Olivier Gevaert

Olivier Gevaert

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Olivier Gevaert

Publications by authors named "Olivier Gevaert"

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78Publications

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Marking the Path Toward Artificial Intelligence-Based Image Classification in Dermatology.

JAMA Dermatol 2019 Aug 14. Epub 2019 Aug 14.

Department of Dermatology, Stanford University School of Medicine, Stanford, California.

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https://jamanetwork.com/journals/jamadermatology/fullarticle
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http://dx.doi.org/10.1001/jamadermatol.2019.1633DOI Listing
August 2019

Development and validation of radiomic signatures of head and neck squamous cell carcinoma molecular features and subtypes.

EBioMedicine 2019 Jul 27;45:70-80. Epub 2019 Jun 27.

Department of Medicine, Stanford Center for Biomedical Informatics Research (BMIR), USA; Department of Biomedical Data Science, Stanford University, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S23523964193041
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http://dx.doi.org/10.1016/j.ebiom.2019.06.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6642281PMC
July 2019

Comparison of single and module-based methods for modeling gene regulatory networks.

Bioinformatics 2019 Jul 9. Epub 2019 Jul 9.

The Stanford Center of Biomedical Informatics Research (BMIR), Department of Medicine, and Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz549DOI Listing
July 2019

The impact of DNA methylation on the cancer proteome.

PLoS Comput Biol 2019 Jul 29;15(7):e1007245. Epub 2019 Jul 29.

Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Palo Alto, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1007245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6695193PMC
July 2019

Deep learning with multimodal representation for pancancer prognosis prediction.

Bioinformatics 2019 Jul;35(14):i446-i454

Department of Medicine and Biomedical Data Science, Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz342DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612862PMC
July 2019

Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations.

AMIA Annu Symp Proc 2017 16;2017:1272-1281. Epub 2018 Apr 16.

Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5977712PMC
April 2019

Artificial intelligence and dermatology: opportunities, challenges, and future directions.

Semin Cutan Med Surg 2019 Mar 1;38(1):E31-37. Epub 2019 Mar 1.

Department of Dermatology, Stanford University, Stanford, California.

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http://dx.doi.org/10.12788/j.sder.2019.DOI Listing
March 2019

Non-invasive genotype prediction of chromosome 1p/19q co-deletion by development and validation of an MRI-based radiomics signature in lower-grade gliomas.

J Neurooncol 2018 Nov 10;140(2):297-306. Epub 2018 Aug 10.

Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, China.

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http://dx.doi.org/10.1007/s11060-018-2953-yDOI Listing
November 2018

MethylMix 2.0: an R package for identifying DNA methylation genes.

Bioinformatics 2018 09;34(17):3044-3046

Stanford Center for Biomedical Informatics, Department of Medicine and Biomedical Data Science, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129298PMC
September 2018

Non-Small Cell Lung Cancer Radiogenomics Map Identifies Relationships between Molecular and Imaging Phenotypes with Prognostic Implications.

Radiology 2018 01 20;286(1):307-315. Epub 2017 Jul 20.

From the Stanford Center for Biomedical Informatics Research, Department of Medicine (M.Z., O.G.), Department of Radiology (A.L., S.E., A.G., S.K.P., D.L.R., S.N.), Division of Thoracic Surgery, Department of Cardiothoracic Surgery (J.B.S.), and Department of Pathology (K.C.J., G.J.B.), Stanford University, 1265 Welch Rd, Stanford, CA 94305-5479.

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http://pubs.rsna.org/doi/10.1148/radiol.2017161845
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http://dx.doi.org/10.1148/radiol.2017161845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5749594PMC
January 2018

Module Analysis Captures Pancancer Genetically and Epigenetically Deregulated Cancer Driver Genes for Smoking and Antiviral Response.

EBioMedicine 2018 Jan 1;27:156-166. Epub 2017 Dec 1.

Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Biomedical Data Science, Stanford University, United States. Electronic address:

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http://dx.doi.org/10.1016/j.ebiom.2017.11.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5828545PMC
January 2018

NSD1 inactivation defines an immune cold, DNA hypomethylated subtype in squamous cell carcinoma.

Sci Rep 2017 12 6;7(1):17064. Epub 2017 Dec 6.

Department of Medicine, Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, USA.

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http://dx.doi.org/10.1038/s41598-017-17298-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5719078PMC
December 2017

Predicting biomedical metadata in CEDAR: A study of Gene Expression Omnibus (GEO).

J Biomed Inform 2017 08 16;72:132-139. Epub 2017 Jun 16.

Stanford Center for Biomedical Informatics Research, Center for Data Annotation and Retrieval, Department of Medicine, Stanford University, Stanford, 94305, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2017.06.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5643580PMC
August 2017

Central focused convolutional neural networks: Developing a data-driven model for lung nodule segmentation.

Med Image Anal 2017 Aug 30;40:172-183. Epub 2017 Jun 30.

CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Key Laboratory of Molecular Imaging, Beijing 100190, China. Electronic address:

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http://dx.doi.org/10.1016/j.media.2017.06.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5661888PMC
August 2017

Magnetic resonance perfusion image features uncover an angiogenic subgroup of glioblastoma patients with poor survival and better response to antiangiogenic treatment.

Neuro Oncol 2017 Jul;19(7):997-1007

Department of Neurosurgery, Stanford University, Stanford, California; Department of Radiology, Stanford University, Stanford, California; Stanford Center for Biomedical Informatics Research and Biomedical Informatics Training Program, Stanford, California; School of Medicine, Stanford University, Stanford, California; Department of Biomolecular Engineering, University of California, Santa Cruz, California.

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http://dx.doi.org/10.1093/neuonc/now270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570189PMC
July 2017

Quantitative imaging outperforms molecular markers when predicting response to chemoradiotherapy for rectal cancer.

Radiother Oncol 2017 07 21;124(1):104-109. Epub 2017 Jun 21.

KU Leuven - University of Leuven, Department of Oncology, B-3000 Leuven, Belgium; University Hospitals Leuven, Radiation Oncology, B-3000 Leuven, Belgium.

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http://dx.doi.org/10.1016/j.radonc.2017.06.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5641595PMC
July 2017

MicroRNA based Pan-Cancer Diagnosis and Treatment Recommendation.

BMC Bioinformatics 2017 Jan 13;18(1):32. Epub 2017 Jan 13.

Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine, and Department of Biomedical Data Science, Stanford University, 1265 Welch Rd, Stanford, CA, USA.

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http://dx.doi.org/10.1186/s12859-016-1421-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5237282PMC
January 2017

Chromatin-Remodeling Complex SWI/SNF Controls Multidrug Resistance by Transcriptionally Regulating the Drug Efflux Pump ABCB1.

Cancer Res 2016 10 8;76(19):5810-5821. Epub 2016 Aug 8.

Department of Biochemistry, Stanford University School of Medicine, Stanford, California. Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5050136PMC
http://dx.doi.org/10.1158/0008-5472.CAN-16-0716DOI Listing
October 2016

Development of prognostic signatures for intermediate-risk papillary thyroid cancer.

BMC Cancer 2016 09 15;16(1):736. Epub 2016 Sep 15.

Stanford Center for Biomedical Informatics Research, Department of Medicine & Department of Biomedical Data Science, Stanford University, Stanford, USA.

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http://dx.doi.org/10.1186/s12885-016-2771-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5025616PMC
September 2016

Single Gene Prognostic Biomarkers in Ovarian Cancer: A Meta-Analysis.

PLoS One 2016 17;11(2):e0149183. Epub 2016 Feb 17.

Dept. of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, SD, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0149183PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4757072PMC
August 2016

CoINcIDE: A framework for discovery of patient subtypes across multiple datasets.

Genome Med 2016 Mar 9;8(1):27. Epub 2016 Mar 9.

The Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine, Stanford University, 1265 Welch Road, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1186/s13073-016-0281-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784276PMC
March 2016

Predicting structured metadata from unstructured metadata.

Database (Oxford) 2016 01;2016

Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1093/database/baw080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4892825PMC
January 2016

Combined Mapping of Multiple clUsteriNg ALgorithms (COMMUNAL): A Robust Method for Selection of Cluster Number, K.

Sci Rep 2015 Nov 19;5:16971. Epub 2015 Nov 19.

Biomedical Informatics Research, Stanford University, Stanford, CA 94305, United States.

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http://www.nature.com/articles/srep16971
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http://dx.doi.org/10.1038/srep16971DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4652212PMC
November 2015

MethylMix: an R package for identifying DNA methylation-driven genes.

Authors:
Olivier Gevaert

Bioinformatics 2015 Jun 20;31(11):1839-41. Epub 2015 Jan 20.

Department of Medicine, Stanford Center for Biomedical Informatics, Stanford, CA 94305-5479, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443673PMC
June 2015

Pancancer analysis of DNA methylation-driven genes using MethylMix.

Genome Biol 2015 Jan 29;16:17. Epub 2015 Jan 29.

Department of Radiology, Stanford University, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1186/s13059-014-0579-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365533PMC
January 2015

Methylation of PITX2, HOXD3, RASSF1 and TDRD1 predicts biochemical recurrence in high-risk prostate cancer.

J Cancer Res Clin Oncol 2014 Nov 18;140(11):1849-61. Epub 2014 Jun 18.

Laboratory of Biosignaling and Therapeutics, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium,

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http://dx.doi.org/10.1007/s00432-014-1738-8DOI Listing
November 2014

Glioblastoma multiforme: exploratory radiogenomic analysis by using quantitative image features.

Radiology 2014 Oct 12;273(1):168-74. Epub 2014 May 12.

From the Departments of Medicine (O.G.), Radiology (O.G., L.A.M., J.X., S.E., S.N., G.Z., S.K.P.), and Neurosurgery (A.S.A., G.K.S., S.H.C.), Stanford University, 1265 Welch Rd, Stanford, CA, 94304-5479.

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http://dx.doi.org/10.1148/radiol.14131731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263772PMC
October 2014

NF-κB protein expression associates with (18)F-FDG PET tumor uptake in non-small cell lung cancer: a radiogenomics validation study to understand tumor metabolism.

Lung Cancer 2014 Feb 13;83(2):189-96. Epub 2013 Nov 13.

Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, United States.

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http://dx.doi.org/10.1016/j.lungcan.2013.11.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3922123PMC
February 2014

Identifying master regulators of cancer and their downstream targets by integrating genomic and epigenomic features.

Pac Symp Biocomput 2013 :123-34

Radiology, Stanford, 1201 Welch Road, Stanford, CA 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3911770PMC
December 2013

Identification of ovarian cancer driver genes by using module network integration of multi-omics data.

Interface Focus 2013 Aug;3(4):20130013

Cancer Center for Systems Biology, Department of Radiology , Stanford University, Lucas Center for Imaging , 1201 Welch Road, Stanford, CA 94305 , USA.

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http://dx.doi.org/10.1098/rsfs.2013.0013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3915833PMC
August 2013

Proteomics analysis of plasma for early diagnosis of endometriosis.

Obstet Gynecol 2012 Feb;119(2 Pt 1):276-85

Department of Obstetrics and Gynaecology, Leuven University Fertility Centre, University Hospital Gasthuisberg, Belgium.

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http://dx.doi.org/10.1097/AOG.0b013e31823fda8dDOI Listing
February 2012

Evaluation of endometrial biomarkers for semi-invasive diagnosis of endometriosis.

Fertil Steril 2011 Mar 30;95(4):1338-43.e1-3. Epub 2010 Aug 30.

Leuven University Fertility Center, and Experimental Gynecology Laboratory, Department of Obstetrics and Gynecology, University Hospital Gasthuisberg, Leuven, Belgium.

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http://dx.doi.org/10.1016/j.fertnstert.2010.06.084DOI Listing
March 2011

Ectopic pregnancy: using the hCG ratio to select women for expectant or medical management.

Acta Obstet Gynecol Scand 2011 Mar 13;90(3):264-72. Epub 2011 Jan 13.

Early Pregnancy and Gynaecological Ultrasound Unit, St George's, University of London, UK.

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http://dx.doi.org/10.1111/j.1600-0412.2010.01053.xDOI Listing
March 2011

Improved microarray-based decision support with graph encoded interactome data.

PLoS One 2010 Apr 19;5(4):e10225. Epub 2010 Apr 19.

Department of Electrical Engineering ESAT/SCD, Katholieke Universiteit Leuven, Leuven, Belgium.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0010225PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2856685PMC
April 2010

Recurrent copy number alterations in BRCA1-mutated ovarian tumors alter biological pathways.

Hum Mutat 2009 Dec;30(12):1693-702

Division of Gynecological Oncology, Department of Obstetrics and Gynecology, University Hospitals Leuven, Katholieke Universiteit Leuven, Belgium.

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http://dx.doi.org/10.1002/humu.21135DOI Listing
December 2009

A taxonomy of epithelial human cancer and their metastases.

BMC Med Genomics 2009 Dec 17;2:69. Epub 2009 Dec 17.

Bioinformatics, Department of Electrical Engineering (ESAT/SCD), Katholieke Universiteit Leuven, Belgium.

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http://dx.doi.org/10.1186/1755-8794-2-69DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806369PMC
December 2009

A kernel-based integration of genome-wide data for clinical decision support.

Genome Med 2009 Apr 3;1(4):39. Epub 2009 Apr 3.

Department of Electrical Engineering (ESAT-SCD), Katholieke Universiteit Leuven, Kasteelpark Arenberg, 3001 Leuven, Belgium.

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http://dx.doi.org/10.1186/gm39DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2684660PMC
April 2009

Supervised classification of array CGH data with HMM-based feature selection.

Pac Symp Biocomput 2009 :468-79

Department of Electrical Engineering, Katholieke Universiteit Leuven, Leuven, Belgium.

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March 2009

Prediction of cancer outcome using DNA microarray technology: past, present and future.

Expert Opin Med Diagn 2009 Mar;3(2):157-65

Katholieke Universiteit Leuven, Department of Electrical Engineering ESAT-SCD-Sista, Kasteelpark Arenberg 10, 3001 Leuven, Belgium +32 16 328646 ; +32 16 32 ;

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http://www.tandfonline.com/doi/full/10.1517/1753005080268017
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http://dx.doi.org/10.1517/17530050802680172DOI Listing
March 2009

Integration of clinical and microarray data with kernel methods.

Conf Proc IEEE Eng Med Biol Soc 2007 ;2007:5411-5

ESAT, Department of Electrical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium.

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http://dx.doi.org/10.1109/IEMBS.2007.4353566DOI Listing
March 2008

Integrating microarray and proteomics data to predict the response on cetuximab in patients with rectal cancer.

Pac Symp Biocomput 2008 :166-77

Katholieke Universiteit Leuven, Department of Electrical Engineering (ESAT), SCD-SISTA (BIOI), Kasteelpark Arenberg 10--bus 2446, B-3001 Leuven, Heverlee, Belgium.

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March 2008

Expression profiling to predict the clinical behaviour of ovarian cancer fails independent evaluation.

BMC Cancer 2008 Jan 22;8:18. Epub 2008 Jan 22.

Department of Electrical Engineering ESAT-SCD-Sista, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium.

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http://dx.doi.org/10.1186/1471-2407-8-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2259320PMC
January 2008

A framework for elucidating regulatory networks based on prior information and expression data.

Ann N Y Acad Sci 2007 Dec 9;1115:240-8. Epub 2007 Oct 9.

Katholieke Universiteit Leuven, Department of Electrical Engineering (ESAT), Kasteelpark Arenberg 10, 3001 Leuven, Belgium.

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http://dx.doi.org/10.1196/annals.1407.002DOI Listing
December 2007

Predicting the prognosis of breast cancer by integrating clinical and microarray data with Bayesian networks.

Bioinformatics 2006 Jul;22(14):e184-90

Department of Electrical Engineering ESAT-SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btl230DOI Listing
July 2006