The Tisch Cancer Institute

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  • 2025

    Automated Hepatocellular Carcinoma Detection and Segmentation in Abbreviated MRI using Vision Transformers

    Yadav, V., Geahchan, A., Fauveau, V., Yasokawa, K., Taouli, B. & Greenspan, H., 2025, Medical Imaging 2025: Computer-Aided Diagnosis. Astley, S. M. & Wismuller, A. (eds.). SPIE, 134071T. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 13407).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • 2023

    Machine Learning Based Prediction of Incident Cases of Crohn’s Disease Using Electronic Health Records from a Large Integrated Health System

    Hugo, J., Ibing, S., Borchert, F., Sachs, J. P., Cho, J., Ungaro, R. C. & Böttinger, E. P., 2023, Artificial Intelligence in Medicine - 21st International Conference on Artificial Intelligence in Medicine, AIME 2023, Proceedings. Juarez, J. M., Marcos, M., Stiglic, G. & Tucker, A. (eds.). Springer Science and Business Media Deutschland GmbH, p. 293-302 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 13897 LNAI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    1 Scopus citations
  • 2022

    Machine Learning Approaches for Early Prostate Cancer Prediction Based on Healthcare Utilization Patterns

    Finkelstein, J., Cui, W., Martin, T. C. & Parsons, R., 2022, Informatics and Technology in Clinical Care and Public Health. Mantas, J., Hasman, A., Househ, M. S., Gallos, P., Zoulias, E. & Liasko, J. (eds.). IOS Press BV, p. 65-68 4 p. (Studies in Health Technology and Informatics; vol. 289).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    Open Access
    1 Scopus citations

  • Usability Inspection of a Mobile Cancer Telerehabilitation System

    Finkelstein, J., Huo, X., Parvanova, I. & Galsky, M., 2022, Informatics and Technology in Clinical Care and Public Health. Mantas, J., Hasman, A., Househ, M. S., Gallos, P., Zoulias, E. & Liasko, J. (eds.). IOS Press BV, p. 405-409 5 p. (Studies in Health Technology and Informatics; vol. 289).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    Open Access
    5 Scopus citations
  • 2021

    Cognitive Testing of an Electronic Consent Platform: Researcher Perspectives

    Robins, D., Brody, R., Parvanova, I. & Finkelstein, J., 15 Dec 2021, Nurses and Midwives in the Digital Age - Selected Papers, Posters and Panels from the 15th International Congress in Nursing Informatics. Honey, M., Ronquillo, C., Lee, T.-T. & Westbrooke, L. (eds.). IOS Press BV, p. 457-462 6 p. (Studies in Health Technology and Informatics; vol. 284).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    Open Access
    2 Scopus citations

  • CureQuest: A digital game for new drug discovery

    Chang, B., Gabrilove, J., Lawson, S., Ruiz, K. & Si, M., 17 May 2021, Proceedings of 2021 7th International Conference of the Immersive Learning Research Network, iLRN 2021. Economou, D., Pena-Rios, A., Dengel, A., Dodds, H., Mentzelopoulos, M., Klippel, A., Erenli, K., Lee, M. J. W. & Richter, J. (eds.). Institute of Electrical and Electronics Engineers Inc., 9459314. (Proceedings of 2021 7th International Conference of the Immersive Learning Research Network, iLRN 2021).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Radiomic texture analysis for the assessment of osteoporosis on low-dose thoracic CT scans

    Fuhrman, J. D., Kremer, L., Zhu, Y., Yip, R., Li, F., Lan, L., Li, H., Jirapatnakul, A., Henschke, C. I., Yankelevitz, D. F. & Giger, M. L., 2021, Medical Imaging 2021: Computer-Aided Diagnosis. Mazurowski, M. A. & Drukker, K. (eds.). SPIE, 1159730. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 11597).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • 2020

    Cascade of U-Nets in the detection and classification of coronary artery calcium in thoracic low-dose CT

    Fuhrman, J. D., Yip, R., Jirapatnakul, A. C., Henschke, C. I., Yankelevitz, D. F. & Giger, M. L., 2020, Medical Imaging 2020: Computer-Aided Diagnosis. Hahn, H. K. & Mazurowski, M. A. (eds.). SPIE, 113140A. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 11314).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    1 Scopus citations

  • Effect of observer variability and training cases on U-Net segmentation performance

    Fuhrman, J. D., Halloran, P., Yip, R., Jirapatnakul, A. C., Henschke, C. I., Yankelevitz, D. F. & Giger, M. L., 2020, Medical Imaging 2020: Image Perception, Observer Performance, and Technology Assessment. Samuelson, F. W. & Taylor-Phillips, S. (eds.). SPIE, 113160T. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 11316).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    1 Scopus citations

  • Towards a highly usable, mobile electronic platform for patient recruitment and consent management

    Robins, D., Brody, R., Jeong, I. C., Parvanova, I., Liu, J. & Finkelstein, J., 16 Jun 2020, Digital Personalized Health and Medicine - Proceedings of MIE 2020. Pape-Haugaard, L. B., Lovis, C., Madsen, I. C., Weber, P., Nielsen, P. H. & Scott, P. (eds.). IOS Press, p. 1066-1070 5 p. (Studies in Health Technology and Informatics; vol. 270).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    8 Scopus citations

  • Towards intelligent integration and sharing of stem cell research data

    Borziak, K., Qi, T., Evangelista, J. E., Clarke, D. J. B., Ma'Ayan, A. & Finkelstein, J., 2020, THE IMPORTANCE OF HEALTH INFORMATICS IN PUBLIC HEALTH DURING A PANDEMIC. Mantas, J., Hasman, A., Househ, M. S., Gallos, P. & Zoulias, E. (eds.). IOS Press, p. 334-337 4 p. (Studies in Health Technology and Informatics; vol. 272).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    5 Scopus citations
  • 2019

    Detection and classification of coronary artery calcifications in low dose thoracic CT using deep learning

    Fuhrman, J. D., Crosby, J., Yip, R., Henschke, C. I., Yankelevitz, D. F. & Giger, M. L., 2019, Medical Imaging 2019: Computer-Aided Diagnosis. Mori, K. & Hahn, H. K. (eds.). SPIE, 1095039. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10950).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    3 Scopus citations
  • 2018

    3D bio-printed model of brain tumor microenvironment with vasculatures

    Lee, V. K., Zou, H., Friedel, R. & Dai, G., 2018, Food, Pharmaceutical and Bioengineering Division 2018 - Core Programming Area at the 2018 AIChE Annual Meeting. AIChE, p. 977-979 3 p. (Food, Pharmaceutical and Bioengineering Division 2018 - Core Programming Area at the 2018 AIChE Annual Meeting; vol. 2).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Fully automated bone mineral density assessment from low-dose chest CT

    Liu, S., Gonzalez, J., Zulueta, J., De-Torres, J. P., Yankelevitz, D. F., Henschke, C. I. & Reeves, A. P., 2018, Medical Imaging 2018: Computer-Aided Diagnosis. Mori, K. & Petrick, N. (eds.). SPIE, 105750M. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10575).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    3 Scopus citations

  • Fully automated gynecomastia quantification from low-dose chest CT

    Liu, S., Sonnenblick, E. B., Azour, L., Yankelevitz, D. F., Henschke, C. I. & Reeves, A. P., 2018, Medical Imaging 2018: Computer-Aided Diagnosis. Mori, K. & Petrick, N. (eds.). SPIE, 1057524. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10575).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    1 Scopus citations
  • 2017

    Fully automated breast density assessment from low-dose chest CT

    Liu, S., Margolies, L. R., Xie, Y., Yankelevitz, D. F., Henschke, C. I. & Reeves, A. P., 2017, Medical Imaging 2017: Computer-Aided Diagnosis. Petrick, N. A. & Armato, S. G. (eds.). SPIE, 101340R. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10134).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    6 Scopus citations

  • Identification of early-stage usual interstitial pneumonia from low-dose chest CT scans using fractional high-density lung distribution

    Xie, Y., Salvatore, M., Liu, S., Jirapatnakul, A., Yankelevitz, D. F., Henschke, C. I. & Reeves, A. P., 2017, Medical Imaging 2017: Computer-Aided Diagnosis. Petrick, N. A. & Armato, S. G. (eds.). SPIE, 1013408. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10134).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    1 Scopus citations

  • Preconditioned random forest regression: Application to genome-wide study for radiotherapy toxicity prediction

    Lee, S., Ostrer, H., Kerns, S., Deasy, J. O., Rosenstein, B. & Oh, J. H., 20 Aug 2017, ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, p. 593 1 p. (ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • 2016

    Gene-Environment Interactions and the Etiology of Birth Defects

    Krauss, R. S. & Hong, M., 2016, Essays on Developmental Biology, Part A, 2016. Wassarman, P. M. (ed.). Academic Press Inc., p. 569-580 12 p. (Current Topics in Developmental Biology; vol. 116).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    62 Scopus citations

  • Sirtuins and the Estrogen Receptor as Regulators of the Mammalian Mitochondrial UPR in Cancer and Aging

    Germain, D., 2016, Advances in Cancer Research, 2016. Tew, K. D. & Fisher, P. B. (eds.). Academic Press Inc., p. 211-256 46 p. (Advances in Cancer Research; vol. 130).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    34 Scopus citations
  • 2015

    Automated measurement of pulmonary artery in low-dose non-contrast chest CT images

    Xie, Y., Liang, M., Yankelevitz, D. F., Henschke, C. I. & Reeves, A. P., 2015, Medical Imaging 2015: Computer-Aided Diagnosis. Hadjiiski, L. M. & Tourassi, G. D. (eds.). SPIE, 94141G. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9414).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    8 Scopus citations

  • Automated segmentation of cardiac visceral fat in low-dose non-contrast chest CT images

    Xie, Y., Liang, M., Yankelevitz, D. F., Henschke, C. I. & Reeves, A. P., 2015, Medical Imaging 2015: Computer-Aided Diagnosis. Hadjiiski, L. M., Hadjiiski, L. M., Tourassi, G. D. & Tourassi, G. D. (eds.). SPIE, 94140G. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9414).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    9 Scopus citations

  • Generation of 3-D glioblastoma-vascular niche using 3-D bioprinting

    Lee, V. K., Dai, G., Zou, H. & Yoo, S. S., 2 Jun 2015, 2015 41st Annual Northeast Biomedical Engineering Conference, NEBEC 2015. Institute of Electrical and Electronics Engineers Inc., 7117111. (2015 41st Annual Northeast Biomedical Engineering Conference, NEBEC 2015).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    29 Scopus citations

  • Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool

    Clark, N. R., Szymkiewicz, M., Wang, Z., Monteiro, C. D., Jones, M. R. & Ma'ayan, A., 16 Dec 2015, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Schapranow, L. M., Zhou, J., Hu, X. T., Ma, B., Rajasekaran, S., Miyano, S., Yoo, I., Pierce, B., Shehu, A., Gombar, V. K., Chen, B., Pai, V. & Huan, J. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 256-262 7 p. 7359689. (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    11 Scopus citations

  • Segmentation of the whole breast from low-dose chest CT images

    Liu, S., Salvatore, M., Yankelevitz, D. F., Henschke, C. I. & Reeves, A. P., 2015, Medical Imaging 2015: Computer-Aided Diagnosis. Hadjiiski, L. M. & Tourassi, G. D. (eds.). SPIE, 94140I. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9414).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    8 Scopus citations
  • 2014

    A prostate MRI atlas of biochemical failures following cancer treatment

    Rusu, M., Kurhanewicz, J., Tewari, A. & Madabhushi, A., 2014, Medical Imaging 2014: Computer-Aided Diagnosis. SPIE, 903513. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9035).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    1 Scopus citations

  • Automated aortic calcification detection in low-dose chest CT images

    Xie, Y., Htwe, Y. M., Padgett, J., Henschke, C., Yankelevitz, D. & Reeves, A. P., 2014, Medical Imaging 2014: Computer-Aided Diagnosis. SPIE, 90350P. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9035).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    8 Scopus citations

  • Automated coronary artery calcification detection on low-dose chest CT images

    Xie, Y., Cham, M. D., Henschke, C., Yankelevitz, D. & Reeves, A. P., 2014, Medical Imaging 2014: Computer-Aided Diagnosis. SPIE, 90350F. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9035).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    21 Scopus citations
  • 2013

    ChEA2: Gene-set libraries from ChIP-X experiments to decode the transcription regulome

    Kou, Y., Chen, E. Y., Clark, N. R., Duan, Q., Tan, C. M. & Ma'ayan, A., 2013, Availability, Reliability, and Security in Information Systems and HCI - IFIP WG 8.4, 8.9, TC 5 International Cross-Domain Conference, CD-ARES 2013, Proceedings. p. 416-430 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8127 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    Open Access
    13 Scopus citations
  • 2012

    Connecting clusters of patient to drug responses of cell lines to suggest personalized therapeutics for breast cancer

    Gordonov, S. & Ma'Ayan, A., 2012, Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012. p. 529-534 6 p. 6470378. (Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Heart region segmentation from low-dose CT scans: An anatomy based approach

    Reeves, A. P., Biancardi, A. M., Yankelevitz, D. F., Cham, M. D. & Henschke, C. I., 2012, Medical Imaging 2012: Image Processing. 83142A. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 8314).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    8 Scopus citations
  • 2011

    Visualization of patient samples by dimensionality reduction of genome-wide measurements

    Xu, H. & Ma'ayan, A., 2011, Information Quality in e-Health - 7th Conference of the Workgroup Human-Computer Interaction and Usability Engineering of the Austrian Computer Society, USAB 2011, Proceedings. p. 15-22 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7058 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    2 Scopus citations
  • 2010

    Inferring the sign of kinase-substrate interactions by combining quantitative phosphoproteomics with a literature-based mammalian kinome network

    Hernandez, M., Lachmann, A., Zhao, S., Xiao, K. & Ma'ayan, A., 2010, 10th IEEE International Conference on Bioinformatics and Bioengineering 2010, BIBE 2010. p. 180-184 5 p. 5521694. (10th IEEE International Conference on Bioinformatics and Bioengineering 2010, BIBE 2010).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    Open Access
    3 Scopus citations
  • 2008

    A modified commercial ultrasound scanner used for in-vivo photoacoustic imaging of nude mice injected with non-targeted contrast agents

    Jankovic, L., Shahzad, K., Wang, Y., Burcher, M., Scholle, F. D., Hauff, P., Mofina, S. & Skobe, M., 2008, Photons Plus Ultrasound: Imaging and Sensing 2008: The Ninth Conference on Biomedical Thermoacoustics, Optoacoustics, and Acousto-optics. 68560O. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 6856).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    2 Scopus citations

  • Hormone refractory prostate cancer: Lessons learned from the pten prostate cancer model

    Mulholland, D. J., Jiao, J. & Wu, H., 2008, Hormonal Carcinogenesis V. Li, J., Li, S., Mohla, S., Rochefort, H., Rochefort, H. & Maudelonde, T. (eds.). p. 87-95 9 p. (Advances in Experimental Medicine and Biology; vol. 617).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    8 Scopus citations

  • In vivo photoacoustic imaging of nude mice vasculature using a photoacoustic imaging system based on a commercial ultrasound scanner

    Jankovic, L., Shahzad, K., Wang, Y., Burcher, M., Scholle, F. D., Hauff, P., Mofina, S. & Skobe, M., 2008, Photons Plus Ultrasound: Imaging and Sensing 2008: The Ninth Conference on Biomedical Thermoacoustics, Optoacoustics, and Acousto-optics. 68560N. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 6856).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    4 Scopus citations
  • 2007

    Connecting seed lists of mammalian proteins using Steiner Trees

    White, A. G. & Ma'ayan, A., 2007, Conference Record of the 41st Asilomar Conference on Signals, Systems and Computers, ACSSC. p. 155-159 5 p. 4487185. (Conference Record - Asilomar Conference on Signals, Systems and Computers).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    5 Scopus citations