Steffen Neumann

发表

Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service

Wout Bittremieux, Simon Rogers, Emma L. Schymanski, 2020 .

Workshop on Knowledge Discovery, Data Mining, and Machine Learning and Workshop on Bioinformatics

Stefan Posch, Ingo Mierswa, Alexander Hinneburg, 2007, LWA.

In silico fragmentation for computer assisted identification of metabolite mass spectra

Matthias Müller-Hannemann, Steffen Neumann, Sebastian Wolf, 2010, BMC Bioinformatics.

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

Franz Kummert, Gerhard Sagerer, Steffen Neumann, 2002, Silico Biol..

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

Matej Oresic, Christoph Steinbeck, Daniel Schober, 2015, Metabolomics.

Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud

Ola Spjuth, Irene Papatheodorou, Yasset Perez-Riverol, 2018, bioRxiv.

Fast Approximate Duplicate Detection for 2D-NMR Spectra

Alexander Hinneburg, Björn Egert, Steffen Neumann, 2007, DILS.

Annotation of LC/ESI-MS Mass Signals

Steffen Neumann, Ralf Tautenhahn, Christoph Böttcher, 2007, BIRD.

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

Emma L. Schymanski, Steffen Neumann, Oliver Fiehn, 2014, Metabolomics.

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

Christoph Steinbeck, Björn Egert, Steffen Neumann, 2008, BMC Bioinformatics.

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

Steffen Neumann, Susanna-Assunta Sansone, Philippe Rocca-Serra, 2014, BMC Bioinformatics.

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

Nigel W. Hardy, Chris F. Taylor, Henning Hermjakob, 2010, Standards in genomic sciences.

Highly sensitive feature detection for high resolution LC/MS

Steffen Neumann, Ralf Tautenhahn, Christoph Böttcher, 2008, BMC Bioinformatics.

PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud

Ola Spjuth, Christoph Steinbeck, David Johnson, 2018 .

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

Steffen Neumann, Kristian Peters, Karin Gorzolka, 2018, Scientific Data.

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

Emma L. Schymanski, Steffen Neumann, Fabien Jourdan, 2018, Metabolites.

Mass Spectrometry Data Processing

Steffen Neumann, Oscar Yanes, Roland Mumm, 2019 .

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

Andrew R. Jones, Steffen Neumann, Reza M. Salek, 2015, Metabolomics.

Expanding the Use of Spectral Libraries in Proteomics.

Johannes Griss, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2018, Journal of proteome research.

Towards standardized evidence descriptors for metabolite annotations

Daniel Schober, Steffen Neumann, Reza M. Salek, 2016, ODLS.

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

Emma L. Schymanski, Steffen Neumann, S. Neumann, 2013, Metabolites.

MetHouse: Raw and Preprocessed Mass Spectrometry Data

Steffen Neumann, Antje Gaida, S. Neumann, 2007, J. Integr. Bioinform..

German Conference on Bioinformatics 2009, 28th to 30th September 2009, Martin Luther University Halle-Wittenberg, Germany

Ivo Grosse, Stefan Posch, Peter F. Stadler, 2009, German Conference on Bioinformatics.

Storage and Processing of Mass Spectrometry Data

Steffen Neumann, Sebastian Klie, S. Neumann, 2006, 17th International Workshop on Database and Expert Systems Applications (DEXA'06).

Database driven test case generation for protein?Cprotein docking

Franz Kummert, Gerhard Sagerer, Steffen Neumann, 2005, Bioinform..

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

Helmut Segner, Thomas Backhaus, Rolf Altenburger, 2015, The Science of the total environment.

Improving MetFrag with statistical learning of fragment annotations

Stefan Posch, Steffen Neumann, Christoph Ruttkies, 2019, BMC Bioinformatics.

MetFrag relaunched: incorporating strategies beyond in silico fragmentation

Emma L. Schymanski, Steffen Neumann, Sebastian Wolf, 2016, Journal of Cheminformatics.

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

Steffen Neumann, Sylvestre Marillonnet, Ramona Gruetzner, 2018 .

SPLASH, a hashed identifier for mass spectra

Tobias Schulze, Emma L. Schymanski, Nuno Bandeira, 2016, Nature Biotechnology.

Feature-based molecular networking in the GNPS analysis environment

Simon Rogers, Justin J. J. van der Hooft, Ngoc Hung Nguyen, 2020, Nature Methods.

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

Steffen Neumann, Emma L Schymanski, Christoph Ruttkies, 2014, Mass spectrometry.

The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience*

Jun Fan, Christoph Steinbeck, Johannes Griss, 2014, Molecular & Cellular Proteomics.

Database supported candidate search for Metabolite identification

Steffen Neumann, Sebastian Wolf, Christian Hildebrandt, 2011, J. Integr. Bioinform..

MetHouse: Raw and Preprocessed Mass Spectrometry Data

Steffen Neumann, Antje Gaida, 2007, J. Integr. Bioinform..

Ontological analysis of controlled vocabularies used in PSI/MSI supported XML standards

Martin Eisenacher, Daniel Schober, Steffen Neumann, 2013, GI-Jahrestagung.

The metaRbolomics Toolbox in Bioconductor and beyond

Emma L. Schymanski, Egon Willighagen, Tobias Schulze, 2019, Metabolites.

Data standards can boost metabolomics research

Christoph Steinbeck, Daniel Schober, Timothy M. D. Ebbels, 2015 .

Tackling CASMI 2012: Solutions from MetFrag and MetFusion

Steffen Neumann, Christoph Ruttkies, Michael Gerlich, 2013, Metabolites.

CASMI: And the Winner is ..

Emma L. Schymanski, Steffen Neumann, S. Neumann, 2013, Metabolites.

Towards Evaluation of Docking Hypotheses using elastic Matching

Gerhard Sagerer, Stefan Posch, Steffen Neumann, 1999, German Conference on Bioinformatics.

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

Steffen Neumann, Clemens Gröpl, Ralf Tautenhahn, 2008, BMC Bioinformatics.

IPO: a tool for automated optimization of XCMS parameters

Steffen Neumann, Thomas R. Pieber, Frank Sinner, 2015, BMC Bioinformatics.

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

Steffen Neumann, Sylvestre Marillonnet, Ramona Gruetzner, 2018, Scientific Reports.

IPHEx: A System For Evaluating Protein Docking Hypothesis Using User Feedback

Franz Kummert, Gerhard Sagerer, Steffen Neumann, 2003 .

mzML—a Community Standard for Mass Spectrometry Data*

Lennart Martens, Henning Hermjakob, Fredrik Levander, 2010, Molecular & Cellular Proteomics.

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

Oliver Hofmann, Chris F. Taylor, Marco Brandizi, 2010, Bioinform..

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

Tobias Schulze, Marja Lamoree, Emma L. Schymanski, 2016, The Science of the total environment.

Critical Assessment of Small Molecule Identification 2016: automated methods

Juho Rousu, Martin Krauss, Emma L. Schymanski, 2017, Journal of Cheminformatics.

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

Christoph Steinbeck, Janna Hastings, Mark Williams, 2012, Nucleic Acids Res..

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

Matej Oresic, Christoph Steinbeck, Dirk Walther, 2015, Metabolomics.

Feature-Based Molecular Networking in the GNPS Analysis Environment

Simon Rogers, Nuno Bandeira, Mingxun Wang, 2019, Nature Methods.

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

Helmut Segner, Thomas Backhaus, Rolf Altenburger, 2015, The Science of the total environment.

Interoperable and scalable data analysis with microservices: Applications in Metabolomics

Ola Spjuth, Christoph Steinbeck, Namrata Kale, 2018 .

TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists*

Lennart Martens, Fredrik Levander, Matthew Chambers, 2011, Molecular & Cellular Proteomics.

Interoperable and scalable data analysis with microservices: applications in metabolomics

Ola Spjuth, Christoph Steinbeck, David Johnson, 2019, Bioinform..

Current challenges in eco-metabolomics

Christoph Steinbeck, Steffen Neumann, Kristian Peters, 2018 .

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

Christoph Steinbeck, Ivo Grosse, Janna Hastings, 2015, BMC Bioinformatics.

Empowering large chemical knowledge bases for exposomics: PubChemLite meets MetFrag

Emma L. Schymanski, Steffen Neumann, Paul A. Thiessen, 2021, Journal of Cheminformatics.

ChemFrag: Chemically meaningful annotation of fragment ion mass spectra.

Matthias Müller-Hannemann, Steffen Neumann, Jördis-Ann Schüler, 2018, Journal of mass spectrometry : JMS.

Current Challenges in Plant Eco-Metabolomics

Christoph Steinbeck, Steffen Neumann, Hendrik Treutler, 2018, International journal of molecular sciences.

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

Ivo Grosse, Steffen Neumann, Diana Trutschel, 2015, Front. Bioeng. Biotechnol..

Bioinformatics can boost metabolomics research.

Steffen Neumann, Hendrik Treutler, Christoph Ruttkies, 2017, Journal of biotechnology.

Side chain flexibility for 1:n protein-protein docking

Gerhard Sagerer, Steffen Neumann, Kerstin Koch, 2002 .

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

Ivo Grosse, Steffen Neumann, Diana Trutschel, 2014, Metabolomics.

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

Steffen Neumann, Christoph Ruttkies, Nadine Strehmel, 2015, Rapid communications in mass spectrometry : RCM.

nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.

Christoph Steinbeck, Daniel Schober, Jie Hao, 2018, Analytical chemistry.

Consensus structure elucidation combining GC/EI-MS, structure generation, and calculated properties.

Martin Krauss, Emma L. Schymanski, Werner Brack, 2012, Analytical chemistry.

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

Martin Eisenacher, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2019, Analytical chemistry.

Metabolome Analysis of Biosynthetic Mutants Reveals a Diversity of Metabolic Changes and Allows Identification of a Large Number of New Compounds in Arabidopsis1[W][OA]

Steffen Neumann, S. Neumann, D. Scheel, 2008, Plant Physiology.

LC-MS Peak Annotation and Identification with CAMERA

Steffen Neumann, Ralf Tautenhahn, S. Neumann, 2009 .

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

Steffen Neumann, S. Neumann, C. Böttcher, 2012, Metabolomics.

Supervised Penalized Canonical Correlation Analysis

Stefan Posch, Steffen Neumann, S. Posch, 2014, 1405.1534.

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

Steffen Neumann, Emmanuel Gaquerel, Carsten Kuhl, 2013, Metabolomics.

Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies.

Andrea Porzel, Steffen Neumann, Hendrik Treutler, 2016, Analytical chemistry.

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

Steffen Neumann, Hendrik Treutler, S. Neumann, 2016, Metabolites.

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

Steffen Neumann, Michael Witting, Christoph Ruttkies, 2017, PloS one.

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

Matej Oresic, Christoph Steinbeck, Dirk Walther, 2015, Metabolomics.

MetFusion: integration of compound identification strategies.

Steffen Neumann, Michael Gerlich, S. Neumann, 2013, Journal of mass spectrometry : JMS.

Chemical Diversity and Classification of Secondary Metabolites in Nine Bryophyte Species

Steffen Neumann, Hendrik Treutler, Thomas Hankemeier, 2019, Metabolites.