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Items: 1 to 50 of 167

1.

PRECISE: a domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors.

Mourragui S, Loog M, van de Wiel MA, Reinders MJT, Wessels LFA.

Bioinformatics. 2019 Jul 15;35(14):i510-i519. doi: 10.1093/bioinformatics/btz372.

2.

Loss of p53 triggers WNT-dependent systemic inflammation to drive breast cancer metastasis.

Wellenstein MD, Coffelt SB, Duits DEM, van Miltenburg MH, Slagter M, de Rink I, Henneman L, Kas SM, Prekovic S, Hau CS, Vrijland K, Drenth AP, de Korte-Grimmerink R, Schut E, van der Heijden I, Zwart W, Wessels LFA, Schumacher TN, Jonkers J, de Visser KE.

Nature. 2019 Aug;572(7770):538-542. doi: 10.1038/s41586-019-1450-6. Epub 2019 Jul 31.

PMID:
31367040
3.

Publisher Correction: Immune induction strategies in metastatic triple-negative breast cancer to enhance the sensitivity to PD-1 blockade: the TONIC trial.

Voorwerk L, Slagter M, Horlings HM, Sikorska K, van de Vijver KK, de Maaker M, Nederlof I, Kluin RJC, Warren S, Ong S, Wiersma TG, Russell NS, Lalezari F, Schouten PC, Bakker NAM, Ketelaars SLC, Peters D, Lange CAH, van Werkhoven E, van Tinteren H, Mandjes IAM, Kemper I, Onderwater S, Chalabi M, Wilgenhof S, Haanen JBAG, Salgado R, de Visser KE, Sonke GS, Wessels LFA, Linn SC, Schumacher TN, Blank CU, Kok M.

Nat Med. 2019 Jul;25(7):1175. doi: 10.1038/s41591-019-0520-5.

PMID:
31209337
4.

Selective Loss of PARG Restores PARylation and Counteracts PARP Inhibitor-Mediated Synthetic Lethality.

Gogola E, Duarte AA, de Ruiter JR, Wiegant WW, Schmid JA, de Bruijn R, James DI, Llobet SG, Vis DJ, Annunziato S, van den Broek B, Barazas M, Kersbergen A, van de Ven M, Tarsounas M, Ogilvie DJ, van Vugt M, Wessels LFA, Bartkova J, Gromova I, Andújar-Sánchez M, Bartek J, Lopes M, van Attikum H, Borst P, Jonkers J, Rottenberg S.

Cancer Cell. 2019 Jun 10;35(6):950-952. doi: 10.1016/j.ccell.2019.05.012. No abstract available.

5.

Identifying Epistasis in Cancer Genomes: A Delicate Affair.

van de Haar J, Canisius S, Yu MK, Voest EE, Wessels LFA, Ideker T.

Cell. 2019 May 30;177(6):1375-1383. doi: 10.1016/j.cell.2019.05.005. Review.

PMID:
31150618
6.

Immune induction strategies in metastatic triple-negative breast cancer to enhance the sensitivity to PD-1 blockade: the TONIC trial.

Voorwerk L, Slagter M, Horlings HM, Sikorska K, van de Vijver KK, de Maaker M, Nederlof I, Kluin RJC, Warren S, Ong S, Wiersma TG, Russell NS, Lalezari F, Schouten PC, Bakker NAM, Ketelaars SLC, Peters D, Lange CAH, van Werkhoven E, van Tinteren H, Mandjes IAM, Kemper I, Onderwater S, Chalabi M, Wilgenhof S, Haanen JBAG, Salgado R, de Visser KE, Sonke GS, Wessels LFA, Linn SC, Schumacher TN, Blank CU, Kok M.

Nat Med. 2019 Jun;25(6):920-928. doi: 10.1038/s41591-019-0432-4. Epub 2019 May 13. Erratum in: Nat Med. 2019 Jun 17;:.

PMID:
31086347
7.

Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency.

Gisler S, Gonçalves JP, Akhtar W, de Jong J, Pindyurin AV, Wessels LFA, van Lohuizen M.

Nat Commun. 2019 Apr 8;10(1):1598. doi: 10.1038/s41467-019-09551-w.

8.

Genetic Factors Associated with a Poor Outcome in Head and Neck Cancer Patients Receiving Definitive Chemoradiotherapy.

Vossen DM, Verhagen CVM, van der Heijden M, Essers PBM, Bartelink H, Verheij M, Wessels LFA, van den Brekel MWM, Vens C.

Cancers (Basel). 2019 Mar 29;11(4). pii: E445. doi: 10.3390/cancers11040445.

9.

Inhibition of the Replication Stress Response Is a Synthetic Vulnerability in SCLC That Acts Synergistically in Combination with Cisplatin.

Nagel R, Avelar AT, Aben N, Proost N, van de Ven M, van der Vliet J, Cozijnsen M, de Vries H, Wessels LFA, Berns A.

Mol Cancer Ther. 2019 Apr;18(4):762-770. doi: 10.1158/1535-7163.MCT-18-0972. Epub 2019 Mar 14.

10.

Comparative oncogenomics identifies combinations of driver genes and drug targets in BRCA1-mutated breast cancer.

Annunziato S, de Ruiter JR, Henneman L, Brambillasca CS, Lutz C, Vaillant F, Ferrante F, Drenth AP, van der Burg E, Siteur B, van Gerwen B, de Bruijn R, van Miltenburg MH, Huijbers IJ, van de Ven M, Visvader JE, Lindeman GJ, Wessels LFA, Jonkers J.

Nat Commun. 2019 Jan 23;10(1):397. doi: 10.1038/s41467-019-08301-2.

11.

Principal component analysis of binary genomics data.

Song Y, Westerhuis JA, Aben N, Michaut M, Wessels LFA, Smilde AK.

Brief Bioinform. 2019 Jan 18;20(1):317-329. doi: 10.1093/bib/bbx119.

PMID:
30657888
12.

Optimized ChIP-seq method facilitates transcription factor profiling in human tumors.

Singh AA, Schuurman K, Nevedomskaya E, Stelloo S, Linder S, Droog M, Kim Y, Sanders J, van der Poel H, Bergman AM, Wessels LF, Zwart W.

Life Sci Alliance. 2018 Dec 28;2(1):e201800115. doi: 10.26508/lsa.201800115. eCollection 2019 Feb.

13.

A role for the unfolded protein response stress sensor ERN1 in regulating the response to MEK inhibitors in KRAS mutant colon cancers.

Šuštić T, van Wageningen S, Bosdriesz E, Reid RJD, Dittmar J, Lieftink C, Beijersbergen RL, Wessels LFA, Rothstein R, Bernards R.

Genome Med. 2018 Nov 27;10(1):90. doi: 10.1186/s13073-018-0600-z.

14.

Integrative epigenetic taxonomy of primary prostate cancer.

Stelloo S, Nevedomskaya E, Kim Y, Schuurman K, Valle-Encinas E, Lobo J, Krijgsman O, Peeper DS, Chang SL, Feng FY, Wessels LFA, Henrique R, Jerónimo C, Bergman AM, Zwart W.

Nat Commun. 2018 Nov 21;9(1):4900. doi: 10.1038/s41467-018-07270-2.

15.

iTOP: inferring the topology of omics data.

Aben N, Westerhuis JA, Song Y, Kiers HAL, Michaut M, Smilde AK, Wessels LFA.

Bioinformatics. 2018 Sep 1;34(17):i988-i996. doi: 10.1093/bioinformatics/bty636.

16.

Comparative Network Reconstruction using mixed integer programming.

Bosdriesz E, Prahallad A, Klinger B, Sieber A, Bosma A, Bernards R, Blüthgen N, Wessels LFA.

Bioinformatics. 2018 Sep 1;34(17):i997-i1004. doi: 10.1093/bioinformatics/bty616.

17.

Role of variant allele fraction and rare SNP filtering to improve cellular DNA repair endpoint association.

Vossen DM, Verhagen CVM, Grénman R, Kluin RJC, Verheij M, van den Brekel MWM, Wessels LFA, Vens C.

PLoS One. 2018 Nov 8;13(11):e0206632. doi: 10.1371/journal.pone.0206632. eCollection 2018.

18.

Molecular characterization of breast and lung tumors by integration of multiple data types with functional sparse-factor analysis.

Bismeijer T, Canisius S, Wessels LFA.

PLoS Comput Biol. 2018 Oct 31;14(10):e1006520. doi: 10.1371/journal.pcbi.1006520. eCollection 2018 Oct.

19.

Transcriptomics and Transposon Mutagenesis Identify Multiple Mechanisms of Resistance to the FGFR Inhibitor AZD4547.

Kas SM, de Ruiter JR, Schipper K, Schut E, Bombardelli L, Wientjens E, Drenth AP, de Korte-Grimmerink R, Mahakena S, Phillips C, Smith PD, Klarenbeek S, van de Wetering K, Berns A, Wessels LFA, Jonkers J.

Cancer Res. 2018 Oct 1;78(19):5668-5679. doi: 10.1158/0008-5472.CAN-18-0757. Epub 2018 Aug 16.

20.

Mouse models in the era of large human tumour sequencing studies.

de Ruiter JR, Wessels LFA, Jonkers J.

Open Biol. 2018 Aug;8(8). pii: 180080. doi: 10.1098/rsob.180080. Review.

21.

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. Epub 2018 Aug 31.

22.

Modelling signalling networks from perturbation data.

Dorel M, Klinger B, Gross T, Sieber A, Prahallad A, Bosdriesz E, Wessels LFA, Blüthgen N.

Bioinformatics. 2018 Dec 1;34(23):4079-4086. doi: 10.1093/bioinformatics/bty473.

PMID:
29931053
23.

Selective Loss of PARG Restores PARylation and Counteracts PARP Inhibitor-Mediated Synthetic Lethality.

Gogola E, Duarte AA, de Ruiter JR, Wiegant WW, Schmid JA, de Bruijn R, James DI, Guerrero Llobet S, Vis DJ, Annunziato S, van den Broek B, Barazas M, Kersbergen A, van de Ven M, Tarsounas M, Ogilvie DJ, van Vugt M, Wessels LFA, Bartkova J, Gromova I, Andújar-Sánchez M, Bartek J, Lopes M, van Attikum H, Borst P, Jonkers J, Rottenberg S.

Cancer Cell. 2018 Jun 11;33(6):1078-1093.e12. doi: 10.1016/j.ccell.2018.05.008. Erratum in: Cancer Cell. 2019 Jun 10;35(6):950-952.

24.

Comparative genomic analysis of oral versus laryngeal and pharyngeal cancer.

Vossen DM, Verhagen CVM, Verheij M, Wessels LFA, Vens C, van den Brekel MWM.

Oral Oncol. 2018 Jun;81:35-44. doi: 10.1016/j.oraloncology.2018.04.006. Epub 2018 Apr 13.

PMID:
29884412
25.

Integrative Modeling Identifies Key Determinants of Inhibitor Sensitivity in Breast Cancer Cell Lines.

Jastrzebski K, Thijssen B, Kluin RJC, de Lint K, Majewski IJ, Beijersbergen RL, Wessels LFA.

Cancer Res. 2018 Aug 1;78(15):4396-4410. doi: 10.1158/0008-5472.CAN-17-2698. Epub 2018 May 29.

26.

Loss of androgen receptor signaling in prostate cancer-associated fibroblasts (CAFs) promotes CCL2- and CXCL8-mediated cancer cell migration.

Cioni B, Nevedomskaya E, Melis MHM, van Burgsteden J, Stelloo S, Hodel E, Spinozzi D, de Jong J, van der Poel H, de Boer JP, Wessels LFA, Zwart W, Bergman AM.

Mol Oncol. 2018 Aug;12(8):1308-1323. doi: 10.1002/1878-0261.12327. Epub 2018 Jul 10.

27.

MAP3K1 and MAP2K4 mutations are associated with sensitivity to MEK inhibitors in multiple cancer models.

Xue Z, Vis DJ, Bruna A, Sustic T, van Wageningen S, Batra AS, Rueda OM, Bosdriesz E, Caldas C, Wessels LFA, Bernards R.

Cell Res. 2018 Jul;28(7):719-729. doi: 10.1038/s41422-018-0044-4. Epub 2018 May 24.

28.

Fanconi anemia and homologous recombination gene variants are associated with functional DNA repair defects in vitro and poor outcome in patients with advanced head and neck squamous cell carcinoma.

Verhagen CVM, Vossen DM, Borgmann K, Hageman F, Grénman R, Verwijs-Janssen M, Mout L, Kluin RJC, Nieuwland M, Severson TM, Velds A, Kerkhoven R, O'Connor MJ, van der Heijden M, van Velthuysen ML, Verheij M, Wreesmann VB, Wessels LFA, van den Brekel MWM, Vens C.

Oncotarget. 2018 Apr 6;9(26):18198-18213. doi: 10.18632/oncotarget.24797. eCollection 2018 Apr 6.

29.

Insertional mutagenesis in a HER2-positive breast cancer model reveals ERAS as a driver of cancer and therapy resistance.

Ikink GJ, Boer M, Bakker ERM, Vendel-Zwaagstra A, Klijn C, Ten Hoeve J, Jonkers J, Wessels LF, Hilkens J.

Oncogene. 2018 Mar;37(12):1594-1609. doi: 10.1038/s41388-017-0031-0. Epub 2018 Jan 12.

30.

Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimates.

Thijssen B, Dijkstra TMH, Heskes T, Wessels LFA.

Bioinformatics. 2018 Mar 1;34(5):803-811. doi: 10.1093/bioinformatics/btx666.

31.

Endogenous androgen receptor proteomic profiling reveals genomic subcomplex involved in prostate tumorigenesis.

Stelloo S, Nevedomskaya E, Kim Y, Hoekman L, Bleijerveld OB, Mirza T, Wessels LFA, van Weerden WM, Altelaar AFM, Bergman AM, Zwart W.

Oncogene. 2018 Jan 18;37(3):313-322. doi: 10.1038/onc.2017.330. Epub 2017 Sep 18.

PMID:
28925401
32.

Mammary tumor-derived CCL2 enhances pro-metastatic systemic inflammation through upregulation of IL1β in tumor-associated macrophages.

Kersten K, Coffelt SB, Hoogstraat M, Verstegen NJM, Vrijland K, Ciampricotti M, Doornebal CW, Hau CS, Wellenstein MD, Salvagno C, Doshi P, Lips EH, Wessels LFA, de Visser KE.

Oncoimmunology. 2017 Jun 19;6(8):e1334744. doi: 10.1080/2162402X.2017.1334744. eCollection 2017.

33.

Predicting clinical benefit from everolimus in patients with advanced solid tumors, the CPCT-03 study.

Weeber F, Cirkel GA, Hoogstraat M, Bins S, Gadellaa-van Hooijdonk CGM, Ooft S, van Werkhoven E, Willems SM, van Stralen M, Veldhuis WB, Besselink NJM, Horlings HM, Steeghs N, de Jonge MJ, Langenberg MHG, Wessels LFA, Cuppen EPJG, Schellens JH, Sleijfer S, Lolkema MP, Voest EE.

Oncotarget. 2017 Mar 8;8(33):55582-55592. doi: 10.18632/oncotarget.16029. eCollection 2017 Aug 15.

34.

Identification of CMTM6 and CMTM4 as PD-L1 protein regulators.

Mezzadra R, Sun C, Jae LT, Gomez-Eerland R, de Vries E, Wu W, Logtenberg MEW, Slagter M, Rozeman EA, Hofland I, Broeks A, Horlings HM, Wessels LFA, Blank CU, Xiao Y, Heck AJR, Borst J, Brummelkamp TR, Schumacher TNM.

Nature. 2017 Sep 7;549(7670):106-110. doi: 10.1038/nature23669. Epub 2017 Aug 16.

35.

Complementary Value of Contralateral Parenchymal Enhancement on DCE-MRI to Prognostic Models and Molecular Assays in High-risk ER+/HER2- Breast Cancer.

van der Velden BHM, Elias SG, Bismeijer T, Loo CE, Viergever MA, Wessels LFA, Gilhuijs KGA.

Clin Cancer Res. 2017 Nov 1;23(21):6505-6515. doi: 10.1158/1078-0432.CCR-17-0176. Epub 2017 Aug 8.

36.

Identification of a Druggable Pathway Controlling Glioblastoma Invasiveness.

Pencheva N, de Gooijer MC, Vis DJ, Wessels LFA, Würdinger T, van Tellingen O, Bernards R.

Cell Rep. 2017 Jul 5;20(1):48-60. doi: 10.1016/j.celrep.2017.06.036.

37.

Insertional mutagenesis identifies drivers of a novel oncogenic pathway in invasive lobular breast carcinoma.

Kas SM, de Ruiter JR, Schipper K, Annunziato S, Schut E, Klarenbeek S, Drenth AP, van der Burg E, Klijn C, Ten Hoeve JJ, Adams DJ, Koudijs MJ, Wesseling J, Nethe M, Wessels LFA, Jonkers J.

Nat Genet. 2017 Aug;49(8):1219-1230. doi: 10.1038/ng.3905. Epub 2017 Jun 26.

PMID:
28650484
38.

Identifying transposon insertions and their effects from RNA-sequencing data.

de Ruiter JR, Kas SM, Schut E, Adams DJ, Koudijs MJ, Wessels LFA, Jonkers J.

Nucleic Acids Res. 2017 Jul 7;45(12):7064-7077. doi: 10.1093/nar/gkx461.

39.

Towards a global cancer knowledge network: dissecting the current international cancer genomic sequencing landscape.

Vis DJ, Lewin J, Liao RG, Mao M, Andre F, Ward RL, Calvo F, Teh BT, Camargo AA, Knoppers BM, Sawyers CL, Wessels LFA, Lawler M, Siu LL, Voest E; Clinical Working Group of the Global Alliance for Genomics and Health.

Ann Oncol. 2017 May 1;28(5):1145-1151. doi: 10.1093/annonc/mdx037.

40.

Systematic functional perturbations uncover a prognostic genetic network driving human breast cancer.

Gallenne T, Ross KN, Visser NL, Salony, Desmet CJ, Wittner BS, Wessels LFA, Ramaswamy S, Peeper DS.

Oncotarget. 2017 Mar 15;8(13):20572-20587. doi: 10.18632/oncotarget.16244.

41.

Estrogen receptor α wields treatment-specific enhancers between morphologically similar endometrial tumors.

Droog M, Nevedomskaya E, Dackus GM, Fles R, Kim Y, Hollema H, Mourits MJ, Nederlof PM, van Boven HH, Linn SC, van Leeuwen FE, Wessels LF, Zwart W.

Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):E1316-E1325. doi: 10.1073/pnas.1615233114. Epub 2017 Feb 6. Erratum in: Proc Natl Acad Sci U S A. 2018 Jan 22;:. Mourits, Marian [corrected to Mourits, Marian J].

43.

Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy.

Knijnenburg TA, Klau GW, Iorio F, Garnett MJ, McDermott U, Shmulevich I, Wessels LF.

Sci Rep. 2016 Nov 23;6:36812. doi: 10.1038/srep36812.

44.

Loss of ARID1A Activates ANXA1, which Serves as a Predictive Biomarker for Trastuzumab Resistance.

Berns K, Sonnenblick A, Gennissen A, Brohée S, Hijmans EM, Evers B, Fumagalli D, Desmedt C, Loibl S, Denkert C, Neven P, Guo W, Zhang F, Knijnenburg TA, Bosse T, van der Heijden MS, Hindriksen S, Nijkamp W, Wessels LF, Joensuu H, Mills GB, Beijersbergen RL, Sotiriou C, Bernards R.

Clin Cancer Res. 2016 Nov 1;22(21):5238-5248. Epub 2016 May 12.

45.

BCM: toolkit for Bayesian analysis of Computational Models using samplers.

Thijssen B, Dijkstra TM, Heskes T, Wessels LF.

BMC Syst Biol. 2016 Oct 21;10(1):100.

46.

Large variety in a panel of human colon cancer organoids in response to EZH2 inhibition.

Koppens MA, Bounova G, Cornelissen-Steijger P, de Vries N, Sansom OJ, Wessels LF, van Lohuizen M.

Oncotarget. 2016 Oct 25;7(43):69816-69828. doi: 10.18632/oncotarget.12002.

47.

TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types.

Aben N, Vis DJ, Michaut M, Wessels LF.

Bioinformatics. 2016 Sep 1;32(17):i413-i420. doi: 10.1093/bioinformatics/btw449.

PMID:
27587657
48.

A Landscape of Pharmacogenomic Interactions in Cancer.

Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, Aben N, Gonçalves E, Barthorpe S, Lightfoot H, Cokelaer T, Greninger P, van Dyk E, Chang H, de Silva H, Heyn H, Deng X, Egan RK, Liu Q, Mironenko T, Mitropoulos X, Richardson L, Wang J, Zhang T, Moran S, Sayols S, Soleimani M, Tamborero D, Lopez-Bigas N, Ross-Macdonald P, Esteller M, Gray NS, Haber DA, Stratton MR, Benes CH, Wessels LFA, Saez-Rodriguez J, McDermott U, Garnett MJ.

Cell. 2016 Jul 28;166(3):740-754. doi: 10.1016/j.cell.2016.06.017. Epub 2016 Jul 7.

49.

RUBIC identifies driver genes by detecting recurrent DNA copy number breaks.

van Dyk E, Hoogstraat M, Ten Hoeve J, Reinders MJ, Wessels LF.

Nat Commun. 2016 Jul 11;7:12159. doi: 10.1038/ncomms12159.

50.

Deletion of Polycomb Repressive Complex 2 From Mouse Intestine Causes Loss of Stem Cells.

Koppens MA, Bounova G, Gargiulo G, Tanger E, Janssen H, Cornelissen-Steijger P, Blom M, Song JY, Wessels LF, van Lohuizen M.

Gastroenterology. 2016 Oct;151(4):684-697.e12. doi: 10.1053/j.gastro.2016.06.020. Epub 2016 Jun 21.

PMID:
27342214

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