Identification of Protein Interactions Involved in Cellular Signaling

Mass spectrometry-based proteomics

Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955

A novel genetic system to detect protein–protein interactions

Fields, S., & Song, O.-K. (1989) · Nature · doi:10.1038/340245a0 · Cited by 6,152

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics

Ong, S.-E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., & Mann, M. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m200025-mcp200 · Cited by 5,574

Targeting of HIF-α to the von Hippel-Lindau Ubiquitylation Complex by O 2 -Regulated Prolyl Hydroxylation

Jaakkola, P., Mole, D. R., Tian, Y.-M., Wilson, M. I., Gielbert, J., Gaskell, S. J., Kriegsheim, A. V., Hebestreit, H. F., Mukherji, M., Schofield, C. J., et al. (2001) · Science · doi:10.1126/science.1059796 · Cited by 5,535

Functional organization of the yeast proteome by systematic analysis of protein complexes

Gavin, A., Böesche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A., Cruciat, C., et al. (2002) · Nature · doi:10.1038/415141a · Cited by 4,729

A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae

Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. (2000) · Nature · doi:10.1038/35001009 · Cited by 4,706

Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents

Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., et al. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m400129-mcp200 · Cited by 4,401

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

Ho, Y., Gruhler, A., Heilbut, A. M., Bader, G. D., Moore, L., Adams, S., Millar, A., Taylor, P. P., Bennett, K. L., Boutilier, K., et al. (2002) · Nature · doi:10.1038/415180a · Cited by 3,573

A comprehensive two-hybrid analysis to explore the yeast protein interactome

Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., & Sakaki, Y. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.061034498 · Cited by 3,566

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

Krogan, N. J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A., et al. (2006) · Nature · doi:10.1038/nature04670 · Cited by 2,964

Leucyl and Cystinyl Aminopeptidase as a Prognostic-Related Biomarker in OV Correlating with Immune Infiltrates

Ma, Q., Chang, L., Wang, W., Che, L., Song, X., Li, G., Zhang, Y., Chen, Y., Gu, Z., & Ge, X. (2023) · Pharmacogenomics and Personalized Medicine · doi:10.2147/pgpm.s400145 · Cited by 1

SAKE-PP: A Spatial-Attention Equivariant Network for Accurate Ranking of Protein–Protein Interaction Models

Xu, Y., Xia, W., Zhang, C., Liu, X., Ju, C., Dai, X., Xie, P., Wang, Y., Chen, G., & Zhang, J. (2026) · JACS Au · doi:10.1021/jacsau.6c00166 · Cited by 1

Systems perspectives on plant growth regulation: integrating omics, signaling networks, and computational models

Zaman, W., & Park, S. (2026) · Plant Growth Regulation · doi:10.1007/s10725-026-01462-3 · Cited by 1

Prediction of protein-protein interactions through support vector machines

Rodriguez, J. D. A., Jaramillo-Garzon, J. A., & Arroyave-Ospina, J. C. (2015) · Symposium on Signal Processing, Images and Computer Vision (STSIVA) · doi:10.1109/stsiva.2015.7330396 · Cited by 1

A Protein Preparation Method for the High-throughput Identification of Proteins Interacting with a Nuclear Cofactor Using LC-MS/MS Analysis

Tsuchiya, M., Karim, M. R., Matsumoto, T., Ogawa, H., & Taniguchi, H. (2017) · Journal of Visualized Experiments · doi:10.3791/55077 · Cited by 1

Advanced Techniques for the Analysis of Proteins and RNAs

Yang, X. (2024) · Chemosensors · doi:10.3390/chemosensors12010012 · Cited by 1

PyVADesign: a python-based cloning tool for one-step generation of large mutant libraries

Kuin, R. C. M., Lamers, M. H., & van Westen, G. J. P. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf433 · Cited by 1

Empirically founded genotype–phenotype maps from mammalian cyclic nucleotide-gated ion channels

Becchetti, A. (2014) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2014.08.038 · Cited by 1

Motifs and interface amino acid–mediated regulation of amyloid biogenesis in microbes to humans: potential targets for intervention

Beg, A. Z., & Khan, A. U. (2020) · Biophysical Reviews · doi:10.1007/s12551-020-00759-5 · Cited by 1

Identification of Hub Genes and Pathways in Cervical Cancer by Statistical and Bioinformatics Analysis

Doulah, M. S. U. (2022) · Bioinformatics & Proteomics Open Access Journal · doi:10.23880/bpoj-16000150 · Cited by 1

Translating Unusual Computational Methods to Drug Discovery: Taking Advantage of Work in Other Fields

Caron, G., & Ermondi, G. (2019) · Future Medicinal Chemistry · doi:10.4155/fmc-2018-0287 · Cited by 1

Candidate Biomarker Identification for the Cancers of Mouth Cavity Using Gene Expression Data

Honagudi, P., Vibhuti, A., & Sheshgiri, M. S. (2014)

Structural studies on protein-protein interactions: Analysis of the regulation of the DYNLL/LC8 binding to Nek9 and characterization of the enzymes composing the arginine deiminase pathway in mycoplasma penetrans

Gallego, P. (2014) · TDX (Tesis Doctorals en Xarxa)

Sequence-based Protein Interaction Site Prediction using Computer Vision and Deep Learning

Purohit, A. (2021) · doi:10.22215/etd/2021-14560

I. Le dispositif cinéma: magie et croyances. Hollywood/Babylone

Feigelson, K. (2010) · CinémAction

Birt-Hogg-Dubé syndrome

Vernooij, M. (2018) · Research Publications (Maastricht University) · doi:10.26481/dis.20181019ms

Research Strategies

(2016) · Elsevier eBooks · doi:10.1016/b978-0-323-34126-4.00006-2

Application of Proteomics in Alzheimer’s Disease: A Mini Review

Sukumaran, P., Bahardin, A. A., Razak, L. H. A., & Senik, M. H. (2023) · Malaysian Journal of Medicine and Health Sciences · doi:10.47836/mjmhs.19.5.38

Proteomics: A Key to Unlocking the Biomarkers and Drug Discovery for Metabolic Syndrome

Beladiya, J., Gandhi, T., & Mehta, A. A. (2024) · Advances in biochemistry in health and disease · doi:10.1007/978-3-031-75686-3_19

Discovery of niclosamide as a p300/transcription factor protein–protein interaction inhibitor

Fitriastuti, D., Miura, K., Okada, S., Hirano, H., Osada, H., & Nakamura, H. (2025) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2025.118114

LSD1 serine 166 is a phosphorylation switch for chromatin landscaping, gene activation, and tissue remodelingPreprint

Sharma, M., Aakula, A., Denisova, O. V., Ceccacci, E., Hayatigolkhatmi, K., Caroli, J., Nätkin, R., Laisne, M.-C., Huhtaniemi, R., Ghimire, S., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.14.653937

Structural features, transcriptional profiles, and potential roles in antiviral immunity of interferon-stimulated 20-kDa exonuclease (ISG20) in red-spotted grouper (Epinephelus akaara)

Sirisena, D. M. K. P., Sandeepani, R. I., Jayasinghe, J. D. H. E., Jeyakanesh, J. T., Tharanga, E. M. T., Kodagoda, Y. K., Park, C. U., Sohn, H., Wan, Q., & Lee, J. (2025) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2025.110481

Quantifying Protein-Protein Interaction with a Spatial Attention Kinetic Graph Neural NetworkPreprint

Xu, Y., Xia, W., Zhang, C., Liu, X., Ju, C., Dai, X., Xie, P., Wang, Y., Chen, G., & Zhang, J. Z. H. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.04.657832

Protein Stability Regulated by Tag- and Site-Specific Ubiquitination and SUMOylation

Arora, S., Das, D., & Ainavarapu, S. R. K. (2026) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.5c03707

Deep evolutionary mining and structural distillation transform human interactome prediction

Ge, W., & Zhao, Q. (2026) · Genomics Communications · doi:10.48130/gcomm-0026-0001

Steric confinement-induced emission probe for monitoring protein conformations in live cells

Jia, H., Yang, L., Yang, Y., Liu, H., Liu, J., Shang, C., Di, Z., He, B., & Zhang, K. (2026) · Communications Chemistry · doi:10.1038/s42004-026-01914-x

Genome-Wide Identification and Expression Analysis of LOX Gene Family in Rice (Oryza sativa L.) Under Abiotic Stress ConditionsPreprint

Tusti, A. D., Hasan, N., Rahman, J. Y., Hoque, H., Chakraborty, A., & Prodhan, S. H. (2026) · Research Square · doi:10.21203/rs.3.rs-8728944/v1

Investigating Escherichia coli Colicin E9 immunity protein interactions with DNA gyrase of Pseudomonas aeruginosa: advanced computational approach for developing novel antimicrobial strategies

Alfaraj, R., Alkathiri, F. A., & Chikhale, R. V. (2026) · Scientific Reports · doi:10.1038/s41598-026-44427-2

Approaches to explore multiplex biological networks and application to study premature aging diseases

Valdeolivas, A. (2019) · theses.fr (ABES) · doi:10.70675/5379aa9cz8f24z45c6z8d81z2e0796525163

Strategies for constructing context-specific protein–protein interaction networks

Nie, S., Kong, X., & Li, D. (2026) · Briefings in Bioinformatics · doi:10.1093/bib/bbag004

Affinity Capillary Electrophoresis for the Study of Biomolecular Interactions: Recent Advances and Future Perspectives

Jin, Y., Zhang, D., & Wang, H. (2026) · Journal of Separation Science · doi:10.1002/jssc.70463

Epitope-guided Detection of a Molecular Glue-induced Ternary Complex Using Engineered Synthetic Antibody Fragments

O’Leary, K. M., Ślężak, T., Le, D. A., & Kossiakoff, A. A. (2026) · Journal of Molecular Biology · doi:10.1016/j.jmb.2026.169953

Amino Acids and Protein Structure

Minden, A. (2026) · Springer eBooks · doi:10.1007/978-3-032-20529-2_4

Synthetic Protein Mimetic Based Therapies for Neurodegeneration

Stillman, N. H. (2025) · Digital Commons - DU (University of Denver) · doi:10.56902/etdcrp.2025.171

Cooperative interaction between ZmKNOX13 and ZmNAC70 improves cold stress response in maize

Zhang, X., Wu, H., Li, X., Liu, Z., Huang, A., Peng, X., Han, G., Ma, Q., Cheng, B., Li, X., et al. (2026) · The Crop Journal · doi:10.1016/j.cj.2026.07.015

Artificial Synthetic Protein Mimetics As Pathology-Targeted Therapeutics

Dohoney, R. A. (2026) · Digital Commons - DU (University of Denver) · doi:10.56902/etdcrp.2026.62

Comprehensive Characterization and Expression Profiling of the LOX Gene Family in Rice (Oryza sativa L.) in Response to Abiotic Stress ConditionsPreprint

Tusti, A. D., Hasan, M. N., Rahman, J. Y., Hoque, H., Chakraborty, A., & Prodhan, S. H. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.7358619

ENVIRONMENTAL CONDITIONS RECURRENCE AND THE STABILIZATION OF GENE REGULATORY FUNCTIONS: TOWARDS A THEORY OF DYNAMIC GENE INTEGRATIONPreprint

López‐Pérez, M., & Fernández, F. J. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.7382207

Artificial Intelligence as a Discovery Engine for Routine Molecular Techniques: Extracting Biological Insight from Western Blotting, ELISA, Immunostaining, and Immunoprecipitation

Almazari, R., Abu‐El‐Rub, E., & Alzu’bi, A. (2026) · Cell Biochemistry and Biophysics · doi:10.1007/s12013-026-02171-4

Unraveling protein folding and structural dynamics

Iram, F., Aiman, A., Khan, L. A., & Islam, A. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-44988-8.00019-8

Proximity labeling technologies for multiscale spatial proteomics: from organelle contact sites to intercellular and inter-organ communication

Chen, D., Zhao, H., Zhao, H., & Wang, J. (2026) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2026.154761

Gold Nanoparticle−Assisted Fluorescence Recovery as a Sensitive Platform for Monitoring α-Synuclein Aggregation

Jahangiri-Manesh, A., Amjadi, N., Nikkhah, M., & Hosseinkhani, S. (2026) · ACS Applied Nano Materials · doi:10.1021/acsanm.6c03247

BindingDB Entry 50023205: Discovery of niclosamide as a p300/transcription factor protein-protein interaction inhibitor.

BindingDB (2026) · UC San Diego · doi:10.7270/q2125zj8

Applications of Two-Hybrid Systems and Mass Spectrometry to Investigate Protein-Protein Interactions

Zhang, Y. (2006) · Letters in Biotechnology

From pathways to networks: Connecting dots by establishing protein–protein interaction networks in signaling pathways using affinity purification and mass spectrometry

Li, X., Wang, W., & Chen, J. (2014) · PROTEOMICS · doi:10.1002/pmic.201400147 · Cited by 24

Illuminating Spatial and Temporal Organization of Protein Interaction Networks by Mass Spectrometry-Based Proteomics

Yang, J., Wagner, S., & Beli, P. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00344 · Cited by 22

Identification of Signaling Protein Complexes by Parallel Affinity Precipitation Coupled with Mass Spectrometry

Heng Lu, Q. L. A. J. Z. (2013) · Cell Communication Insights · doi:10.4137/cci.s12484 · Cited by 1

Simple and Effective Affinity Purification Procedures for Mass Spectrometry-Based Identification of Protein-Protein Interactions in Cell Signaling Pathways

Kwan, J., & Emili, A. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-3341-9_13 · Cited by 4