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Items: 1 to 50 of 105

1.

Eleven grand challenges in single-cell data science.

Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo TH, Lelieveldt BPF, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Raczkowski L, Reinders M, Ridder J, Saliba AE, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A.

Genome Biol. 2020 Feb 7;21(1):31. doi: 10.1186/s13059-020-1926-6. Review.

2.

Integrated proteogenomic approach identifying a protein signature of COPD and a new splice variant of SORBS1.

Brandsma CA, Guryev V, Timens W, Ciconelle A, Postma DS, Bischoff R, Johansson M, Ovchinnikova ES, Malm J, Marko-Varga G, Fehniger TE, van den Berge M, Horvatovich P.

Thorax. 2020 Feb;75(2):180-183. doi: 10.1136/thoraxjnl-2019-213200. Epub 2020 Jan 14.

3.

Gene network approach reveals co-expression patterns in nasal and bronchial epithelium.

Imkamp K, Bernal V, Grzegorzcyk M, Horvatovich P, Vermeulen CJ, Heijink IH, Guryev V, Kerstjens HAM, van den Berge M, Faiz A.

Sci Rep. 2019 Nov 1;9(1):15835. doi: 10.1038/s41598-019-50963-x.

4.

breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data.

Porubsky D, Sanders AD, Taudt A, Colomé-Tatché M, Lansdorp PM, Guryev V.

Bioinformatics. 2020 Feb 15;36(4):1260-1261. doi: 10.1093/bioinformatics/btz681.

PMID:
31504176
5.

Proteogenomics: From next-generation sequencing (NGS) and mass spectrometry-based proteomics to precision medicine.

Ang MY, Low TY, Lee PY, Wan Mohamad Nazarie WF, Guryev V, Jamal R.

Clin Chim Acta. 2019 Nov;498:38-46. doi: 10.1016/j.cca.2019.08.010. Epub 2019 Aug 14. Review.

PMID:
31421119
6.

Peptide microarray of pediatric acute myeloid leukemia is related to relapse and reveals involvement of DNA damage response and repair.

Mahmud H, Ter Elst A, Scherpen FJG, Boer TM, Kampen KR, de Haas V, Guryev V, Peppelenbosch MM, Kornblau SM, de Bont ESJM.

Oncotarget. 2019 Jul 23;10(45):4679-4690. doi: 10.18632/oncotarget.27086. eCollection 2019 Jul 23.

7.

Nasal gene expression changes with inhaled corticosteroid treatment in asthma.

Boudewijn IM, Lan A, Faiz A, Cox CA, Brouwer S, Schokker S, Vroegop SJ, Nawijn MC, Woodruff PG, Christenson SA, Hagedoorn P, Frijlink HW, Choy DF, Brouwer U, Wisman M, Postma DS, Fingleton J, Beasley R, van den Berge M, Guryev V.

Allergy. 2020 Jan;75(1):191-194. doi: 10.1111/all.13952. Epub 2019 Jul 15. No abstract available.

PMID:
31230369
8.

Exact hypothesis testing for shrinkage-based Gaussian graphical models.

Bernal V, Bischoff R, Guryev V, Grzegorczyk M, Horvatovich P.

Bioinformatics. 2019 Dec 1;35(23):5011-5017. doi: 10.1093/bioinformatics/btz357.

9.

Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C.

Nat Commun. 2019 Apr 16;10(1):1784. doi: 10.1038/s41467-018-08148-z.

10.

AGER expression and alternative splicing in bronchial biopsies of smokers and never smokers.

Faiz A, van den Berge M, Vermeulen CJ, Ten Hacken NHT, Guryev V, Pouwels SD.

Respir Res. 2019 Apr 10;20(1):70. doi: 10.1186/s12931-019-1038-6.

11.

TGF-β activation impairs fibroblast ability to support adult lung epithelial progenitor cell organoid formation.

Ng-Blichfeldt JP, de Jong T, Kortekaas RK, Wu X, Lindner M, Guryev V, Hiemstra PS, Stolk J, Königshoff M, Gosens R.

Am J Physiol Lung Cell Mol Physiol. 2019 Jul 1;317(1):L14-L28. doi: 10.1152/ajplung.00400.2018. Epub 2019 Apr 10.

PMID:
30969812
12.

Gene expression variability: the other dimension in transcriptome analysis.

de Jong TV, Moshkin YM, Guryev V.

Physiol Genomics. 2019 May 1;51(5):145-158. doi: 10.1152/physiolgenomics.00128.2018. Epub 2019 Mar 15.

PMID:
30875273
13.

Age-related gene and miRNA expression changes in airways of healthy individuals.

Ong J, Woldhuis RR, Boudewijn IM, van den Berg A, Kluiver J, Kok K, Terpstra MM, Guryev V, de Vries M, Vermeulen CJ, Timens W, van den Berge M, Brandsma CA.

Sci Rep. 2019 Mar 6;9(1):3765. doi: 10.1038/s41598-019-39873-0.

14.

Quantification of Aneuploidy in Mammalian Systems.

van den Bos H, Bakker B, Taudt A, Guryev V, Colomé-Tatché M, Lansdorp PM, Foijer F, Spierings DCJ.

Methods Mol Biol. 2019;1896:159-190. doi: 10.1007/978-1-4939-8931-7_15.

PMID:
30474848
15.

VEGFC Antibody Therapy Drives Differentiation of AML.

Kampen KR, Scherpen FJG, Mahmud H, Ter Elst A, Mulder AB, Guryev V, Verhagen HJMP, De Keersmaecker K, Smit L, Kornblau SM, De Bont ESJM.

Cancer Res. 2018 Oct 15;78(20):5940-5948. doi: 10.1158/0008-5472.CAN-18-0250. Epub 2018 Sep 5.

16.

Cigarette smoke exposure decreases CFLAR expression in the bronchial epithelium, augmenting susceptibility for lung epithelial cell death and DAMP release.

Faiz A, Heijink IH, Vermeulen CJ, Guryev V, van den Berge M, Nawijn MC, Pouwels SD.

Sci Rep. 2018 Aug 20;8(1):12426. doi: 10.1038/s41598-018-30602-7.

17.

Proteomic alterations in early stage cervical cancer.

Güzel C, Govorukhina NI, Wisman GBA, Stingl C, Dekker LJM, Klip HG, Hollema H, Guryev V, Horvatovich PL, van der Zee AGJ, Bischoff R, Luider TM.

Oncotarget. 2018 Apr 6;9(26):18128-18147. doi: 10.18632/oncotarget.24773. eCollection 2018 Apr 6.

18.

Reduced expression of C/EBPβ-LIP extends health and lifespan in mice.

Müller C, Zidek LM, Ackermann T, de Jong T, Liu P, Kliche V, Zaini MA, Kortman G, Harkema L, Verbeek DS, Tuckermann JP, von Maltzahn J, de Bruin A, Guryev V, Wang ZQ, Calkhoven CF.

Elife. 2018 Jun 4;7. pii: e34985. doi: 10.7554/eLife.34985.

19.

Identification of Two Protein-Signaling States Delineating Transcriptionally Heterogeneous Human Medulloblastoma.

Zomerman WW, Plasschaert SLA, Conroy S, Scherpen FJ, Meeuwsen-de Boer TGJ, Lourens HJ, Guerrero Llobet S, Smit MJ, Slagter-Menkema L, Seitz A, Gidding CEM, Hulleman E, Wesseling P, Meijer L, van Kempen LC, van den Berg A, Warmerdam DO, Kruyt FAE, Foijer F, van Vugt MATM, den Dunnen WFA, Hoving EW, Guryev V, de Bont ESJM, Bruggeman SWM.

Cell Rep. 2018 Mar 20;22(12):3206-3216. doi: 10.1016/j.celrep.2018.02.089.

20.

Nasal epithelium as a proxy for bronchial epithelium for smoking-induced gene expression and expression Quantitative Trait Loci.

Imkamp K, Berg M, Vermeulen CJ, Heijink IH, Guryev V, Kerstjens HAM, Koppelman GH, van den Berge M, Faiz A.

J Allergy Clin Immunol. 2018 Jul;142(1):314-317.e15. doi: 10.1016/j.jaci.2018.01.047. Epub 2018 Mar 6. No abstract available.

PMID:
29522853
21.

Resilience to aging in the regeneration-capable flatworm Macrostomum lignano.

Mouton S, Grudniewska M, Glazenburg L, Guryev V, Berezikov E.

Aging Cell. 2018 Jun;17(3):e12739. doi: 10.1111/acel.12739. Epub 2018 Feb 28.

22.

BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes.

van Wietmarschen N, Merzouk S, Halsema N, Spierings DCJ, Guryev V, Lansdorp PM.

Nat Commun. 2018 Jan 18;9(1):271. doi: 10.1038/s41467-017-02760-1.

23.

A p300 and SIRT1 Regulated Acetylation Switch of C/EBPα Controls Mitochondrial Function.

Zaini MA, Müller C, de Jong TV, Ackermann T, Hartleben G, Kortman G, Gührs KH, Fusetti F, Krämer OH, Guryev V, Calkhoven CF.

Cell Rep. 2018 Jan 9;22(2):497-511. doi: 10.1016/j.celrep.2017.12.061.

24.

Nasal gene expression differentiates COPD from controls and overlaps bronchial gene expression.

Boudewijn IM, Faiz A, Steiling K, van der Wiel E, Telenga ED, Hoonhorst SJM, Ten Hacken NHT, Brandsma CA, Kerstjens HAM, Timens W, Heijink IH, Jonker MR, de Bruin HG, Sebastiaan Vroegop J, Pasma HR, Boersma WG, Wielders P, van den Elshout F, Mansour K, Spira A, Lenburg ME, Guryev V, Postma DS, van den Berge M.

Respir Res. 2017 Dec 21;18(1):213. doi: 10.1186/s12931-017-0696-5.

25.

Efficient transgenesis and annotated genome sequence of the regenerative flatworm model Macrostomum lignano.

Wudarski J, Simanov D, Ustyantsev K, de Mulder K, Grelling M, Grudniewska M, Beltman F, Glazenburg L, Demircan T, Wunderer J, Qi W, Vizoso DB, Weissert PM, Olivieri D, Mouton S, Guryev V, Aboobaker A, Schärer L, Ladurner P, Berezikov E.

Nat Commun. 2017 Dec 14;8(1):2120. doi: 10.1038/s41467-017-02214-8.

26.

Genome-wide mapping of sister chromatid exchange events in single yeast cells using Strand-seq.

Claussin C, Porubský D, Spierings DC, Halsema N, Rentas S, Guryev V, Lansdorp PM, Chang M.

Elife. 2017 Dec 12;6. pii: e30560. doi: 10.7554/eLife.30560.

27.

Lung tissue gene-expression signature for the ageing lung in COPD.

de Vries M, Faiz A, Woldhuis RR, Postma DS, de Jong TV, Sin DD, Bossé Y, Nickle DC, Guryev V, Timens W, van den Berge M, Brandsma CA.

Thorax. 2017 Dec 6. pii: thoraxjnl-2017-210074. doi: 10.1136/thoraxjnl-2017-210074. [Epub ahead of print]

PMID:
29212667
28.

Parental DNA Methylation States Are Associated with Heterosis in Epigenetic Hybrids.

Lauss K, Wardenaar R, Oka R, van Hulten MHA, Guryev V, Keurentjes JJB, Stam M, Johannes F.

Plant Physiol. 2018 Feb;176(2):1627-1645. doi: 10.1104/pp.17.01054. Epub 2017 Dec 1.

29.

Dense and accurate whole-chromosome haplotyping of individual genomes.

Porubsky D, Garg S, Sanders AD, Korbel JO, Guryev V, Lansdorp PM, Marschall T.

Nat Commun. 2017 Nov 3;8(1):1293. doi: 10.1038/s41467-017-01389-4.

30.

Peptide microarray profiling identifies phospholipase C gamma 1 (PLC-γ1) as a potential target for t(8;21) AML.

Mahmud H, Scherpen FJG, de Boer TM, Lourens HJ, Schoenherr C, Eder M, Scherr M, Guryev V, De Bont ES.

Oncotarget. 2017 Jun 27;8(40):67344-67354. doi: 10.18632/oncotarget.18631. eCollection 2017 Sep 15.

31.

Unmasking Transcriptional Heterogeneity in Senescent Cells.

Hernandez-Segura A, de Jong TV, Melov S, Guryev V, Campisi J, Demaria M.

Curr Biol. 2017 Sep 11;27(17):2652-2660.e4. doi: 10.1016/j.cub.2017.07.033. Epub 2017 Aug 30.

32.

Population specific analysis of Yakut exomes.

Zlobin AS, Sharapov SS, Guryev VP, Bevova MR, Tsepilov YA, Sivtseva TM, Boyarskih UA, Sokolova EA, Aulchenko YS, Filipenko ML, Osakovsky VL.

Dokl Biochem Biophys. 2017 May;474(1):213-216. doi: 10.1134/S1607672917030188. Epub 2017 Jul 20.

PMID:
28726087
33.

Assessment of variant pathogenicity in a highly admixed population.

Guryev V.

Hum Mutat. 2017 Jul;38(7):749. doi: 10.1002/humu.23241. No abstract available.

PMID:
28609575
34.

Identification of an RNA Polymerase III Regulator Linked to Disease-Associated Protein Aggregation.

Sin O, de Jong T, Mata-Cabana A, Kudron M, Zaini MA, Aprile FA, Seinstra RI, Stroo E, Prins RW, Martineau CN, Wang HH, Hogewerf W, Steinhof A, Wanker EE, Vendruscolo M, Calkhoven CF, Reinke V, Guryev V, Nollen EA.

Mol Cell. 2017 Mar 16;65(6):1096-1108.e6. doi: 10.1016/j.molcel.2017.02.022.

35.

Direct chromosome-length haplotyping by single-cell sequencing.

Porubský D, Sanders AD, van Wietmarschen N, Falconer E, Hills M, Spierings DC, Bevova MR, Guryev V, Lansdorp PM.

Genome Res. 2016 Nov;26(11):1565-1574. Epub 2016 Sep 19.

36.

Characterizing polymorphic inversions in human genomes by single-cell sequencing.

Sanders AD, Hills M, Porubský D, Guryev V, Falconer E, Lansdorp PM.

Genome Res. 2016 Nov;26(11):1575-1587. Epub 2016 Jul 29.

37.

A high-quality human reference panel reveals the complexity and distribution of genomic structural variants.

Hehir-Kwa JY, Marschall T, Kloosterman WP, Francioli LC, Baaijens JA, Dijkstra LJ, Abdellaoui A, Koval V, Thung DT, Wardenaar R, Renkens I, Coe BP, Deelen P, de Ligt J, Lameijer EW, van Dijk F, Hormozdiari F; Genome of the Netherlands Consortium, Uitterlinden AG, van Duijn CM, Eichler EE, de Bakker PI, Swertz MA, Wijmenga C, van Ommen GB, Slagboom PE, Boomsma DI, Schönhuth A, Ye K, Guryev V.

Nat Commun. 2016 Oct 6;7:12989. doi: 10.1038/ncomms12989.

38.

Proteogenomics: Key Driver for Clinical Discovery and Personalized Medicine.

Barbieri R, Guryev V, Brandsma CA, Suits F, Bischoff R, Horvatovich P.

Adv Exp Med Biol. 2016;926:21-47. Review.

PMID:
27686804
39.

Erratum to: Single-cell whole genome sequencing reveals no evidence for common aneuploidy in normal and Alzheimer's disease neurons.

van den Bos H, Spierings DC, Taudt A, Bakker B, Porubský D, Falconer E, Novoa C, Halsema N, Kazemier HG, Hoekstra-Wakker K, Guryev V, den Dunnen WF, Foijer F, Colomé-Tatché M, Boddeke HW, Landsdorp PM.

Genome Biol. 2016 Jun 30;17(1):143. No abstract available.

40.

Single-cell whole genome sequencing reveals no evidence for common aneuploidy in normal and Alzheimer's disease neurons.

van den Bos H, Spierings DC, Taudt AS, Bakker B, Porubský D, Falconer E, Novoa C, Halsema N, Kazemier HG, Hoekstra-Wakker K, Guryev V, den Dunnen WF, Foijer F, Tatché MC, Boddeke HW, Lansdorp PM.

Genome Biol. 2016 May 31;17(1):116. doi: 10.1186/s13059-016-0976-2. Erratum in: Genome Biol. 2016 Jun 30;17(1):143.

41.

Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies.

Bakker B, Taudt A, Belderbos ME, Porubsky D, Spierings DC, de Jong TV, Halsema N, Kazemier HG, Hoekstra-Wakker K, Bradley A, de Bont ES, van den Berg A, Guryev V, Lansdorp PM, Colomé-Tatché M, Foijer F.

Genome Biol. 2016 May 31;17(1):115. doi: 10.1186/s13059-016-0971-7.

42.

Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster.

Chereji RV, Kan TW, Grudniewska MK, Romashchenko AV, Berezikov E, Zhimulev IF, Guryev V, Morozov AV, Moshkin YM.

Nucleic Acids Res. 2016 Feb 18;44(3):1036-51. doi: 10.1093/nar/gkv978. Epub 2015 Oct 1.

43.

Protein biogenesis machinery is a driver of replicative aging in yeast.

Janssens GE, Meinema AC, González J, Wolters JC, Schmidt A, Guryev V, Bischoff R, Wit EC, Veenhoff LM, Heinemann M.

Elife. 2015 Dec 1;4:e08527. doi: 10.7554/eLife.08527.

44.

Genomic variability and protein species - Improving sequence coverage for proteogenomics.

Bischoff R, Permentier H, Guryev V, Horvatovich P.

J Proteomics. 2016 Feb 16;134:25-36. doi: 10.1016/j.jprot.2015.09.021. Epub 2015 Sep 21. Review.

PMID:
26394375
45.

Effect of IKZF1 deletions on signal transduction pathways in Philadelphia chromosome negative pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL).

van der Sligte NE, Scherpen FJ, Ter Elst A, Guryev V, van Leeuwen FN, de Bont ES.

Exp Hematol Oncol. 2015 Aug 12;4:23. doi: 10.1186/s40164-015-0017-y. eCollection 2015.

46.

Essential role for cyclic-AMP responsive element binding protein 1 (CREB) in the survival of acute lymphoblastic leukemia.

van der Sligte NE, Kampen KR, ter Elst A, Scherpen FJ, Meeuwsen-de Boer TG, Guryev V, van Leeuwen FN, Kornblau SM, de Bont ES.

Oncotarget. 2015 Jun 20;6(17):14970-81.

47.

Genome-wide patterns and properties of de novo mutations in humans.

Francioli LC, Polak PP, Koren A, Menelaou A, Chun S, Renkens I; Genome of the Netherlands Consortium, van Duijn CM, Swertz M, Wijmenga C, van Ommen G, Slagboom PE, Boomsma DI, Ye K, Guryev V, Arndt PF, Kloosterman WP, de Bakker PIW, Sunyaev SR.

Nat Genet. 2015 Jul;47(7):822-826. doi: 10.1038/ng.3292. Epub 2015 May 18.

48.

Association analysis of copy numbers of FC-gamma receptor genes for rheumatoid arthritis and other immune-mediated phenotypes.

Franke L, el Bannoudi H, Jansen DT, Kok K, Trynka G, Diogo D, Swertz M, Fransen K, Knevel R, Gutierrez-Achury J, Ärlestig L, Greenberg JD, Kremer J, Pappas DA, Kanterakis A, Weersma RK, van der Helm-van Mil AH, Guryev V, Rantapää-Dahlqvist S, Gregersen PK, Plenge RM, Wijmenga C, Huizinga TW, Ioan-Facsinay A, Toes RE, Zhernakova A.

Eur J Hum Genet. 2016 Feb;24(2):263-70. doi: 10.1038/ejhg.2015.95. Epub 2015 May 13.

49.

Genomic landscape of rat strain and substrain variation.

Hermsen R, de Ligt J, Spee W, Blokzijl F, Schäfer S, Adami E, Boymans S, Flink S, van Boxtel R, van der Weide RH, Aitman T, Hübner N, Simonis M, Tabakoff B, Guryev V, Cuppen E.

BMC Genomics. 2015 May 6;16:357. doi: 10.1186/s12864-015-1594-1.

50.

Characteristics of de novo structural changes in the human genome.

Kloosterman WP, Francioli LC, Hormozdiari F, Marschall T, Hehir-Kwa JY, Abdellaoui A, Lameijer EW, Moed MH, Koval V, Renkens I, van Roosmalen MJ, Arp P, Karssen LC, Coe BP, Handsaker RE, Suchiman ED, Cuppen E, Thung DT, McVey M, Wendl MC; Genome of Netherlands Consortium, Uitterlinden A, van Duijn CM, Swertz MA, Wijmenga C, van Ommen GB, Slagboom PE, Boomsma DI, Schönhuth A, Eichler EE, de Bakker PI, Ye K, Guryev V.

Genome Res. 2015 Jun;25(6):792-801. doi: 10.1101/gr.185041.114. Epub 2015 Apr 16.

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