Protein networks in disease

Cited by (817)

Items 501–600 of 817

1. Pathway crosstalk analysis based on protein-protein network analysis in prostate cancer.
   Wang Jm, J-T Wu, Sun Dk, P Zhang, L Wang · 2012 · PubMed
2. Understanding chronic disease comorbidities from baseline networks
   Arif M. Khan, Shahadat Uddin, Uma Shankari Srinivasan · 2016 · Australasian Computer Science Week Multiconference (ACSW)
3. Construction of the spatial and temporal active protein interaction network for identifying protein complexes
   Xiangmao Meng, Min Li, Jianxin Wang, Fang‐Xiang Wu, Yi Feng Pan · 2016 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
4. A Computational Selection of Metabolite Biomarkers Using Emerging Pattern Mining: A Case Study in Human Hepatocellular Carcinoma
   Guillaume Poezevara, Sylvain Lozano, Bertrand Cuissart, Ronan Bureau, Pierre Bureau, Vincent Croixmarie, Philippe Vayer, Alban Lepailleur · 2017 · Journal of Proteome Research
5. Proteomics and Non-proteomics Approaches to Study Stable and Transient Protein-Protein Interactions
   Armand G. Ngounou Wetie, Izabela Sokolowska, Devika Channaveerappa, Emmalyn J. Dupree, Madhuri Jayathirtha, Alisa G. Woods, Costel C. Darie · 2019 · Advances in experimental medicine and biology
6. We need to keep a reproducible trace of facts, predictions, and hypotheses from gene to function in the era of big data
   Simon Kasif, Richard J. Roberts · 2020 · PLoS Biology
7. Heterogeneity within and across Pediatric Pulmonary Infections: From Bipartite Networks to At-Risk Subphenotypes.
   Suresh K. Bhavnani, Bryant Dang, Maria Caro, Gowtham Bellala, Shyam Visweswaran, Asunción Mejías, Rohit Dilip Divekar · 2014 · Europe PMC (PubMed Central)
8. Network-Based Analysis for Biological Discovery
   Lokesh P. Tripathi, Y. Ann Chen, Kenji Mizuguchi, Yoichi Murakami · 2018 · Elsevier eBooks
9. diaPASEF-Powered Chemoproteomics Enables Deep Kinome Interaction Profiling
   Kathryn Woods, Alexandria M. Chan, Thankhoe A. Rants’o, Tanmay Sapre, Grace E. Mastin, Kathleen M. Maguire, Shao‐En Ong, Martin G. Golkowski · 2025 · Journal of Proteome Research
10. Joint representation of molecular networks from multiple species improves gene classification
    Christopher A Mancuso, Kayla A Johnson, Renming Liu, Arjun Krishnan · 2024 · PLoS Computational Biology
11. Prioritizing drug targets by perturbing biological network response functions
    Matthew C. Perrone, Michael G. Lerner, Matthew Dunworth, Andrew J. Ewald, Joel S. Bader · 2024 · PLoS Computational Biology
12. Network-based gene deletion analysis identifies candidate genes and molecular mechanism involved in clear cell renal cell carcinoma
    G. K. Udayaraja, Isaac Arnold Emerson · 2021 · Journal of Genetics
13. Shared Proteins and Pathways of Cardiovascular and Cognitive Diseases: Relation to Vascular Cognitive Impairment
    Melisa Ece Zeylan, Simge Senyuz, Pol Picón-Pagès, Anna García-Elías, Marta Tajes, Francisco J. Muñoz, Baldomero Oliva, Jordi García‐Ojalvo, Eduard Barbu, Raúl Vicente et al. · 2024 · Journal of Proteome Research
14. Transcriptional regulatory network and protein–protein interaction to reveal the mechanism of pancreatic cancer
    Hongli Sun, Bing Han, Xinhua Cheng, Kai Ma · 2013 · Molecular Biology Reports
15. The role of genes co-amplified with nicastrin in breast invasive carcinoma
    Anida Sarajlić, Aleksandra Filipović, Vuk Janjić, R. Charles Coombes, Nataša Pržulj · 2013 · Breast Cancer Research and Treatment
16. Construction of a Pig Physical Interactome Using Sequence Homology and a Comprehensive Reference Human Interactome
    Felix Dreher, Atanas Kamburov, Ralf Herwig · 2012 · Evolutionary Bioinformatics
17. Comparative Analysis of Prostate Cancer Gene Regulatory Networks via Hub Type Variation.
    Pegah Khosravi, Vahid Gazestani, Mohammad Akbarzadeh, Samira Mirkhalaf, Mehdi Sadeghi, Bahram Goliaei · 2015 · PubMed Central
18. Diffusion kernel to identify missing PPIs in protein network biomarker
    Dominic K. Bett, Ananda Mohan Mondal · 2015 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
19. AtPID: a genome-scale resource for genotype–phenotype associations in Arabidopsis
    Qi Lv, Yiheng Lan, Yan Shi, Huan Wang, Xia Pan, Peng Li, Tieliu Shi · 2016 · Nucleic Acids Research
20. Construction and Analysis of Protein-Protein Interaction Network to Identify the Molecular Mechanism in Laryngeal Cancer
    Sarahani Harun, Nurulisa Zulkifle · 2018 · Sains Malaysiana
21. Interdependent Patterns in Protein-Protein Interaction Networks
    Peng Gang Sun, Yining Quan, Qiguang Miao · 2020 · IEEE Transactions on Network Science and Engineering
22. Disease Gene Classification with Metagraph Representations
    Sezin Kircali Ata, Yuan Fang, Min Wu, Xiaoli Li, Xiaokui Xiao · 2018 · Methods in molecular biology
23. Prestige centrality-based functional outlier detection in gene expression analysis
    Ali Torkamani, Nicholas J. Schork · 2009 · Bioinformatics
24. Inferring gene regulatory networks from asynchronous microarray data with AIRnet
    David Oviatt, Mark Clement, Quinn O. Snell, Kenneth Sundberg, Chun Wan Jeffrey Lai, Jared Allen, Randall J. Roper · 2010 · BMC Genomics
25. Gene regulatory network reconstruction incorporating 3D chromosomal architecture reveals key transcription factors and DNA elements driving neural lineage commitment
    Valeriya Malysheva, Marco Antonio Mendoza-Parra, Matthias Blum, Mikhail Spivakov, Hinrich Gronemeyer · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
26. Implications of systems biology in understanding the pathophysiology of neurological diseases
    Sanjana Mishra, Ananya Singh, Wayez Naqvi, Prekshi Garg, Neha Srivastava, Prachi Srivastava · 2024 · Elsevier eBooks
27. Network-based analysis of genotype–phenotype correlations between different inheritance modes
    Dapeng Hao, Chuanxing Li, Shaojun Zhang, Jianping Lu, Yongshuai Jiang, Shiyuan Wang, Meng Zhou · 2014 · Bioinformatics
28. Estimating the Number of Communities in Weighted Networks
    Huan Qing · 2023 · Entropy
29. The Extent of Edgetic Perturbations in the Human Interactome Caused by Population-Specific Mutations
    Hongzhu Cui, Suhas Srinivasan, Ziyang Gao, Dmitry Korkin · 2023 · Biomolecules
30. G-Protein Signaling in Alzheimer's Disease: Spatial Expression Validation of Semi-supervised Deep Learning-Based Computational Framework
    Daniel F. Zhang, Timothy Penwell, Yanhua Chen, Addison Koehler, Rui Wu, Shayan Nik Akhtar, Qun Lu · 2024 · Journal of Neuroscience
31. Joint Analysis for Integrating Two Related Studies of Different Data Types and Different Study Designs Using Hierarchical Modeling Approaches
    Rui Li, David V. Conti, David Díaz-Sánchez, Frank D. Gilliland, Duncan C. Thomas · 2012 · Human Heredity
32. Global risk transformative prioritization for prostate cancer candidate genes in molecular networks
    Lina Chen, Jingxie Tai, Liangcai Zhang, Yukui Shang, Xu Li, Xiaoli Qu, Weiguo Li, Zhengqiang Miao, Jia Xu, Hong Wang et al. · 2011 · Molecular BioSystems
33. A random walk based approach for improving protein-protein interaction network and protein complex prediction
    Chengwei Lei, Jianhua Ruan · 2012 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
34. Study on Incompatibility of Traditional Chinese Medicine: Evidence from Formula Network, Chemical Space, and Metabolism Room
    Wei Long, Xiaodong Zhang, Hongying Wu, Jin Jin, Guang-Yun Yu, Xin He, Hao Wang, Xiu Shen, Zewei Zhou, Peixun Liu et al. · 2013 · Evidence-based Complementary and Alternative Medicine
35. Network Medicine: New Paradigm in the -Omics Era
    Nancy Lan Guo · 2011 · Anatomy & Physiology
36. Genome and network visualization facilitates the analyses of the effects of drugs and mutations on protein-protein and drug-protein networks
    Arnaud Gerard Michel Ceol, Lisette G. G. C. Verhoef, Mark R. Wade, Heiko Müller · 2016 · BMC Bioinformatics
37. Function Analysis of Human Protein Interactions Based on a Novel Minimal Loop Algorithm
    Mingyang Jiang, Zhili Pei, Xiaojing Fan, Jingqing Jiang, Qinghu Wang, Zhifeng Zhang · 2018 · Current Bioinformatics
38. Lower connectivity of tumor coexpression networks is not specific to cancer
    Ertuğrul Dalgıç, Özlen Konu, Zehra Safi Öz, Christina Chan · 2019 · In Silico Biology
39. iBRET Screen of the ABCD1 Peroxisomal Network and Mutation-Induced Network Perturbations
    Amelie Sophia Lotz-Havla, Mathias Woidy, Philipp Guder, Caroline C. Friedel, Julian M. Klingbeil, Ana‐Maria Bulau, Anja Schultze, Ilona Dahmen, Heidi Noll‐Puchta, Stephan Kemp et al. · 2021 · Journal of Proteome Research
40. Improving Identification of Key Players in Aging via Network De-Noising and Core Inference
    Boyoung Yoo, Fazle E. Faisal, Huili Chen, Tijana Milenković · 2015 · IEEE Transactions on Computational Biology and Bioinformatics
41. Viewing the Meso-Scale Structures in Protein-Protein Interaction Networks Using 2-Clubs
    Songwei Jia, Lin Gao, Yong Gao, James Nastos, Wen Xiao, Xiaotai Huang, Haiyang Wang · 2018 · IEEE Access
42. A novel network model for molecular prognosis
    Ying‐Wooi Wan, Swetha B. Nutakki, James Denvir, Nancy Lan Guo · 2010 · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)
43. Network Based Prioritization of Disease Genes
    Mehmet Sinan Erten · 2009 · OhioLink ETD Center (Ohio Library and Information Network)
44. Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks
    Mark D’Souza, Dinanath Sulakhe, Sheng Wang, Bing Xie, Somaye Sadat Hashemifar, Andrew Taylor, Inna L Dubchak, T. Conrad Gilliam, Natalia Maltsev · 2017 · Methods in molecular biology
45. Primer on Protein–Protein Interaction Maps
    Nora Marín‐de la Rosa, Pascal Falter‐Braun · 2015 · Wiley eBooks
46. Computational Biology
    Thomas Lengauer, Mario Albrecht, Francisco S. Domingues · 2012 · Wiley-VCH eBooks
47. Discriminating physiological from non-physiological interfaces in structures of protein complexes: a community-wide study
    Hugo Schweke, Qifang Xu, Gerardo Tauriello, Lorenzo Pantolini, Torsten F. Schwede, Frédéric Cazals, Alix Lhéritier, Juan Fernández‐Recio, Luis Angel Rodríguez‐Lumbreras, Ora Schueler‐Furman et al. · 2023
48. A quantitative comparison of the deleteriousness of missense and nonsense mutations using the structurally resolved human protein interactome
    Ting‐Yi Su, Yu Xia · 2025 · Protein Science
49. Temporal Ordered Clustering in Dynamic Networks: Unsupervised and Semi-Supervised Learning Algorithms
    Krzysztof Turowski, Jithin Kazhuthuveettil Sreedharan, Wojciech Szpankowski A · 2021 · IEEE Transactions on Network Science and Engineering
50. Photoswitchable, Water‐Soluble Bisazobenzene Cross‐Linkers with Enhanced Properties for Biological Applications
    Jana Volarić, Sebastian Thallmair, Ben L. Feringa, Wiktor Szymański · 2022 · ChemPhotoChem
51. WDR54 exerts oncogenic roles in T‐cell acute lymphoblastic leukemia
    Huan Li, Danlan Zhang, Qiuxia Fu, Shang Wang, Xin Zhang, Zhixian Lin, Zhongyuan Wang, Jiaxing Song, Zijie Su, Vivian Weiwen Xue et al. · 2023 · Cancer Science
52. Single-cell biclustering for cell-specific transcriptomic perturbation detection in AD progression
    Yuqiao Gong, Jingsi Xu, Maoying Wu, Ruitian Gao, Jianle Sun, Zhangsheng Yu, Yue Zhang · 2024 · Cell Reports Methods
53. Prospective Investigation Unravels Plasma Proteomic Links to Dementia
    Jincheng Li, Jialin Li, Shuaizhou Chen, Zhenqiu Liu, Jiacheng Dai, Yingzhe Wang, Mei Cui, Chen Suo, Kelin Xu, Jin Li et al. · 2025 · Molecular Neurobiology
54. Performance of Hybrid Strategies Combining MDockPP and AlphaFold2 in CAPRI Rounds 47–55
    Rui Duan, Xianjin Xu, Liming Qiu, Shuang Zhang, Xiaoqin Zou · 2025 · Proteins Structure Function and Bioinformatics
55. COUNTERPOINT: Do not opine before it's time
    Isaac S. Kohane, David M. Margulies · 2011 · Nature Biotechnology
56. Interconnectivity of human cellular metabolism and disease prevalence
    Deok‐Sun Lee · 2010 · Journal of Statistical Mechanics Theory and Experiment
57. Improving identification of key players in aging via network de-noising
    Boyoung Yoo, Huili Chen, Fazle E. Faisal, Tijana Milenković · 2014 · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)
58. Model organism proteomics
    Christian H. Ahrens, Sabine Schrimpf, Erich Brunner, Ruedi H. Aebersold · 2010 · Journal of Proteomics
59. Reverse engineering molecular hypergraphs
    Ahsanur Rahman, Christopher L. Poirel, David J. Badger, T. M. Murali · 2012 · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)
60. Comparative study of network-based prioritization of protein domains associated with human complex diseases
    Wangshu Zhang, Yong Chen, Rui Jiang · 2010 · Frontiers of Electrical and Electronic Engineering in China
61. Mini Review: The Application of Omics in Targeted Anticancer Biopharmaceuticals Development
    Lufang Zhou · 2014
62. [Genomics in medicine].
    Ruth Ruiz-Esparza Garrido, Miguel Ángel Velázquez-Flores, Diego Julio Arenas-Aranda, Fabio Salamanca-Gómez · 2014 · PubMed
63. Graph Theoretic Concepts as the Building Blocks for Disease Initiation and Progression at Protein Network Level: Identification and Challenges
    Ananda Mohan Mondal, Cornelia Ada Schultz, Markea Sheppard, Jasmine Carson, Raihanul Bari Tanvir, Tasmia Aqila · 2018 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
64. Introduction to Network Biology
    Mehmet Koyutürk, Shankar Subramaniam, Ananth Y. Grama · 2011 · Springer eBooks
65. Reconstruction of a Comprehensive Interactome and Experimental Data Analysis of FRA10AC1 May Provide Insights into Its Biological Role in Health and Disease
    Theologia Sarafidou, Eleni Galliopoulou, Despina Apostolopoulou, Georgios A. Fragkiadakis, Nicholas Κ. Moschonas · 2023 · Genes
66. Subtype-specific network organization of molecular complexes in breast cancer
    Swapnil Kumar, Ramakrishna Ramaswamy, Vaibhav Vindal, Alok Srivastava · 2023 · Journal of Biosciences
67. HMNPPID—human malignant neoplasm protein–protein interaction database
    Qingqing Li, Zhihao Yang, Zhehuan Zhao, Ling Luo, Zhiheng Li, Lei Wang, Yin Zhang, Hongfei Lin, Jian Wang, Yijia Zhang · 2019 · Human Genomics
68. Bioinformatics‐Driven New Immune Target Discovery in Disease
    C. Yang, P. Chen, WENJIA ZHANG, Hongyan Du · 2016 · Scandinavian Journal of Immunology
69. The Integration and Annotation of the Human Interactome in the UniHI Database
    Gautam Chaurasia, Matthias Erwin Futschik · 2011 · Methods in molecular biology
70. Computational Systems Analysis on Polycystic Ovarian Syndrome (PCOS)
    Nor Afiqah‐Aleng, Zeti‐Azura Mohamed‐Hussein · 2020 · IntechOpen eBooks
71. Visualization and analysis of the interaction network of proteins associated with blood-cell targeting autoimmune diseases
    Athina I. Amanatidou, Katerina C. Nastou, Ourania Tsitsilonis, Vassiliki A. Iconomidou · 2020 · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease
72. The Hallmarks of Cancer Revisited Through Systems Biology and Network Modelling
    Charles Auffray, Trey Ideker, David J. Galas, Leroy Hood · 2011 · Springer eBooks
73. Computational approaches for disease gene identification
    Peng Yang · 2014
74. The periphery and the core properties explain the omnigenic model in the human interactome
    Bingbo Wang, Kimberly Glass, Annika Röhl, Marc Santolini, Damien C. Croteau‐Chonka, Scott T. Weiss, Benjamin A. Raby, Amitabh Sharma · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
75. Aspects algorithmiques de la comparaison d'éléments biologiques
    Florian Sikora · 2011 · theses.fr (ABES)
76. Thermal Proteome Profiling Reveals Meltome Upon NLRP3 Inflammasome Activation
    Chen Yang, Ling Wang, Yuchen Liu, Yuehui Zhang, Chaozhi Jin, Jiale Cheng, Limin Shang, Longlong Fang, Shanshan Wu, Chuan Chen et al. · 2025 · Molecular & Cellular Proteomics
77. Dissecting the role of bHLH transcription factors in the potato spindle tuber viroid (PSTVd)-tomato pathosystem using network approaches
    Katia Aviña‐Padilla, Octavio Zambada-Moreno, Marco A. Jimenez-Limas, Rosemarie W. Hammond, Maribel Hernández-Rosales · 2025 · PLoS ONE
78. A method for estimating coherence of molecular mechanisms in major human disease and traits
    Mikhail G. Dozmorov, Kellen G. Cresswell, Silviu‐Alin Bacanu, Carl F. Craver, Mark Reimers, Kenneth S. Kendler · 2020 · BMC Bioinformatics
79. Strategy for Modern Research of Traditional Chinese Medicine Formulae
    Shikai Yan, Jing Zhao, Dale G. Nagle, Yudong Zhou, Weidong Zhang · 2018 · Elsevier eBooks
80. Tau Pathology
    Ankush Bansal, Mehul Salaria, Tiratha Raj Singh · 2018 · Advances in medical diagnosis, treatment, and care (AMDTC) book series
81. Prediction of Autism-Related Genes Using a New Clustering-Based Under-Sampling Method
    Xuan Tho Dang, Duong Hung Bui, Thi Hong Nguyen, Tran Quoc Vinh Nguyen, Dang Hung Tran · 2019 · International Conference on Knowledge and Systems Engineering/Proceedings
82. Network-Driven Drug Discovery
    J. Wray, Alan V. Whitmore · 2021 · Methods in molecular biology
83. Structural Aspects of Protein–Protein Interactions
    Krishna Mohan Poluri, Khushboo Gulati, Sharanya Sarkar · 2021 · Springer eBooks
84. Transcriptional progressive patterns from mild to severe renal ischemia/reperfusion-induced kidney injury in mice
    Dong Lai, Lei Wang, Jia-Rui Li, Chen Chen, Wenlei Zhao, Qing Yuan, Xin Ma, Xu Zhang · 2022 · Frontiers in Genetics
85. A systems biology approach towards oral cancer using computational tools and techniques
    Yadav Keerti Kumar, Anil Kumar, Ajay Kumar Singh · 2022 · Chemometrics and Intelligent Laboratory Systems
86. Introduction to Systems Biology
    Nitish Rai, Namita Ashish Singh, Vivek Jain, Preet Jain, Alexander Choi, Saurabh Kumar Sinha · 2024 · Springer eBooks
87. PPI Prediction from Sequences via Transfer Learning on Balanced but yet Biased Datasets: An Open Problem
    Alba Nogueira-Rodríguez, Daniel Glez‐Peña, Cristina P. Vieira, Jorge Vieira, Hugo López-Fernández · 2025 · Lecture notes in networks and systems
88. Transcriptional regulation of the genes involved in protein metabolism and processing inSaccharomyces cerevisiae
    Duygu Dikicioǧlu, Daniel J. H. Nightingale, Valerie Wood, Kathryn Susan Lilley, Stephen G. Oliver · 2019 · FEMS Yeast Research
89. Retinoschisis and Norrie disease: a missing link
    Rahini Rajendran, Dhandayuthapani Sudha, Subbulakshmi Chidambaram, Hemavathy Nagarajan, Umashankar Vetrivel, Jayamuruga Pandian Arunachalam · 2021 · BMC Research Notes
90. A survey of disease connections for CD4+ T cell master genes and their directly linked genes
    Wentian Li, Jesús Espinal Enríquez, Kim R. Simpfendorfer, Enrique Hernandez Lemus · 2015 · Computational Biology and Chemistry
91. Using Biological Networks in Protein Function Prediction and Gene Expression Analysis
    Limsoon Wong · 2011 · Internet Mathematics
92. Bias of Phenotype Similarity Scores between Diseases
    Jing Wang, Xianxiao Zhou, Jing Zhu, Zheng Guo · 2010 · International Conference on Bioinformatics and Biomedical Engineering
93. Evaluating predictive performance of network biomarkers with network structures
    Shang Gao, Ibrahim Karakira, Salim Afra, Ghada Naji, Reda Alhajj, Jia Zeng, Douglas J. Demetrick · 2014 · Journal of Bioinformatics and Computational Biology
94. A seed-based approach to identify risk disease sub-networks in human lung cancer
    Yibin Wang, Yongmei Cheng, Shao‐Wu Zhang, Wei Chen · 2012 · IEEE International Conference on Systems Biology
95. Exploring phenotype-associated modules in an oral cavity tumor using an integrated framework
    Zhirong Sun, Jie Luo, Yun Zhou, Junjie Luo, Ke Liu, Wenting Li · 2009 · Bioinformatics
96. Disrupted pathways associated with neonatal sepsis: Combination of protein-protein interactions and pathway data
    Xin J. Qiao, Silian Zhu, Shujiao Zhang, Hongmei Dong · 2016 · BioChip Journal
97. Module Finding Approaches for Protein Interaction Networks
    Tero A. Aittokallio · 2009 · IGI Global eBooks
98. Pan-interactomics and its applications
    Gyan Prakash Srivastava, Neelam Yadav, Bhupendra Narayan Singh Yadav, Rajiv Kumar Yadav, Dinesh Kumar Yadav · 2020 · Elsevier eBooks
99. Context-Specific Coordinately Regulatory Network Prioritize Breast Cancer Genetic Risk Factors
    Shuyuan Wang, Wencan Wang, Weida Wang, Peng Xia, Lei Yu, Ye Feng Lu, Xiaowen Chen, Chaohan Xu, Hui Liu · 2020 · Frontiers in Genetics
100. Detect the early-warning signals of diseases based on signaling pathway perturbations on a single sample
     Yanhao Huo, Geng Zhao, Luoshan Ruan, Peng Xu, Gang Fang, Fengyue Zhang, Zhenshen Bao, Xin Li · 2022 · BMC Bioinformatics