Publications

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

Top 50 most recent publications:

1: 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.


2: 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. 2017 Jul 20:161845. doi:
10.1148/radiol.2017161845. [Epub ahead of print] PubMed PMID: 28727543.


3: 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.


4: 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.


5: 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.


6: 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.


7: 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.


8: 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.


9: 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.


10: 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.


11: 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. 2016 Dec 22. pii: now270. doi: 10.1093/neuonc/now270. [Epub ahead of
print] PubMed PMID: 28007759; PubMed Central PMCID: PMC5570189.


12: 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.


13: 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.


14: 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.


15: 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.


16: 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.


17: 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.


18: 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.


19: 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.


20: 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.


21: 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.


22: 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.


23: 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.


24: 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.


25: 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.


26: 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.


27: 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.


28: 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.


29: 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.


30: 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.


31: 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.


32: 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.


33: 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.


34: 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.


35: 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.


36: 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.


37: 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.


38: 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.


39: 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.


40: 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.


41: 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.


42: 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.


43: 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.


44: 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.


45: 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.


46: 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.


47: 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.


48: 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.


49: 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.


50: 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.