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For: Snoek LB, Sterken MG, Volkers RJ, Klatter M, Bosman KJ, Bevers RP, Riksen JA, Smant G, Cossins AR, Kammenga JE. A rapid and massive gene expression shift marking adolescent transition in C. elegans. Sci Rep 2014;4:3912. [PMID: 24468752 DOI: 10.1038/srep03912] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 01/13/2014] [Indexed: 11/26/2022]  Open
Number Cited by Other Article(s)
1
Inskeep TR, Groen SC. Network properties constrain natural selection on gene expression in Caenorhabditis elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.19.639144. [PMID: 40060403 PMCID: PMC11888156 DOI: 10.1101/2025.02.19.639144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/17/2025]
2
van Eijnatten AL, Sterken MG, Kammenga JE, Nijveen H, Snoek BL. The effect of developmental variation on expression QTLs in a multi parental Caenorhabditis elegans population. G3 (BETHESDA, MD.) 2024;14:jkad273. [PMID: 38015660 PMCID: PMC10849341 DOI: 10.1093/g3journal/jkad273] [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: 09/21/2023] [Revised: 09/21/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023]
3
Ceron-Noriega A, Almeida MV, Levin M, Butter F. Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis. Genome Res 2023;33:112-128. [PMID: 36653121 PMCID: PMC9977148 DOI: 10.1101/gr.277070.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/18/2022] [Indexed: 01/19/2023]
4
Real age prediction from the transcriptome with RAPToR. Nat Methods 2022;19:969-975. [PMID: 35817937 DOI: 10.1038/s41592-022-01540-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 05/25/2022] [Indexed: 11/08/2022]
5
Inferring biological age from the transcriptome with RAPToR. Nat Methods 2022;19:936-937. [PMID: 35817939 DOI: 10.1038/s41592-022-01542-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
6
van Sluijs L, Bosman KJ, Pankok F, Blokhina T, Wilten JIHA, te Molder DM, Riksen JAG, Snoek BL, Pijlman GP, Kammenga JE, Sterken MG. Balancing Selection of the Intracellular Pathogen Response in Natural Caenorhabditis elegans Populations. Front Cell Infect Microbiol 2022;11:758331. [PMID: 35174100 PMCID: PMC8841876 DOI: 10.3389/fcimb.2021.758331] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/21/2021] [Indexed: 12/17/2022]  Open
7
Snoek BL, Sterken MG, Nijveen H, Volkers RJM, Riksen J, Rosenstiel PC, Schulenburg H, Kammenga JE. The genetics of gene expression in a Caenorhabditis elegans multiparental recombinant inbred line population. G3 (BETHESDA, MD.) 2021;11:jkab258. [PMID: 34568931 PMCID: PMC8496280 DOI: 10.1093/g3journal/jkab258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/17/2021] [Indexed: 11/29/2022]
8
Faerberg DF, Gurarie V, Ruvinsky I. Inferring temporal organization of postembryonic development from high-content behavioral tracking. Dev Biol 2021;475:54-64. [PMID: 33636188 PMCID: PMC8107144 DOI: 10.1016/j.ydbio.2021.02.007] [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: 11/18/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 11/22/2022]
9
Sterken MG, van Wijk MH, Quamme EC, Riksen JAG, Carnell L, Mathies LD, Davies AG, Kammenga JE, Bettinger JC. Transcriptional analysis of the response of C. elegans to ethanol exposure. Sci Rep 2021;11:10993. [PMID: 34040055 PMCID: PMC8155136 DOI: 10.1038/s41598-021-90282-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/07/2021] [Indexed: 11/30/2022]  Open
10
Sterken MG, Bevers RPJ, Volkers RJM, Riksen JAG, Kammenga JE, Snoek BL. Dissecting the eQTL Micro-Architecture in Caenorhabditis elegans. Front Genet 2020;11:501376. [PMID: 33240309 PMCID: PMC7670075 DOI: 10.3389/fgene.2020.501376] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 10/13/2020] [Indexed: 01/11/2023]  Open
11
Snoek BL, Sterken MG, Hartanto M, van Zuilichem AJ, Kammenga JE, de Ridder D, Nijveen H. WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans. Database (Oxford) 2020;2020:baz149. [PMID: 31960906 PMCID: PMC6971878 DOI: 10.1093/database/baz149] [Citation(s) in RCA: 11] [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: 10/14/2019] [Revised: 11/30/2019] [Accepted: 12/13/2019] [Indexed: 12/19/2022]
12
Jovic K, Grilli J, Sterken MG, Snoek BL, Riksen JAG, Allesina S, Kammenga JE. Transcriptome resilience predicts thermotolerance in Caenorhabditis elegans. BMC Biol 2019;17:102. [PMID: 31822273 PMCID: PMC6905072 DOI: 10.1186/s12915-019-0725-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/18/2019] [Indexed: 12/11/2022]  Open
13
Hart MP. Stress-Induced Neuron Remodeling Reveals Differential Interplay Between Neurexin and Environmental Factors in Caenorhabditis elegans. Genetics 2019;213:1415-1430. [PMID: 31558583 PMCID: PMC6893388 DOI: 10.1534/genetics.119.302415] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 09/24/2019] [Indexed: 01/30/2023]  Open
14
Wang YA, Snoek BL, Sterken MG, Riksen JAG, Stastna JJ, Kammenga JE, Harvey SC. Genetic background modifies phenotypic and transcriptional responses in a C. elegans model of α-synuclein toxicity. BMC Genomics 2019;20:232. [PMID: 30894116 PMCID: PMC6427842 DOI: 10.1186/s12864-019-5597-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 03/11/2019] [Indexed: 11/13/2022]  Open
15
Snoek BL, Volkers RJM, Nijveen H, Petersen C, Dirksen P, Sterken MG, Nakad R, Riksen JAG, Rosenstiel P, Stastna JJ, Braeckman BP, Harvey SC, Schulenburg H, Kammenga JE. A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits. BMC Biol 2019;17:24. [PMID: 30866929 PMCID: PMC6417139 DOI: 10.1186/s12915-019-0642-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/26/2019] [Indexed: 01/29/2023]  Open
16
Jovic K, Sterken MG, Grilli J, Bevers RPJ, Rodriguez M, Riksen JAG, Allesina S, Kammenga JE, Snoek LB. Temporal dynamics of gene expression in heat-stressed Caenorhabditis elegans. PLoS One 2017;12:e0189445. [PMID: 29228038 PMCID: PMC5724892 DOI: 10.1371/journal.pone.0189445] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/25/2017] [Indexed: 12/21/2022]  Open
17
Kim B, Suo B, Emmons SW. Gene Function Prediction Based on Developmental Transcriptomes of the Two Sexes in C. elegans. Cell Rep 2017;17:917-928. [PMID: 27732864 PMCID: PMC5656000 DOI: 10.1016/j.celrep.2016.09.051] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 08/03/2016] [Accepted: 09/16/2016] [Indexed: 11/29/2022]  Open
18
Snoek BL, Sterken MG, Bevers RPJ, Volkers RJM, Van't Hof A, Brenchley R, Riksen JAG, Cossins A, Kammenga JE. Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans. BMC Genomics 2017;18:500. [PMID: 28662696 PMCID: PMC5492678 DOI: 10.1186/s12864-017-3899-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/22/2017] [Indexed: 11/10/2022]  Open
19
Variation in gene expression within clones of the earthworm Dendrobaena octaedra. PLoS One 2017;12:e0174960. [PMID: 28384196 PMCID: PMC5383104 DOI: 10.1371/journal.pone.0174960] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 03/19/2017] [Indexed: 12/23/2022]  Open
20
Singh KD, Roschitzki B, Snoek LB, Grossmann J, Zheng X, Elvin M, Kamkina P, Schrimpf SP, Poulin GB, Kammenga JE, Hengartner MO. Natural Genetic Variation Influences Protein Abundances in C. elegans Developmental Signalling Pathways. PLoS One 2016;11:e0149418. [PMID: 26985669 PMCID: PMC4795773 DOI: 10.1371/journal.pone.0149418] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 01/30/2016] [Indexed: 12/11/2022]  Open
21
Kamkina P, Snoek LB, Grossmann J, Volkers RJM, Sterken MG, Daube M, Roschitzki B, Fortes C, Schlapbach R, Roth A, von Mering C, Hengartner MO, Schrimpf SP, Kammenga JE. Natural Genetic Variation Differentially Affects the Proteome and Transcriptome in Caenorhabditis elegans. Mol Cell Proteomics 2016;15:1670-80. [PMID: 26944343 DOI: 10.1074/mcp.m115.052548] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Indexed: 11/06/2022]  Open
22
Roux J, Rosikiewicz M, Robinson-Rechavi M. What to compare and how: Comparative transcriptomics for Evo-Devo. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015;324:372-82. [PMID: 25864439 PMCID: PMC4949521 DOI: 10.1002/jez.b.22618] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/19/2015] [Indexed: 12/30/2022]
23
The laboratory domestication of Caenorhabditis elegans. Trends Genet 2015;31:224-31. [PMID: 25804345 DOI: 10.1016/j.tig.2015.02.009] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 02/19/2015] [Accepted: 02/20/2015] [Indexed: 12/17/2022]
24
Francesconi M, Lehner B. Reconstructing and analysing cellular states, space and time from gene expression profiles of many cells and single cells. MOLECULAR BIOSYSTEMS 2015;11:2690-8. [DOI: 10.1039/c5mb00339c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
25
George-Raizen JB, Shockley KR, Trojanowski NF, Lamb AL, Raizen DM. Dynamically-expressed prion-like proteins form a cuticle in the pharynx of Caenorhabditis elegans. Biol Open 2014;3:1139-49. [PMID: 25361578 PMCID: PMC4232772 DOI: 10.1242/bio.20147500] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
26
Snoek LB, Orbidans HE, Stastna JJ, Aartse A, Rodriguez M, Riksen JAG, Kammenga JE, Harvey SC. Widespread genomic incompatibilities in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2014;4:1813-23. [PMID: 25128438 PMCID: PMC4199689 DOI: 10.1534/g3.114.013151] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/17/2014] [Indexed: 01/18/2023]
27
Loss-of-function of β-catenin bar-1 slows development and activates the Wnt pathway in Caenorhabditis elegans. Sci Rep 2014;4:4926. [PMID: 24819947 PMCID: PMC4019968 DOI: 10.1038/srep04926] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/23/2014] [Indexed: 02/07/2023]  Open
28
Snoek LB, Joeri van der Velde K, Li Y, Jansen RC, Swertz MA, Kammenga JE. Worm variation made accessible: Take your shopping cart to store, link, and investigate! WORM 2014;3:e28357. [PMID: 24843834 PMCID: PMC4024057 DOI: 10.4161/worm.28357] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 02/17/2014] [Accepted: 02/25/2014] [Indexed: 11/20/2022]
29
Sterken MG, Snoek LB, Bosman KJ, Daamen J, Riksen JAG, Bakker J, Pijlman GP, Kammenga JE. A heritable antiviral RNAi response limits Orsay virus infection in Caenorhabditis elegans N2. PLoS One 2014;9:e89760. [PMID: 24587016 PMCID: PMC3933659 DOI: 10.1371/journal.pone.0089760] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 01/23/2014] [Indexed: 11/21/2022]  Open
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