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For: van Hilten A, Kushner SA, Kayser M, Ikram MA, Adams HHH, Klaver CCW, Niessen WJ, Roshchupkin GV. GenNet framework: interpretable deep learning for predicting phenotypes from genetic data. Commun Biol 2021;4:1094. [PMID: 34535759 DOI: 10.1038/s42003-021-02622-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 08/26/2021] [Indexed: 12/31/2022]  Open
Number Cited by Other Article(s)
1
Shokor F, Croiseau P, Gangloff H, Saintilan R, Tribout T, Mary-Huard T, Cuyabano BCD. Deep learning and genomic best linear unbiased prediction integration: An approach to identify potential nonlinear genetic relationships between traits. J Dairy Sci 2025;108:6174-6189. [PMID: 40252763 DOI: 10.3168/jds.2024-26057] [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: 11/21/2024] [Accepted: 03/24/2025] [Indexed: 04/21/2025]
2
Hu G, Zhou T, Zhou P, Yau SST. Novel natural vector with asymmetric covariance for classifying biological sequences. Gene 2025;962:149532. [PMID: 40367998 DOI: 10.1016/j.gene.2025.149532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2025] [Revised: 04/07/2025] [Accepted: 04/23/2025] [Indexed: 05/16/2025]
3
Zavorskas J, Edwards H, Marten MR, Harris S, Srivastava R. Generalizable Metamaterials Design Techniques Inspire Efficient Mycelial Materials Inverse Design. ACS Biomater Sci Eng 2025;11:1897-1920. [PMID: 39898596 DOI: 10.1021/acsbiomaterials.4c01986] [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] [Indexed: 02/04/2025]
4
Lee I, Wallace ZS, Wang Y, Park S, Nam H, Majithia AR, Ideker T. A genotype-phenotype transformer to assess and explain polygenic risk. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.10.23.619940. [PMID: 40291728 PMCID: PMC12026415 DOI: 10.1101/2024.10.23.619940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2025]
5
Zheng W, Ma W, Chen Z, Wang C, Sun T, Dong W, Zhang W, Zhang S, Tang Z, Li K, Zhao Y, Liu Y. DPImpute: A Genotype Imputation Framework for Ultra-Low Coverage Whole-Genome Sequencing and its Application in Genomic Selection. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025;12:e2412482. [PMID: 40013759 PMCID: PMC12021046 DOI: 10.1002/advs.202412482] [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: 10/07/2024] [Revised: 02/05/2025] [Indexed: 02/28/2025]
6
Thapa K, Kinali M, Pei S, Luna A, Babur Ö. Strategies to include prior knowledge in omics analysis with deep neural networks. PATTERNS (NEW YORK, N.Y.) 2025;6:101203. [PMID: 40182174 PMCID: PMC11963003 DOI: 10.1016/j.patter.2025.101203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/05/2025]
7
Xi X, Li J, Jia J, Meng Q, Li C, Wang X, Wei L, Zhang X. A mechanism-informed deep neural network enables prioritization of regulators that drive cell state transitions. Nat Commun 2025;16:1284. [PMID: 39900922 PMCID: PMC11790924 DOI: 10.1038/s41467-025-56475-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Accepted: 01/15/2025] [Indexed: 02/05/2025]  Open
8
Gromiha MM, Pandey M, Kulandaisamy A, Sharma D, Ridha F. Progress on the development of prediction tools for detecting disease causing mutations in proteins. Comput Biol Med 2025;185:109510. [PMID: 39637461 DOI: 10.1016/j.compbiomed.2024.109510] [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: 07/13/2024] [Revised: 11/27/2024] [Accepted: 11/29/2024] [Indexed: 12/07/2024]
9
Zeng R, Li Z, Li J, Zhang Q. DNA promoter task-oriented dictionary mining and prediction model based on natural language technology. Sci Rep 2025;15:153. [PMID: 39747934 PMCID: PMC11697570 DOI: 10.1038/s41598-024-84105-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2024] [Accepted: 12/19/2024] [Indexed: 01/04/2025]  Open
10
Arab A, Kashani B, Cordova-Delgado M, Scott EN, Alemi K, Trueman J, Groeneweg G, Chang WC, Loucks CM, Ross CJD, Carleton BC, Ester M. Machine learning model identifies genetic predictors of cisplatin-induced ototoxicity in CERS6 and TLR4. Comput Biol Med 2024;183:109324. [PMID: 39488053 DOI: 10.1016/j.compbiomed.2024.109324] [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: 04/30/2024] [Revised: 10/20/2024] [Accepted: 10/22/2024] [Indexed: 11/04/2024]
11
Ghose U, Sproviero W, Winchester L, Amin N, Zhu T, Newby D, Ulm BS, Papathanasiou A, Shi L, Liu Q, Fernandes M, Adams C, Albukhari A, Almansouri M, Choudhry H, van Duijn C, Nevado-Holgado A. Genome-wide association neural networks identify genes linked to family history of Alzheimer's disease. Brief Bioinform 2024;26:bbae704. [PMID: 39775791 PMCID: PMC11707606 DOI: 10.1093/bib/bbae704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Revised: 11/29/2024] [Accepted: 12/23/2024] [Indexed: 01/11/2025]  Open
12
Islam UI, Campelo dos Santos AL, Kanjilal R, Assis R. Learning genotype-phenotype associations from gaps in multi-species sequence alignments. Brief Bioinform 2024;26:bbaf022. [PMID: 39976386 PMCID: PMC11840556 DOI: 10.1093/bib/bbaf022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 12/16/2024] [Accepted: 01/08/2025] [Indexed: 02/21/2025]  Open
13
He R, Fu J, Ren J, Pan W. Trait imputation enhances nonlinear genetic prediction for some traits. Genetics 2024;228:iyae148. [PMID: 39255064 PMCID: PMC12098936 DOI: 10.1093/genetics/iyae148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 08/29/2024] [Accepted: 09/03/2024] [Indexed: 09/12/2024]  Open
14
Jo Y, Webster MJ, Kim S, Lee D. Interpretation of SNP combination effects on schizophrenia etiology based on stepwise deep learning with multi-precision data. Brief Funct Genomics 2024;23:663-671. [PMID: 37738675 PMCID: PMC11428150 DOI: 10.1093/bfgp/elad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 07/17/2023] [Accepted: 08/22/2023] [Indexed: 09/24/2023]  Open
15
Xie Z, Weng L, He J, Feng X, Xu X, Ma Y, Bai P, Kong Q. PNNGS, a multi-convolutional parallel neural network for genomic selection. FRONTIERS IN PLANT SCIENCE 2024;15:1410596. [PMID: 39290743 PMCID: PMC11405342 DOI: 10.3389/fpls.2024.1410596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 08/19/2024] [Indexed: 09/19/2024]
16
van Hilten A, van Rooij J, Ikram MA, Niessen WJ, van Meurs JBJ, Roshchupkin GV. Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data. NPJ Syst Biol Appl 2024;10:81. [PMID: 39095438 PMCID: PMC11297229 DOI: 10.1038/s41540-024-00405-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 07/12/2024] [Indexed: 08/04/2024]  Open
17
van Hilten A, Katz S, Saccenti E, Niessen WJ, Roshchupkin GV. Designing interpretable deep learning applications for functional genomics: a quantitative analysis. Brief Bioinform 2024;25:bbae449. [PMID: 39293804 PMCID: PMC11410376 DOI: 10.1093/bib/bbae449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 08/07/2024] [Accepted: 08/28/2024] [Indexed: 09/20/2024]  Open
18
Ding X, Zhang L, Fan M, Li L. TME-NET: an interpretable deep neural network for predicting pan-cancer immune checkpoint inhibitor responses. Brief Bioinform 2024;25:bbae410. [PMID: 39167797 PMCID: PMC11337220 DOI: 10.1093/bib/bbae410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/17/2024] [Accepted: 08/02/2024] [Indexed: 08/23/2024]  Open
19
Wang X, Li F, Zhang Y, Imoto S, Shen HH, Li S, Guo Y, Yang J, Song J. Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects. Brief Bioinform 2024;25:bbae446. [PMID: 39276327 PMCID: PMC11401448 DOI: 10.1093/bib/bbae446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 08/08/2024] [Accepted: 08/27/2024] [Indexed: 09/16/2024]  Open
20
Martins D, Abbasi M, Egas C, Arrais JP. Detecting outliers in case-control cohorts for improving deep learning networks on Schizophrenia prediction. J Integr Bioinform 2024;21:jib-2023-0042. [PMID: 39004922 PMCID: PMC11377398 DOI: 10.1515/jib-2023-0042] [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: 10/18/2023] [Accepted: 06/06/2024] [Indexed: 07/16/2024]  Open
21
Huang X, Rymbekova A, Dolgova O, Lao O, Kuhlwilm M. Harnessing deep learning for population genetic inference. Nat Rev Genet 2024;25:61-78. [PMID: 37666948 DOI: 10.1038/s41576-023-00636-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2023] [Indexed: 09/06/2023]
22
Sigala RE, Lagou V, Shmeliov A, Atito S, Kouchaki S, Awais M, Prokopenko I, Mahdi A, Demirkan A. Machine Learning to Advance Human Genome-Wide Association Studies. Genes (Basel) 2023;15:34. [PMID: 38254924 PMCID: PMC10815885 DOI: 10.3390/genes15010034] [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: 11/16/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024]  Open
23
Chen SF, Loguercio S, Chen KY, Lee SE, Park JB, Liu S, Sadaei HJ, Torkamani A. Artificial Intelligence for Risk Assessment on Primary Prevention of Coronary Artery Disease. CURRENT CARDIOVASCULAR RISK REPORTS 2023;17:215-231. [DOI: 10.1007/s12170-023-00731-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2023] [Indexed: 01/04/2025]
24
Wang Q, Zhang J, Liu Z, Duan Y, Li C. Integrative approaches based on genomic techniques in the functional studies on enhancers. Brief Bioinform 2023;25:bbad442. [PMID: 38048082 PMCID: PMC10694556 DOI: 10.1093/bib/bbad442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/22/2023] [Accepted: 11/08/2023] [Indexed: 12/05/2023]  Open
25
Li P, Wei J, Zhu Y. CellGO: a novel deep learning-based framework and webserver for cell-type-specific gene function interpretation. Brief Bioinform 2023;25:bbad417. [PMID: 37995133 PMCID: PMC10790717 DOI: 10.1093/bib/bbad417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/09/2023] [Accepted: 10/29/2023] [Indexed: 11/25/2023]  Open
26
Kaynar G, Cakmakci D, Bund C, Todeschi J, Namer IJ, Cicek AE. PiDeeL: metabolic pathway-informed deep learning model for survival analysis and pathological classification of gliomas. Bioinformatics 2023;39:btad684. [PMID: 37952175 PMCID: PMC10663986 DOI: 10.1093/bioinformatics/btad684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/19/2023] [Accepted: 11/10/2023] [Indexed: 11/14/2023]  Open
27
Esser-Skala W, Fortelny N. Reliable interpretability of biology-inspired deep neural networks. NPJ Syst Biol Appl 2023;9:50. [PMID: 37816807 PMCID: PMC10564878 DOI: 10.1038/s41540-023-00310-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/15/2023] [Indexed: 10/12/2023]  Open
28
Verplaetse N, Passemiers A, Arany A, Moreau Y, Raimondi D. Large sample size and nonlinear sparse models outline epistatic effects in inflammatory bowel disease. Genome Biol 2023;24:224. [PMID: 37798735 PMCID: PMC10552306 DOI: 10.1186/s13059-023-03064-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023]  Open
29
Balnis J, Lauria EJM, Yucel R, Singer HA, Alisch RS, Jaitovich A. Peripheral Blood Omics and Other Multiplex-based Systems in Pulmonary and Critical Care Medicine. Am J Respir Cell Mol Biol 2023;69:383-390. [PMID: 37379507 PMCID: PMC10557924 DOI: 10.1165/rcmb.2023-0153ps] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/28/2023] [Indexed: 06/30/2023]  Open
30
Cheng KP, Shen WX, Jiang YY, Chen Y, Chen YZ, Tan Y. Deep learning of 2D-Restructured gene expression representations for improved low-sample therapeutic response prediction. Comput Biol Med 2023;164:107245. [PMID: 37480677 DOI: 10.1016/j.compbiomed.2023.107245] [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: 04/26/2023] [Revised: 06/27/2023] [Accepted: 07/07/2023] [Indexed: 07/24/2023]
31
Ghosh Roy G, Geard N, Verspoor K, He S. MPVNN: Mutated Pathway Visible Neural Network architecture for interpretable prediction of cancer-specific survival risk. Bioinformatics 2022;38:5026-5032. [PMID: 36124954 DOI: 10.1093/bioinformatics/btac636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 08/04/2022] [Accepted: 09/16/2022] [Indexed: 12/24/2022]  Open
32
Baratta AM, Brandner AJ, Plasil SL, Rice RC, Farris SP. Advancements in Genomic and Behavioral Neuroscience Analysis for the Study of Normal and Pathological Brain Function. Front Mol Neurosci 2022;15:905328. [PMID: 35813067 PMCID: PMC9259865 DOI: 10.3389/fnmol.2022.905328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022]  Open
33
Divate M, Tyagi A, Richard DJ, Prasad PA, Gowda H, Nagaraj SH. Deep Learning-Based Pan-Cancer Classification Model Reveals Tissue-of-Origin Specific Gene Expression Signatures. Cancers (Basel) 2022;14:cancers14051185. [PMID: 35267493 PMCID: PMC8909043 DOI: 10.3390/cancers14051185] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/03/2022] [Accepted: 02/17/2022] [Indexed: 12/24/2022]  Open
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