• 66999 Citations
  • 112 h-Index
1971 …2020

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2020

Fluorescent imaging technologies for in situ measurement of drug target engagement and cell signaling pathways

McMahon, N. P., Solanki, A., Jones, J., Kwon, S., Chang, Y. H., Chin, K., Nederlof, M. A., Gray, J. W. & Gibbs, S. L., Jan 1 2020, Visualizing and Quantifying Drug Distribution in Tissue IV. Chan, K. F. & Evans, C. L. (eds.). SPIE, 112190O. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 11219).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2019

cmIF: A Python Library for Scalable Multiplex Imaging Pipelines

Eng, J., Bucher, E., Gray, E., Campbell, L. G., Thibault, G., Heiser, L., Gibbs, S., Gray, J. W., Chin, K. & Chang, Y. H., Jan 1 2019, Mathematical and Computational Oncology - 1st International Symposium, ISMCO 2019, Proceedings. Bebis, G., Benos, T., Chen, K., Jahn, K. & Lima, E. (eds.). Springer, p. 37-43 7 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11826 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Signal removal methods for highly multiplexed immunofluorescent staining using antibody conjugated oligonucleotides

McMahon, N., Jones, J., Eng, J., Kwon, S., Chang, Y. H., Thibault, G., Chin, K., Nederlof, M., Gray, J. & Gibbs, S. L., Jan 1 2019, Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XVII. Leary, J. F., Tarnok, A. & Farkas, D. L. (eds.). SPIE, 108810X. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10881).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Variational autoencoding tissue response to microenvironment perturbation

Schau, G. F., Thibault, G., Dane, M. A., Gray, J., Heiser, L. & Chang, Y. H., Jan 1 2019, Medical Imaging 2019: Image Processing. Landman, B. A., Angelini, E. D., Angelini, E. D. & Angelini, E. D. (eds.). SPIE, 109491M. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10949).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2018

SHIFT: Speedy histopathological-To-immunofluorescent translation of whole slide images using conditional generative adversarial networks

Burlingame, E. A., Margolin, A., Gray, J. & Chang, Y. H., Jan 1 2018, Medical Imaging 2018: Digital Pathology. SPIE, Vol. 10581. 1058105

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations
2017

Breast cancer histopathology image analysis pipeline for tumor purity estimation

Azimi, V., Chang, Y. H., Thibault, G., Smith, J., Tsujikawa, T., Kukull, B., Jensen, B., Corless, C., Margolin, A. & Gray, J., Jun 15 2017, 2017 IEEE 14th International Symposium on Biomedical Imaging, ISBI 2017. IEEE Computer Society, p. 1137-1140 4 p. 7950717

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Deep learning based Nucleus Classification in pancreas histological images

Chang, Y. H., Thibault, G., Madin, O., Azimi, V., Meyers, C., Johnson, B., Link, J., Margolin, A. & Gray, J., Sep 13 2017, 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Smarter Technology for a Healthier World, EMBC 2017 - Proceedings. Institute of Electrical and Electronics Engineers Inc., p. 672-675 4 p. 8036914

Research output: Chapter in Book/Report/Conference proceedingConference contribution

10 Scopus citations

Integrative analysis on histopathological image for identifying cellular heterogeneity

Chang, Y. H., Thibault, G., Johnson, B., Margolin, A. & Gray, J., 2017, Medical Imaging 2017: Digital Pathology. SPIE, Vol. 10140. 101400T

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Multiplexed immunohistochemistry image analysis using sparse coding

Chang, Y. H., Tsujikawa, T., Margolin, A., Coussens, L. & Gray, J., Sep 13 2017, 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Smarter Technology for a Healthier World, EMBC 2017 - Proceedings. Institute of Electrical and Electronics Engineers Inc., p. 4046-4049 4 p. 8037744

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations
2016

Quantitative analysis of histological tissue image based on cytological profiles and spatial statistics

Chang, Y. H., Thibault, G., Azimi, V., Johnson, B., Jorgens, D., Link, J., Margolin, A. & Gray, J., Oct 13 2016, 2016 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2016. Institute of Electrical and Electronics Engineers Inc., Vol. 2016-October. p. 1175-1178 4 p. 7590914

Research output: Chapter in Book/Report/Conference proceedingConference contribution

7 Scopus citations

Retrieving common dynamics of gene regulatory networks under various perturbations

Chang, Y. H., Dobbe, R., Bhushan, P., Gray, J. & Tomlin, C. J., Feb 8 2016, Proceedings of the IEEE Conference on Decision and Control. Institute of Electrical and Electronics Engineers Inc., Vol. 2016-February. p. 2531-2536 6 p. 7402597

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations
2015

Heterogeneity in cancer dynamics: A convex formulation to dissect dynamic trajectories and infer LTV models of networked systems

Dobbe, R., Chang, Y. H., Korkola, J., Gray, J. & Tomlin, C., Jul 28 2015, ACC 2015 - 2015 American Control Conference. Institute of Electrical and Electronics Engineers Inc., p. 4398-4403 6 p. 7172021. (Proceedings of the American Control Conference; vol. 2015-July).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations
2013

Adaptive H-extrema for automatic immunogold particle detection

Thibault, G., Iljin, K., Arthur, C., Shafran, I. & Gray, J., Dec 1 2013, Progress in Pattern Recognition, Image Analysis, Computer Vision, and Applications - 18th Iberoamerican Congress, CIARP 2013, Proceedings. PART 2 ed. p. 238-245 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8259 LNCS, no. PART 2).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2012

Learning invariant features of tumor signatures

Le, Q. V., Han, J., Gray, J. W., Spellman, P. T., Borowsky, A. & Parvin, B., Aug 15 2012, 2012 9th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2012 - Proceedings. p. 302-305 4 p. 6235544. (Proceedings - International Symposium on Biomedical Imaging).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

23 Scopus citations
2011

Comparison of sparse coding and kernel methods for histopathological classification of gliobastoma multiforme

Han, J., Chang, H., Loss, L., Zhang, K., Baehner, F. L., Gray, J. W., Spellman, P. & Parvin, B., Nov 2 2011, 2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11. p. 711-714 4 p. 5872505. (Proceedings - International Symposium on Biomedical Imaging).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

22 Scopus citations

Optimization-based inference for temporally evolving Boolean networks with applications in biology

Chang, Y. H., Gray, J. & Tomlin, C., Sep 29 2011, Proceedings of the 2011 American Control Conference, ACC 2011. p. 4129-4134 6 p. 5991347. (Proceedings of the American Control Conference).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations
2010

An ODE model for the HER2/3-AKT signaling pathway in cancers that overexpress HER2

Itani, S., Gray, J. & Tomlin, C. J., Oct 15 2010, Proceedings of the 2010 American Control Conference, ACC 2010. p. 1235-1241 7 p. 5531034. (Proceedings of the 2010 American Control Conference, ACC 2010).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations
2009

Morphometric subtyping for a panel of breast cancer cell lines

Han, J., Chang, H., Fontenay, G., Wang, N. J., Gray, J. W. & Parvin, B., Nov 17 2009, Proceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009. p. 791-794 4 p. 5193168. (Proceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations
2008

Ovarian cancer: Linking genomics to new target discovery and molecular markers - The way ahead

Hennessy, B. T., Murph, M., Nanjundan, M., Carey, M., Auersperg, N., Almeida, J., Coombes, K. R., Liu, J., Lu, Y., Gray, J. W. & Mills, G. B., Dec 1 2008, Hormonal Carcinogenesis V. Li, J., Li, S., Mohla, S., Rochefort, H., Rochefort, H. & Maudelonde, T. (eds.). p. 23-40 18 p. (Advances in Experimental Medicine and Biology; vol. 617).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

10 Scopus citations
2007

Spectral decomposition of signaling networks

Parvin, B., Ghosh, N., Heiser, L., Knapp, M., Talcott, C., Laderoute, K., Gray, J. & Spellman, P., Dec 1 2007, 2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology, CIBCB 2007. p. 76-81 6 p. 4221207. (2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology, CIBCB 2007).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2005

Nanoplasmonic biomolecular ruler with a 2 NM spatial resolution for probing restricted digestion of nucleic acids

Liu, G. L., Chen, F., Gerion, D., Yin, Y., Paul Alivisatos, A., Gray, J. W. & Lee, L. P., Jan 1 2005, Micro Total Analysis Systems - Proceedings of MicroTAS 2005 Conference: 9th International Conference on Miniaturized Systems for Chemistry and Life Sciences. Transducer Research Foundation, p. 1513-1515 3 p. (Micro Total Analysis Systems - Proceedings of MicroTAS 2005 Conference: 9th International Conference on Miniaturized Systems for Chemistry and Life Sciences; vol. 1).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1999

Measurement of genetic instability in breast cancer by confocal microscopy and 3D image analysis

Ortiz de Solorzano, C., Chin, K., Chou, W. S., Knowles, D., Gray, J. W. & Lockett, S. J., Dec 1 1999, Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings. IEEE, 1 p. (Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings; vol. 2).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1995

Interactive algorithms for rapid enumeration of hybridization signals in individual whole-cell nuclei inside intact-tissue specimens

Lockett, S. J., Thompson, C. T., Mullikin, J. C., Sudar, D., Khavari, R., Hyun, W., Pinkel, D. & Gray, J. W., Jan 1 1995, Proceedings of SPIE - The International Society for Optical Engineering. Wilson, T. & Cogswell, C. J. (eds.). Society of Photo-Optical Instrumentation Engineers, p. 43-49 7 p. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 2412).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations
1993

Application of x rays to the analysis of DNA packaging in mammalian sperm

Balhorn, R., Corzett, M., Allen, M. J., Lee, C., Barbee, T. W., Koch, J. A., MacGowan, B. J., Matthews, D. L., Mrowka, S. J., Trebes, J. E., McNulty, I., Da Silva, L. B., Gray, J. W., Anderson, E. H., Kern, D. & Attwood, D. T., Jan 1 1993, Proceedings of SPIE - The International Society for Optical Engineering. Publ by Int Soc for Optical Engineering, p. 374-385 12 p. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 1741).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

7 Scopus citations

Imaging microscopy with x-ray lasers at LLNL

Da Silva, L. B., Trebes, J. E., Mrowka, S. J., MacGowan, B. J., Koch, J. A., Matthews, D. L., Barbee, T. W., Balhorn, R., Gray, J. W., Anderson, E. H., Kern, D. & Attwood, D. T., Jan 1 1993, Proceedings of SPIE - The International Society for Optical Engineering. Publ by Int Soc for Optical Engineering, p. 154-159 6 p. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 1741).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1990

X-ray laser holography of biological microstructures

Trebes, J., Brase, J., Gray, J., London, R., Matthews, D., Peters, D., Pinkel, D., Stone, G., Rosen, M. & Yorkey, T., Dec 1 1990, Institute of Physics Conference Series. 116 ed. Publ by Inst of Physics Publ Ltd, p. 279-287 9 p. (Institute of Physics Conference Series; no. 116).

Research output: Chapter in Book/Report/Conference proceedingConference contribution