• 64653 Citations
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1971 …2020
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Research Output 1971 2020

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Conference contribution
2019

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

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

oligonucleotides
Oligonucleotides
staining
antibodies
Antibodies

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

learning
Learning
Tissue
annotations
perturbation
2018
2 Citations (Scopus)

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

Hematoxylin
Eosine Yellowish-(YS)
chutes
Coloring Agents
Imaging techniques
2017
1 Citation (Scopus)

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

Image analysis
Tumors
Pipelines
Breast Neoplasms
Neoplasms
6 Citations (Scopus)

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

Pancreas
Learning
Tumors
Neoplasms
Explosions

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

Spatial Analysis
Lymphocytes
Spatial distribution
Tumors
lymphocytes

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

Image analysis
Immunohistochemistry
Tissue
Biomarkers
Tumors
2016
7 Citations (Scopus)

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

Statistics
Tissue
Chemical analysis
Spatial Analysis
Hematoxylin
2 Citations (Scopus)

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

Gene Regulatory Network
Genes
Perturbation
Proteomics
Graph in graph theory
2015
1 Citation (Scopus)

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, Proceedings of the American Control Conference. Institute of Electrical and Electronics Engineers Inc., Vol. 2015-July. p. 4398-4403 6 p. 7172021

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

Cells
Trajectories
Tumors
Cell signaling
Proteins
2013

Adaptive H-extrema for automatic immunogold particle detection

Thibault, G., Iljin, K., Arthur, C., Shafran, I. & Gray, J., 2013, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PART 2 ed. Vol. 8259 LNCS. 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

Extremum
Multiple Classifiers
Classifiers
Multiple Scales
Gold
2012
23 Citations (Scopus)

Learning invariant features of tumor signatures

Le, Q. V., Han, J., Gray, J., Spellman, P., Borowsky, A. & Parvin, B., 2012, Proceedings - International Symposium on Biomedical Imaging. p. 302-305 4 p. 6235544

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

Tumors
Learning
Tissue
Network layers
Neoplasms
2011
21 Citations (Scopus)

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., Spellman, P. & Parvin, B., 2011, Proceedings - International Symposium on Biomedical Imaging. p. 711-714 4 p. 5872505

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

Histology
Discriminant analysis
Glossaries
Restoration
Support vector machines
4 Citations (Scopus)

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

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

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

Cost functions
Systems Biology
2010
3 Citations (Scopus)

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

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

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

Drug therapy
Oncology
Mathematical models
Epidermal Growth Factor
2009
1 Citation (Scopus)

Morphometric subtyping for a panel of breast cancer cell lines

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

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

Cells
Breast Neoplasms
Cell Line
Assays
Pipelines
2008
10 Citations (Scopus)

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. & Mills, G., 2008, Advances in Experimental Medicine and Biology. Vol. 617. p. 23-40 18 p. (Advances in Experimental Medicine and Biology; vol. 617).

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

Human Genome
Tumor Biomarkers
Genomics
Ovarian Neoplasms
2007

Spectral decomposition of signaling networks

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

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

Decomposition
Proteins
Petri nets
Directed graphs
Cells
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. & Lee, L. P., 2005, Micro Total Analysis Systems - Proceedings of MicroTAS 2005 Conference: 9th International Conference on Miniaturized Systems for Chemistry and Life Sciences. Transducer Research Foundation, Vol. 1. p. 1513-1515 3 p.

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

Nucleic acids
Nucleic Acids
DNA
Nanoconjugates
Biochemistry
2003

In Situ Quantification of Genomic Instability in Breast Cancer Progression

Ortiz De Solórzano, C., Chin, K-Y., Gray, J. & Lockett, S. J., 2003, Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings. Leder, R. S. (ed.). Vol. 4. p. 3578-3581 4 p.

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

Telomerase
Image analysis
Fluorescence
Tissue
2002
3 Citations (Scopus)

Technical approaches for efficient, high precision nucleic acid analysis using DNA microarrays

Pinkel, D., Hamilton, G., Brown, N., Segraves, R., Huey, B., Snijders, A., Blackwood, S., Hindle, K., Law, S., Gray, J., Jain, A., Hanson, J., Nordmeyer, R. & Albertson, D., 2002, Proceedings of SPIE - The International Society for Optical Engineering. Bornhop, D. J., Dunn, D. A., Mariella, Jr., R. P., Murphy, C. J. & and others, O. (eds.). Vol. 4626. p. 82-88 7 p.

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

Nucleic acids
nucleic acids
Microarrays
DNA
deoxyribonucleic acid
1999

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

Ortiz de Solorzano, C., Chin, K-Y., Chou, W. S., Knowles, D., Gray, J. & Lockett, S. J., 1999, Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings. IEEE, Vol. 2. p. 822 1 p.

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

Confocal microscopy
Image analysis
Tissue
Chromosomes
Tumors
1998

Interactive system for registering adjacent tissue sections

Lockett, S. J., Fernandez, C., Rodriguez, E., Wesselmann, U., Bastian, B. C., Sudar, D., Pinkel, D. & Gray, J., 1998, Proceedings of SPIE - The International Society for Optical Engineering. Farkas, D. L., Leif, R. C. & Tromberg, B. J. (eds.). Vol. 3260. p. 154-161 8 p.

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

Tissue
Labeling
Microscopes
chutes
markers

Segmentation of Cell Nuclei from Confocal Microscope Images of Thick Tissue Samples

Ortiz de Solorzano, C., Sarti, A., Rodriguez, E. G., Jones, A., Sudar, D., Pinkel, D., Gray, J., Malladi, R. & Lockett, S. J., 1998, Proceedings of the Joint Conference on Information Sciences. Li, K., Pan, Y., Wang, P. P., Al-Dhelaan, A., Da Cheng, H., Pan, Y., Wang, P. P., Li, K., Al-Dhelaan, A. & Da Cheng, H. (eds.). Vol. 4. p. 187-190 4 p.

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

Hough transforms
Microscopes
Visualization
Cells
Tissue
1995
2 Citations (Scopus)

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., 1995, Proceedings of SPIE - The International Society for Optical Engineering. Wilson, T. & Cogswell, C. J. (eds.). Society of Photo-Optical Instrumentation Engineers, Vol. 2412. p. 43-49 7 p.

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

enumeration
Fluorescence
Cells
Tissue
nuclei
1994
1 Citation (Scopus)

Digital imaging microscopy for molecular cytogenetics

Gray, J., Lockett, S., Mascio, L., Mullikin, J., Pinkel, D., Piper, J., Sudar, D. & Thompson, C., 1994, Proceedings - Annual Meeting, Microscopy Society of America. Bailey, G. W. & Garratt-Reed, A. J. (eds.). p. 82-83 2 p.

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

Histology
Image acquisition
Microscopic examination
Genes
Display devices
1993
7 Citations (Scopus)

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., Anderson, E. H., Kern, D. & Attwood, D. T., 1993, Proceedings of SPIE - The International Society for Optical Engineering. Publ by Int Soc for Optical Engineering, Vol. 1741. p. 374-385 12 p.

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

packaging
Packaging
DNA
deoxyribonucleic acid
X rays

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., Anderson, E. H., Kern, D. & Attwood, D. T., 1993, Proceedings of SPIE - The International Society for Optical Engineering. Publ by Int Soc for Optical Engineering, Vol. 1741. p. 154-159 6 p.

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

x ray lasers
Microscopic examination
microscopy
Imaging techniques
X rays
1990
3 Citations (Scopus)

X-ray holography for sequencing DNA

Yorkey, T., Brase, J., Trebes, J., Lane, S. & Gray, J., 1990, Proceedings of SPIE - The International Society for Optical Engineering. Knauer, J. P. & Shenoy, G. K. (eds.). Publ by Int Soc for Optical Engineering, Vol. 1345. p. 255-259 5 p.

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

sequencing
Holography
holography
DNA
deoxyribonucleic acid
2 Citations (Scopus)

X-ray holography for sequencing DNA

Yorkey, T., Brase, J., Trebes, J., Lane, S. & Gray, J., 1990, Proceedings of SPIE - The International Society for Optical Engineering. Javidi, B. (ed.). Publ by Int Soc for Optical Engineering, Vol. 1347. p. 474-478 5 p.

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

sequencing
Holography
holography
DNA
deoxyribonucleic acid

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., 1990, Institute of Physics Conference Series. 116 ed. Publ by Inst of Physics Publ Ltd, p. 279-287 9 p.

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

X ray lasers
Holography
Chromosomes
Gold
Imaging techniques