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Items: 36

1.

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.

2.

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.

3.

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.

4.

Urinary metabolites predict prolonged duration of delayed graft function in DCD kidney transplant recipients.

Kostidis S, Bank JR, Soonawala D, Nevedomskaya E, van Kooten C, Mayboroda OA, de Fijter JW.

Am J Transplant. 2019 Jan;19(1):110-122. doi: 10.1111/ajt.14941. Epub 2018 Jun 15.

PMID:
29786954
5.

Recent Advances in Prostate Cancer Treatment and Drug Discovery.

Nevedomskaya E, Baumgart SJ, Haendler B.

Int J Mol Sci. 2018 May 4;19(5). pii: E1359. doi: 10.3390/ijms19051359. Review.

6.

The adaptive immune system promotes initiation of prostate carcinogenesis in a human c-Myc transgenic mouse model.

Melis MHM, Nevedomskaya E, van Burgsteden J, Cioni B, van Zeeburg HJT, Song JY, Zevenhoven J, Hawinkels LJAC, de Visser KE, Bergman AM.

Oncotarget. 2017 Sep 28;8(55):93867-93877. doi: 10.18632/oncotarget.21305. eCollection 2017 Nov 7.

7.

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
8.

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].

9.

Comparative Cistromics Reveals Genomic Cross-talk between FOXA1 and ERα in Tamoxifen-Associated Endometrial Carcinomas.

Droog M, Nevedomskaya E, Kim Y, Severson T, Flach KD, Opdam M, Schuurman K, Gradowska P, Hauptmann M, Dackus G, Hollema H, Mourits M, Nederlof P, van Boven H, Linn SC, Wessels L, van Leeuwen FE, Zwart W.

Cancer Res. 2016 Jul 1;76(13):3773-84. doi: 10.1158/0008-5472.CAN-14-1813. Epub 2016 May 6. Erratum in: Cancer Res. 2018 May 1;78(9):2446.

10.

Neoadjuvant tamoxifen synchronizes ERα binding and gene expression profiles related to outcome and proliferation.

Severson TM, Nevedomskaya E, Peeters J, Kuilman T, Krijgsman O, van Rossum A, Droog M, Kim Y, Koornstra R, Beumer I, Glas AM, Peeper D, Wesseling J, Simon IM, Wessels L, Linn SC, Zwart W.

Oncotarget. 2016 Jun 7;7(23):33901-18. doi: 10.18632/oncotarget.8983.

11.

mTOR pathway activation is a favorable prognostic factor in human prostate adenocarcinoma.

Stelloo S, Sanders J, Nevedomskaya E, de Jong J, Peters D, van Leenders GJ, Jenster G, Bergman AM, Zwart W.

Oncotarget. 2016 May 31;7(22):32916-24. doi: 10.18632/oncotarget.8767.

12.

Androgen receptor DNA binding and chromatin accessibility profiling in prostate cancer.

Nevedomskaya E, Stelloo S, van der Poel HG, de Jong J, Wessels LF, Bergman AM, Zwart W.

Genom Data. 2015 Dec 28;7:124-6. doi: 10.1016/j.gdata.2015.12.020. eCollection 2016 Mar.

13.

Mastermind-Like 3 Controls Proliferation and Differentiation in Neuroblastoma.

Heynen GJ, Nevedomskaya E, Palit S, Jagalur Basheer N, Lieftink C, Schlicker A, Zwart W, Bernards R, Bajpe PK.

Mol Cancer Res. 2016 May;14(5):411-22. doi: 10.1158/1541-7786.MCR-15-0291-T. Epub 2016 Jan 19.

14.

Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9.

Korkmaz G, Lopes R, Ugalde AP, Nevedomskaya E, Han R, Myacheva K, Zwart W, Elkon R, Agami R.

Nat Biotechnol. 2016 Feb;34(2):192-8. doi: 10.1038/nbt.3450. Epub 2016 Jan 11.

PMID:
26751173
15.

A Systems Oncology Approach Identifies NT5E as a Key Metabolic Regulator in Tumor Cells and Modulator of Platinum Sensitivity.

Nevedomskaya E, Perryman R, Solanki S, Syed N, Mayboroda OA, Keun HC.

J Proteome Res. 2016 Jan 4;15(1):280-90. doi: 10.1021/acs.jproteome.5b00793. Epub 2015 Dec 17.

16.

Genome-wide epigenetic profiling of breast cancer tumors treated with aromatase inhibitors.

Nevedomskaya E, Wessels L, Zwart W.

Genom Data. 2014 Jul 8;2:195-8. doi: 10.1016/j.gdata.2014.06.023. eCollection 2014 Dec.

17.

Systematic integration of molecular profiles identifies miR-22 as a regulator of lipid and folate metabolism in breast cancer cells.

Koufaris C, Valbuena GN, Pomyen Y, Tredwell GD, Nevedomskaya E, Lau CH, Yang T, Benito A, Ellis JK, Keun HC.

Oncogene. 2016 May;35(21):2766-76. doi: 10.1038/onc.2015.333. Epub 2015 Oct 19.

18.

Androgen receptor profiling predicts prostate cancer outcome.

Stelloo S, Nevedomskaya E, van der Poel HG, de Jong J, van Leenders GJ, Jenster G, Wessels LF, Bergman AM, Zwart W.

EMBO Mol Med. 2015 Nov;7(11):1450-64. doi: 10.15252/emmm.201505424.

19.

APOBEC3B-Mediated Cytidine Deamination Is Required for Estrogen Receptor Action in Breast Cancer.

Periyasamy M, Patel H, Lai CF, Nguyen VTM, Nevedomskaya E, Harrod A, Russell R, Remenyi J, Ochocka AM, Thomas RS, Fuller-Pace F, Győrffy B, Caldas C, Navaratnam N, Carroll JS, Zwart W, Coombes RC, Magnani L, Buluwela L, Ali S.

Cell Rep. 2015 Oct 6;13(1):108-121. doi: 10.1016/j.celrep.2015.08.066. Epub 2015 Sep 24.

20.

SRC3 Phosphorylation at Serine 543 Is a Positive Independent Prognostic Factor in ER-Positive Breast Cancer.

Zwart W, Flach KD, Rudraraju B, Abdel-Fatah TM, Gojis O, Canisius S, Moore D, Nevedomskaya E, Opdam M, Droog M, Hofland I, Chan S, Shaw J, Ellis IO, Coombes RC, Carroll JS, Ali S, Palmieri C.

Clin Cancer Res. 2016 Jan 15;22(2):479-91. doi: 10.1158/1078-0432.CCR-14-3277. Epub 2015 Sep 14.

21.

CopywriteR: DNA copy number detection from off-target sequence data.

Kuilman T, Velds A, Kemper K, Ranzani M, Bombardelli L, Hoogstraat M, Nevedomskaya E, Xu G, de Ruiter J, Lolkema MP, Ylstra B, Jonkers J, Rottenberg S, Wessels LF, Adams DJ, Peeper DS, Krijgsman O.

Genome Biol. 2015 Feb 27;16:49. doi: 10.1186/s13059-015-0617-1.

22.

Exploratory analysis of urinary tract infection using a GC-APCI-MS platform.

Pacchiarotta T, Derks RJ, Nevedomskaya E, van der Starre W, van Dissel J, Deelder A, Mayboroda OA.

Analyst. 2015 Apr 21;140(8):2834-41. doi: 10.1039/c5an00033e. Epub 2015 Mar 2.

PMID:
25730398
23.

Complex formation and function of estrogen receptor α in transcription requires RIP140.

Rosell M, Nevedomskaya E, Stelloo S, Nautiyal J, Poliandri A, Steel JH, Wessels LF, Carroll JS, Parker MG, Zwart W.

Cancer Res. 2014 Oct 1;74(19):5469-79. doi: 10.1158/0008-5472.CAN-13-3429. Epub 2014 Aug 21.

24.

Phosphorylation of activating transcription factor-2 (ATF-2) within the activation domain is a key determinant of sensitivity to tamoxifen in breast cancer.

Rudraraju B, Droog M, Abdel-Fatah TM, Zwart W, Giannoudis A, Malki MI, Moore D, Patel H, Shaw J, Ellis IO, Chan S, Brooke GN, Nevedomskaya E, Lo Nigro C, Carroll J, Coombes RC, Bevan C, Ali S, Palmieri C.

Breast Cancer Res Treat. 2014 Sep;147(2):295-309. doi: 10.1007/s10549-014-3098-0. Epub 2014 Aug 22.

PMID:
25141981
25.

VAV3 mediates resistance to breast cancer endocrine therapy.

Aguilar H, Urruticoechea A, Halonen P, Kiyotani K, Mushiroda T, Barril X, Serra-Musach J, Islam A, Caizzi L, Di Croce L, Nevedomskaya E, Zwart W, Bostner J, Karlsson E, Pérez Tenorio G, Fornander T, Sgroi DC, Garcia-Mata R, Jansen MP, García N, Bonifaci N, Climent F, Soler MT, Rodríguez-Vida A, Gil M, Brunet J, Martrat G, Gómez-Baldó L, Extremera AI, Figueras A, Balart J, Clarke R, Burnstein KL, Carlson KE, Katzenellenbogen JA, Vizoso M, Esteller M, Villanueva A, Rodríguez-Peña AB, Bustelo XR, Nakamura Y, Zembutsu H, Stål O, Beijersbergen RL, Pujana MA.

Breast Cancer Res. 2014 May 28;16(3):R53. doi: 10.1186/bcr3664.

26.

(1)H NMR-based metabolic profiling of urinary tract infection: combining multiple statistical models and clinical data.

Nevedomskaya E, Pacchiarotta T, Artemov A, Meissner A, van Nieuwkoop C, van Dissel JT, Mayboroda OA, Deelder AM.

Metabolomics. 2012 Dec;8(6):1227-1235. Epub 2012 Feb 29.

27.

Fibrinogen alpha chain O-glycopeptides as possible markers of urinary tract infection.

Pacchiarotta T, Hensbergen PJ, Wuhrer M, van Nieuwkoop C, Nevedomskaya E, Derks RJ, Schoenmaker B, Koeleman CA, van Dissel J, Deelder AM, Mayboroda OA.

J Proteomics. 2012 Jan 4;75(3):1067-73. doi: 10.1016/j.jprot.2011.10.021. Epub 2011 Oct 31.

PMID:
22075168
28.

Cross-platform analysis of longitudinal data in metabolomics.

Nevedomskaya E, Mayboroda OA, Deelder AM.

Mol Biosyst. 2011 Dec;7(12):3214-22. doi: 10.1039/c1mb05280b. Epub 2011 Sep 22.

PMID:
21947311
29.

Evaluation of GC-APCI/MS and GC-FID as a complementary platform.

Pacchiarotta T, Nevedomskaya E, Carrasco-Pancorbo A, Deelder AM, Mayboroda OA.

J Biomol Tech. 2010 Dec;21(4):205-13.

30.

Metabolic profiling of human urine by CE-MS using a positively charged capillary coating and comparison with UPLC-MS.

Ramautar R, Nevedomskaya E, Mayboroda OA, Deelder AM, Wilson ID, Gika HG, Theodoridis GA, Somsen GW, de Jong GJ.

Mol Biosyst. 2011 Jan;7(1):194-9. doi: 10.1039/c0mb00032a. Epub 2010 Nov 5.

PMID:
21052608
31.

CE-MS for metabolic profiling of volume-limited urine samples: application to accelerated aging TTD mice.

Nevedomskaya E, Ramautar R, Derks R, Westbroek I, Zondag G, van der Pluijm I, Deelder AM, Mayboroda OA.

J Proteome Res. 2010 Sep 3;9(9):4869-74. doi: 10.1021/pr100634d.

PMID:
20690666
32.

Exploratory analysis of human urine by LC-ESI-TOF MS after high intake of olive oil: understanding the metabolism of polyphenols.

García-Villalba R, Carrasco-Pancorbo A, Nevedomskaya E, Mayboroda OA, Deelder AM, Segura-Carretero A, Fernández-Gutiérrez A.

Anal Bioanal Chem. 2010 Sep;398(1):463-75. doi: 10.1007/s00216-010-3899-x. Epub 2010 Jun 27.

PMID:
20582699
33.

Metabolic profiling of accelerated aging ERCC1 d/- mice.

Nevedomskaya E, Meissner A, Goraler S, de Waard M, Ridwan Y, Zondag G, van der Pluijm I, Deelder AM, Mayboroda OA.

J Proteome Res. 2010 Jul 2;9(7):3680-7. doi: 10.1021/pr100210k.

PMID:
20507129
34.

Gas chromatography/atmospheric pressure chemical ionization-time of flight mass spectrometry: analytical validation and applicability to metabolic profiling.

Carrasco-Pancorbo A, Nevedomskaya E, Arthen-Engeland T, Zey T, Zurek G, Baessmann C, Deelder AM, Mayboroda OA.

Anal Chem. 2009 Dec 15;81(24):10071-9. doi: 10.1021/ac9006073.

PMID:
19924863
35.

Alignment of capillary electrophoresis-mass spectrometry datasets using accurate mass information.

Nevedomskaya E, Derks R, Deelder AM, Mayboroda OA, Palmblad M.

Anal Bioanal Chem. 2009 Dec;395(8):2527-33. doi: 10.1007/s00216-009-3166-1. Epub 2009 Oct 14.

PMID:
19826795
36.

Explorative analysis of urine by capillary electrophoresis-mass spectrometry in chronic patients with complex regional pain syndrome.

Ramautar R, van der Plas AA, Nevedomskaya E, Derks RJ, Somsen GW, de Jong GJ, van Hilten JJ, Deelder AM, Mayboroda OA.

J Proteome Res. 2009 Dec;8(12):5559-67. doi: 10.1021/pr900651k.

PMID:
19821589

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