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Items: 25

1.

Genomic data integration by WON-PARAFAC identifies interpretable factors for predicting drug-sensitivity in vivo.

Kim Y, Bismeijer T, Zwart W, Wessels LFA, Vis DJ.

Nat Commun. 2019 Nov 6;10(1):5034. doi: 10.1038/s41467-019-13027-2.

2.

Patient-derived organoids can predict response to chemotherapy in metastatic colorectal cancer patients.

Ooft SN, Weeber F, Dijkstra KK, McLean CM, Kaing S, van Werkhoven E, Schipper L, Hoes L, Vis DJ, van de Haar J, Prevoo W, Snaebjornsson P, van der Velden D, Klein M, Chalabi M, Boot H, van Leerdam M, Bloemendal HJ, Beerepoot LV, Wessels L, Cuppen E, Clevers H, Voest EE.

Sci Transl Med. 2019 Oct 9;11(513). pii: eaay2574. doi: 10.1126/scitranslmed.aay2574.

PMID:
31597751
3.

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.

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, 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.

5.

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.

6.

Pathogenic and targetable genetic alterations in 70 urachal adenocarcinomas.

Reis H, van der Vos KE, Niedworok C, Herold T, Módos O, Szendrői A, Hager T, Ingenwerth M, Vis DJ, Behrendt MA, de Jong J, van der Heijden MS, Peyronnet B, Mathieu R, Wiesweg M, Ablat J, Okon K, Tolkach Y, Keresztes D, Nagy N, Bremmer F, Gaisa NT, Chlosta P, Kriegsmann J, Kovalszky I, Timar J, Kristiansen G, Radzun HJ, Knüchel R, Schuler M, Black PC, Rübben H, Hadaschik BA, Schmid KW, van Rhijn BWG, Nyirády P, Szarvas T.

Int J Cancer. 2018 Oct 1;143(7):1764-1773. doi: 10.1002/ijc.31547. Epub 2018 May 10.

7.

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.

8.

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.

9.

Second-line Chemotherapy in Older Patients With Metastatic Urothelial Carcinoma: Pooled Analysis of 10 Second-line Studies.

Salah S, Lee JL, Rozzi A, Kitamura H, Matsumoto K, Vis DJ, Srinivas S, Morales-Barrera R, Carles J, Al-Rimawi D, Lee S, Kim KH, Izumi K, Lewin J.

Clin Genitourin Cancer. 2017 Aug;15(4):e563-e571. doi: 10.1016/j.clgc.2016.12.014. Epub 2016 Dec 22.

PMID:
28065418
10.

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
11.

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.

12.

Multilevel models improve precision and speed of IC50 estimates.

Vis DJ, Bombardelli L, Lightfoot H, Iorio F, Garnett MJ, Wessels LF.

Pharmacogenomics. 2016 May;17(7):691-700. doi: 10.2217/pgs.16.15. Epub 2016 May 16.

13.

Facilitating a culture of responsible and effective sharing of cancer genome data.

Siu LL, Lawler M, Haussler D, Knoppers BM, Lewin J, Vis DJ, Liao RG, Andre F, Banks I, Barrett JC, Caldas C, Camargo AA, Fitzgerald RC, Mao M, Mattison JE, Pao W, Sellers WR, Sullivan P, Teh BT, Ward RL, ZenKlusen JC, Sawyers CL, Voest EE.

Nat Med. 2016 May 5;22(5):464-71. doi: 10.1038/nm.4089.

14.

Integration of genomic, transcriptomic and proteomic data identifies two biologically distinct subtypes of invasive lobular breast cancer.

Michaut M, Chin SF, Majewski I, Severson TM, Bismeijer T, de Koning L, Peeters JK, Schouten PC, Rueda OM, Bosma AJ, Tarrant F, Fan Y, He B, Xue Z, Mittempergher L, Kluin RJ, Heijmans J, Snel M, Pereira B, Schlicker A, Provenzano E, Ali HR, Gaber A, O'Hurley G, Lehn S, Muris JJ, Wesseling J, Kay E, Sammut SJ, Bardwell HA, Barbet AS, Bard F, Lecerf C, O'Connor DP, Vis DJ, Benes CH, McDermott U, Garnett MJ, Simon IM, Jirström K, Dubois T, Linn SC, Gallagher WM, Wessels LF, Caldas C, Bernards R.

Sci Rep. 2016 Jan 5;6:18517. doi: 10.1038/srep18517.

15.

Subunit composition of VRAC channels determines substrate specificity and cellular resistance to Pt-based anti-cancer drugs.

Planells-Cases R, Lutter D, Guyader C, Gerhards NM, Ullrich F, Elger DA, Kucukosmanoglu A, Xu G, Voss FK, Reincke SM, Stauber T, Blomen VA, Vis DJ, Wessels LF, Brummelkamp TR, Borst P, Rottenberg S, Jentsch TJ.

EMBO J. 2015 Dec 14;34(24):2993-3008. doi: 10.15252/embj.201592409. Epub 2015 Nov 3.

16.

Intra- and inter-tumor heterogeneity in a vemurafenib-resistant melanoma patient and derived xenografts.

Kemper K, Krijgsman O, Cornelissen-Steijger P, Shahrabi A, Weeber F, Song JY, Kuilman T, Vis DJ, Wessels LF, Voest EE, Schumacher TN, Blank CU, Adams DJ, Haanen JB, Peeper DS.

EMBO Mol Med. 2015 Sep;7(9):1104-18. doi: 10.15252/emmm.201404914.

17.

Correlated measurement error hampers association network inference.

Kaduk M, Hoefsloot HC, Vis DJ, Reijmers T, van der Greef J, Smilde AK, Hendriks MM.

J Chromatogr B Analyt Technol Biomed Life Sci. 2014 Sep 1;966:93-9. doi: 10.1016/j.jchromb.2014.04.048. Epub 2014 May 2.

PMID:
24951433
18.

Network identification of hormonal regulation.

Vis DJ, Westerhuis JA, Hoefsloot HC, Roelfsema F, van der Greef J, Hendriks MM, Smilde AK.

PLoS One. 2014 May 22;9(5):e96284. doi: 10.1371/journal.pone.0096284. eCollection 2014.

19.

Inferring differences in the distribution of reaction rates across conditions.

Hendrickx DM, Hoefsloot HC, Hendriks MM, Vis DJ, Canelas AB, Teusink B, Smilde AK.

Mol Biosyst. 2012 Sep;8(9):2415-23. Epub 2012 Jul 11.

PMID:
22782002
20.

Detecting regulatory mechanisms in endocrine time series measurements.

Vis DJ, Westerhuis JA, Hoefsloot HC, Roelfsema F, Hendriks MM, Smilde AK.

PLoS One. 2012;7(3):e32985. doi: 10.1371/journal.pone.0032985. Epub 2012 Mar 26.

21.

Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness.

Zakrzewska A, van Eikenhorst G, Burggraaff JE, Vis DJ, Hoefsloot H, Delneri D, Oliver SG, Brul S, Smits GJ.

Mol Biol Cell. 2011 Nov;22(22):4435-46. doi: 10.1091/mbc.E10-08-0721. Epub 2011 Sep 30.

22.

Dynamic metabolomic data analysis: a tutorial review.

Smilde AK, Westerhuis JA, Hoefsloot HC, Bijlsma S, Rubingh CM, Vis DJ, Jellema RH, Pijl H, Roelfsema F, van der Greef J.

Metabolomics. 2010 Mar;6(1):3-17. Epub 2009 Dec 4.

23.

Endocrine pulse identification using penalized methods and a minimum set of assumptions.

Vis DJ, Westerhuis JA, Hoefsloot HC, Pijl H, Roelfsema F, van der Greef J, Smilde AK.

Am J Physiol Endocrinol Metab. 2010 Feb;298(2):E146-55. doi: 10.1152/ajpendo.00048.2009. Epub 2009 Oct 27.

24.

Phenotyping tea consumers by nutrikinetic analysis of polyphenolic end-metabolites.

van Velzen EJ, Westerhuis JA, van Duynhoven JP, van Dorsten FA, Grün CH, Jacobs DM, Duchateau GS, Vis DJ, Smilde AK.

J Proteome Res. 2009 Jul;8(7):3317-30. doi: 10.1021/pr801071p.

PMID:
19374449
25.

Statistical validation of megavariate effects in ASCA.

Vis DJ, Westerhuis JA, Smilde AK, van der Greef J.

BMC Bioinformatics. 2007 Aug 30;8:322.

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