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For: Li HD, Menon R, Omenn GS, Guan Y. The emerging era of genomic data integration for analyzing splice isoform function. Trends Genet 2014;30:340-7. [PMID: 24951248 DOI: 10.1016/j.tig.2014.05.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/21/2014] [Accepted: 05/23/2014] [Indexed: 01/17/2023]
Number Cited by Other Article(s)
1
Abulfaraj AA, Alshareef SA. Concordant Gene Expression and Alternative Splicing Regulation under Abiotic Stresses in Arabidopsis. Genes (Basel) 2024;15:675. [PMID: 38927612 PMCID: PMC11202685 DOI: 10.3390/genes15060675] [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: 04/16/2024] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024]  Open
2
Lin CY, Zhang YM, Li BZ, Shu MA, Xu WB. Identification and characterization of mitogen-activated protein kinase kinase 4 (MKK4) from the mud crab Scylla paramamosain in response to Vibrio alginolyticus and White Spot Syndrome Virus (WSSV). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023;147:104755. [PMID: 37295629 DOI: 10.1016/j.dci.2023.104755] [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: 03/07/2023] [Revised: 06/03/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
3
Mann JT, Riley BA, Baker SF. All differential on the splicing front: Host alternative splicing alters the landscape of virus-host conflict. Semin Cell Dev Biol 2023;146:40-56. [PMID: 36737258 DOI: 10.1016/j.semcdb.2023.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
4
Liu Y, Li HD, Xu Y, Liu YW, Peng X, Wang J. IsoCell: An Approach to Enhance Single Cell Clustering by Integrating Isoform-Level Expression Through Orthogonal Projection. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:465-475. [PMID: 35100120 DOI: 10.1109/tcbb.2022.3147193] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
5
Raina P, Guinea R, Chatsirisupachai K, Lopes I, Farooq Z, Guinea C, Solyom CA, de Magalhães JP. GeneFriends: gene co-expression databases and tools for humans and model organisms. Nucleic Acids Res 2022;51:D145-D158. [PMID: 36454018 PMCID: PMC9825523 DOI: 10.1093/nar/gkac1031] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 12/05/2022]  Open
6
Castaldi PJ, Abood A, Farber CR, Sheynkman GM. Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease. Hum Mol Genet 2022;31:R123-R136. [PMID: 35960994 PMCID: PMC9585682 DOI: 10.1093/hmg/ddac196] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 02/04/2023]  Open
7
Qiu S, Yu G, Lu X, Domeniconi C, Guo M. Isoform function prediction by Gene Ontology embedding. Bioinformatics 2022;38:4581-4588. [PMID: 35997558 DOI: 10.1093/bioinformatics/btac576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/13/2022] [Accepted: 08/22/2022] [Indexed: 12/24/2022]  Open
8
Yu G, Huang Q, Zhang X, Guo M, Wang J. Tissue Specificity Based Isoform Function Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:3048-3059. [PMID: 34185647 DOI: 10.1109/tcbb.2021.3093167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
9
Dominant transcript expression profiles of human protein-coding genes interrogated with GTEx dataset. Sci Rep 2022;12:6969. [PMID: 35484179 PMCID: PMC9050722 DOI: 10.1038/s41598-022-10619-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 04/11/2022] [Indexed: 12/27/2022]  Open
10
Li H, Eksi R, Yi D, Godfrey B, Mathew LR, O’Connor CL, Bitzer M, Kretzler M, Menon R, Guan Y. Micro-dissection and integration of long and short reads to create a robust catalog of kidney compartment-specific isoforms. PLoS Comput Biol 2022;18:e1010040. [PMID: 35468141 PMCID: PMC9037928 DOI: 10.1371/journal.pcbi.1010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 03/19/2022] [Indexed: 11/19/2022]  Open
11
Lin CX, Li HD, Deng C, Liu W, Erhardt S, Wu FX, Zhao XM, Guan Y, Wang J, Wang D, Hu B, Wang J. An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer’s disease. Brief Bioinform 2021;23:6483067. [DOI: 10.1093/bib/bbab522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/26/2021] [Accepted: 11/13/2021] [Indexed: 11/12/2022]  Open
12
Yu G, Zhou G, Zhang X, Domeniconi C, Guo M. DMIL-IsoFun: predicting isoform function using deep multi-instance learning. Bioinformatics 2021;37:4818-4825. [PMID: 34282449 DOI: 10.1093/bioinformatics/btab532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/20/2021] [Accepted: 07/16/2021] [Indexed: 11/14/2022]  Open
13
Li HD, Xu Y, Zhu X, Liu Q, Omenn GS, Wang J. ClusterMine: A knowledge-integrated clustering approach based on expression profiles of gene sets. J Bioinform Comput Biol 2021;18:2040009. [PMID: 32698720 DOI: 10.1142/s0219720020400090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
14
Li H, Funk CC, McFarland K, Dammer EB, Allen M, Carrasquillo MM, Levites Y, Chakrabarty P, Burgess JD, Wang X, Dickson D, Seyfried NT, Duong DM, Lah JJ, Younkin SG, Levey AI, Omenn GS, Ertekin‐Taner N, Golde TE, Price ND. Integrative functional genomic analysis of intron retention in human and mouse brain with Alzheimer's disease. Alzheimers Dement 2021;17:984-1004. [PMID: 33480174 PMCID: PMC8248162 DOI: 10.1002/alz.12254] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 10/08/2020] [Accepted: 10/17/2020] [Indexed: 12/21/2022]
15
McDougall LI, Powell RM, Ratajska M, Lynch-Sutherland CF, Hossain SM, Wiggins GAR, Harazin-Lechowska A, Cybulska-Stopa B, Motwani J, Macaulay EC, Reid G, Walker LC, Ryś J, Eccles MR. Differential Expression of BARD1 Isoforms in Melanoma. Genes (Basel) 2021;12:320. [PMID: 33672422 PMCID: PMC7927127 DOI: 10.3390/genes12020320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/12/2021] [Accepted: 02/20/2021] [Indexed: 12/11/2022]  Open
16
Tung KF, Pan CY, Chen CH, Lin WC. Top-ranked expressed gene transcripts of human protein-coding genes investigated with GTEx dataset. Sci Rep 2020;10:16245. [PMID: 33004865 PMCID: PMC7530651 DOI: 10.1038/s41598-020-73081-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]  Open
17
Ping L, Kundinger SR, Duong DM, Yin L, Gearing M, Lah JJ, Levey AI, Seyfried NT. Global quantitative analysis of the human brain proteome and phosphoproteome in Alzheimer's disease. Sci Data 2020;7:315. [PMID: 32985496 PMCID: PMC7522715 DOI: 10.1038/s41597-020-00650-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/18/2020] [Indexed: 12/27/2022]  Open
18
Khan AH, Lin A, Wang RT, Bloom JS, Lange K, Smith DJ. Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells. Genome Res 2020;30:1458-1467. [PMID: 32878976 PMCID: PMC7605260 DOI: 10.1101/gr.262204.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022]
19
Yu G, Wang K, Domeniconi C, Guo M, Wang J. Isoform function prediction based on bi-random walks on a heterogeneous network. Bioinformatics 2020;36:303-310. [PMID: 31250882 DOI: 10.1093/bioinformatics/btz535] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 06/21/2019] [Accepted: 06/26/2019] [Indexed: 01/29/2023]  Open
20
Sulakhe D, D'Souza M, Wang S, Balasubramanian S, Athri P, Xie B, Canzar S, Agam G, Gilliam TC, Maltsev N. Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. Brief Bioinform 2020;20:1754-1768. [PMID: 29931155 DOI: 10.1093/bib/bby047] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/02/2018] [Indexed: 12/30/2022]  Open
21
Zhao Y, Wang J, Chen J, Zhang X, Guo M, Yu G. A Literature Review of Gene Function Prediction by Modeling Gene Ontology. Front Genet 2020;11:400. [PMID: 32391061 PMCID: PMC7193026 DOI: 10.3389/fgene.2020.00400] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/30/2020] [Indexed: 12/14/2022]  Open
22
Isoform-Disease Association Prediction by Data Fusion. BIOINFORMATICS RESEARCH AND APPLICATIONS 2020. [DOI: 10.1007/978-3-030-57821-3_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
23
Kandoi G, Dickerson JA. Tissue-specific mouse mRNA isoform networks. Sci Rep 2019;9:13949. [PMID: 31562339 PMCID: PMC6765046 DOI: 10.1038/s41598-019-50119-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/05/2019] [Indexed: 02/06/2023]  Open
24
Tang Z, Chen T, Ren X, Zhang Z. Identification of transcriptional isoforms associated with survival in cancer patient. J Genet Genomics 2019;46:413-421. [PMID: 31630971 DOI: 10.1016/j.jgg.2019.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 08/04/2019] [Accepted: 08/21/2019] [Indexed: 11/26/2022]
25
Chen H, Shaw D, Zeng J, Bu D, Jiang T. DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning. Bioinformatics 2019;35:i284-i294. [PMID: 31510699 PMCID: PMC6612874 DOI: 10.1093/bioinformatics/btz367] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]  Open
26
Pacini C, Koziol MJ. Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing. Philos Trans R Soc Lond B Biol Sci 2019;373:rstb.2017.0073. [PMID: 29685977 PMCID: PMC5915717 DOI: 10.1098/rstb.2017.0073] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2017] [Indexed: 02/07/2023]  Open
27
Pandeswari PB, Sabareesh V. Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry. RSC Adv 2018;9:313-344. [PMID: 35521579 PMCID: PMC9059502 DOI: 10.1039/c8ra07200k] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/11/2018] [Indexed: 12/27/2022]  Open
28
Ashraf U, Benoit-Pilven C, Lacroix V, Navratil V, Naffakh N. Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing. Trends Microbiol 2018;27:268-281. [PMID: 30577974 DOI: 10.1016/j.tim.2018.11.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/19/2018] [Accepted: 11/09/2018] [Indexed: 12/14/2022]
29
Zhang X, Yu S, Yang Q, Wang K, Zhang S, Pan C, Yan H, Dang R, Lei C, Chen H, Lan X. Goat Boule: Isoforms identification, mRNA expression in testis and functional study and promoter methylation profiles. Theriogenology 2018;116:53-63. [PMID: 29778921 DOI: 10.1016/j.theriogenology.2018.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 05/03/2018] [Accepted: 05/04/2018] [Indexed: 10/16/2022]
30
Yu KH, Lee TLM, Wang CS, Chen YJ, Ré C, Kou SC, Chiang JH, Kohane IS, Snyder M. Systematic Protein Prioritization for Targeted Proteomics Studies through Literature Mining. J Proteome Res 2018;17:1383-1396. [PMID: 29505266 DOI: 10.1021/acs.jproteome.7b00772] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
31
Jyotsana N, Heuser M. Exploiting differential RNA splicing patterns: a potential new group of therapeutic targets in cancer. Expert Opin Ther Targets 2017;22:107-121. [PMID: 29235382 DOI: 10.1080/14728222.2018.1417390] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
32
Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism. Proc Natl Acad Sci U S A 2017;114:E9740-E9749. [PMID: 29078384 DOI: 10.1073/pnas.1713050114] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
33
Yang S, Shao F, Duan W, Zhao Y, Chen F. Variance component testing for identifying differentially expressed genes in RNA-seq data. PeerJ 2017;5:e3797. [PMID: 28929020 PMCID: PMC5592911 DOI: 10.7717/peerj.3797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/21/2017] [Indexed: 01/28/2023]  Open
34
Yu G, Fu G, Lu C, Ren Y, Wang J. BRWLDA: bi-random walks for predicting lncRNA-disease associations. Oncotarget 2017;8:60429-60446. [PMID: 28947982 PMCID: PMC5601150 DOI: 10.18632/oncotarget.19588] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 06/19/2017] [Indexed: 12/20/2022]  Open
35
Pantazatos SP, Huang YY, Rosoklija GB, Dwork AJ, Arango V, Mann JJ. Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity. Mol Psychiatry 2017;22:760-773. [PMID: 27528462 PMCID: PMC5313378 DOI: 10.1038/mp.2016.130] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/04/2016] [Accepted: 06/07/2016] [Indexed: 12/30/2022]
36
Tranchevent LC, Aubé F, Dulaurier L, Benoit-Pilven C, Rey A, Poret A, Chautard E, Mortada H, Desmet FO, Chakrama FZ, Moreno-Garcia MA, Goillot E, Janczarski S, Mortreux F, Bourgeois CF, Auboeuf D. Identification of protein features encoded by alternative exons using Exon Ontology. Genome Res 2017;27:1087-1097. [PMID: 28420690 PMCID: PMC5453322 DOI: 10.1101/gr.212696.116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 03/28/2017] [Indexed: 12/16/2022]
37
Transcriptome profile of the human placenta. Funct Integr Genomics 2017;17:551-563. [PMID: 28251419 PMCID: PMC5561170 DOI: 10.1007/s10142-017-0555-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/09/2017] [Accepted: 02/16/2017] [Indexed: 01/09/2023]
38
Guerrero CR, Jagtap PD, Johnson JE, Griffin TJ. Using Galaxy for Proteomics. PROTEOME INFORMATICS 2016. [DOI: 10.1039/9781782626732-00289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
39
Yu W, Li Y, Wang Z, Liu L, Liu J, Ding F, Zhang X, Cheng Z, Chen P, Dou J. Transcriptomic changes in human renal proximal tubular cells revealed under hypoxic conditions by RNA sequencing. Int J Mol Med 2016;38:894-902. [PMID: 27432315 DOI: 10.3892/ijmm.2016.2677] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 07/07/2016] [Indexed: 11/05/2022]  Open
40
Panwar B, Menon R, Eksi R, Li HD, Omenn GS, Guan Y. Genome-Wide Functional Annotation of Human Protein-Coding Splice Variants Using Multiple Instance Learning. J Proteome Res 2016;15:1747-53. [PMID: 27142340 DOI: 10.1021/acs.jproteome.5b00883] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
41
Guan Y, Martini S, Mariani LH. Genes Caught In Flagranti: Integrating Renal Transcriptional Profiles With Genotypes and Phenotypes. Semin Nephrol 2016. [PMID: 26215861 DOI: 10.1016/j.semnephrol.2015.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
42
A Network of Splice Isoforms for the Mouse. Sci Rep 2016;6:24507. [PMID: 27079421 PMCID: PMC4832266 DOI: 10.1038/srep24507] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/30/2016] [Indexed: 01/08/2023]  Open
43
Hsu MK, Pan CL, Chen FC. Functional divergence and convergence between the transcript network and gene network in lung adenocarcinoma. Onco Targets Ther 2016;9:335-47. [PMID: 26834492 PMCID: PMC4716766 DOI: 10.2147/ott.s94897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]  Open
44
Li HD, Omenn GS, Guan Y. A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling. Brief Bioinform 2016;17:1024-1031. [PMID: 26740460 DOI: 10.1093/bib/bbv109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/03/2015] [Indexed: 01/23/2023]  Open
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Schweizer RM, Robinson J, Harrigan R, Silva P, Galverni M, Musiani M, Green RE, Novembre J, Wayne RK. Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves. Mol Ecol 2015;25:357-79. [DOI: 10.1111/mec.13467] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 11/04/2015] [Accepted: 11/06/2015] [Indexed: 12/29/2022]
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Zhao S, Xi L, Zhang B. Union Exon Based Approach for RNA-Seq Gene Quantification: To Be or Not to Be? PLoS One 2015;10:e0141910. [PMID: 26559532 PMCID: PMC4641603 DOI: 10.1371/journal.pone.0141910] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/14/2015] [Indexed: 11/24/2022]  Open
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AlFadhli S, Ghanem AAM, Nizam R. Genome-wide peripheral blood transcriptome analysis of Arab female lupus and lupus nephritis. Gene 2015;570:230-8. [PMID: 26072163 DOI: 10.1016/j.gene.2015.06.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/16/2015] [Accepted: 06/07/2015] [Indexed: 01/11/2023]
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Li HD, Menon R, Govindarajoo B, Panwar B, Zhang Y, Omenn GS, Guan Y. Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project. J Proteome Res 2015. [PMID: 26216192 DOI: 10.1021/acs.jproteome.5b00494] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Panwar B, Menon R, Eksi R, Omenn GS, Guan Y. MI-PVT: A Tool for Visualizing the Chromosome-Centric Human Proteome. J Proteome Res 2015. [PMID: 26204236 DOI: 10.1021/acs.jproteome.5b00525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Menon R, Panwar B, Eksi R, Kleer C, Guan Y, Omenn GS. Computational Inferences of the Functions of Alternative/Noncanonical Splice Isoforms Specific to HER2+/ER-/PR- Breast Cancers, a Chromosome 17 C-HPP Study. J Proteome Res 2015;14:3519-29. [PMID: 26147891 DOI: 10.1021/acs.jproteome.5b00498] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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