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For: Yu K, Lung PY, Zhao T, Zhao P, Tseng YY, Zhang J. Automatic extraction of protein-protein interactions using grammatical relationship graph. BMC Med Inform Decis Mak 2018;18:42. [PMID: 30066644 PMCID: PMC6069288 DOI: 10.1186/s12911-018-0628-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]  Open
Number Cited by Other Article(s)
1
Zhang Y, Sui X, Pan F, Yu K, Li K, Tian S, Erdengasileng A, Han Q, Wang W, Wang J, Wang J, Sun D, Chung H, Zhou J, Zhou E, Lee B, Zhang P, Qiu X, Zhao T, Zhang J. A comprehensive large scale biomedical knowledge graph for AI powered data driven biomedical research. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2023.10.13.562216. [PMID: 38168218 PMCID: PMC10760044 DOI: 10.1101/2023.10.13.562216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
2
Li J, Zhang H, Wang J, Deng M, Li Z, Jiang W, Xu K, Wu L, Dong Z, Liu J, Ding Q, Yu H. Development and Validation of an AI-Driven System for Automatic Literature Analysis and Molecular Regulatory Network Construction. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2405395. [PMID: 39373342 PMCID: PMC11600262 DOI: 10.1002/advs.202405395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 09/06/2024] [Indexed: 10/08/2024]
3
Rehana H, Çam NB, Basmaci M, Zheng J, Jemiyo C, He Y, Özgür A, Hur J. Evaluating GPT and BERT models for protein-protein interaction identification in biomedical text. BIOINFORMATICS ADVANCES 2024;4:vbae133. [PMID: 39319026 PMCID: PMC11419952 DOI: 10.1093/bioadv/vbae133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 08/16/2024] [Accepted: 09/09/2024] [Indexed: 09/26/2024]
4
Cai J, Han R, Li J, Hao J, Zhao Z, Jing D. Exploring mechanobiology network of bone and dental tissue based on Natural Language Processing. J Biomech 2024;174:112271. [PMID: 39159585 DOI: 10.1016/j.jbiomech.2024.112271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 07/04/2024] [Accepted: 08/08/2024] [Indexed: 08/21/2024]
5
Jadhav A, Kumar T, Raghavendra M, Loganathan T, Narayanan M. Predicting cross-tissue hormone-gene relations using balanced word embeddings. Bioinformatics 2022;38:4771-4781. [PMID: 36000859 PMCID: PMC9563690 DOI: 10.1093/bioinformatics/btac578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 07/29/2022] [Accepted: 08/23/2022] [Indexed: 11/12/2022]  Open
6
Le TD, Nguyen PD, Korkin D, Thieu T. PHILM2Web: A high-throughput database of macromolecular host–pathogen interactions on the Web. Database (Oxford) 2022;2022:6625823. [PMID: 35776535 PMCID: PMC9248916 DOI: 10.1093/database/baac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 04/27/2022] [Accepted: 05/31/2022] [Indexed: 12/02/2022]
7
Sharma VS, Fossati A, Ciuffa R, Buljan M, Williams EG, Chen Z, Shao W, Pedrioli PGA, Purcell AW, Martínez MR, Song J, Manica M, Aebersold R, Li C. PCfun: a hybrid computational framework for systematic characterization of protein complex function. Brief Bioinform 2022;23:6611913. [PMID: 35724564 PMCID: PMC9310514 DOI: 10.1093/bib/bbac239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/05/2022] [Accepted: 05/21/2022] [Indexed: 11/14/2022]  Open
8
Lou P, Dong Y, Jimeno Yepes A, Li C. A representation model for biological entities by fusing structured axioms with unstructured texts. Bioinformatics 2021;37:1156-1163. [PMID: 33107905 DOI: 10.1093/bioinformatics/btaa913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/04/2020] [Accepted: 10/13/2020] [Indexed: 11/14/2022]  Open
9
Badal VD, Kundrotas PJ, Vakser IA. Text mining for modeling of protein complexes enhanced by machine learning. Bioinformatics 2021;37:497-505. [PMID: 32960948 PMCID: PMC8088328 DOI: 10.1093/bioinformatics/btaa823] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 11/14/2022]  Open
10
Zhao S, Su C, Lu Z, Wang F. Recent advances in biomedical literature mining. Brief Bioinform 2021;22:bbaa057. [PMID: 32422651 PMCID: PMC8138828 DOI: 10.1093/bib/bbaa057] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/22/2020] [Accepted: 03/25/2020] [Indexed: 01/26/2023]  Open
11
Azer K, Kaddi CD, Barrett JS, Bai JPF, McQuade ST, Merrill NJ, Piccoli B, Neves-Zaph S, Marchetti L, Lombardo R, Parolo S, Immanuel SRC, Baliga NS. History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications. Front Physiol 2021;12:637999. [PMID: 33841175 PMCID: PMC8027332 DOI: 10.3389/fphys.2021.637999] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/25/2021] [Indexed: 12/24/2022]  Open
12
Qu J, Steppi A, Zhong D, Hao J, Wang J, Lung PY, Zhao T, He Z, Zhang J. Triage of documents containing protein interactions affected by mutations using an NLP based machine learning approach. BMC Genomics 2020;21:773. [PMID: 33167858 PMCID: PMC7654050 DOI: 10.1186/s12864-020-07185-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 10/26/2020] [Indexed: 11/17/2022]  Open
13
Deng Z, Yin K, Bao Y, Armengol VD, Wang C, Tiwari A, Barzilay R, Parmigiani G, Braun D, Hughes KS. Validation of a Semiautomated Natural Language Processing-Based Procedure for Meta-Analysis of Cancer Susceptibility Gene Penetrance. JCO Clin Cancer Inform 2020;3:1-9. [PMID: 31419182 DOI: 10.1200/cci.19.00043] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
14
A novel machine learning framework for automated biomedical relation extraction from large-scale literature repositories. NAT MACH INTELL 2020. [DOI: 10.1038/s42256-020-0189-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
15
Poverennaya EV, Kiseleva OI, Ivanov AS, Ponomarenko EA. Methods of Computational Interactomics for Investigating Interactions of Human Proteoforms. BIOCHEMISTRY (MOSCOW) 2020;85:68-79. [PMID: 32079518 DOI: 10.1134/s000629792001006x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
16
Lou P, Jimeno Yepes A, Zhang Z, Zheng Q, Zhang X, Li C. BioNorm: deep learning-based event normalization for the curation of reaction databases. Bioinformatics 2020;36:611-620. [PMID: 31350561 DOI: 10.1093/bioinformatics/btz571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/27/2019] [Accepted: 07/19/2019] [Indexed: 11/13/2022]  Open
17
Extracellular Matrix Networks: From Connections to Functions. EXTRACELLULAR MATRIX OMICS 2020. [DOI: 10.1007/978-3-030-58330-9_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
18
Caufield JH, Ping P. New advances in extracting and learning from protein-protein interactions within unstructured biomedical text data. Emerg Top Life Sci 2019;3:357-369. [PMID: 33523203 DOI: 10.1042/etls20190003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/11/2019] [Accepted: 07/16/2019] [Indexed: 12/14/2022]
19
Lung PY, He Z, Zhao T, Yu D, Zhang J. Extracting chemical-protein interactions from literature using sentence structure analysis and feature engineering. Database (Oxford) 2019;2019:5280305. [PMID: 30624652 PMCID: PMC6323317 DOI: 10.1093/database/bay138] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 12/04/2018] [Accepted: 12/06/2018] [Indexed: 12/14/2022]
20
He Z, Tao C, Bian J, Zhang R, Huang J. Introduction: selected extended articles from the 2nd International Workshop on Semantics-Powered Data Analytics (SEPDA 2017). BMC Med Inform Decis Mak 2018;18:56. [PMID: 30066636 PMCID: PMC6069756 DOI: 10.1186/s12911-018-0624-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
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