List of works - Folker Meyer

A Predator Unmasked: Life Cycle of Bdellovibrio bacteriovorus from a Genomic Perspective

scientific article

A metagenomics portal for a democratized sequencing world

scientific article

A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE.

scientific article

A scalable data analysis platform for metagenomics

An experience report: porting the MG-RAST rapid metagenomics analysis pipeline to the cloud

Annotation of bacterial and archaeal genomes: improving accuracy and consistency

scientific article published on 21 July 2007

BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison

scientific article published on 28 October 2004

BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae)

scientific article

BRIGEP--the BRIDGE-based genome-transcriptome-proteome browser

scientific article

Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants

scientific article published on 10 July 2013

Bioinformatics support for high-throughput proteomics

scientific article published on December 2003

Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology

scientific article

COVID-19 pandemic reveals the peril of ignoring metadata standards

scientific article published on 19 June 2020

Combined transcriptome profiling reveals a novel family of arbuscular mycorrhizal-specific Medicago truncatula lectin genes

scientific article published in August 2005

Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331.

scientific article

Comparing expression level-dependent features in codon usage with protein abundance: an analysis of 'predictive proteomics'.

scientific article published in January 2004

Complete genome sequence and analysis of Wolinella succinogenes

scientific article

Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora

scientific article

Complete genome sequence of the myxobacterium Sorangium cellulosum

scientific article

Conceptualizing a Genomics Software Institute (GSI)

scientific article (publication date: 19 March 2012)

Connecting genotype to phenotype in the era of high-throughput sequencing.

scientific article published on 21 March 2011

Consent insufficient for data release-Response

scientific article published on 01 May 2019

Construction and validation of a Sinorhizobium meliloti whole genome DNA microarray: genome-wide profiling of osmoadaptive gene expression

article

Construction and validation of cDNA-based Mt6k-RIT macro- and microarrays to explore root endosymbioses in the model legume Medicago truncatula

scientific article published in March 2004

Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti

scientific article published in June 2006

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

scientific article published in February 2018

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

article

Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses

scientific article

Development of joint application strategies for two microbial gene finders

scientific article published on 26 February 2004

Draft genome sequence of Achromobacter piechaudii strain HLE

scientific article

Draft genome sequence of Agrobacterium albertimagni strain AOL15

scientific article

Draft genome sequence of Alcaligenes faecalis subsp. faecalis NCIB 8687 (CCUG 2071).

scientific article

EMMA: a platform for consistent storage and efficient analysis of microarray data

scientific article

FIGfams: yet another set of protein families

scientific article published on 17 September 2009

Federation in genomics pipelines: techniques and challenges.

scientific article published on 29 August 2017

Finding novel genes in bacterial communities isolated from the environment

article

From genomics to metagenomics

scientific article

Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG

scientific article

Functional predictions from inference and observation in sequence-based inflammatory bowel disease research

scientific article

GISMO--gene identification using a support vector machine for ORF classification

scientific article published on 14 December 2006

GenDB--an open source genome annotation system for prokaryote genomes

scientific article

Genome of the Epsilonproteobacterial Chemolithoautotroph Sulfurimonas denitrificans

scientific article

Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis

scientific article

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains

scientific article published in August 2014

Genomic standards consortium projects

scientific article

Hybrid pathogenicity island PAGI-5 contributes to the highly virulent phenotype of a Pseudomonas aeruginosa isolate in mammals

scientific article published on 29 August 2008

Insights into Genome Plasticity and Pathogenicity of the Plant Pathogenic Bacterium Xanthomonas campestris pv. vesicatoria Revealed by the Complete Genome Sequence

scientific article

Intestinal tissues induce an SNP mutation in Pseudomonas aeruginosa that enhances its virulence: possible role in anastomotic leak

scientific article published in 2012

KBase: The United States Department of Energy Systems Biology Knowledgebase

article

Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon

scientific article

MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function

scientific article

MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.

scientific article

Maternal activation of gap genes in the hover fly Episyrphus

article

Maternal activation of gap genes in the hover fly Episyrphus.

scientific article published in May 2010

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10

scientific article (publication date: 25 December 2010)

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9

scientific article (publication date: 4 December 2010)

Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010.

scientific article

Meeting report of the RNA Ontology Consortium January 8-9, 2011.

scientific article

Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010

scientific article (publication date: 15 December 2010)

Meeting report: the 2 annual argonne soils workshop, argonne national laboratory, chicago illinois, USA, october 6-8, 2010

scientific article published on 15 November 2011

Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel

scientific article

Metagenomic profiling of a microbial assemblage associated with the California mussel: a node in networks of carbon and nitrogen cycling

scientific article

Metagenomics - a guide from sampling to data analysis

scientific article

Metagenomics: A foundling finds its feet

scientific article

Metazen - metadata capture for metagenomes

scientific article

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

scientific article

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

scientific article

REGANOR

scientific article published on 01 January 2006

Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes

scientific article

Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012

scientific article (publication date: 25 May 2012)

Short-read reading-frame predictors are not created equal: sequence error causes loss of signal

scientific article

Structure, fluctuation and magnitude of a natural grassland soil metagenome.

scientific article

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

2012 scientific article

The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010.

scientific article

The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes

scientific article

The Genomic Standards Consortium

scientific article (publication date: June 2011)

The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools

scientific article

The MG-RAST API explorer: an on-ramp for RESTful query composition

scientific article published on 08 November 2019

The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes

article

The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation

scientific article published on December 2006

The RAST Server: rapid annotations using subsystems technology

scientific article

The Sequence Analysis and Management System -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies

scientific article

The United States of America and scientific research

scientific article

The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins

scientific article

The complete genome sequence for putative H₂- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome

scientific article

The future of microbial metagenomics (or is ignorance bliss?).

scientific article

The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2

scientific article

The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity

scientific article (publication date: March 2008)

The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes

scientific article

The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae

scientific article

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

scientific article

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

Toward unrestricted use of public genomic data:

scientific article

Transcriptional profiling of Medicago truncatula roots after infection with Aphanomyces euteiches (oomycota) identifies novel genes upregulated during this pathogenic interaction

article

Unlocking the potential of metagenomics through replicated experimental design

scientific article published on 7 June 2012

Using clouds for metagenomics: A case study

article published in 2009

Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes

scientific article published in January 2010

Whole genome analysis of the marine Bacteroidetes'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter

scientific article published on December 2006

Whole genome shotgun sequencing guided by bioinformatics pipelines--an optimized approach for an established technique

scientific article

Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes

scientific article published on 25 August 2006

List of works by Folker Meyer

A Predator Unmasked: Life Cycle of Bdellovibrio bacteriovorus from a Genomic Perspective

A metagenomics portal for a democratized sequencing world

A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE.

A scalable data analysis platform for metagenomics

An experience report: porting the MG-RAST rapid metagenomics analysis pipeline to the cloud

Annotation of bacterial and archaeal genomes: improving accuracy and consistency

BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison

BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae)

BRIGEP--the BRIDGE-based genome-transcriptome-proteome browser

Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants

Bioinformatics support for high-throughput proteomics

Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology

COVID-19 pandemic reveals the peril of ignoring metadata standards

Combined transcriptome profiling reveals a novel family of arbuscular mycorrhizal-specific Medicago truncatula lectin genes

Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331.

Comparing expression level-dependent features in codon usage with protein abundance: an analysis of 'predictive proteomics'.

Complete genome sequence and analysis of Wolinella succinogenes

Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora

Complete genome sequence of the myxobacterium Sorangium cellulosum

Conceptualizing a Genomics Software Institute (GSI)

Connecting genotype to phenotype in the era of high-throughput sequencing.

Consent insufficient for data release-Response

Construction and validation of a Sinorhizobium meliloti whole genome DNA microarray: genome-wide profiling of osmoadaptive gene expression

Construction and validation of cDNA-based Mt6k-RIT macro- and microarrays to explore root endosymbioses in the model legume Medicago truncatula

Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses

Development of joint application strategies for two microbial gene finders

Draft genome sequence of Achromobacter piechaudii strain HLE

Draft genome sequence of Agrobacterium albertimagni strain AOL15

Draft genome sequence of Alcaligenes faecalis subsp. faecalis NCIB 8687 (CCUG 2071).

EMMA: a platform for consistent storage and efficient analysis of microarray data

FIGfams: yet another set of protein families

Federation in genomics pipelines: techniques and challenges.

Finding novel genes in bacterial communities isolated from the environment

From genomics to metagenomics

Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG

Functional predictions from inference and observation in sequence-based inflammatory bowel disease research

GISMO--gene identification using a support vector machine for ORF classification

GenDB--an open source genome annotation system for prokaryote genomes

Genome of the Epsilonproteobacterial Chemolithoautotroph Sulfurimonas denitrificans

Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains

Genomic standards consortium projects

Hybrid pathogenicity island PAGI-5 contributes to the highly virulent phenotype of a Pseudomonas aeruginosa isolate in mammals

Insights into Genome Plasticity and Pathogenicity of the Plant Pathogenic Bacterium Xanthomonas campestris pv. vesicatoria Revealed by the Complete Genome Sequence

Intestinal tissues induce an SNP mutation in Pseudomonas aeruginosa that enhances its virulence: possible role in anastomotic leak

KBase: The United States Department of Energy Systems Biology Knowledgebase

Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon

MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function

MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.

Maternal activation of gap genes in the hover fly Episyrphus

Maternal activation of gap genes in the hover fly Episyrphus.

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9

Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010.

Meeting report of the RNA Ontology Consortium January 8-9, 2011.

Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010

Meeting report: the 2 annual argonne soils workshop, argonne national laboratory, chicago illinois, USA, october 6-8, 2010

Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel

Metagenomic profiling of a microbial assemblage associated with the California mussel: a node in networks of carbon and nitrogen cycling

Metagenomics - a guide from sampling to data analysis

Metagenomics: A foundling finds its feet

Metazen - metadata capture for metagenomes

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

REGANOR

Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes

Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012

Short-read reading-frame predictors are not created equal: sequence error causes loss of signal

Structure, fluctuation and magnitude of a natural grassland soil metagenome.

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010.

The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes

The Genomic Standards Consortium

The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools

The MG-RAST API explorer: an on-ramp for RESTful query composition

The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes