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For: Monlong J, Calvo M, Ferreira PG, Guigó R. Identification of genetic variants associated with alternative splicing using sQTLseekeR. Nat Commun 2014;5:4698. [PMID: 25140736 DOI: 10.1038/ncomms5698] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 07/11/2014] [Indexed: 02/05/2023]  Open
Number Cited by Other Article(s)
1
Kaminska D. Alternative Splicing Regulation in Metabolic Disorders. Obes Rev 2025:e13950. [PMID: 40425033 DOI: 10.1111/obr.13950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 03/20/2025] [Accepted: 05/08/2025] [Indexed: 05/29/2025]
2
Humphrey J, Brophy E, Kosoy R, Zeng B, Coccia E, Mattei D, Ravi A, Naito T, Efthymiou AG, Navarro E, De Sanctis C, Flores-Almazan V, Muller BZ, Snijders GJLJ, Allan A, Münch A, Kitata RB, Kleopoulos SP, Argyriou S, Malakates P, Psychogyiou K, Shao Z, Francoeur N, Tsai CF, Gritsenko MA, Monroe ME, Paurus VL, Weitz KK, Shi T, Sebra R, Liu T, de Witte LD, Goate AM, Bennett DA, Haroutunian V, Hoffman GE, Fullard JF, Roussos P, Raj T. Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing. Nat Genet 2025;57:604-615. [PMID: 40033057 DOI: 10.1038/s41588-025-02099-0] [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: 09/13/2023] [Accepted: 01/23/2025] [Indexed: 03/05/2025]
3
Xavier JM, Magno R, Russell R, de Almeida BP, Jacinta-Fernandes A, Besouro-Duarte A, Dunning M, Samarajiwa S, O'Reilly M, Maia AM, Rocha CL, Rosli N, Ponder BAJ, Maia AT. Identification of candidate causal variants and target genes at 41 breast cancer risk loci through differential allelic expression analysis. Sci Rep 2024;14:22526. [PMID: 39341862 PMCID: PMC11438911 DOI: 10.1038/s41598-024-72163-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: 02/01/2024] [Accepted: 09/04/2024] [Indexed: 10/01/2024]  Open
4
Einson J, Minaeva M, Rafi F, Lappalainen T. The impact of genetically controlled splicing on exon inclusion and protein structure. PLoS One 2024;19:e0291960. [PMID: 38478511 PMCID: PMC10936842 DOI: 10.1371/journal.pone.0291960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 09/08/2023] [Indexed: 03/17/2024]  Open
5
Baker MR, Lee AS, Rajadhyaksha AM. L-type calcium channels and neuropsychiatric diseases: Insights into genetic risk variant-associated genomic regulation and impact on brain development. Channels (Austin) 2023;17:2176984. [PMID: 36803254 PMCID: PMC9980663 DOI: 10.1080/19336950.2023.2176984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/01/2023] [Indexed: 02/21/2023]  Open
6
Humphrey J, Brophy E, Kosoy R, Zeng B, Coccia E, Mattei D, Ravi A, Efthymiou AG, Navarro E, Muller BZ, Snijders GJLJ, Allan A, Münch A, Kitata RB, Kleopoulos SP, Argyriou S, Shao Z, Francoeur N, Tsai CF, Gritsenko MA, Monroe ME, Paurus VL, Weitz KK, Shi T, Sebra R, Liu T, de Witte LD, Goate AM, Bennett DA, Haroutunian V, Hoffman GE, Fullard JF, Roussos P, Raj T. Long-read RNA-seq atlas of novel microglia isoforms elucidates disease-associated genetic regulation of splicing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.01.23299073. [PMID: 38076956 PMCID: PMC10705658 DOI: 10.1101/2023.12.01.23299073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
7
Garrido-Martín D, Calvo M, Reverter F, Guigó R. A fast non-parametric test of association for multiple traits. Genome Biol 2023;24:230. [PMID: 37828616 PMCID: PMC10571397 DOI: 10.1186/s13059-023-03076-8] [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: 04/25/2022] [Accepted: 09/27/2023] [Indexed: 10/14/2023]  Open
8
Pan L, Zheng C, Yang Z, Pawitan Y, Vu TN, Shen X. Hidden Genetic Regulation of Human Complex Traits via Brain Isoforms. PHENOMICS (CHAM, SWITZERLAND) 2023;3:217-227. [PMID: 37325708 PMCID: PMC10260721 DOI: 10.1007/s43657-023-00100-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 06/17/2023]
9
Cotto KC, Feng YY, Ramu A, Richters M, Freshour SL, Skidmore ZL, Xia H, McMichael JF, Kunisaki J, Campbell KM, Chen THP, Rozycki EB, Adkins D, Devarakonda S, Sankararaman S, Lin Y, Chapman WC, Maher CA, Arora V, Dunn GP, Uppaluri R, Govindan R, Griffith OL, Griffith M. Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer. Nat Commun 2023;14:1589. [PMID: 36949070 PMCID: PMC10033906 DOI: 10.1038/s41467-023-37266-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/08/2023] [Indexed: 03/24/2023]  Open
10
Deshpande D, Chhugani K, Chang Y, Karlsberg A, Loeffler C, Zhang J, Muszyńska A, Munteanu V, Yang H, Rotman J, Tao L, Balliu B, Tseng E, Eskin E, Zhao F, Mohammadi P, P. Łabaj P, Mangul S. RNA-seq data science: From raw data to effective interpretation. Front Genet 2023;14:997383. [PMID: 36999049 PMCID: PMC10043755 DOI: 10.3389/fgene.2023.997383] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 02/24/2023] [Indexed: 03/14/2023]  Open
11
Ogiya D, Chyra Z, Verselis SJ, O'Keefe M, Cobb J, Abiatari I, Talluri S, Sithara AA, Hideshima T, Chu MP, Hájek R, Dorfman DM, Pilarski LM, Anderson KC, Adamia S. Identification of disease-related aberrantly spliced transcripts in myeloma and strategies to target these alterations by RNA-based therapeutics. Blood Cancer J 2023;13:23. [PMID: 36737429 PMCID: PMC9898564 DOI: 10.1038/s41408-023-00791-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 12/17/2022] [Accepted: 01/12/2023] [Indexed: 02/05/2023]  Open
12
de Menezes RX, Rauschenberger A, 't Hoen PAC, Jonker MA. A powerful global test for spliceQTL effects. Biom J 2023;65:e2100123. [PMID: 35818126 DOI: 10.1002/bimj.202100123] [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: 04/21/2021] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 01/17/2023]
13
Identification of Candidate mRNA Isoforms for Prostate Cancer-Risk SNPs Utilizing Iso-eQTL and sQTL Methods. Int J Mol Sci 2022;23:ijms232012406. [PMID: 36293264 PMCID: PMC9604153 DOI: 10.3390/ijms232012406] [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: 08/13/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 11/17/2022]  Open
14
Zhou YH, Gallins PJ, Etheridge AS, Jima D, Scholl E, Wright FA, Innocenti F. A resource for integrated genomic analysis of the human liver. Sci Rep 2022;12:15151. [PMID: 36071064 PMCID: PMC9452507 DOI: 10.1038/s41598-022-18506-z] [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: 07/27/2021] [Accepted: 08/08/2022] [Indexed: 11/18/2022]  Open
15
Splicing QTL analysis focusing on coding sequences reveals mechanisms for disease susceptibility loci. Nat Commun 2022;13:4659. [PMID: 36002455 PMCID: PMC9402578 DOI: 10.1038/s41467-022-32358-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 07/26/2022] [Indexed: 12/26/2022]  Open
16
Genetic control of RNA splicing and its distinct role in complex trait variation. Nat Genet 2022;54:1355-1363. [PMID: 35982161 PMCID: PMC9470536 DOI: 10.1038/s41588-022-01154-4] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/08/2022] [Indexed: 12/11/2022]
17
Wright CJ, Smith CWJ, Jiggins CD. Alternative splicing as a source of phenotypic diversity. Nat Rev Genet 2022;23:697-710. [PMID: 35821097 DOI: 10.1038/s41576-022-00514-4] [Citation(s) in RCA: 190] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2022] [Indexed: 12/27/2022]
18
Yang W, Liu H, Zhang R, Freedman JA, Han Y, Hung RJ, Brhane Y, McLaughlin J, Brennan P, Bickeboeller H, Rosenberger A, Houlston RS, Caporaso NE, Landi MT, Brueske I, Risch A, Christiani DC, Amos CI, Chen X, Patierno SR, Wei Q. Deciphering associations between three RNA splicing-related genetic variants and lung cancer risk. NPJ Precis Oncol 2022;6:48. [PMID: 35773316 PMCID: PMC9247007 DOI: 10.1038/s41698-022-00281-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 05/20/2022] [Indexed: 01/12/2023]  Open
19
Tian Y, Soupir A, Liu Q, Wu L, Huang CC, Park JY, Wang L. Novel role of prostate cancer risk variant rs7247241 on PPP1R14A isoform transition through allelic TF binding and CpG methylation. Hum Mol Genet 2022;31:1610-1621. [PMID: 34849858 PMCID: PMC9122641 DOI: 10.1093/hmg/ddab347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/21/2022]  Open
20
Deyssenroth MA, Peng S, Hao K, Marsit CJ, Chen J. Placental Gene Transcript Proportions are Altered in the Presence of In Utero Arsenic and Cadmium Exposures, Genetic Variants, and Birth Weight Differences. Front Genet 2022;13:865449. [PMID: 35646058 PMCID: PMC9136297 DOI: 10.3389/fgene.2022.865449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/07/2022] [Indexed: 11/26/2022]  Open
21
Flynn E, Lappalainen T. Functional Characterization of Genetic Variant Effects on Expression. Annu Rev Biomed Data Sci 2022;5:119-139. [PMID: 35483347 DOI: 10.1146/annurev-biodatasci-122120-010010] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
22
Brotman SM, Raulerson CK, Vadlamudi S, Currin KW, Shen Q, Parsons VA, Iyengar AK, Roman TS, Furey TS, Kuusisto J, Collins FS, Boehnke M, Laakso M, Pajukanta P, Mohlke KL. Subcutaneous adipose tissue splice quantitative trait loci reveal differences in isoform usage associated with cardiometabolic traits. Am J Hum Genet 2022;109:66-80. [PMID: 34995504 PMCID: PMC8764203 DOI: 10.1016/j.ajhg.2021.11.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/23/2021] [Indexed: 01/13/2023]  Open
23
Clark KC, Kwitek AE. Multi-Omic Approaches to Identify Genetic Factors in Metabolic Syndrome. Compr Physiol 2021;12:3045-3084. [PMID: 34964118 PMCID: PMC9373910 DOI: 10.1002/cphy.c210010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
24
Dankó B, Szikora P, Pór T, Szeifert A, Sebestyén E. SplicingFactory-splicing diversity analysis for transcriptome data. Bioinformatics 2021;38:384-390. [PMID: 34499147 PMCID: PMC8722757 DOI: 10.1093/bioinformatics/btab648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/31/2021] [Accepted: 09/06/2021] [Indexed: 02/03/2023]  Open
25
Aygün N, Elwell AL, Liang D, Lafferty MJ, Cheek KE, Courtney KP, Mory J, Hadden-Ford E, Krupa O, de la Torre-Ubieta L, Geschwind DH, Love MI, Stein JL. Brain-trait-associated variants impact cell-type-specific gene regulation during neurogenesis. Am J Hum Genet 2021;108:1647-1668. [PMID: 34416157 PMCID: PMC8456186 DOI: 10.1016/j.ajhg.2021.07.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 07/23/2021] [Indexed: 12/21/2022]  Open
26
Yang Y, Paul A, Bach TN, Huang ZJ, Zhang MQ. Single-cell alternative polyadenylation analysis delineates GABAergic neuron types. BMC Biol 2021;19:144. [PMID: 34301239 PMCID: PMC8299648 DOI: 10.1186/s12915-021-01076-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 06/17/2021] [Indexed: 01/10/2023]  Open
27
Deep transcriptome sequencing of subgenual anterior cingulate cortex reveals cross-diagnostic and diagnosis-specific RNA expression changes in major psychiatric disorders. Neuropsychopharmacology 2021;46:1364-1372. [PMID: 33558674 PMCID: PMC8134494 DOI: 10.1038/s41386-020-00949-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 01/29/2023]
28
Dent CI, Singh S, Mukherjee S, Mishra S, Sarwade RD, Shamaya N, Loo KP, Harrison P, Sureshkumar S, Powell D, Balasubramanian S. Quantifying splice-site usage: a simple yet powerful approach to analyze splicing. NAR Genom Bioinform 2021;3:lqab041. [PMID: 34017946 PMCID: PMC8121094 DOI: 10.1093/nargab/lqab041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/24/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023]  Open
29
Wang K, Basu M, Malin J, Hannenhalli S. A transcription-centric model of SNP-age interaction. PLoS Genet 2021;17:e1009427. [PMID: 33770080 PMCID: PMC7997000 DOI: 10.1371/journal.pgen.1009427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 02/16/2021] [Indexed: 12/23/2022]  Open
30
Garrido-Martín D, Borsari B, Calvo M, Reverter F, Guigó R. Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome. Nat Commun 2021;12:727. [PMID: 33526779 PMCID: PMC7851174 DOI: 10.1038/s41467-020-20578-2] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022]  Open
31
Li Y, Wang D, Wang H, Huang X, Wen Y, Wang B, Xu C, Gao J, Liu J, Tong J, Wang M, Su P, Ren S, Ma F, Li H, Bresnick EH, Zhou J, Shi L. A splicing factor switch controls hematopoietic lineage specification of pluripotent stem cells. EMBO Rep 2021;22:e50535. [PMID: 33319461 PMCID: PMC7788460 DOI: 10.15252/embr.202050535] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 10/26/2020] [Accepted: 11/12/2020] [Indexed: 11/09/2022]  Open
32
Calonga‐Solís V, Amorim LM, Farias TDJ, Petzl‐Erler ML, Malheiros D, Augusto DG. Variation in genes implicated in B-cell development and antibody production affects susceptibility to pemphigus. Immunology 2021;162:58-67. [PMID: 32926429 PMCID: PMC7730027 DOI: 10.1111/imm.13259] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/23/2020] [Accepted: 08/29/2020] [Indexed: 12/12/2022]  Open
33
Population-scale genetic control of alternative polyadenylation and its association with human diseases. QUANTITATIVE BIOLOGY 2021. [DOI: 10.15302/j-qb-021-0252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
34
Demirdjian L, Xu Y, Bahrami-Samani E, Pan Y, Stein S, Xie Z, Park E, Wu YN, Xing Y. Detecting Allele-Specific Alternative Splicing from Population-Scale RNA-Seq Data. Am J Hum Genet 2020;107:461-472. [PMID: 32781045 PMCID: PMC7477012 DOI: 10.1016/j.ajhg.2020.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 07/10/2020] [Indexed: 12/20/2022]  Open
35
Thom CS, Voight BF. Genetic colocalization atlas points to common regulatory sites and genes for hematopoietic traits and hematopoietic contributions to disease phenotypes. BMC Med Genomics 2020;13:89. [PMID: 32600345 PMCID: PMC7325014 DOI: 10.1186/s12920-020-00742-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/17/2020] [Indexed: 02/08/2023]  Open
36
Cano-Gamez E, Trynka G. From GWAS to Function: Using Functional Genomics to Identify the Mechanisms Underlying Complex Diseases. Front Genet 2020;11:424. [PMID: 32477401 PMCID: PMC7237642 DOI: 10.3389/fgene.2020.00424] [Citation(s) in RCA: 338] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 04/06/2020] [Indexed: 12/19/2022]  Open
37
Bou Sleiman M, Frochaux MV, Andreani T, Osman D, Guigo R, Deplancke B. Enteric infection induces Lark-mediated intron retention at the 5' end of Drosophila genes. Genome Biol 2020;21:4. [PMID: 31948480 PMCID: PMC6966827 DOI: 10.1186/s13059-019-1918-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 12/09/2019] [Indexed: 01/15/2023]  Open
38
Balliu B, Durrant M, Goede OD, Abell N, Li X, Liu B, Gloudemans MJ, Cook NL, Smith KS, Knowles DA, Pala M, Cucca F, Schlessinger D, Jaiswal S, Sabatti C, Lind L, Ingelsson E, Montgomery SB. Genetic regulation of gene expression and splicing during a 10-year period of human aging. Genome Biol 2019;20:230. [PMID: 31684996 PMCID: PMC6827221 DOI: 10.1186/s13059-019-1840-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022]  Open
39
Khokhar W, Hassan MA, Reddy ASN, Chaudhary S, Jabre I, Byrne LJ, Syed NH. Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2019;10:1160. [PMID: 31632417 PMCID: PMC6785726 DOI: 10.3389/fpls.2019.01160] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/26/2019] [Indexed: 05/27/2023]
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Reble E, Feng Y, Wigg KG, Barr CL. DNA Variant in the RPGRIP1L Gene Influences Alternative Splicing. MOLECULAR NEUROPSYCHIATRY 2019;5:97-106. [PMID: 32399473 DOI: 10.1159/000502199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 06/18/2019] [Indexed: 12/22/2022]
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Vandiedonck C. Genetic association of molecular traits: A help to identify causative variants in complex diseases. Clin Genet 2019;93:520-532. [PMID: 29194587 DOI: 10.1111/cge.13187] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/14/2022]
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Hu Y, Lin J, Hu J, Hu G, Wang K, Zhang H, Reilly MP, Li M. PennDiff: detecting differential alternative splicing and transcription by RNA sequencing. Bioinformatics 2019;34:2384-2391. [PMID: 29474557 DOI: 10.1093/bioinformatics/bty097] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 02/20/2018] [Indexed: 11/13/2022]  Open
43
Mariella E, Marotta F, Grassi E, Gilotto S, Provero P. The Length of the Expressed 3' UTR Is an Intermediate Molecular Phenotype Linking Genetic Variants to Complex Diseases. Front Genet 2019;10:714. [PMID: 31475030 PMCID: PMC6707137 DOI: 10.3389/fgene.2019.00714] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/05/2019] [Indexed: 11/13/2022]  Open
44
Buchberger E, Reis M, Lu TH, Posnien N. Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary Studies. Genes (Basel) 2019;10:E492. [PMID: 31261769 PMCID: PMC6678813 DOI: 10.3390/genes10070492] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/20/2019] [Accepted: 06/26/2019] [Indexed: 12/20/2022]  Open
45
Wang X, Yang M, Ren D, Terzaghi W, Deng XW, He G. Cis-regulated alternative splicing divergence and its potential contribution to environmental responses in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019;97:555-570. [PMID: 30375060 DOI: 10.1111/tpj.14142] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/19/2018] [Accepted: 10/23/2018] [Indexed: 05/14/2023]
46
Understanding human DNA variants affecting pre-mRNA splicing in the NGS era. ADVANCES IN GENETICS 2019;103:39-90. [PMID: 30904096 DOI: 10.1016/bs.adgen.2018.09.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
47
Ebrahimi D, Richards CM, Carpenter MA, Wang J, Ikeda T, Becker JT, Cheng AZ, McCann JL, Shaban NM, Salamango DJ, Starrett GJ, Lingappa JR, Yong J, Brown WL, Harris RS. Genetic and mechanistic basis for APOBEC3H alternative splicing, retrovirus restriction, and counteraction by HIV-1 protease. Nat Commun 2018;9:4137. [PMID: 30297863 PMCID: PMC6175962 DOI: 10.1038/s41467-018-06594-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/13/2018] [Indexed: 12/11/2022]  Open
48
Wan Y, Larson DR. Splicing heterogeneity: separating signal from noise. Genome Biol 2018;19:86. [PMID: 29986741 PMCID: PMC6036703 DOI: 10.1186/s13059-018-1467-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
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Chen Q, Han Y, Liu H, Wang X, Sun J, Zhao B, Li W, Tian J, Liang Y, Yan J, Yang X, Tian F. Genome-Wide Association Analyses Reveal the Importance of Alternative Splicing in Diversifying Gene Function and Regulating Phenotypic Variation in Maize. THE PLANT CELL 2018;30:1404-1423. [PMID: 29967286 PMCID: PMC6096592 DOI: 10.1105/tpc.18.00109] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/23/2018] [Accepted: 06/27/2018] [Indexed: 05/22/2023]
50
Li Y, McGrail DJ, Xu J, Mills GB, Sahni N, Yi S. Gene Regulatory Network Perturbation by Genetic and Epigenetic Variation. Trends Biochem Sci 2018;43:576-592. [PMID: 29941230 DOI: 10.1016/j.tibs.2018.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 04/25/2018] [Accepted: 05/27/2018] [Indexed: 01/28/2023]
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