Publication List

publication transparent Publications List

GenomeScan is proud to have contributed to a number of publications in prestigious journals, both on basic science and on clinical research. Combining our customized next generation offerings with expertise in bioinformatics, we help researchers move from experiments to meaningful, ready-to-present results faster and easier.

2020

Genome-wide characterization of 5-hydoxymethylcytosine in melanoma reveals major differences with nevus. Salgado C, Oosting J, Janssen B, Kumar R, Gruis N, van Doorn R. Genes Chromosomes Cancer. 2020 Jun;59(6):366-374. doi: 10.1002/gcc.22837. PMID: 32017278

Prioritization of novel ADPKD drug candidates from disease-stage specific gene expression profiles. Malas TB, Leonhard WN, Bange H, Granchi Z, Hettne KM, Van Westen GJP, Price LS, ‘t Hoen PAC, Peters DJM. EBioMedicine. 2020 Jan;51:102585. doi: 10.1016/j.ebiom.2019.11.046. PMID: 31879244

Molecular characterization of colorectal adenomas reveals POFUT1 as a candidate driver of tumor progression. Komor MA, de Wit M, van den Berg J, Martens de Kemp SR, Delis-van Diemen PM, Bolijn AS, Tijssen M, Schelfhorst T, Piersma SR, Chiasserini D, Sanders J, Rausch C, Hoogstrate Y, Stubbs AP, de Jong M, Jenster G, Carvalho B, Meijer GA, Jimenez CR, Fijneman RJA; NGS-ProToCol Consortium. Int J Cancer. 2020 Apr 1;146(7):1979-1992. doi: 10.1002/ijc.32627. PMID: 31411736

Comprehensive diagnostics of acute myeloid leukemia by whole transcriptome RNA sequencing. Arindrarto W, Borràs DM, de Groen RAL, van den Berg RR, Locher IJ, van Diessen SAME, van der Holst R, van der Meijden ED, Honders MW, de Leeuw RH, Verlaat W, Jedema I, Kroes WGM, Knijnenburg J, van Wezel T, Vermaat JSP, Valk PJM, Janssen B, de Knijff P, van Bergen CAM, van den Akker EB, Hoen PAC’, Kiełbasa SM, Laros JFJ, Griffioen M, Veelken H. Leukemia. 2020 Mar 3. doi: 10.1038/s41375-020-0762-8. PMID: 32127641

2019

RNA-Seq in 296 phased trios provides a high-resolution map of genomic imprinting. Jadhav B, Monajemi R, Gagalova KK, Ho D, Draisma HHM, van de Wiel MA, Franke L, Heijmans BT, van Meurs J, Jansen R; GoNL Consortium; BIOS Consortium, ‘t Hoen PAC, Sharp AJ, Kiełbasa SM. BMC Biol. 2019 Jun 24;17(1):50. doi: 10.1186/s12915-019-0674-0. PMID: 31234833

Widespread and Functional RNA Circularization in Localized Prostate Cancer. Chen S, Huang V, Xu X, Livingstone J, Soares F, Jeon J, Zeng Y, Hua JT, Petricca J, Guo H, Wang M, Yousif F, Zhang Y, Donmez N, Ahmed M, Volik S, Lapuk A, Chua MLK, Heisler LE, Foucal A, Fox NS, Fraser M, Bhandari V, Shiah YJ, Guan J, Li J, Orain M, Picard V, Hovington H, Bergeron A, Lacombe L, Fradet Y, Têtu B, Liu S, Feng F, Wu X, Shao YW, Komor MA, Sahinalp C, Collins C, Hoogstrate Y, de Jong M, Fijneman RJA, Fei T, Jenster G, van der Kwast T, Bristow RG, Boutros PC, He HH. Cell. 2019 Feb 7;176(4):831-843.e22. doi: 10.1016/j.cell.2019.01.025. PMID: 30735634

BacTag – a pipeline for fast and accurate gene and allele typing in bacterial sequencing data based on database preprocessing. Khachatryan L, Kraakman MEM, Bernards AT, Laros JFJ. BMC Genomics. 2019 May 6;20(1):338. doi: 10.1186/s12864-019-5723-0. PMID: 31060512

Skewed X-inactivation is common in the general female population. Shvetsova E, Sofronova A, Monajemi R, Gagalova K, Draisma HHM, White SJ, Santen GWE, Chuva de Sousa Lopes SM, Heijmans BT, van Meurs J, Jansen R, Franke L, Kiełbasa SM, den Dunnen JT, ‘t Hoen PAC; BIOS consortium; GoNL consortium. Eur J Hum Genet. 2019 Mar;27(3):455-465. doi: 10.1038/s41431-018-0291-3. PMID:30552425

2018

Consensus molecular subtype classification of colorectal adenomas. Komor MA, Bosch LJ, Bounova G, Bolijn AS, Delis-van Diemen PM, Rausch C, Hoogstrate Y, Stubbs AP, de Jong M, Jenster G, van Grieken NC, Carvalho B, Wessels LF, Jimenez CR, Fijneman RJ, Meijer GA; NGS-ProToCol Consortium. J Pathol. 2018 Nov;246(3):266-276. doi: 10.1002/path.5129. PMID: 29968252

Physiological Responses to Swimming-Induced Exercise in the Adult Zebrafish Regenerating Heart. Rovira M, Borràs DM, Marques IJ, Puig C, Planas JV. Front Physiol. 2018 Oct 1;9:1362. doi: 10.3389/fphys.2018.01362. eCollection 2018. PMID: 30327615

Genome sequence of Rhizomucor pusillus FCH 5.7, a thermophilic zygomycete involved in plant biomass degradation harbouring putative GH9 endoglucanases. Hüttner S, Granchi Z, Nguyen TT, van Pelt S, Larsbrink J, Thanh VN, Olsson L. Biotechnol Rep (Amst). 2018 Aug 31;20:e00279. doi: 10.1016/j.btre.2018.e00279. eCollection 2018. PMID: 30211016

Talaromyces borbonicus, sp. nov., a novel fungus from biodegraded Arundo donax with potential abilities in lignocellulose conversion. Varriale S, Houbraken J, Granchi Z, Pepe O, Cerullo G, Ventorino V, Chin-A-Woeng T, Meijer M, Riley R, Grigoriev IV, Henrissat B, de Vries RP, Faraco V. Mycologia. 2018 Mar-Apr;110(2):316-324. doi: 10.1080/00275514.2018.1456835. PMID: 29843575

Draft Genome Sequence of the Basidiomycete White-Rot Fungus Phlebia centrifuga. Mäkelä MR, Peng M, Granchi Z, Chin-A-Woeng T, Hegi R, van Pelt SI, Ahrendt S, Riley R, Hainaut M, Henrissat B, Grigoriev IV, de Vries RP, Hildén KS. Genome Announc. 2018 Apr 5;6(14). pii: e01414-17. doi: 10.1128/genomeA.01414-17. PMID: 29622620

Meta-analysis of polycystic kidney disease expression profiles defines strong involvement of injury repair processes. Malas TB, Formica C, Leonhard WN, Rao P, Granchi Z, Roos M, Peters DJ, ‘t Hoen PA. Am J Physiol Renal Physiol. 2017 Apr 1;312(4):F806-F817. doi: 10.1152/ajprenal.00653.2016. Epub 2017 Feb 1. Erratum in: Am J Physiol Renal Physiol. 2018 Jan 1;314(1):F140. PMID: 28148532

Draft Genome Sequence of Talaromyces adpressus. Cerullo G, Houbraken J, Granchi Z, Pepe O, Varriale S, Ventorino V, Chin-A-Woeng T, Meijer M, de Vries RP, Faraco V. Genome Announc. 2018 Jan 11;6(2). pii: e01430-17. doi: 10.1128/genomeA.01430-17. PMID: 29326215

Osteolytic cancer cells induce vascular/axon guidance processes in the bone/bone marrow stroma. Hensel J, Wetterwald A, Temanni R, Keller I, Riether C, van der Pluijm G, Cecchini MG, Thalmann GN. Oncotarget. 2018 Jun 22;9(48):28877-28896. doi: 10.18632/oncotarget.25608. eCollection 2018 Jun 22. PMID: 29988965

2017

Combined genome and transcriptome sequencing to investigate the plant cell wall degrading enzyme system in the thermophilic fungus Malbranchea cinnamomea. Hüttner S, Nguyen TT, Granchi Z, Chin-A-Woeng T, Ahrén D, Larsbrink J, Thanh VN, Olsson L. Biotechnol Biofuels. 2017 Nov 13;10:265. doi: 10.1186/s13068-017-0956-0. eCollection 2017. PMID: 29158777

Genome Sequence of the Basidiomycete White-Rot Fungus Trametes pubescens FBCC735. Granchi Z, Peng M, Chi-A-Woeng T, de Vries RP, Hildén K, Mäkelä MR. Genome Announc. 2017 Feb 23;5(8). pii: e01643-16. doi: 10.1128/genomeA.01643-16. PMID: 28232439

The draft genome sequence of the ascomycete fungus Penicillium subrubescens reveals a highly enriched content of plant biomass related CAZymes compared to related fungi. Peng M, Dilokpimol A, Mäkelä MR, Hildén K, Bervoets S, Riley R, Grigoriev IV, Hainaut M, Henrissat B, de Vries RP, Granchi Z. J Biotechnol. 2017 Mar 20;246:1-3. doi: 10.1016/j.jbiotec.2017.02.012. Epub 2017 Feb 16. PMID: 28216099

Coding and small non-coding transcriptional landscape of tuberous sclerosis complex cortical tubers: implications for pathophysiology and treatment. Mills JD, Iyer AM, van Scheppingen J, Bongaarts A, Anink JJ, Janssen B, Zimmer TS, Spliet WG, van Rijen PC, Jansen FE, Feucht M, Hainfellner JA, Krsek P, Zamecnik J, Kotulska K, Jozwiak S, Jansen A, Lagae L, Curatolo P, Kwiatkowski DJ, Pasterkamp RJ, Senthilkumar K, von Oerthel L, Hoekman MF, Gorter JA, Crino PB, Mühlebner A, Scicluna BP, Aronica E. Sci Rep. 2017 Aug 14;7(1):8089. doi: 10.1038/s41598-017-06145-8. PMID: 28808237

Genome Sequence of the Thermophilic Biomass-Degrading Fungus Malbranchea cinnamomea FCH 10.5. Granchi Z, van Pelt S, Thanh VN, Olsson L, Hüttner S. Genome Announc. 2017 Aug 17;5(33). pii: e00779-17. doi: 10.1128/genomeA.00779-17. PMID: 28818895

Differentiation-Defective Human Induced Pluripotent Stem Cells Reveal Strengths and Limitations of the Teratoma Assay and In Vitro Pluripotency Assays. Bouma MJ, van Iterson M, Janssen B, Mummery CL, Salvatori DCF, Freund C. Stem Cell Reports. 2017 May 9;8(5):1340-1353. doi: 10.1016/j.stemcr.2017.03.009. PMID: 28494940

Critical points for an accurate human genome analysis. White SJ, Laros JFJ, Bakker E, Cambon-Thomsen A, Eden M, Leonard S, Lochmüller H, Matthijs G, Mattocks C, Patton S, Payne K, Scheffer H, Souche E, Thomassen E, Thompson R, Traeger-Synodinos J, Van Vooren S, Janssen B, den Dunnen JT. Hum Mutat. 2017 Aug;38(8):912-921. doi: 10.1002/humu.23238. PMID: 28471515

Functional characterization of a multi-cancer risk locus on chr5p15.33 reveals regulation of TERT by ZNF148. Fang J, Jia J, Makowski M, Xu M, Wang Z, Zhang T, Hoskins JW, Choi J, Han Y, Zhang M, Thomas J, Kovacs M, Collins I, Dzyadyk M, Thompson A, O’Neill M, Das S, Lan Q, Koster R; PanScan Consortium; TRICL Consortium; GenoMEL Consortium, Stolzenberg-Solomon RS, Kraft P, Wolpin BM, Jansen PWTC, Olson S, McGlynn KA, Kanetsky PA, Chatterjee N, Barrett JH, Dunning AM, Taylor JC, Newton-Bishop JA, Bishop DT, Andresson T, Petersen GM, Amos CI, Iles MM, Nathanson KL, Landi MT, Vermeulen M, Brown KM, Amundadottir LT. Nat Commun. 2017 May 2;8:15034. doi: 10.1038/ncomms15034. PMID: 28447668

Detecting PKD1 variants in polycystic kidney disease patients by single-molecule long-read sequencing. Borràs DM, Vossen RHAM, Liem M, Buermans HPJ, Dauwerse H, van Heusden D, Gansevoort RT, den Dunnen JT, Janssen B, Peters DJM, Losekoot M, Anvar SY. Hum Mutat. 2017 Jul;38(7):870-879. doi: 10.1002/humu.23223. PMID: 28378423

Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos. Rauwerda H, Pagano JF, de Leeuw WC, Ensink W, Nehrdich U, de Jong M, Jonker M, Spaink HP, Breit TM. BMC Genomics. 2017 Apr 11;18(1):287. doi: 10.1186/s12864-017-3672-z. PMID: 28399811

Meta-analysis of polycystic kidney disease expression profiles defines strong involvement of injury repair processes. Malas TB, Formica C, Leonhard WN, Rao P, Granchi Z, Roos M, Peters DJ, ‘t Hoen PA. Am J Physiol Renal Physiol. 2017 Apr 1;312(4):F806-F817. doi: 10.1152/ajprenal.00653.2016. Epub 2017 Feb 1. Erratum in: Am J Physiol Renal Physiol. 2018 Jan 1;314(1):F140. PMID: 28148532

Insulin-like growth factor 1 receptor activation promotes mammary gland tumor development by increasing glycolysis and promoting biomass production. Ter Braak B, Siezen CL, Lee JS, Rao P, Voorhoeve C, Ruppin E, van der Laan JW, van de Water B. Breast Cancer Res. 2017 Feb 7;19(1):14. doi: 10.1186/s13058-017-0802-0. PMID:28173837

2016

Silencing of Profilin-1 suppresses cell adhesion and tumor growth via predicted alterations in integrin and Ca2+ signaling in T24M-based bladder cancer models. Frantzi M, Klimou Z, Makridakis M, Zoidakis J, Latosinska A, Borràs DM, Janssen B, Giannopoulou I, Lygirou V, Lazaris AC, Anagnou NP, Mischak H, Roubelakis MG, Vlahou A. Oncotarget. 2016 Oct 25;7(43):70750-70768. doi: 10.18632/oncotarget.12218. PMID: 27683119

Integrative analysis of extracellular and intracellular bladder cancer cell line proteome with transcriptome: improving coverage and validity of -omics findings. Latosinska A, Makridakis M, Frantzi M, Borràs DM, Janssen B, Mullen W, Zoidakis J, Merseburger AS, Jankowski V, Mischak H, Vlahou A. Sci Rep. 2016 May 11;6:25619. doi: 10.1038/srep25619. PMID: 27167498

Genome Sequence of Madurella mycetomatis mm55, Isolated from a Human Mycetoma Case in Sudan. Smit S, Derks MF, Bervoets S, Fahal A, van Leeuwen W, van Belkum A, van de Sande WW. Genome Announc. 2016 May 26;4(3). pii: e00418-16. doi: 10.1128/genomeA.00418-16. PMID: 27231361

Incorporation of an invasive plant into a native insect herbivore food web. Schilthuizen M, Santos Pimenta LP, Lammers Y, Steenbergen PJ, Flohil M, Beveridge NG, van Duijn PT, Meulblok MM, Sosef N, van de Ven R, Werring R, Beentjes KK, Meijer K, Vos RA, Vrieling K, Gravendeel B, Choi Y, Verpoorte R, Smit C, Beukeboom LW. PeerJ. 2016 May 10;4:e1954. doi: 10.7717/peerj.1954. eCollection 2016. PMID: 27190702

2015

Copy number alterations and allelic ratio in relation to recurrence of rectal cancer. Goossens-Beumer IJ, Oosting J, Corver WE, Janssen MJ, Janssen B, van Workum W, Zeestraten EC, van de Velde CJ, Morreau H, Kuppen PJ, van Wezel T. BMC Genomics. 2015 Jun 6;16:438. doi: 10.1186/s12864-015-1550-0. PMID: 26048403

Paternally Inherited IGF2 Mutation and Growth Restriction. Begemann M, Zirn B, Santen G, Wirthgen E, Soellner L, Büttel HM, Schweizer R, van Workum W, Binder G, Eggermann T. N Engl J Med. 2015 Jul 23;373(4):349-56. doi: 10.1056/NEJMoa1415227. PMID: 26154720

Next-generation sequencing-based genome diagnostics across clinical genetics centers: implementation choices and their effects. Vrijenhoek T, Kraaijeveld K, Elferink M, de Ligt J, Kranendonk E, Santen G, Nijman IJ, Butler D, Claes G, Costessi A, Dorlijn W, van Eyndhoven W, Halley DJ, van den Hout MC, van Hove S, Johansson LF, Jongbloed JD, Kamps R, Kockx CE, de Koning B, Kriek M, Lekanne Dit Deprez R, Lunstroo H, Mannens M, Mook OR, Nelen M, Ploem C, Rijnen M, Saris JJ, Sinke R, Sistermans E, van Slegtenhorst M, Sleutels F, van der Stoep N, van Tienhoven M, Vermaat M, Vogel M, Waisfisz Q, Marjan Weiss J, van den Wijngaard A, van Workum W, Ijntema H, van der Zwaag B, van IJcken WF, den Dunnen J, Veltman JA, Hennekam R, Cuppen E. Eur J Hum Genet. 2015 Sep;23(9):1142-50. doi: 10.1038/ejhg.2014.279. PMID: 25626705

Formalin-fixed, paraffin-embedded (FFPE) tissue epigenomics using Infinium HumanMethylation450 BeadChip assays. de Ruijter TC, de Hoon JP, Slaats J, de Vries B, Janssen MJ, van Wezel T, Aarts MJ, van Engeland M, Tjan-Heijnen VC, Van Neste L, Veeck J. Lab Invest. 2015 Jul;95(7):833-42. doi: 10.1038/labinvest.2015.53. PMID: 25867767

Quantitative and qualitative analysis of small RNAs in human endothelial cells and exosomes provides insights into localized RNA processing, degradation and sorting. van Balkom BW, Eisele AS, Pegtel DM, Bervoets S, Verhaar MC. J Extracell Vesicles. 2015 May 29;4:26760. doi: 10.3402/jev.v4.26760. eCollection 2015. PMID: 26027894

Next-generation sequencing reveals novel rare fusion events with functional implication in prostate cancer. Teles Alves I, Hartjes T, McClellan E, Hiltemann S, Böttcher R, Dits N, Temanni MR, Janssen B, van Workum W, van der Spek P, Stubbs A, de Klein A, Eussen B, Trapman J, Jenster G. Oncogene. 2015 Jan 29;34(5):568-77. doi: 10.1038/onc.2013.591. PMID: 24488012

Fine mapping of genetic susceptibility loci for melanoma reveals a mixture of single variant and multiple variant regions. Barrett JH, Taylor JC, Bright C, Harland M, Dunning AM, Akslen LA, Andresen PA, Avril MF, Azizi E, Bianchi Scarrà G, Brossard M, Brown KM, Dębniak T, Elder DE, Friedman E, Ghiorzo P, Gillanders EM, Gruis NA, Hansson J, Helsing P, Hočevar M, Höiom V, Ingvar C, Landi MT, Lang J, Lathrop GM, Lubiński J, Mackie RM, Molven A, Novaković S, Olsson H, Puig S, Puig-Butille JA, van der Stoep N, van Doorn R, van Workum W, Goldstein AM, Kanetsky PA, Pharoah PD, Demenais F, Hayward NK, Newton Bishop JA, Bishop DT, Iles MM; GenoMEL Consortium. Int J Cancer. 2015 Mar 15;136(6):1351-60. doi: 10.1002/ijc.29099. PMID: 25077817

2012

Short-term erythropoietin treatment does not substantially modulate monocyte transcriptomes of patients with combined heart and renal failure. Jie KE, van der Putten K, Wesseling S, Joles JA, Bergevoet MW, Pepers-de Kort F, Doevendans PA, Yasui Y, Liu Q, Verhaar MC, Gaillard CA. PloS one. 2012;7(9). doi: 10.1371/journal.pone.0041339. PMID: 22957013

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