Jelle J Goeman

Jelle J Goeman

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Jelle J Goeman

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Postmortem T2*- Weighted MRI Imaging of Cortical Iron Reflects Severity of Alzheimer's Disease.

J Alzheimers Dis 2018 ;65(4):1125-1137

Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands.

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http://dx.doi.org/10.3233/JAD-180317DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218127PMC
August 2019

Tissue-sparing properties of Mohs micrographic surgery for infiltrative basal cell carcinoma.

J Am Acad Dermatol 2019 Jun 31;80(6):1700-1703. Epub 2019 Jan 31.

Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands; Department of Dermatology, Roosevelt Clinic, Leiden, The Netherlands. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S01909622193016
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http://dx.doi.org/10.1016/j.jaad.2019.01.057DOI Listing
June 2019

Large-scale plasma metabolome analysis reveals alterations in HDL metabolism in migraine.

Neurology 2019 Apr 3;92(16):e1899-e1911. Epub 2019 Apr 3.

From the Departments of Neurology (G.L.J.O., J.A.P., D.A.K., R.Z., I.d.B., M.D.F., G.M.T., A.M.J.M.v.d.M.), Human Genetics (A.D., L.S.V., P.A.C.'tH., A.M.J.M.v.d.M.), Molecular Epidemiology (M.B., P.E.S.), Radiology (D.A.K.), and Medical Statistics (J.J.G.), Leiden University Medical Centre; Department of Biological Psychology (L.L., R.P., D.I.B.), Vrije Universiteit Amsterdam; Amsterdam Public Health Institute (L.L.); Amsterdam Neuroscience and Amsterdam Public Health (M.B., C.S.T., Y.M., D.I.B., B.W.P.); Department of Psychiatry (M.B., C.S.T., Y.M., B.W.P.), VU University Medical Centre/GGZ inGeest, Amsterdam; Departments of Epidemiology (A.D., J.L., K.-x.W., N.A., M.A.I., C.M.v.D.) and Neurology (M.A.I.), Erasmus Medical Centre, Rotterdam; Departments of Genetics (J.F., L.F., C.W.) and Pediatrics (J.F.), University Medical Centre Groningen; Department of Internal Medicine (C.J.H.v.d.K., F.H.M.V., M.M.J.v.G., M.T.S., C.D.A.S.) and Heart and Vascular Center (M.T.S.), Maastricht University Medical Centre; CARIM School for Cardiovascular Diseases (C.J.H.v.d.K., M.M.J.v.G., I.C.W.A., M.T.S., P.C.D., C.D.A.S.), Department of Epidemiology (I.C.W.A.), MaCSBio Maastricht Centre for Systems Biology (I.C.W.A.), and Department of Epidemiology (P.C.D.), Maastricht University; Department of Radiology (M.A.I.), Erasmus MC University Medical Centre, Rotterdam; Leiden Academic Centre in Drug Research, Faculty Science (C.M.v.D.), Leiden University; and Centre for Molecular and Biomolecular Informatics (P.A.C.'tH.), Radboud University Medical Centre Nijmegen, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands.

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http://dx.doi.org/10.1212/WNL.0000000000007313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6550500PMC
April 2019

Deacetylation Inhibition Reverses PABPN1-Dependent Muscle Wasting.

iScience 2019 Feb 22;12:318-332. Epub 2019 Jan 22.

Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2019.01.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6370712PMC
February 2019

Hommel's procedure in linear time.

Biom J 2019 01 5;61(1):73-82. Epub 2018 Sep 5.

Biomedical Data Sciences, Leiden University Medical Center, Postbus, RC Leiden, The Netherlands.

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http://dx.doi.org/10.1002/bimj.201700316DOI Listing
January 2019

All-Resolutions Inference for brain imaging.

Neuroimage 2018 11 27;181:786-796. Epub 2018 Jul 27.

Department of Biomedical Data Sciences, Leiden University Medical Center, The Netherlands.

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http://dx.doi.org/10.1016/j.neuroimage.2018.07.060DOI Listing
November 2018

Gaining power in multiple testing of interval hypotheses via conditionalization.

Biostatistics 2018 Sep 21. Epub 2018 Sep 21.

Biomedical Data Sciences, Leiden University Medical Center, Postbus 9600, 2300 RC, Leiden, The Netherlands.

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http://dx.doi.org/10.1093/biostatistics/kxy042DOI Listing
September 2018

A test for detecting differential indirect trans effects between two groups of samples.

Stat Appl Genet Mol Biol 2018 07 31;17(5). Epub 2018 Jul 31.

Afdeling Epidemiologie en Biostatistiek, Amsterdam Public Health Research Institute, Medische Faculteit (F-vleugel), VU Medisch Centrum, 1007 MB Amsterdam, The Netherlands.

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http://dx.doi.org/10.1515/sagmb-2017-0058DOI Listing
July 2018

What (not) to expect when classifying rare events.

Brief Bioinform 2018 03;19(2):341-349

Leiden University Medical Center, Department of Medical Statistics and Bioinformatics, Leiden, The Netherlands.

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http://dx.doi.org/10.1093/bib/bbw107DOI Listing
March 2018

Blinded histopathological characterisation of POLE exonuclease domain-mutant endometrial cancers: sheep in wolf's clothing.

Histopathology 2018 Jan 10;72(2):248-258. Epub 2017 Oct 10.

Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands.

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http://dx.doi.org/10.1111/his.13338DOI Listing
January 2018

Contribution to the discussion of "A critical evaluation of the current 'p-value controversy"'.

Authors:
Jelle J Goeman

Biom J 2017 09 25;59(5):884-885. Epub 2017 Apr 25.

Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Postzone S5-P, Postbus 9600, 2300 RC, Leiden, The Netherlands.

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http://dx.doi.org/10.1002/bimj.201700028DOI Listing
September 2017

Minimally adaptive BH: A tiny but uniform improvement of the procedure of Benjamini and Hochberg.

Biom J 2017 Jul 18;59(4):776-780. Epub 2016 May 18.

Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Postzone S5-P, Postbus 9600, 2300 RC Leiden, The Netherlands.

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http://dx.doi.org/10.1002/bimj.201500253DOI Listing
July 2017

A global × global test for testing associations between two large sets of variables.

Biom J 2017 Jan 25;59(1):145-158. Epub 2016 May 25.

Biostatistics, Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1002/bimj.201500106DOI Listing
January 2017

Multiple Testing of Gene Sets from Gene Ontology: Possibilities and Pitfalls.

Brief Bioinform 2016 09 7;17(5):808-18. Epub 2015 Oct 7.

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http://dx.doi.org/10.1093/bib/bbv091DOI Listing
September 2016

A Cochran-Armitage-type and a score-free global test for multivariate ordinal data.

Stat Med 2016 07 28;35(16):2754-69. Epub 2016 Feb 28.

Biostatistics, Institute for Molecular Life Sciences, Radboud university medical center, P.O. Box 9101, Nijmegen, 6500 HB, The Netherlands.

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http://dx.doi.org/10.1002/sim.6898DOI Listing
July 2016

Plea for routinely presenting prediction intervals in meta-analysis.

BMJ Open 2016 07 12;6(7):e010247. Epub 2016 Jul 12.

Radboud University Medical Center, Radboud Institute for Health Sciences (RIHS), Nijmegen, The Netherlands.

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http://dx.doi.org/10.1136/bmjopen-2015-010247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4947751PMC
July 2016

Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack.

BMC Bioinformatics 2016 Feb 9;17:77. Epub 2016 Feb 9.

Department of Pediatric Oncology and Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands.

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http://dx.doi.org/10.1186/s12859-016-0926-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4746904PMC
February 2016

Genes involved in the osteoarthritis process identified through genome wide expression analysis in articular cartilage; the RAAK study.

PLoS One 2014 23;9(7):e103056. Epub 2014 Jul 23.

Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands; The Netherlands Genomics Initiative, sponsored by the NCHA, Leiden-Rotterdam, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0103056PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108379PMC
November 2015

Focused human gene expression profiling using dual-color reverse transcriptase multiplex ligation-dependent probe amplification.

Vaccine 2015 Sep 24;33(40):5282-8. Epub 2015 Apr 24.

Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.vaccine.2015.04.054DOI Listing
September 2015

Small studies are more heterogeneous than large ones: a meta-meta-analysis.

J Clin Epidemiol 2015 Aug 2;68(8):860-9. Epub 2015 Apr 2.

Radboud Institute for Health Sciences (RIHS), Radboud University Medical Center, Mailbox 133, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands.

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http://dx.doi.org/10.1016/j.jclinepi.2015.03.017DOI Listing
August 2015

Drug Survival Studies in Dermatology:Principles, Purposes, and Pitfalls.

J Invest Dermatol 2015 Jul;135(7):1-5

Department of Dermatology, Radboud University Medical Center, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1038/jid.2015.171DOI Listing
July 2015

KeyGenes, a Tool to Probe Tissue Differentiation Using a Human Fetal Transcriptional Atlas.

Stem Cell Reports 2015 Jun 28;4(6):1112-24. Epub 2015 May 28.

Department of Anatomy and Embryology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands; Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2015.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4472038PMC
June 2015

Assessing the translational landscape of myogenic differentiation by ribosome profiling.

Nucleic Acids Res 2015 May 14;43(9):4408-28. Epub 2015 Apr 14.

Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands

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http://dx.doi.org/10.1093/nar/gkv281DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4482065PMC
May 2015

An alternative approach to multiple testing for methylation QTL mapping reduces the proportion of falsely identified CpGs.

Bioinformatics 2015 Feb 4;31(3):340-5. Epub 2014 Oct 4.

Department of Molecular Epidemiology, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, 2333 ZC Leiden and Biostatistics, Department for Health Evidence, Radboud University Nijmegen Medical Center, 6500 HB Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btu654DOI Listing
February 2015

MicroRNA classifier and nomogram for metastasis prediction in colon cancer.

Cancer Epidemiol Biomarkers Prev 2015 Jan 14;24(1):187-97. Epub 2014 Oct 14.

Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands.

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http://dx.doi.org/10.1158/1055-9965.EPI-14-0544-TDOI Listing
January 2015

A multiple testing method for hypotheses structured in a directed acyclic graph.

Biom J 2015 Jan 13;57(1):123-43. Epub 2014 Nov 13.

Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Postzone S5-P, P.O. Box 9604, 2300 RC Leiden, The Netherlands.

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http://dx.doi.org/10.1002/bimj.201300253DOI Listing
January 2015

Promoter CpG island hypermethylation in dysplastic nevus and melanoma: CLDN11 as an epigenetic biomarker for malignancy.

J Invest Dermatol 2014 Dec 7;134(12):2957-2966. Epub 2014 Jul 7.

Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands; The first two and last three authors contributed equally to this work. Electronic address:

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http://dx.doi.org/10.1038/jid.2014.270DOI Listing
December 2014

Rotation-based multiple testing in the multivariate linear model.

Biometrics 2014 Dec 30;70(4):954-61. Epub 2014 Sep 30.

Department of Economics, Management and Statistics, University of Milano-Bicocca, Milan, Italy.

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http://paduaresearch.cab.unipd.it/7115/1/2013_3_201302011547
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http://doi.wiley.com/10.1111/biom.12238
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http://dx.doi.org/10.1111/biom.12238DOI Listing
December 2014

A test for comparing two groups of samples when analyzing multiple omics profiles.

BMC Bioinformatics 2014 Jul 8;15:236. Epub 2014 Jul 8.

Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-15-236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227098PMC
July 2014

Multiple hypothesis testing in genomics.

Stat Med 2014 May 8;33(11):1946-78. Epub 2014 Jan 8.

Biostatistics, Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands.

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http://dx.doi.org/10.1002/sim.6082DOI Listing
May 2014

Fused lasso algorithm for Cox' proportional hazards and binomial logit models with application to copy number profiles.

Biom J 2014 May 3;56(3):477-92. Epub 2014 Feb 3.

Epidemiology and Biostatistics, Vrije Universiteit Medical Center, Amsterdam, The Netherlands; Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.1002/bimj.201200241DOI Listing
May 2014

Human leukocyte antigen-DO regulates surface presentation of human leukocyte antigen class II-restricted antigens on B cell malignancies.

Biol Blood Marrow Transplant 2014 May 14;20(5):742-7. Epub 2014 Feb 14.

Department of Hematology, Leiden University Medical Center, RC Leiden, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.bbmt.2014.02.005DOI Listing
May 2014

Meta-analysis on blood transcriptomic studies identifies consistently coexpressed protein-protein interaction modules as robust markers of human aging.

Aging Cell 2014 Apr 19;13(2):216-25. Epub 2013 Nov 19.

Department of Molecular Epidemiology, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands; The Delft Bioinformatics Lab, Delft University of Technology, PO Box 5031, 2600 GA, Delft, The Netherlands.

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http://dx.doi.org/10.1111/acel.12160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4331790PMC
April 2014

The footprint of genome architecture in the largest genome expansion in RNA viruses.

PLoS Pathog 2013 18;9(7):e1003500. Epub 2013 Jul 18.

Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.

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http://dx.doi.org/10.1371/journal.ppat.1003500DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715407PMC
February 2014

Major aging-associated RNA expressions change at two distinct age-positions.

BMC Genomics 2014 Feb 14;15:132. Epub 2014 Feb 14.

Department of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-15-132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930826PMC
February 2014

Efficient approximate k-fold and leave-one-out cross-validation for ridge regression.

Biom J 2013 Mar 24;55(2):141-55. Epub 2013 Jan 24.

Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Postzone S5-P, P.O. Box 9604, 2300 RC Leiden, The Netherlands.

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http://dx.doi.org/10.1002/bimj.201200088DOI Listing
March 2013

Testing goodness of fit in regression: a general approach for specified alternatives.

Stat Med 2012 Dec 25;31(28):3656-66. Epub 2012 Jul 25.

Department of Statistics, University of Milano-Bicocca, via Bicocca degli Arcimboldi 8, 20126, Milan, Italy.

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http://dx.doi.org/10.1002/sim.5417DOI Listing
December 2012

Different gene sets contribute to different symptom dimensions of depression and anxiety.

Am J Med Genet B Neuropsychiatr Genet 2012 Jul 9;159B(5):519-28. Epub 2012 May 9.

Department of Psychiatry, Leiden University Medical Centre, Leiden, The Netherlands.

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http://dx.doi.org/10.1002/ajmg.b.32058DOI Listing
July 2012

Resolving confusion of tongues in statistics and machine learning: a primer for biologists and bioinformaticians.

Proteomics 2012 Feb 23;12(4-5):543-9. Epub 2012 Jan 23.

Center for Human and Clinical Genetics, Leiden University Medical Center, The Netherlands.

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http://doi.wiley.com/10.1002/pmic.201100395
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http://dx.doi.org/10.1002/pmic.201100395DOI Listing
February 2012

Tracking the progression of the human inner cell mass during embryonic stem cell derivation.

Nat Biotechnol 2012 Feb 26;30(3):278-82. Epub 2012 Feb 26.

Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium.

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http://dx.doi.org/10.1038/nbt.2135DOI Listing
February 2012

The inheritance procedure: multiple testing of tree-structured hypotheses.

Stat Appl Genet Mol Biol 2012 Jan 21;11(1):Article 11. Epub 2012 Jan 21.

Leiden University Medical Center.

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http://dx.doi.org/10.1515/1544-6115.1554DOI Listing
January 2012

Literature-aided interpretation of gene expression data with the weighted global test.

Brief Bioinform 2011 Sep 22;12(5):518-29. Epub 2010 Dec 22.

Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.

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http://dx.doi.org/10.1093/bib/bbq082DOI Listing
September 2011

Three-sided hypothesis testing: simultaneous testing of superiority, equivalence and inferiority.

Stat Med 2010 Sep;29(20):2117-25

Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands.

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http://dx.doi.org/10.1002/sim.4002DOI Listing
September 2010

L1 penalized estimation in the Cox proportional hazards model.

Authors:
Jelle J Goeman

Biom J 2010 Feb;52(1):70-84

Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands.

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http://dx.doi.org/10.1002/bimj.200900028DOI Listing
February 2010

Autocorrelated logistic ridge regression for prediction based on proteomics spectra.

Authors:
Jelle J Goeman

Stat Appl Genet Mol Biol 2008 21;7(2):Article10. Epub 2008 Feb 21.

Leiden University Medical Center.

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http://dx.doi.org/10.2202/1544-6115.1344DOI Listing
April 2008

Multiple testing on the directed acyclic graph of gene ontology.

Bioinformatics 2008 Feb 18;24(4):537-44. Epub 2008 Jan 18.

Department of Medical Statistics, Postzone S5-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btm628DOI Listing
February 2008

Genetic susceptibility to respiratory syncytial virus bronchiolitis is predominantly associated with innate immune genes.

J Infect Dis 2007 Sep 10;196(6):826-34. Epub 2007 Aug 10.

Laboratory for Toxicology, Pathology, and Genetics, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.

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http://dx.doi.org/10.1086/520886DOI Listing
September 2007

Analyzing gene expression data in terms of gene sets: methodological issues.

Bioinformatics 2007 Apr 15;23(8):980-7. Epub 2007 Feb 15.

Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btm051DOI Listing
April 2007

A goodness-of-fit test for multinomial logistic regression.

Biometrics 2006 Dec;62(4):980-5

Department of Medical Statistics, Leiden University Medical Center, P.O. Box 9604, 2300 RC Leiden, The Netherlands.

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http://dx.doi.org/10.1111/j.1541-0420.2006.00581.xDOI Listing
December 2006

Testing association of a pathway with survival using gene expression data.

Bioinformatics 2005 May 18;21(9):1950-7. Epub 2005 Jan 18.

Department of Medical Statistics, Leiden University Medical Center, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/bti267DOI Listing
May 2005

Enhancing scatterplots with smoothed densities.

Bioinformatics 2004 Mar 22;20(5):623-8. Epub 2004 Jan 22.

Department of Medical Statistics, Leiden University Medical Centre, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btg454DOI Listing
March 2004

A global test for groups of genes: testing association with a clinical outcome.

Bioinformatics 2004 Jan;20(1):93-9

Department of Medical Statistics, Leiden University Medical Center, P.O. Box 9604, 2300 RC Leiden, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btg382DOI Listing
January 2004