Publications

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

 

1: 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.


2: 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 Jun 25. pii: ocv048. doi:
10.1093/jamia/ocv048. [Epub ahead of print] PubMed PMID: 26112029.


3: 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.


4: 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.


5: 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.


6: 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.


7: 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.


8: 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.


9: 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.


10: 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.


11: 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.


12: 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.


13: 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.


14: 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.


15: 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.


16: 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.


17: 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.


18: 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.


19: 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.


20: 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.


21: 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.


22: 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.


23: 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.


24: 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.


25: 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. 2011 Apr
6;9(1):44. doi: 10.1186/1477-7827-9-44. PubMed PMID: 25927325; PubMed Central
PMCID: PMC3079635.


26: 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.


27: 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.


28: 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.


29: 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.


30: 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.


31: 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.


32: 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.


33: 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.


34: 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.


35: 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.


36: 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.


37: 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.


38: 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.


39: 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.


40: 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.


41: 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.


42: 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.


43: 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.


44: 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.


45: 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.


46: 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.


47: 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.


48: 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.


49: 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.


50: 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.