Lodewyk F A Wessels

Lodewyk F A Wessels

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Lodewyk F A Wessels

Publications by authors named "Lodewyk F A Wessels"

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Identifying Epistasis in Cancer Genomes: A Delicate Affair.

Cell 2019 May;177(6):1375-1383

Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Program in Bioinformatics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Cancer Cell Map Initiative, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.05.005DOI Listing
May 2019

Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency.

Nat Commun 2019 04 8;10(1):1598. Epub 2019 Apr 8.

Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.

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http://dx.doi.org/10.1038/s41467-019-09551-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6453899PMC
April 2019

Principal component analysis of binary genomics data.

Brief Bioinform 2019 01;20(1):317-329

Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.

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https://academic.oup.com/bib/article/20/1/317/4372404
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http://dx.doi.org/10.1093/bib/bbx119DOI Listing
January 2019

Modelling signalling networks from perturbation data.

Bioinformatics 2018 12;34(23):4079-4086

Institute of Pathology, Charité Universitätsmedizin, Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bty473DOI Listing
December 2018

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

PLoS Comput Biol 2018 10 31;14(10):e1006520. Epub 2018 Oct 31.

Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.

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http://dx.plos.org/10.1371/journal.pcbi.1006520
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http://dx.doi.org/10.1371/journal.pcbi.1006520DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6231682PMC
October 2018

Comparative Network Reconstruction using mixed integer programming.

Bioinformatics 2018 09;34(17):i997-i1004

Division of Molecular Carcinogenesis, The Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/bty616DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129277PMC
September 2018

iTOP: inferring the topology of omics data.

Bioinformatics 2018 09;34(17):i988-i996

Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/bty636DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129292PMC
September 2018

Integrative Modeling Identifies Key Determinants of Inhibitor Sensitivity in Breast Cancer Cell Lines.

Cancer Res 2018 08 29;78(15):4396-4410. Epub 2018 May 29.

Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-2698DOI Listing
August 2018

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

Cell Res 2018 07 24;28(7):719-729. Epub 2018 May 24.

Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.

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http://dx.doi.org/10.1038/s41422-018-0044-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028652PMC
July 2018

Comparative genomic analysis of oral versus laryngeal and pharyngeal cancer.

Oral Oncol 2018 Jun 13;81:35-44. Epub 2018 Apr 13.

Department of Head and Neck Oncology and Surgery, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Institute of Phonetic Sciences, University of Amsterdam, Amsterdam, The Netherlands; Department of Oral and Maxillofacial Surgery, Academic Medical Center, Amsterdam, The Netherlands. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S13688375183012
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http://dx.doi.org/10.1016/j.oraloncology.2018.04.006DOI Listing
June 2018

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

Bioinformatics 2018 03;34(5):803-811

Computational Cancer Biology, Division of Molecular Carcinogenesis, Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btx666DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6192208PMC
March 2018

Complementary Value of Contralateral Parenchymal Enhancement on DCE-MRI to Prognostic Models and Molecular Assays in High-risk ER/HER2 Breast Cancer.

Clin Cancer Res 2017 Nov 8;23(21):6505-6515. Epub 2017 Aug 8.

Image Sciences Institute, University Medical Center Utrecht, Utrecht, the Netherlands.

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http://dx.doi.org/10.1158/1078-0432.CCR-17-0176DOI Listing
November 2017

Identifying transposon insertions and their effects from RNA-sequencing data.

Nucleic Acids Res 2017 Jul;45(12):7064-7077

Division of Molecular Pathology and Cancer Genomics Netherlands, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkx461DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499543PMC
July 2017

Identification of a Druggable Pathway Controlling Glioblastoma Invasiveness.

Cell Rep 2017 07;20(1):48-60

Division of Molecular Carcinogenesis and Cancer Genomics Center Netherlands, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.06.036DOI Listing
July 2017

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

Genome Biol 2016 12 16;17(1):261. Epub 2016 Dec 16.

Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.

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http://dx.doi.org/10.1186/s13059-016-1114-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5162102PMC
December 2016

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

Sci Rep 2016 11 23;6:36812. Epub 2016 Nov 23.

Netherlands Cancer Institute, Amsterdam, and The Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1038/srep36812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120272PMC
November 2016

Deletion of Polycomb Repressive Complex 2 From Mouse Intestine Causes Loss of Stem Cells.

Gastroenterology 2016 10 21;151(4):684-697.e12. Epub 2016 Jun 21.

Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Cancer Genomics Centre Netherlands, Utrecht, The Netherlands. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2016.06.020DOI Listing
October 2016

BCM: toolkit for Bayesian analysis of Computational Models using samplers.

BMC Syst Biol 2016 10 21;10(1):100. Epub 2016 Oct 21.

Computational Cancer Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/s12918-016-0339-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5073811PMC
October 2016

TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types.

Bioinformatics 2016 09;32(17):i413-i420

Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands, Faculty of EEMCS, Delft University of Technology, Delft 2628CD, The Netherlands Cancer Genomics Netherlands, Utrecht 3584CT, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btw449DOI Listing
September 2016

Sensitizing Triple-Negative Breast Cancer to PI3K Inhibition by Cotargeting IGF1R.

Mol Cancer Ther 2016 07 11;15(7):1545-56. Epub 2016 May 11.

Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands. Cancer Systems Biology Center (CSBC), The Netherlands Cancer Institute, Amsterdam, the Netherlands. The NKI Robotics and Screening Center (NRSC), The Netherlands Cancer Institute, Amsterdam, the Netherlands.

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http://dx.doi.org/10.1158/1535-7163.MCT-15-0865DOI Listing
July 2016

RUBIC identifies driver genes by detecting recurrent DNA copy number breaks.

Nat Commun 2016 07 11;7:12159. Epub 2016 Jul 11.

Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands.

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http://dx.doi.org/10.1038/ncomms12159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4942583PMC
July 2016

Defining chromosomal translocation risks in cancer.

Proc Natl Acad Sci U S A 2016 06 14;113(26):E3649-56. Epub 2016 Jun 14.

Division of Biological Stress Response, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;

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http://dx.doi.org/10.1073/pnas.1602025113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4932958PMC
June 2016

OncoScape: Exploring the cancer aberration landscape by genomic data fusion.

Sci Rep 2016 06 20;6:28103. Epub 2016 Jun 20.

Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1038/srep28103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4913322PMC
June 2016

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

Genom Data 2016 Mar 28;7:124-6. Epub 2015 Dec 28.

Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.gdata.2015.12.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4778643PMC
March 2016

xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model.

Bioinformatics 2015 Oct 27;31(19):3147-55. Epub 2015 May 27.

Life Sciences, Centrum Wiskunde & Informatica (CWI), Amsterdam, The Netherlands, Centre for Integrative Bioinformatics VU, VU University Amsterdam, The Netherlands, Erable Team, INRIA, Lyon, France.

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http://bioinformatics.oxfordjournals.org/content/31/19/3147.
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http://bioinformatics.oxfordjournals.org/lookup/doi/10.1093/
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http://dx.doi.org/10.1093/bioinformatics/btv316DOI Listing
October 2015

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

Chin J Cancer 2015 Sep 14;34(10):439-49. Epub 2015 Sep 14.

Institute for Systems Biology, Seattle, WA, 98109, USA.

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http://dx.doi.org/10.1186/s40880-015-0050-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4593384PMC
September 2015

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

Nat Chem Biol 2015 Jul 11;11(7):472-80. Epub 2015 May 11.

1] Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands. [2] Institute for Chemical Immunology, the Netherlands.

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http://dx.doi.org/10.1038/nchembio.1811DOI Listing
July 2015

Lack of genomic heterogeneity at high-resolution aCGH between primary breast cancers and their paired lymph node metastases.

PLoS One 2014 1;9(8):e103177. Epub 2014 Aug 1.

Division of Molecular Pathology, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands; Division of Medical Oncology, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0103177PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118860PMC
April 2015

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

Cell Res 2015 Apr 6;25(4):445-58. Epub 2015 Feb 6.

Department of Biochemistry, The Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada.

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http://dx.doi.org/10.1038/cr.2015.16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4387553PMC
April 2015

Applications of DNA integrating elements: Facing the bias bully.

Mob Genet Elements 2014 Nov-Dec;4(6):1-6. Epub 2015 Mar 9.

Division of Molecular Genetics; The Netherlands Cancer Institute ; Amsterdam, The Netherlands.

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http://dx.doi.org/10.4161/2159256X.2014.992694DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4588226PMC
March 2015

Breast cancer subtype specific classifiers of response to neoadjuvant chemotherapy do not outperform classifiers trained on all subtypes.

PLoS One 2014 18;9(2):e88551. Epub 2014 Feb 18.

Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands ; Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0088551PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3928239PMC
January 2015

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

Nat Protoc 2014 8;9(6):1255-81. Epub 2014 May 8.

1] Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands. [2] Cancer Genomics Centre, The Netherlands.

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http://dx.doi.org/10.1038/nprot.2014.072DOI Listing
December 2014

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

Cancer Res 2014 Oct 21;74(19):5469-79. Epub 2014 Aug 21.

Division of Molecular Pathology, the Netherlands Cancer Institute, Amsterdam, the Netherlands.

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http://dx.doi.org/10.1158/0008-5472.CAN-13-3429DOI Listing
October 2014

USP9X downregulation renders breast cancer cells resistant to tamoxifen.

Cancer Res 2014 Jul;74(14):3810-20

Authors' Affiliations: Division of Molecular Carcinogenesis and Cancer Genomics Center Netherlands; and

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http://dx.doi.org/10.1158/0008-5472.CAN-13-1960DOI Listing
July 2014

Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis.

Proc Natl Acad Sci U S A 2014 Apr 2;111(15):5747-52. Epub 2014 Apr 2.

Department of Biological Sciences, Columbia University, New York, NY 10027.

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http://dx.doi.org/10.1073/pnas.1309293111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3992641PMC
April 2014

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

Front Genet 2013 23;4:289. Epub 2013 Dec 23.

Life Sciences, Centrum Wiskunde & Informatica Amsterdam, Netherlands ; Operations Research and Bioinformatics, Faculty of Sciences, VU University Amsterdam Amsterdam, Netherlands.

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http://dx.doi.org/10.3389/fgene.2013.00289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3870302PMC
January 2014

Selection of patients for hepatic surgery of colorectal cancer liver metastasis based on genomic aberrations.

Ann Surg Oncol 2013 Dec 20;20 Suppl 3:S560-9. Epub 2013 Jun 20.

Division of Experimental Therapy, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands,

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http://dx.doi.org/10.1245/s10434-013-2985-7DOI Listing
December 2013

Timely deposition of macromolecular structures is necessary for peer review.

Acta Crystallogr D Biol Crystallogr 2013 Dec 19;69(Pt 12):2293-5. Epub 2013 Nov 19.

Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.

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http://dx.doi.org/10.1107/S0907444913024621DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852646PMC
December 2013

Identifying subgroup markers in heterogeneous populations.

Nucleic Acids Res 2013 Nov 22;41(21):e200. Epub 2013 Sep 22.

Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands, Division of Molecular Biology, The Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands, Division of Medical Oncology, The Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands and Faculty of EEMCS, Delft University of Technology, 2628 CN, Delft, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkt845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3834840PMC
November 2013

Chromatin position effects assayed by thousands of reporters integrated in parallel.

Cell 2013 Aug;154(4):914-27

Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.

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http://dx.doi.org/10.1016/j.cell.2013.07.018DOI Listing
August 2013

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

Breast Cancer Res Treat 2013 Jun 14;139(2):317-27. Epub 2013 May 14.

Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1007/s10549-013-2558-2DOI Listing
June 2013

A scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control.

Nucleic Acids Res 2013 May 8;41(9):e100. Epub 2013 Mar 8.

Bioinformatics and Statistics group, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkt155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3643574PMC
May 2013

Large-scale genotyping identifies 41 new loci associated with breast cancer risk.

Authors:
Kyriaki Michailidou Per Hall Anna Gonzalez-Neira Maya Ghoussaini Joe Dennis Roger L Milne Marjanka K Schmidt Jenny Chang-Claude Stig E Bojesen Manjeet K Bolla Qin Wang Ed Dicks Andrew Lee Clare Turnbull Nazneen Rahman Olivia Fletcher Julian Peto Lorna Gibson Isabel Dos Santos Silva Heli Nevanlinna Taru A Muranen Kristiina Aittomäki Carl Blomqvist Kamila Czene Astrid Irwanto Jianjun Liu Quinten Waisfisz Hanne Meijers-Heijboer Muriel Adank Rob B van der Luijt Rebecca Hein Norbert Dahmen Lars Beckman Alfons Meindl Rita K Schmutzler Bertram Müller-Myhsok Peter Lichtner John L Hopper Melissa C Southey Enes Makalic Daniel F Schmidt Andre G Uitterlinden Albert Hofman David J Hunter Stephen J Chanock Daniel Vincent François Bacot Daniel C Tessier Sander Canisius Lodewyk F A Wessels Christopher A Haiman Mitul Shah Robert Luben Judith Brown Craig Luccarini Nils Schoof Keith Humphreys Jingmei Li Børge G Nordestgaard Sune F Nielsen Henrik Flyger Fergus J Couch Xianshu Wang Celine Vachon Kristen N Stevens Diether Lambrechts Matthieu Moisse Robert Paridaens Marie-Rose Christiaens Anja Rudolph Stefan Nickels Dieter Flesch-Janys Nichola Johnson Zoe Aitken Kirsimari Aaltonen Tuomas Heikkinen Annegien Broeks Laura J Van't Veer C Ellen van der Schoot Pascal Guénel Thérèse Truong Pierre Laurent-Puig Florence Menegaux Frederik Marme Andreas Schneeweiss Christof Sohn Barbara Burwinkel M Pilar Zamora Jose Ignacio Arias Perez Guillermo Pita M Rosario Alonso Angela Cox Ian W Brock Simon S Cross Malcolm W R Reed Elinor J Sawyer Ian Tomlinson Michael J Kerin Nicola Miller Brian E Henderson Fredrick Schumacher Loic Le Marchand Irene L Andrulis Julia A Knight Gord Glendon Anna Marie Mulligan Annika Lindblom Sara Margolin Maartje J Hooning Antoinette Hollestelle Ans M W van den Ouweland Agnes Jager Quang M Bui Jennifer Stone Gillian S Dite Carmel Apicella Helen Tsimiklis Graham G Giles Gianluca Severi Laura Baglietto Peter A Fasching Lothar Haeberle Arif B Ekici Matthias W Beckmann Hermann Brenner Heiko Müller Volker Arndt Christa Stegmaier Anthony Swerdlow Alan Ashworth Nick Orr Michael Jones Jonine Figueroa Jolanta Lissowska Louise Brinton Mark S Goldberg France Labrèche Martine Dumont Robert Winqvist Katri Pylkäs Arja Jukkola-Vuorinen Mervi Grip Hiltrud Brauch Ute Hamann Thomas Brüning Paolo Radice Paolo Peterlongo Siranoush Manoukian Bernardo Bonanni Peter Devilee Rob A E M Tollenaar Caroline Seynaeve Christi J van Asperen Anna Jakubowska Jan Lubinski Katarzyna Jaworska Katarzyna Durda Arto Mannermaa Vesa Kataja Veli-Matti Kosma Jaana M Hartikainen Natalia V Bogdanova Natalia N Antonenkova Thilo Dörk Vessela N Kristensen Hoda Anton-Culver Susan Slager Amanda E Toland Stephen Edge Florentia Fostira Daehee Kang Keun-Young Yoo Dong-Young Noh Keitaro Matsuo Hidemi Ito Hiroji Iwata Aiko Sueta Anna H Wu Chiu-Chen Tseng David Van Den Berg Daniel O Stram Xiao-Ou Shu Wei Lu Yu-Tang Gao Hui Cai Soo Hwang Teo Cheng Har Yip Sze Yee Phuah Belinda K Cornes Mikael Hartman Hui Miao Wei Yen Lim Jen-Hwei Sng Kenneth Muir Artitaya Lophatananon Sarah Stewart-Brown Pornthep Siriwanarangsan Chen-Yang Shen Chia-Ni Hsiung Pei-Ei Wu Shian-Ling Ding Suleeporn Sangrajrang Valerie Gaborieau Paul Brennan James McKay William J Blot Lisa B Signorello Qiuyin Cai Wei Zheng Sandra Deming-Halverson Martha Shrubsole Jirong Long Jacques Simard Montse Garcia-Closas Paul D P Pharoah Georgia Chenevix-Trench Alison M Dunning Javier Benitez Douglas F Easton

Nat Genet 2013 Apr;45(4):353-61, 361e1-2

Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.

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https://umexpert.um.edu.my/file/publication/00000868_105106.
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http://www.nature.com/doifinder/10.1038/ng.2563
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http://dx.doi.org/10.1038/ng.2563DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3771688PMC
April 2013

Integration of clinical and gene expression data has a synergetic effect on predicting breast cancer outcome.

PLoS One 2012 11;7(7):e40358. Epub 2012 Jul 11.

Delft Bioinformatics Laboratory, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg, Delft, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040358PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394805PMC
March 2013

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes.

Authors:
Andrew V Biankin Nicola Waddell Karin S Kassahn Marie-Claude Gingras Lakshmi B Muthuswamy Amber L Johns David K Miller Peter J Wilson Ann-Marie Patch Jianmin Wu David K Chang Mark J Cowley Brooke B Gardiner Sarah Song Ivon Harliwong Senel Idrisoglu Craig Nourse Ehsan Nourbakhsh Suzanne Manning Shivangi Wani Milena Gongora Marina Pajic Christopher J Scarlett Anthony J Gill Andreia V Pinho Ilse Rooman Matthew Anderson Oliver Holmes Conrad Leonard Darrin Taylor Scott Wood Qinying Xu Katia Nones J Lynn Fink Angelika Christ Tim Bruxner Nicole Cloonan Gabriel Kolle Felicity Newell Mark Pinese R Scott Mead Jeremy L Humphris Warren Kaplan Marc D Jones Emily K Colvin Adnan M Nagrial Emily S Humphrey Angela Chou Venessa T Chin Lorraine A Chantrill Amanda Mawson Jaswinder S Samra James G Kench Jessica A Lovell Roger J Daly Neil D Merrett Christopher Toon Krishna Epari Nam Q Nguyen Andrew Barbour Nikolajs Zeps Nipun Kakkar Fengmei Zhao Yuan Qing Wu Min Wang Donna M Muzny William E Fisher F Charles Brunicardi Sally E Hodges Jeffrey G Reid Jennifer Drummond Kyle Chang Yi Han Lora R Lewis Huyen Dinh Christian J Buhay Timothy Beck Lee Timms Michelle Sam Kimberly Begley Andrew Brown Deepa Pai Ami Panchal Nicholas Buchner Richard De Borja Robert E Denroche Christina K Yung Stefano Serra Nicole Onetto Debabrata Mukhopadhyay Ming-Sound Tsao Patricia A Shaw Gloria M Petersen Steven Gallinger Ralph H Hruban Anirban Maitra Christine A Iacobuzio-Donahue Richard D Schulick Christopher L Wolfgang Richard A Morgan Rita T Lawlor Paola Capelli Vincenzo Corbo Maria Scardoni Giampaolo Tortora Margaret A Tempero Karen M Mann Nancy A Jenkins Pedro A Perez-Mancera David J Adams David A Largaespada Lodewyk F A Wessels Alistair G Rust Lincoln D Stein David A Tuveson Neal G Copeland Elizabeth A Musgrove Aldo Scarpa James R Eshleman Thomas J Hudson Robert L Sutherland David A Wheeler John V Pearson John D McPherson Richard A Gibbs Sean M Grimmond

Nature 2012 Nov 24;491(7424):399-405. Epub 2012 Oct 24.

The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, Sydney, New South Wales 2010, Australia.

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http://dx.doi.org/10.1038/nature11547DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530898PMC
November 2012

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

Methods 2012 Oct 23;58(2):171-87. Epub 2012 Jul 23.

Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S10462023120017
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http://dx.doi.org/10.1016/j.ymeth.2012.07.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597438PMC
October 2012

A regression model for estimating DNA copy number applied to capture sequencing data.

Bioinformatics 2012 Sep 13;28(18):2357-65. Epub 2012 Jul 13.

Department of Bioinformatics and Statistics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/bts448DOI Listing
September 2012

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

Breast Cancer Res 2011 Oct 27;13(5):R107. Epub 2011 Oct 27.

Department of Experimental Therapy, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/bcr3049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3262220PMC
October 2011

Computational identification of insertional mutagenesis targets for cancer gene discovery.

Nucleic Acids Res 2011 Aug 7;39(15):e105. Epub 2011 Jun 7.

Bioinformatics and Statistics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkr447DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159484PMC
August 2011

Radiation-associated breast tumors display a distinct gene expression profile.

Int J Radiat Oncol Biol Phys 2010 Feb;76(2):540-7

Division of Experimental Therapy, The Netherlands Cancer Institute, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.ijrobp.2009.09.004DOI Listing
February 2010

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

Breast Cancer Res Treat 2010 Jan 8;119(1):119-26. Epub 2009 Aug 8.

Department of Bioinformatics and Statistics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1007/s10549-009-0499-6DOI Listing
January 2010

Fewer permutations, more accurate P-values.

Bioinformatics 2009 Jun;25(12):i161-8

Institute for Systems Biology, Seattle, WA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687965PMC
June 2009

Knowledge driven decomposition of tumor expression profiles.

BMC Bioinformatics 2009 Jan 30;10 Suppl 1:S20. Epub 2009 Jan 30.

Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-10-S1-S20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648763PMC
January 2009

Analysis of mass spectrometry data using sub-spectra.

BMC Bioinformatics 2009 Jan 30;10 Suppl 1:S51. Epub 2009 Jan 30.

Bioinformatics and Statistics, Department of Molecular Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-10-S1-S51DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648731PMC
January 2009