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Items: 1 to 50 of 55

1.

Comparison of Different Classifiers with Active Learning to Support Quality Control in Nucleus Segmentation in Pathology Images.

Wen S, Kurc TM, Hou L, Saltz JH, Gupta RR, Batiste R, Zhao T, Nguyen V, Samaras D, Zhu W.

AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:227-236. eCollection 2018.

2.

Classification of Pancreatic Cysts in Computed Tomography Images Using a Random Forest and Convolutional Neural Network Ensemble.

Dmitriev K, Kaufman AE, Javed AA, Hruban RH, Fishman EK, Lennon AM, Saltz JH.

Med Image Comput Comput Assist Interv. 2017 Sep;10435:150-158. doi: 10.1007/978-3-319-66179-7_18. Epub 2017 Sep 4.

3.

PanCancer insights from The Cancer Genome Atlas: the pathologist's perspective.

Cooper LA, Demicco EG, Saltz JH, Powell RT, Rao A, Lazar AJ.

J Pathol. 2018 Apr;244(5):512-524. doi: 10.1002/path.5028. Epub 2018 Feb 22. Review.

PMID:
29288495
4.

An Assessment of Imaging Informatics for Precision Medicine in Cancer.

Chennubhotla C, Clarke LP, Fedorov A, Foran D, Harris G, Helton E, Nordstrom R, Prior F, Rubin D, Saltz JH, Shalley E, Sharma A.

Yearb Med Inform. 2017 Aug;26(1):110-119. doi: 10.15265/IY-2017-041. Epub 2017 Sep 11. Review.

5.

A Methodology for Texture Feature-based Quality Assessment in Nucleus Segmentation of Histopathology Image.

Wen S, Kurc TM, Gao Y, Zhao T, Saltz JH, Zhu W.

J Pathol Inform. 2017 Sep 7;8:38. doi: 10.4103/jpi.jpi_43_17. eCollection 2017.

6.

Development of a Framework for Large Scale Three-Dimensional Pathology and Biomarker Imaging and Spatial Analytics.

Liang Y, Wang F, Zhang P, Saltz JH, Brat DJ, Kong J.

AMIA Jt Summits Transl Sci Proc. 2017 Jul 26;2017:75-84. eCollection 2017.

7.

Center-Focusing Multi-task CNN with Injected Features for Classification of Glioma Nuclear Images.

Murthy V, Hou L, Samaras D, Kurc TM, Saltz JH.

IEEE Winter Conf Appl Comput Vis. 2017 Mar;2017:834-841. doi: 10.1109/WACV.2017.98. Epub 2017 May 15.

8.

Algorithm sensitivity analysis and parameter tuning for tissue image segmentation pipelines.

Teodoro G, Kurç TM, Taveira LFR, Melo ACMA, Gao Y, Kong J, Saltz JH.

Bioinformatics. 2017 Apr 1;33(7):1064-1072. doi: 10.1093/bioinformatics/btw749.

9.

Patch-based Convolutional Neural Network for Whole Slide Tissue Image Classification.

Hou L, Samaras D, Kurc TM, Gao Y, Davis JE, Saltz JH.

Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2016 Jun-Jul;2016:2424-2433.

10.

Efficient irregular wavefront propagation algorithms on Intel® Xeon Phi.

Gomes JM, Teodoro G, de Melo A, Kong J, Kurc T, Saltz JH.

Proc Symp Comput Archit High Perform Comput. 2015 Oct;2015:25-32.

11.

Efficient Execution of Microscopy Image Analysis on CPU, GPU, and MIC Equipped Cluster Systems.

Andrade G, Ferreira R, Teodoro G, Rocha L, Saltz JH, Kurc T.

Proc Symp Comput Archit High Perform Comput. 2014 Oct;2014:89-96.

12.

GlycoPattern: a web platform for glycan array mining.

Agravat SB, Saltz JH, Cummings RD, Smith DF.

Bioinformatics. 2014 Dec 1;30(23):3417-8. doi: 10.1093/bioinformatics/btu559. Epub 2014 Aug 20.

13.

Temporal abstraction-based clinical phenotyping with Eureka!

Post AR, Kurc T, Willard R, Rathod H, Mansour M, Pai AK, Torian WM, Agravat S, Sturm S, Saltz JH.

AMIA Annu Symp Proc. 2013 Nov 16;2013:1160-9. eCollection 2013.

14.

Semantic ETL into i2b2 with Eureka!

Post AR, Krc T, Rathod H, Agravat S, Mansour M, Torian W, Saltz JH.

AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:203-7. eCollection 2013.

15.

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.

16.

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.

17.

Tumor-infiltrating lymphocytes in glioblastoma are associated with specific genomic alterations and related to transcriptional class.

Rutledge WC, Kong J, Gao J, Gutman DA, Cooper LA, Appin C, Park Y, Scarpace L, Mikkelsen T, Cohen ML, Aldape KD, McLendon RE, Lehman NL, Miller CR, Schniederjan MJ, Brennan CW, Saltz JH, Moreno CS, Brat DJ.

Clin Cancer Res. 2013 Sep 15;19(18):4951-60. doi: 10.1158/1078-0432.CCR-13-0551. Epub 2013 Jul 17.

18.

Caveats for the use of operational electronic health record data in comparative effectiveness research.

Hersh WR, Weiner MG, Embi PJ, Logan JR, Payne PR, Bernstam EV, Lehmann HP, Hripcsak G, Hartzog TH, Cimino JJ, Saltz JH.

Med Care. 2013 Aug;51(8 Suppl 3):S30-7. doi: 10.1097/MLR.0b013e31829b1dbd.

19.

Liver steatosis assessment: correlations among pathology, radiology, clinical data and automated image analysis software.

Lee MJ, Bagci P, Kong J, Vos MB, Sharma P, Kalb B, Saltz JH, Martin DR, Adsay NV, Farris AB.

Pathol Res Pract. 2013 Jun;209(6):371-9. doi: 10.1016/j.prp.2013.04.001. Epub 2013 Apr 17.

PMID:
23707550
20.

High-throughput Analysis of Large Microscopy Image Datasets on CPU-GPU Cluster Platforms.

Teodoro G, Pan T, Kurc TM, Kong J, Cooper LA, Podhorszki N, Klasky S, Saltz JH.

IPDPS. 2013 May;2013:103-114.

21.

A high-performance spatial database based approach for pathology imaging algorithm evaluation.

Wang F, Kong J, Gao J, Cooper LA, Kurc T, Zhou Z, Adler D, Vergara-Niedermayr C, Katigbak B, Brat DJ, Saltz JH.

J Pathol Inform. 2013 Mar 14;4:5. doi: 10.4103/2153-3539.108543. Print 2013.

22.

Future vision for the quality assurance of oncology clinical trials.

Fitzgerald TJ, Bishop-Jodoin M, Bosch WR, Curran WJ, Followill DS, Galvin JM, Hanusik R, King SR, Knopp MV, Laurie F, O'Meara E, Michalski JM, Saltz JH, Schnall MD, Schwartz L, Ulin K, Xiao Y, Urie M.

Front Oncol. 2013 Mar 15;3:31. doi: 10.3389/fonc.2013.00031. eCollection 2013.

23.

The Analytic Information Warehouse (AIW): a platform for analytics using electronic health record data.

Post AR, Kurc T, Cholleti S, Gao J, Lin X, Bornstein W, Cantrell D, Levine D, Hohmann S, Saltz JH.

J Biomed Inform. 2013 Jun;46(3):410-24. doi: 10.1016/j.jbi.2013.01.005. Epub 2013 Feb 9.

24.

Accelerating Pathology Image Data Cross-Comparison on CPU-GPU Hybrid Systems.

Wang K, Huai Y, Lee R, Wang F, Zhang X, Saltz JH.

Proceedings VLDB Endowment. 2012 Jul;5(11):1543-1554.

25.

Towards Building a High Performance Spatial Query System for Large Scale Medical Imaging Data.

Aji A, Wang F, Saltz JH.

Proc ACM SIGSPATIAL Int Conf Adv Inf. 2012 Nov 6;2012:309-318.

26.

Automated motif discovery from glycan array data.

Cholleti SR, Agravat S, Morris T, Saltz JH, Song X, Cummings RD, Smith DF.

OMICS. 2012 Oct;16(10):497-512. Epub 2012 Aug 9.

27.

Accelerating Large Scale Image Analyses on Parallel, CPU-GPU Equipped Systems.

Teodoro G, Kurc TM, Pan T, Cooper LA, Kong J, Widener P, Saltz JH.

IPDPS. 2012 May;2012:1093-1104.

28.
29.

The tumor microenvironment strongly impacts master transcriptional regulators and gene expression class of glioblastoma.

Cooper LA, Gutman DA, Chisolm C, Appin C, Kong J, Rong Y, Kurc T, Van Meir EG, Saltz JH, Moreno CS, Brat DJ.

Am J Pathol. 2012 May;180(5):2108-19. doi: 10.1016/j.ajpath.2012.01.040. Epub 2012 Mar 20.

30.

A proprotein convertase/MMP-14 proteolytic cascade releases a novel 40 kDa vasculostatin from tumor suppressor BAI1.

Cork SM, Kaur B, Devi NS, Cooper L, Saltz JH, Sandberg EM, Kaluz S, Van Meir EG.

Oncogene. 2012 Dec 13;31(50):5144-52. doi: 10.1038/onc.2012.1. Epub 2012 Feb 13.

31.

Integrated morphologic analysis for the identification and characterization of disease subtypes.

Cooper LA, Kong J, Gutman DA, Wang F, Gao J, Appin C, Cholleti S, Pan T, Sharma A, Scarpace L, Mikkelsen T, Kurc T, Moreno CS, Brat DJ, Saltz JH.

J Am Med Inform Assoc. 2012 Mar-Apr;19(2):317-23. doi: 10.1136/amiajnl-2011-000700. Epub 2012 Jan 24.

32.

MORPHOLOGICAL SIGNATURES AND GENOMIC CORRELATES IN GLIOBLASTOMA.

Cooper LA, Kong J, Wang F, Kurc T, Moreno CS, Brat DJ, Saltz JH.

Proc IEEE Int Symp Biomed Imaging. 2011 Mar 30:1624-1627.

33.

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.

34.

ImageMiner: a software system for comparative analysis of tissue microarrays using content-based image retrieval, high-performance computing, and grid technology.

Foran DJ, Yang L, Chen W, Hu J, Goodell LA, Reiss M, Wang F, Kurc T, Pan T, Sharma A, Saltz JH.

J Am Med Inform Assoc. 2011 Jul-Aug;18(4):403-15. doi: 10.1136/amiajnl-2011-000170. Epub 2011 May 23.

35.

The proneural molecular signature is enriched in oligodendrogliomas and predicts improved survival among diffuse gliomas.

Cooper LA, Gutman DA, Long Q, Johnson BA, Cholleti SR, Kurc T, Saltz JH, Brat DJ, Moreno CS.

PLoS One. 2010 Sep 3;5(9):e12548. doi: 10.1371/journal.pone.0012548.

36.

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.

37.

Computer-aided Prognosis of Neuroblastoma on Whole-slide Images: Classification of Stromal Development.

Sertel O, Kong J, Shimada H, Catalyurek UV, Saltz JH, Gurcan MN.

Pattern Recognit. 2009 Jun;42(6):1093-1103.

38.

A new model-based estimation of ellipses for object representation.

Kong J, Boyer KL, Saltz JH, Huang K.

Conf Proc IEEE Eng Med Biol Soc. 2009;2009:3637-40. doi: 10.1109/IEMBS.2009.5333149.

PMID:
19964084
39.

A caGRID-ENABLED, LEARNING BASED IMAGE SEGMENTATION METHOD FOR HISTOPATHOLOGY SPECIMENS.

Foran DJ, Yang L, Tuzel O, Chen W, Hu J, Kurc TM, Ferreira R, Saltz JH.

Proc IEEE Int Symp Biomed Imaging. 2009 Jul 1;6:1306-1309.

40.

An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules.

Qin H, Chan MW, Liyanarachchi S, Balch C, Potter D, Souriraj IJ, Cheng AS, Agosto-Perez FJ, Nikonova EV, Yan PS, Lin HJ, Nephew KP, Saltz JH, Showe LC, Huang TH, Davuluri RV.

BMC Syst Biol. 2009 Jul 17;3:73. doi: 10.1186/1752-0509-3-73.

41.

Computer-aided evaluation of neuroblastoma on whole-slide histology images: Classifying grade of neuroblastic differentiation.

Kong J, Sertel O, Shimada H, Boyer KL, Saltz JH, Gurcan MN.

Pattern Recognit. 2009 Jun;42(6):1080-1092. doi: 10.1016/j.patcog.2008.10.035.

42.

Leveraging an existing data warehouse to annotate workflow models for operations research and optimization.

Borlawsky T, LaFountain J, Petty L, Saltz JH, Payne PR.

AMIA Annu Symp Proc. 2008 Nov 6:885.

PMID:
18999220
43.

Integrating heterogeneous rules-engine technologies with caGrid.

Saltz JH, Oster S, Hastings SL, Langella S, Ervin D, Payne PR.

AMIA Annu Symp Proc. 2007 Oct 11:1099.

PMID:
18694196
44.

A framework for workflow-based clinical research billing disambiguation.

Payne PR, Borlawsky T, Kamal J, Saltz JH.

AMIA Annu Symp Proc. 2007 Oct 11:1071.

PMID:
18694169
45.

Computer-assisted grading of neuroblastic differentiation.

Kong J, Sertel O, Boyer KL, Saltz JH, Gurcan MN, Shimada H.

Arch Pathol Lab Med. 2008 Jun;132(6):903-4; author reply 904. doi: 10.1043/1543-2165(2008)132[903:CGOND]2.0.CO;2. No abstract available.

PMID:
18517267
46.

Large-scale biomedical image analysis in grid environments.

Kumar VS, Rutt B, Kurc T, Catalyurek UV, Pan TC, Chow S, Lamont S, Martone M, Saltz JH.

IEEE Trans Inf Technol Biomed. 2008 Mar;12(2):154-61. doi: 10.1109/TITB.2007.908466.

47.

An application of a service-oriented system to support array annotation in custom chip design for epigenomic analysis.

Han J, Potter D, Kurc T, Singer G, Yan PS, Hao S, Hastings S, Langella S, Oster S, Davuluri RV, Huang TH, Saltz JH.

Cancer Inform. 2008;6:111-25. Epub 2008 Apr 10.

48.

Informatics in radiology: GridCAD: grid-based computer-aided detection system.

Pan TC, Gurcan MN, Langella SA, Oster SW, Hastings SL, Sharma A, Rutt BG, Ervin DW, Kurc TM, Siddiqui KM, Saltz JH, Siegel EL.

Radiographics. 2007 May-Jun;27(3):889-97. Review.

PMID:
17495299
49.
50.

An XML-based system for synthesis of data from disparate databases.

Kurc T, Janies DA, Johnson AD, Langella S, Oster S, Hastings S, Habib F, Camerlengo T, Ervin D, Catalyurek UV, Saltz JH.

J Am Med Inform Assoc. 2006 May-Jun;13(3):289-301. Epub 2006 Feb 24.

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