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A meta-analysis of caloric restriction gene expression profiles to infer common signatures and regulatory mechanisms.
Plank M, Wuttke D, van Dam S, Clarke SA, de Magalhães JP. Plank M, et al. Among authors: van dam s. Mol Biosyst. 2012 Apr;8(4):1339-49. doi: 10.1039/c2mb05255e. Epub 2012 Feb 10. Mol Biosyst. 2012. PMID: 22327899
Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging.
Wood SH, van Dam S, Craig T, Tacutu R, O'Toole A, Merry BJ, de Magalhães JP. Wood SH, et al. Among authors: van dam s. Genome Biol. 2015 Dec 22;16:285. doi: 10.1186/s13059-015-0847-2. Genome Biol. 2015. PMID: 26694192 Free PMC article.
A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels.
Monaco G, van Dam S, Casal Novo Ribeiro JL, Larbi A, de Magalhães JP. Monaco G, et al. Among authors: van dam s. BMC Evol Biol. 2015 Nov 20;15:259. doi: 10.1186/s12862-015-0534-7. BMC Evol Biol. 2015. PMID: 26589719 Free PMC article.
Insights into the evolution of longevity from the bowhead whale genome.
Keane M, Semeiks J, Webb AE, Li YI, Quesada V, Craig T, Madsen LB, van Dam S, Brawand D, Marques PI, Michalak P, Kang L, Bhak J, Yim HS, Grishin NV, Nielsen NH, Heide-Jørgensen MP, Oziolor EM, Matson CW, Church GM, Stuart GW, Patton JC, George JC, Suydam R, Larsen K, López-Otín C, O'Connell MJ, Bickham JW, Thomsen B, de Magalhães JP. Keane M, et al. Among authors: van dam s. Cell Rep. 2015 Jan 6;10(1):112-22. doi: 10.1016/j.celrep.2014.12.008. Cell Rep. 2015. PMID: 25565328 Free PMC article.
GeneFriends: a human RNA-seq-based gene and transcript co-expression database.
van Dam S, Craig T, de Magalhães JP. van Dam S, et al. Nucleic Acids Res. 2015 Jan;43(Database issue):D1124-32. doi: 10.1093/nar/gku1042. Epub 2014 Oct 31. Nucleic Acids Res. 2015. PMID: 25361971 Free PMC article.
GeneFriends: an online co-expression analysis tool to identify novel gene targets for aging and complex diseases.
van Dam S, Cordeiro R, Craig T, van Dam J, Wood SH, de Magalhães JP. van Dam S, et al. Among authors: van dam j. BMC Genomics. 2012 Oct 6;13:535. doi: 10.1186/1471-2164-13-535. BMC Genomics. 2012. PMID: 23039964 Free PMC article.
Gathering insights on disease etiology from gene expression profiles of healthy tissues.
Silva AS, Wood SH, van Dam S, Berres S, McArdle A, de Magalhães JP. Silva AS, et al. Among authors: van dam s. Bioinformatics. 2011 Dec 1;27(23):3300-5. doi: 10.1093/bioinformatics/btr559. Epub 2011 Oct 11. Bioinformatics. 2011. PMID: 21994229
Gene co-expression analysis for functional classification and gene-disease predictions.
van Dam S, Võsa U, van der Graaf A, Franke L, de Magalhães JP. van Dam S, et al. Brief Bioinform. 2018 Jul 20;19(4):575-592. doi: 10.1093/bib/bbw139. Brief Bioinform. 2018. PMID: 28077403 Free PMC article.
Improving the diagnostic yield of exome- sequencing by predicting gene-phenotype associations using large-scale gene expression analysis.
Deelen P, van Dam S, Herkert JC, Karjalainen JM, Brugge H, Abbott KM, van Diemen CC, van der Zwaag PA, Gerkes EH, Zonneveld-Huijssoon E, Boer-Bergsma JJ, Folkertsma P, Gillett T, van der Velde KJ, Kanninga R, van den Akker PC, Jan SZ, Hoorntje ET, Te Rijdt WP, Vos YJ, Jongbloed JDH, van Ravenswaaij-Arts CMA, Sinke R, Sikkema-Raddatz B, Kerstjens-Frederikse WS, Swertz MA, Franke L. Deelen P, et al. Among authors: van dam s. Nat Commun. 2019 Jun 28;10(1):2837. doi: 10.1038/s41467-019-10649-4. Nat Commun. 2019. PMID: 31253775 Free PMC article.
Overlapping SETBP1 gain-of-function mutations in Schinzel-Giedion syndrome and hematologic malignancies.
Acuna-Hidalgo R, Deriziotis P, Steehouwer M, Gilissen C, Graham SA, van Dam S, Hoover-Fong J, Telegrafi AB, Destree A, Smigiel R, Lambie LA, Kayserili H, Altunoglu U, Lapi E, Uzielli ML, Aracena M, Nur BG, Mihci E, Moreira LM, Borges Ferreira V, Horovitz DD, da Rocha KM, Jezela-Stanek A, Brooks AS, Reutter H, Cohen JS, Fatemi A, Smitka M, Grebe TA, Di Donato N, Deshpande C, Vandersteen A, Marques Lourenço C, Dufke A, Rossier E, Andre G, Baumer A, Spencer C, McGaughran J, Franke L, Veltman JA, De Vries BB, Schinzel A, Fisher SE, Hoischen A, van Bon BW. Acuna-Hidalgo R, et al. Among authors: van dam s. PLoS Genet. 2017 Mar 27;13(3):e1006683. doi: 10.1371/journal.pgen.1006683. eCollection 2017 Mar. PLoS Genet. 2017. PMID: 28346496 Free PMC article.
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