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51

[Lecture Notes in Computer Science] Pattern Recognition in Bioinformatics Volume 7036 ||

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

Year:

2011

Language:

english

File:

PDF, 12.82 MB

english, 2011

52

Timely deposition of macromolecular structures is necessary for peer review

Joosten, Robbie P., Soueidan, Hayssam, Wessels, Lodewyk F. A., Perrakis, Anastassis

Journal:

Acta Crystallographica Section D Biological Crystallography

Year:

2013

Language:

english

File:

PDF, 2.39 MB

english, 2013

53

Applications of DNA integrating elements: Facing the bias bully

de Jong, Johann, Wessels, Lodewyk F A, van Lohuizen, Maarten, de Ridder, Jeroen, Akhtar, Waseem

Journal:

Mobile Genetic Elements

Year:

2014

Language:

english

File:

PDF, 523 KB

english, 2014

54

Identification of Networks of Co-Occurring, Tumor-Related DNA Copy Number Changes Using a Genome-Wide Scoring Approach

Klijn, Christiaan, Bot, Jan, Adams, David J., Reinders, Marcel, Wessels, Lodewyk, Jonkers, Jos, Noble, William Stafford

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 3.05 MB

english, 2010

55

Chromatin Landscapes of Retroviral and Transposon Integration Profiles

de Jong, Johann, Akhtar, Waseem, Badhai, Jitendra, Rust, Alistair G., Rad, Roland, Hilkens, John, Berns, Anton, van Lohuizen, Maarten, Wessels, Lodewyk F. A., de Ridder, Jeroen, Roth, Monica J.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.38 MB

english, 2014

56

Detecting Statistically Significant Common Insertion Sites in Retroviral Insertional Mutagenesis Screens

de Ridder, Jeroen, Uren, Anthony, Kool, Jaap, Reinders, Marcel, Wessels, Lodewyk

Journal:

PLoS Computational Biology

Year:

2006

Language:

english

File:

PDF, 1.11 MB

english, 2006

57

SMARCE1 suppresses EGFR expression and controls responses to MET and ALK inhibitors in lung cancer

Papadakis, Andreas I, Sun, Chong, Knijnenburg, Theo A, Xue, Yibo, Grernrum, Wipawadee, Hölzel, Michael, Nijkamp, Wouter, Wessels, Lodewyk FA, Beijersbergen, Roderick L, Bernards, Rene, Huang, Sidong

Journal:

Year:

2015

Language:

english

File:

PDF, 2.10 MB

english, 2015

58

Corrigendum: Using TRIP for genome-wide position effect analysis in cultured cells

Akhtar, Waseem, Pindyurin, Alexey V, de Jong, Johann, Pagie, Ludo, ten Hoeve, Jelle, Berns, Anton, Wessels, Lodewyk F A, van Steensel, Bas, van Lohuizen, Maarten

Journal:

Nature Protocols

Year:

2015

Language:

english

File:

PDF, 538 KB

english, 2015

59

Do predictive signatures really predict response to cancer chemotherapy?

Borst, Piet, Wessels, Lodewyk

Journal:

Year:

2010

Language:

english

File:

PDF, 1.01 MB

english, 2010

60

Multilevel models improve precision and speed of IC 50 estimates

Vis, Daniel J, Bombardelli, Lorenzo, Lightfoot, Howard, Iorio, Francesco, Garnett, Mathew J, Wessels, Lodewyk FA

Journal:

Pharmacogenomics

Year:

2016

Language:

english

File:

PDF, 1.61 MB

english, 2016

61

Androgen receptor DNA binding and chromatin accessibility profiling in prostate cancer

Nevedomskaya, Ekaterina, Stelloo, Suzan, van der Poel, Henk G., de Jong, Jeroen, Wessels, Lodewyk F.A., Bergman, Andries M., Zwart, Wilbert

Journal:

Year:

2016

Language:

english

File:

PDF, 337 KB

english, 2016

62

A multilevel pan-cancer map links gene mutations to cancer hallmarks

Knijnenburg, Theo A., Bismeijer, Tycho, Wessels, Lodewyk F. A., Shmulevich, Ilya

Journal:

Chinese Journal of Cancer

Year:

2015

Language:

english

File:

PDF, 1.57 MB

english, 2015

63

Defining chromosomal translocation risks in cancer

Hogenbirk, Marc A., Heideman, Marinus R., de Rink, Iris, Velds, Arno, Kerkhoven, Ron M., Wessels, Lodewyk F. A., Jacobs, Heinz

Journal:

Proceedings of the National Academy of Sciences

Year:

2016

Language:

english

File:

PDF, 769 KB

english, 2016

64

SPIE Proceedings [SPIE International Symposium on Biomedical Optics - San Jose, CA (Saturday 19 January 2002)] Biomedical Nanotechnology Architectures and Applications - Computer-based optimization of high-throughput peptide screening

van der Veen, Peter J., Wessels, Lodewyk F. A., Slootstra, Jerry W., Meloen, Rob H., Reinders, Marcel J. T., Hellendoorn, J., Bornhop, Darryl J., Dunn, David A., Mariella, Jr., Raymond P., Murphy, Cat

Year:

2002

Language:

english

File:

PDF, 332 KB

english, 2002

65

SPIE Proceedings [SPIE BiOS 2001 The International Symposium on Biomedical Optics - San Jose, CA (Saturday 20 January 2001)] Microarrays: Optical Technologies and Informatics - Genetic network models: a comparative study

van Someren, Eugene P., Wessels, Lodewyk F. A., Reinders, Marcel J. T., Bittner, Michael L., Chen, Yidong, Dorsel, Andreas N., Dougherty, Edward R.

Year:

2001

Language:

english

File:

PDF, 1.12 MB

english, 2001

66

SPIE Proceedings [SPIE International Symposium on Biomedical Optics - San Jose, CA (Saturday 19 January 2002)] Functional Monitoring and Drug-Tissue Interaction - Reverse engineering of genetic networks through multicriterion optimization

van Someren, Eugene P., Wessels, Lodewyk F. A., Reinders, Marcel J. T., Backer, Eric, Kessler, Manfred D., Mueller, Gerhard J.

Year:

2002

Language:

english

File:

PDF, 1.60 MB

english, 2002

67

PTEN Loss in E-Cadherin-Deficient Mouse Mammary Epithelial Cells Rescues Apoptosis and Results in Development of Classical Invasive Lobular Carcinoma

Boelens, Mirjam C., Nethe, Micha, Klarenbeek, Sjoerd, de Ruiter, Julian R., Schut, Eva, Bonzanni, Nicola, Zeeman, Amber L., Wientjens, Ellen, van der Burg, Eline, Wessels, Lodewyk, van Amerongen, René

Journal:

Year:

2016

Language:

english

File:

PDF, 9.15 MB

english, 2016

68

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

Knijnenburg, Theo A., Klau, Gunnar W., Iorio, Francesco, Garnett, Mathew J., McDermott, Ultan, Shmulevich, Ilya, Wessels, Lodewyk F. A.

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 678 KB

english, 2016

69

RUBIC identifies driver genes by detecting recurrent DNA copy number breaks

van Dyk, Ewald, Hoogstraat, Marlous, ten Hoeve, Jelle, Reinders, Marcel J. T., Wessels, Lodewyk F. A.

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 866 KB

english, 2016

70

OncoScape: Exploring the cancer aberration landscape by genomic data fusion

Schlicker, Andreas, Michaut, Magali, Rahman, Rubayte, Wessels, Lodewyk F. A.

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 1.58 MB

english, 2016

71

A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence

Canisius, Sander, Martens, John W. M., Wessels, Lodewyk F. A.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.19 MB

english, 2016

72

Corrigendum: 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, van Steensel, Bas

Journal:

Year:

2013

File:

PDF, 27 KB

2013

73

Androgen receptor profiling predicts prostate cancer outcome

Stelloo, Suzan, Nevedomskaya, Ekaterina, van der Poel, Henk G, de Jong, Jeroen, van Leenders, Geert JLH, Jenster, Guido, Wessels, Lodewyk FA, Bergman, Andries M, Zwart, Wilbert

Journal:

EMBO Molecular Medicine

Year:

2015

Language:

english

File:

PDF, 3.16 MB

english, 2015

74

Identifying transposon insertions and their effects from RNA-sequencing data

de Ruiter, Julian R., Kas, Sjors M., Schut, Eva, Adams, David J., Koudijs, Marco J., Wessels, Lodewyk F. A., Jonkers, Jos

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 1.07 MB

english, 2017

75

Identification of a Druggable Pathway Controlling Glioblastoma Invasiveness

Pencheva, Nora, de Gooijer, Mark C., Vis, Daniel J., Wessels, Lodewyk F.A., Würdinger, Tom, van Tellingen, Olaf, Bernards, René

Journal:

Year:

2017

Language:

english

File:

PDF, 7.79 MB

english, 2017

76

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, Bas H.M., Elias, Sjoerd G., Bismeijer, Tycho, Loo, Claudette E, Viergever, Max A., Wessels, Lodewyk F.A., Gilhuijs, Kenneth G.A.

Journal:

Clinical Cancer Research

Year:

2017

Language:

english

File:

PDF, 6.30 MB

english, 2017

77

Principal component analysis of binary genomics data

Song, Yipeng, Westerhuis, Johan A, Aben, Nanne, Michaut, Magali, Wessels, Lodewyk F A, Smilde, Age K

Journal:

Briefings in Bioinformatics

Year:

2017

Language:

english

File:

PDF, 1.07 MB

english, 2017

78

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

Thijssen, Bram, Dijkstra, Tjeerd M H, Heskes, Tom, Wessels, Lodewyk F A

Journal:

Year:

2017

Language:

english

File:

PDF, 1022 KB

english, 2017

79

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

Ikink, Gerjon J., Boer, Mandy, Bakker, Elvira R. M., Vendel-Zwaagstra, Annabel, Klijn, Chris, ten Hoeve, Jelle, Jonkers, Jos, Wessels, Lodewyk F., Hilkens, John

Journal:

Year:

2018

Language:

english

File:

PDF, 5.40 MB

english, 2018

80

Comparative genomic analysis of oral versus laryngeal and pharyngeal cancer

Vossen, David M., Verhagen, Caroline V.M., Verheij, Marcel, Wessels, Lodewyk F.A., Vens, Conchita, van den Brekel, Michiel W.M.

Journal:

Year:

2018

Language:

english

File:

PDF, 887 KB

english, 2018

81

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

Xue, Zheng, Vis, Daniel J., Bruna, Alejandra, Sustic, Tonci, van Wageningen, Sake, Batra, Ankita Sati, Rueda, Oscar M., Bosdriesz, Evert, Caldas, Carlos, Wessels, Lodewyk F. A., Bernards, René

Journal:

Year:

2018

Language:

english

File:

PDF, 4.45 MB

english, 2018

82

Integrative modeling identifies key determinants of inhibitor sensitivity in breast cancer cell lines

Jastrzebski, Katarzyna, Thijssen, Bram, Kluin, Roelof JC, de Lint, Klaas, Majewski, Ian J, Beijersbergen, Roderick L., Wessels, Lodewyk F.A.

Journal:

Cancer Research

Year:

2018

Language:

english

File:

PDF, 10.81 MB

english, 2018

83

Module-Based Outcome Prediction Using Breast Cancer Compendia

van Vliet, Martin H., Klijn, Christiaan N., Wessels, Lodewyk F. A., Reinders, Marcel J. T., Wu, Xiaolin

Journal:

Year:

2007

Language:

english

File:

PDF, 409 KB

english, 2007

84

Ubiquitin E3 Ligase Ring1b/Rnf2 of Polycomb Repressive Complex 1 Contributes to Stable Maintenance of Mouse Embryonic Stem Cells

van der Stoop, Petra, Boutsma, Erwin A., Hulsman, Danielle, Noback, Sonja, Heimerikx, Mike, Kerkhoven, Ron M., Voncken, J. Willem, Wessels, Lodewyk F. A., van Lohuizen, Maarten, Williams, Simon

Journal:

Year:

2008

Language:

english

File:

PDF, 626 KB

english, 2008

85

A Critical Evaluation of Network and Pathway-Based Classifiers for Outcome Prediction in Breast Cancer

Staiger, Christine, Cadot, Sidney, Kooter, Raul, Dittrich, Marcus, Müller, Tobias, Klau, Gunnar W., Wessels, Lodewyk F. A., Dopazo, Joaquín

Journal:

Year:

2012

Language:

english

File:

PDF, 1.22 MB

english, 2012

86

Lack of Genomic Heterogeneity at High-Resolution aCGH between Primary Breast Cancers and Their Paired Lymph Node Metastases

Vollebergh, Marieke A., Klijn, Christiaan, Schouten, Philip C., Wesseling, Jelle, Israeli, Danielle, Ylstra, Bauke, Wessels, Lodewyk F.A., Jonkers, Jos, Linn, Sabine C., van Diest, Paul J.

Journal:

Year:

2014

Language:

english

File:

PDF, 4.70 MB

english, 2014

87

Modelling Signalling Networks from Perturbation Data

Dorel, Mathurin, Klinger, Bertram, Gross, Torsten, Sieber, Anja, Prahallad, Anirudh, Bosdriesz, Evert, Wessels, Lodewyk, Blüthgen, Nils, Valencia, Alfonso

Journal:

Year:

2018

Language:

english

File:

PDF, 524 KB

english, 2018

88

Current composite-feature classification methods do not outperform simple single-genes classifiers in breast cancer prognosis

Staiger, Christine, Cadot, Sidney, Györffy, Balázs, Wessels, Lodewyk F. A., Klau, Gunnar W.

Journal:

Frontiers in Genetics

Year:

2013

Language:

english

File:

PDF, 2.57 MB

english, 2013

89

Comparative Network Reconstruction using mixed integer programming

Bosdriesz, Evert, Prahallad, Anirudh, Klinger, Bertram, Sieber, Anja, Bosma, Astrid, Bernards, René, Blüthgen, Nils, Wessels, Lodewyk F A

Journal:

Year:

2018

Language:

english

File:

PDF, 799 KB

english, 2018

90

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

Bismeijer, Tycho, Canisius, Sander, Wessels, Lodewyk F. A., Leslie, Christina S.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.04 MB

english, 2018

91

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

Vossen, David M., Verhagen, Caroline V. M., Grénman, Reidar, Kluin, Roelof J. C., Verheij, Marcel, van den Brekel, Michiel W. M., Wessels, Lodewyk F. A., Vens, Conchita, Sobol, Robert W.

Journal:

Year:

2018

Language:

english

File:

PDF, 538 KB

english, 2018

92

iTOP: inferring the topology of omics data

Aben, Nanne, Westerhuis, Johan A, Song, Yipeng, Kiers, Henk A L, Michaut, Magali, Smilde, Age K, Wessels, Lodewyk F A

Journal:

Year:

2018

Language:

english

File:

PDF, 843 KB

english, 2018

93

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

Šuštić, Tonći, van Wageningen, Sake, Bosdriesz, Evert, Reid, Robert J. D., Dittmar, John, Lieftink, Cor, Beijersbergen, Roderick L., Wessels, Lodewyk F. A., Rothstein, Rodney, Bernards, René

Journal:

Genome Medicine

Year:

2018

Language:

english

File:

PDF, 3.63 MB

english, 2018

94

Detection of Colorectal Cancer by Serum and Tissue Protein Profiling: A Prospective Study in a Population at Risk

Engwegen, Judith Y.M.N., Depla, Annekatrien C.T.M., Smits, Marianne E., Cats, Annemieke, Tuynman, Henriëtte, Van Heukelem, Henk A., Snel, Pleun, Meuleman, Wouter, Wessels, Lodewyk F., Schellens, Jan H

Journal:

Biomarker Insights

Year:

2008

Language:

english

File:

PDF, 370 KB

english, 2008

95

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

Mourragui, Soufiane, Loog, Marco, van de Wiel, Mark A, Reinders, Marcel J T, Wessels, Lodewyk F A

Journal:

Year:

2019

Language:

english

File:

PDF, 751 KB

english, 2019

96

Are contralateral parenchymal enhancement on dynamic contrast-enhanced MRI and genomic ER-pathway activity in ER-positive/HER2-negative breast cancer related?

van der Velden, Bas H.M., Bismeijer, Tycho, Canisius, Sander, Loo, Claudette E., Lips, Esther H., Wesseling, Jelle, Viergever, Max A., Wessels, Lodewyk F.A., Gilhuijs, Kenneth G.A.

Journal:

European Journal of Radiology

Year:

2019

Language:

english

File:

PDF, 490 KB

english, 2019

97

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

Kim, Yongsoo, Bismeijer, Tycho, Zwart, Wilbert, Wessels, Lodewyk F. A., Vis, Daniel J.

Journal:

Nature Communications

Year:

2019

Language:

english

File:

PDF, 3.83 MB

english, 2019

98

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

Kim, Yongsoo, Bismeijer, Tycho, Zwart, Wilbert, Wessels, Lodewyk F. A., Vis, Daniel J.

Journal:

Nature Communications

Year:

2019

File:

PDF, 3.83 MB

2019

99

CD4+ T cell help creates memory CD8+ T cells with innate and help-independent recall capacities

Ahrends, Tomasz, Busselaar, Julia, Severson, Tesa M., Bąbała, Nikolina, de Vries, Evert, Bovens, Astrid, Wessels, Lodewyk, van Leeuwen, Fred, Borst, Jannie

Journal:

Nature Communications

Year:

2019

File:

PDF, 2.68 MB

2019

100

Heterofusion: Fusing genomics data of different measurement scales

Smilde, Age K., Song, Yipeng, Westerhuis, Johan A., Kiers, Henk A. L., Aben, Nanne, Wessels, Lodewyk F. A.

Journal:

Journal of Chemometrics

Year:

2020

Language:

english

File:

PDF, 2.73 MB

english, 2020