Publications

You can find my google scholar profile here and my Stanford CAP profile here

Preprints on bioRxiv

Deep Recurrent Attention Models for Histopathological Image Analysis Alexandre Momeni, Marc Thibault, Olivier Gevaert 
bioRxiv 438341; doi: https://doi.org/10.1101/438341

Dropout-Enabled Ensemble Learning for Multi-Scale Biomedical Data Alexandre Momeni, Marc Thibault, Olivier Gevaert
. bioRxiv 440362; doi: https://doi.org/10.1101/440362

A deep learning framework for imputing missing values in genomic data Yeping Lina Qiu, Hong Zheng, Olivier Gevaert. 
bioRxiv 406066; doi: https://doi.org/10.1101/406066

Comparison of single gene and module-based methods for modeling gene regulatory networks Mikel Hernaez, Olivier Gevaert. bioRxiv 307884; doi: https://doi.org/10.1101/307884

Proteogenomic view of cancer epigenetics: the impact of DNA methylation on the cancer proteome Majed Mohamed Magzoub, Marcos Prunello, Kevin Brennan, Olivier Gevaert
. bioRxiv 340760; doi: https://doi.org/10.1101/340760

Benchmark of lncRNA Quantification for RNA-Seq of Cancer Samples Hong Zheng, Kevin Brennan, Mikel Hernaez, Olivier Gevaert
. bioRxiv 241869; doi: https://doi.org/10.1101/241869


Locoregional Radiogenomic Models Capture Gene Expression Heterogeneity in Glioblastoma Adrien Depeursinge, Tunde Szilagyi, Yan Liu, Kazmer Kovacs, Reena Thomas, Kristen Yeom, NancyFischbein, Daniel Rubin, Michael Iv, Olivier Gevaert
. bioRxiv 304105; doi: https://doi.org/10.1101/304105

Journal publications

1: Bakr S, Gevaert O, Echegaray S, Ayers K, Zhou M, Shafiq M, Zheng H, Benson JA,

Zhang W, Leung ANC, Kadoch M, D Hoang C, Shrager J, Quon A, Rubin DL, Plevritis
SK, Napel S. A radiogenomic dataset of non-small cell lung cancer. Sci Data. 2018
Oct 16;5:180202. doi: 10.1038/sdata.2018.202. PubMed PMID: 30325352.


2: Han Y, Xie Z, Zang Y, Zhang S, Gu D, Zhou M, Gevaert O, Wei J, Li C, Chen H,
Du J, Liu Z, Dong D, Tian J, Zhou D. 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 Aug 10. doi:
10.1007/s11060-018-2953-y. [Epub ahead of print] PubMed PMID: 30097822.


3: Martínez-Romero M, O'Connor MJ, Shankar RD, Panahiazar M, Willrett D, Egyedi
AL, Gevaert O, Graybeal J, Musen MA. Fast and Accurate Metadata Authoring Using
Ontology-Based Recommendations. AMIA Annu Symp Proc. 2018 Apr 16;2017:1272-1281.
eCollection 2017. PubMed PMID: 29854196; PubMed Central PMCID: PMC5977712.


4: Cedoz PL, Prunello M, Brennan K, Gevaert O. MethylMix 2.0: an R package for
identifying DNA methylation genes. Bioinformatics. 2018 Apr 14. doi:
10.1093/bioinformatics/bty156. [Epub ahead of print] PubMed PMID: 29668835;
PubMed Central PMCID: PMC6129298.


5: Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN,
Kamińska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwińska P, Mazurek
S, Mishra L, Heyn H, Krasnitz A, Godwin AK, Lazar AJ; Cancer Genome Atlas
Research Network, Stuart JM, Hoadley KA, Laird PW, Noushmehr H, Wiznerowicz M.
Machine Learning Identifies Stemness Features Associated with Oncogenic
Dedifferentiation. Cell. 2018 Apr 5;173(2):338-354.e15. doi:
10.1016/j.cell.2018.03.034. PubMed PMID: 29625051; PubMed Central PMCID:
PMC5902191.


6: Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C,
Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD,
Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S,
Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A,
Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW,
Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER,
Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK; Cancer Genome Atlas
Research Network, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M,
Pickering CR, Chen Z, Van Waes C. Genomic, Pathway Network, and Immunologic
Features Distinguishing Squamous Carcinomas. Cell Rep. 2018 Apr
3;23(1):194-212.e6. doi: 10.1016/j.celrep.2018.03.063. PubMed PMID: 29617660;
PubMed Central PMCID: PMC6002769.


7: Bulens P, Couwenberg A, Haustermans K, Debucquoy A, Vandecaveye V, Philippens
M, Zhou M, Gevaert O, Intven M. Development and validation of an MRI-based model
to predict response to chemoradiotherapy for rectal cancer. Radiother Oncol. 2018
Mar;126(3):437-442. doi: 10.1016/j.radonc.2018.01.008. Epub 2018 Jan 31. PubMed
PMID: 29395287; PubMed Central PMCID: PMC5990635.


8: Champion M, Brennan K, Croonenborghs T, Gentles AJ, Pochet N, Gevaert O.
Module Analysis Captures Pancancer Genetically and Epigenetically Deregulated
Cancer Driver Genes for Smoking and Antiviral Response. EBioMedicine. 2018
Jan;27:156-166. doi: 10.1016/j.ebiom.2017.11.028. Epub 2017 Dec 1. PubMed PMID:
29331675; PubMed Central PMCID: PMC5828545.


9: Brennan K, Shin JH, Tay JK, Prunello M, Gentles AJ, Sunwoo JB, Gevaert O. NSD1
inactivation defines an immune cold, DNA hypomethylated subtype in squamous cell
carcinoma. Sci Rep. 2017 Dec 6;7(1):17064. doi: 10.1038/s41598-017-17298-x.
PubMed PMID: 29213088; PubMed Central PMCID: PMC5719078.


10: Williams LM, Pines A, Goldstein-Piekarski AN, Rosas LG, Kullar M, Sacchet MD,
Gevaert O, Bailenson J, Lavori PW, Dagum P, Wandell B, Correa C, Greenleaf W,
Suppes T, Perry LM, Smyth JM, Lewis MA, Venditti EM, Snowden M, Simmons JM, Ma J.
The ENGAGE study: Integrating neuroimaging, virtual reality and smartphone
sensing to understand self-regulation for managing depression and obesity in a
precision medicine model. Behav Res Ther. 2018 Feb;101:58-70. doi:
10.1016/j.brat.2017.09.012. Epub 2017 Oct 7. PubMed PMID: 29074231.


11: Shuo Wang, Mu Zhou, Gevaert O, Zhenchao Tang, Di Dong, Zhenyu Liu, Jie Tian.
A multi-view deep convolutional neural networks for lung nodule segmentation.
Conf Proc IEEE Eng Med Biol Soc. 2017 Jul;2017:1752-1755. doi:
10.1109/EMBC.2017.8037182. PubMed PMID: 29060226.


12: Zhou M, Scott J, Chaudhury B, Hall L, Goldgof D, Yeom KW, Iv M, Ou Y,
Kalpathy-Cramer J, Napel S, Gillies R, Gevaert O, Gatenby R. Radiomics in Brain
Tumor: Image Assessment, Quantitative Feature Descriptors, and Machine-Learning
Approaches. AJNR Am J Neuroradiol. 2018 Feb;39(2):208-216. doi:
10.3174/ajnr.A5391. Epub 2017 Oct 5. Review. PubMed PMID: 28982791; PubMed
Central PMCID: PMC5812810.


13: Minamimoto R, Jamali M, Gevaert O, Echegaray S, Khuong A, Hoang CD, Shrager
JB, Plevritis SK, Rubin DL, Leung AN, Napel S, Quon A. Prediction of EGFR and
KRAS mutation in non-small cell lung cancer using quantitative (18)F FDG-PET/CT
metrics. Oncotarget. 2017 May 10;8(32):52792-52801. doi:
10.18632/oncotarget.17782. eCollection 2017 Aug 8. PubMed PMID: 28881771; PubMed
Central PMCID: PMC5581070.


14: Bakr S, Echegaray S, Shah R, Kamaya A, Louie J, Napel S, Kothary N, Gevaert
O. Noninvasive radiomics signature based on quantitative analysis of computed
tomography images as a surrogate for microvascular invasion in hepatocellular
carcinoma: a pilot study. J Med Imaging (Bellingham). 2017 Oct;4(4):041303. doi:
10.1117/1.JMI.4.4.041303. Epub 2017 Aug 21. PubMed PMID: 28840174; PubMed Central
PMCID: PMC5565686.


15: Zhou M, Leung A, Echegaray S, Gentles A, Shrager JB, Jensen KC, Berry GJ,
Plevritis SK, Rubin DL, Napel S, Gevaert O. Non-Small Cell Lung Cancer
Radiogenomics Map Identifies Relationships between Molecular and Imaging
Phenotypes with Prognostic Implications. Radiology. 2018 Jan;286(1):307-315. doi:
10.1148/radiol.2017161845. Epub 2017 Jul 20. PubMed PMID: 28727543; PubMed
Central PMCID: PMC5749594.


16: Wang S, Zhou M, Liu Z, Liu Z, Gu D, Zang Y, Dong D, Gevaert O, Tian J.
Central focused convolutional neural networks: Developing a data-driven model for
lung nodule segmentation. Med Image Anal. 2017 Aug;40:172-183. doi:
10.1016/j.media.2017.06.014. Epub 2017 Jun 30. PubMed PMID: 28688283; PubMed
Central PMCID: PMC5661888.


17: Yan KS, Gevaert O, Zheng GXY, Anchang B, Probert CS, Larkin KA, Davies PS,
Cheng ZF, Kaddis JS, Han A, Roelf K, Calderon RI, Cynn E, Hu X, Mandleywala K,
Wilhelmy J, Grimes SM, Corney DC, Boutet SC, Terry JM, Belgrader P, Ziraldo SB,
Mikkelsen TS, Wang F, von Furstenberg RJ, Smith NR, Chandrakesan P, May R,
Chrissy MAS, Jain R, Cartwright CA, Niland JC, Hong YK, Carrington J, Breault DT,
Epstein J, Houchen CW, Lynch JP, Martin MG, Plevritis SK, Curtis C, Ji HP, Li L,
Henning SJ, Wong MH, Kuo CJ. Intestinal Enteroendocrine Lineage Cells Possess
Homeostatic and Injury-Inducible Stem Cell Activity. Cell Stem Cell. 2017 Jul
6;21(1):78-90.e6. doi: 10.1016/j.stem.2017.06.014. PubMed PMID: 28686870; PubMed
Central PMCID: PMC5642297.


18: Joye I, Debucquoy A, Deroose CM, Vandecaveye V, Cutsem EV, Wolthuis A,
D'Hoore A, Sagaert X, Zhou M, Gevaert O, Haustermans K. Quantitative imaging
outperforms molecular markers when predicting response to chemoradiotherapy for
rectal cancer. Radiother Oncol. 2017 Jul;124(1):104-109. doi:
10.1016/j.radonc.2017.06.013. Epub 2017 Jun 21. PubMed PMID: 28647399; PubMed
Central PMCID: PMC5641595.


19: Panahiazar M, Dumontier M, Gevaert O. Predicting biomedical metadata in
CEDAR: A study of Gene Expression Omnibus (GEO). J Biomed Inform. 2017
Aug;72:132-139. doi: 10.1016/j.jbi.2017.06.017. Epub 2017 Jun 16. PubMed PMID:
28625880; PubMed Central PMCID: PMC5643580.


20: Echegaray S, Nair V, Kadoch M, Leung A, Rubin D, Gevaert O, Napel S. A Rapid
Segmentation-Insensitive "Digital Biopsy" Method for Radiomic Feature Extraction:
Method and Pilot Study Using CT Images of Non-Small Cell Lung Cancer. Tomography.
2016 Dec;2(4):283-294. doi: 10.18383/j.tom.2016.00163. PubMed PMID: 28612050;
PubMed Central PMCID: PMC5466872.


21: Brennan K, Koenig JL, Gentles AJ, Sunwoo JB, Gevaert O. Identification of an
atypical etiological head and neck squamous carcinoma subtype featuring the CpG
island methylator phenotype. EBioMedicine. 2017 Mar;17:223-236. doi:
10.1016/j.ebiom.2017.02.025. Epub 2017 Mar 1. PubMed PMID: 28314692; PubMed
Central PMCID: PMC5360591.


22: Gevaert O, Echegaray S, Khuong A, Hoang CD, Shrager JB, Jensen KC, Berry GJ,
Guo HH, Lau C, Plevritis SK, Rubin DL, Napel S, Leung AN. Predictive
radiogenomics modeling of EGFR mutation status in lung cancer. Sci Rep. 2017 Jan
31;7:41674. doi: 10.1038/srep41674. PubMed PMID: 28139704; PubMed Central PMCID:
PMC5282551.


23: Cheerla N, Gevaert O. MicroRNA based Pan-Cancer Diagnosis and Treatment
Recommendation. BMC Bioinformatics. 2017 Jan 13;18(1):32. doi:
10.1186/s12859-016-1421-y. PubMed PMID: 28086747; PubMed Central PMCID:
PMC5237282.


24: Liu TT, Achrol AS, Mitchell LA, Rodriguez SA, Feroze A, Iv M, Kim C,
Chaudhary N, Gevaert O, Stuart JM, Harsh GR, Chang SD, Rubin DL. 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 1;19(7):997-1007. doi: 10.1093/neuonc/now270. PubMed PMID:
28007759; PubMed Central PMCID: PMC5570189.


25: Brennan K, Holsinger C, Dosiou C, Sunwoo JB, Akatsu H, Haile R, Gevaert O.
Development of prognostic signatures for intermediate-risk papillary thyroid
cancer. BMC Cancer. 2016 Sep 15;16(1):736. doi: 10.1186/s12885-016-2771-6. PubMed
PMID: 27633254; PubMed Central PMCID: PMC5025616.


26: Dubey R, Lebensohn AM, Bahrami-Nejad Z, Marceau C, Champion M, Gevaert O,
Sikic BI, Carette JE, Rohatgi R. Chromatin-Remodeling Complex SWI/SNF Controls
Multidrug Resistance by Transcriptionally Regulating the Drug Efflux Pump ABCB1.
Cancer Res. 2016 Oct 1;76(19):5810-5821. Epub 2016 Aug 8. PubMed PMID: 27503929;
PubMed Central PMCID: PMC5050136.


27: Planey CR, Gevaert O. CoINcIDE: A framework for discovery of patient subtypes
across multiple datasets. Genome Med. 2016 Mar 9;8(1):27. doi:
10.1186/s13073-016-0281-4. PubMed PMID: 26961683; PubMed Central PMCID:
PMC4784276.


28: Willis S, Villalobos VM, Gevaert O, Abramovitz M, Williams C, Sikic BI,
Leyland-Jones B. Single Gene Prognostic Biomarkers in Ovarian Cancer: A
Meta-Analysis. PLoS One. 2016 Feb 17;11(2):e0149183. doi:
10.1371/journal.pone.0149183. eCollection 2016. PubMed PMID: 26886260; PubMed
Central PMCID: PMC4757072.


29: Posch L, Panahiazar M, Dumontier M, Gevaert O. Predicting structured metadata
from unstructured metadata. Database (Oxford). 2016 Jan 1;2016. doi:
10.1093/database/baw080. PubMed PMID: 28637268; PubMed Central PMCID: PMC4892825.


30: Echegaray S, Gevaert O, Shah R, Kamaya A, Louie J, Kothary N, Napel S. Core
samples for radiomics features that are insensitive to tumor segmentation: method
and pilot study using CT images of hepatocellular carcinoma. J Med Imaging
(Bellingham). 2015 Oct;2(4):041011. doi: 10.1117/1.JMI.2.4.041011. Epub 2015 Nov
18. PubMed PMID: 26587549; PubMed Central PMCID: PMC4650964.


31: Sweeney TE, Chen AC, Gevaert O. Combined Mapping of Multiple clUsteriNg
ALgorithms (COMMUNAL): A Robust Method for Selection of Cluster Number, K. Sci
Rep. 2015 Nov 19;5:16971. doi: 10.1038/srep16971. PubMed PMID: 26581809; PubMed
Central PMCID: PMC4652212.


32: Itakura H, Achrol AS, Mitchell LA, Loya JJ, Liu T, Westbroek EM, Feroze AH,
Rodriguez S, Echegaray S, Azad TD, Yeom KW, Napel S, Rubin DL, Chang SD, Harsh GR
4th, Gevaert O. Magnetic resonance image features identify glioblastoma
phenotypic subtypes with distinct molecular pathway activities. Sci Transl Med.
2015 Sep 2;7(303):303ra138. doi: 10.1126/scitranslmed.aaa7582. PubMed PMID:
26333934; PubMed Central PMCID: PMC4666025.


33: Musen MA, Bean CA, Cheung KH, Dumontier M, Durante KA, Gevaert O,
Gonzalez-Beltran A, Khatri P, Kleinstein SH, O'Connor MJ, Pouliot Y, Rocca-Serra
P, Sansone SA, Wiser JA; CEDAR team. The center for expanded data annotation and
retrieval. J Am Med Inform Assoc. 2015 Nov;22(6):1148-52. doi:
10.1093/jamia/ocv048. Epub 2015 Jun 25. PubMed PMID: 26112029; PubMed Central
PMCID: PMC5009916.


34: Gevaert O, Mitchell LA, Achrol AS, Xu J, Echegaray S, Steinberg GK, Cheshier
SH, Napel S, Zaharchuk G, Plevritis SK. Glioblastoma Multiforme: Exploratory
Radiogenomic Analysis by Using Quantitative Image Features. Radiology. 2015
Jul;276(1):313. doi: 10.1148/radiol.2015154019. PubMed PMID: 26101929; PubMed
Central PMCID: PMC4725327.


35: Litovkin K, Van Eynde A, Joniau S, Lerut E, Laenen A, Gevaert T, Gevaert O,
Spahn M, Kneitz B, Gramme P, Helleputte T, Isebaert S, Haustermans K, Bollen M.
DNA Methylation-Guided Prediction of Clinical Failure in High-Risk Prostate
Cancer. PLoS One. 2015 Jun 18;10(6):e0130651. doi: 10.1371/journal.pone.0130651.
eCollection 2015. PubMed PMID: 26086362; PubMed Central PMCID: PMC4472347.


36: Verstraete M, Debucquoy A, Dekervel J, van Pelt J, Verslype C, Devos E,
Chiritescu G, Dumon K, D'Hoore A, Gevaert O, Sagaert X, Van Cutsem E, Haustermans
K. Combining bevacizumab and chemoradiation in rectal cancer. Translational
results of the AXEBeam trial. Br J Cancer. 2015 Apr 14;112(8):1314-25. doi:
10.1038/bjc.2015.93. Epub 2015 Mar 17. PubMed PMID: 25867261; PubMed Central
PMCID: PMC4402460.


37: Gevaert O, Tibshirani R, Plevritis SK. Pancancer analysis of DNA
methylation-driven genes using MethylMix. Genome Biol. 2015 Jan 29;16:17. doi:
10.1186/s13059-014-0579-8. PubMed PMID: 25631659; PubMed Central PMCID:
PMC4365533.


38: Gevaert O. MethylMix: an R package for identifying DNA methylation-driven
genes. Bioinformatics. 2015 Jun 1;31(11):1839-41. doi:
10.1093/bioinformatics/btv020. Epub 2015 Jan 20. PubMed PMID: 25609794; PubMed
Central PMCID: PMC4443673.


39: Manolakos A, Ochoa I, Venkat K, Goldsmith AJ, Gevaert O. CaMoDi: a new method
for cancer module discovery. BMC Genomics. 2014;15 Suppl 10:S8. doi:
10.1186/1471-2164-15-S10-S8. Epub 2014 Dec 12. Review. PubMed PMID: 25560933;
PubMed Central PMCID: PMC4304219.


40: Nicolasjilwan M, Hu Y, Yan C, Meerzaman D, Holder CA, Gutman D, Jain R, Colen
R, Rubin DL, Zinn PO, Hwang SN, Raghavan P, Hammoud DA, Scarpace LM, Mikkelsen T,
Chen J, Gevaert O, Buetow K, Freymann J, Kirby J, Flanders AE, Wintermark M; TCGA
Glioma Phenotype Research Group. Addition of MR imaging features and genetic
biomarkers strengthens glioblastoma survival prediction in TCGA patients. J
Neuroradiol. 2015 Jul;42(4):212-21. doi: 10.1016/j.neurad.2014.02.006. Epub 2014
Jul 2. PubMed PMID: 24997477; PubMed Central PMCID: PMC5511631.


41: Litovkin K, Joniau S, Lerut E, Laenen A, Gevaert O, Spahn M, Kneitz B,
Isebaert S, Haustermans K, Beullens M, Van Eynde A, Bollen M. Methylation of
PITX2, HOXD3, RASSF1 and TDRD1 predicts biochemical recurrence in high-risk
prostate cancer. J Cancer Res Clin Oncol. 2014 Nov;140(11):1849-61. doi:
10.1007/s00432-014-1738-8. Epub 2014 Jun 18. PubMed PMID: 24938434.


42: Li X, Nadauld L, Ootani A, Corney DC, Pai RK, Gevaert O, Cantrell MA, Rack
PG, Neal JT, Chan CW, Yeung T, Gong X, Yuan J, Wilhelmy J, Robine S, Attardi LD,
Plevritis SK, Hung KE, Chen CZ, Ji HP, Kuo CJ. Oncogenic transformation of
diverse gastrointestinal tissues in primary organoid culture. Nat Med. 2014
Jul;20(7):769-77. doi: 10.1038/nm.3585. Epub 2014 May 25. PubMed PMID: 24859528;
PubMed Central PMCID: PMC4087144.


43: Gevaert O, Mitchell LA, Achrol AS, Xu J, Echegaray S, Steinberg GK, Cheshier
SH, Napel S, Zaharchuk G, Plevritis SK. Glioblastoma multiforme: exploratory
radiogenomic analysis by using quantitative image features. Radiology. 2014
Oct;273(1):168-74. doi: 10.1148/radiol.14131731. Epub 2014 May 12. Erratum in:
Radiology. 2015 Jul;276(1):313. PubMed PMID: 24827998; PubMed Central PMCID:
PMC4263772.


44: Gevaert O, Villalobos V, Sikic BI, Plevritis SK. Identification of ovarian
cancer driver genes by using module network integration of multi-omics data.
Interface Focus. 2013 Aug 6;3(4):20130013. doi: 10.1098/rsfs.2013.0013. Erratum
in: Interface Focus. 2014 Jun 6;4(3):20140023. PubMed PMID: 24511378; PubMed
Central PMCID: PMC3915833.


45: Nair VS, Gevaert O, Davidzon G, Plevritis SK, West R. 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;83(2):189-96. doi: 10.1016/j.lungcan.2013.11.001. Epub 2013 Nov
13. PubMed PMID: 24355259; PubMed Central PMCID: PMC3922123.


46: Van Bockstal M, Lambein K, Gevaert O, De Wever O, Praet M, Cocquyt V, Van den
Broecke R, Braems G, Denys H, Libbrecht L. Stromal architecture and periductal
decorin are potential prognostic markers for ipsilateral locoregional recurrence
in ductal carcinoma in situ of the breast. Histopathology. 2013 Oct;63(4):520-33.
doi: 10.1111/his.12188. Epub 2013 Jul 26. PubMed PMID: 23889174.


47: Gevaert O, Plevritis S. Identifying master regulators of cancer and their
downstream targets by integrating genomic and epigenomic features. Pac Symp
Biocomput. 2013:123-34. PubMed PMID: 23424118; PubMed Central PMCID: PMC3911770.


48: Vicent S, Sayles LC, Vaka D, Khatri P, Gevaert O, Chen R, Zheng Y, Gillespie
AK, Clarke N, Xu Y, Shrager J, Hoang CD, Plevritis S, Butte AJ, Sweet-Cordero EA.
Cross-species functional analysis of cancer-associated fibroblasts identifies a
critical role for CLCF1 and IL-6 in non-small cell lung cancer in vivo. Cancer
Res. 2012 Nov 15;72(22):5744-56. doi: 10.1158/0008-5472.CAN-12-1097. Epub 2012
Sep 7. PubMed PMID: 22962265; PubMed Central PMCID: PMC3856949.


49: Vodolazkaia A, El-Aalamat Y, Popovic D, Mihalyi A, Bossuyt X, Kyama CM,
Fassbender A, Bokor A, Schols D, Huskens D, Meuleman C, Peeraer K, Tomassetti C,
Gevaert O, Waelkens E, Kasran A, De Moor B, D'Hooghe TM. Evaluation of a panel of
28 biomarkers for the non-invasive diagnosis of endometriosis. Hum Reprod. 2012
Sep;27(9):2698-711. doi: 10.1093/humrep/des234. Epub 2012 Jun 26. PubMed PMID:
22736326.


50: Gevaert O, Xu J, Hoang CD, Leung AN, Xu Y, Quon A, Rubin DL, Napel S,
Plevritis SK. Non-small cell lung cancer: identifying prognostic imaging
biomarkers by leveraging public gene expression microarray data--methods and
preliminary results. Radiology. 2012 Aug;264(2):387-96. doi:
10.1148/radiol.12111607. Epub 2012 Jun 21. PubMed PMID: 22723499; PubMed Central
PMCID: PMC3401348.


51: Nair VS, Gevaert O, Davidzon G, Napel S, Graves EE, Hoang CD, Shrager JB,
Quon A, Rubin DL, Plevritis SK. Prognostic PET 18F-FDG uptake imaging features
are associated with major oncogenomic alterations in patients with resected
non-small cell lung cancer. Cancer Res. 2012 Aug 1;72(15):3725-34. doi:
10.1158/0008-5472.CAN-11-3943. Epub 2012 Jun 18. Erratum in: Cancer Res. 2012 Sep
15;72(18):4870-1. PubMed PMID: 22710433; PubMed Central PMCID: PMC3596510.


52: Fassbender A, Verbeeck N, Börnigen D, Kyama CM, Bokor A, Vodolazkaia A,
Peeraer K, Tomassetti C, Meuleman C, Gevaert O, Van de Plas R, Ojeda F, De Moor
B, Moreau Y, Waelkens E, D'Hooghe TM. Combined mRNA microarray and proteomic
analysis of eutopic endometrium of women with and without endometriosis. Hum
Reprod. 2012 Jul;27(7):2020-9. doi: 10.1093/humrep/des127. Epub 2012 May 3.
PubMed PMID: 22556377.


53: Fassbender A, Waelkens E, Verbeeck N, Kyama CM, Bokor A, Vodolazkaia A, Van
de Plas R, Meuleman C, Peeraer K, Tomassetti C, Gevaert O, Ojeda F, De Moor B,
D'Hooghe T. Proteomics analysis of plasma for early diagnosis of endometriosis.
Obstet Gynecol. 2012 Feb;119(2 Pt 1):276-85. doi: 10.1097/AOG.0b013e31823fda8d.
PubMed PMID: 22270279.


54: Beert E, Brems H, Daniëls B, De Wever I, Van Calenbergh F, Schoenaers J,
Debiec-Rychter M, Gevaert O, De Raedt T, Van Den Bruel A, de Ravel T, Cichowski
K, Kluwe L, Mautner V, Sciot R, Legius E. Atypical neurofibromas in
neurofibromatosis type 1 are premalignant tumors. Genes Chromosomes Cancer. 2011
Dec;50(12):1021-32. doi: 10.1002/gcc.20921. Epub 2011 Aug 24. PubMed PMID:
21987445.


55: Kirk E, Van Calster B, Condous G, Papageorghiou AT, Gevaert O, Van Huffel S,
De Moor B, Timmerman D, Bourne T. Ectopic pregnancy: using the hCG ratio to
select women for expectant or medical management. Acta Obstet Gynecol Scand. 2011
Mar;90(3):264-72. doi: 10.1111/j.1600-0412.2010.01053.x. Epub 2011 Jan 13. PubMed
PMID: 21306315.


56: Smeets A, Daemen A, Vanden Bempt I, Gevaert O, Claes B, Wildiers H,
Drijkoningen R, Van Hummelen P, Lambrechts D, De Moor B, Neven P, Sotiriou C,
Vandorpe T, Paridaens R, Christiaens MR. Prediction of lymph node involvement in
breast cancer from primary tumor tissue using gene expression profiling and
miRNAs. Breast Cancer Res Treat. 2011 Oct;129(3):767-76. doi:
10.1007/s10549-010-1265-5. Epub 2010 Nov 30. PubMed PMID: 21116709.


57: Fassbender A, Simsa P, Kyama CM, Waelkens E, Mihalyi A, Meuleman C, Gevaert
O, Van de Plas R, de Moor B, D'Hooghe TM. TRIzol treatment of secretory phase
endometrium allows combined proteomic and mRNA microarray analysis of the same
sample in women with and without endometriosis. Reprod Biol Endocrinol. 2010 Oct
21;8:123. doi: 10.1186/1477-7827-8-123. Erratum in: Reprod Biol Endocrinol.
2011;9:44. PubMed PMID: 20964823; PubMed Central PMCID: PMC2987945.


58: Kyama CM, Mihalyi A, Gevaert O, Waelkens E, Simsa P, Van de Plas R, Meuleman
C, De Moor B, D'Hooghe TM. Evaluation of endometrial biomarkers for semi-invasive
diagnosis of endometriosis. Fertil Steril. 2011 Mar 15;95(4):1338-43.e1-3. doi:
10.1016/j.fertnstert.2010.06.084. Epub 2010 Aug 30. PubMed PMID: 20800833.


59: van Malenstein H, Gevaert O, Libbrecht L, Daemen A, Allemeersch J, Nevens F,
Van Cutsem E, Cassiman D, De Moor B, Verslype C, van Pelt J. A seven-gene set
associated with chronic hypoxia of prognostic importance in hepatocellular
carcinoma. Clin Cancer Res. 2010 Aug 15;16(16):4278-88. doi:
10.1158/1078-0432.CCR-09-3274. Epub 2010 Jun 30. PubMed PMID: 20592013.


60: Daemen A, Signoretto M, Gevaert O, Suykens JA, De Moor B. Improved
microarray-based decision support with graph encoded interactome data. PLoS One.
2010 Apr 19;5(4):e10225. doi: 10.1371/journal.pone.0010225. PubMed PMID:
20419106; PubMed Central PMCID: PMC2856685.


61: Gevaert O, Daemen A, De Moor B, Libbrecht L. A taxonomy of epithelial human
cancer and their metastases. BMC Med Genomics. 2009 Dec 17;2:69. doi:
10.1186/1755-8794-2-69. PubMed PMID: 20017941; PubMed Central PMCID: PMC2806369.


62: Mihalyi A, Gevaert O, Kyama CM, Simsa P, Pochet N, De Smet F, De Moor B,
Meuleman C, Billen J, Blanckaert N, Vodolazkaia A, Fulop V, D'Hooghe TM.
Non-invasive diagnosis of endometriosis based on a combined analysis of six
plasma biomarkers. Hum Reprod. 2010 Mar;25(3):654-64. doi: 10.1093/humrep/dep425.
Epub 2009 Dec 9. PubMed PMID: 20007161.


63: Gravendeel LA, Kouwenhoven MC, Gevaert O, de Rooi JJ, Stubbs AP, Duijm JE,
Daemen A, Bleeker FE, Bralten LB, Kloosterhof NK, De Moor B, Eilers PH, van der
Spek PJ, Kros JM, Sillevis Smitt PA, van den Bent MJ, French PJ. Intrinsic gene
expression profiles of gliomas are a better predictor of survival than histology.
Cancer Res. 2009 Dec 1;69(23):9065-72. doi: 10.1158/0008-5472.CAN-09-2307. Epub
2009 Nov 17. PubMed PMID: 19920198.


64: Leunen K, Gevaert O, Daemen A, Vanspauwen V, Michils G, De Moor B, Moerman P,
Vergote I, Legius E. Recurrent copy number alterations in BRCA1-mutated ovarian
tumors alter biological pathways. Hum Mutat. 2009 Dec;30(12):1693-702. doi:
10.1002/humu.21135. PubMed PMID: 19802895.


65: Bokor A, Kyama CM, Vercruysse L, Fassbender A, Gevaert O, Vodolazkaia A, De
Moor B, Fülöp V, D'Hooghe T. Density of small diameter sensory nerve fibres in
endometrium: a semi-invasive diagnostic test for minimal to mild endometriosis.
Hum Reprod. 2009 Dec;24(12):3025-32. doi: 10.1093/humrep/dep283. Epub 2009 Aug
18. PubMed PMID: 19690351.


66: Daemen A, Gevaert O, Ojeda F, Debucquoy A, Suykens JA, Sempoux C, Machiels
JP, Haustermans K, De Moor B. A kernel-based integration of genome-wide data for
clinical decision support. Genome Med. 2009 Apr 3;1(4):39. doi: 10.1186/gm39.
PubMed PMID: 19356222; PubMed Central PMCID: PMC2684660.


67: Debucquoy A, Haustermans K, Daemen A, Aydin S, Libbrecht L, Gevaert O, De
Moor B, Tejpar S, McBride WH, Penninckx F, Scalliet P, Stroh C, Vlassak S,
Sempoux C, Machiels JP. Molecular response to cetuximab and efficacy of
preoperative cetuximab-based chemoradiation in rectal cancer. J Clin Oncol. 2009
Jun 10;27(17):2751-7. doi: 10.1200/JCO.2008.18.5033. Epub 2009 Mar 30. PubMed
PMID: 19332731.


68: Gevaert O, De Moor B. Prediction of cancer outcome using DNA microarray
technology: past, present and future. Expert Opin Med Diagn. 2009
Mar;3(2):157-65. doi: 10.1517/17530050802680172. PubMed PMID: 23485162.


69: Daemen A, Gevaert O, Leunen K, Legius E, Vergote I, De Moor B. Supervised
classification of array CGH data with HMM-based feature selection. Pac Symp
Biocomput. 2009:468-79. PubMed PMID: 19209723.


70: Van den Bosch T, Daemen A, Gevaert O, De Moor B, Timmerman D. Building
decision trees for diagnosing intracavitary uterine pathology. Facts Views Vis
Obgyn. 2009;1(3):182-8. Review. PubMed PMID: 25489463; PubMed Central PMCID:
PMC4255509.


71: Van den Bosch T, Verguts J, Daemen A, Gevaert O, Domali E, Claerhout F,
Vandenbroucke V, De Moor B, Deprest J, Timmerman D. Pain experienced during
transvaginal ultrasound, saline contrast sonohysterography, hysteroscopy and
office sampling: a comparative study. Ultrasound Obstet Gynecol. 2008
Mar;31(3):346-51. doi: 10.1002/uog.5263. PubMed PMID: 18307203.


72: Gevaert O, Van Vooren S, de Moor B. Integration of microarray and textual
data improves the prognosis prediction of breast, lung and ovarian cancer
patients. Pac Symp Biocomput. 2008:279-90. PubMed PMID: 18229693.


73: Daemen A, Gevaert O, De Bie T, Debucquoy A, Machiels JP, De Moor B,
Haustermans K. Integrating microarray and proteomics data to predict the response
on cetuximab in patients with rectal cancer. Pac Symp Biocomput. 2008:166-77.
PubMed PMID: 18229684.


74: Gevaert O, De Smet F, Van Gorp T, Pochet N, Engelen K, Amant F, De Moor B,
Timmerman D, Vergote I. Expression profiling to predict the clinical behaviour of
ovarian cancer fails independent evaluation. BMC Cancer. 2008 Jan 22;8:18. doi:
10.1186/1471-2407-8-18. PubMed PMID: 18211668; PubMed Central PMCID: PMC2259320.


75: Daemen A, Gevaert O, De Moor B. Integration of clinical and microarray data
with kernel methods. Conf Proc IEEE Eng Med Biol Soc. 2007;2007:5411-5. PubMed
PMID: 18003232.


76: Gevaert O, Van Vooren S, De Moor B. A framework for elucidating regulatory
networks based on prior information and expression data. Ann N Y Acad Sci. 2007
Dec;1115:240-8. Epub 2007 Oct 9. PubMed PMID: 17925352.


77: Gevaert O, De Smet F, Timmerman D, Moreau Y, De Moor B. Predicting the
prognosis of breast cancer by integrating clinical and microarray data with
Bayesian networks. Bioinformatics. 2006 Jul 15;22(14):e184-90. PubMed PMID:
16873470.


78: Gevaert O, Pochet N, De Smet F, Van Gorp T, De Moor B, Timmerman D, Amant F,
Vergote I. Molecular profiling of platinum resistant ovarian cancer: use of the
model in clinical practice. Int J Cancer. 2006 Sep 15;119(6):1511; author reply
1512. PubMed PMID: 16619247.


79: Gevaert O, De Smet F, Kirk E, Van Calster B, Bourne T, Van Huffel S, Moreau
Y, Timmerman D, De Moor B, Condous G. Predicting the outcome of pregnancies of
unknown location: Bayesian networks with expert prior information compared to
logistic regression. Hum Reprod. 2006 Jul;21(7):1824-31. Epub 2006 Apr 6. PubMed
PMID: 16601010.


80: Condous G, Kirk E, Lu C, Van Huffel S, Gevaert O, De Moor B, De Smet F,
Timmerman D, Bourne T. Diagnostic accuracy of varying discriminatory zones for
the prediction of ectopic pregnancy in women with a pregnancy of unknown
location. Ultrasound Obstet Gynecol. 2005 Dec;26(7):770-5. PubMed PMID: 16308901.