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1. Full Text Network medicine: A new paradigm for cardiovascular disease research and beyond
by Menche, Jörg
Cardiovascular Research, ISSN 0008-6363, 08/2017, Volume 113, Issue 10, pp. e29 - e30
VARIANTS | MOLECULAR NETWORKS | CARDIAC & CARDIOVASCULAR SYSTEMS | Cardiovascular Diseases - metabolism | Signal Transduction | Humans | Cardiovascular Diseases - therapy | Biomedical Research - trends | Gene Regulatory Networks | Cardiovascular Diseases - genetics | Protein Interaction Maps | Systems Biology - methods | Systems Biology - trends | Diffusion of Innovation | Biomedical Research - methods | Cardiology - trends | Cardiology - methods | Cardiovascular Diseases - diagnosis
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2. Full Text A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome
by Ghiassian, Susan Dina and Menche, Jörg and Barabási, Albert-László
PLoS Computational Biology, ISSN 1553-734X, 04/2015, Volume 11, Issue 4, p. e1004120
The observation that disease associated proteins often interact with each other has fueled the development of network-based approaches to elucidate the... 
INTERACTION NETWORK | PROFILES | RANDOM-WALKS | PROTEOME-SCALE MAP | COVER TIME | GENES | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | COMPREHENSIVE RESOURCE | MEDICINE | GENOME | GRAPHS | Usage | Algorithms | Health aspects | Protein-protein interactions | Proteins | Neighborhoods | Disease | Genes | Connectivity | Methods
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3. Full Text Human symptoms-disease network
by Zhou, Xuezhong and Menche, Jörg and Barabási, Albert-László and Sharma, Amitabh
Nature Communications, ISSN 2041-1723, 06/2014, Volume 5, Issue 1, p. 4212
In the post-genomic era, the elucidation of the relationship between the molecular origins of diseases and their resulting phenotypes is a crucial task for... 
COMMUNITY | PHENOTYPE ONTOLOGY | GENETICS | ELECTRONIC HEALTH RECORDS | ALZHEIMERS-DISEASE | INFORMATION | MULTIDISCIPLINARY SCIENCES | GENES | MODEL | MEDICINE | INTERACTOME | Models, Theoretical | Proteins - genetics | Systems Theory | Genetic Predisposition to Disease | Phenotype | Disease - genetics | Humans
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4. Full Text Uncovering disease-disease relationships through the incomplete interactome
by Menche, Jörg and Sharma, Amitabh and Kitsak, Maksim and Ghiassian, Susan Dina and Vidal, Marc and Loscalzo, Joseph and Barabási, Albert-László
Science, ISSN 0036-8075, 02/2015, Volume 347, Issue 6224, pp. 841 - 1257601
According to the diseasemodule hypothesis, the cellular components associated with a disease segregate in the same neighborhood of the human interactome,... 
PROTEIN-INTERACTION NETWORKS | GWAS DATA | MULTIDISCIPLINARY SCIENCES | CANDIDATE GENES | BIOLOGY | MOLECULAR NETWORKS | INTERACTION DATASETS | DISORDERS | MEDICINE | GENOME-WIDE ASSOCIATION | CELIAC-DISEASE | Disease | Molecular biology | Genes | Proteins | Networks | Maps | Similarity | Mathematical analysis | Modules | Disease control
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5. Full Text Network-based in silico drug efficacy screening
by Guney, Emre and Menche, Jörg and Vidal, Marc and Barábasi, Albert-László
Nature Communications, ISSN 2041-1723, 02/2016, Volume 7, Issue 1, p. 10331
The increasing cost of drug development together with a significant drop in the number of new drug approvals raises the need for innovative approaches for... 
ALZHEIMER-DISEASE | PROFILES | HUMAN-DISEASE | PROTEIN | INTEGRATION | MULTIDISCIPLINARY SCIENCES | COMPREHENSIVE RESOURCE | PATHOLOGY | IDENTIFICATION | GENOME-WIDE ASSOCIATION | INTERACTOME
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6. Full Text Tissue Specificity of Human Disease Module
by Kitsak, Maksim and Sharma, Amitabh and Menche, Jörg and Guney, Emre and Ghiassian, Susan Dina and Loscalzo, Joseph and Barabási, Albert-László
Scientific Reports, ISSN 2045-2322, 10/2016, Volume 6, Issue 1, p. 35241
Genes carrying mutations associated with genetic diseases are present in all human cells; yet, clinical manifestations of genetic diseases are usually highly... 
PROTEIN INTERACTION NETWORK | GENOTYPE | ALZHEIMERS-DISEASE | SCALE MAP | MULTIDISCIPLINARY SCIENCES | GENES | COMPLEXES | PHENOTYPE | MEDICINE | EXPRESSION | GENOME-WIDE ASSOCIATION | Disease | Genetic disorders
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7. Full Text The immune system as a social network
by Bergthaler, Andreas and Menche, Jörg
Nature Immunology, ISSN 1529-2908, 04/2017, Volume 18, Issue 5, pp. 481 - 482
The immune system employs a multitude of molecules, cells and organs that act together throughout the entire body to guard human health. Much like in a social... 
IMMUNOLOGY | Cell Communication | Immune System - immunology | Humans | Proteomics | Social Support | Cellular proteins | Genetic aspects | Properties | Immune system | Immunological research
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8. Full Text Endophenotype Network Models: Common Core of Complex Diseases
by Ghiassian, Susan Dina and Menche, Jörg and Chasman, Daniel I and Giulianini, Franco and Wang, Ruisheng and Ricchiuto, Piero and Aikawa, Masanori and Iwata, Hiroshi and Müller, Christian and Zeller, Tania and Sharma, Amitabh and Wild, Philipp and Lackner, Karl and Singh, Sasha and Ridker, Paul M and Blankenberg, Stefan and Barabási, Albert-László and Loscalzo, Joseph
Scientific Reports, ISSN 2045-2322, 06/2016, Volume 6, Issue 1, p. 27414
Historically, human diseases have been differentiated and categorized based on the organ system in which they primarily manifest. Recently, an alternative view... 
CELLS | ACTIVATION | THROMBOSIS | CASPASE 7 | INFLAMMATION | MULTIDISCIPLINARY SCIENCES | ATHEROSCLEROSIS | MECHANISMS | PROTEIN-INTERACTION NETWORK | MACROPHAGE POLARIZATION | EXPRESSION | Endophenotypes - metabolism | Inflammation - metabolism | Thrombosis - metabolism | Inflammasomes - metabolism | Cardiovascular Diseases - metabolism | Humans | Gene Regulatory Networks - physiology | Proteomics - methods | Fibrosis - metabolism
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9. Full Text From comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration
by Gomez-Cabrero, David and Menche, Jörg and Vargas, Claudia and Cano, Isaac and Maier, Dieter and Barabási, Albert-László and Tegnér, Jesper and Roca, Josep and Synergy-COPD Consortia and on behalf of Synergy-COPD Consortia
BMC Bioinformatics, ISSN 1471-2105, 11/2016, Volume 17, Issue S15, pp. 23 - 35
Background: Deep mining of healthcare data has provided maps of comorbidity relationships between diseases. In parallel, integrative multi-omics investigations... 
IMPACT | CODES | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | EXACERBATIONS | ENRICHMENT | RISK | GENE ONTOLOGY | ICD9 | COPD | Lung diseases, Obstructive | Electronic data processing | Comorbidity | Statistics | Methods | Prevalence studies (Epidemiology) | Mineria de dades | Bioinformàtica | Comorbiditat | Malalties pulmonars obstructives cròniques | Marcadors bioquímics | Malalties de l'aparell digestiu | Digestive system diseases | Data mining | Chronic obstructive pulmonary diseases | Bioinformatics | Biochemical markers
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10. Full Text Map of synthetic rescue interactions for the Fanconi anemia DNA repair pathway identifies USP48
by Velimezi, Georgia and Robinson-Garcia, Lydia and Muñoz-Martínez, Francisco and Wiegant, Wouter W and Ferreira Da Silva, Joana and Owusu, Michel and Moder, Martin and Wiedner, Marc and Rosenthal, Sara Brin and Fisch, Kathleen M and Moffat, Jason and Menche, Jörg and Van Attikum, Haico and Jackson, Stephen P and Loizou, Joanna I
Nature Communications, ISSN 2041-1723, 12/2018, Volume 9, Issue 1, pp. 2280 - 14
Defects in DNA repair can cause various genetic diseases with severe pathological phenotypes. Fanconi anemia ( FA) is a rare disease characterized by bone... 
UBIQUITINATION | DAMAGE RESPONSE | CHROMATIN | CROSS-LINK REPAIR | HUMAN-CELLS | MULTIDISCIPLINARY SCIENCES | SENSITIVITY | HOMOLOGOUS RECOMBINATION | BRCA1 | ENRICHMENT ANALYSIS | ASSOCIATION | Genetic Therapy | Ubiquitin-Specific Proteases - genetics | Fanconi Anemia Complementation Group D2 Protein - genetics | Fanconi Anemia - metabolism | Humans | DNA Repair - physiology | DNA Repair - genetics | Fanconi Anemia Complementation Group C Protein - genetics | Fanconi Anemia Complementation Group A Protein - genetics | Fanconi Anemia Complementation Group D2 Protein - deficiency | Fanconi Anemia Complementation Group A Protein - metabolism | Fanconi Anemia Complementation Group Proteins - metabolism | Ubiquitination | Fanconi Anemia Complementation Group G Protein - genetics | Ubiquitin-Specific Proteases - deficiency | Fanconi Anemia Complementation Group G Protein - deficiency | BRCA1 Protein - metabolism | Fanconi Anemia - genetics | Ubiquitin-Specific Proteases - metabolism | Chromosomal Instability | Rad51 Recombinase - metabolism | Cell Line | Fanconi Anemia Complementation Group Proteins - deficiency | Fanconi Anemia Complementation Group Proteins - genetics | Fanconi Anemia Complementation Group G Protein - metabolism | Gene Knockout Techniques | Fanconi Anemia Complementation Group C Protein - metabolism | Fanconi Anemia Complementation Group D2 Protein - metabolism | Fanconi Anemia Complementation Group A Protein - deficiency | CRISPR-Cas Systems | Fanconi Anemia Complementation Group C Protein - deficiency | Fanconi Anemia - therapy | DNA Damage | Histones - metabolism | Mutation
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11. Full Text Canonical genetic signatures of the adult human brain
by Hawrylycz, Michael and Miller, Jeremy A and Menon, Vilas and Feng, David and Dolbeare, Tim and Guillozet-Bongaarts, Angela L and Jegga, Anil G and Aronow, Bruce J and Lee, Chang-Kyu and Bernard, Amy and Glasser, Matthew F and Dierker, Donna L and Menche, Jörg and Szafer, Aaron and Collman, Forrest and Grange, Pascal and Berman, Kenneth A and Mihalas, Stefan and Yao, Zizhen and Stewart, Lance and Barabási, Albert-László and Schulkin, Jay and Phillips, John and Ng, Lydia and Dang, Chinh and R Haynor, David and Jones, Allan and Van Essen, David C and Koch, Christof and Lein, Ed
Nature Neuroscience, ISSN 1097-6256, 11/2015, Volume 18, Issue 12, pp. 1832 - 1844
The structure and function of the human brain are highly stereotyped, implying a conserved molecular program responsible for its development, cellular... 
NETWORK ANALYSIS | MOUSE-BRAIN | EXPRESSION PATTERNS | ORGANIZATION | TRANSCRIPTOME | ALZHEIMERS-DISEASE | FUNCTIONAL CONNECTIVITY | GENERATION | HUMAN CONNECTOME PROJECT | NEUROSCIENCES | GENOME-WIDE ASSOCIATION | Animals | Gene Regulatory Networks - genetics | Humans | Adult | Mice | Transcriptome - genetics | Brain - physiology | Nerve Net - physiology | Neural circuitry | Brain research | Brain mapping | Genetic research | Genetic aspects | Research | Gene expression | Methods
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12. Full Text Non-classical monocytes as mediators of tissue destruction in arthritis
by Puchner, Antonia and Saferding, Victoria and Bonelli, Michael and Mikami, Yohei and Hofmann, Melanie and Brunner, Julia S and Caldera, Michael and Goncalves-Alves, Eliana and Binder, Nikolaus B and Fischer, Anita and Simader, Elisabeth and Steiner, Carl-Walter and Leiss, Harald and Hayer, Silvia and Niederreiter, Birgit and Karonitsch, Thomas and Koenders, Marije I and Podesser, Bruno K and O’Shea, John J and Menche, Jörg and Smolen, Josef S and Redlich, Kurt and Blüml, Stephan
Annals of the Rheumatic Diseases, ISSN 0003-4967, 10/2018, Volume 77, Issue 10, pp. 1490 - 1497
ObjectivesBone destruction in rheumatoid arthritis is mediated by osteoclasts (OC), which are derived from precursor cells of the myeloid lineage. The role of... 
cytokines | arthritis | inflammation | synovitis | tnf-alpha | RHEUMATOID-ARTHRITIS | DC-STAMP | CELLS | TUMOR-NECROSIS-FACTOR | EXPERIMENTAL AUTOIMMUNE ENCEPHALOMYELITIS | BONE-MARROW | JOINT DESTRUCTION | INFLAMMATORY ARTHRITIS | MICE | RHEUMATOLOGY | GENE ONTOLOGY | Bone Resorption - etiology | Bone Resorption - physiopathology | RANK Ligand - metabolism | Arthritis, Experimental - physiopathology | Arthritis, Experimental - complications | Arthritis, Rheumatoid - complications | Receptors, CCR2 - metabolism | Animals | Flow Cytometry | TNF Receptor-Associated Factor 6 - metabolism | Signal Transduction - physiology | Cell Differentiation | Mice | Osteoclasts - physiology | Receptor Activator of Nuclear Factor-kappa B - metabolism | Monocytes - physiology | Arthritis, Rheumatoid - physiopathology | Disease Models, Animal | CC chemokine receptors | Flow cytometry | TRAF6 protein | Transcription | Cloning | Genomics | Nervous system | Inflammation | Gene expression | Phosphatase | Ribonucleic acid--RNA | Proteins | Monocytes | CCR2 protein | Rheumatoid arthritis | Immunotherapy | Rodents | Osteoclasts | Transduction | TRANCE protein | Chemokines | Monocyte chemoattractant protein 1 | 2311 | Basic and Translational Research | 1506
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13. Full Text Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein
by Khamina, Kseniya and Lercher, Alexander and Caldera, Michael and Schliehe, Christopher and Vilagos, Bojan and Sahin, Mehmet and Kosack, Lindsay and Bhattacharya, Anannya and Májek, Peter and Stukalov, Alexey and Sacco, Roberto and James, Leo C and Pinschewer, Daniel D and Bennett, Keiryn L and Menche, Jörg and Bergthaler, Andreas
PLoS Pathogens, ISSN 1553-7366, 12/2017, Volume 13, Issue 12, p. e1006758
RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic... 
MASS-SPECTROMETRY DATA | PERSISTENCE | INFLUENZA | MICROBIOLOGY | RECEPTOR TRIM21 | IDENTIFICATION | SOFTWARE | I INTERFERON | VIROLOGY | INFECTION | VIRAL-RNA SYNTHESIS | PARASITOLOGY | PROTEOMICS | Viral proteins | Physiological aspects | Genetic aspects | Arenaviruses | Research | Health aspects | RNA polymerases | Visualization | Ontology | Chronic infection | Amino acids | Viruses | Infections | Genomes | Open source software | Proteins | Spectrometry | Immunology | Virions | Life cycle engineering | Genetics | Bioinformatics | Research centers | Supervision | CRISPR | RNA viruses | L protein | Virology | Medicine | Ribonucleic acids | Proteomics | Scientific imaging | Gene mapping | Protein interaction | Mass spectrometry | Viral infections | Life cycles
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