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1

Cross-validated Cox regression on microarray gene expression data

Hans C. van Houwelingen, Tako Bruinsma, Augustinus A. M. Hart, Laura J. van't Veer, Lodewyk F. A. Wessels

Journal:

Statistics in Medicine

Year:

2006

Language:

english

File:

PDF, 230 KB

english, 2006

2

An expression profile for diagnosis of lymph node metastases from primary head and neck squamous cell carcinomas

Roepman, Paul, Wessels, Lodewyk F A, Kettelarij, Nienke, Kemmeren, Patrick, Miles, Antony J, Lijnzaad, Philip, Tilanus, Marcel G J, Koole, Ronald, Hordijk, Gert-Jan, van der Vliet, Peter C

Journal:

Nature Genetics

Year:

2005

Language:

english

File:

PDF, 328 KB

english, 2005

3

Synthetic Lethality in Cancer Therapeutics

Beijersbergen, Roderick L., Wessels, Lodewyk F.A., Bernards, René

Journal:

Annual Review of Cancer Biology

Year:

2017

Language:

english

File:

PDF, 1.16 MB

english, 2017

4

Identifying Epistasis in Cancer Genomes: A Delicate Affair

van de Haar, Joris, Canisius, Sander, Yu, Michael K., Voest, Emile E., Wessels, Lodewyk F.A., Ideker, Trey

Journal:

Year:

2019

Language:

english

File:

PDF, 4.02 MB

english, 2019

5

Chromatin Position Effects Assayed by Thousands of Reporters Integrated in Parallel

Akhtar, Waseem, de Jong, Johann, Pindyurin, Alexey V., Pagie, Ludo, Meuleman, Wouter, de Ridder, Jeroen, Berns, Anton, Wessels, Lodewyk F.A., van Lohuizen, Maarten, van Steensel, Bas

Journal:

Year:

2013

Language:

english

File:

PDF, 8.90 MB

english, 2013

6

Classification in the presence of class noise using a probabilistic Kernel Fisher method

Yunlei Li, Lodewyk F.A. Wessels, Dick de Ridder, Marcel J.T. Reinders

Journal:

Pattern Recognition

Year:

2007

Language:

english

File:

PDF, 290 KB

english, 2007

7

Erratum to “Classification in the presence of class noise using a probabilistic kernel fisher method”: [Pattern Recognition 40 (12) 3349–3357]

Yunlei Li, Lodewyk F.A. Wessels, Dick de Ridder, Marcel J.T. Reinders

Journal:

Pattern Recognition

Year:

2008

Language:

english

File:

PDF, 80 KB

english, 2008

8

Artifacts of Markov blanket filtering based on discretized features in small sample size applications

Theo A. Knijnenburg, Marcel J.T. Reinders, Lodewyk F.A. Wessels

Journal:

Pattern Recognition Letters

Year:

2006

Language:

english

File:

PDF, 153 KB

english, 2006

9

Random subspace method for multivariate feature selection

Carmen Lai, Marcel J.T. Reinders, Lodewyk Wessels

Journal:

Pattern Recognition Letters

Year:

2006

Language:

english

File:

PDF, 207 KB

english, 2006

10

Radiation-Associated Breast Tumors Display a Distinct Gene Expression Profile

Annegien Broeks, Linde M. Braaf, Lodewyk F.A. Wessels, Marc van de Vijver, Marie L. De Bruin, Marilyn Stovall, Nicola S. Russell, Flora E. van Leeuwen, Laura J. Van 't Veer

Journal:

International Journal of Radiation Oncology*Biology*Physics

Year:

2010

Language:

english

File:

PDF, 382 KB

english, 2010

11

Prediction ofBRCA1-association in hereditary non-BRCA1/2breast carcinomas with array-CGH

Simon A. Joosse, Erik H. van Beers, Ivon H. G. Tielen, Hugo Horlings, Johannes L. Peterse, Nicoline Hoogerbrugge, Marjolijn J. Ligtenberg, Lodewyk F. A. Wessels, Priscilla Axwijk, Senno Verhoef, Frans

Journal:

Breast Cancer Research and Treatment

Year:

2009

Language:

english

File:

PDF, 562 KB

english, 2009

12

Concordance of clinical and molecular breast cancer subtyping in the context of preoperative chemotherapy response

Jorma J. de Ronde, Juliane Hannemann, Hans Halfwerk, Lennart Mulder, Marieke E. Straver, Marie-Jeanne T. F. D. Vrancken Peeters, Jelle Wesseling, Marc van de Vijver, Lodewyk F. A. Wessels, Sjoerd Rode

Journal:

Breast Cancer Research and Treatment

Year:

2010

Language:

english

File:

PDF, 189 KB

english, 2010

13

PKA-induced phosphorylation of ERα at serine 305 and high PAK1 levels is associated with sensitivity to tamoxifen in ER-positive breast cancer

Marleen Kok, Wilbert Zwart, Caroline Holm, Renske Fles, Michael Hauptmann, Laura J. Van’t Veer, Lodewyk F. A. Wessels, Jacques Neefjes, Olle Stål, Sabine C. Linn, Göran Landberg, Rob Michalides

Journal:

Breast Cancer Research and Treatment

Year:

2011

Language:

english

File:

PDF, 683 KB

english, 2011

14

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

Guelen, Lars, Pagie, Ludo, Brasset, Emilie, Meuleman, Wouter, Faza, Marius B., Talhout, Wendy, Eussen, Bert H., de Klein, Annelies, Wessels, Lodewyk, de Laat, Wouter

Journal:

Year:

2008

Language:

english

File:

PDF, 1.27 MB

english, 2008

15

MMTV insertional mutagenesis identifies genes, gene families and pathways involved in mammary cancer

Theodorou, Vassiliki, Kimm, Melanie A, Boer, Mandy, Wessels, Lodewyk, Theelen, Wendy, Jonkers, Jos, Hilkens, John

Journal:

Nature Genetics

Year:

2007

Language:

english

File:

PDF, 284 KB

english, 2007

16

Analysis of mass spectrometry data using sub-spectra

Wouter Meuleman, Judith YMN Engwegen, Marie-Christine W Gast, Lodewyk FA Wessels, Marcel JT Reinders

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 504 KB

english, 2009

17

A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets

Carmen Lai, Marcel JT Reinders, Laura J van't Veer, Lodewyk FA Wessels

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 333 KB

english, 2006

18

SIRAC: Supervised Identification of Regions of Aberration in aCGH datasets

Carmen Lai, Hugo M Horlings, Marc J van de Vijver, Eric H van Beers, Petra M Nederlof, Lodewyk FA Wessels, Marcel JT Reinders

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 1.07 MB

english, 2007

19

Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data

Wouter Meuleman, Judith YMN Engwegen, Marie-Christine W Gast, Jos H Beijnen, Marcel JT Reinders, Lodewyk FA Wessels

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 378 KB

english, 2008

20

Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: A quantitative analysis of a compendium of chemostat-based transcriptome data

Theo A Knijnenburg, Jean-Marc G Daran, Marcel A van den Broek, Pascale AS Daran-Lapujade, Johannes H de Winde, Jack T Pronk, Marcel JT Reinders, Lodewyk FA Wessels

Journal:

Year:

2009

Language:

english

File:

PDF, 1.20 MB

english, 2009

21

Converting a breast cancer microarray signature into a high-throughput diagnostic test

Annuska M Glas, Arno Floore, Leonie JMJ Delahaye, Anke T Witteveen, Rob CF Pover, Niels Bakx, Jaana ST Lahti-Domenici, Tako J Bruinsma, Marc O Warmoes, René Bernards, Lodewyk FA Wessels, Laura J Van't

Journal:

Year:

2006

Language:

english

File:

PDF, 3.68 MB

english, 2006

22

Exploiting combinatorial cultivation conditions to infer transcriptional regulation

Theo A Knijnenburg, Johannes H de Winde, Jean-Marc Daran, Pascale Daran-Lapujade, Jack T Pronk, Marcel JT Reinders, Lodewyk FA Wessels

Journal:

Year:

2007

Language:

english

File:

PDF, 570 KB

english, 2007

23

Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability

Martin H van Vliet, Fabien Reyal, Hugo M Horlings, Marc J van de Vijver, Marcel JT Reinders, Lodewyk FA Wessels

Journal:

Year:

2008

Language:

english

File:

PDF, 536 KB

english, 2008

24

Cross-species comparison of aCGH data from mouse and humanBRCA1- andBRCA2-mutated breast cancers

Henne Holstege, Erik van Beers, Arno Velds, Xiaoling Liu, Simon A Joosse, Sjoerd Klarenbeek, Eva Schut, Ron Kerkhoven, Christiaan N Klijn, Lodewyk FA Wessels, Petra M Nederlof, Jos Jonkers

Journal:

Year:

2010

Language:

english

File:

PDF, 3.61 MB

english, 2010

25

Specific genomic aberrations in primary colorectal cancer are associated with liver metastases

Sjoerd C Bruin, Christiaan Klijn, Gerrit-Jan Liefers, Linde M Braaf, Simon A Joosse, Eric H van Beers, Victor J Verwaal, Hans Morreau, Lodewyk F Wessels, Marie-Louise F van Velthuysen, Rob AEM Tollena

Journal:

Year:

2010

Language:

english

File:

PDF, 682 KB

english, 2010

26

KC-SMARTR: An R package for detection of statistically significant aberrations in multi-experiment aCGH data

Jorma J de Ronde, Christiaan Klijn, Arno Velds, Henne Holstege, Marcel JT Reinders, Jos Jonkers, Lodewyk FA Wessels

Journal:

BMC Research Notes

Year:

2010

Language:

english

File:

PDF, 945 KB

english, 2010

27

O20: Discovering genetic profiles by array-CGH in familial breast tumors

Erik H. van Beers, Simon A. Joosse, Frans B. Hogervorst, Lodewyk F. Wessels, Rogier A. Oldenburg, Peter Devilee, Cees J. Cornelisse, Senno Verhoef, Laura J. van t Veer, Petra M. Nederlof

Journal:

European Journal of Medical Genetics

Year:

2005

Language:

english

File:

PDF, 52 KB

english, 2005

28

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

Daan Peric-Hupkes, Wouter Meuleman, Ludo Pagie, Sophia W.M. Bruggeman, Irina Solovei, Wim Brugman, Stefan Gräf, Paul Flicek, Ron M. Kerkhoven, Maarten van Lohuizen, Marcel Reinders, Lodewyk Wessels, B

Journal:

Year:

2010

Language:

english

File:

PDF, 1.54 MB

english, 2010

29

Orbital rhabdomyosarcoma presenting as an apparent orbital subperiosteal abscess

Riaz Y Seedat, Pieter D Hamilton, Lodewyk P de Jager, Wessel Strydom, Catherine A Beukes

Journal:

International Journal of Pediatric Otorhinolaryngology

Year:

2000

Language:

english

File:

PDF, 373 KB

english, 2000

30

Molecular subtyping of breast cancer: ready to use?

Jorma de Ronde, Lodewyk Wessels, Jelle Wesseling

Journal:

The Lancet Oncology

Year:

2010

Language:

english

File:

PDF, 181 KB

english, 2010

31

Bioinformatic analysis of barcoded cDNA libraries for small RNA profiling by next-generation sequencing

Thalia A. Farazi, Miguel Brown, Pavel Morozov, Jelle J. ten Hoeve, Iddo Z. Ben-Dov, Volker Hovestadt, Markus Hafner, Neil Renwick, Aleksandra Mihailović, Lodewyk F.A. Wessels, Thomas Tuschl

Journal:

Year:

2012

Language:

english

File:

PDF, 2.23 MB

english, 2012

32

Quantitative copy number analysis by Multiplex Ligation-dependent Probe Amplification (MLPA) of BRCA1-associated breast cancer regions identifies BRCAness

Esther H Lips, Nadja Laddach, Suvi P Savola, Marieke A Vollebergh, Anne MM Oonk, Alex LT Imholz, Lodewyk FA Wessels, Jelle Wesseling, Petra M Nederlof, Sjoerd Rodenhuis

Journal:

Breast Cancer Research

Year:

2011

Language:

english

File:

PDF, 276 KB

english, 2011

33

SERPINA6, BEX1, AGTR1, SLC26A3, and LAPTM4B are markers of resistance to neoadjuvant chemotherapy in HER2-negative breast cancer

Jorma J. de Ronde, Esther H. Lips, Lennart Mulder, Andrew D. Vincent, Jelle Wesseling, Marja Nieuwland, Ron Kerkhoven, Marie-Jeanne T. F. D. Vrancken Peeters, Gabe S. Sonke, Sjoerd Rodenhuis, Lodewyk

Journal:

Breast Cancer Research and Treatment

Year:

2013

Language:

english

File:

PDF, 614 KB

english, 2013

34

Knowledge driven decomposition of tumor expression profiles

Martin H van Vliet, Lodewyk FA Wessels, Marcel JT Reinders

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 504 KB

english, 2009

35

Concordance among Gene-Expression–Based Predictors for Breast Cancer

Fan, Cheng, Oh, Daniel S., Wessels, Lodewyk, Weigelt, Britta, Nuyten, Dimitry S.A., Nobel, Andrew B., van't Veer, Laura J., Perou, Charles M.

Journal:

Boston Medical and Surgical Journal

Year:

2006

Language:

english

File:

PDF, 279 KB

english, 2006

36

[Lecture Notes in Computer Science] Pattern Recognition in Bioinformatics Volume 7036 || Biclustering of Expression Microarray Data Using Affinity Propagation

Loog, Marco, Wessels, Lodewyk, Reinders, Marcel J. T., de Ridder, Dick

Year:

2011

Language:

english

File:

PDF, 306 KB

english, 2011

37

Selection of Patients for Hepatic Surgery of Colorectal Cancer Liver Metastasis Based on Genomic Aberrations

Bruin, Sjoerd C., Ronde, Jorma J., Wiering, Bas, Braaf, Linde M., Wilt, J. H. W., Vincent, Andrew D., Velthuysen, Marie-Louise F., Ruers, T. J., Wessels, Lodewyk F.A., Veer, Laura J.

Journal:

Annals of Surgical Oncology

Year:

2013

Language:

english

File:

PDF, 599 KB

english, 2013

38

[Lecture Notes in Computer Science] Pattern Recognition in Bioinformatics Volume 7036 || A New Gene Selection Method Based on Random Subspace Ensemble for Microarray Cancer Classification

Loog, Marco, Wessels, Lodewyk, Reinders, Marcel J. T., de Ridder, Dick

Year:

2011

Language:

english

File:

PDF, 183 KB

english, 2011

39

[Lecture Notes in Computer Science] Pattern Recognition in Bioinformatics Volume 7036 || A New Framework for Co-clustering of Gene Expression Data

Loog, Marco, Wessels, Lodewyk, Reinders, Marcel J. T., de Ridder, Dick

Year:

2011

Language:

english

File:

PDF, 839 KB

english, 2011

40

[Lecture Notes in Computer Science] Pattern Recognition in Bioinformatics Volume 7036 || PAAA: A Progressive Iterative Alignment Algorithm Based on Anchors

Loog, Marco, Wessels, Lodewyk, Reinders, Marcel J. T., de Ridder, Dick

Year:

2011

Language:

english

File:

PDF, 209 KB

english, 2011

41

Platform comparisons for identification of breast cancers with a BRCA-like copy number profile

Schouten, Philip C., Dyk, Ewald, Braaf, Linde M., Mulder, Lennart, Lips, Esther H., Ronde, Jorma J., Holtman, Laura, Wesseling, Jelle, Hauptmann, Michael, Wessels, Lodewyk F. A., Linn, Sabine C., Nede

Journal:

Breast Cancer Research and Treatment

Year:

2013

Language:

english

File:

PDF, 1.04 MB

english, 2013

42

Genomic patterns resemblingBRCA1- andBRCA2-mutated breast cancers predict benefit of intensified carboplatin-based chemotherapy

Vollebergh, Marieke A, Lips, Esther H, Nederlof, Petra M, Wessels, Lodewyk FA, Wesseling, Jelle, vd Vijver, Marc J, de Vries, Elisabeth GE, van Tinteren, Harm, Jonkers, Jos, Hauptmann, Michael, Rodenh

Journal:

Breast Cancer Research

Year:

2014

Language:

english

File:

PDF, 673 KB

english, 2014

43

Multiscale representation of genomic signals

Knijnenburg, Theo A, Ramsey, Stephen A, Berman, Benjamin P, Kennedy, Kathleen A, Smit, Arian F A, Wessels, Lodewyk F A, Laird, Peter W, Aderem, Alan, Shmulevich, Ilya

Journal:

Year:

2014

Language:

english

File:

PDF, 808 KB

english, 2014

44

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

Nevedomskaya, Ekaterina, Wessels, Lodewyk, Zwart, Wilbert

Journal:

Year:

2014

Language:

english

File:

PDF, 1.26 MB

english, 2014

45

ElevatedAPOBEC3BCorrelates with Poor Outcomes for Estrogen-Receptor-Positive Breast Cancers

Sieuwerts, Anieta M., Willis, Scooter, Burns, Michael B., Look, Maxime P., Gelder, Marion E. Meijer-Van, Schlicker, Andreas, Heideman, Marinus R., Jacobs, Heinz, Wessels, Lodewyk, Leyland-Jones, Brian

Journal:

Hormones and Cancer

Year:

2014

Language:

english

File:

PDF, 728 KB

english, 2014

46

Biclustering Sparse Binary Genomic Data

Uitert, Miranda van, Meuleman, Wouter, Wessels, Lodewyk

Journal:

Journal of Computational Biology

Year:

2008

Language:

english

File:

PDF, 601 KB

english, 2008

47

Quantitative imaging of focal adhesion dynamics and their regulation by HGF and Rap1 signaling

Spanjaard, Emma, Smal, Ihor, Angelopoulos, Nicos, Verlaan, Ingrid, Matov, Alexandre, Meijering, Erik, Wessels, Lodewyk, Bos, Hans, de Rooij, Johan

Journal:

Experimental Cell Research

Year:

2015

Language:

english

File:

PDF, 5.32 MB

english, 2015

48

PROTEIN COMPLEX PREDICTION USING AN INTEGRATIVE BIOINFORMATICS APPROACH

VAN BERLO, ROGIER J. P., WESSELS, LODEWYK F. A., DE RIDDER, DICK, REINDERS, MARCEL J. T.

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2007

Language:

english

File:

PDF, 638 KB

english, 2007

49

Chemical profiling of the genome with anti-cancer drugs defines target specificities

Pang, Baoxu, de Jong, Johann, Qiao, Xiaohang, Wessels, Lodewyk F A, Neefjes, Jacques

Journal:

Nature Chemical Biology

Year:

2015

Language:

english

File:

PDF, 2.43 MB

english, 2015

50

Identification of distinct miRNA target regulation between breast cancer molecular subtypes using AGO2-PAR-CLIP and patient datasets

Farazi, Thalia A, ten Hoeve, Jelle J, Brown, Miguel, Mihailovic, Aleksandra, Horlings, Hugo M, van de Vijver, Marc J, Tuschl, Thomas, Wessels, Lodewyk FA

Journal:

Year:

2014

Language:

english

File:

PDF, 1.04 MB

english, 2014