4.7 Article

Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Plant Sciences

Environment and host identity structure communities of green algal symbionts in lichens

Francesco Dal Grande et al.

NEW PHYTOLOGIST (2018)

Article Biochemistry & Molecular Biology

metaSPAdes: a new versatile metagenomic assembler

Sergey Nurk et al.

GENOME RESEARCH (2017)

Review Biochemistry & Molecular Biology

Symbiosis-inspired approaches to antibiotic discovery

Navid Adnani et al.

NATURAL PRODUCT REPORTS (2017)

Article Biochemistry & Molecular Biology

antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification

Kai Blin et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Multidisciplinary Sciences

Panmixia and dispersal from the Mediterranean Basin to Macaronesian Islands of a macrolichen species

David Alors et al.

SCIENTIFIC REPORTS (2017)

Article Biochemical Research Methods

MetaQUAST: evaluation of metagenome assemblies

Alla Mikheenko et al.

BIOINFORMATICS (2016)

Article Biochemistry & Molecular Biology

Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens

Bastian Greshake et al.

MOLECULAR ECOLOGY RESOURCES (2016)

Article Ecology

High Life Expectancy of Bacteria on Lichens

Tomislav Cernava et al.

MICROBIAL ECOLOGY (2016)

Article Biochemistry & Molecular Biology

From barcodes to genomes: extending the concept of DNA barcoding

Eric Coissac et al.

MOLECULAR ECOLOGY (2016)

Article Biochemistry & Molecular Biology

GenBank

Dennis A. Benson et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Multidisciplinary Sciences

Basidiomycete yeasts in the cortex of ascomycete macrolichens

Toby Spribille et al.

SCIENCE (2016)

Article Biochemical Research Methods

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

Daniel H. Huson et al.

PLOS COMPUTATIONAL BIOLOGY (2016)

Review Microbiology

Understanding Microbial Multi-Species Symbioses

Ines A. Aschenbrenner et al.

FRONTIERS IN MICROBIOLOGY (2016)

Article Multidisciplinary Sciences

An evaluation of the accuracy and speed of metagenome analysis tools

Stinus Lindgreen et al.

SCIENTIFIC REPORTS (2016)

Article Biochemical Research Methods

NxTrim: optimized trimming of Illumina mate pair reads

Jared O'Connell et al.

BIOINFORMATICS (2015)

Article Biochemical Research Methods

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

Felipe A. Simao et al.

BIOINFORMATICS (2015)

Editorial Material Biochemistry & Molecular Biology

Metagenome skimming for phylogenetic community ecology: a new era in biodiversity research

Anna Papadopoulou et al.

MOLECULAR ECOLOGY (2015)

Review Microbiology

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

Eric A. Franzosa et al.

NATURE REVIEWS MICROBIOLOGY (2015)

Review Biochemistry & Molecular Biology

Systems-based approaches to unravel multi-species microbial community functioning

Florence Abram

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2015)

Article Biochemical Research Methods

Fast and sensitive protein alignment using DIAMOND

Benjamin Buchfink et al.

NATURE METHODS (2015)

Article Biochemical Research Methods

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

Jiajie Zhang et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

Omega: an Overlap-graph de novo Assembler for Metagenomics

Bahlul Haider et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

InterProScan 5: genome-scale protein function classification

Philip Jones et al.

BIOINFORMATICS (2014)

Article Multidisciplinary Sciences

Tackling soil diversity with the assembly of large, complex metagenomes

Adina Chuang Howe et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Review Genetics & Heredity

Sequence assembly demystified

Niranjan Nagarajan et al.

NATURE REVIEWS GENETICS (2013)

Article Multidisciplinary Sciences

Metagenomic natural product discovery in lichen provides evidence for a family of biosynthetic pathways in diverse symbioses

Annette Kampa et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemical Research Methods

Taxonomic binning of metagenome samples generated by next-generation sequencing technologies

Johannes Droege et al.

BRIEFINGS IN BIOINFORMATICS (2012)

Article Biochemical Research Methods

Reference databases for taxonomic assignment in metagenomics

Monica Santamaria et al.

BRIEFINGS IN BIOINFORMATICS (2012)

Article Biochemical Research Methods

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

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Review Biochemistry & Molecular Biology

Vertical and horizontal photobiont transmission within populations of a lichen symbiosis

F. Dal Grande et al.

MOLECULAR ECOLOGY (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

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

Toshiaki Namiki et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Microbiology

The binning of rnetagenomic contings for physiology of mixed cultures

Marc Strous et al.

FRONTIERS IN MICROBIOLOGY (2012)

Article Biotechnology & Applied Microbiology

Toward almost closed genomes with GapFiller

Marten Boetzer et al.

GENOME BIOLOGY (2012)

Article Biochemical Research Methods

Scaffolding pre-assembled contigs using SSPACE

Marten Boetzer et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

Meta-IDBA: a de Novo assembler for metagenomic data

Yu Peng et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

Carson Holt et al.

BMC BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

Integrative analysis of environmental sequences using MEGAN4

Daniel H. Huson et al.

GENOME RESEARCH (2011)

Article Biochemical Research Methods

TopHat: discovering splice junctions with RNA-Seq

Cole Trapnell et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

BLAST plus : architecture and applications

Christiam Camacho et al.

BMC BIOINFORMATICS (2009)

Article Biochemical Research Methods

Genome assembly reborn: recent computational challenges

Mihai Pop

BRIEFINGS IN BIOINFORMATICS (2009)

Review Chemistry, Applied

Lichen extracts as raw materials in perfumery. Part 1: oakmoss

Daniel Joulain et al.

FLAVOUR AND FRAGRANCE JOURNAL (2009)

Review Chemistry, Applied

Lichen extracts as raw materials in perfumery. Part 2: treemoss

Daniel Joulain et al.

FLAVOUR AND FRAGRANCE JOURNAL (2009)

Article Biochemistry & Molecular Biology

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

Vardges Ter-Hovhannisyan et al.

GENOME RESEARCH (2008)

Article Biochemistry & Molecular Biology

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

Daniel R. Zerbino et al.

GENOME RESEARCH (2008)

Article Biochemical Research Methods

Choosing BLAST options for better detection of orthologs as reciprocal best hits

Gabriel Moreno-Hagelsieb et al.

BIOINFORMATICS (2008)

Review Biochemistry & Molecular Biology

Standardizing methods to address clonality in population studies

S. Arnaud-Haond et al.

MOLECULAR ECOLOGY (2007)

Article Biochemical Research Methods

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genornes

Genis Parra et al.

BIOINFORMATICS (2007)

Article Biochemistry & Molecular Biology

MEGAN analysis of metagenomic data

Daniel H. Huson et al.

GENOME RESEARCH (2007)

Article Biochemistry & Molecular Biology

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

Kim D. Pruitt et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Multidisciplinary Sciences

Symbiosis insights through metagenomic analysis of a microbial consortium

Tanja Woyke et al.

NATURE (2006)

Review Microbiology

The metagenomics of soil

R Daniel

NATURE REVIEWS MICROBIOLOGY (2005)

Article Multidisciplinary Sciences

Comparative metagenomics of microbial communities

SG Tringe et al.

SCIENCE (2005)

Article Biochemical Research Methods

Gene finding in novel genomes

I Korf

BMC BIOINFORMATICS (2004)