Identification of Protein Interactions Involved in Cellular Signaling

Mass spectrometry-based proteomics

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A novel genetic system to detect protein–protein interactions

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

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

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

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A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae

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

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Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

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

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Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

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The Critical Node Detection Problem in networks: A survey

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European contribution to the study of ROS: A summary of the findings and prospects for the future from the COST action BM1203 (EU-ROS)

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Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple ‘Omic’ Layers

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Affinity purification–mass spectrometry and network analysis to understand protein-protein interactions

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Systematic Targeting of Protein–Protein Interactions

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Transcriptional co-activators: emerging roles in signaling pathways and potential therapeutic targets for diseases

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Functionalization of Silk Fibroin Materials at Mesoscale

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Legume genomics and transcriptomics: From classic breeding to modern technologies

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Insulin Induces Microtubule Stabilization and Regulates the Microtubule Plus-end Tracking Protein Network in Adipocytes

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Characterization of the CLASP2 Protein Interaction Network Identifies SOGA1 as a Microtubule-Associated Protein

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Predicting protein-peptide binding sites with a deep convolutional neural network

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Live cell imaging of signaling and metabolic activities

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An insight into PI3k/Akt pathway and associated protein–protein interactions in metabolic syndrome: A recent update

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Microscale Thermophoresis as a Tool to Study Protein Interactions and Their Implication in Human Diseases

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Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology

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Benchmarking all-atom biomolecular structure prediction with FoldBench

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Pyruvate kinase M2 in chronic inflammations: a potpourri of crucial protein–protein interactions

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Few shot learning for phenotype-driven diagnosis of patients with rare genetic diseases

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The PtdIns3‐phosphatase MTMR3 interacts with mTORC1 and suppresses its activity

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Peptide-Based Subunit Vaccine Design of T- and B-Cells Multi-Epitopes against Zika Virus Using Immunoinformatics Approaches

Prasasty, V. D., Grazzolie, K., Rosmalena, R., Yazid, F., Ivan, F. X., & Sinaga, E. (2019) · Microorganisms · doi:10.3390/microorganisms7080226 · Cited by 33

Combining Chemical Protein Synthesis and Random Nonstandard Peptides Integrated Discovery for Modulating Biological Processes

Saha, A., Suga, H., & Brik, A. (2023) · Accounts of Chemical Research · doi:10.1021/acs.accounts.3c00178 · Cited by 31

Disease‐specific interactome alterations via epichaperomics: the case for Alzheimer’s disease

Ginsberg, S. D., Neubert, T. A., Sharma, S., Digwal, C. S., Yan, P., Timbus, C., Wang, T., & Chiosis, G. (2021) · FEBS Journal · doi:10.1111/febs.16031 · Cited by 28

Dynamic Tracking of Biological Processes Using Near-Infrared Fluorescent Single-Walled Carbon Nanotubes

Basu, S., Hendler‐Neumark, A., & Bisker, G. (2024) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.4c10955 · Cited by 24

The disruption of protein-protein interactions as a therapeutic strategy for prostate cancer

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Mitochondrial ribosomal small subunit proteins (MRPS) MRPS6 and MRPS23 show dysregulation in breast cancer affecting tumorigenic cellular processes

Oviya, R. P., Gopisetty, G., Shirley, S., Velusamy, S., Jayavelu, S., & Rajkumar, T. (2021) · Gene · doi:10.1016/j.gene.2021.145697 · Cited by 24

High-dimensionality Data Analysis of Pharmacological Systems Associated with Complex Diseases

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The Value of Mechanistic Biophysical Information for Systems-Level Understanding of Complex Biological Processes Such as Cytokinesis

Pollard, T. D. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.10.031 · Cited by 23

Relevance Rank Platform (RRP) for Functional Filtering of High Content Protein–Protein Interaction Data*

Pokharel, Y. R., Saarela, J., Szwajda, A., Rupp, C., Rokka, A., Karna, S. K. L., Teittinen, K. J., Corthals, G. L., Kallioniemi, O., Wennerberg, K., et al. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m115.050773 · Cited by 20

TRP Channels Regulation of Rho GTPases in Brain Context and Diseases

Lavanderos, B. J., Silva, I., Cruz, P., Orellana‐Serradell, O., Saldías, M. P., & Cerda, O. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.582975 · Cited by 18

MK2 degradation as a sensor of signal intensity that controls stress-induced cell fate

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DNA-Nanostructure-Guided Assembly of Proteins into Programmable Shapes

Lu, Q., Xu, Y., Poppleton, E., Zhou, K., Šulc, P., Stephanopoulos, N., & Ke, Y. (2024) · Nano Letters · doi:10.1021/acs.nanolett.3c04497 · Cited by 17

MS/MS‐based strategies for proteomic profiling of invasive cell structures

Havrylov, S., & Park, M. (2014) · PROTEOMICS · doi:10.1002/pmic.201400220 · Cited by 18

Approaches to Investigating the Protein Interactome of PTEN

Smith, S. L., Pitt, A. R., & Spickett, C. M. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00570 · Cited by 16

Exploring the mechanistic insights of Cas scaffolding protein family member 4 with protein tyrosine kinase 2 in Alzheimer’s disease by evaluating protein interactions through molecular docking and dynamic simulations

Hassan, M., Shahzadi, S., Alashwal, H., Zaki, N., Seo, S., & Moustafa, A. A. (2018) · Neurological Sciences · doi:10.1007/s10072-018-3430-2 · Cited by 17

A Web of Possibilities: Network-Based Discovery of Protein Interaction Codes

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Understand the Functions of Scaffold Proteins in Cell Signaling by a Mesoscopic Simulation Method

Su, Z., Dhusia, K., & Wu, Y. (2020) · Biophysical Journal · doi:10.1016/j.bpj.2020.10.002 · Cited by 15

Network approaches for omics studies of neurodegenerative diseases

Zhao, N., Quicksall, Z., Asmann, Y. W., & Ren, Y. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.984338 · Cited by 18

Fast Quantitative Validation of 3D Models of Low-Affinity Protein–Ligand Complexes by STD NMR Spectroscopy

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Ripor2 is involved in auditory hair cell stereociliary bundle structure and orientation

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Mechanistic insights into TNFR1/MADD death domains in Alzheimer’s disease through conformational molecular dynamic analysis

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Ion-Mediated Morphological Diversity in Protein Amyloid Systems

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A review on evolution, structural characteristics, interactions, and regulation of the membrane transport protein: The family of Rab proteins

Parray, Z. A. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.139828 · Cited by 15

GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks

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Chemical proteomics and its impact on the drug discovery process

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Interaction of ribosomal protein L22 with casein kinase 2α: A novel mechanism for understanding the biology of non-small cell lung cancer

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Exploring Proteomic Drug Targets, Therapeutic Strategies and Protein - Protein Interactions in Cancer: Mechanistic View

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The art of designed coiled-coils for the regulation of mammalian cells

Plaper, T., Rihtar, E., Ramuta, T. Ž., Forstnerič, V., Jazbec, V., Ivanovski, F., Benčina, M., & Jerala, R. (2024) · Cell chemical biology · doi:10.1016/j.chembiol.2024.06.001 · Cited by 15

Tandem Immunoaffinity Purification Using Anti-FLAG and Anti-HA AntibodiesPreprint

DeCaprio, J. A., & Kohl, T. O. (2019) · Cold Spring Harbor Protocols · doi:10.1101/pdb.prot098657 · Cited by 14

Microfluidic Antibody Affinity Profiling for In-Solution Characterisation of Alloantibody - HLA Interactions in Human SerumPreprint

Schneider, M. M., Scheidt, T., Priddey, A. J., Xu, C. K., Hu, M., Devenish, S. R. A., Meisl, G., Dobson, C. M., Kosmoliaptsis, V., & Knowles, T. P. J. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.14.296442 · Cited by 14

Trends in co-fractionation mass spectrometry: A new gold-standard in global protein interaction network discovery

Goel, R. K., Bithi, N., & Emili, A. (2024) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2024.102880 · Cited by 15

Molecular characterization of COVID-19 therapeutics: luteolin as an allosteric modulator of the spike protein of SARS-CoV-2

Alvarado, W., Pérez-Lemus, G. R., Menéndez, C. A., Byléhn, F., & Pablo, J. (2021) · Molecular Systems Design & Engineering · doi:10.1039/d1me00119a · Cited by 14

Building Bridges Between Structural and Network-Based Systems Biology

Chasapis, C. T. (2019) · Molecular Biotechnology · doi:10.1007/s12033-018-0146-8 · Cited by 15

Single-cell chemoproteomics identifies metastatic activity signatures in breast cancer

Pillai, K. S., Laxton, O. C., Li, G., Lin, J., Karginova, O. A., Nanda, R., Olopade, O. I., Tay, S., & Moellering, R. E. (2024) · Science Advances · doi:10.1126/sciadv.adp2622 · Cited by 12

Structure and thermodynamics of transient protein-protein complexes by chemometric decomposition of SAXS datasets

Sagar, A., Herranz-Trillo, F., Langkilde, A. E., Vestergaard, B., & Bernadó, P. (2021) · Structure · doi:10.1016/j.str.2021.03.017 · Cited by 12

Genome-wide identification and characterization of NCED gene family in soybean (Glycine max L.) and their expression profiles in response to various abiotic stress treatments

Islam, M. S. U., Shing, P., Ahmed, M., Zohra, F. T., Rownaq, A., Paul, S. K., Rahman, S. M., & Sarkar, M. A. R. (2025) · PLoS ONE · doi:10.1371/journal.pone.0319952 · Cited by 11

The development of microfluidic-based western blotting: Technical advances and future perspectives

Desire, C. T., Arrua, R. D., Strudwick, X. L., Kopecki, Z., Cowin, A. J., & Hilder, E. F. (2023) · Journal of Chromatography A · doi:10.1016/j.chroma.2023.463813 · Cited by 11

Identification of novel long non-coding RNA involved in Sertoli cell of non-obstructive azoospermia based on microarray and bioinformatics analysis

Karoii, D. H., Abroudi, A. S., Darvar, M., Djamali, M., Azizi, H., & Skutella, T. (2025) · Genomics · doi:10.1016/j.ygeno.2025.111046 · Cited by 11

Design and synthesis of a new orthogonally protected glutamic acid analog and its use in the preparation of high affinity polo-like kinase 1 polo-box domain – binding peptide macrocycles

Hymel, D., Tsuji, K., Grant, R. A., Chingle, R. M., Kunciw, D. L., Yaffe, M. B., & Burke, T. R. (2021) · Organic & Biomolecular Chemistry · doi:10.1039/d1ob01120k · Cited by 11

Recent developments in Phos-tag electrophoresis for the analysis of phosphoproteins in proteomics

Hirano, H., & Shirakawa, J. (2022) · Expert Review of Proteomics · doi:10.1080/14789450.2022.2052850 · Cited by 11

Conducting bioinformatics analysis to predict sulforaphane-triggered adverse outcome pathways in healthy human cells

Božić, D., Živančević, K., Baralić, K., Miljaković, E. A., Djordjević, A. B., Ćurčić, M., Bulat, Z., Antonijević, B., & Đukić-Ćosić, D. (2023) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2023.114316 · Cited by 11

A Noise-Filtering Method for Link Prediction in Complex Networks

Ouyang, B., Jiang, L., & Teng, Z. (2016) · PLoS ONE · doi:10.1371/journal.pone.0146925 · Cited by 10

AraPPISite: a database of fine-grained protein–protein interaction site annotations for Arabidopsis thaliana

Li, H., Yang, S., Wang, C., Zhou, Y., & Zhang, Z. (2016) · Plant Molecular Biology · doi:10.1007/s11103-016-0498-z · Cited by 10

The paradox of autophagy in cancer: NEAT1's role in tumorigenesis and therapeutic resistance

Almujri, S. S., & Almalki, W. H. (2024) · Pathology - Research and Practice · doi:10.1016/j.prp.2024.155523 · Cited by 9

Nonbonded Force Field Parameters Derived from Atoms-in-Molecules Methods Reproduce Interactions in Proteins from First-Principles

Castillo-Orellana, C., Heidar‐Zadeh, F., & Vöhringer‐Martinez, E. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c01406 · Cited by 9

Blocking Allergic Reaction through Targeting Surface-Bound IgE with Low-Affinity Anti-IgE Antibodies

Zhang, K., Liu, J., Truong, T., Zukin, E., Chen, W., & Saxon, A. (2017) · The Journal of Immunology · doi:10.4049/jimmunol.1602022 · Cited by 9

In vitro Determination of Rapamycin-triggered FKBP-FRB Interactions Using a Molecular Tension Probe

Kim, S. B., Nishihara, R., Fujii, R., Paulmurugan, R., Citterio, D., & Suzuki, K. A. O. (2018) · Analytical Sciences · doi:10.2116/analsci.18sdp08 · Cited by 9

Development of a bioluminescence assay for BIR2- caspase3 interaction through split luciferase complementary assay

Mostafavi, M., Ataei, F., Hamidieh, A. A., & Hosseinkhani, S. (2022) · Biochemical Engineering Journal · doi:10.1016/j.bej.2022.108584 · Cited by 8

Mixed Stereochemistry Macrocycle Acts as a Helix-Stabilizing Peptide N-Cap

Hink, F., Aduriz‐Arrizabalaga, J., López, X., Suga, H., Sancho, D. D., & Rogers, J. M. (2024) · Journal of the American Chemical Society · doi:10.1021/jacs.4c05378 · Cited by 9

Computational investigation of mechanistic insights of Aβ42 interactions against extracellular domain of nAChRα7 in Alzheimer’s disease

Hassan, M., Shahzadi, S., Raza, H., Abbasi, M. A., Alashwal, H., Zaki, N., Moustafa, A. A., & Seo, S. (2018) · International Journal of Neuroscience · doi:10.1080/00207454.2018.1543670 · Cited by 8

In-cellulo chemical cross-linking to visualize protein-protein interactions

Saha, S., Ranjan, A. K., Godara, M., & Shukla, A. K. (2022) · Methods in cell biology · doi:10.1016/bs.mcb.2021.12.024 · Cited by 7

An ESRG-interacting protein, COXII, is involved in pro-apoptosis of human embryonic stem cells

Shi, J., Ren, C., Liu, H., Wang, L., Zhu, B., Huang, W., Liu, W., Liu, J., Liu, Y., Xia, X., et al. (2015) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2015.02.130 · Cited by 8

A deep learning framework for improving protein interaction prediction using sequence propertiesPreprint

Guo, Y., & Chen, X. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/843755 · Cited by 7

Label-Free Multimetric Measurement of Molecular Binding Kinetics by Electrical Modulation of a Flexible Nanobiolayer

Zhou, X., Ma, G., Wan, Z., & Wang, S. (2022) · ACS Sensors · doi:10.1021/acssensors.2c01804 · Cited by 7

Additive energetic contributions of multiple peptide positions determine the relative promiscuity of viral and human sequences for PDZ domain targets

Tahti, E. F., Blount, J. M., Jackson, S. N., Gao, M., Gill, N. P., Smith, S. N., Pederson, N. J., Rumph, S. N., Struyvenberg, S. A., Mackley, I. G. P., et al. (2023) · Protein Science · doi:10.1002/pro.4611 · Cited by 7

Analysis of FAIMS for the study of affinity-purified protein complexes using the orbitrap ascend tribrid mass spectrometer

Goswami, P., Cesare, J., Rekowski, M. J., Clark, Z., Thornton, J., & Washburn, M. P. (2025) · Molecular Omics · doi:10.1039/d5mo00038f · Cited by 6

Microfluidics for protein interaction studies: current methods, challenges, and future perspectives

Schneider, M. M., Knowles, T. P. J., Keller, S., & Krainer, G. (2025) · European Biophysics Journal · doi:10.1007/s00249-025-01763-x · Cited by 6

Reprogrammable 3D Shapes from 1D Metamaterial

Abu, E. B., Zigelman, A., Veksler, Y., Givli, S., Filipov, E. T., Lipson, H., & Gat, A. D. (2024) · Advanced Materials Technologies · doi:10.1002/admt.202401113 · Cited by 7

Molecular engineering strategies for visualizing low-affinity protein complexes

Ming, Q., González-Pérez, D., & Luca, V. C. (2019) · Experimental Biology and Medicine · doi:10.1177/1535370219855401 · Cited by 6

In Vivo Quantitative Estimation of DNA-Dependent Interaction of Sox2 and Oct4 Using BirA-Catalyzed Site-Specific Biotinylation

Kulyyassov, A., & Ogryzko, V. V. (2020) · Biomolecules · doi:10.3390/biom10010142 · Cited by 6

Target Recognition in Tandem WW Domains: Complex Structures for Parallel and Antiparallel Ligand Orientation in h-FBP21 Tandem WW

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Prediction of Protein-Protein Interactions: Looking Through the Kaleidoscope

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