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An integrative approach for in silico glioma research.

Cooper LA, Kong J, Gutman DA, Wang F, Cholleti SR, Pan TC, Widener PM, Sharma A, Mikkelsen T, Flanders AE, Rubin DL, Van Meir EG, Kurc TM, Moreno CS, Brat DJ, Saltz JH.

IEEE Trans Biomed Eng. 2010 Oct;57(10):2617-21. doi: 10.1109/TBME.2010.2060338. Epub 2010 Jul 23.


Integrative, multimodal analysis of glioblastoma using TCGA molecular data, pathology images, and clinical outcomes.

Kong J, Cooper LA, Wang F, Gutman DA, Gao J, Chisolm C, Sharma A, Pan T, Van Meir EG, Kurc TM, Moreno CS, Saltz JH, Brat DJ.

IEEE Trans Biomed Eng. 2011 Dec;58(12):3469-74. doi: 10.1109/TBME.2011.2169256. Epub 2011 Sep 23.


Multiscale integration of -omic, imaging, and clinical data in biomedical informatics.

Phan JH, Quo CF, Cheng C, Wang MD.

IEEE Rev Biomed Eng. 2012;5:74-87. doi: 10.1109/RBME.2012.2212427. Review.


Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data.

Gutman DA, Cobb J, Somanna D, Park Y, Wang F, Kurc T, Saltz JH, Brat DJ, Cooper LA.

J Am Med Inform Assoc. 2013 Nov-Dec;20(6):1091-8. doi: 10.1136/amiajnl-2012-001469. Epub 2013 Jul 25.


Atlas - a data warehouse for integrative bioinformatics.

Shah SP, Huang Y, Xu T, Yuen MM, Ling J, Ouellette BF.

BMC Bioinformatics. 2005 Feb 21;6:34.


Towards building computerized image analysis framework for nucleus discrimination in microscopy images of diffuse glioma.

Kong J, Cooper L, Kurc T, Brat D, Saltz J.

Conf Proc IEEE Eng Med Biol Soc. 2011;2011:6605-8. doi: 10.1109/IEMBS.2011.6091629.


Machine-based morphologic analysis of glioblastoma using whole-slide pathology images uncovers clinically relevant molecular correlates.

Kong J, Cooper LA, Wang F, Gao J, Teodoro G, Scarpace L, Mikkelsen T, Schniederjan MJ, Moreno CS, Saltz JH, Brat DJ.

PLoS One. 2013 Nov 13;8(11):e81049. doi: 10.1371/journal.pone.0081049. eCollection 2013.


A biosegmentation benchmark for evaluation of bioimage analysis methods.

Drelie Gelasca E, Obara B, Fedorov D, Kvilekval K, Manjunath B.

BMC Bioinformatics. 2009 Nov 1;10:368. doi: 10.1186/1471-2105-10-368.


Automated image computing reshapes computational neuroscience.

Peng H, Roysam B, Ascoli GA.

BMC Bioinformatics. 2013 Oct 4;14:293. doi: 10.1186/1471-2105-14-293.


GLISTR: glioma image segmentation and registration.

Gooya A, Pohl KM, Bilello M, Cirillo L, Biros G, Melhem ER, Davatzikos C.

IEEE Trans Med Imaging. 2012 Oct;31(10):1941-54. doi: 10.1109/TMI.2012.2210558. Epub 2012 Aug 13.


Bioimage Informatics in the context of Drosophila research.

Jug F, Pietzsch T, Preibisch S, Tomancak P.

Methods. 2014 Jun 15;68(1):60-73. doi: 10.1016/j.ymeth.2014.04.004. Epub 2014 Apr 13. Review.


Multimodal fusion of biomedical data at different temporal and dimensional scales.

Viceconti M, Clapworthy G, Testi D, Taddei F, McFarlane N.

Comput Methods Programs Biomed. 2011 Jun;102(3):227-37. doi: 10.1016/j.cmpb.2010.04.017. Epub 2010 May 26.


High speed data processing for imaging MS-based molecular histology using graphical processing units.

Jones EA, van Zeijl RJ, Andrén PE, Deelder AM, Wolters L, McDonnell LA.

J Am Soc Mass Spectrom. 2012 Apr;23(4):745-52. doi: 10.1007/s13361-011-0327-1. Epub 2012 Feb 4.


Multireference level set for the characterization of nuclear morphology in glioblastoma multiforme.

Chang H, Han J, Spellman PT, Parvin B.

IEEE Trans Biomed Eng. 2012 Dec;59(12):3460-7. doi: 10.1109/TBME.2012.2218107. Epub 2012 Sep 10.


Identification of mutated core cancer modules by integrating somatic mutation, copy number variation, and gene expression data.

Zhang J, Zhang S, Wang Y, Zhang XS.

BMC Syst Biol. 2013;7 Suppl 2:S4. doi: 10.1186/1752-0509-7-S2-S4. Epub 2013 Oct 14.


OMERO.searcher: content-based image search for microscope images.

Cho BH, Cao-Berg I, Bakal JA, Murphy RF.

Nat Methods. 2012 Jun 28;9(7):633-4. doi: 10.1038/nmeth.2086. No abstract available.


Atlas-based neuroinformatics via MRI: harnessing information from past clinical cases and quantitative image analysis for patient care.

Mori S, Oishi K, Faria AV, Miller MI.

Annu Rev Biomed Eng. 2013;15:71-92. doi: 10.1146/annurev-bioeng-071812-152335. Epub 2013 Apr 29. Review.


Novel computational methods and tools in biomedicine and biopharmacy.

Cai Y, Huang T, Chen L, Gao S, Zhang N.

Comput Math Methods Med. 2014;2014:127515. doi: 10.1155/2014/127515. Epub 2014 Jun 5. No abstract available.


Detection and segmentation of cell nuclei in virtual microscopy images: a minimum-model approach.

Wienert S, Heim D, Saeger K, Stenzinger A, Beil M, Hufnagl P, Dietel M, Denkert C, Klauschen F.

Sci Rep. 2012;2:503. doi: 10.1038/srep00503. Epub 2012 Jul 11.

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