List of works - Steffen Neumann

A Modular and Expandable Ecosystem for Metabolomics Data Annotation in R

scientific article published on 11 February 2022

A cross-platform toolkit for mass spectrometry and proteomics

scientific article

Annotation of metabolites from gas chromatography/atmospheric pressure chemical ionization tandem mass spectrometry data using an in silico generated compound database and MetFrag

scientific article

BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology

scientific article

Bioinformatics can boost metabolomics research

scientific article

Bioschemas Resource Index for Chem and Plants

Building blocks for automated elucidation of metabolites: machine learning methods for NMR prediction

scientific article

CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets

scientific article

CASMI: And the Winner is . .

scientific article (publication date: 24 May 2013)

CDK-Taverna 2.0: migration and enhancements of an open-source pipelining solution

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

scientific article

Central venous catheter-related infections in hematology and oncology: 2012 updated guidelines on diagnosis, management and prevention by the Infectious Diseases Working Party of the German Society of Hematology and Medical Oncology

scientific article published on 7 January 2014

ChemFrag: Chemically meaningful annotation of fragment ion mass spectra

scientific article published on 01 November 2018

Chemical Diversity and Classification of Secondary Metabolites in Nine Bryophyte Species

scientific article published on 11 October 2019

Cheminformatics for Users

chapter in a proceedings

Comparative expression profiling reveals a role of the root apoplast in local phosphate response

scientific article

Comparing bound and unbound protein structures using energy calculation and rotamer statistics.

scientific article

Computational annotation of plant metabolomics profiles via a novel network-assisted approach

article

Computational mass spectrometry for metabolomics: Identification of metabolites and small molecules ⬇️

scientific article published on October 9, 2010

Computational workflow to study the seasonal variation of secondary metabolites in nine different bryophytes

Consensus Structure Elucidation Combining GC/EI-MS, Structure Generation, and Calculated Properties

scientific article published in 2012

Critical Assessment of Small Molecule Identification 2016: automated methods

scientific article

Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements

scientific article

Current Challenges in Plant Eco-Metabolomics.

scientific article published on 6 May 2018

Data format standards in analytical chemistry

scientific article published in 2022

Data standards can boost metabolomics research, and if there is a will, there is a way

scientific article

Database driven test case generation for protein-protein docking

scientific article published on 12 October 2004

Database supported candidate search for metabolite identification

scientific article published on July 7, 2011

Diagnosis and antimicrobial therapy of lung infiltrates in febrile neutropenic patients (allogeneic SCT excluded): updated guidelines of the Infectious Diseases Working Party (AGIHO) of the German Society of Hematology and Medical Oncology (DGHO).

scientific article

Diagnosis and empirical treatment of fever of unknown origin (FUO) in adult neutropenic patients: guidelines of the Infectious Diseases Working Party (AGIHO) of the German Society of Hematology and Medical Oncology (DGHO).

scientific article published on 30 August 2017

Diagnosis and management of gastrointestinal complications in adult cancer patients: evidence-based guidelines of the Infectious Diseases Working Party (AGIHO) of the German Society of Hematology and Oncology (DGHO) ⬇️

scientific article published on February 10, 2013

Digitalizing the Chemical Landscape:

scientific article published on 7 September 2023

Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies.

scientific article

ELIXIR and Toxicology: a community in development

scientific article published on 3 October 2023

Effect-directed analysis supporting monitoring of aquatic environments--An in-depth overview

scientific article

Embedding standards in metabolomics: the Metabolomics Society data standards task group

Empowering large chemical knowledge bases for exposomics: PubChemLite meets MetFrag

scientific article published on 08 March 2021

Erratum to: COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

scholarly article published in Metabolomics

Expanding the use of spectral libraries in proteomics

Experiment design beyond gut feeling: statistical tests and power to detect differential metabolites in mass spectrometry data

scientific article published in 2014

Feature-based molecular networking in the GNPS analysis environment

scientific article published on 24 August 2020

Functional Traits 2.0: The power of the metabolome for ecology

scientific article published on 12 January 2022

Future water quality monitoring--adapting tools to deal with mixtures of pollutants in water resource management

scientific article published on 31 January 2015

Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud

Golden Mutagenesis: An efficient multi-site-saturation mutagenesis approach by Golden Gate cloning with automated primer design

scientific article published on 29 July 2019

Highly sensitive feature detection for high resolution LC/MS

scientific article

Host Tree and Geography Induce Metabolic Shifts in the Epiphytic Liverwort Radula complanata

scientific article published in 2023

IPO: a tool for automated optimization of XCMS parameters

scientific article

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level

scientific article (publication date: 15 September 2010)

Impact of in vitro phytohormone treatments on the metabolome of the leafy liverwort Radula complanata (L.) Dumort

scientific article published in 2023

Improving MetFrag with statistical learning of fragment annotations

scientific article published on 05 July 2019

In silico fragmentation for computer assisted identification of metabolite mass spectra

scientific article

Interim Report NFDI4Chem 2023

scientific article published on 4 July 2024

Interoperable and scalable data analysis with microservices: Applications in Metabolomics

scientific article published in 2019

Joint Analysis of Dependent Features within Compound Spectra Can Improve Detection of Differential Features.

scientific article published on 24 September 2015

LC-MS/MS data analysis with xcms

Leaf metabolic traits reveal hidden dimensions of plant form and function

scientific article published in 2023

LipidFrag: Improving reliability of in silico fragmentation of lipids and application to the Caenorhabditis elegans lipidome

scientific article

Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics

scientific article (publication date: 26 May 2012)

Mass spectral databases for LC/MS- and GC/MS-based metabolomics: State of the field and future prospects

scientific article (publication date: April 2016)

Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

scientific article published in 2021

MassBank: a public repository for sharing mass spectral data for life sciences

scientific article (publication date: 7 July 2010)

Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop

scientific article (publication date: 25 December 2010)

MetFrag relaunched: incorporating strategies beyond in silico fragmentation

scientific article (publication date: 29 January 2016)

MetFusion: integration of compound identification strategies

scientific article

MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data

scientific article (publication date: 2013)

Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid

scientific article published on 22 September 2021

Metabolite identification: are you sure? And how do your peers gauge your confidence?

article

Metabolite profiling and beyond: approaches for the rapid processing and annotation of human blood serum mass spectrometry data

scientific article

Metabolome analysis of biosynthetic mutants reveals a diversity of metabolic changes and allows identification of a large number of new compounds in Arabidopsis ⬇️

scientific article

Mind the Gap: Mapping Mass Spectral Databases in Genome-Scale Metabolic Networks Reveals Poorly Covered Areas

scholarly article by Clément Frainay published in September 2018

Minimum Information Standards in Chemistry: A Call for Better Research Data Management Practices

scientific article published on 8 November 2022

NFDI4Chem - Towards a National Research Data Infrastructure for Chemistry in Germany

scientific article published on 26 June 2020

Natural variation of root exudates in Arabidopsis thaliana-linking metabolomic and genomic data

scientific article

Nearline acquisition and processing of liquid chromatography-tandem mass spectrometry data

Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation

scientific article published on 08 March 2022

Ontologies4Chem: the landscape of ontologies in chemistry

scientific article published in 2022

PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud

scholarly article by Kristian Peters et al published 7 December 2018 in GigaScience

Plant-to-Plant Variability in Root Metabolite Profiles of 19 Arabidopsis thaliana Accessions Is Substance-Class-Dependent ⬇️

scientific article

PredRet: prediction of retention time by direct mapping between multiple chromatographic systems

scientific article published on 20 August 2015

Prediction, Detection, and Validation of Isotope Clusters in Mass Spectrometry Data

scientific article (publication date: 20 October 2016)

Primary prophylaxis of bacterial infections and Pneumocystis jirovecii pneumonia in patients with hematological malignancies and solid tumors : guidelines of the Infectious Diseases Working Party (AGIHO) of the German Society of Hematology and Oncol

scientific article published on 15 February 2013

Reshaping of the Arabidopsis thaliana proteome landscape and co-regulation of proteins in development and immunity

scientific article published on 29 September 2020

SPLASH, a hashed identifier for mass spectra ⬇️

scientific article

Seasonal variation of secondary metabolites in nine different bryophytes

scientific article published in 2018

Solving CASMI 2013 with MetFrag, MetFusion and MOLGEN-MS/MS.

scientific article published on 16 August 2014

Supporting non-target identification by adding hydrogen deuterium exchange MS/MS capabilities to MetFrag

scientific article published on 17 June 2019

Tackling CASMI 2012: Solutions from MetFrag and MetFusion

scientific article

The Critical Assessment of Small Molecule Identification (CASMI): Challenges and Solutions

scientific article

The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again

scientific article

The SOLUTIONS project: challenges and responses for present and future emerging pollutants in land and water resources management

scientific article

The current landscape of author guidelines in chemistry through the lens of research data sharing

scientific article published in 2023

The future of metabolomics in ELIXIR

scientific article published in 2017

The future of metabolomics in ELIXIR.

scientific article

The metaRbolomics Toolbox in Bioconductor and beyond

scientific article published on 23 September 2019

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience

scientific article

The significance of tree-tree interactions for forest ecosystem functioning

scientific article published on 09 February 2021

Toward interoperable bioscience data

scientific article (publication date: 27 January 2012)

TraML--a standard format for exchange of selected reaction monitoring transition lists

scientific article published on 12 December 2011

Tree species richness differentially affects the chemical composition of leaves, roots and root exudates in four subtropical tree species

scientific article published in 2021

Untargeted In Silico Compound Classification—A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes

scientific article published on 23 March 2021

Untargeted Metabolomics for Integrative Taxonomy: Metabolomics, DNA Marker-Based Sequencing, and Phenotype Bioimaging

scientific article published in 2023

mzML--a community standard for mass spectrometry data

2011 scientific article

mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics

scientific article published on 13 February 2019

nmrML: a community supported open data standard for the description, storage, and exchange of NMR data

scientific article published on 16 October 2017

List of works by Steffen Neumann

A Modular and Expandable Ecosystem for Metabolomics Data Annotation in R

A cross-platform toolkit for mass spectrometry and proteomics

Annotation of metabolites from gas chromatography/atmospheric pressure chemical ionization tandem mass spectrometry data using an in silico generated compound database and MetFrag

BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology

Bioinformatics can boost metabolomics research

Bioschemas Resource Index for Chem and Plants

Building blocks for automated elucidation of metabolites: machine learning methods for NMR prediction

CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets

CASMI: And the Winner is . .

CDK-Taverna 2.0: migration and enhancements of an open-source pipelining solution

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

Central venous catheter-related infections in hematology and oncology: 2012 updated guidelines on diagnosis, management and prevention by the Infectious Diseases Working Party of the German Society of Hematology and Medical Oncology

ChemFrag: Chemically meaningful annotation of fragment ion mass spectra

Chemical Diversity and Classification of Secondary Metabolites in Nine Bryophyte Species

Cheminformatics for Users

Comparative expression profiling reveals a role of the root apoplast in local phosphate response

Comparing bound and unbound protein structures using energy calculation and rotamer statistics.

Computational annotation of plant metabolomics profiles via a novel network-assisted approach

Computational mass spectrometry for metabolomics: Identification of metabolites and small molecules ⬇️

Computational workflow to study the seasonal variation of secondary metabolites in nine different bryophytes

Consensus Structure Elucidation Combining GC/EI-MS, Structure Generation, and Calculated Properties

Critical Assessment of Small Molecule Identification 2016: automated methods

Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements

Current Challenges in Plant Eco-Metabolomics.

Data format standards in analytical chemistry

Data standards can boost metabolomics research, and if there is a will, there is a way

Database driven test case generation for protein-protein docking

Database supported candidate search for metabolite identification

Diagnosis and antimicrobial therapy of lung infiltrates in febrile neutropenic patients (allogeneic SCT excluded): updated guidelines of the Infectious Diseases Working Party (AGIHO) of the German Society of Hematology and Medical Oncology (DGHO).

Diagnosis and empirical treatment of fever of unknown origin (FUO) in adult neutropenic patients: guidelines of the Infectious Diseases Working Party (AGIHO) of the German Society of Hematology and Medical Oncology (DGHO).

Diagnosis and management of gastrointestinal complications in adult cancer patients: evidence-based guidelines of the Infectious Diseases Working Party (AGIHO) of the German Society of Hematology and Oncology (DGHO) ⬇️

Digitalizing the Chemical Landscape:

Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies.

ELIXIR and Toxicology: a community in development

ELIXIR and Toxicology: a community in development

Effect-directed analysis supporting monitoring of aquatic environments--An in-depth overview

Embedding standards in metabolomics: the Metabolomics Society data standards task group

Empowering large chemical knowledge bases for exposomics: PubChemLite meets MetFrag

Erratum to: COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

Expanding the use of spectral libraries in proteomics

Experiment design beyond gut feeling: statistical tests and power to detect differential metabolites in mass spectrometry data

Feature-based molecular networking in the GNPS analysis environment

Functional Traits 2.0: The power of the metabolome for ecology

Future water quality monitoring--adapting tools to deal with mixtures of pollutants in water resource management

Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud

Golden Mutagenesis: An efficient multi-site-saturation mutagenesis approach by Golden Gate cloning with automated primer design

Highly sensitive feature detection for high resolution LC/MS

Host Tree and Geography Induce Metabolic Shifts in the Epiphytic Liverwort Radula complanata

IPO: a tool for automated optimization of XCMS parameters

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level

Impact of in vitro phytohormone treatments on the metabolome of the leafy liverwort Radula complanata (L.) Dumort

Improving MetFrag with statistical learning of fragment annotations

In silico fragmentation for computer assisted identification of metabolite mass spectra

Interim Report NFDI4Chem 2023

Interoperable and scalable data analysis with microservices: Applications in Metabolomics

Interoperable and scalable data analysis with microservices: Applications in Metabolomics

Interoperable and scalable data analysis with microservices: Applications in Metabolomics

Joint Analysis of Dependent Features within Compound Spectra Can Improve Detection of Differential Features.

LC-MS/MS data analysis with xcms

Leaf metabolic traits reveal hidden dimensions of plant form and function

LipidFrag: Improving reliability of in silico fragmentation of lipids and application to the Caenorhabditis elegans lipidome

Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics

Mass spectral databases for LC/MS- and GC/MS-based metabolomics: State of the field and future prospects

Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

MassBank: a public repository for sharing mass spectral data for life sciences

Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop

MetFrag relaunched: incorporating strategies beyond in silico fragmentation

MetFusion: integration of compound identification strategies

MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data

Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid

Metabolite identification: are you sure? And how do your peers gauge your confidence?

Metabolite profiling and beyond: approaches for the rapid processing and annotation of human blood serum mass spectrometry data

Metabolome analysis of biosynthetic mutants reveals a diversity of metabolic changes and allows identification of a large number of new compounds in Arabidopsis ⬇️

Mind the Gap: Mapping Mass Spectral Databases in Genome-Scale Metabolic Networks Reveals Poorly Covered Areas

Minimum Information Standards in Chemistry: A Call for Better Research Data Management Practices

NFDI4Chem - Towards a National Research Data Infrastructure for Chemistry in Germany

Natural variation of root exudates in Arabidopsis thaliana-linking metabolomic and genomic data

Nearline acquisition and processing of liquid chromatography-tandem mass spectrometry data

Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation