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1

Intensity-based analysis of dual-color gene expression data as an alternative to ratio-based analysis to enhance reproducibility

Koen Bossers, Bauke Ylstra, Ruud H Brakenhoff, Serge J Smeets, Joost Verhaagen, Mark A van de Wiel

Journal:

Year:

2010

Language:

english

File:

PDF, 986 KB

english, 2010

2

MOLECULAR CONTROL AND GENETIC MODIFICATION OF FLOWER DEVELOPMENT.

van Tunen, Arjen J., Franken, J., Busscher, J., Angenent, Gerco C., Ylstra, B., Dons, Hans J.M.

Journal:

Acta Horticulturae

Year:

1995

File:

PDF, 183 KB

1995

3

Investigation of a patient with a partial trisomy 16q including the fat mass and obesity associated gene (FTO): Fine mapping and FTO gene expression study

Linda van den Berg, Henriette Delemarre-van de Waal, Joan C. Han, Bauke Ylstra, Paul Eijk, Maria Nesterova, Peter Heutink, Constantine A. Stratakis

Journal:

American Journal of Medical Genetics Part A

Year:

2010

Language:

english

File:

PDF, 190 KB

english, 2010

4

Altered promoter usage characterizes monoallelic transcription arising with ERBB2 amplification in human breast cancers

Christopher C. Benz, Vita Fedele, Fan Xu, Bauke Ylstra, David Ginzinger, Mamie Yu, Dan Moore, Rayna Kneuper Hall, Daynna J. Wolff, Mary L. Disis, Serenella Eppenberger-Castori, Urs Eppenberger, France

Journal:

Genes, Chromosomes and Cancer

Year:

2006

Language:

english

File:

PDF, 270 KB

english, 2006

5

Co-amplification of 8p12 and 11q13 in breast cancers is not the result of a single genomic event

Anna L. Paterson, Jessica C. M. Pole, Katherine A. Blood, Maria J. Garcia, Susanna L. Cooke, Andrew E. Teschendorff, Yanzhong Wang, Suet-Feung Chin, Bauke Ylstra, Carlos Caldas, Paul A. W. Edwards

Journal:

Genes, Chromosomes and Cancer

Year:

2007

Language:

english

File:

PDF, 885 KB

english, 2007

6

Integrated genomic and transcriptional profiling identifies chromosomal loci with altered gene expression in cervical cancer

Saskia M. Wilting, Jillian de Wilde, Chris J. L. M. Meijer, Johannes Berkhof, Yajun Yi, Wessel N. van Wieringen, Boudewijn J. M. Braakhuis, Gerrit A. Meijer, Bauke Ylstra, Peter J. F. Snijders, Renske

Journal:

Genes, Chromosomes and Cancer

Year:

2008

Language:

english

File:

PDF, 301 KB

english, 2008

7

Across array comparative genomic hybridization: A strategy to reduce reference channel hybridizations

Tineke E. Buffart, Daniëlle Israeli, Marianne Tijssen, Sjoerd J. Vosse, Alan Mršić, Gerrit A. Meijer, Bauke Ylstra

Journal:

Genes, Chromosomes and Cancer

Year:

2008

Language:

english

File:

PDF, 388 KB

english, 2008

8

Identification of genes putatively involved in the pathogenesis of diffuse large B-cell lymphomas by integrative genomics

Joost J. Oudejans, Wessel N. van Wieringen, Serge J. Smeets, Marianne Tijssen, Sjoerd J. Vosse, Chris J. L. M. Meijer, Gerrit A. Meijer, Mark A. van de Wiel, Bauke Ylstra

Journal:

Genes, Chromosomes and Cancer

Year:

2009

Language:

english

File:

PDF, 235 KB

english, 2009

9

Copy number gain at 8q12.1-q22.1 is associated with a malignant tumor phenotype in salivary gland myoepitheliomas

Hedy Vékony, Kerstin Röser, Thomas Löning, Bauke Ylstra, Gerrit A. Meijer, Wessel N. van Wieringen, Mark A. van de Wiel, Beatriz Carvalho, Klaas Kok, C. René Leemans, Isaäc van der Waal, Elisabeth Blo

Journal:

Genes, Chromosomes and Cancer

Year:

2009

Language:

english

File:

PDF, 285 KB

english, 2009

10

CGH arrays compared for DNA isolated from formalin-fixed, paraffin-embedded material

Oscar Krijgsman, Danielle Israeli, Josien C. Haan, Hendrik F. van Essen, Serge J. Smeets, Paul P. Eijk, Renske D. M. Steenbergen, Klaas Kok, Sabine Tejpar, Gerrit A. Meijer, Bauke Ylstra

Journal:

Genes, Chromosomes and Cancer

Year:

2012

Language:

english

File:

PDF, 1.59 MB

english, 2012

11

Genome-wide analysis of genetic changes in intestinal-type sinonasal adenocarcinoma

Mario A. Hermsen, José Luis Llorente, Jhudit Pérez-Escuredo, Fernando López, Bauke Ylstra, César Álvarez-Marcos, Carlos Suárez

Journal:

Year:

2009

Language:

english

File:

PDF, 631 KB

english, 2009

12

Gene expression profiling to identify markers associated with deregulated hTERT in HPV-transformed keratinocytes and cervical cancer

Jillian de Wilde, Saskia M. Wilting, Chris J.L.M. Meijer, Mark A. van de Wiel, Bauke Ylstra, Peter J.F. Snijders, Renske D.M. Steenbergen

Journal:

International Journal of Cancer

Year:

2008

Language:

english

File:

PDF, 437 KB

english, 2008

13

Phenotypic and genomic analysis of an exceptional case of enteropathy associated T-cell lymphoma

Greetje J. Tack, Wieke H.M. Verbeek, Jolanda M.W. van de Water, B. Mary E. von Blomberg, Shama L. Bhola, Bauke Ylstra, Chris J.J. Mulder, Marco W.J. Schreurs

Journal:

Leukemia Research

Year:

2010

Language:

english

File:

PDF, 1012 KB

english, 2010

14

Methodological contributions to the microbiological determination of tryptophane

Journal:

Analytica Chimica Acta

Year:

1948

Language:

english

File:

PDF, 327 KB

english, 1948

15

Flavonols and fertilization in Petunia hybrida: localization and mode of action during pollen tube growth

Bauke Ylstra, Jacqueline Busscher, John Franken, Peter C.H. Hollman, Joseph N.M. Mol, Arjen J. Van Tunen

Journal:

The Plant Journal

Year:

1994

Language:

english

File:

PDF, 19.83 MB

english, 1994

16

Analysis of mRNA stabilities during pollen development and in BY2 cells

Bauke Ylstra, Sheila McCormick

Journal:

The Plant Journal

Year:

1999

Language:

english

File:

PDF, 215 KB

english, 1999

17

NMD inhibition fails to identify tumour suppressor genes in microsatellite stable gastric cancer cell lines

Tineke E Buffart, Marianne Tijssen, Jamila El-Bchiri, Alex Duval, A van de Mark Wiel, Bauke Ylstra, Gerrit A Meijer, Beatriz Carvalho

Journal:

BMC Medical Genomics

Year:

2009

Language:

english

File:

PDF, 1.21 MB

english, 2009

18

Genomic profiling identifies common HPV-associated chromosomal alterations in squamous cell carcinomas of cervix and head and neck

Saskia M Wilting, Serge J Smeets, Peter JF Snijders, Wessel N van Wieringen, Mark A van de Wiel, Gerrit A Meijer, Bauke Ylstra, C René Leemans, Chris JLM Meijer, Ruud H Brakenhoff, Boudewijn JM Braakh

Journal:

BMC Medical Genomics

Year:

2009

Language:

english

File:

PDF, 2.13 MB

english, 2009

19

Gastric cancers of Western European and African patients show different patterns of genomic instability

Tineke E Buffart, Melanie Louw, Nicole CT van Grieken, Marianne Tijssen, Beatriz Carvalho, Bauke Ylstra, Heike Grabsch, Chris JJ Mulder, Cornelis JH van de Velde, Schalk W van der Merwe, Gerrit A Meij

Journal:

BMC Medical Genomics

Year:

2011

Language:

english

File:

PDF, 742 KB

english, 2011

20

Determination of amplicon boundaries at 20q13.2 in tissue samples of human gastric adenocarcinomas by high-resolution microarray comparative genomic hybridization

Marjan M Weiss, Antoine M Snijders, Ernst J Kuipers, Bauke Ylstra, Daniel Pinkel, Stefan GM Meuwissen, Paul J van Diest, Donna G Albertson, Gerrit A Meijer

Journal:

The Journal of Pathology

Year:

2003

Language:

english

File:

PDF, 159 KB

english, 2003

21

Increased gene copy numbers at chromosome 20q are frequent in both squamous cell carcinomas and adenocarcinomas of the cervix

SM Wilting, PJF Snijders, GA Meijer, B Ylstra, PRLA van den IJssel, AM Snijders, DG Albertson, J Coffa, JP Schouten, MA van de Wiel, CJLM Meijer, RDM Steenbergen

Journal:

The Journal of Pathology

Year:

2006

Language:

english

File:

PDF, 430 KB

english, 2006

22

Gastric cancers in young and elderly patients show different genomic profiles

TE Buffart, B Carvalho, E Hopmans, V Brehm, E Klein Kranenbarg, TBM Schaaij-Visser, PP Eijk, NCT van Grieken, B Ylstra, CJH van de Velde, GA Meijer

Journal:

The Journal of Pathology

Year:

2007

Language:

english

File:

PDF, 235 KB

english, 2007

23

Candidate driver genes in focal chromosomal aberrations of stage II colon cancer

Rebecca PM Brosens, Josien C Haan, Beatriz Carvalho, François Rustenburg, Heike Grabsch, Philip Quirke, Alexander F Engel, Miguel A Cuesta, Nicola Maughan, Marcel Flens, Gerrit A Meijer, Bauke Ylstra

Journal:

The Journal of Pathology

Year:

2010

Language:

english

File:

PDF, 353 KB

english, 2010

24

The effect of ultraviolet light on some components of the nucleic acids: II: In rapidly frozen solutions

R. Beukers, J. Ylstra, W. Berends

Journal:

Recueil des Travaux Chimiques des Pays-Bas

Year:

1958

Language:

english

File:

PDF, 194 KB

english, 1958

25

Interaction between dimethylpyruvic acid and biotin with a mould

J. N. Brouwer, J. Ylstra, W. Berends

Journal:

Recueil des Travaux Chimiques des Pays-Bas

Year:

1959

Language:

english

File:

PDF, 269 KB

english, 1959

26

Flavonols arenotessential for fertilization inArabidopsis thaliana

Bauke Ylstra, Mariëlle Muskens, Arjen J. Tunen

Journal:

Plant Molecular Biology

Year:

1996

Language:

english

File:

PDF, 1.32 MB

english, 1996

27

Comparison of different techniques for gene transfer into mature and immature tobacco pollen

Eva Stöger, Rosa Maria Benito Moreno, Bauke Ylstra, Oscar Vicente, Erwin Heberle-Bors

Journal:

Transgenic Research

Year:

1992

Language:

english

File:

PDF, 3.09 MB

english, 1992

28

Pollen tubes of flavonol-deficientPetuniashow striking alterations in wall structure leading to tube disruption

Jan Derksen, René van Wezel, Bart Knuiman, Bauke Ylstra, Arjen J. van Tunen

Journal:

Year:

1999

Language:

english

File:

PDF, 582 KB

english, 1999

29

High resolution analysis of DNA copy-number aberrations of chromosomes 8, 13, and 20 in gastric cancers

Tineke E. Buffart, Nicole C. T. van Grieken, Marianne Tijssen, Jordy Coffa, Bauke Ylstra, Heike I. Grabsch, Cornelis J. H. van de Velde, Beatriz Carvalho, Gerrit A. Meijer

Journal:

Virchows Archiv

Year:

2009

Language:

english

File:

PDF, 257 KB

english, 2009

30

Identification of key genes for carcinogenic pathways associated with colorectal adenoma-to-carcinoma progression

Anke H. Sillars-Hardebol, Beatriz Carvalho, Meike de Wit, Cindy Postma, Pien M. Delis-van Diemen, Sandra Mongera, Bauke Ylstra, Mark A. van de Wiel, Gerrit A. Meijer, Remond J. A. Fijneman

Journal:

Year:

2010

Language:

english

File:

PDF, 302 KB

english, 2010

31

Deletion of chromosome 4q predicts outcome in Stage II colon cancer patients

R. P. M. Brosens, E. J. T. H. Belt, J. C. Haan, T. E. Buffart, B. Carvalho, H. Grabsch, P. Quirke, M. A. Cuesta, A. F. Engel, B. Ylstra, G. A. Meijer

Journal:

Cellular Oncology

Year:

2011

Language:

english

File:

PDF, 395 KB

english, 2011

32

Colorectal adenoma to carcinoma progression is accompanied by changes in gene expression associated with ageing, chromosomal instability, and fatty acid metabolism

Beatriz Carvalho, Anke H. Sillars-Hardebol, Cindy Postma, Sandra Mongera, Jochim Terhaar Sive Droste, Askar Obulkasim, Mark van de Wiel, Wim van Criekinge, Bauke Ylstra, Remond J. A. Fijneman, Gerrit

Journal:

Cellular Oncology

Year:

2012

Language:

english

File:

PDF, 196 KB

english, 2012

33

Profiling of apoptosis genes allows for clinical stratification of primary nodal diffuse large B-cell lymphomas

J. J. F. Muris, B. Ylstra, S. A. G. M. Cillessen, G. J. Ossenkoppele, J. C. Kluin-Nelemans, P. P. Eijk, B. Nota, M. Tijssen, W. P. H. De Boer, M. Van De Wiel, P. R. L. A. Van Den Ijssel, P. Jansen, P.

Journal:

British Journal of Haematology

Year:

2007

Language:

english

File:

PDF, 875 KB

english, 2007

34

Sugar sweet springtails: on the transcriptional response of Folsomia candida (Collembola) to desiccation stress

M. J. T. N. Timmermans, D. Roelofs, B. Nota, B. Ylstra, M. Holmstrup

Journal:

Insect Molecular Biology

Year:

2009

Language:

english

File:

PDF, 519 KB

english, 2009

35

Gene expression microarray analysis of heat stress in the soil invertebrate Folsomia candida

B. Nota, N. M. Van Straalen, B. Ylstra, D. Roelofs

Journal:

Insect Molecular Biology

Year:

2010

Language:

english

File:

PDF, 158 KB

english, 2010

36

Adaptive differences in gene expression associated with heavy metal tolerance in the soil arthropod Orchesella cincta

DICK ROELOFS, THIERRY K. S. JANSSENS, MARTIJN J. T. N. TIMMERMANS, BENJAMIN NOTA, JANINE MARIËN, ZOLTÁN BOCHDANOVITS, BAUKE YLSTRA, NICO M. VAN STRAALEN

Journal:

Molecular Ecology

Year:

2009

Language:

english

File:

PDF, 2.77 MB

english, 2009

37

Transcriptional plasticity of a soil arthropod across different ecological conditions

TJALF E. DE BOER, ADRIANA BIRLUTIU, ZOLTAN BOCHDANOVITS, MARTIJN J. T. N. TIMMERMANS, TJEERD M. H. DIJKSTRA, NICO M. VAN STRAALEN, BAUKE YLSTRA, DICK ROELOFS

Journal:

Molecular Ecology

Year:

2011

Language:

english

File:

PDF, 713 KB

english, 2011

38

Microarray-based comparative genomic hybridization and its applications in human genetics

AE Oostlander, GA Meijer, B Ylstra

Journal:

Clinical Genetics

Year:

2004

Language:

english

File:

PDF, 579 KB

english, 2004

39

Reduced expression of neuropeptide genes in a genome-wide screen of a secretion-deficient mouse

J. Bouwman, S. Spijker, D. Schut, B. Wächtler, B. Ylstra, A. B. Smit, M. Verhage

Journal:

Journal of Neurochemistry

Year:

2006

Language:

english

File:

PDF, 1.25 MB

english, 2006

40

10.1038/75985

Albertson, Donna G., Ylstra, Bauke, Segraves, Richard, Collins, Colin, Dairkee, Shanaz H., Kowbel, David, Kuo, Wen-Lin, Gray, Joe W., Pinkel, Daniel

Journal:

Nature Genetics

Year:

2000

Language:

english

File:

PDF, 357 KB

english, 2000

41

ErbB2 Activation of ESX gene expression

Neve, Richard M, Ylstra, Bauke, Chang, Chuan-Hsiung, Albertson, Donna G, Benz, Christopher C

Journal:

Year:

2002

Language:

english

File:

PDF, 180 KB

english, 2002

42

Genome-wide DNA copy number alterations in head and neck squamous cell carcinomas with or without oncogene-expressing human papillomavirus

Smeets, S J, Braakhuis, B J M, Abbas, S, Snijders, P J F, Ylstra, B, van de Wiel, M A, Meijer, G A, Leemans, C R, Brakenhoff, R H

Journal:

Year:

2005

Language:

english

File:

PDF, 234 KB

english, 2005

43

The genomic profile of human malignant glioma is altered early in primary cell culture and preserved in spheroids

De Witt Hamer, P C, Van Tilborg, A A G, Eijk, P P, Sminia, P, Troost, D, Van Noorden, C J F, Ylstra, B, Leenstra, S

Journal:

Year:

2007

Language:

english

File:

PDF, 315 KB

english, 2007

44

Trifluorothymidine Resistance Is Associated with Decreased Thymidine Kinase and Equilibrative Nucleoside Transporter Expression or Increased Secretory Phospholipase A2

Temmink, O. H., Bijnsdorp, I. V., Prins, H. J., Losekoot, N., Adema, A. D., Smid, K., Honeywell, R. J., Ylstra, B., Eijk, P. P., Fukushima, M.

Journal:

Molecular Cancer Therapeutics

Year:

2010

Language:

english

File:

PDF, 430 KB

english, 2010

45

Chromosomal profiles of high-grade cervical intraepithelial neoplasia relate to duration of preceding high-risk human papillomavirus infection

Mariska Bierkens, Saskia M. Wilting, Wessel N. van Wieringen, Folkert J. van Kemenade, Maaike C.G. Bleeker, Ekaterina S. Jordanova, Marjolein Bekker-Lettink, Mark A. van de Wiel, Bauke Ylstra, Chris J

Journal:

International Journal of Cancer

Year:

2012

Language:

english

File:

PDF, 614 KB

english, 2012

46

The promise of DNA copy number-based classification for diagnostic applications

Serge J. Smeets, Ulrike Harjes, Wessel N. van Wieringen, Bauke Ylstra

Journal:

Cancer Genetics and Cytogenetics

Year:

2010

Language:

english

File:

PDF, 32 KB

english, 2010

47

DNA copy number alterations in flat colorectal adenomas

Q.J.M. Voorham, B. Carvalho, A.J. Spiertz, N.C.T. van Grieken, H.I. Grabsch, B. Rembacken, M. Kliment, M.A. van de Wiel, B. Ylstra, A.P. de Bruïne, C.J.J. Mulder, M. van Engeland, G.A. Meijer

Journal:

Cancer Genetics and Cytogenetics

Year:

2010

Language:

english

File:

PDF, 40 KB

english, 2010

48

Salivary gland carcinosarcoma: Oligonucleotide array CGH reveals similar genomic profiles in epithelial and mesenchymal components

Hedy Vékony, C. René Leemans, Bauke Ylstra, Gerrit A. Meijer, Isaäc van der Waal, Elisabeth Bloemena

Journal:

Year:

2009

Language:

english

File:

PDF, 2.83 MB

english, 2009

49

Array Comparative Genomic Hybridization Copy Number Profiling: A New Tool for Translational Research in Solid Malignancies

José Luis Costa, Gerrit Meijer, Bauke Ylstra, Carlos Caldas

Journal:

Seminars in Radiation Oncology

Year:

2008

Language:

english

File:

PDF, 857 KB

english, 2008

50

CGHpower: exploring sample size calculations for chromosomal copy number experiments

Ilari Scheinin, José A Ferreira, Sakari Knuutila, Gerrit A Meijer, Mark A van de Wiel, Bauke Ylstra

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 541 KB

english, 2010