Publications - Center for Biomedical Imaging & Informatics Skip to main content

Publications

2022

David J Foran, Eric B Durbin, Wenjin Chen, Evita Sadimin, Ashish Sharma, Imon Banerjee, Tahsin Kurc, Nan Li, Antoinette M Stroup, Gerald Harris, Annie Gu, Maria Schymura, Rajarsi Gupta, Erich Bremer, Joseph Balsamo, Tammy DiPrima, Feiqiao Wang, Shahira Abousamra, Dimitris Samaras, Isaac Hands, Kevin Ward, Joel H Saltz. An expandable informatics framework for enhancing central cancer registries with digital pathology specimens, computational imaging tools, and advanced mining capabilities. J Pathol Inform 2022;13:5, 1-11.  http://www.jpathinformatics.org/text.asp?2022/13/1/5/334787

2021

Zeeshan Ahmed, David J. Foran, XinQi Dong, Frederic Wondisford, Integrative Clinical, Genomics and Metabolomics Data Analysis for Mainstream Precision Medicine to Investigate COVID-19. BMJ: British Medical Journals/British Medical Association, Innovation. Accepted for publication.

Qi X, Brown L, Foran DJ, Nosher J, Hacihaliloglu I. Chest X-ray image phase features for improved diagnosis of COVID-19 using convolutional neural networks. International Journal of Computer Assisted Radiology and Surgery. 2021 January; :-. doi: 10.1007/s11548-020-02305-w.

2020

Panayides AS, Amini A, Filipovic ND, Sharma A, Tsaftaris SA, Young A, Foran D, Do N, Golemati S, Kurc T, Huang K, Nikita KS, Veasey BP, Zervakis M, Saltz JH, Pattichis CS. AI in Medical Imaging Informatics: Current Challenges and Future Directions. IEEE J Biomed Health Inform. 2020 Jul;24(7):1837-1857. doi: 10.1109/JBHI.2020.2991043. PMID: 32609615; PMCID: PMC8580417.

Adana A.M. Llanos, Song Yao, Amartya Singh, John B. Aremu, Hossein Khiabanian, Yong Lin, Coral Omene, Angela R. Omilian, Thaer Khoury, Chi‑Chen Hong, Shridar Ganesan, David J.Foran, Michael J. Higgins, Christine B. Ambrosone, Elisa V. Bandera1, Kitaw Demissie. Gene expression of adipokines and dipokine receptors in the tumor microenvironment: associations of lower expression with more aggressive breast tumor features. Breast Cancer Research and Treatment. https://doi.org/10.1007/s10549-020-05972-0

David J. Foran and Wenjin Chen. PathMiner: An Intelligent Platform for Diagnostic Pathology. European Medical and Biological Engineering Conference. Portoroz, Slovenia. Dec. 1, 2020. EMBEC 2020 Proceedings. In press.

Wong C, Tang LH, Davidson C, Vosburgh E, Chen W, Foran DJ, Notterman DA, Levine AJ, and Xu EY. Two well-differentiated pancreatic neuroendocrine tumor mouse models. Cell Death Differ. 2020;27(1):269-283. doi:10.1038/s41418-019-0355-0. DOI: 10.1038/s41418-019-0355-0

2019

Ren J, Hacihaliloglu I, Singer EA, Foran DJ, and Qi X. (2019) Unsupervised Domain Adaptation for Classification of Histopathology Whole-Slide Images. Frontiers in Bioengineering and Biotechnology. https://doi.org/10.3389/fbioe.2019.00102

Ren J, Singer EA, Sadimin E, Foran DJ, Qi X. Statistical Analysis of Survival Models Using Feature Quantification on Prostate Cancer Histopathological Images. J Pathol Inform. 2019;10:30. Published 2019 Sep 27. https://doi.org/10.4103/jpi.jpi_85_18 

Ren J, Li Z, Yang J, Xu N, Yang T, and Foran DJ. (2019) EIGEN: Ecologically-Inspired GENetic Approach for Neural Network Structure Searching from Scratch. CVPR. https://arxiv.org/abs/1806.01940

2018

Qi X, Karagoz Kubra, Ren J, Foran, DJ, Gatza M. (2018). Differentiation among prostate cancer patients with Gleason score of 7 using histopathology image and genomic data. 1. 10.1117/12.2293193.

Ren J, Karagoz K, Gatza ML, Singer E, Sadimin E, Foran D, Qi, X. (2018). Recurrence analysis on prostate cancer patients with Gleason score 7 using integrated histopathology whole-slide images and genomic data through deep neural networks. Journal of Medical Imaging. 5. 1. 10.1117/1.JMI.5.4.047501.

Ren J, Hacihaliloglu I, Singer EA, Foran DJ, Qi X. Adversarial Domain Adaptation for Classification of Prostate Histopathology Whole-Slide Images. Med Image Comput Comput Assist Interv. 2018 September ; 11071: 201–209. doi:10.1007/978-3-030-00934-2_23

Ren J, Sadimin E, Foran DJ, Qi X.Computer aided analysis of prostate histopathology images to support a refined Gleason grading system.  Proceedings Volume 10133, Medical Imaging 2017: Image Processing; 101331V (2017) https://doi.org/10.1117/12.2253887

Park K, Chen W, Chekmareva MA, Foran DJ, Desai JP. Electromechanical Coupling Factor of Breast Tissue as a Biomarker for Breast Cancer. IEEE Trans Biomed Eng. 2018 Jan;65(1):96-103. doi: 10.1109/TBME.2017.2695103. Epub 2017 Apr 19. http://ieeexplore.ieee.org/document/7904656/

Zaldana F, Qi X, Ren J, Chen W, Sadimin E, Plazonic K, Nemoyer R, Do N, Langenfeld J, Foran DJ, and Minerowicz C. Analysis of Lung Adenocarcinoma Based on Nuclear Features and WHO Subtype Classification using Deep Convolutional Neural Networks on Histopathology Images. American Association for Cancer Research Special Conference Convergence: Artificial Intelligence, Big Data, and Prediction in Cancer (October 14-17, 2018) Rhode Island, United States

2017

Chennubhotla C, Clarke LP, Fedorov A, Foran DJ, Harris G, Helton E, Nordstrom R, Prior F, Rubin D, Saltz JH, Shalley E, Sharma A. An Assessment of Imaging Informatics for Precision Medicine in Cancer. Yearb Med Inform. 2017 Aug;26(1):110-119. doi: 10.15265/IY-2017-041. Epub 2017 Sep 11. PMID: 29063549 https://pdfs.semanticscholar.org/4b89/06ed7e476ac039858041bf813fae1ef61941.pdf 

Karagoz, K., Ren, J., Foran, D.J., Gatza, M., Qi, X., Differentiation among prostate cancer patients with Gleason score of 7 using histopathology image and genomic data, SPIE Medical Imaging 2018, M107-24, 1-4 (Accepted)

Ren, J., Sadimin, E., Foran, D.J., Qi, X., Computer aided analysis of prostate histopathology images to support a refined Gleason grading system, SPIE Medical Imaging 2017, MI101, 1-4 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4917302/ 

Su, H., Shen, Y., Xing, F., Qi, X., Hirshfield, K.M., Yang, L., Foran, D.J., Robust automatic breast cancer staging using a combination of functional genomics and image-omics, Conf Proc. IEEE Eng Med Bio Soc, (EBMC) 2015, 7226-9 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918467/

Foran DJ, Chen W, Chu H, Sadimin E, Loh D, Riedlinger G, Goodell LA, Ganesan S, Hirshfield K, Rodriguez L, DiPaola RS. Roadmap to a Comprehensive Clinical Data Warehouse for Precision Medicine Applications in Oncology. Cancer Inform. 2017 Mar 2;16:1176935117694349. doi: 10.1177/1176935117694349. eCollection 2017. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5392017/

2016

Pandya HJ, Park K, Chen W, Goodell LA, Foran DJ, Desai JP. Toward a Portable Cancer Diagnostic Tool Using a Disposable MEMS-Based Biochip. IEEE Trans Biomed Eng. 2016 Jul;63(7):1347-53. doi: 10.1109/TBME.2016.2535364. PubMed PMID: 26930673; PubMed Central PMCID: PMC4917475. http://ieeexplore.ieee.org/document/7420666/?arnumber=7420666&tag=1 

Yildirim E, Foran D. Parallel vs. Distributed Data Access for Giga-pixel-resolution Histology Images: Challenges and Opportunities. IEEE J Biomed Health Inform. 2016 Jun 13. [Epub ahead of print] PubMed PMID: 27323383. http://ieeexplore.ieee.org/abstract/document/7490364/ 

Boregowda RK, Medina DJ, Markert E, Bryan MA, Chen W, Chen S, Rabkin A, Vido MJ, Gunderson SI, Chekmareva M, Foran DJ, Lasfar A, Goydos JS, Cohen-Solal KA. The transcription factor RUNX2 regulates receptor tyrosine kinase expression in melanoma. Oncotarget. 2016 May 17;7(20):29689-707. doi: 10.18632/oncotarget.8822. PubMed PMID: 27102439; PubMed Central PMCID: PMC5045426. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045426/

2015

Kurc, T., Qi, X., Wang, D., Wang, F., Teodoro, G., Cooper, L., Nalisnik, M., Yang, L., Saltz, J., Foran, D.J., Scalable analysis of big pathology image data cohorts using efficient methods and high-performance computing strategies, BMC Bioinformatics, BMC Bioinformatics201516:399 https://doi.org/10.1186/s12859-015-0831-6 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0831-6

Ren, J., Diaz-Montes, J., Saltz, J., Kurc, T., Parashar, M., Foran, J.D., Qi, X., Nuclei detection ensemble workflows across clustered infrastructure, High Performance Computing workshop associated with International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Munich, Germany 2015

Wang, D., Parashar, M., Foran, J.D., Qi, X., Enabling large-scale image analysis workflows on Federated high-performance resources, High Performance Computing workshop associated with International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Munich, Germany 2015

Wang, D., Foran, J.D., Ren, J., Zhong, H., Kim, I.Y., Qi, X., Exploring automatic prostate histopathology image Gleason grading via local structure modeling, Proceeding of 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society 2015 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920598/

Ren, J., Sadimin, E.T., Wang, D., Epstein, J.I., Foran, D.J., Qi, X., Computer aided analysis of prostate histopathology images Gleason grading especially for Gleason score 7, Proceeding of 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society 2015 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4917302/

Ren J, Sadimin ET, Wang D, Epstein JI, Foran DJ, Qi X. Computer aided analysis of prostate histopathology images Gleason grading especially for Gleason score 7. Conf Proc IEEE Eng Med Biol Soc. 2015;2015:3013-6. doi: 10.1109/EMBC.2015.7319026. PubMed PMID: 26736926; PubMed Central PMCID: PMC4917302. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4917302/

Su H, Shen Y, Xing F, Qi X, Hirshfield KM, Yang L, Foran DJ. Robust automatic breast cancer staging using a combination of functional genomics and image-omics. Conf Proc IEEE Eng Med Biol Soc. 2015;2015:7226-9. doi: 10.1109/EMBC.2015.7320059. PubMed PMID: 26737959; PubMed Central PMCID: PMC4918467. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918467/ 

Pandya HJ, Park K, Chen W, Chekmareva MA, Foran DJ, Desai JP. Simultaneous MEMS-based electro-mechanical phenotyping of breast cancer. Lab Chip. 2015;15(18):3695-706. doi: 10.1039/c5lc00491h. PubMed PMID: 26224116; PubMed Central PMCID: PMC4550491. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4550491/

2014

Chen W, Brandes Z, Roy R, Chekmareva M, Pandya HJ, Desai JP, Foran DJ. Robot-Guided Atomic Force Microscopy for Mechano-Visual Phenotyping of Cancer Specimens. Microsc Microanal. 2015 Oct;21(5):1224-35. doi: 10.1017/S1431927615015007. PubMed PMID: 26343283; PubMed Central PMCID: PMC4729564.

Pandya HJ, Roy R, Chen W, Chekmareva MA, Foran DJ, Desai JP. Accurate characterization of benign and cancerous breast tissues: Aspecific patient studies using piezoresistive microcantilevers. Biosensors & bioelectronics. 2015;63:414-24. Epub 2014/08/17. doi: 10.1016/j.bios.2014.08.002. PubMed PMID: 25128621.

Yang L, Qi X, Xing F, Kurc T, Saltz J, Foran DJ. Parallel content-based sub-image retrieval using hierarchical searching. Bioinformatics. 2014 Apr 1;30(7):996-1002. doi: 10.1093/bioinformatics/btt623. PubMed PMID: 24215030; PubMed Central PMCID: PMC3967099.

Chen W, Wong C, Vosburgh E, Levine AJ, Foran DJ, Xu EY. High-throughput image analysis of tumor spheroids: a user-friendly software application to measure the size of spheroids automatically and accurately. Journal of visualized experiments : JoVE. 2014(89). Epub 2014/07/22. doi: 10.3791/51639. PubMed PMID: 25046278.http://www.ncbi.nlm.nih.gov/pubmed/25046278

Qi X, Wang D, Rodero I, Diaz-Montes J, Gensure RH, Xing F, et al. Content-based histopathology image retrieval using CometCloud. BMC Bioinformatics. 2014;15(1):287. Epub 2014/08/27. doi: 10.1186/1471-2105-15-287. PubMed PMID: 25155691. http://www.ncbi.nlm.nih.gov/pubmed/25155691 

Wang D, Diaz-Granados M, Diaz-Montes J, Rodero I, Yang L, Parashar M, et al. High-throughput automatic Gleason-grading system for prostate histopathology images using CometCloud. The 7th International Workshop on High Performance Computing for Biomedical Image Analysis (HPC-MICCAI); September 14, 2014; Boston, MA2014. p. 21-30.

Yang L, Qi X, Xing F, Kurc T, Saltz J, Foran DJ. Parallel content-based sub-image retrieval using hierarchical searching. Bioinformatics. 2014;30(7):996-1002. Epub 2013/11/12. doi: 10.1093/bioinformatics/btt623. PubMed PMID: 24215030; PubMed Central PMCID: PMC3967099. http://www.ncbi.nlm.nih.gov/pubmed/24215030

Boregowda RK, Olabisi OO, Abushahba W, Jeong BS, Haenssen KK, Chen W, et al. RUNX2 is overexpressed in melanoma cells and mediates their migration and invasion. Cancer Lett. 2014;348(1-2):61-70. Epub 2014/03/25. doi: 10.1016/j.canlet.2014.03.011. PubMed PMID: 24657655; PubMed Central PMCID: PMC4041161.http://www.ncbi.nlm.nih.gov/pubmed/24657655

Pandya HJ, Chen W, Goodell L, Foran DJ, Jaydev D. Mechanical phenotyping of breast cancer using MEMS: A method to demarcate benign and cancerous breast tissue. Lab Chip. 2014 Dec 7; 14(23): 4523–4532.doi: 10.1039/c4lc00594e PMCID: PMC4224189 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224189/
Pandya HJ, Kim HT, Roy R, Chen W, Cong L, Zhong H, et al. Towards an Automated MEMS-based Characterization of Benign and Cancerous Breast Tissue using Bioimpedance Measurements. Sensors and actuators B, Chemical. 2014;199:259-68. Epub 2014/07/12. doi: 10.1016/j.snb.2014.03.065. PubMed PMID: 25013305; PubMed Central PMCID: PMC4084740. http://www.ncbi.nlm.nih.gov/pubmed/25013305 

Roy R, Chen W, Cong L, Goodell LA, Foran DJ, Desai JP. Probabilistic estimation of mechanical properties of biomaterials using atomic force microscopy. IEEE Trans Biomed Eng. 2014;61(2):547-56. Epub 2013/10/02. doi: 10.1109/TBME.2013.2283597. PubMed PMID: 24081838; PubMed Central PMCID: PMC3966978.http://www.ncbi.nlm.nih.gov/pubmed/24081838 

2013

Foran DJ, Chen W, Yang L. Automated image interpretation and computer-assisted diagnostics. Stud Health Technol Inform. 2013;185:77-108. Epub 2013/04/02. PubMed PMID: 23542932.http://www.ncbi.nlm.nih.gov/pubmed/23542932

Qi X, Gensure RH, Foran DJ, Yang L, editors. Content-based white blood cell retrieval on bright-field pathology images. SPIE Medical Imaging Symposium 2013: Digital Pathology, February 10, 2013 – February 11, 2013; 2013; Lake Buena Vista, FL, United states: SPIE. http://dx.doi.org/10.1117/12.2006439 

Roy R, Chen W, Cong L, Goodell LA, Foran DJ, Desai JP. A Semi-Automated Positioning System for contact-mode Atomic Force Microscopy (AFM). IEEE transactions on automation science and engineering : a publication of the IEEE Robotics and Automation Society. 2013;10(2). Epub 2013/12/03. doi: 10.1109/TASE.2012.2226154. PubMed PMID: 24294144; PubMed Central PMCID: PMC3840952. http://www.ncbi.nlm.nih.gov/pubmed/24294144 

2012

Miletti-González KE, Murphy K, Kumaran MN, Ravindranath AK, Wernyj RP, Kaur S, Miles GD, Lim E, Chan R, Chekmareva M, Heller DS, Foran D, Chen W, Reiss M, Bandera EV, Scotto K, Rodríguez-Rodríguez L. Identification of function for CD44 intracytoplasmic domain (CD44-ICD): modulation of matrix metalloproteinase 9 (MMP-9) transcription via novel promoter response element. J Biol Chem. 2012 Jun 1;287(23):18995-9007. doi: 10.1074/jbc.M111.318774. PubMed PMID: 22433859; PubMed Central PMCID: PMC3365933. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365933/

Sadimin ET, Foran DJ. Pathology Imaging Informatics for Clinical Practice and Investigative and Translational Research. N Am J Med Sci (Boston). 2012 Apr;5(2):103-109. PubMed PMID: 22855694; PubMed Central PMCID: PMC3407842. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3407842/

Qi X, Xing F, Foran DJ, Yang L. Robust segmentation of overlapping cells in histopathology specimens using parallel seed detection and repulsive level set. IEEE Trans Biomed Eng. 2012 Mar;59(3):754-65. doi: 10.1109/TBME.2011.2179298. PubMed PMID: 22167559; PubMed Central PMCID: PMC3655778. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3655778/

Sadimin ET, Foran DJ. Pathology Imaging Informatics for Clinical Practice and Investigative and Translational Research. North American journal of medicine & science. 2012;5(2):103-9. Epub 2012/08/03. PubMed PMID: 22855694; PubMed Central PMCID: PMC3407842. http://www.ncbi.nlm.nih.gov/pubmed/22855694

Xing F, Liu B, Qi X, Foran DJ, Yang L, editors. Digital tissue microarray classification using sparse reconstruction. Medical Imaging 2012: Image Processing, February 6, 2012 – February 9, 2012; 2012; San Diego, CA, United states: SPIE. http://dx.doi.org/10.1117/12.911900

Cukierski WJ, Nandy K, Gudla P, Meaburn KJ, Misteli T, Foran DJ, et al. Ranked retrieval of segmented nuclei for objective assessment of cancer gene repositioning. BMC Bioinformatics. 2012;13:232. Epub 2012/09/14. doi: 10.1186/1471-2105-13-232. PubMed PMID: 22971117; PubMed Central PMCID: PMC3484015. http://www.ncbi.nlm.nih.gov/pubmed/22971117 

Gensure RH, Foran DJ, Lee VM, Gendel VM, Jabbour SK, Carpizo DR, et al. Evaluation of hepatic tumor response to yttrium-90 radioembolization therapy using texture signatures generated from contrast-enhanced CT images. Acad Radiol. 2012;19(10):1201-7. Epub 2012/07/31. doi: 10.1016/j.acra.2012.04.015. PubMed PMID: 22841288; PubMed Central PMCID: PMC3438382. http://www.ncbi.nlm.nih.gov/pubmed/22841288

Qi X, Kim H, Xing F, Parashar M, Foran DJ, Yang L. The analysis of image feature robustness using cometcloud. J Pathol Inform. 2012;3:33. Epub 2012/12/19. doi: 10.4103/2153-3539.101782. PubMed PMID: 23248759; PubMed Central PMCID: PMC3519094. http://www.ncbi.nlm.nih.gov/pubmed/23248759

Qi X, Xing F, Foran DJ, Yang L. A fast, automatic segmentation algorithm for locating and delineating touching cell boundaries in imaged histopathology. Methods Inf Med. 2012;51(3):260-7. Epub 2012/04/25. doi: 10.3414/ME11-02-0015. PubMed PMID: 22526139; PubMed Central PMCID: PMC3650677. http://www.ncbi.nlm.nih.gov/pubmed/22526139

Qi X, Xing F, Foran DJ, Yang L. Robust segmentation of overlapping cells in histopathology specimens using parallel seed detection and repulsive level set. IEEE Trans Biomed Eng. 2012;59(3):754-65. Epub 2011/12/15. doi: 10.1109/TBME.2011.2179298. PubMed PMID: 22167559; PubMed Central PMCID: PMC3655778.http://www.ncbi.nlm.nih.gov/pubmed/22167559 

2011

Foran DJ, Yang L, Chen W, Hu J, Goodell LA, Reiss M, Wang F, Kurc T, Pan T, Sharma A, Saltz JH. ImageMiner: a software system for comparative analysis of tissue microarrays using content-based image retrieval, high-performance computing, and grid technology. J Am Med Inform Assoc. 2011 Jul-Aug;18(4):403-15. doi: 10.1136/amiajnl-2011-000170. PubMed PMID: 21606133; PubMed Central PMCID: PMC3128405. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3128405/ 

Foran DJ, Chen W, Yang L. Automated image interpretation computer-assisted diagnostics. Anal Cell Pathol (Amst). 2011;34(6):279-300. Epub 2011/11/16. doi: 10.3233/ACP-2011-0046. PubMed PMID: 22082571; PubMed Central PMCID: PMC3685404. http://www.ncbi.nlm.nih.gov/pubmed/22082571 

Foran DJ, Yang L, Chen WJ, Hu J, Goodell LA, Reiss M, et al. ImageMiner: a software system for comparative analysis of tissue microarrays using content-based image retrieval, high-performance computing, and grid technology. Journal of the American Medical Informatics Association. 2011;18(4):403-15. doi: DOI 10.1136/amiajnl-2011-000170. PubMed PMID: ISI:000292061700011.

Qi X, Xing F, Foran DJ, Yang L, editors. Comparative performance analysis of stained histopathology specimens using RGB and multispectral imaging. Medical Imaging 2011: Computer-Aided Diagnosis, February 15, 2011 – February 17, 2011; 2011; Lake Buena Vista, FL, United states: SPIE. http://dx.doi.org/10.1117/12.878325

Sadimin E, Chen W, Osband A, Reitsma W, Laskow D, Joseph J, et al. Telemicroscopy for the Evaluation of Donor Kidney Biopsies. United States and Canadian Academy of Pathology Annual Meeting: Modern Pathology; 2011. p. 350A.

Wang F, Kong J, Cooper L, Pan T, Kurc T, Chen W, et al. A data model and database for high-resolution pathology analytical image informatics. J Pathol Inform. 2011;2:32. Epub 2011/08/17. doi: 10.4103/2153-3539.83192. PubMed PMID: 21845230; PubMed Central PMCID: PMC3153692. http://www.ncbi.nlm.nih.gov/pubmed/21845230

Cohen-Solal K, Merrigan K, Chan J, Goydos J, Chen W, Foran D, et al. Constitutive Smad linker phosphorylation in melanoma: A mechanism of resistance to Transforming Growth Factor-β-mediated growth inhibition. Pigment Cell Melanoma Res. 2011 Jun; 24(3): 512–524. Published online 2011 Apr 28. doi: 10.1111/j.1755-148X.2011.00858.x PMCID: PMC3108265 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3108265/

Roy R, Chen W, Cong L, Goodell LA, Foran DJ, Desai JP. Towards automated mechanical characterization of biological samples using atomic force microscopy (AFM). 2011 SAME Dynamic Systems and Control Conference; October, 30; Washington, DC2011. http://proceedings.asmedigitalcollection.asme.org/proceeding.aspx?articleid=1638

Yang L, Kim H, Parashar M, Foran DJ. High Throughput Landmark Based Image Registration Using Cloud Computing. Workshop on High Performance and Distributed Computing for Medical Imaging. Proceedings of the 14th International Conference on Medical Image Computing for Image-Assisted Clinical Intervention and Decision-Making. Toronto, Canada, 2011.

2010

Qi X, Cukierski W, Foran DJ, editors. A comparative performance study characterizing breast tissue microarrays using standard RGB and multispectral imaging. Multimodal Biomedical Imaging V, January 23, 2010 – January 25, 2010; 2010; San Francisco, CA, United states: SPIE. http://dx.doi.org/10.1117/12.842067

Qi X, Xing F, Foran DJ, Yang L, editors. GPU Enabled Parallel Touching Cell Segmentation Using Mean Shift Based Seed Detection and Repulsive Level Set. High Performance Computing (HP) workshop associated with Proc International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI); 2010.

Roy R, Chen W, Goodell LA, Hu J, Foran DJ, Desai JP, editors. Microarray-facilitated mechanical characterization of breast tissue pathology samples using contact-mode Atomic Force Microscopy (AFM). Biomedical Robotics and Biomechatronics (BioRob), 2010 3rd IEEE RAS and EMBS International Conference on; 2010: IEEE.

Roy R, Chen W, Hu J, Goodell LA, Foran DJ, Desai JP. Tissue Microarray Facilitated Mechanical Characterization of Cancerous Breast Tissue using Atomic Force Microscopy. Archives in Pathology & Laboratory Medicine. 2010;134:939.

Cukierski WJ, Foran DJ. Metamerism in Multispectral Imaging of Histopathology Specimens. Proc IEEE Int Symp Biomed Imaging. 2010;2010:145-8. Epub 2010/12/15. doi: 10.1109/ISBI.2010.5490392. PubMed PMID: 21151845; PubMed Central PMCID: PMC2998912. http://www.ncbi.nlm.nih.gov/pubmed/21151845 

Goodell L, Chen W, Javidian P, Chekmareva M, Hu J, Foran DJ. Use of Computer Assisted Analysis to Facilitate Tissue Microarray Interpretation. United States and Canadian Academy of Pathology 2010 Annual Meeting; March 20-26, 2010; Washington, D.C.2010.

Liu B, Yang L, Kulikowski C, Zhou J, Gong L, Foran DJ, et al. An Adaptive Tracking Algorithm of Lung Tumors in Fluoroscopy Using Online Learned Collaborative Trackers. Proc IEEE Int Symp Biomed Imaging. 2010;2010:209-12. Epub 2010/07/14. doi: 10.1109/ISBI.2010.5490376. PubMed PMID: 20622932; PubMed Central PMCID: PMC2900817.http://www.ncbi.nlm.nih.gov/pubmed/20622932

Liu B, Yang L, Kulikowski C, Zhou J, Gong L, Foran DJ, et al., editors. An adaptive tracking algorithm of lung tumors in fluoroscopy using online learned collaborative trackers. 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010, April 14, 2010 – April 17, 2010; 2010; Rotterdam, Netherlands: IEEE Computer Society.http://dx.doi.org/10.1109/ISBI.2010.5490376 

Widener P, Chen W, Wang F, Yang L, Hu J, Chu V, Saltz JH, Foran DJ, Kurc T. Grid-Enabled, High-performance Microscopy Image Analysis. The 2nd International Workshop on High-Performance Medical Image Computing for Image-Assisted Clinical Intervention and Decision-Making. Bejing, China. Invited Paper. Pages 70-79, 2010.

2009

Chen W, Chu V, Hu J, Yang L, Wang F, Kurc T, et al. ImageMiner: a medical image analysis and image management UML data model. APIII: Advancing Practice, Instruction & Innovation Through Informatics; September; Pittsburgh, PA2009.

Cukierski WJ, Qi X, Foran DJ. Moving Beyond Color: The Case for Multispectral Imaging in Brightfield Pathology. Proc IEEE Int Symp Biomed Imaging. 2009;5193251:1111-4. Epub 2009/12/10. doi: 10.1109/ISBI.2009.5193251. PubMed PMID: 19997528; PubMed Central PMCID: PMC2789468. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citati…

Foran DJ, Yang L, Tuzel O, Chen W, Hu J, Kurc TM, et al. A caGRID-ENABLED, LEARNING BASED IMAGE SEGMENTATION METHOD FOR HISTOPATHOLOGY SPECIMENS. Proc IEEE Int Symp Biomed Imaging. 2009;6:1306-9. Epub 2009/11/26. doi: 10.1109/ISBI.2009.5193304. PubMed PMID: 19936299; PubMed Central PMCID: PMC2779045.http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citati… 

Kim H, Parashar M, Foran DJ, Yang L. Investigating the Use of Cloudbursts for High-Throughput Medical Image Registration. Proceedings of the IEEE/ACM International Conference on Grid Computing IEEE/ACM International Conference on Grid Computing. 2009;2009:34-41. Epub 2010/07/20. doi: 10.1109/GRID.2009.5353065. PubMed PMID: 20640235; PubMed Central PMCID: PMC2904524. http://www.ncbi.nlm.nih.gov/pubmed/20640235 

Lin Y, Wenjin C, Meer P, Salaru G, Goodell LA, Berstis V, et al. Virtual microscopy and grid-enabled decision support for large-scale analysis of imaged pathology specimens. Ieee Transactions on Information Technology in Biomedicine. 2009;13(4):636-44. doi: 10.1109/titb.2009.2020159. http://dx.doi.org/10.1109/TITB.2009.2020159

Niculescu G, Nosher JL, Schneider MD, Foran DJ. A deformable model for tracking tumors across consecutive imaging studies. Int J Comput Assist Radiol Surg. 2009;4(4):337-47. Epub 2009/09/24. doi: 10.1007/s11548-009-0298-x. PubMed PMID: 19774096; PubMed Central PMCID: PMC2747734. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citati…
Yang L, Gong L, Zhang H, Nosher JL, Foran DJ. A multicore based parallel image registration method. Conf Proc IEEE Eng Med Biol Soc. 2009;2009:98-101. Epub 2009/12/08. doi: 10.1109/IEMBS.2009.5334782. PubMed PMID: 19964921; PubMed Central PMCID: PMC3360576. http://www.ncbi.nlm.nih.gov/pubmed/19964921 

Yang L, Gong L, Zhang H, Nosher JL, Foran DJ. A Parallel Point Matching Algorithm for Landmark Based Image Registration Using Multicore Platform. EURO-PAR ‘ : International EURO-PAR Conference : proceedings International EURO-PAR Conference. 2009;5704. Epub 2009/12/01. doi: 10.1007/978-3-642-03869-3_86. PubMed PMID: 24308014; PubMed Central PMCID: PMC3845531. http://www.ncbi.nlm.nih.gov/pubmed/24308014 

Yang L, Tuzel O, Chen W, Meer P, Salaru G, Goodell LA, et al. PathMiner: a Web-based tool for computer-assisted diagnostics in pathology. IEEE Trans Inf Technol Biomed. 2009;13(3):291-9. Epub 2009/01/28. doi: 10.1109/TITB.2008.2008801. PubMed PMID: 19171530; PubMed Central PMCID: PMC3683402. http://www.ncbi.nlm.nih.gov/pubmed/19171530 

Zhang H, Yang L, Foran DJ, Nosher JL, Yim PJ. 3d Segmentation of the Liver Using Free-Form Deformation Based on Boosting and Deformation Gradients. Proc IEEE Int Symp Biomed Imaging. 2009;5193092:494-7. Epub 2009/12/10. doi: 10.1109/ISBI.2009.5193092. PubMed PMID: 19997530; PubMed Central PMCID: PMC2789470.http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citati… 

Kim H, Parashar M, Foran DJ, Yang L, editors. Investigating the use of autonomic cloudbursts for high-throughput medical image registration. Grid Computing, 2009 10th IEEE/ACM International Conference on; 2009: IEEE. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2904524/ 
Yang L, Gong L, Zhang H, Nosher JL and Foran DJ. Landmark-Based Co-Registration of Consecutive Imaging Studies using High Performance Parallel Computing. European Conference on Parallel Computing. Vol. 1: 936–947, 2009.

2008

Yang L, Tuzel O, Meer P, Foran DJ. Automatic image analysis of histopathology specimens using concave vertex graph. Med Image Comput Comput Assist Interv. 2008;11(Pt 1):833-41. Epub 2008/11/05. PubMed PMID: 18979823; PubMed Central PMCID: PMC3683135. http://www.ncbi.nlm.nih.gov/pubmed/18979823

Cukierski WJ, Foran DJ, editors. Using betweenness centrality to identify manifold shortcuts. IEEE International Conference on Data Mining Workshops, ICDM Workshops 2008, December 15, 2008 – December 19, 2008; 2008; Pisa, Italy: Inst. of Elec. and Elec. Eng. Computer Society. http://dx.doi.org/10.1109/ICDMW.2008.39

DiPaola RS, Dvorzhinski D, Thalasila A, Garikapaty V, Doram D, May M, et al. Therapeutic starvation and autophagy in prostate cancer: a new paradigm for targeting metabolism in cancer therapy. Prostate. 2008;68(16):1743-52. Epub 2008/09/04. doi: 10.1002/pros.20837. PubMed PMID: 18767033. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citati…

Hall BH, Ianosi-Irimie M, Javidian P, Chen W, Ganesan S, Foran DJ. Computer-assisted assessment of the human epidermal growth factor receptor 2 immunohistochemical assay in imaged histologic sections using a membrane isolation algorithm and quantitative analysis of positive controls. BMC Med Imaging. 2008;8:11. Epub 2008/06/07. doi: 10.1186/1471-2342-8-11. PubMed PMID: 18534031; PubMed Central PMCID: PMC2447833. http://www.ncbi.nlm.nih.gov/pubmed/18534031

Yang L, Georgescu B, Zheng Y, Foran DJ, Comaniciu D. A Fast and Accurate Tracking Algorithm of Left Ventricles in 3d Echocardiography. Proc IEEE Int Symp Biomed Imaging. 2008;5:221-4. Epub 2008/05/14. doi: 10.1109/ISBI.2008.4540972. PubMed PMID: 19936301; PubMed Central PMCID: PMC2779051. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citati… 

2007

Yang L, Meer P, Foran DJ. Multiple Class Segmentation Using A Unified Framework over Mean-Shift Patches. Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2007 Jul 16;2007(4270254):1-8. PubMed PMID: 19295664; PubMed Central PMCID: PMC2654774. http://ieeexplore.ieee.org/document/4270254/?arnumber=4270254 

Chen W, Foran DJ. A Computer-Assisted Microscopy System for Automated Image Analysis of Pathology Specimens and Tissue Microarrays. In: Einstein) EH-SWaAJ, editor. Image Analysis in Medical Microscopy and Pathology. New York, NY: Research Signpost; 2007. http://www.ressign.com/UserBookDetail.aspx?bkid=535&catid=150#

Hall B, Chen W, Reiss M, Foran DJ. A clinically motivated 2-fold framework for quantifying and classifying immunohistochemically stained specimens. Med Image Comput Comput Assist Interv. 2007;10(Pt 2):287-94. Epub 2007/11/30. PubMed PMID: 18044580. http://www.ncbi.nlm.nih.gov/pubmed/18044580

Niculescu G, Foran DJ, Nosher J. Non-rigid registration of the liver in consecutive CT studies for assessment of tumor response to radiofrequency ablation. Conf Proc IEEE Eng Med Biol Soc. 2007;2007:856-9. Epub 2007/11/16. doi: 10.1109/IEMBS.2007.4352425. PubMed PMID: 18002091. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citati… 

Tuzel O, Yang L, Meer P, Foran DJ. Classification of hematologic malignancies using texton signatures. Pattern Anal Appl. 2007;10(4):277-90. Epub 2007/10/01. doi: 10.1007/s10044-007-0066-x. PubMed PMID: 19890460; PubMed Central PMCID: PMC2772183. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citati… 

Yang L, Chen W, Meer P, Salaru G, Feldman MD, Foran DJ. High throughput analysis of breast cancer specimens on the grid. Med Image Comput Comput Assist Interv. 2007;10(Pt 1):617-25. Epub 2007/12/07. PubMed PMID: 18051110; PubMed Central PMCID: PMC3366434. http://www.ncbi.nlm.nih.gov/pubmed/18051110

Yang L, Meer P, Foran DJ. Multiple Class Segmentation Using A Unified Framework over Mean-Shift Patches. Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2007;2007(4270254):1-8. Epub 2007/07/16. doi: 10.1109/CVPR.2007.383229. PubMed PMID: 19295664; PubMed Central PMCID: PMC2654774.http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citati…

Yang L, Chen W, Meer P, Salaru G, Feldman MD, Foran DJ. High throughput analysis of breast cancer specimens on the grid. Med Image Comput Comput Assist Interv. 2007;10(Pt 1):617-25. PubMed PMID: 18051110; PubMed Central PMCID: PMC3366434. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3366434/

2006

Chen W, Foran DJ. Advances in cancer tissue microarray technology: Towards improved understanding and diagnostics. Anal Chim Acta. 2006;564(1):74-81. Epub 2007/08/29. doi: S0003-2670(05)01978-1 [pii] 10.1016/j.aca.2005.11.083. PubMed PMID: 17723364; PubMed Central PMCID: PMC2583100. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citati… 

Chen W, Schmidt C, Parashar M, Reiss M, Foran DJ. Decentralized data sharing of tissue microarrays for investigative research in oncology. Cancer Inform. 2006;2:373-88. Epub 2007/06/06. PubMed PMID: 19081778; PubMed Central PMCID: PMC2600512. http://www.ncbi.nlm.nih.gov/pubmed/19081778

Yang L, Foran DJ. A Variational Framework for Partially Occluded Image Segmentation Using Coarse to Fine Shape Alignment and Semi-Parametric Density Approximation. Proc Int Conf Image Proc. 2006;1(4378885):137-40. Epub 2006/01/01. doi: 10.1109/ICIP.2007.4378885. PubMed PMID: 19305512; PubMed Central PMCID: PMC2657958.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657958/

2005

Yang L, Meer P, Foran DJ. Unsupervised segmentation based on robust estimation and color active contour models. IEEE Transactions on Information Technology in Biomedicine. 2005 Sep;9(3):475-86. http://ieeexplore.ieee.org/document/1504818/?arnumber=1504818

Chen W, Meer P, Georgescu B, He W, Goodell LA, Foran DJ. Image mining for investigative pathology using optimized feature extraction and data fusion. Comput Methods Programs Biomed. 2005;79(1):59-72. Epub 2005/05/24. doi: S0169-2607(05)00080-5 [pii] 10.1016/j.cmpb.2005.03.006. PubMed PMID: 15908036. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citati…

Yang L, Meer P, Foran DJ. Unsupervised segmentation based on robust estimation and color active contour models. IEEE Trans Inf Technol Biomed. 2005;9(3):475-86. Epub 2005/09/20. PubMed PMID: 16167702. http://www.ncbi.nlm.nih.gov/pubmed/16167702

2004

Chen W, Reiss M, Foran DJ. A prototype for unsupervised analysis of tissue microarrays for cancer research and diagnostics. IEEE Trans Inf Technol Biomed. 2004;8(2):89-96. Epub 2004/06/26. PubMed PMID: 15217253. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citati…

2003

Foran DJ, Nosher JL, Siegel R, Schmidling M, Raskova J. Dynamic quiz bank: a portable tool set for authoring and managing distributed, Web-based educational programs in radiology. Acad Radiol. 2003;10(1):52-7. Epub 2003/01/17. PubMed PMID: 12529029. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citati… 

Lin W, Wilder J, Grossman S, Foran DJ. A network-reactive model for distributed telemicroscopy. J Telemed Telecare. 2003;9(2):78-83. Epub 2003/04/18. doi: 10.1258/135763303321327920. PubMed PMID: 12699576. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citati… 

Silver FH, Snowhill PB, Foran DJ. Mechanical behavior of vessel wall: a comparative study of aorta, vena cava, and carotid artery. Ann Biomed Eng. 2003;31(7):793-803. Epub 2003/09/16. PubMed PMID: 12971612. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citati…

2002

Chen W, Foran DJ, Reiss M. Unsupervised imaging, registration and archiving of tissue microarrays. Proc AMIA Symp. 2002:136-9. Epub 2002/12/05. doi: D020002272 [pii]. PubMed PMID: 12463802; PubMed Central PMCID: PMC2244557. http://www.ncbi.nlm.nih.gov/pubmed/12463802

Silver FH, Horvath I, Foran DJ. Mechanical implications of the domain structure of fiber-forming collagens: comparison of the molecular and fibrillar flexibilities of the alpha1-chains found in types I-III collagen. J Theor Biol. 2002;216(2):243-54. Epub 2002/06/25. doi: 10.1006/jtbi.2002.2542 S0022519302925427 [pii]. PubMed PMID: 12079374.http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citati… 

2001

Silver FH, Horvath I, Foran DJ. Viscoelasticity of the vessel wall: the role of collagen and elastic fibers. Crit Rev Biomed Eng. 2001;29(3):279-301. Epub 2001/12/04. PubMed PMID: 11730097. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citati…

2000

Foran DJ, Comaniciu D, Meer P, Goodell LA. Computer-assisted discrimination among malignant lymphomas and leukemia using immunophenotyping, intelligent image repositories, and telemicroscopy. IEEE Trans Inf Technol Biomed. 2000;4(4):265-73. Epub 2001/02/24. PubMed PMID: 11206811. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citati…

1999

Comaniciu D, Meer P, Foran DJ. Image-guided decision support system for pathology. Machine Vision and Applications. 1999;11(4):213-24. doi: 10.1007/s001380050104.https://link.springer.com/article/10.1007%2Fs001380050104?LI=true 

1998

Comaniciu D, Foran D, Meer P, editors. Shape-based image indexing and retrieval for diagnostic pathology. 14th International Conference on Pattern Recognition, ICPR 1998, August 16, 1998 – August 20, 1998; 1998; Brisbane, QLD, Australia: Institute of Electrical and Electronics Engineers Inc. DOI: 10.1109/ICPR.1998.711297 http://ieeexplore.ieee.org/document/711297/

Comaniciu D, Meer P, Foran D, Medl A. Bimodal system for interactive indexing and retrieval of pathology images.  Proceedings Fourth IEEE workshop on Applications of Computer Vision WACV’98; Oct, 1998; Princeton, NJ, USA1998. p. 76-81. DOI: 10.1109/ACV.1998.732861 http://ieeexplore.ieee.org/document/732861/

1997

Foran DJ, Meer PP, Papathomas T, Marsic I. Compression guidelines for diagnostic telepathology. IEEE Trans Inf Technol Biomed. 1997;1(1):55-60. Epub 1997/03/01. PubMed PMID: 11020810.DOI: 10.1109/4233.594046 http://ieeexplore.ieee.org/document/594046/ 

1996

Foran DJ, Winkelmann DA, Goodell LA, Trelstad RL. A network-based prototype for interactive telemedicine & automated management of distributed, clinical databases. J Clin Eng. 1996;21(5):383-91. Epub 1996/09/01. PubMed PMID: 10161804. https://www.ncbi.nlm.nih.gov/pubmed/10161804

Trelstad RL, Amenta PS, Foran DJ, Smilow PC. The role for regional autopsy centers in the evaluation of covered deaths. Survey of opinions of US and Canadian chairs of pathology and major health insurers in the United States. Arch Pathol Lab Med. 1996;120(8):753-8. Epub 1996/08/01. PubMed PMID: 8718901. https://www.ncbi.nlm.nih.gov/pubmed/8718901

1994

Foran DJ, Berg RA. A method for quantitative image assessment based on redundant feature measurements and statistical reasoning. Comput Methods Programs Biomed. 1994;45(4):291-305. Epub 1994/12/01. doi: 0169-2607(94)01590-C [pii] 10.1016/0169-2607(94)01590-C. PubMed PMID: 7736731. http://www.sciencedirect.com/science/article/pii/016926079401590C

1991

Foran DJ, Cahn F, Eikenberry EF. Assessment of cell proliferation on porous microcarriers by means of image analysis. Anal Quant Cytol Histol. 1991;13(3):215-22. Epub 1991/06/01. PubMed PMID: 1910423. http://europepmc.org/abstract/med/1910423