Robust disease module mining via enumeration of diverse prize-collecting Steiner trees

DOMINO: a network‐based active module identification algorithm with reduced rate of false calls

(2021) Hagai Levi et al.   Molecular Systems Biology

On the limits of active module identification

(2021) Olga Lazareva et al.   BRIEFINGS IN BIOINFORMATICS

The AIMe registry for artificial intelligence in biomedical research

(2021) Julian Matschinske et al.   NATURE METHODS

Effects of Peroxiredoxin 2 in Neurological Disorders: A Review of its Molecular Mechanisms

(2020) Jifei Liu et al.   NEUROCHEMICAL RESEARCH

NetCore: a network propagation approach using node coreness

(2020) Gal Barel et al.   NUCLEIC ACIDS RESEARCH

Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing

(2020) Sepideh Sadegh et al.   Nature Communications

Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data

(2019) Juan Fernández-Tajes et al.   Genome Medicine

APID database: redefining protein–protein interaction experimental evidences and binary interactomes

(2019) Diego Alonso-López et al.   Database-The Journal of Biological Databases and Curation

OUP accepted manuscript

(2018)   BIOINFORMATICS

Network-Based Disease Module Discovery by a Novel Seed Connector Algorithm with Pathobiological Implications

(2018) Rui-Sheng Wang et al.   JOURNAL OF MOLECULAR BIOLOGY

NEDD9 targetsCOL3A1to promote endothelial fibrosis and pulmonary arterial hypertension

(2018) Andriy O. Samokhin et al.   Science Translational Medicine

IID 2018 update: context-specific physical protein–protein interactions in human, model organisms and domesticated species

(2018) Max Kotlyar et al.   NUCLEIC ACIDS RESEARCH

OMIM.org: leveraging knowledge across phenotype–gene relationships

(2018) Joanna S Amberger et al.   NUCLEIC ACIDS RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2019 update

(2018) Rose Oughtred et al.   NUCLEIC ACIDS RESEARCH

Thioredoxin-1, redox factor-1 and thioredoxin-interacting protein, mRNAs are differentially expressed in Multiple Sclerosis patients exposed and non-exposed to interferon and immunosuppressive treatments

(2017) Elham Mahmoudian et al.   GENE

Expression of the Antioxidative Enzyme Peroxiredoxin 2 in Multiple Sclerosis Lesions in Relation to Inflammation

(2017) David Voigt et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

KeyPathwayMinerWeb: online multi-omics network enrichment

(2016) Markus List et al.   NUCLEIC ACIDS RESEARCH

APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks

(2016) Diego Alonso-López et al.   NUCLEIC ACIDS RESEARCH

Transition steps in peroxide reduction and a molecular switch for peroxide robustness of prokaryotic peroxiredoxins

(2016) Neelagandan Kamariah et al.   Scientific Reports

A disease module in the interactome explains disease heterogeneity, drug response and captures novel pathways and genes in asthma

(2015) Amitabh Sharma et al.   HUMAN MOLECULAR GENETICS

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Uncovering disease-disease relationships through the incomplete interactome

(2015) J. Menche et al.   SCIENCE

A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome

(2015) Susan Dina Ghiassian et al.   PLoS Computational Biology

Steiner Tree Approximation via Iterative Randomized Rounding

(2013) Jarosław Byrka et al.   JOURNAL OF THE ACM

Network information improves cancer outcome prediction

(2012) J. Roy et al.   BRIEFINGS IN BIOINFORMATICS

Galectin-1 Deactivates Classically Activated Microglia and Protects from Inflammation-Induced Neurodegeneration

(2012) Sarah C. Starossom et al.   IMMUNITY

COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method

(2011) Haisu Ma et al.   BIOINFORMATICS

Nrf2 and DJ1 are consistently upregulated in inflammatory multiple sclerosis lesions

(2010) Jack van Horssen et al.   FREE RADICAL BIOLOGY AND MEDICINE

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Correlation between DJ-1 levels in the cerebrospinal fluid and the progression of disabilities in multiple sclerosis patients

(2008) M Hirotani et al.   Multiple Sclerosis Journal

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH