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List of works by Martin Hofmann-Apitius

@neuLink: a service-oriented application for biomedical knowledge discovery

scientific article published on January 2008

@neurIST - Towards a System Architecture for Advanced Disease Management through Integration of Heterogeneous Data, Computing, and Complex Processing Services

article

A Computational Approach for Mapping Heme Biology in the Context of Hemolytic Disorders

scientific article published on 06 March 2020

A Systems Biology Approach for Hypothesizing the Effect of Genetic Variants on Neuroimaging Features in Alzheimer’s Disease

scientific article

A comprehensive, cell specific microRNA catalogue of human peripheral blood.

scientific article

A computational approach for mapping heme biology in the context of hemolytic disorders

scholarly article

A human homologue of the rat metastasis-associated variant of CD44 is expressed in colorectal carcinomas and adenomatous polyps

scientific article

A hybrid approach unveils drug repurposing candidates targeting an Alzheimer pathophysiology mechanism

scientific article published on 26 January 2022

A link between ras and metastatic behavior of tumor cells: ras induces CD44 promoter activity and leads to low-level expression of metastasis-specific variants of CD44 in CREF cells.

scientific article published on April 1993

A network model of genomic hormone interactions underlying dementia and its translational validation through serendipitous off-target effect ⬇️

scientific article published on July 26, 2013

A new variant of glycoprotein CD44 confers metastatic potential to rat carcinoma cells ⬇️

scientific article published on April 5, 1991

A robust framework for rapid deployment of a virtual screening laboratory

scientific article published on 01 January 2009

A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities

preprint

A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities

scientific article

ADO: A disease ontology representing the domain knowledge specific to Alzheimer's disease ⬇️

scientific article published on 03 July 2013

ANMerge: A Comprehensive and Accessible Alzheimer's Disease Patient-Level Dataset

scientific article published on 01 December 2020

Abstracts versus Full Texts and Patents: A Quantitative Analysis of Biomedical Entities

Alternative to Consensus Scoring — A New Approach Toward the Qualitative Combination of Docking Algorithms

Alternative to consensus scoring--a new approach toward the qualitative combination of docking algorithms

scientific article published on 11 May 2007

An Improved Weighted-Residue Profile Based Method of Using Protein-Ligand Interaction Information in Increasing Hits Selection from Virtual Screening: A Study on Virtual Screening of Human GPCR A2A Receptor Antagonists

scientific article

Analytical Strategy to Prioritize Alzheimer's Disease Candidate Genes in Gene Regulatory Networks Using Public Expression Data

scientific article published on 08 August 2017

Anterior Communicating Artery Aneurysms Are More Likely to be Discovered Ruptured in the Male Population

Automatic Recognition of Chemical Images

Automatic Recognition of Chemical Images

BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language

preprint

BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language

scholarly article

BEL2ABM: agent-based simulation of static models in Biological Expression Language

scientific article published in July 2018

Big data and data repurposing - using existing data to answer new questions in vascular dementia research

scientific article

Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders

scientific article

Biomarker-guided translation of brain imaging into disease pathway models

scientific article published on 29 November 2013

Boosting translational research on Alzheimer's disease in Europe: The Innovative Medicine Initiative AD research platform

scientific article

CD44 expression and regulation during mammary gland development and function

scientific article published on July 2000

CD44 is the principal mediator of hyaluronic-acid-induced melanoma cell proliferation

scientific article published on 01 January 2001

CD44 splice variants confer metastatic behavior in rats: homologous sequences are expressed in human tumor cell lines ⬇️

scientific article published on October 1, 1991

CLEP: A Hybrid Data- and Knowledge- Driven Framework for Generating Patient Representations

preprint published on 04 November 2020

COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology

scientific article published on 15 April 2020

COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology

scientific article published on 25 September 2020

CSEO - the Cigarette Smoke Exposure Ontology

scientific article

Challenges and opportunities for oncology biomarker discovery ⬇️

scientific article published on December 29, 2012

Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers

scientific article

Challenges of Integrative Disease Modeling in Alzheimer's Disease

scholarly article

Characterisation of the murine gene encoding the intracellular hyaluronan receptor IHABP (RHAMM).

scientific article published in January 1999

Clustering of Alzheimer's and Parkinson's disease based on genetic burden of shared molecular mechanisms

scientific article published on 05 November 2020

ComPath: An ecosystem for exploring, analyzing, and curating mappings across pathway databases

preprint

ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases

scholarly article

Comorbidity Analysis between Alzheimer's Disease and Type 2 Diabetes Mellitus (T2DM) Based on Shared Pathways and the Role of T2DM Drugs

scientific article published on 8 September 2017

Computable cause-and-effect models of healthy and Alzheimer's disease states and their mechanistic differential analysis

scientific article published on 4 April 2015

Computational Modelling Approaches on Epigenetic Factors in Neurodegenerative and Autoimmune Diseases and Their Mechanistic Analysis

scientific article

Concept-based semi-automatic classification of drugs.

scientific article

Construction of biological networks from unstructured information based on a semi-automated curation workflow

scientific article published on 17 June 2015

Contribution of syndecans to cellular internalization and fibrillation of amyloid-β(1-42)

scientific article published in Scientific Reports

Contribution of syndecans to cellular uptake and fibrillation of α-synuclein and tau

scientific article published on 12 November 2019

Corrigendum: The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

scientific article published on 29 April 2020

Data science in neurodegenerative disease: its capabilities, limitations, and perspectives

scientific article published on 01 April 2020

Data-Driven Modeling of Knowledge Assemblies in Understanding Comorbidity Between Type 2 Diabetes Mellitus and Alzheimer's Disease

scientific article published on 08 September 2020

Deep learning for clustering of multivariate clinical patient trajectories with missing values

scientific article published on 01 November 2019

Design of New Plasmepsin Inhibitors: A Virtual High Throughput Screening Approach on the EGEE Grid

Design of new plasmepsin inhibitors: a virtual high throughput screening approach on the EGEE grid

scientific article

Detecting miRNA Mentions and Relations in Biomedical Literature

scientific article published on 28 August 2014

Detection of IUPAC and IUPAC-like chemical names

scientific article (publication date: 27 June 2008)

Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports

scientific article published on 25 April 2012

Differences in cohort study data affect external validation of artificial intelligence models for predictive diagnostics of dementia - lessons for translation into clinical practice

scientific article published on 22 June 2020

DockFlow - a prototypic PharmaGrid for virtual screening integrating four different docking tools.

scientific article published on January 2009

Drug2ways: Reasoning over causal paths in biological networks for drug discovery

scientific article published on 02 December 2020

Effect of alpha-lipoic acid on the progression of endothelial cell damage and albuminuria in patients with diabetes mellitus: an exploratory study

scientific article published in June 2001

Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets

scientific article published on 01 January 2022

Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets

scientific article published on 15 June 2022

Erratum: Publisher Correction: ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases

scientific article published on 07 March 2019

Evaluating the Alzheimer's disease data landscape

scientific article published on 16 December 2020

Exploring novel mechanistic insights in Alzheimer's disease by assessing reliability of protein interactions

scientific article

Expression of CD44 isoforms carrying metastasis-associated sequences in newborn and adult rats ⬇️

scientific article published on January 1, 1993

From integrative disease modeling to predictive, preventive, personalized and participatory (P4) medicine

From integrative disease modeling to predictive, preventive, personalized and participatory (P4) medicine ⬇️

scientific article

Gene expression patterns associated with the metastatic phenotype in rodent and human tumors

scientific article published on 01 February 2001

Grid-added value to address malaria

scientific article published on March 2008

GuiltyTargets: Prioritization of Novel Therapeutic Targets with Deep Network Representation Learning

preprint

GuiltyTargets: Prioritization of Novel Therapeutic Targets with Deep Network Representation Learning

scientific article published on 19 June 2020

HuPSON: the human physiology simulation ontology

scientific article

Identification of IHABP, a 95 kDa intracellular hyaluronate binding protein ⬇️

scientific article published on June 1, 1998

Identification of gene co-expression clusters in liver tissues from multiple porcine populations with high and low backfat androstenone phenotype

scientific article

Identification of histone modifications in biomedical text for supporting epigenomic research

scientific article

Identification of new drug classification terms in textual resources

scientific article published in July 2007

Identifying Drug Repositioning Candidates using Comparative Mechanism Enrichment in Neurodegenerative Diseases ⬇️

conference poster

Identifying Drug Repositioning Candidates using Representation Learning on Heterogeneous Networks ⬇️

conference poster

Identifying gene-specific variations in biomedical text

scientific article published in December 2007

Identifying multimodal signatures underlying the somatic comorbidity of psychosis: the COMMITMENT roadmap

scientific article published on 15 October 2020

In silico drug discovery approaches on grid computing infrastructures.

scientific article

Insights into the Folding of Disulfide-Rich μ-Conotoxins

scientific article published on 01 October 2018

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

scientific article

Integration of Structured Biological Data Sources using Biological Expression Language

BioRxiv scholarly article describing Bio2BEL

Integrative data semantics through a model-enabled data stewardship

scientific article published in 2022

Is dementia research ready for big data approaches?

scientific article

Knowledge environments representing molecular entities for the virtual physiological human

scientific article published on September 2008

Knowledge retrieval from PubMed abstracts and electronic medical records with the Multiple Sclerosis Ontology

scientific article

Knowledge-driven computational modeling in Alzheimer's disease research: Current state and future trends

scientific article

Linking hypothetical knowledge patterns to disease molecular signatures for biomarker discovery in Alzheimer's disease

scientific article published on 03 December 2014

Maintenance and Enrichment of Disease Maps in Biological Expression Language ⬇️

conference poster

Mining biomarker information in biomedical literature

scientific article

Multi-omic approach decodes paradoxes of the triple-negative breast cancer: lessons for predictive, preventive and personalised medicine

scientific article published on 16 December 2017

MultiPaths: a python framework for analyzing multi-layer biological networks using diffusion algorithms

scientific article published on 26 December 2020

Multimodal Mechanistic Signatures for Neurodegenerative Diseases (NeuroMMSig): a web server for mechanism enrichment

scientific article

NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease

scientific article

NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases

scientific article published on 16 October 2015

Neuroimaging Feature Terminology: A Controlled Terminology for the Annotation of Brain Imaging Features

scientific article published on 18 July 2017

Novel approaches to develop community-built biological network models for potential drug discovery

scientific article published on 06 June 2017

OSIRISv1.2: a named entity recognition system for sequence variants of genes in biomedical literature

scientific article published on 5 February 2008

Of Mice and Men: Comparative Analysis of Neuro-Inflammatory Mechanisms in Human and Mouse Using Cause-and-Effect Models

scientific article published on 17 July 2017

PDON: Parkinson's disease ontology for representation and modeling of the Parkinson's disease knowledge domain

scientific article

PLIO: an ontology for formal description of protein–ligand interactions ⬇️

scientific article published on 05 May 2011

PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures

preprint

PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures

scientific article published on 05 June 2020

PTSD Biomarker Database: deep dive metadatabase for PTSD biomarkers, visualizations and analysis tools

scientific article published on 01 January 2019

PathMe: Merging and exploring mechanistic pathway knowledge

PathMe: merging and exploring mechanistic pathway knowledge

scholarly article

Pathway based analysis of genes and interactions influencing porcine testis samples from boars with divergent androstenone content in back fat.

scientific article

Prevention of tumor metastasis formation by anti-variant CD44.

scientific article published on February 1993

ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs ⬇️

Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm

scientific article published on 11 October 2019

Re-curation and Rational Enrichment of Knowledge Graphs in Biological Expression Language

BioRxiv article

Re-curation and rational enrichment of knowledge graphs in Biological Expression Language.

scientific article

Realistic simulation of virtual multi-scale, multi-modal patient trajectories using Bayesian networks and sparse auto-encoders

scientific article published on 03 July 2020

Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases

scientific article published on 5 August 2015

Recent advances in the genetics of metastasis

scientific article published on January 1994

Reconstruction of chemical molecules from images

scientific article

Regulated clustering of variant CD44 proteins increases their hyaluronate binding capacity

scientific article published on November 1996

STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs

preprint published on 18 August 2021

STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs

scientific article published on 5 January 2022

SVM Based Descriptor Selection and Classification of Neurodegenerative Disease Drugs for Pharmacological Modeling

scientific article

Soluble CD44 inhibits melanoma tumor growth by blocking cell surface CD44 binding to hyaluronic acid

scientific article

Splicing choice from ten variant exons establishes CD44 variability

scientific article published on March 1993

Synthesis and secretion of plasminogen activators and plasminogen activator inhibitors in cell lines of different groups of human lung tumors

scientific article published on December 1989

Systems approach for the selection of micro-RNAs as therapeutic biomarkers of anti-EGFR monoclonal antibody treatment in colorectal cancer

scientific article

Text mining for systems biology

scientific article published on 23 September 2013

Text mining in livestock animal science: introducing the potential of text mining to animal sciences

scientific article

The @neurIST project

scientific article published in 2008

The COVID-19 Ontology

scientific article published on 21 December 2020

The Human Brain Pharmacome: An Overview ⬇️

conference poster

The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

preprint

The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

scientific article published on 22 November 2019

The two major CD44 proteins expressed on a metastatic rat tumor cell line are derived from different splice variants: each one individually suffices to confer metastatic behavior.

scientific article published on March 1993

Tissue factor antigen is elevated in patients with microvascular complications of diabetes mellitus ⬇️

scientific article published on 01 January 1997

Towards a 21st-century roadmap for biomedical research and drug discovery: consensus report and recommendations.

scientific article published on 28 October 2016

Towards a Pathway Inventory of the Human Brain for Modeling Disease Mechanisms Underlying Neurodegeneration

scientific article

Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms

scientific article published on 11 June 2021

Towards a mechanism-based taxonomy of Alzheimer’s and Parkinson’s disease ⬇️

conference poster

Towards the taxonomy of human disease

scientific article published in February 2015

Trial watch: Tracing investment in drug development for Alzheimer disease

scientific article published on 23 October 2017

Unravelling the debate on heme effects in COVID-19 infections

scientific article

Urokinase-type and tissue-type plasminogen activators are essential for in vitro invasion of human melanoma cells

scientific article published on 01 February 1991

Using Drugs as Molecular Probes: A Computational Chemical Biology Approach in Neurodegenerative Diseases

scientific article (publication date: 2017)

Using Multi-Scale Genetic, Neuroimaging and Clinical Data for Predicting Alzheimer's Disease and Reconstruction of Relevant Biological Mechanisms

scientific article published in Scientific Reports

Variational Autoencoder Modular Bayesian Networks for Simulation of Heterogeneous Clinical Study Data

publication published on 28 May 2020

Virtual high throughput screening (vHTS) on an optical high speed testbed.

scientific article published in January 2008

WISDOM-II: screening against multiple targets implicated in malaria using computational grid infrastructures

scientific article

[The Wolfram syndrome: diabetes mellitus, hypacusis, optic atrophy and short stature in STH deficiency]

scientific article published on 01 January 1997

‘HypothesisFinder:’ A Strategy for the Detection of Speculative Statements in Scientific Text ⬇️

scientific article published on July 25, 2013

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