List of works - Michael Schroeder

A Corpus-Driven Approach for Design, Evolution and Alignment of Ontologies

A Maximum-Entropy approach for accurate document annotation in the biomedical domain

scientific article (publication date: 24 April 2012)

A deliberative and reactive diagnosis agent based on logic programming

scientific article published in 1997

A knowledge-based search engine to navigate the information thicket of nanotoxicology ⬇️

scientific article published on September 17, 2010

A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language

scientific article

A novel pattern recognition algorithm to classify membrane protein unfolding pathways with high-throughput single-molecule force spectroscopy.

scientific article

A roadmap of clustering algorithms: finding a match for a biomedical application

scientific article published on 24 February 2009

A user-centred evaluation framework for the Sealife semantic web browsers

scientific article published in October 2009

Agents in bioinformatics, computational and systems biology

scientific article published on 26 May 2006

An overview of the BIOASQ large-scale biomedical semantic indexing and question answering competition

scientific article

Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer

Automated Patent Categorization and Guided Patent Search using IPC as Inspired by MeSH and PubMed

scientific article

Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases.

scientific article

Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy

scientific article

Clustering by common friends finds locally significant proteins mediating modules

scientific article published on 21 February 2007

Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map).

scientific article published on 24 May 2005

Computational Drug Repositioning by Target Hopping: A Use Case in Chagas Disease

scientific article published on 12 February 2016

Computational polypharmacology with text mining and ontologies

scientific article published on March 2011

Correction: Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key

scientific article (publication date: 20 December 2013)

Discovering relations between indirectly connected biomedical concepts

scientific article published on 6 July 2015

Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key

scientific article (publication date: 2013)

Drug repositioning through incomplete bi-cliques in an integrated drug–target–disease network ⬇️

scientific article published on April 26, 2012

Drug target prioritization by perturbed gene expression and network information

scientific article published on 30 November 2015

Equivalent binding sites reveal convergently evolved interaction motifs

scientific article

Examination of apoptosis signaling in pancreatic cancer by computational signal transduction analysis

scientific article

Extending ontologies by finding siblings using set expansion techniques ⬇️

scientific article (publication date: 15 June 2012)

Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies?

scientific article

Formalizing biomedical concepts from textual definitions

scientific article

From malaria to cancer: Computational drug repositioning of amodiaquine using PLIP interaction patterns

scientific article published on 12 September 2017

Gene mention normalization and interaction extraction with context models and sentence motifs.

scientific article published on September 2008

Genome-wide expression profiling and functional network analysis upon neuroectodermal conversion of human mesenchymal stem cells suggest HIF-1 and miR-124a as important regulators

scientific article

Go3R - semantic Internet search engine for alternative methods to animal testing.

scientific article published on January 2009

GoGene: gene annotation in the fast lane

scientific article published on 22 May 2009

GoPubMed: exploring PubMed with the Gene Ontology

scientific article

GoWeb: a semantic search engine for the life science web

scientific article (publication date: October 2009)

Google goes cancer: improving outcome prediction for cancer patients by network-based ranking of marker genes

scientific article

Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction.

scientific article published on 2 June 2011

Improved mutation tagging with gene identifiers applied to membrane protein stability prediction

scientific article published on 27 August 2009

Inter-species normalization of gene mentions with GNAT.

scientific article published on August 2008

LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation

scientific article published on 24 September 2006

Large-scale de novo prediction of physical protein-protein association ⬇️

scientific article

LipidXplorer: a software for consensual cross-platform lipidomics

scientific article

MeMotif: a database of linear motifs in alpha-helical transmembrane proteins

scientific article (publication date: 2010)

Meta-analysis of Cancer Gene Profiling Data

scientific article

MetaDBSite: a meta approach to improve protein DNA-binding sites prediction ⬇️

scientific article published on June 20, 2011

Negotiation in multi-agent systems

Network compression as a quality measure for protein interaction networks

scientific article

Network information improves cancer outcome prediction

scientific article published on 18 December 2012

New HSP27 inhibitors efficiently suppress drug resistance development in cancer cells

scientific article published on 08 September 2016

Old friends in new guise: repositioning of known drugs with structural bioinformatics ⬇️

scientific article published on March 26, 2011

Ontologies and Text Mining as a Basis for a Semantic Web for the Life Sciences

PLIP: fully automated protein-ligand interaction profiler

scientific article published on 14 April 2015

PSIbase: a database of Protein Structural Interactome map (PSIMAP).

scientific article published on 3 March 2005

Pioneering topological methods for network-based drug-target prediction by exploiting a brain-network self-organization theory.

scientific article published on 26 April 2017

Polypharmacology rescored: protein-ligand interaction profiles for remote binding site similarity assessment

scientific article

Prediction of drug gene associations via ontological profile similarity with application to drug repositioning

scientific article published on 08 December 2014

Protein interactions in 3D: from interface evolution to drug discovery

scientific article published on May 2012

REVISE: Logic programming and diagnosis

scientific article published in 1997

Rapid changes of mRNA-binding protein levels following glucose and 3-isobutyl-1-methylxanthine stimulation of insulinoma INS-1 cells

scientific article published on 14 October 2008

SCOPPI: a structural classification of protein-protein interfaces

scientific article

SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces

scientific article published on 2 March 2006

Sealife: a semantic grid browser for the life sciences applied to the study of infectious diseases.

scientific article

Semi-automated ontology generation within OBO-Edit

scientific article (publication date: 15 June 2010)

Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins

scientific article

Structural modeling of histone methyltransferase complex Set1C from Saccharomyces cerevisiae using constraint‐based docking ⬇️

scientific article published on December 1, 2010

Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data

scientific article

SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions

scientific article

Systematic drug perturbations on cancer cells reveal diverse exit paths from proliferative state

scientific article

Terminologies for text-mining; an experiment in the lipoprotein metabolism domain

scientific article

The GNAT library for local and remote gene mention normalization

scientific article

The many faces of protein-protein interactions: A compendium of interface geometry

scientific article

Triangle network motifs predict complexes by complementing high-error interactomes with structural information

scientific article

Unraveling protein networks with power graph analysis

scientific article

Using Extended Logic Programming for Alarm-Correlation in Cellular Phone Networks

scientific article published in 1999

Using convex hulls to extract interaction interfaces from known structures.

scientific article published on July 2004

Using protein binding site prediction to improve protein docking

scientific article published on 14 June 2008

Using structural motif descriptors for sequence-based binding site prediction

scientific article

Visualisation and graph-theoretic analysis of a large-scale protein structural interactome

scientific article

Vivid agents: Theory, architecture, and applications

article by Michael Schroeder et al published August 2000 in Applied Artificial Intelligence

Whole blood genome-wide expression profiling and network analysis suggest MELAS master regulators

scientific article

Word Sense Disambiguation in biomedical ontologies with term co-occurrence analysis and document clustering

scientific article published on January 2008

Xenopus meiotic microtubule-associated interactome

scientific article

List of works by Michael Schroeder

A Corpus-Driven Approach for Design, Evolution and Alignment of Ontologies

A Maximum-Entropy approach for accurate document annotation in the biomedical domain

A deliberative and reactive diagnosis agent based on logic programming

A knowledge-based search engine to navigate the information thicket of nanotoxicology ⬇️

A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language

A novel pattern recognition algorithm to classify membrane protein unfolding pathways with high-throughput single-molecule force spectroscopy.

A roadmap of clustering algorithms: finding a match for a biomedical application

A user-centred evaluation framework for the Sealife semantic web browsers

Agents in bioinformatics, computational and systems biology

An overview of the BIOASQ large-scale biomedical semantic indexing and question answering competition

Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer

Automated Patent Categorization and Guided Patent Search using IPC as Inspired by MeSH and PubMed

Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases.

Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy

Clustering by common friends finds locally significant proteins mediating modules

Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map).

Computational Drug Repositioning by Target Hopping: A Use Case in Chagas Disease

Computational polypharmacology with text mining and ontologies

Correction: Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key

Discovering relations between indirectly connected biomedical concepts

Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key

Drug repositioning through incomplete bi-cliques in an integrated drug–target–disease network ⬇️

Drug target prioritization by perturbed gene expression and network information

Equivalent binding sites reveal convergently evolved interaction motifs

Examination of apoptosis signaling in pancreatic cancer by computational signal transduction analysis

Extending ontologies by finding siblings using set expansion techniques ⬇️

Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies?

Formalizing biomedical concepts from textual definitions

From malaria to cancer: Computational drug repositioning of amodiaquine using PLIP interaction patterns

Gene mention normalization and interaction extraction with context models and sentence motifs.

Genome-wide expression profiling and functional network analysis upon neuroectodermal conversion of human mesenchymal stem cells suggest HIF-1 and miR-124a as important regulators

Go3R - semantic Internet search engine for alternative methods to animal testing.

GoGene: gene annotation in the fast lane

GoPubMed: exploring PubMed with the Gene Ontology

GoWeb: a semantic search engine for the life science web

Google goes cancer: improving outcome prediction for cancer patients by network-based ranking of marker genes

Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction.

Improved mutation tagging with gene identifiers applied to membrane protein stability prediction

Inter-species normalization of gene mentions with GNAT.

LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation

Large-scale de novo prediction of physical protein-protein association ⬇️

LipidXplorer: a software for consensual cross-platform lipidomics

MeMotif: a database of linear motifs in alpha-helical transmembrane proteins

Meta-analysis of Cancer Gene Profiling Data

MetaDBSite: a meta approach to improve protein DNA-binding sites prediction ⬇️

Negotiation in multi-agent systems

Network compression as a quality measure for protein interaction networks

Network information improves cancer outcome prediction

New HSP27 inhibitors efficiently suppress drug resistance development in cancer cells

Old friends in new guise: repositioning of known drugs with structural bioinformatics ⬇️

Ontologies and Text Mining as a Basis for a Semantic Web for the Life Sciences

PLIP: fully automated protein-ligand interaction profiler

PSIbase: a database of Protein Structural Interactome map (PSIMAP).

Pioneering topological methods for network-based drug-target prediction by exploiting a brain-network self-organization theory.

Polypharmacology rescored: protein-ligand interaction profiles for remote binding site similarity assessment

Prediction of drug gene associations via ontological profile similarity with application to drug repositioning

Protein interactions in 3D: from interface evolution to drug discovery

REVISE: Logic programming and diagnosis

Rapid changes of mRNA-binding protein levels following glucose and 3-isobutyl-1-methylxanthine stimulation of insulinoma INS-1 cells

SCOPPI: a structural classification of protein-protein interfaces

SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces

Sealife: a semantic grid browser for the life sciences applied to the study of infectious diseases.

Semi-automated ontology generation within OBO-Edit

Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins

Structural modeling of histone methyltransferase complex Set1C from Saccharomyces cerevisiae using constraint‐based docking ⬇️

Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data

SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions

Systematic drug perturbations on cancer cells reveal diverse exit paths from proliferative state

Terminologies for text-mining; an experiment in the lipoprotein metabolism domain

The GNAT library for local and remote gene mention normalization

The many faces of protein-protein interactions: A compendium of interface geometry

Triangle network motifs predict complexes by complementing high-error interactomes with structural information

Unraveling protein networks with power graph analysis

Using Extended Logic Programming for Alarm-Correlation in Cellular Phone Networks

Using convex hulls to extract interaction interfaces from known structures.

Using protein binding site prediction to improve protein docking

Using structural motif descriptors for sequence-based binding site prediction

Visualisation and graph-theoretic analysis of a large-scale protein structural interactome

Vivid agents: Theory, architecture, and applications