June 2018

Versatile and open software for comparing large genomes

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21 June 2018

Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Bacteriophage infections in the industrial acetone butanol (AB) fermentation process.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Clostridium ljungdahlii sp. nov., an acetogenic species in clostridial rRNA homology group I.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

21 June 2018

Life with CO or CO2 and H2 as a source of carbon and energy

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21 June 2018

Phylogenetic basis for a taxonomic dissection of the genus Clostridium

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21 January 2018

Comparative analysis of CRISPR loci in lactic acid bacteria genomes.

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21 January 2018

Ethanol and acetate production by Clostridium ljungdahlii and Clostridium autoethanogenum using resting cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4022347

30 October 2018

Fermentative production of ethanol from carbon monoxide

1 reference

https://pubmed.ncbi.nlm.nih.gov/24655715

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/1754-6834-7-40

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Dimensions Publication ID

1 reference

https://scigraph.springernature.com/pub.10.1186/1754-6834-7-40

9 September 2019

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

ResearchGate publication ID

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