Jelle Goeman
Professor Analysis of high-dimensional medical data
- Name
- Prof.dr. J.J. Goeman
- Telephone
- +31 71 526 9700
- j.j.goeman@lumc.nl
- ORCID iD
- null
Jelle J. Goeman is professor of biostatistics at the department of Biomedical Data Sciences at Leiden University Medical Center. His specialization is the analysis of high-dimensional medical data. For his research he was awarded a VENI and a VIDI grant.
Jelle J. Goeman is professor of biostatistics at the department of Biomedical Data Sciences at Leiden University Medical Center. His specialization is the analysis of high-dimensional medical data. For his research he was awarded a VENI and a VIDI grant.
Biostatistics
In medical research more and more data are gathered using advanced technologies. For example in genetics the activity of tens of thousands of genes can be measured simultaneously; in brain research the acivity of tens of thousands of brain segments is measured. Finding patterns in such data is like finding a needle in a haystack. To help research in these areas there is a need for new and advanced statistical methods. Jelle Goeman develops such methods. He works on methods for multiple hypothesis testing and on high-dimensional prediction models.
Academic career
Jelle Goeman studied mathematics and history at Leiden University, where he obtained his PhD on March 8, 2006 with his thesis “Statistical methods for microarray data”. He worked as a researcher at Leiden University and at imperial College in London. In 2013 he was appointed professor of biostatistics at Radboud University. He returned to Leiden University in 2016 where he gave an inaugural address on November 17, 2017: Statistical methods for Microarray data: pathway analysis, prediction methods and visualization tools
Prizes and honourable appointments
Jelle Goeman received the C.J. Kok prize in 2011 for extraordinary acievements in mathamatics and/or medicine. In 2012 he was awarded the Biometry Award for his article “Multiple testing for exploratory research”.
Professor Analysis of high-dimensional medical data
- Faculteit Geneeskunde
- Divisie 4
- Divisie 4
- Kapteijn, M.Y.; Lanting, V.R.; Kaptein, F.H.J.; Guman, N.A.M.; Laghmani, E.H.; Kuipers, T.B.; Mei, H.L.; Goeman, J.J.; Mulder, F.I.; Duinen, S.G. van; Taphoorn, M.J.B.; Dirven, L.; Broekman, M.L.D.; Es, N. van; Klok, F.A.; Koekkoek, J.A.F.; Versteeg, H.H. & Buijs, J.T. (2023), RNA-sequencing to discover genes and signaling pathways associated with venous thromboembolism in glioblastoma patients, Thrombosis Research: Vascular Obstruction, Hemorrhage and Hemostasis 232: 27-34.
- Kapteijn, M.Y.; Lanting, V.R.; Kaptein, F.H.J.; Guman, N.A.M.; Laghmani, E.H.; Kuipers, T.B.; Mei, H.L.; Goeman, J.J.; Mulder, F.I.; Duinen, S.G. van; Taphoorn, M.J.B.; Dirven, L.; Broekman, M.L.D.; Es, N. van; Klok, F.A.; Koekkoek, J.A.F.; Versteeg, H.H. & Buijs, J.T. (2023), RNA-sequencing to discover genes and signaling pathways associated with venous thromboembolism in glioblastoma patients, Thrombosis Research: Vascular Obstruction, Hemorrhage and Hemostasis 232: 27-34.
- Li-Gao, R.; Lu, C.; Hughes, D.A.; Klinken, J.B. van; Mutsert, R. de; Rosendaal, F.R.; Timpson, N.J.; Mook-Kanamori, D.O.; Goeman, J.J.; Putter, H. & Dijk, K.W. van (2023), The associations between metabolomic responses to a liquid mixed meal and incidence of type 2 diabetes: Are there novel biomarkers beyond glucose and triglyceride response?, Diabetologia 66(SUPPL 1): S14-S14.
- Andreella, A.; Hemerik, J.; Finos, L.; Weeda, W. & Goeman, J. (2023), Permutation-based true discovery proportions for functional magnetic resonance imaging cluster analysis, Statistics in Medicine 42(14): 2311-2340.
- Vesely, A.; Finos, L. & Goeman, J.J. (2023), Permutation-based true discovery guarantee by sum tests, Journal of the Royal Statistical Society: Statistical Methodology Series B 85(3): 664-683.
- Kluivers, K.B.; Lince, S.L.; Ruiz-Zapata, A.M.; Post, W.M.; Cartwright, R.; Kerkhof, M.H.; Widomska, J.; Witte, W. de; Pecanka, J.; Kiemeney, L.A.; Vermeulen, S.H.; Goeman, J.J.; Allen-Brady, K.; Oosterwijk, E. & Poelmans, G. (2023), Molecular landscape of pelvic organ prolapse provides insights into disease etiology, International Journal of Molecular Sciences 24(7).
- Marsidi, N.; Scheepens, K.M.J.; Goeman, J.J.; Horeman, T. & Genders, R.E. (2023), Dynamic characteristics of skin reaction force in different body postures, Scientific Reports 13(1).
- Goeman, J.J.; Górecki, P.; Monajemi, R.; Chen, X.; Nichols, T.E. & Weeda, W. (2023), Cluster extent inference revisited, Journal of the Royal Statistical Society: Statistical Methodology Series B 85(4): 1128-1153.
- Onderwater, G.L.J.; Dongen, R.M. van; Harms, A.C.; Zielman, R.; Oosterhout, W.P.J. van; Klinken, J.B. van; Goeman, J.J.; Terwindt, G.M.; Maagdenberg, A.M.J.M. van den; Hankemeier, T. & Ferrari, M.D. (2023), Cerebrospinal fluid and plasma amine profiles in interictal migraine, Annals of Neurology 93(4).
- Dang, H.; Harryvan, T.J.; Liao, C.Y.; Danen, E.H.J.; Spalburg, V.N.L.N.; Kielbasa, S.M.; Mei, H.L.; Goeman, J.J.; Jonge-Muller, E.S. de; Janson, S.G.T.; Reijden, J.J. van der; Crobach, S.; Hardwick, J.C.H.; Boonstra, J.J.; Miranda, N.F.C.C. de & Hawinkels, L.J.A.C. (2023), Cancer-associated fibroblasts are key determinants of cancer cell Invasion in the earliest stage of colorectal cancer, Cellular and Molecular Gastroenterology and Hepatology 16(1): 107-131.
- Ipenburg, N.A.; Sharouni, M.A. el; Doorn, R. van; Diest, P.J. van; Leerdam, M.E. van; Rhee, J.I. van der; Goeman, J.; Kukutsch, N.A. & Netherlands Fdn Detection (2022), Lack of association between CDKN2A germline mutations and survival in patients with melanoma: A retrospective cohort study.
- Marsidi, N.; Ottevanger, R.; Bavinck, J.N.B.; Krekel-Taminiau, N.M.A.; Goeman, J.J. & Genders, R.E. (2022), Risk factors for incomplete excision of cutaneous squamous cell carcinoma, Journal of the European Academy of Dermatology and Venereology 36(8): 1229-1234.
- Oosterveer, T.T.M.; Erp, G.C.M. van; Hendriks, P.; Broersen, A.; Overduin, C.G.; Rijswijk, C.S.P. van; Erkel, A.R. van; Meer, R.W. van der; Tushuizen, M.E.; Moelker, A.; Meijerink, M.R.; Delden, O.M. van; Jong, K.P. de; Leij, C. van der; Smits, M.L.J.; Urlings, T.A.J.; Braak, J.P.B.M.; Kranenbarg, E.M.K.; Duijn-de Vreugd, B. van; Zeijdner, E.; Goeman, J.J.; Futterer, J.J.; Coenraad, M.J.; Dijkstra, J. & Burgmans, M.C. (2022), Study protocol PROMETHEUS, CardioVascular and Interventional Radiology 45.
- Holswilder, G.; Stuart, M.P.M.E.; Dompeling, T.; Kruyt, N.D.; Goeman, J.J.; Lugt, A. van der; Schonewille, W.J.; Nijeholt, G.J.L.A.; Majoie, C.B.L.M.; Yo, L.S.F.; Meijer, F.J.A.; Marquering, H.A.; Wermer, M.J.H.; Walderveen, M.A.A. van & MR CLEAN (2022), The prognostic value of extracranial vascular characteristics on procedural duration and revascularization success in endovascularly treated acute ischemic stroke patients, European Stroke Journal 7(1): 48-56.
- Aiyer, K.T.S.; Doeleman, T.; Ryan, N.A.; Nielsen, M.; Crosbie, E.J.; Smit, V.T.H.B.M.; Morreau, H.; Goeman, J.J. & Bosse, T. (2022), Validity of a two-antibody testing algorithm for mismatch repair deficiency testing in cancer, Modern Pathology 35(12).
- Tong, T.M.L.; Samim, M.; Kapiteijn, E.; Meijer, T.S.; Speetjens, F.M.; Bruning, R.; Schroeder, T.H.; El-Sanosy, S.; Maschke, H.; Wacker, F.K.; Vogel, A.; Dewald, C.L.A.; Goeman, J.J. & Burgmans, M.C. (2022), Predictive parameters in patients undergoing percutaneous hepatic perfusion with melphalan for unresectable liver metastases from uveal melanoma, CardioVascular and Interventional Radiology 45(9): 1304-1313.
- Cai, M.L.; Vesely, A.; Chen, X.; Li, L.M. & Goeman, J.J. (2022), NetTDP, Briefings in Bioinformatics 23(6).
- Lu, C.Y.; Goeman, J. & Putter, H. (2022), Maximum likelihood estimation in the additive hazards model, Biometrics.
- Tian, J.J.; Chen, X.; Katsevich, E.; Goeman, J. & Ramdas, A. (2022), Large-scale simultaneous inference under dependence, Scandinavian Journal of Statistics 50(2).
- Ducarmon, Q.R.; Smits, W.K.; Goeman, J.J. & Kuijper, E.J. (2022), International travel, the gut microbiome, and ESBL-E coli carriage.
- Zlei, M.; Sidorov, I.A.; Joosten, S.A.; Heemskerk, M.H.M.; Myeni, S.K.; Pothast, C.R.; Brouwer, C.S. de; Boomaars-van der Zanden, A.L.; Meijgaarden, K.E. van; Morales, S.T.; Wessels, E.; Janse, J.J.; Goeman, J.J.; Cobbaert, C.M.; Kroes, A.C.M.; Cannegieter, S.C.; Roestenberg, M.; Visser, L.G.; Kikkert, M.; Feltkamp, M.C.W.; Arbous, S.M.; Staal, F.J.T.; Ottenhoff, T.H.M.; Dongen, J.J.M. van; Roukens, A.H.E.; Vries, J.J.C. de; Collaboration BEAT-COVID & Collaboration LUMC COVID (2022), Immune determinants of viral clearance in hospitalised COVID-19 patients, Cells 11(17).
- Vendrik, K.E.W.; Baktash, A.; Goeman, J.J.; Harmanus, C.; Notermans, D.W.; Greeff, S.C. de; Kuijper, E.J. & C Difficile Surveillance Study Grp (2022), Comparison of trends in Clostridioides difficile infections in hospitalised patients during the first and second waves of the COVID-19 pandemic, The Lancet Regional Health Europe 19.
- Xu, N.N.; Solari, A. & Goeman, J.J. (2022), Closed testing with Globaltest, with application in metabolomics, Biometrics.
- Edelmann, D. & Goeman, J. (2022), A regression perspective on generalized distance covariance and the Hilbert-Schmidt Independence Criterion, Statistical Science 37(4): 562-579.
- Goeman, J.J.; Hemerik, J. & Solari, A. (2021), Only closed testing procedures are admissible for controlling false discovery proportions, Annals of Statistics 49(2): 1218-1238.
- Ebrahimpoor, M.; Spitali, P.; Goeman, J.J. & Tsonaka, R. (2021), Pathway testing for longitudinal metabolomics, Statistics in Medicine 40(13).
- Bulk, M.; Harten, T. van; Kenkhuis, B.; Inglese, F.; Hegeman, I.; Duinen, S. van; Ercan, E.; Magro-Checa, C.; Goeman, J.; Mawrin, C.; Buchem, M. van; Steup-Beekman, G.; Huizinga, T.; Weerd, L. van der & Ronen, I. (2021), Quantitative susceptibility mapping in the thalamus and basal ganglia of systemic lupus erythematosus patients with neuropsychiatric complaints, NeuroImage: Clinical 30.
- Mohamad, D. al; Zwet, E. van; Solari, A. & Goeman, J. (2021), Simultaneous confidence intervals for ranks using the partitioning principle, Electronic Journal of Statistics 15(1): 2608-2646.
- Mohamad, D. al; Goeman, J.J. & Zwet, E.W. van (2021), Simultaneous confidence intervals for ranks with application to ranking institutions, Biometrics 78(1).
- Jong, S.E. de; Unen, V. van; Manurung, M.D.; Stam, K.A.; Goeman, J.J.; Jochems, S.P.; Hollt, T.; Pezzotti, N.; Mouwenda, Y.D.; Ongwe, M.E.B.; Lorenz, F.R.; Kruize, Y.C.M.; Azimi, S.; Konig, M.H.; Vilanova, A.; Eisemann, E.; Lelieveldt, B.P.F.; Roestenberg, M.; Sim, B.K.L.; Reinders, M.J.T.; Fendel, R.; Hoffman, S.L.; Kremsner, P.G.; Koning, F.; Mordmuller, B.; Lell, B. & Yazdanbakhsh, M. (2021), Systems analysis and controlled malaria infection in Europeans and Africans elucidate naturally acquired immunity, Nature Immunology 22(5): 654-+.
- Silvagni, E.; Inglese, F.; Bortoluzzi, A.; Borrelli, M.; Goeman, J.J.; Revenaz, A.; Groppo, E.; Steup-Beekman, G.M.; Huizinga, T.W.J.; Ronen, I.; Bresser, J. de; Fainardi, E.; Govoni, M. & Ercan, E. (2021), Longitudinal changes in cerebral white matter microstructure in newly diagnosed systemic lupus erythematosus patients, Rheumatology 60(6): 2678-2687.
- Xu, N.N.; Solari, A. & Goeman, J. (2021), Globaltest confidence regions and their application to ridge regression, Biometrical Journal 63(7).
- Rosenblatt, J.D.; Benjamini, Y.; Gilron, R.; Mukamel, R. & Goeman, J.J. (2021), Better-than-chance classification for signal detection, Biostatistics 22(2): 365-380.
- Carbo, E.C.; Blankenspoor, I.; Goeman, J.J.; Kroes, A.C.M.; Claas, E.C.J. & Vries, J.J.C. de (2021), Viral metagenomic sequencing in the diagnosis of meningoencephalitis, Expert Review of Molecular Diagnostics 21(11).
- Juffermans, J.F.; Minderhoud, S.C.S.; Wittgren, J.; Kilburg, A.; Ese, A.; Fidock, B.; Zheng, Y.C.; Zhang, J.M.; Blanken, C.P.S.; Lamb, H.J.; Goeman, J.J.; Carlsson, M.; Zhao, S.H.; Planken, R.N.; Ooij, P. van; Zhong, L.; Chen, X.Y.; Garg, P.; Emrich, T.; Hirsch, A.; Toger, J. & Westenberg, J.J.M. (2021), Multicenter Consistency Assessment of Valvular Flow Quantification With Automated Valve Tracking in 4D Flow CMR, JACC: Cardiovascular Imaging 14(7): 1354-1366.
- Ebrahimpoor, M. & Goeman, J.J. (2021), Inflated false discovery rate due to volcano plots: problem and solutions, Briefings in Bioinformatics 22(5).
- Pont, L.M.H. de; Steekelenburg, J.M. van; Verhagen, T.O.; Houben, M.; Goeman, J.J.; Verbist, B.M.; Buchem, M.A. van; Bommelje, C.C.; Blom, H.M. & Hammer, S. (2021), Hydropic ear disease: correlation between audiovestibular symptoms, endolymphatic hydrops and blood-labyrinth barrier impairment, Frontiers in Surgery 8.
- Ghorzang, E.; Koning, M.N.C. de; Bavinck, J.N.B.; Gussekloo, J.; Quint, K.D.; Goeman, J.J.; Feltkamp, M.C.W.; Bruggink, S.C. & Eekhof, J.A.H. (2021), HPV type-specific distribution among family members and linen in households of cutaneous wart patients, Journal of the European Academy of Dermatology and Venereology 36(1).
- Westenberg, J.J.M.; Assen, H.C.; Boogaard, P.J. den; Goeman, J.J.; Saaid, H.; Voorneveld, J.; Bosch, J.; Kenjeres, S.; Claessens, T.; Garg, P.; Kouwenhoven, M. & Lamb, H.J. (2021), Echo planar imaging-induced errors in intracardiac 4D flow MRI quantification, Magnetic Resonance in Medicine 87(5).
- Goeman, J.J. & Solari, A. (2021), Comparing three groups, American Statistician 76(2).
- Groenwold, R.H.H.; Goeman, J.J.; Cessie, S. le & Dekkers, O.M. (2021), Multiple testing, European Journal of Endocrinology 184(2): E11-E14.
- Rijnberg, F.M.; Assen, H.C. van; Juffermans, J.F.; Kroft, L.J.M.; Boogaard, P.J. van den; Koning, P.J.H. de; Hazekamp, M.G.; Woude, S.F.S. van der; Warmerdam, E.G.; Leiner, T.; Grotenhuis, H.B.; Goeman, J.J.; Lamb, H.J.; Roest, A.A.W. & Westenberg, J.J.M. (2021), Reduced scan time and superior image quality with 3D flow MRI compared to 4D flow MRI for hemodynamic evaluation of the Fontan pathway, Scientific Reports 11(1).
- Hemerik, J.; Goeman, J.J. & Finos, L. (2020), Robust testing in generalized linear models by sign flipping score contributions, Journal of the Royal Statistical Society: Statistical Methodology Series B 82(3): 841-864.
- Overduin, L.A.; Soentjens, P.H.P.; Goeman, J.J.; Berkowska, M.A.; Dongen, J.J.M. van & Visser, L.G. (2020), Redefining non-inferiority in anamnestic antibody responses using the mean increase of log-transformed antibody titers after revaccination, Vaccines 8(4).
- Blagus, R. & Goeman, J.J. (2020), Mean squared error of ridge estimators in logistic regression, Statistica Neerlandica 74(2).
- Genders, R.E.; Marsidi, N.; Michi, M.; Henny, E.P.; Goeman, J.J. & Kester, M.S. van (2020), Incomplete excision of cutaneous squamous cell carcinoma; systematic review of the literature, Acta Dermato-Venereologica 100(3).
- Ellis, J.L.; Pecanka, J. & Goeman, J.J. (2020), Gaining power in multiple testing of interval hypotheses via conditionalization, Biostatistics 21(2): E65-E79.
- Ducarmon, Q.R.; Hoogerwerf, M.A.; Janse, J.J.; Geelen, A.R.; Koopman, J.P.R.; Zwittink, R.D.; Goeman, J.J.; Kuijper, E.J. & Roestenberg, M. (2020), Dynamics of the bacterial gut microbiota during controlled human infection with Necator americanus larvae, Gut Microbes 12(1).
- Ebrahimpoor, M.; Spitali, P.; Hettne, K.; Tsonaka, R. & Goeman, J. (2020), Simultaneous enrichment analysis of all possible gene-sets: unifying self-contained and competitive methods, Briefings in Bioinformatics 21(4): 1302-1312.
- Goeman, J.J. & Bohringer, S. (2020), Comments on: hierarchical inference for genome-wide association studies by Jelle J. Goeman and Stefan Bohringer, Computational Statistics 35(1): 53-58.
- Cessie, S. le; Goeman, J.J. & Dekkers, O.M. (2020), Authors' reply: Who is afraid of non-normal data? Choosing between t-tests and non-parametric tests.
- Botvinik-Nezer, R.; Holzmeister, F.; Camerer, C.F.; Dreber, A.; Huber, J.; Johannesson, M.; Kirchler, M.; Iwanir, R.; Mumford, J.A.; Adcock, R.A.; Avesani, P.; Baczkowski, B.M.; Bajracharya, A.; Bakst, L.; Ball, S.; Barilari, M.; Bault, N.; Beaton, D.; Beitner, J.; Benoit, R.G.; Berkers, R.M.W.J.; Bhanji, J.P.; Biswal, B.B.; Bobadilla-Suarez, S.; Bortolini, T.; Bottenhorn, K.L.; Bowring, A.; Braem, S.; Brooks, H.R.; Brudner, E.G.; Calderon, C.B.; Camilleri, J.A.; Castrellon, J.J.; Cecchetti, L.; Cieslik, E.C.; Cole, Z.J.; Collignon, O.; Cox, R.W.; Cunningham, W.A.; Czoschke, S.; Dadi, K.; Davis, C.P.; Luca, A.D.; Delgado, M.R.; Demetriou, L.; Dennison, J.B.; , X. di; Dickie, E.W.; Dobryakova, E.; Donnat, C.L.; Dukart, J.; Duncan, N.W.; Durnez, J.; Eed, A.; Eickhoff, S.B.; Erhart, A.; Fontanesi, L.; Fricke, G.M.; Fu, S.G.; Galvan, A.; Gau, R.; Genon, S.; Glatard, T.; Glerean, E.; Goeman, J.J.; Golowin, S.A.E.; Gonzalez-Garcia, C.; Gorgolewski, K.J.; Grady, C.L.; Green, M.A.; Moreira, J.F.G.; Guest, O.; Hakimi, S.; Hamilton, J.P.; Hancock, R.; Handjaras, G.; Harry, B.B.; Hawco, C.; Herholz, P.; Herman, G.; Heunis, S.; Hoffstaedter, F.; Hogeveen, J.; Holmes, S.; Hu, C.P.; Huettel, S.A.; Hughes, M.E.; Iacovella, V.; Iordan, A.D.; Isager, P.M.; Isik, A.I.; Jahn, A.; Johnson, M.R.; Johnstone, T.; Joseph, M.J.E.; Juliano, A.C.; Kable, J.W.; Kassinopoulos, M.; Koba, C.; Kong, X.Z.; Koscik, T.R.; Kucukboyaci, N.E.; Kuhl, B.A.; Kupek, S.; Laird, A.R.; Lamm, C.; Langner, R.; Lauharatanahirun, N.; Lee, H.M.; Lee, S.G.; Leemans, A.; Leo, A.; Lesage, E.; Li, F.R.; Li, M.Y.C.; Lim, P.C.; Lintz, E.N.; Liphardt, S.W.; Vermeer, A.L.B.; Love, B.C.; Mack, M.L.; Malpica, N.; Marins, T.; Maumet, C.; McDonald, K.; McGuire, J.T.; Melero, H.; Leal, A.M.S.; Meyer, B.; Meyer, K.N.; Mihai, G.; Mitsis, G.D.; Moll, J.; Nielson, D.M.; Nilsonne, G.; Notter, M.P.; Olivetti, E.; Onicas, A.I.; Papale, P.; Patil, K.R.; Peelle, J.E.; Perez, A.; Pischedda, D.; Poline, J.B.; Prystauka, Y.; Ray, S.; Reuter-Lorenz, P.A.; Reynolds, R.C.; Ricciardi, E.; Rieck, J.R.; Rodriguez-Thompson, A.M.; Romyn, A.; Salo, T.; Samanez-Larkin, G.R.; Sanz-Morales, E.; Schlichting, M.L.; Schultz, D.H.; Shen, Q.; Sheridan, M.A.; Silvers, J.A.; Skagerlund, K.; Smith, A.; Smith, D.V.; Sokol-Hessner, P.; Steinkamp, S.R.; Tashjian, S.M.; Thirion, B.; Thorp, J.N.; Tinghog, G.; Tisdall, L.; Tompson, S.H.; Toro-Serey, C.; Tresols, J.J.T.; Tozzi, L.; Truong, V.; Turella, L.; Veer, A.E. van 't; Verguts, T.; Vettel, J.M.; Vijayarajah, S.; Vo, K.; Wall, M.B.; Weeda, W.D.; Weis, S.; White, D.J.; Wisniewski, D.; Xifra-Porxas, A.; Yearling, E.A.; Yoon, S.; Yuan, R.; Yuen, K.S.L.; Zhang, L.; Zhang, X.; Zosky, J.E.; Nichols, T.E.; Poldrack, R.A. & Schonberg, T. (2020), Variability in the analysis of a single neuroimaging dataset by many teams, Nature 582(7810): 84-+.
- Dizier, B.; Callegaro, A.; Debois, M.; Dreno, B.; Hersey, P.; Gogas, H.J.; Kirkwood, J.M.; Vansteenkiste, J.F.; Sequist, L.V.; Atanackovic, D.; Goeman, J.; Houwelingen, H. van; Salceda, S.; Wang, F.; Therasse, P.; Debruyne, C.; Spiessens, B.; Brichard, V.G.; Louahed, J. & Ulloa-Montoya, F. (2020), A Th1/IFN gamma gene signature is prognostic in the adjuvant setting of resectable high-risk melanoma but not in non-small cell lung cancer, Clinical Cancer Research 26(7): 1725-1735.
- Hemerik, J. & Goeman, J.J. (2020), Another look at the lady tasting tea and differences between permutation tests and randomisation tests, International Statistical Review 89(2).
- Edelmann, D.; Saadati, M.; Putter, H. & Goeman, J. (2020), A global test for competing risks survival analysis, Statistical Methods in Medical Research 29(12): 3666-3683.
- Raz, Y.; Akker, E.B. van den; Roest, T.; Riaz, M.; Rest, O. van de; Suchiman, H.E.D.; Lakenberg, N.; Stassen, S.A.; Putten, M. van; Feskens, E.J.M.; Reinders, M.J.T.; Goeman, J.; Beekman, M.; Raz, V. & Slagboom, P.E. (2020), A data-driven methodology reveals novel myofiber clusters in older human muscles, FASEB Journal 34(4): 5525-5537.
- Mohamad, D. al; Zwet, E.W. van; Cator, E. & Goeman, J.J. (2020), Adaptive critical value for constrained likelihood ratio testing, Biometrika 107(3): 677-688.
- Cessie, S. le; Goeman, J.J. & Dekkers, O.M. (2020), Who is afraid of non-normal data?, European Journal of Endocrinology 182(2): E1-E3.
- Tio-Coma, M.; Hooij, A. van; Bobosha, K.; Ploeg-van Schip, J.J. van der; Banu, S.; Khadge, S.; Thapa, P.; Kunwar, C.B.; Goulart, I.M.; Bekele, Y.; Hagge, D.A.; Moraes, M.O.; Teles, R.M.B.; Pinheiro, R.O.; Zwet, E.W. van; Goeman, J.J.; Aseffa, A.; Haks, M.C.; Ottenhoff, T.H.M.; Modlin, R.L. & Geluk, A. (2019), Whole blood RNA signatures in leprosy patients identify reversal reactions before clinical onset: a prospective, multicenter study, Scientific Reports 9.
- Kester, M.S. van; Goeman, J.J. & Genders, R.E. (2019), Tissue-sparing properties of Mohs micrographic surgery for infiltrative basal cell carcinoma, Journal of The American Academy of Dermatology 80(6): 1700-1703.
- Goeman, J.J.; Rosenblatt, J.D. & Nichols, T.E. (2019), The harmonic mean p-value: Strong versus weak control, and the assumption of independence, Proceedings of the National Academy of Sciences 116(47): 23382-23383.
- Fest, J.; Vijfhuizen, L.S.; Goeman, J.J.; Veth, O.; Joensuu, A.; Perola, M.; Mannisto, S.; Ness-Jensen, E.; Hveem, K.; Haller, T.; Tonisson, N.; Mikkel, K.; Metspalu, A.; Duijn, C.M. van; Ikram, A.; Stricker, B.H.; Ruiter, R.; Eijck, C.H.J. van; Ommen, G.J.B. van & Hoen, P.A.C. 't (2019), Search for Early Pancreatic Cancer Blood Biomarkers in Five European Prospective Population Biobanks Using Metabolomics, Endocrinology 160(7): 1731-1742.
- Onderwater, G.L.J.; Ligthart, L.; Bot, M.; Demirkan, A.; Fu, J.Y.; Kallen, C.J.H. van der; Vijfhuizen, L.S.; Pool, R.; Liu, J.; Vanmolkot, F.H.M.; Beekman, M.; Wen, K.X.; Amin, N.; Thesing, C.S.; Pijpers, J.A.; Kies, D.A.; Zielman, R.; Boer, I. de; Greevenbroek, M.M.J. van; Arts, I.C.W.; Milaneschi, Y.; Schram, M.T.; Dagnelie, P.C.; Franke, L.; Ikram, M.A.; Ferrari, M.D.; Goeman, J.J.; Slagboom, P.E.; Wijmenga, C.; Stehouwer, C.D.A.; Boomsma, D.I.; Duijn, C.M. van; Penninx, B.W.; Hoen, P.A.C. 't; Terwindt, G.M.; Maagdenberg, A.M.J.M. van den & BBMRI Metabolomics Consortium (2019), Large-scale plasma metabolome analysis reveals alterations in HDL metabolism in migraine, Neurology 92(16): E1899-E1911.
- Meijer, R.J.; Krebs, T.J.P. & Goeman, J.J. (2019), Hommel's procedure in linear time, Biometrical Journal 61(1): 73-82.
- Rosenblatt, J.D.; Ritov, Y. & Goeman, J.J. (2019), Discussion of "Gene hunting with hidden Markov model knockoffs', Biometrika 106(1): 29-33.
- Olie, C.S.; Riaz, M.; Konietzny, R.; Charles, P.D.; Pinto-Fernandez, A.; Kielbasa, S.M.; Aartsma-Rus, A.; Goeman, J.J.; Kessler, B.M. & Raz, V. (2019), Deacetylation Inhibition Reverses PABPN1-Dependent Muscle Wasting, iScience 12: 318-+.
- Hiller, M.; Falzarano, M.S.; Garcia-Jimenez, I.; Sardone, V.; Verheul, R.C.; Popplewell, L.; Anthony, K.; Ruiz-Del-Yerro, E.; Osman, H.; Goeman, J.J.; Mamchaoui, K.; Dickson, G.; Ferlini, A.; Muntoni, F.; Aartsma-Rus, A.; Arechavala-Gomeza, V.; Datson, N.A. & Spitali, P. (2018), A multicenter comparison of quantification methods for antisense oligonucleotide- induced DMD exon 51 skipping in Duchenne muscular dystrophy cell cultures, PLoS ONE 13(10).
- Chaturvedi, N.; Menezes, R.X. de; Goeman, J.J. & Wieringen, W. van (2018), A test for detecting differential indirect trans effects between two groups of samples, Statistical Applications in Genetics and Molecular Biology 17(5).
- Hemerik, J. & Goeman, J. (2018), Exact testing with random permutations, TEST 27(4): 811-825.
- Lemmers, R.J.L.F.; Vliet, P.J. van der; Balog, J.; Goeman, J.J.; Arindrarto, W.; Krom, Y.D.; Straasheijm, K.R.; Debipersad, R.D.; Ozel, G.; Sowden, J.; Snider, L.; Mul, K.; Sacconi, S.; Engelen, B. van; Tapscott, S.J.; Tawil, R. & Maarel, S.M. van der (2018), Deep characterization of a common D4Z4 variant identifies biallelic DUX4 expression as a modifier for disease penetrance in FSHD2, European Journal of Human Genetics 26(1): 94-106.
- Spitali, P.; Hettne, K.; Tsonaka, R.; Sabir, E.; Seyer, A.; Hemerik, J.B.A.; Goeman, J.J.; Picillo, E.; Ergoli, M.; Politano, L. & Aartsma-Rus, A. (2018), Cross-sectional serum metabolomic study of multiple forms of muscular dystrophy, Journal of Cellular and Molecular Medicine 22(4): 2442-2448.
- Bulk, M.; Weerd, L. van der; Breimer, W.; Lebedev, N.; Webb, A.; Goeman, J.J.; Ward, R.J.; Huber, M.; Oosterkamp, T.H. & Bossoni, L. (2018), Quantitative comparison of different iron forms in the temporal cortex of Alzheimer patients and control subjects, Scientific Reports 8.
- Toonen, L.J.A.; Overzier, M.; Evers, M.M.; Leon, L.G.; Zeeuw, S.A.J. van der; Mei, H.L.; Kielbasa, S.M.; Goeman, J.J.; Hettne, K.M.; Magnusson, O.T.; Poirel, M.; Seyer, A.; Hoen, P.A.C. 't & Roon-Mom, W.M.C. van (2018), Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model, Molecular Neurodegeneration 13.
- Meijgaarden, K.E. van; Khatri, B.; Smith, S.G.; Drittij, A.M.F.H.; Paus, R.A. de; Goeman, J.J.; Ho, M.M.; Dockrell, H.M.; McShane, H.; Joosten, S.A. & Ottenhoff, T.H.M. (2018), Cross-laboratory evaluation of multiplex bead assays including independent common reference standards for immunological monitoring of observational and interventional human studies, PLoS ONE 13(9).
- Blagus, R. & Goeman, J.J. (2018), What (not) to expect when classifying rare events, Briefings in Bioinformatics 19(2): 341-349.
- Bulk, M.; Kenkhuis, B.; Graaf, L.M. van der; Goeman, J.J.; Natte, R. & Weerd, L. van der (2018), Postmortem T-2* - Weighted MRI Imaging of Cortical Iron Reflects Severity of Alzheimer's Disease, Journal of Alzheimer's Disease 65(4): 1125-1137.
- Spitali, P.; Hettne, K.; Tsonaka, R.; Sabir, E.; Seyer, A.; Hemerik, J.B.A.; Goeman, J.J.; Picillo, E.; Ergoli, M.; Politano, L. & Aartsma-Rus, A. (2018), Metabolomics analysis in serum of muscular dystrophy patients, Neuromuscular Disorders 28: S9-S10.
- Dreno, B.; Thompson, J.F.; Smithers, B.M.; Santinami, M.; Jouary, T.; Gutzmer, R.; Levchenko, E.; Rutkowski, P.; Grob, J.J.; Korovin, S.; Drucis, K.; Grange, F.; Machet, L.; Hersey, P.; Krajsova, I.; Testori, A.; Conry, R.; Guillot, B.; Kruit, W.H.J.; Demidov, L.; Thompson, J.A.; Bondarenko, I.; Jaroszek, J.; Puig, S.; Cinat, G.; Hauschild, A.; Goeman, J.J.; Houwelingen, H.C. van; Ulloa-Montoya, F.; Callegaro, A.; Dizier, B.; Spiessens, B.; Debois, M.; Brichard, V.G.; Louahed, J.; Therasse, P.; Debruyne, C. & Kirkwood, J.M. (2018), MAGE-A3 immunotherapeutic as adjuvant therapy for patients with resected, MAGE-A3-positive, stage III melanoma (DERMA): a double-blind, randomised, placebo-controlled, phase 3 trial, Lancet Oncology 19(7): 916-929.
- Rovito, R.; Warnatz, H.J.; Kielbasa, S.M.; Mei, H.; Amstislayskiy, V.; Arens, R.; Yaspo, M.L.; Lehrach, H.; Kroes, A.C.M.; Goeman, J.J. & Vossen, A.C.T.M. (2018), Impact of congenital cytomegalovirus infection on transcriptomes from archived dried blood spots in relation to long-term clinical outcome, PLoS ONE 13(7).
- Bavinck, J.N.B.; Feltkamp, M.C.W.; Green, A.C.; Fiocco, M.; Euvrard, S.; Harwood, C.A.; Nasir, S.; Thomson, J.; Proby, C.M.; Naldi, L.; Diphoorn, J.C.D.; Venturuzzo, A.; Tessari, G.; Nindl, I.; Sampogna, F.; Abeni, D.; Neale, R.E.; Goeman, J.J.; Quint, K.D.; Halk, A.B.; Sneek, C.; Genders, R.E.; Koning, M.N.C. de; Quint, W.G.V.; Wieland, U.; Weissenborn, S.; Waterboer, T.; Pawlita, M.; Pfister, H. & EPI-HPV-UV-CA Grp (2018), Human papillomavirus and posttransplantation cutaneous squamous cell carcinoma: A multicenter, prospective cohort study, American Journal of Transplantation 18(5): 1220-1230.
- Goeman, J.J. & Jong, N.H. de (2018), How Well Does the Sum Score Summarize the Test? Summability as a Measure of Internal Consistency, Educational Measurement: Issues and Practice 37(2): 54-63.
- Rosenblatt, J.D.; Finos, L.; Weeda, W.D.; Solari, A. & Goeman, J.J. (2018), All-Resolutions Inference for brain imaging, NeuroImage 181: 786-796.
- Hemerik, J. & Goeman, J.J. (2018), False discovery proportion estimation by permutations: confidence for significance analysis of microarrays, Journal of the Royal Statistical Society: Series B 80(1): 137-155.
- Gool, I.C. van; Ubachs, J.E.H.; Stelloo, E.; Kroon, C.D. de; Goeman, J.J.; Smit, V.T.H.B.M.; Creutzberg, C.L. & Bosse, T. (2018), Blinded histopathological characterisation of POLE exonuclease domain-mutant endometrial cancers: sheep in wolf's clothing, Histopathology 72(2): 248-258.
- Vogelaar, I.P.; Post, R.S. van der; Krieken, J.H.J.M. van; Spruijt, L.; Zelst-Stams, W.A.G. van; Kets, C.M.; Lubinski, J.; Jakubowska, A.; Teodorczyk, U.; Aalfs, C.M.; Hest, L.P. van; Pinheiro, H.; Oliveira, C.; Jhangiani, S.N.; Muzny, D.M.; Gibbs, R.A.; Lupski, J.R.; Ligt, J. de; Vissers, L.E.L.M.; Hoischen, A.; Gilissen, C.; Vorst, M. van de; Goeman, J.J.; Schackert, H.K.; Ranzani, G.N.; Molinaro, V.; Garcia, E.B.G.; Hes, F.J.; Holinski-Feder, E.; Genuardi, M.; Ausems, M.G.E.M.; Sijmons, R.H.; Wagner, A.; Kolk, L.E. van der; Bjornevoll, I.; Hoberg-Vetti, H.; Kessel, A.G. van; Kuiper, R.P.; Ligtenberg, M.J.L. & Hoogerbrugge, N. (2017), Unraveling genetic predisposition to familial or early onset gastric cancer using germline whole-exome sequencing, European Journal of Human Genetics 25(11): 1246-1252.
- Pecanka, J. & Goeman, J. (2017), Robin Hood: A cost-efficient two-stage approach to large-scale simultaneous inference with non-homogeneous sparse effects, Statistical Applications in Genetics and Molecular Biology 16(2): 107-132.
- Solari, A. & Goeman, J.J. (2017), Minimally adaptive BH: A tiny but uniform improvement of the procedure of Benjamini and Hochberg, Biometrical Journal 59(4): 776-780.
- Timmerman, H.; Steegers, M.A.H.; Huygen, F.J.P.M.; Goeman, J.J.; Dasselaar, N.T. van; Schenkels, M.J.; Wilder-Smith, O.H.G.; Wolff, A.A.P. & Vissers, K.C.P. (2017), Investigating the validity of the DN4 in a consecutive population of patients with chronic pain, PLoS ONE 12(11).
- Lince, S.L.; Kluivers, K.B.; Cartwright, R.; Ruiz-Zapata, A.M.; Kerkhof, M.H.; Pecanka, J.; Kiemeney, L.A.; Vermeulen, S.H.; Goeman, J.J.; Allen-Brady, K.; Norton, P.A.; Oosterwijk, E. & Poelmans, G. (2017), Exome chip study provides novel insights into the genetics of pelvic organ prolapse, European Journal of Obstetrics and Gynecology and Reproductive Biology 211: 207-207.
- Goeman, J.J. (2017), Contribution to the discussion of "A critical evaluation of the current "p-value controversy"', Biometrical Journal 59(5): 884-885.
- Chaturvedi, N.; Menezes, R.X. de & Goeman, J.J. (2017), A global x global test for testing associations between two large sets of variables, Biometrical Journal 59(1): 145-158.
- Vulto-van Silfhout, A.T.; Gilissen, C.; Goeman, J.J.; Jansen, S.; Amen-Hellebrekers, C.J.M. van; Bon, B.W.M. van; Koolen, D.A.; Sistermans, E.A.; Brunner, H.G.; Brouwer, A.P.M. de & Vries, B.B.A. de (2017), Quantification of Phenotype Information Aids the Identification of Novel Disease Genes, Human Mutation 38(5): 594-599.
- Meijer, R.J. & Goeman, J.J. (2016), Multiple Testing of Gene Sets from Gene Ontology: Possibilities and Pitfalls, Briefings in Bioinformatics 17(5): 808-818.
- Pont, M.J.; Honders, M.W.; Kremer, A.N.; Kooten, C. van; Out, C.; Hiemstra, P.S.; Boer, H.C. de; Jager, M.J.; Schmelzer, E.; Vries, R.G.; Hinai, A.S. al; Kroes, W.G.; Monajemi, R.; Goeman, J.J.; Bohringer, S.; Marijt, W.A.F.; Falkenburg, J.H.F. & Griffioen, M. (2016), Microarray Gene Expression Analysis to Evaluate Cell Type Specific Expression of Targets Relevant for Immunotherapy of Hematological Malignancies, PLoS ONE 11(5).
- Doorn, R. van; Slieker, R.C.; Boonk, S.E.; Zoutman, W.H.; Goeman, J.J.; Bagot, M.; Michel, L.; Tensen, C.P.; Willemze, R.; Heijmans, B.T. & Vermeer, M.H. (2016), Epigenomic Analysis of Sezary Syndrome Defines Patterns of Aberrant DNA Methylation and Identifies Diagnostic Markers, Journal of Investigative Dermatology 136(9): 1876-1884.
- Menezes, R.X.; Mohammadi, L.; Goeman, J.J. & Boer, J.M. (2016), Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack, BMC Bioinformatics 17.
- Jelizarow, M.; Mansmann, U. & Goeman, J.J. (2016), A Cochran-Armitage-type and a score-free global test for multivariate ordinal data, Statistics in Medicine 35(16): 2754-2769.
- Mina, E.; Roon-Mom, W. van; Hettne, K.; Zwet, E. van; Goeman, J.; Neri, C.; Hoen, P.A.C. 't; Mons, B. & Roos, M. (2016), Common disease signatures from gene expression analysis in Huntington's disease human blood and brain, Orphanet Journal of Rare Diseases 11.
- Meijer, R.J. & Goeman, J.J. (2015), A multiple testing method for hypotheses structured in a directed acyclic graph, Biometrical Journal 57(1): 123-143.
- Anastasios Mastrokolias1, Yavuz Ariyurek2, Jelle J Goeman3,4, Erik van Duijn5,6, Raymund AC Roos7, Roos C van der Mast5, GertJan B van Ommen1, Johan T den Dunnen1,2 & Peter AC 't Hoen1 and Willeke MC van Roon-Mom1 (2015), Huntington’s disease biomarker progression profile identified by transcriptome sequencing in peripheral blood, European Journal of Human Genetics 23.
- Goossens-Beumer, I.J.; Derr, R.S.; Buermans, H.P.J.; Goeman, J.J.; Bohringer, S.; Morreau, H.; Nitsche, U.; Janssen, K.P.; Velde, C.J.H. van de & Kuppen, P.J.K. (2015), MicroRNA Classifier and Nomogram for Metastasis Prediction in Colon Cancer, Cancer Epidemiology, Biomarkers and Prevention 24(1): 187-197.
- Klerk, E. de; Fokkema, I.F.A.C.; Thiadens, K.A.M.H.; Goeman, J.J.; Palmblad, M.; Dunnen, J.T. den; Lindern, M. von & Hoen, P.A.C. 't (2015), Assessing the translational landscape of myogenic differentiation by ribosome profiling, Nucleic Acids Research 43(9): 4408-4428.
- Lemmers, R.J.L.F.; Goeman, J.J.; Vliet, P.J. van der; Nieuwenhuizen, M.P. van; Balog, J.; Vos-Versteeg, M.; Camano, P.; Arroyo, M.A.R.; Jerico, I.; Rogers, M.T.; Miller, D.G.; Upadhyaya, M.; Verschuuren, J.J.G.M.; Arregui, A.L.D.; Engelen, B.G.M. van; Padberg, G.W.; Sacconi, S.; Tawil, R.; Tapscott, S.J.; Bakker, B. & Maarel, S.M. van der (2015), Inter-individual differences in CpG methylation at D4Z4 correlate with clinical variability in FSHD1 and FSHD2, Human Molecular Genetics 24(3): 659-669.
- Haks, M.C.; Goeman, J.J.; Magis-Escurra, C. & Ottenhoff, T.H.M. (2015), Focused human gene expression profiling using dual-color reverse transcriptase multiplex ligation-dependent probe amplification, Vaccine 33(40): 5282-5288.
- Mastrokolias, A.; Ariyurek, Y.; Goeman, J.J.; Duijn, E. van; Roos, R.A.C.; Mast, R.C. van der; Ommen, G.B. van; Dunnen, J.T. den; Hoen, P.A.C. 't & Roon-Mom, W.M.C. van (2015), Huntington's disease biomarker progression profile identified by transcriptome sequencing in peripheral blood, European Journal of Human Genetics 23(10): 1349-1356.
- Meijer, R.J.; Krebs, T.J.P. & Goeman, J.J. (2015), A region-based multiple testing method for hypotheses ordered in space or time, Statistical Applications in Genetics and Molecular Biology 14(1): 1-19.
- Wilde, A.H. de; Wannee, K.F.; Scholte, F.E.M.; Goeman, J.J.; Dijke, P. ten; Snijder, E.J.; Kikkert, M. & Hemert, M.J. van (2015), A Kinome-Wide Small Interfering RNA Screen Identifies Proviral and Antiviral Host Factors in Severe Acute Respiratory Syndrome Coronavirus Replication, Including Double-Stranded RNA-Activated Protein Kinase and Early Secretory Pathway Proteins, Journal of Virology 89(16): 8318-8333.
- Luijk, R.; Goeman, J.J.; Slagboom, E.P.; Heijmans, B.T. & Zwet, E.W. van (2015), An alternative approach to multiple testing for methylation QTL mapping reduces the proportion of falsely identified CpGs, Bioinformatics 31(3): 340-345.
- Roost, M.S.; Iperen, L. van; Ariyurek, Y.; Buermans, H.P.; Arindrarto, W.; Devalla, H.D.; Passier, R.; Mummery, C.L.; Carlotti, F.; Koning, E.J.P. de; Zwet, E.W. van; Goeman, J.J. & Lopes, S.M.C.D. (2015), KeyGenes, a Tool to Probe Tissue Differentiation Using a Human Fetal Transcriptional Atlas, Stem Cell Reports 4(6): 1112-1124.
- Ramos, Y.F.M.; Hollander, W. den; Bovee, J.V.M.G.; Bomer, N.; Breggen, R. van der; Lakenberg, N.; Keurentjes, J.C.; Goeman, J.J.; Slagboom, P.E.; Nelissen, R.G.H.H.; Bos, S.D. & Meulenbelt, I. (2014), Genes Involved in the Osteoarthritis Process Identified through Genome Wide Expression Analysis in Articular Cartilage; the RAAK Study, PLoS ONE 9(7).
- Vermeer, M.H.; Zoutman, W.; Boonk, S.; Tensen, K.; Bagot, M.; Fits, L. van der; Goeman, J.; Heijmans, B. & Doorn, R. van (2014), Genome-wide analysis of DNA methylation in Sezary syndrome, Journal of Investigative Dermatology 134: S18-S18.
- Kremer, A.N.; Meijden, E.D. van der; Honders, M.W.; Pont, M.J.; Goeman, J.J.; Falkenburg, J.H.F. & Griffioen, M. (2014), Human Leukocyte Antigen-DO Regulates Surface Presentation of Human Leukocyte Antigen Class-II Restricted Antigens on B Cell Malignancies, Biology of Blood and Marrow Transplantation 20(5): 742-747.
- Sanders, M.A.; Hoogenboezem, R.; Groschel, S.; Zeilemaker, A.; Geertsma-Kleinekoort, W.M.; Delwel, R.; Goeman, J.J. & Valk, P.J. (2014), IMPROVED COPY NUMBER VARIATION ESTIMATION FROM NEXT GENERATION SEQUENCING DATA REVEALS FOCAL GENETIC LESIONS SUCH AS MLL-PTD IN ACUTE MYELOID LEUKEMIA, Haematologica 99: 17-17.
- Gheorghe, M.; Snoeck, M.; Emmerich, M.; Back, T.; Goeman, J.J. & Raz, V. (2014), Major aging-associated RNA expressions change at two distinct age-positions, BMC Genomics 15.
- Akker, E.B. van den; Passtoors, W.M.; Jansen, R.; Zwet, E.W. van; Goeman, J.J.; Hulsman, M.; Emilsson, V.; Perola, M.; Willemsen, G.; Penninx, B.W.J.H.; Heijmans, B.T.; Maier, A.B.; Boomsma, D.I.; Kok, J.N.; Slagboom, P.E.; Reinders, M.J.T. & Beekman, M. (2014), Meta- analysis on blood transcriptomic studies identifies consistently coexpressed protein- protein interaction modules as robust markers of human aging, Aging Cell 13(2): 216-225.
- Goeman, J.J. & Solari, A. (2014), Multiple hypothesis testing in genomics, Statistics in Medicine 33(11): 1946-1978.
- Gao, L.; Hurk, K. van den; Moerkerk, P.T.M.; Goeman, J.J.; Beck, S.; Gruis, N.A.; Oord, J.J. van den; Winnepenninckx, V.J.; Engeland, M. van & Doorn, R. van (2014), Promoter CpG Island Hypermethylation in Dysplastic Nevus and Melanoma: CLDN11 as an Epigenetic Biomarker for Malignancy, Journal of Investigative Dermatology 134(12): 2957-2966.
- Chaturvedi, N.; Goeman, J.J.; Boer, J.M.; Wieringen, W.N. van & Menezes, R.X. de (2014), A test for comparing two groups of samples when analyzing multiple omics profiles, BMC Bioinformatics 15.
- Bokenkamp, R.; Brempt, R. van; Munsteren, J.C. van; Wijngaert, I. van den; Hoogt, R. de; Finos, L.; Goeman, J.; Gittenberger-de Groot, A.C.; Poelmann, R.E.; Blom, N.A. & DeRuiter, M.C. (2014), Dlx1 and Rgs5 in the Ductus Arteriosus: Vessel-Specific Genes Identified by Transcriptional Profiling of Laser-Capture Microdissected Endothelial and Smooth Muscle Cells, PLoS ONE 9(1).
- Tobi, E.W.; Goeman, J.J.; Monajemi, R.; Gu, H.C.; Putter, H.; Zhang, Y.J.; Slieker, R.C.; Stok, A.P.; Thijssen, P.E.; Muller, F.; Zwet, E.W. van; Bock, C.; Meissner, A.; Lumey, L.H.; Slagboom, P.E. & Heijmans, B.T. (2014), DNA methylation signatures link prenatal famine exposure to growth and metabolism, Nature Communications 5.
- Chaturvedi, N.; Menezes, R.X. de & Goeman, J.J. (2014), Fused lasso algorithm for Cox proportional hazards and binomial logit models with application to copy number profiles, Biometrical Journal 56(3): 477-492.
- Lauber, C.; Goeman, J.J.; Parquet, M.D.; Nga, P.T.; Snijder, E.J.; Morita, K. & Gorbalenya, A.E. (2013), The Footprint of Genome Architecture in the Largest Genome Expansion in RNA Viruses, PLoS Pathogens 9(7).
- Hettne, K.M.; Boorsma, A.; Dartel, D.A.M. van; Goeman, J.J.; Jong, E. de; Piersma, A.H.; Stierum, R.H.; Kleinjans, J.C. & Kors, J.A. (2013), Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data, BMC Medical Genomics 6.
- Goeman, J.J. & Solari, A. (2013), Multiple testing for exploratory research (vol 26, pg 584, 2011).
- Tillaart, S.A.H.M. van den; Corver, W.E.; Neto, D.R.; Haar, N.T. ter; Goeman, J.J.; Trimbos, J.B.M.Z.; Fleuren, G.J. & Oosting, J. (2013), Loss of Heterozygosity and Copy Number Alterations in Flow-Sorted Bulky Cervical Cancer, PLoS ONE 8(7).
- Slieker, R.C.; Bos, S.D.; Goeman, J.J.; Bovee, J.V.M.G.; Talens, R.P.; Breggen, R. van der; Suchiman, H.E.D.; Lameijer, E.W.; Putter, H.; Akker, E.B. van den; Zhang, Y.J.; Jukema, J.W.; Slagboom, P.E.; Meulenbelt, I. & Heijmans, B.T. (2013), Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array, Epigenetics and Chromatin 6.
- Meijer, R.J. & Goeman, J.J. (2013), Efficient approximate k-fold and leave-one-out cross-validation for ridge regression, Biometrical Journal 55(2): 141-155.
- Anvar, S.Y.; Raz, Y.; Verwey, N.; Sluijs, B. van der; Venema, A.; Goeman, J.J.; Vissing, J.; Maarel, S.M. van der; Hoen, P.A.C. 't; Engelen, B.G.M. van & Raz, V. (2013), A decline in PABPN1 induces progressive muscle weakness in Oculopharyngeal muscle dystrophy and in muscle aging, Aging 5(6): 412-426.
- Meijer, R.J. & Goeman, J.J. (2013), Efficient approximate k-fold and leave-one-out cross-validation for ridge regression., Biometrical Journal.
- Gao, L.; Smit, M.; Oord, J. van den; Goeman, J.; Verdegaal, E.; Burg, S. van der; Stas, M.; Beck, S.; Gruis, N.; Tensen, C.; Willemze, R.; Peeper, D. & Doorn, R. van (2013), Comprehensive promoter methylation analysis identifies epigenetic silencing of MAPK13 in primary cutaneous melanoma, Journal of Investigative Dermatology 133: S228-S228.
- Gao, L.; Smit, M.A.; Oord, J.J. van den; Goeman, J.J.; Verdegaal, E.M.E.; Burg, S.H. van der; Stas, M.; Beck, S.; Gruis, N.A.; Tensen, C.P.; Willemze, R.; Peeper, D.S. & Doorn, R. van (2013), Genome-wide promoter methylation analysis identifies epigenetic silencing of MAPK13 in primary cutaneous melanoma, Pigment Cell and Melanoma Research 26(4).
- O'Leary, T.; Heindryckx, B.; Lierman, S.; Bruggen, D. van; Goeman, J.J.; Vandewoestyne, M.; Deforce, D.; Lopes, S.M.C.D. & Sutter, P. de (2012), Tracking the progression of the human inner cell mass during embryonic stem cell derivation, Nature Biotechnology 30(3): 278-+.
- Dahm, A.E.A.; Eilertsen, A.L.; Goeman, J.; Olstad, O.K.; Ovstebo, R.; Kierulf, P.; Mowinckel, M.C.; Skretting, G. & Sandset, P.M. (2012), A microarray study on the effect of four hormone therapy regimens on gene transcription in whole blood from healthy postmenopausal women, Thrombosis Research 130(1): 45-51.
- Osanto, S.; Qin, Y.J.; Buermans, H.P.; Berkers, J.; Lerut, E.; Goeman, J.J. & Poppel, H. van (2012), Genome-Wide MicroRNA Expression Analysis of Clear Cell Renal Cell Carcinoma by Next Generation Deep Sequencing, PLoS ONE 7(6): -.
- Passtoors, W.M.; Boer, J.M.; Goeman, J.J.; Akker, E.B. van den; Deelen, J.; Zwaan, B.J.; Scarborough, A.; Breggen, R. van der; Vossen, R.H.A.M.; Houwing-Duistermaat, J.J.; Ommen, G.J.B. van; Westendorp, R.G.J.; Heemst, D. van; Craen, A.J.M. de; White, A.J.; Gunn, D.A.; Beekman, M. & Slagboom, P.E. (2012), Transcriptional Profiling of Human Familial Longevity Indicates a Role for ASF1A and IL7R., PLoS ONE 7(1): e27759.
- Iterson, M. van; Haagen, H.H.H.B.M. van & Goeman, J.J. (2012), Resolving confusion of tongues in statistics and machine learning: A primer for biologists and bioinformaticians, Proteomics 12(4-5): 543-549.
- Visser, R.; Landman, E.B.M.; Goeman, J.; Wit, J.M. & Karperien, M. (2012), Sotos Syndrome Is Associated with Deregulation of the MAPK/ERK-Signaling Pathway, PLoS ONE 7(11): -.
- Joosten, S.A.; Goeman, J.J.; Sutherland, J.S.; Opmeer, L.; Boer, K.G. de; Jacobsen, M.; Kaufmann, S.H.E.; Finos, L.; Magis-Escurra, C.; Ota, M.O.C.; Ottenhoff, T.H.M. & Haks, M.C. (2012), Identification of biomarkers for tuberculosis disease using a novel dual-color RT-MLPA assay, Genes and Immunity 13(1): 71-82.
- Passtoors, W.M.; Boer, J.M.; Goeman, J.J.; Akker, E.B. van den; Deelen, J.; Zwaan, B.J.; Scarborough, A.; Breggen, R. van der; Vossen, R.H.A.M.; Houwing-Duistermaat, J.J.; Ommen, G.J.B. van; Westendorp, R.G.J.; Heemst, D. van; Craen, A.J.M. de; White, A.J.; Gunn, D.A.; Beekman, M. & Slagboom, P.E. (2012), Transcriptional Profiling of Human Familial Longevity Indicates a Role for ASF1A and IL7R, PLoS ONE 7(1): -.
- Klerk, E. de; Venema, A.; Anvar, S.Y.; Goeman, J.J.; Hu, O.H.; Trollet, C.; Dickson, G.; Dunnen, J.T. den; Maarel, S.M. van der; Raz, V. & Hoen, P.A.C. 't (2012), Poly(A) binding protein nuclear 1 levels affect alternative polyadenylation, Nucleic Acids Research 40(18): 9089-9101.
- Solari, A.; Cessie, S. le & Goeman, J.J. (2012), Testing goodness of fit in regression: a general approach for specified alternatives, Statistics in Medicine 31(28): 3656-3666.
- Veen, T. van; Goeman, J.J.; Monajemi, R.; Wardenaar, K.J.; Hartman, C.A.; Snieder, H.; Nolte, I.M.; Penninx, B.W.J.H. & Zitman, F.G. (2012), Different gene sets contribute to different symptom dimensions of depression and anxiety, American Journal of Medical Genetics Part B: Neuropsychiatric Genetics 159B(5): 519-528.
- Roozen, P.; Luis, T.; Naber, B.; Haas, E. de; Bres-Vloermans, A.; Brugman, M.; Fibbe, W.; Fodde, R.; Goeman, J. & Staal, F. (2012), MECHANISMS UNDERLYING THE DOSE DEPENDENT EFFECTS OF CANONICAL WNT SIGNALLING IN HEMATOPOIETIC STEM CELLS, Experimental Hematology: Journal for Hematology, Stem Cell Biology and Transplantation 40(8): S92-S92.
- Goeman, J.J. & Finos, L. (2012), The Inheritance Procedure: Multiple Testing of Tree-structured Hypotheses, Statistical Applications in Genetics and Molecular Biology 11(1): -.
- Kremer, A.N.; Meijden, E.D. van der; Honders, M.W.; Goeman, J.J.; Wiertz, E.J.H.J.; Falkenburg, J.H.F. & Griffioen, M. (2012), Endogenous HLA class II epitopes that are immunogenic in vivo show distinct behavior toward HLA-DM and its natural inhibitor HLA-DO, Blood 120(16): 3246-3255.
- Gool, S.A. van; Emons, J.A.M.; Leijten, J.C.H.; Decker, E.; Sticht, C.; Houwelingen, J.C. van; Goeman, J.J.; Kleijburg, C.; Scherjon, S.A.; Gretz, N.; Wit, J.M.; Rappold, G.; Post, J.N. & Karperien, M. (2012), Fetal Mesenchymal Stromal Cells Differentiating towards Chondrocytes Acquire a Gene Expression Profile Resembling Human Growth Plate Cartilage, PLoS ONE 7(11): -.
- Deelen, J.; Uh, H.W.; Monajemi, R.; Heemst, D. van; Thijssen, P.E.; Bohringer, S.; Akker, E.B. van den; Craen, A.J.M. de; Rivadeneira, F.; Uitterlinden, A.G.; Westendorp, R.G.J.; Goeman, J.J.; Slagboom, P.E.; Houwing-Duistermaat, J.J. & Beekman, M. (2011), Gene set analysis of GWAS data for human longevity highlights the relevance of the insulin/IGF-1 signaling and telomere maintenance pathways., AGE.
- Miclea, R.L.; Siebelt, M.; Finos, L.; Goeman, J.J.; Lowik, C.W.G.M.; Oostdijk, W.; Weinans, H.; Wit, J.M.; Robanus-Maandag, E.C. & Karperien, M. (2011), Inhibition of Gsk3β in cartilage induces osteoarthritic features through activation of the canonical Wnt signaling pathway., Osteoarthritis and Cartilage 19(11): 1363-72.
- Joosten, S.A.; Goeman, J.J.; Sutherland, J.S.; Opmeer, L.; Boer, K.G. de; Jacobsen, M.; Kaufmann, S.H.E.; Finos, L.; Magis-Escurra, C.; Ota, M.O.C.; Ottenhoff, T.H.M. & Haks, M.C. (2011), Identification of biomarkers for tuberculosis disease using a novel dual-color RT-MLPA assay., Genes and Immunity.
- Goeman, J.J.; Houwelingen, H.C. van & Finos, L. (2011), Testing against a high-dimensional alternative in the generalized linear model: asymptotic type I error control, Biometrika 98(2): 381-390.
- Jelier, R.; Goeman, J.J.; Hettne, K.M.; Schuemie, M.J.; Dunnen, J. den & Hoen, P.A.C. 't (2011), Literature-aided interpretation of gene expression data with the weighted global test, Briefings in Bioinformatics 12(5): 518-529.
- Dahm, A.E.A.; Eilertsen, A.L.; Goeman, J.; Olstad, O.K.; Ovestebo, R.; Kierulf, P.; Mowinchel, M.C.; Skretting, G. & Sandset, P.M. (2011), A microarray study on the effect of four hormone therapy regimens on gene transcription in leucocytes from healthy postmenopausal women, Thrombosis Research 127: S124S124.
- Goeman, J.J. & Solari, A. (2011), Rejoinder, Statistical Science 26(4): 608-612.
- Goeman, J.J. & Solari, A. (2011), Multiple Testing for Exploratory Research.
- Miclea, R.L.; Siebelt, M.; Finos, L.; Goeman, J.J.; Lowik, C.W.G.M.; Oostdijk, W.; Weinans, H.; Wit, J.M.; Robanus-Maandag, E.C. & Karperien, M. (2011), Inhibition of Gsk3 beta in cartilage induces osteoarthritic features through activation of the canonical Wnt signaling pathway, Osteoarthritis and Cartilage 19(11): 1363-1372.
- Alkemade, F.E.; Vliet, P. van; Henneman, P.; Dijk, K.W. van; Hierck, B.P.; Munsteren, J.C. van; Scheerman, J.A.; Goeman, J.J.; Havekes, L.M.; Gittenberger-de Groot, A.C.; Elsen, P.J. van den & DeRuiter, M.C. (2010), Prenatal exposure to apoE deficiency and postnatal hypercholesterolemia are associated with altered cell-specific lysine methyltransferase and histone methylation patterns in the vasculature.
- Goeman, J.J. & Solari, A. (2010), THE SEQUENTIAL REJECTION PRINCIPLE OF FAMILYWISE ERROR CONTROL, Annals of Statistics 38(6): 3782-3810.
- Datson, N.A.; Speksnijder, N.; Mayer, J.L.; Steenbergen, P.J.; Korobko, O.; Goeman, J.; Kloet, E.R. de; Joels, M. & Lucassen, P.J. (2010), The transcriptional response to chronic stress and glucocorticoid receptor blockade in the hippocampal dentate gyrus., Hippocampus.
- Goeman, J.J. (2010), L-1 Penalized Estimation in the Cox Proportional Hazards Model, Biometrical Journal 52(1): 70-84.
- Alkemade, F.E.; Vliet, P. van; Henneman, P.; Dijk, K.W. van; Hierck, B.P.; Munsteren, J.C. van; Scheerman, J.A.; Goeman, J.J.; Havekes, L.M.; Gittenberger-de Groot, A.C.; Elsen, P.J. van den & DeRuiter, M.C. (2010), Prenatal Exposure to apoE Deficiency and Postnatal Hypercholesterolemia Are Associated with Altered Cell-Specific Lysine Methyltransferase and Histone Methylation Patterns in the Vasculature, American Journal of Pathology 176(2): 542-548.
- Goeman, J.J. (2010), L1 penalized estimation in the Cox proportional hazards model., Biometrical Journal 52(1): 70-84.
- Goeman JJ & Solari A (2010), The sequential rejection principle of familiywise error control, Annals of Statistics.
- Goeman, J.J.; Solari, A. & Stijnen, T. (2010), Three-sided hypothesis testing: Simultaneous testing of superiority, equivalence and inferiority, Statistics in Medicine 29(20): 2117-2125.
- Goeman JJ & Solari A (2010), The sequential rejection principle of family wise error control, Annals of Statistics.
- Emons JAM, Leijten J, van Zwet E, Goeman J, Decker E, Chagin A, Sticht C, Yu XL, van Gool SA, Pirzer H, Rappold GA, Gretz N, Wit JM, Savendahl L & Karperien M (2009), Genome wide screening and morphological analysis of the human growth plate during pubertal development, Hormone Research 72: 275-276.
- Hensen, E.F.; Goeman, J.J.; Oosting, J.; Mey, A.G.L. van der; Hogendoorn, P.C.W.; Cremers, C.W.R.J.; Devilee, P. & Cornelisse, C.J. (2009), Similar gene expression profiles of sporadic, PGL2-, and SDHD-linked paragangliomas suggest a common pathway to tumorigenesis, BMC Medical Genomics 2.
- Out AA, van Minderhout IJ, Goeman JJ, Ariyurek Y, Ossowski S, Schneeberger K, Weigel D, van Galen M, Taschner PE, Tops CM, Breuning MH, van Ommen GJ, den Dunnen JT, Devilee P & Hes FJ (2009), Deep sequencing to reveal new variants in pooled DNA samples., Human Mutation 30(12): 1703-12.
- Out AA, van Minderhout IJHM, Goeman JJ, Ariyurek Y, Ossowski S, Schneeberger K, Weigel D, van Galen M, Taschner PEM, Tops CMJ, Breuning MH, van Ommen GJB, den Dunnen JT, Devilee P & Hes FJ (2009), Deep Sequencing to Reveal New Variants in Pooled DNA Samples, Human Mutation 30(12): 1703-1712.
- Goeman JJ (2008), Autocorrelated logistic ridge regression for prediction based on proteomics spectra, Statistical Applications in Genetics and Molecular Biology 7(2).
- Goeman JJ & Mansmann U (2008), Multiple testing on the directed acyclic graph of gene ontology, Bioinformatics 24(4).
- Van Gool SA, Emons JAM, Decker E, Yu X, Van Houwelingen JC, Goeman J, Kleijburg C, Scherjon S, Gretz N, Wit JM, Rappold G & Karperien M (2008), Human mesenchymal stem cells as a model for chondrocyte differentiation, Hormone Research 70: 37-37.
- Visser R, Goeman J, Wit JM & Karperien M (2008), Sotos syndrome is associated with a deregulation of the MAPK signaling pathway, Hormone Research 70: 3-3.
- Goeman JJ (2008), Autocorrelated logistic ridge regression for prediction based on proteomics spectra., Statistical Applications in Genetics and Molecular Biology 7(2): Article10.
- Goeman JJ & Mansmann U (2008), Multiple testing on the directed acyclic graph of gene ontology., Bioinformatics 24(4): 537-44.
- Hensen EF, De Herdt MJ, Goeman JJ, Oosting J, Smit VTHBM, Cornelisse CJ & de Jong RJB (2008), Gene-expression of metastasized versus non-metastasized primary head and neck squamous cell carcinomas: A pathway-based analysis, BMC Cancer 8.
- Janssen R, Bont L, Siezen CLE, Hodemaekers HM, Ermers MJ, Doornbos G, van't Slot R, Wijmenga C, Goeman JJ, Kimpen JLL, van Houwelingen HC, Kimman TG & Hoebee B (2007), Genetic susceptibility to respiratory syncytial virus bronchiolitis is predominantly associated with innate immune genes, Journal of Infectious Diseases 196(6).
- Goeman JJ & Buhlmann P (2007), Analyzing gene expression data in terms of gene sets: methodological issues, Bioinformatics 23(8).
- Goeman Jelle Jurjen (8 March 2006), Statistical methods for microarray data (Dissertatie, Faculty of Medicine, Leiden University Medical Center (LUMC), Leiden University). Supervisor(s): Houwelingen J.C. van & Geer S.A. van de.
- Goeman JJ, van de Geer SA & van Houwelingen HC (2006), Testing against a high dimensional alternative, Journal of the Royal Statistical Society: Series B 68.
- Goeman JJ & le Cessie S (2006), A goodness-of-fit test for multinomial logistic regression, Biometrics 62(4).
- Goeman JJ, Oosting J, Cleton-Jansen AM, Anninga JK & van Houwelingen HC (2005), Testing association of a pathway with survival using gene expression data, Bioinformatics 21(9).
- Goeman JJ, van de Geer SA, de Kort F & van Houwelingen HC (2004), A global test for groups of genes: testing association with a clinical outcome, Bioinformatics 20(1).
- Eilers PHC & Goeman JJ (2004), Enhancing scatterplots with smoothed densities, Bioinformatics 20(5).
- Goeman JJ, Le Cessie S, de Jong RJB & van de Geer SA (2004), Predicting survival using disease history: a model combining relative survival and frailty, Statistica Neerlandica 58(1).