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Items: 1 to 20 of 44

1.

The molecular genetic make-up of male breast cancer.

Moelans CB, de Ligt J, van der Groep P, Prins P, Besselink NJM, Hoogstraat M, Ter Hoeve ND, Lacle MM, Kornegoor R, van der Pol CC, de Leng WWJ, Barbé E, van der Vegt B, Martens J, Bult P, Smit VTHBM, Koudijs MJ, Nijman IJ, Voest EE, Selenica P, Weigelt B, Reis-Filho JS, van der Wall E, Cuppen E, van Diest PJ.

Endocr Relat Cancer. 2019 Oct;26(10):779-794. doi: 10.1530/ERC-19-0278.

PMID:
31340200
2.

Scalable Workflows and Reproducible Data Analysis for Genomics.

Strozzi F, Janssen R, Wurmus R, Crusoe MR, Githinji G, Di Tommaso P, Belhachemi D, Möller S, Smant G, de Ligt J, Prins P.

Methods Mol Biol. 2019;1910:723-745. doi: 10.1007/978-1-4939-9074-0_24.

PMID:
31278683
3.

Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer.

Jager M, Blokzijl F, Kuijk E, Bertl J, Vougioukalaki M, Janssen R, Besselink N, Boymans S, de Ligt J, Pedersen JS, Hoeijmakers J, Pothof J, van Boxtel R, Cuppen E.

Genome Res. 2019 Jul;29(7):1067-1077. doi: 10.1101/gr.246223.118. Epub 2019 Jun 20.

4.

Long-term expanding human airway organoids for disease modeling.

Sachs N, Papaspyropoulos A, Zomer-van Ommen DD, Heo I, Böttinger L, Klay D, Weeber F, Huelsz-Prince G, Iakobachvili N, Amatngalim GD, de Ligt J, van Hoeck A, Proost N, Viveen MC, Lyubimova A, Teeven L, Derakhshan S, Korving J, Begthel H, Dekkers JF, Kumawat K, Ramos E, van Oosterhout MF, Offerhaus GJ, Wiener DJ, Olimpio EP, Dijkstra KK, Smit EF, van der Linden M, Jaksani S, van de Ven M, Jonkers J, Rios AC, Voest EE, van Moorsel CH, van der Ent CK, Cuppen E, van Oudenaarden A, Coenjaerts FE, Meyaard L, Bont LJ, Peters PJ, Tans SJ, van Zon JS, Boj SF, Vries RG, Beekman JM, Clevers H.

EMBO J. 2019 Feb 15;38(4). pii: e100300. doi: 10.15252/embj.2018100300. Epub 2019 Jan 14.

5.

Natural helix 9 mutants of PPARγ differently affect its transcriptional activity.

Broekema MF, Massink MPG, Donato C, de Ligt J, Schaarschmidt J, Borgman A, Schooneman MG, Melchers D, Gerding MN, Houtman R, Bonvin AMJJ, Majithia AR, Monajemi H, van Haaften GW, Soeters MR, Kalkhoven E.

Mol Metab. 2019 Feb;20:115-127. doi: 10.1016/j.molmet.2018.12.005. Epub 2018 Dec 16.

6.

A Single Complex Agpat2 Allele in a Patient With Partial Lipodystrophy.

Broekema MF, Massink MPG, De Ligt J, Stigter ECA, Monajemi H, De Ridder J, Burgering BMT, van Haaften GW, Kalkhoven E.

Front Physiol. 2018 Sep 26;9:1363. doi: 10.3389/fphys.2018.01363. eCollection 2018.

7.

A System-wide Approach to Monitor Responses to Synergistic BRAF and EGFR Inhibition in Colorectal Cancer Cells.

Ressa A, Bosdriesz E, de Ligt J, Mainardi S, Maddalo G, Prahallad A, Jager M, de la Fonteijne L, Fitzpatrick M, Groten S, Altelaar AFM, Bernards R, Cuppen E, Wessels L, Heck AJR.

Mol Cell Proteomics. 2018 Oct;17(10):1892-1908. doi: 10.1074/mcp.RA117.000486. Epub 2018 Jul 3.

8.

Cancer cells copy migratory behavior and exchange signaling networks via extracellular vesicles.

Steenbeek SC, Pham TV, de Ligt J, Zomer A, Knol JC, Piersma SR, Schelfhorst T, Huisjes R, Schiffelers RM, Cuppen E, Jimenez CR, van Rheenen J.

EMBO J. 2018 Aug 1;37(15). pii: e98357. doi: 10.15252/embj.201798357. Epub 2018 Jun 14.

9.

A Living Biobank of Breast Cancer Organoids Captures Disease Heterogeneity.

Sachs N, de Ligt J, Kopper O, Gogola E, Bounova G, Weeber F, Balgobind AV, Wind K, Gracanin A, Begthel H, Korving J, van Boxtel R, Duarte AA, Lelieveld D, van Hoeck A, Ernst RF, Blokzijl F, Nijman IJ, Hoogstraat M, van de Ven M, Egan DA, Zinzalla V, Moll J, Boj SF, Voest EE, Wessels L, van Diest PJ, Rottenberg S, Vries RGJ, Cuppen E, Clevers H.

Cell. 2018 Jan 11;172(1-2):373-386.e10. doi: 10.1016/j.cell.2017.11.010. Epub 2017 Dec 7.

10.

Mapping and phasing of structural variation in patient genomes using nanopore sequencing.

Cretu Stancu M, van Roosmalen MJ, Renkens I, Nieboer MM, Middelkamp S, de Ligt J, Pregno G, Giachino D, Mandrile G, Espejo Valle-Inclan J, Korzelius J, de Bruijn E, Cuppen E, Talkowski ME, Marschall T, de Ridder J, Kloosterman WP.

Nat Commun. 2017 Nov 6;8(1):1326. doi: 10.1038/s41467-017-01343-4.

11.

Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer.

Drost J, van Boxtel R, Blokzijl F, Mizutani T, Sasaki N, Sasselli V, de Ligt J, Behjati S, Grolleman JE, van Wezel T, Nik-Zainal S, Kuiper RP, Cuppen E, Clevers H.

Science. 2017 Oct 13;358(6360):234-238. doi: 10.1126/science.aao3130. Epub 2017 Sep 14.

12.

Unraveling genetic predisposition to familial or early onset gastric cancer using germline whole-exome sequencing.

Vogelaar IP, van der Post RS, van Krieken JHJ, Spruijt L, van Zelst-Stams WA, Kets CM, Lubinski J, Jakubowska A, Teodorczyk U, Aalfs CM, van Hest LP, Pinheiro H, Oliveira C, Jhangiani SN, Muzny DM, Gibbs RA, Lupski JR, de Ligt J, Vissers LELM, Hoischen A, Gilissen C, van de Vorst M, Goeman JJ, Schackert HK, Ranzani GN, Molinaro V, Gómez García EB, Hes FJ, Holinski-Feder E, Genuardi M, Ausems MGEM, Sijmons RH, Wagner A, van der Kolk LE, Bjørnevoll I, Høberg-Vetti H, van Kessel AG, Kuiper RP, Ligtenberg MJL, Hoogerbrugge N.

Eur J Hum Genet. 2017 Nov;25(11):1246-1252. doi: 10.1038/ejhg.2017.138. Epub 2017 Sep 6.

13.

Genetic dissection of colorectal cancer progression by orthotopic transplantation of engineered cancer organoids.

Fumagalli A, Drost J, Suijkerbuijk SJ, van Boxtel R, de Ligt J, Offerhaus GJ, Begthel H, Beerling E, Tan EH, Sansom OJ, Cuppen E, Clevers H, van Rheenen J.

Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):E2357-E2364. doi: 10.1073/pnas.1701219114. Epub 2017 Mar 7.

14.

Molecular dissection of germline chromothripsis in a developmental context using patient-derived iPS cells.

Middelkamp S, van Heesch S, Braat AK, de Ligt J, van Iterson M, Simonis M, van Roosmalen MJ, Kelder MJ, Kruisselbrink E, Hochstenbach R, Verbeek NE, Ippel EF, Adolfs Y, Pasterkamp RJ, Kloosterman WP, Kuijk EW, Cuppen E.

Genome Med. 2017 Jan 26;9(1):9. doi: 10.1186/s13073-017-0399-z.

15.

Novel mutations in LRP6 highlight the role of WNT signaling in tooth agenesis.

Ockeloen CW, Khandelwal KD, Dreesen K, Ludwig KU, Sullivan R, van Rooij IALM, Thonissen M, Swinnen S, Phan M, Conte F, Ishorst N, Gilissen C, RoaFuentes L, van de Vorst M, Henkes A, Steehouwer M, van Beusekom E, Bloemen M, Vankeirsbilck B, Bergé S, Hens G, Schoenaers J, Poorten VV, Roosenboom J, Verdonck A, Devriendt K, Roeleveldt N, Jhangiani SN, Vissers LELM, Lupski JR, de Ligt J, Von den Hoff JW, Pfundt R, Brunner HG, Zhou H, Dixon J, Mangold E, van Bokhoven H, Dixon MJ, Kleefstra T, Hoischen A, Carels CEL.

Genet Med. 2016 Nov;18(11):1158-1162. doi: 10.1038/gim.2016.10. Epub 2016 Mar 10.

16.

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.

17.

Tissue-specific mutation accumulation in human adult stem cells during life.

Blokzijl F, de Ligt J, Jager M, Sasselli V, Roerink S, Sasaki N, Huch M, Boymans S, Kuijk E, Prins P, Nijman IJ, Martincorena I, Mokry M, Wiegerinck CL, Middendorp S, Sato T, Schwank G, Nieuwenhuis EE, Verstegen MM, van der Laan LJ, de Jonge J, IJzermans JN, Vries RG, van de Wetering M, Stratton MR, Clevers H, Cuppen E, van Boxtel R.

Nature. 2016 Oct 13;538(7624):260-264. doi: 10.1038/nature19768. Epub 2016 Oct 3.

18.

The Genomic Scrapheap Challenge; Extracting Relevant Data from Unmapped Whole Genome Sequencing Reads, Including Strain Specific Genomic Segments, in Rats.

van der Weide RH, Simonis M, Hermsen R, Toonen P, Cuppen E, de Ligt J.

PLoS One. 2016 Aug 8;11(8):e0160036. doi: 10.1371/journal.pone.0160036. eCollection 2016.

19.

Allelic Mutations of KITLG, Encoding KIT Ligand, Cause Asymmetric and Unilateral Hearing Loss and Waardenburg Syndrome Type 2.

Zazo Seco C, Serrão de Castro L, van Nierop JW, Morín M, Jhangiani S, Verver EJ, Schraders M, Maiwald N, Wesdorp M, Venselaar H, Spruijt L, Oostrik J, Schoots J; Baylor-Hopkins Center for Mendelian Genomics, van Reeuwijk J, Lelieveld SH, Huygen PL, Insenser M, Admiraal RJ, Pennings RJ, Hoefsloot LH, Arias-Vásquez A, de Ligt J, Yntema HG, Jansen JH, Muzny DM, Huls G, van Rossum MM, Lupski JR, Moreno-Pelayo MA, Kunst HP, Kremer H.

Am J Hum Genet. 2015 Nov 5;97(5):647-60. doi: 10.1016/j.ajhg.2015.09.011. Epub 2015 Oct 29.

20.

Novel genetic causes for cerebral visual impairment.

Bosch DG, Boonstra FN, de Leeuw N, Pfundt R, Nillesen WM, de Ligt J, Gilissen C, Jhangiani S, Lupski JR, Cremers FP, de Vries BB.

Eur J Hum Genet. 2016 May;24(5):660-5. doi: 10.1038/ejhg.2015.186. Epub 2015 Sep 9.

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