STRING: a database of predicted functional associations between proteins

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

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The microglial sensome revealed by direct RNA sequencing

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Interaction network containing conserved and essential protein complexes in Escherichia coli

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Protein networks in disease

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The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data

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Emerging methods in protein co-evolution

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Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut

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A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions

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Systematic Discovery of New Recognition Peptides Mediating Protein Interaction Networks

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Systematic Evaluation of Molecular Networks for Discovery of Disease Genes

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A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans

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Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data

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Suppressing the KIF20A/NUAK1/Nrf2/GPX4 signaling pathway induces ferroptosis and enhances the sensitivity of colorectal cancer to oxaliplatin

Yang, C., Zhang, Y., Lin, S., Liu, Y., & Li, W. (2021) · Aging · doi:10.18632/aging.202774 · Cited by 174

SynaptomeDB: an ontology-based knowledgebase for synaptic genes

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Expansion of Biological Pathways Based on Evolutionary Inference

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Toolbox model of evolution of prokaryotic metabolic networks and their regulation

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Time-Dependent Changes in Microglia Transcriptional Networks Following Traumatic Brain Injury

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Significance of chitinase-3-like protein 1 in the pathogenesis of inflammatory diseases and cancer

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Proteomics-Based Methods for Discovery, Quantification, and Validation of Protein–Protein Interactions

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Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15

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Quercetin as a potential treatment for COVID-19-induced acute kidney injury: Based on network pharmacology and molecular docking study

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Human and mouse proteomics reveals the shared pathways in Alzheimer’s disease and delayed protein turnover in the amyloidome

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Molecular mechanism of triple‑negative breast cancer‑associated BRCA1 and the identification of signaling pathways

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Assessment of the key regulatory genes and their interologs for Turner syndrome employing network approach

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Modeling complex genetic and environmental influences on comorbid bipolar disorder with tobacco use disorder

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The interactome of CCT complex—a computational analysis

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A large-scale benchmark for network inference from single-cell perturbation data

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Weight loss with GLP-1 medicines does not result in a disproportionate loss of muscle mass or function in obese mice and humans

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Synergistic Antifungal Activity of Berberine Derivative B-7b and Fluconazole

Li, L. P., Liu, W., Liu, H., Zhu, F., Zhang, D. Z., Shen, H., Xu, Z., Qi, Y. P., Zhang, S. Q., Chen, S. M., et al. (2015) · PLOS ONE · doi:10.1371/journal.pone.0126393 · Cited by 17

Unveiling the molecular complexity of proliferative diabetic retinopathy through scRNA-seq, AlphaFold 2, and machine learning

Wang, J., Sun, H., Mou, L., Lu, Y., Wu, Z., Pu, Z., & Yang, M.-M. (2024) · Frontiers in Endocrinology · doi:10.3389/fendo.2024.1382896 · Cited by 13

Identification of key genes and pathways associated with classical Hodgkin lymphoma by bioinformatics analysis

Kuang, Z., Guo, L., & Li, X. (2017) · Molecular Medicine Reports · doi:10.3892/mmr.2017.7158 · Cited by 11

Effect of Poria cocos Terpenes: Verifying Modes of Action Using Molecular Docking, Drug-Induced Transcriptomes, and Diffusion Network Analyses

Park, M., Yi, J.-M., Kim, N. S., Lee, S.-Y., & Lee, H. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25094636 · Cited by 11

Main methods and tools for peptide development based on protein-protein interactions (PPIs)

Baeza, J., Bedoya, M., Cruz, P., Ojeda, P., Adasme-Carreño, F., Cerda, O., & González, W. (2025) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2025.151623 · Cited by 8

EXOSC3 S1-domain variants implicated in PCH1b alter RNA exosome cap subunit abundance and thermal stability disrupting rRNA processing and targeting of AU-rich mRNA

Runnebohm, A. M., Wijeratne, H. R. S., Barron, M. P., Smith-Kinnaman, W. R., Rooney, J. D., Peck Justice, S. A., Cureton, L. A., Holland, A., Ghalei, H., Pelletier, S., et al. (2025) · doi:10.1101/2025.05.31.657176 · Cited by 4

De Novo Multi-Omics Pathway Analysis Designed for Prior Data Independent Inference of Cell Signaling Pathways

Vaparanta, K., Merilahti, J. A. M., Ojala, V. K., & Elenius, K. (2024) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2024.100780 · Cited by 3

CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset

Nishimura, Y., Omae, K., Tominaga, K., & Iwasaki, W. (2025) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaf182 · Cited by 1