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For: Moore JH, Williams SM. Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesis. Bioessays 2005;27:637-46. [PMID: 15892116 DOI: 10.1002/bies.20236] [Citation(s) in RCA: 214] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Number Cited by Other Article(s)
1
Zuo Y, Pei Y, Li Y, Wen S, Ren X, Li L, Wu Y, Hu Z. The synergism between metabolic and target-site resistance enhances the intensity of resistance to pyrethroids in Spodoptera exigua. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2025;180:104313. [PMID: 40233841 DOI: 10.1016/j.ibmb.2025.104313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2025] [Revised: 03/20/2025] [Accepted: 04/13/2025] [Indexed: 04/17/2025]
2
Li S, Arora S, Attaoua R, Hamet P, Tremblay J, Bihlo A, Liu B, Rutter G. Leveraging hierarchical structures for genetic block interaction studies using the hierarchical transformer. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2024.11.18.24317486. [PMID: 39606365 PMCID: PMC11601704 DOI: 10.1101/2024.11.18.24317486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
3
Sha Z, Freda PJ, Bhandary P, Ghosh A, Matsumoto N, Moore JH, Hu T. Distinct network patterns emerge from Cartesian and XOR epistasis models: a comparative network science analysis. BioData Min 2024;17:61. [PMID: 39732697 DOI: 10.1186/s13040-024-00413-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 12/09/2024] [Indexed: 12/30/2024]  Open
4
Tutaj H, Tomala K, Pirog A, Marszałek M, Korona R. Extreme positive epistasis for fitness in monosomic yeast strains. eLife 2024;12:RP87455. [PMID: 39417696 PMCID: PMC11486488 DOI: 10.7554/elife.87455] [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] [Indexed: 10/19/2024]  Open
5
Freda PJ, Ye S, Zhang R, Moore JH, Urbanowicz RJ. Assessing the limitations of relief-based algorithms in detecting higher-order interactions. BioData Min 2024;17:37. [PMID: 39354639 PMCID: PMC11443793 DOI: 10.1186/s13040-024-00390-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Accepted: 09/04/2024] [Indexed: 10/03/2024]  Open
6
Toral-Rios D, Pichardo-Rojas P, Ruiz-Sánchez E, Rosas-Carrasco Ó, Carvajal-García R, Gálvez-Coutiño DC, Martínez-Rodríguez NL, Rubio-Chávez AD, Alcántara-Flores M, López-Ramírez A, Martínez-Rosas AR, Ruiz-Chow ÁA, Alonso-Vanegas M, Campos-Peña V. Synergistic Effect between the APOE ε4 Allele with Genetic Variants of GSK3B and MAPT: Differential Profile between Refractory Epilepsy and Alzheimer Disease. Int J Mol Sci 2024;25:10228. [PMID: 39337715 PMCID: PMC11432663 DOI: 10.3390/ijms251810228] [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: 08/14/2024] [Revised: 09/13/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024]  Open
7
Jang MJ, Tan LJ, Park MY, Shin S, Kim JM. Identification of interactions between genetic risk scores and dietary patterns for personalized prevention of kidney dysfunction in a population-based cohort. Nutr Diabetes 2024;14:62. [PMID: 39143076 PMCID: PMC11325018 DOI: 10.1038/s41387-024-00316-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 07/09/2024] [Accepted: 07/16/2024] [Indexed: 08/16/2024]  Open
8
Batista S, Madar VS, Freda PJ, Bhandary P, Ghosh A, Matsumoto N, Chitre AS, Palmer AA, Moore JH. Interaction models matter: an efficient, flexible computational framework for model-specific investigation of epistasis. BioData Min 2024;17:7. [PMID: 38419006 PMCID: PMC10900690 DOI: 10.1186/s13040-024-00358-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/20/2024] [Indexed: 03/02/2024]  Open
9
Yang X, Li X, Bao Q, Wang Z, He S, Qu X, Tang Y, Song B, Huang J, Yi G. Uncovering Evolutionary Adaptations in Common Warthogs through Genomic Analyses. Genes (Basel) 2024;15:166. [PMID: 38397156 PMCID: PMC10888464 DOI: 10.3390/genes15020166] [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: 11/20/2023] [Revised: 01/15/2024] [Accepted: 01/20/2024] [Indexed: 02/25/2024]  Open
10
Singhal P, Verma SS, Ritchie MD. Gene Interactions in Human Disease Studies-Evidence Is Mounting. Annu Rev Biomed Data Sci 2023;6:377-395. [PMID: 37196359 DOI: 10.1146/annurev-biodatasci-102022-120818] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
11
Melograna F, Li Z, Galazzo G, van Best N, Mommers M, Penders J, Stella F, Van Steen K. Edge and modular significance assessment in individual-specific networks. Sci Rep 2023;13:7868. [PMID: 37188794 PMCID: PMC10185658 DOI: 10.1038/s41598-023-34759-8] [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: 09/19/2022] [Accepted: 05/07/2023] [Indexed: 05/17/2023]  Open
12
Czaja AJ. Missing Causality and Heritability of Autoimmune Hepatitis. Dig Dis Sci 2023;68:1585-1604. [PMID: 36261672 DOI: 10.1007/s10620-022-07728-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 10/10/2022] [Indexed: 12/09/2022]
13
Learning high-order interactions for polygenic risk prediction. PLoS One 2023;18:e0281618. [PMID: 36763605 PMCID: PMC9916647 DOI: 10.1371/journal.pone.0281618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/27/2023] [Indexed: 02/11/2023]  Open
14
Saha S, Perrin L, Röder L, Brun C, Spinelli L. Epi-MEIF: detecting higher order epistatic interactions for complex traits using mixed effect conditional inference forests. Nucleic Acids Res 2022;50:e114. [PMID: 36107776 PMCID: PMC9639209 DOI: 10.1093/nar/gkac715] [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: 04/06/2022] [Revised: 07/29/2022] [Accepted: 09/12/2022] [Indexed: 12/04/2022]  Open
15
Brandes N, Weissbrod O, Linial M. Open problems in human trait genetics. Genome Biol 2022;23:131. [PMID: 35725481 PMCID: PMC9208223 DOI: 10.1186/s13059-022-02697-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 05/30/2022] [Indexed: 12/21/2022]  Open
16
D'Silva S, Chakraborty S, Kahali B. Concurrent outcomes from multiple approaches of epistasis analysis for human body mass index associated loci provide insights into obesity biology. Sci Rep 2022;12:7306. [PMID: 35508500 PMCID: PMC9068779 DOI: 10.1038/s41598-022-11270-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 04/18/2022] [Indexed: 12/13/2022]  Open
17
Slim L, Chatelain C, Foucauld HD, Azencott CA. A systematic analysis of gene-gene interaction in multiple sclerosis. BMC Med Genomics 2022;15:100. [PMID: 35501860 PMCID: PMC9063218 DOI: 10.1186/s12920-022-01247-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/28/2022] [Indexed: 12/03/2022]  Open
18
Maculewicz E, Antkowiak B, Antkowiak O, Borecka A, Mastalerz A, Leońska-Duniec A, Humińska-Lisowska K, Michałowska-Sawczyn M, Garbacz A, Lorenz K, Szarska E, Dziuda Ł, Cywińska A, Cięszczyk P. The interactions between interleukin-1 family genes: IL1A, IL1B, IL1RN, and obesity parameters. BMC Genomics 2022;23:112. [PMID: 35139823 PMCID: PMC8830010 DOI: 10.1186/s12864-021-08258-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 12/14/2021] [Indexed: 12/23/2022]  Open
19
Duroux D, Climente-González H, Azencott CA, Van Steen K. Interpretable network-guided epistasis detection. Gigascience 2022;11:giab093. [PMID: 35134928 PMCID: PMC8848319 DOI: 10.1093/gigascience/giab093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 10/12/2021] [Accepted: 12/13/2021] [Indexed: 11/15/2022]  Open
20
Walakira A, Ocira J, Duroux D, Fouladi R, Moškon M, Rozman D, Van Steen K. Detecting gene-gene interactions from GWAS using diffusion kernel principal components. BMC Bioinformatics 2022;23:57. [PMID: 35105309 PMCID: PMC8805268 DOI: 10.1186/s12859-022-04580-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/18/2022] [Indexed: 11/10/2022]  Open
21
Frankel S, Rogina B. Evolution, Chance, and Aging. Front Genet 2021;12:733184. [PMID: 34567083 PMCID: PMC8458753 DOI: 10.3389/fgene.2021.733184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/13/2021] [Indexed: 12/15/2022]  Open
22
Liu D, Ban HJ, El Sergani AM, Lee MK, Hecht JT, Wehby GL, Moreno LM, Feingold E, Marazita ML, Cha S, Szabo-Rogers HL, Weinberg SM, Shaffer JR. PRICKLE1 × FOCAD Interaction Revealed by Genome-Wide vQTL Analysis of Human Facial Traits. Front Genet 2021;12:674642. [PMID: 34434215 PMCID: PMC8381734 DOI: 10.3389/fgene.2021.674642] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022]  Open
23
Odenkirk MT, Reif DM, Baker ES. Multiomic Big Data Analysis Challenges: Increasing Confidence in the Interpretation of Artificial Intelligence Assessments. Anal Chem 2021;93:7763-7773. [PMID: 34029068 PMCID: PMC8465926 DOI: 10.1021/acs.analchem.0c04850] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
24
Bruger EL, Chubiz LM, Rojas Echenique JI, Renshaw CJ, Espericueta NV, Draghi JA, Marx CJ. Genetic Context Significantly Influences the Maintenance and Evolution of Degenerate Pathways. Genome Biol Evol 2021;13:6245841. [PMID: 33885815 PMCID: PMC8214414 DOI: 10.1093/gbe/evab082] [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] [Accepted: 04/19/2021] [Indexed: 11/16/2022]  Open
25
Sheppard B, Rappoport N, Loh PR, Sanders SJ, Zaitlen N, Dahl A. A model and test for coordinated polygenic epistasis in complex traits. Proc Natl Acad Sci U S A 2021;118:e1922305118. [PMID: 33833052 PMCID: PMC8053945 DOI: 10.1073/pnas.1922305118] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
26
Orlenko A, Moore JH. A comparison of methods for interpreting random forest models of genetic association in the presence of non-additive interactions. BioData Min 2021;14:9. [PMID: 33514397 PMCID: PMC7847145 DOI: 10.1186/s13040-021-00243-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 01/13/2021] [Indexed: 01/19/2023]  Open
27
Taha K, Davuluri R, Yoo P, Spencer J. Personizing the prediction of future susceptibility to a specific disease. PLoS One 2021;16:e0243127. [PMID: 33406077 PMCID: PMC7787538 DOI: 10.1371/journal.pone.0243127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/17/2020] [Indexed: 01/22/2023]  Open
28
Aristodimou A, Antoniades A, Dardiotis E, Loizidou E, Spyrou G, Votsi C, Kyproula C, Pantzaris M, Grigoriadis N, Hadjigeorgiou G, Kyriakides T, Pattichi C. A Framework for Efficient N-Way Interaction Testing in Case/Control Studies With Categorical Data. IEEE OPEN JOURNAL OF ENGINEERING IN MEDICINE AND BIOLOGY 2021;2:256-262. [PMID: 35402966 PMCID: PMC8901013 DOI: 10.1109/ojemb.2021.3100416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 07/08/2021] [Accepted: 07/22/2021] [Indexed: 11/26/2022]  Open
29
Sierksma A, Lu A, Mancuso R, Fattorelli N, Thrupp N, Salta E, Zoco J, Blum D, Buée L, De Strooper B, Fiers M. Novel Alzheimer risk genes determine the microglia response to amyloid-β but not to TAU pathology. EMBO Mol Med 2020;12:e10606. [PMID: 31951107 PMCID: PMC7059012 DOI: 10.15252/emmm.201910606] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 12/20/2022]  Open
30
Rahit KMTH, Tarailo-Graovac M. Genetic Modifiers and Rare Mendelian Disease. Genes (Basel) 2020;11:E239. [PMID: 32106447 PMCID: PMC7140819 DOI: 10.3390/genes11030239] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 02/21/2020] [Indexed: 12/11/2022]  Open
31
Moore JH, Olson RS, Schmitt P, Chen Y, Manduchi E. How Computational Experiments Can Improve Our Understanding of the Genetic Architecture of Common Human Diseases. ARTIFICIAL LIFE 2020;26:23-37. [PMID: 32027528 DOI: 10.1162/artl_a_00308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
32
Sio YY, Matta SA, Ng YT, Chew FT. Epistasis between phenylethanolamine N-methyltransferase and β2-adrenergic receptor influences extracellular epinephrine level and associates with the susceptibility to allergic asthma. Clin Exp Allergy 2020;50:352-363. [PMID: 31855300 DOI: 10.1111/cea.13552] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 12/03/2019] [Accepted: 12/08/2019] [Indexed: 12/14/2022]
33
Selecting Closely-Linked SNPs Based on Local Epistatic Effects for Haplotype Construction Improves Power of Association Mapping. G3-GENES GENOMES GENETICS 2019;9:4115-4126. [PMID: 31604824 PMCID: PMC6893203 DOI: 10.1534/g3.119.400451] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
34
Chattopadhyay A, Lu TP. Gene-gene interaction: the curse of dimensionality. ANNALS OF TRANSLATIONAL MEDICINE 2019;7:813. [PMID: 32042829 DOI: 10.21037/atm.2019.12.87] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
35
Cao X, Yu G, Ren W, Guo M, Wang J. DualWMDR: Detecting epistatic interaction with dual screening and multifactor dimensionality reduction. Hum Mutat 2019;41:719-734. [DOI: 10.1002/humu.23951] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 09/10/2019] [Accepted: 11/07/2019] [Indexed: 12/14/2022]
36
Alzoubi D, Desouki AA, Lercher MJ. Flux balance analysis with or without molecular crowding fails to predict two thirds of experimentally observed epistasis in yeast. Sci Rep 2019;9:11837. [PMID: 31413270 PMCID: PMC6694147 DOI: 10.1038/s41598-019-47935-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 07/08/2019] [Indexed: 12/15/2022]  Open
37
Joiret M, Mahachie John JM, Gusareva ES, Van Steen K. Confounding of linkage disequilibrium patterns in large scale DNA based gene-gene interaction studies. BioData Min 2019;12:11. [PMID: 31198442 PMCID: PMC6558841 DOI: 10.1186/s13040-019-0199-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/09/2019] [Indexed: 01/07/2023]  Open
38
Hill GE, Havird JC, Sloan DB, Burton RS, Greening C, Dowling DK. Assessing the fitness consequences of mitonuclear interactions in natural populations. Biol Rev Camb Philos Soc 2019;94:1089-1104. [PMID: 30588726 PMCID: PMC6613652 DOI: 10.1111/brv.12493] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022]
39
Van Steen K, Moore JH. How to increase our belief in discovered statistical interactions via large-scale association studies? Hum Genet 2019;138:293-305. [PMID: 30840129 PMCID: PMC6483943 DOI: 10.1007/s00439-019-01987-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 02/20/2019] [Indexed: 12/31/2022]
40
Hou TT, Lin F, Bai S, Cleves MA, Xu HM, Lou XY. Generalized multifactor dimensionality reduction approaches to identification of genetic interactions underlying ordinal traits. Genet Epidemiol 2018;43:24-36. [PMID: 30387901 DOI: 10.1002/gepi.22169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/31/2018] [Accepted: 09/21/2018] [Indexed: 12/11/2022]
41
Campbell RF, McGrath PT, Paaby AB. Analysis of Epistasis in Natural Traits Using Model Organisms. Trends Genet 2018;34:883-898. [PMID: 30166071 PMCID: PMC6541385 DOI: 10.1016/j.tig.2018.08.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 06/06/2018] [Accepted: 08/03/2018] [Indexed: 12/16/2022]
42
Urbanowicz RJ, Olson RS, Schmitt P, Meeker M, Moore JH. Benchmarking relief-based feature selection methods for bioinformatics data mining. J Biomed Inform 2018;85:168-188. [PMID: 30030120 PMCID: PMC6299838 DOI: 10.1016/j.jbi.2018.07.015] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 06/30/2018] [Accepted: 07/14/2018] [Indexed: 11/23/2022]
43
Manduchi E, Williams SM, Chesi A, Johnson ME, Wells AD, Grant SFA, Moore JH. Leveraging epigenomics and contactomics data to investigate SNP pairs in GWAS. Hum Genet 2018;137:413-425. [PMID: 29797095 PMCID: PMC5996751 DOI: 10.1007/s00439-018-1893-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/20/2018] [Indexed: 12/29/2022]
44
Sharbrough J, Havird JC, Noe GR, Warren JM, Sloan DB. The Mitonuclear Dimension of Neanderthal and Denisovan Ancestry in Modern Human Genomes. Genome Biol Evol 2018;9:1567-1581. [PMID: 28854627 PMCID: PMC5509035 DOI: 10.1093/gbe/evx114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2017] [Indexed: 12/15/2022]  Open
45
Fang L, Tang BS, Fan K, Wan CM, Yan XX, Guo JF. Alzheimer's disease susceptibility genes modify the risk of Parkinson disease and Parkinson's disease-associated cognitive impairment. Neurosci Lett 2018;677:55-59. [PMID: 29698690 DOI: 10.1016/j.neulet.2018.04.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 04/19/2018] [Accepted: 04/22/2018] [Indexed: 12/16/2022]
46
Piette ER, Moore JH. Improving machine learning reproducibility in genetic association studies with proportional instance cross validation (PICV). BioData Min 2018;11:6. [PMID: 29713384 PMCID: PMC5907739 DOI: 10.1186/s13040-018-0167-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 04/03/2018] [Indexed: 11/10/2022]  Open
47
Ritchie MD, Van Steen K. The search for gene-gene interactions in genome-wide association studies: challenges in abundance of methods, practical considerations, and biological interpretation. ANNALS OF TRANSLATIONAL MEDICINE 2018;6:157. [PMID: 29862246 DOI: 10.21037/atm.2018.04.05] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
48
Uppu S, Krishna A, Gopalan RP. A Review on Methods for Detecting SNP Interactions in High-Dimensional Genomic Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018;15:599-612. [PMID: 28060710 DOI: 10.1109/tcbb.2016.2635125] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
49
Cole BS, Hall MA, Urbanowicz RJ, Gilbert‐Diamond D, Moore JH. Analysis of Gene‐Gene Interactions. ACTA ACUST UNITED AC 2018;95:1.14.1-1.14.10. [DOI: 10.1002/cphg.45] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
50
Verma SS, Ritchie MD. Another Round of "Clue" to Uncover the Mystery of Complex Traits. Genes (Basel) 2018;9:E61. [PMID: 29370075 PMCID: PMC5852557 DOI: 10.3390/genes9020061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/19/2017] [Accepted: 01/15/2018] [Indexed: 12/13/2022]  Open
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