Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 78

1.

Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations.

Martínez-Romero M, O'Connor MJ, Shankar RD, Panahiazar M, Willrett D, Egyedi AL, Gevaert O, Graybeal J, Musen MA.

AMIA Annu Symp Proc. 2018 Apr 16;2017:1272-1281. eCollection 2017.

2.

MethylMix 2.0: an R package for identifying DNA methylation genes.

Cedoz PL, Prunello M, Brennan K, Gevaert O.

Bioinformatics. 2018 Apr 14. doi: 10.1093/bioinformatics/bty156. [Epub ahead of print]

PMID:
29668835
3.

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.

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.

Cell. 2018 Apr 5;173(2):338-354.e15. doi: 10.1016/j.cell.2018.03.034.

4.

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas.

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.

Cell Rep. 2018 Apr 3;23(1):194-212.e6. doi: 10.1016/j.celrep.2018.03.063.

5.

Development and validation of an MRI-based model to predict response to chemoradiotherapy for rectal cancer.

Bulens P, Couwenberg A, Haustermans K, Debucquoy A, Vandecaveye V, Philippens M, Zhou M, Gevaert O, Intven M.

Radiother Oncol. 2018 Mar;126(3):437-442. doi: 10.1016/j.radonc.2018.01.008. Epub 2018 Jan 31.

PMID:
29395287
6.

Module Analysis Captures Pancancer Genetically and Epigenetically Deregulated Cancer Driver Genes for Smoking and Antiviral Response.

Champion M, Brennan K, Croonenborghs T, Gentles AJ, Pochet N, Gevaert O.

EBioMedicine. 2018 Jan;27:156-166. doi: 10.1016/j.ebiom.2017.11.028. Epub 2017 Dec 1.

7.

NSD1 inactivation defines an immune cold, DNA hypomethylated subtype in squamous cell carcinoma.

Brennan K, Shin JH, Tay JK, Prunello M, Gentles AJ, Sunwoo JB, Gevaert O.

Sci Rep. 2017 Dec 6;7(1):17064. doi: 10.1038/s41598-017-17298-x.

8.

The ENGAGE study: Integrating neuroimaging, virtual reality and smartphone sensing to understand self-regulation for managing depression and obesity in a precision medicine model.

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.

Behav Res Ther. 2018 Feb;101:58-70. doi: 10.1016/j.brat.2017.09.012. Epub 2017 Oct 7.

PMID:
29074231
9.

A multi-view deep convolutional neural networks for lung nodule segmentation.

Shuo Wang, Mu Zhou, Gevaert O, Zhenchao Tang, Di Dong, Zhenyu Liu, Jie Tian.

Conf Proc IEEE Eng Med Biol Soc. 2017 Jul;2017:1752-1755. doi: 10.1109/EMBC.2017.8037182.

PMID:
29060226
10.

Radiomics in Brain Tumor: Image Assessment, Quantitative Feature Descriptors, and Machine-Learning Approaches.

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.

AJNR Am J Neuroradiol. 2018 Feb;39(2):208-216. doi: 10.3174/ajnr.A5391. Epub 2017 Oct 5. Review.

PMID:
28982791
11.

Prediction of EGFR and KRAS mutation in non-small cell lung cancer using quantitative 18F FDG-PET/CT metrics.

Minamimoto R, Jamali M, Gevaert O, Echegaray S, Khuong A, Hoang CD, Shrager JB, Plevritis SK, Rubin DL, Leung AN, Napel S, Quon A.

Oncotarget. 2017 May 10;8(32):52792-52801. doi: 10.18632/oncotarget.17782. eCollection 2017 Aug 8.

12.

Noninvasive radiomics signature based on quantitative analysis of computed tomography images as a surrogate for microvascular invasion in hepatocellular carcinoma: a pilot study.

Bakr S, Echegaray S, Shah R, Kamaya A, Louie J, Napel S, Kothary N, Gevaert O.

J Med Imaging (Bellingham). 2017 Oct;4(4):041303. doi: 10.1117/1.JMI.4.4.041303. Epub 2017 Aug 21.

PMID:
28840174
13.

Non-Small Cell Lung Cancer Radiogenomics Map Identifies Relationships between Molecular and Imaging Phenotypes with Prognostic Implications.

Zhou M, Leung A, Echegaray S, Gentles A, Shrager JB, Jensen KC, Berry GJ, Plevritis SK, Rubin DL, Napel S, Gevaert O.

Radiology. 2018 Jan;286(1):307-315. doi: 10.1148/radiol.2017161845. Epub 2017 Jul 20.

PMID:
28727543
14.

Central focused convolutional neural networks: Developing a data-driven model for lung nodule segmentation.

Wang S, Zhou M, Liu Z, Liu Z, Gu D, Zang Y, Dong D, Gevaert O, Tian J.

Med Image Anal. 2017 Aug;40:172-183. doi: 10.1016/j.media.2017.06.014. Epub 2017 Jun 30.

15.

Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity.

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.

Cell Stem Cell. 2017 Jul 6;21(1):78-90.e6. doi: 10.1016/j.stem.2017.06.014.

16.

Quantitative imaging outperforms molecular markers when predicting response to chemoradiotherapy for rectal cancer.

Joye I, Debucquoy A, Deroose CM, Vandecaveye V, Cutsem EV, Wolthuis A, D'Hoore A, Sagaert X, Zhou M, Gevaert O, Haustermans K.

Radiother Oncol. 2017 Jul;124(1):104-109. doi: 10.1016/j.radonc.2017.06.013. Epub 2017 Jun 21.

17.

Predicting biomedical metadata in CEDAR: A study of Gene Expression Omnibus (GEO).

Panahiazar M, Dumontier M, Gevaert O.

J Biomed Inform. 2017 Aug;72:132-139. doi: 10.1016/j.jbi.2017.06.017. Epub 2017 Jun 16.

18.

A Rapid Segmentation-Insensitive "Digital Biopsy" Method for Radiomic Feature Extraction: Method and Pilot Study Using CT Images of Non-Small Cell Lung Cancer.

Echegaray S, Nair V, Kadoch M, Leung A, Rubin D, Gevaert O, Napel S.

Tomography. 2016 Dec;2(4):283-294. doi: 10.18383/j.tom.2016.00163.

19.

Identification of an atypical etiological head and neck squamous carcinoma subtype featuring the CpG island methylator phenotype.

Brennan K, Koenig JL, Gentles AJ, Sunwoo JB, Gevaert O.

EBioMedicine. 2017 Mar;17:223-236. doi: 10.1016/j.ebiom.2017.02.025. Epub 2017 Mar 1.

20.

Predictive radiogenomics modeling of EGFR mutation status in lung cancer.

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.

Sci Rep. 2017 Jan 31;7:41674. doi: 10.1038/srep41674.

21.

MicroRNA based Pan-Cancer Diagnosis and Treatment Recommendation.

Cheerla N, Gevaert O.

BMC Bioinformatics. 2017 Jan 13;18(1):32. doi: 10.1186/s12859-016-1421-y.

22.

Magnetic resonance perfusion image features uncover an angiogenic subgroup of glioblastoma patients with poor survival and better response to antiangiogenic treatment.

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.

Neuro Oncol. 2017 Jul 1;19(7):997-1007. doi: 10.1093/neuonc/now270.

23.

Development of prognostic signatures for intermediate-risk papillary thyroid cancer.

Brennan K, Holsinger C, Dosiou C, Sunwoo JB, Akatsu H, Haile R, Gevaert O.

BMC Cancer. 2016 Sep 15;16(1):736. doi: 10.1186/s12885-016-2771-6.

24.

Chromatin-Remodeling Complex SWI/SNF Controls Multidrug Resistance by Transcriptionally Regulating the Drug Efflux Pump ABCB1.

Dubey R, Lebensohn AM, Bahrami-Nejad Z, Marceau C, Champion M, Gevaert O, Sikic BI, Carette JE, Rohatgi R.

Cancer Res. 2016 Oct 1;76(19):5810-5821. Epub 2016 Aug 8.

25.

CoINcIDE: A framework for discovery of patient subtypes across multiple datasets.

Planey CR, Gevaert O.

Genome Med. 2016 Mar 9;8(1):27. doi: 10.1186/s13073-016-0281-4.

26.

Single Gene Prognostic Biomarkers in Ovarian Cancer: A Meta-Analysis.

Willis S, Villalobos VM, Gevaert O, Abramovitz M, Williams C, Sikic BI, Leyland-Jones B.

PLoS One. 2016 Feb 17;11(2):e0149183. doi: 10.1371/journal.pone.0149183. eCollection 2016.

27.

Predicting structured metadata from unstructured metadata.

Posch L, Panahiazar M, Dumontier M, Gevaert O.

Database (Oxford). 2016 Jan 1;2016. doi: 10.1093/database/baw080.

28.

Core samples for radiomics features that are insensitive to tumor segmentation: method and pilot study using CT images of hepatocellular carcinoma.

Echegaray S, Gevaert O, Shah R, Kamaya A, Louie J, Kothary N, Napel S.

J Med Imaging (Bellingham). 2015 Oct;2(4):041011. doi: 10.1117/1.JMI.2.4.041011. Epub 2015 Nov 18.

29.

Combined Mapping of Multiple clUsteriNg ALgorithms (COMMUNAL): A Robust Method for Selection of Cluster Number, K.

Sweeney TE, Chen AC, Gevaert O.

Sci Rep. 2015 Nov 19;5:16971. doi: 10.1038/srep16971.

30.

Magnetic resonance image features identify glioblastoma phenotypic subtypes with distinct molecular pathway activities.

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.

Sci Transl Med. 2015 Sep 2;7(303):303ra138. doi: 10.1126/scitranslmed.aaa7582.

31.

The center for expanded data annotation and retrieval.

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.

J Am Med Inform Assoc. 2015 Nov;22(6):1148-52. doi: 10.1093/jamia/ocv048. Epub 2015 Jun 25.

32.

Glioblastoma Multiforme: Exploratory Radiogenomic Analysis by Using Quantitative Image Features.

Gevaert O, Mitchell LA, Achrol AS, Xu J, Echegaray S, Steinberg GK, Cheshier SH, Napel S, Zaharchuk G, Plevritis SK.

Radiology. 2015 Jul;276(1):313. doi: 10.1148/radiol.2015154019. No abstract available.

33.

DNA Methylation-Guided Prediction of Clinical Failure in High-Risk Prostate Cancer.

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.

PLoS One. 2015 Jun 18;10(6):e0130651. doi: 10.1371/journal.pone.0130651. eCollection 2015.

34.

Combining bevacizumab and chemoradiation in rectal cancer. Translational results of the AXEBeam trial.

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.

Br J Cancer. 2015 Apr 14;112(8):1314-25. doi: 10.1038/bjc.2015.93. Epub 2015 Mar 17.

35.

Pancancer analysis of DNA methylation-driven genes using MethylMix.

Gevaert O, Tibshirani R, Plevritis SK.

Genome Biol. 2015 Jan 29;16:17. doi: 10.1186/s13059-014-0579-8.

36.

MethylMix: an R package for identifying DNA methylation-driven genes.

Gevaert O.

Bioinformatics. 2015 Jun 1;31(11):1839-41. doi: 10.1093/bioinformatics/btv020. Epub 2015 Jan 20.

37.

CaMoDi: a new method for cancer module discovery.

Manolakos A, Ochoa I, Venkat K, Goldsmith AJ, Gevaert O.

BMC Genomics. 2014;15 Suppl 10:S8. doi: 10.1186/1471-2164-15-S10-S8. Epub 2014 Dec 12. Review.

38.

Addition of MR imaging features and genetic biomarkers strengthens glioblastoma survival prediction in TCGA patients.

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.

J Neuroradiol. 2015 Jul;42(4):212-21. doi: 10.1016/j.neurad.2014.02.006. Epub 2014 Jul 2.

39.

Methylation of PITX2, HOXD3, RASSF1 and TDRD1 predicts biochemical recurrence in high-risk prostate cancer.

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.

J Cancer Res Clin Oncol. 2014 Nov;140(11):1849-61. doi: 10.1007/s00432-014-1738-8. Epub 2014 Jun 18.

PMID:
24938434
40.

Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture.

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.

Nat Med. 2014 Jul;20(7):769-77. doi: 10.1038/nm.3585. Epub 2014 May 25.

41.

Glioblastoma multiforme: exploratory radiogenomic analysis by using quantitative image features.

Gevaert O, Mitchell LA, Achrol AS, Xu J, Echegaray S, Steinberg GK, Cheshier SH, Napel S, Zaharchuk G, Plevritis SK.

Radiology. 2014 Oct;273(1):168-74. doi: 10.1148/radiol.14131731. Epub 2014 May 12. Erratum in: Radiology. 2015 Jul;276(1):313.

42.

Identification of ovarian cancer driver genes by using module network integration of multi-omics data.

Gevaert O, Villalobos V, Sikic BI, Plevritis SK.

Interface Focus. 2013 Aug 6;3(4):20130013. doi: 10.1098/rsfs.2013.0013. Erratum in: Interface Focus. 2014 Jun 6;4(3):20140023.

43.

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.

Nair VS, Gevaert O, Davidzon G, Plevritis SK, West R.

Lung Cancer. 2014 Feb;83(2):189-96. doi: 10.1016/j.lungcan.2013.11.001. Epub 2013 Nov 13.

44.

Stromal architecture and periductal decorin are potential prognostic markers for ipsilateral locoregional recurrence in ductal carcinoma in situ of the breast.

Van Bockstal M, Lambein K, Gevaert O, De Wever O, Praet M, Cocquyt V, Van den Broecke R, Braems G, Denys H, Libbrecht L.

Histopathology. 2013 Oct;63(4):520-33. doi: 10.1111/his.12188. Epub 2013 Jul 26.

PMID:
23889174
46.

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.

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.

Cancer Res. 2012 Nov 15;72(22):5744-56. doi: 10.1158/0008-5472.CAN-12-1097. Epub 2012 Sep 7.

47.

Evaluation of a panel of 28 biomarkers for the non-invasive diagnosis of endometriosis.

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.

Hum Reprod. 2012 Sep;27(9):2698-711. doi: 10.1093/humrep/des234. Epub 2012 Jun 26.

PMID:
22736326
48.

Non-small cell lung cancer: identifying prognostic imaging biomarkers by leveraging public gene expression microarray data--methods and preliminary results.

Gevaert O, Xu J, Hoang CD, Leung AN, Xu Y, Quon A, Rubin DL, Napel S, Plevritis SK.

Radiology. 2012 Aug;264(2):387-96. doi: 10.1148/radiol.12111607. Epub 2012 Jun 21.

49.

Prognostic PET 18F-FDG uptake imaging features are associated with major oncogenomic alterations in patients with resected non-small cell lung cancer.

Nair VS, Gevaert O, Davidzon G, Napel S, Graves EE, Hoang CD, Shrager JB, Quon A, Rubin DL, Plevritis SK.

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.

50.

Combined mRNA microarray and proteomic analysis of eutopic endometrium of women with and without endometriosis.

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.

Hum Reprod. 2012 Jul;27(7):2020-9. doi: 10.1093/humrep/des127. Epub 2012 May 3.

PMID:
22556377

Supplemental Content

Loading ...
Support Center