• 3303 SW Bond Avenue, CH13B, Portland OR 97239

  • 362 Citations
  • 8 h-Index
20052020
If you made any changes in Pure, your changes will be visible here soon.

Research Output 2005 2020

  • 362 Citations
  • 8 h-Index
  • 28 Conference contribution
  • 22 Article
  • 1 Chapter
2020
1 Citation (Scopus)
Single-Cell Analysis
Tumor-Infiltrating Lymphocytes
Fluorescent Antibody Technique
Breast Neoplasms
Neoplasms
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

Python
Pipelines
Imaging
Imaging techniques
Reproducibility

High-throughput single-particle tracking reveals 1 nested membrane domains that dictate krasg12d 2 diffusion and trafficking

Lee, Y., Phelps, C., Huang, T., Mostofian, B., Wu, L., Zhang, Y., Tao, K., Chang, Y. H., Stork, P. J. S., Gray, J. W., Zuckerman, D. M. & Nan, X., Nov 2019, In : eLife. 8

Research output: Contribution to journalArticle

Open Access
Throughput
Membranes
Recycling
Microscopy
Microscopic examination
7 Citations (Scopus)

Modeling Tumor Phenotypes In Vitro with Three-Dimensional Bioprinting

Langer, E. M., Allen-Petersen, B. L., King, S. M., Kendsersky, N. D., Turnidge, M. A., Kuziel, G. M., Riggers, R., Samatham, R., Amery, T. S., Jacques, S., Sheppard, B., Korkola, J., Muschler, J., Thibault, G., Chang, Y. H., Gray, J., Presnell, S. C., Nguyen, D. G. & Sears, R., Jan 15 2019, In : Cell Reports. 26, 3, p. 608-623.e6

Research output: Contribution to journalArticle

Bioprinting
Tumors
Tissue
Phenotype
Scaffolds
1 Citation (Scopus)

Robust Cell Detection and Segmentation for Image Cytometry Reveal Th17 Cell Heterogeneity

Tsujikawa, T., Thibault, G., Azimi, V., Sivagnanam, S., Banik, G., Means, C., Kawashima, R., Clayburgh, D., Gray, J., Coussens, L. & Chang, Y. H., Jan 1 2019, In : Cytometry Part A.

Research output: Contribution to journalArticle

Image Cytometry
Th17 Cells
Papillomaviridae
Immunohistochemistry
Biomarkers

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
1 Citation (Scopus)

A method for quantification of calponin expression in myoepithelial cells in immunohistochemical images of ductal carcinoma in situ

Gray, E., Mitchell, E., Jindal, S., Schedin, P. & Chang, Y. H., May 23 2018, 2018 IEEE 15th International Symposium on Biomedical Imaging, ISBI 2018. IEEE Computer Society, Vol. 2018-April. p. 796-799 4 p.

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

Carcinoma, Intraductal, Noninfiltrating
Chemotherapy
Biomarkers
Ducts
Breast Neoplasms
2 Citations (Scopus)

Computational measurement of tumor immune microenvironment in gastric adenocarcinomas

Chang, Y. H., Heo, Y. J., Cho, J., Song, S. Y., Lee, J. & Kim, K. M., Dec 1 2018, In : Scientific Reports. 8, 1, 13887.

Research output: Contribution to journalArticle

Tumor Microenvironment
Human Herpesvirus 4
Stomach
Adenocarcinoma
Tumor-Infiltrating Lymphocytes
17 Citations (Scopus)

IFNγ-activated dermal lymphatic vessels inhibit cytotoxic T cells in melanoma and inflamed skin

Lane, R. S., Femel, J., Breazeale, A. P., Loo, C. P., Thibault, G., Kaempf, A., Mori, M. T., Tsujikawa, T., Chang, Y. H. & Lund, A., Dec 1 2018, In : Journal of Experimental Medicine. 215, 12, p. 3057-3074 18 p.

Research output: Contribution to journalArticle

Lymphatic Vessels
Melanoma
T-Lymphocytes
Skin
Immunity
13 Citations (Scopus)

Secure estimation based Kalman Filter for cyber–physical systems against sensor attacks

Chang, Y. H., Hu, Q. & Tomlin, C. J., Sep 1 2018, In : Automatica. 95, p. 399-412 14 p.

Research output: Contribution to journalArticle

Kalman filters
Sensors
Error correction
Unmanned aerial vehicles (UAV)
Sensor nodes
4 Citations (Scopus)

Secure state estimation and control for cyber security of the nonlinear power systems

Hu, Q., Fooladivanda, D., Chang, Y. H. & Tomlin, C. J., Sep 1 2018, In : IEEE Transactions on Control of Network Systems. 5, 3, p. 1310-1321 12 p., 7929374.

Research output: Contribution to journalArticle

Electric power system interconnection
Interconnected Systems
State Estimation
State estimation
Power System
3 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
48 Citations (Scopus)

Toward Minimal Residual Disease-Directed Therapy in Melanoma

Rambow, F., Rogiers, A., Marin-Bejar, O., Aibar, S., Femel, J., Dewaele, M., Karras, P., Brown, D., Chang, Y. H., Debiec-Rychter, M., Adriaens, C., Radaelli, E., Wolter, P., Bechter, O., Dummer, R., Levesque, M., Piris, A., Frederick, D. T., Boland, G., Flaherty, K. T. & 5 others, van den Oord, J., Voet, T., Aerts, S., Lund, A. & Marine, J. C., Aug 9 2018, In : Cell. 174, 4, p. 843-855.e19

Research output: Contribution to journalArticle

Residual Neoplasm
Melanoma
Therapeutics
Biopsy
RNA Sequence Analysis
6 Citations (Scopus)

VIPER is a genetically encoded peptide tag for fluorescence and electron microscopy

Doh, J. K., White, J. D., Zane, H. K., Chang, Y. H., Lopez, C., Enns, C. & Beatty, K., Dec 18 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 51, p. 12961-12966 6 p.

Research output: Contribution to journalArticle

Fluorescence Microscopy
Electron Microscopy
Peptides
Proteins
Technology
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
101 Citations (Scopus)

Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis

Tsujikawa, T., Kumar, S., Borkar, R. N., Azimi, V., Thibault, G., Chang, Y. H., Balter, A., Kawashima, R., Choe, G., Sauer, D., El Rassi, E., Clayburgh, D., Kulesz-Martin, M., Lutz, E. R., Zheng, L., Jaffee, E. M., Leyshock, P., Margolin, A., Mori, M. T., Gray, J. & 2 others, Flint, P. & Coussens, L., Apr 4 2017, In : Cell Reports. 19, 1, p. 203-217 15 p.

Research output: Contribution to journalArticle

Tumors
Immunohistochemistry
Tissue
Biomarkers
Papillomaviridae
3 Citations (Scopus)

Secure state estimation for Cyber Physical Systems with sparse malicious packet drops

Fiore, G., Chang, Y. H., Hu, Q., Di Benedetto, M. D. & Tomlin, C. J., Jun 29 2017, 2017 American Control Conference, ACC 2017. Institute of Electrical and Electronics Engineers Inc., p. 1898-1903 6 p. 7963229

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

State estimation
Unmanned aerial vehicles (UAV)
Linear systems
Actuators
Controllers
7 Citations (Scopus)

Secure state estimation for nonlinear power systems under cyber attacks

Hu, Q., Fooladivanda, D., Chang, Y. H. & Tomlin, C. J., Jun 29 2017, 2017 American Control Conference, ACC 2017. Institute of Electrical and Electronics Engineers Inc., p. 2779-2784 6 p. 7963372

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

State estimation
Nonlinear systems
Electric power system interconnection
Nonlinear dynamical systems
Communication
2016

Iterative function separation for gene regulatory function identification

Bhushan, P., Chang, Y. H. & 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. 133-138 6 p. 7402098

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

Genes
Gene
Level measurement
Iterative Scheme
Iterative methods

Primer for image informatics in personalized medicine

Chang, Y. H., Foley, P., Azimi, V., Borkar, R. & Lefman, J., 2016, In : Unknown Journal. 159, p. 58-65 8 p.

Research output: Contribution to journalArticle

Precision Medicine
Informatics
Medicine
Software
Social Media
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

Reconstruction of Gene Regulatory Networks Based on Repairing Sparse Low-Rank Matrices

Chang, Y. H., Dobbe, R., Bhushan, P., Gray, J. & Tomlin, C. J., Jul 1 2016, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 13, 4, p. 767-777 11 p., 7182286.

Research output: Contribution to journalArticle

Low-rank Matrices
Gene Regulatory Networks
Gene Regulatory Network
Sparse matrix
Genes
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
3 Citations (Scopus)

Secure estimation for unmanned aerial vehicles against adversarial cyber attacks

Hu, Q., Chang, Y. H. & Tomlin, C. J., 2016, 30th Congress of the International Council of the Aeronautical Sciences, ICAS 2016. International Council of the Aeronautical Sciences

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

Unmanned aerial vehicles (UAV)
Sensors
Kalman filters
Dynamical systems
31 Citations (Scopus)

Sparse network identifiability via Compressed Sensing

Hayden, D., Chang, Y. H., Goncalves, J. & Tomlin, C. J., 2016, In : Automatica. 68, p. 9-17 9 p.

Research output: Contribution to journalArticle

Compressed sensing
Experiments
2015
3 Citations (Scopus)

Accelerating submovement decomposition with search-space reduction heuristics

Gowda, S., Overduin, S. A., Chen, M., Chang, Y. H., Tomlin, C. J. & Carmena, J. M., Oct 1 2015, In : IEEE Transactions on Biomedical Engineering. 62, 10, p. 2508-2515 8 p., 2434595.

Research output: Contribution to journalArticle

Decomposition
Innovation
Set theory
1 Citation (Scopus)

Disentangling multidimensional spatio-temporal data into their common and aberrant responses

Chang, Y. H., Korkola, J., Amin, D. N., Moasser, M. M., Carmena, J. M., Gray, J. & Tomlin, C. J., Apr 22 2015, In : PLoS One. 10, 4, e0121607.

Research output: Contribution to journalArticle

Experiments
Gene expression
Principal component analysis
Time series
methodology
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
2014
2 Citations (Scopus)

A design of neural decoder by reducing discrepancy between Manual Control (MC) and Brain Control (BC)

Chang, Y. H., Chen, M., Shanechi, M., Carmena, J. M. & Tomlin, C., Jul 22 2014, 2014 European Control Conference, ECC 2014. Institute of Electrical and Electronics Engineers Inc., p. 516-521 6 p. 6862547

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

Manual control
Brain
Kalman filters
Parameter estimation
Decoding

Design of a neural decoder by sensory prediction and error correction

Lu, J., Chen, M., Chang, Y. H., Tomizuka, M., Carmena, J. M. & Tomlin, C. J., 2014, In : Unknown Journal. 2015-February, February, p. 6999-7004 6 p., 7040489.

Research output: Contribution to journalArticle

Brain-Computer Interfaces
Error correction
Error Correction
Biological Models
Prediction
21 Citations (Scopus)

Exact reconstruction of gene regulatory networks using compressive sensing

Chang, Y. H., Gray, J. & Tomlin, C. J., 2014, In : BMC Bioinformatics. 15, p. 400 1 p.

Research output: Contribution to journalArticle

Compressive Sensing
Gene Regulatory Networks
Gene Regulatory Network
Genes
Connectivity
3 Citations (Scopus)

Reconstruction of gene regulatory networks with hidden nodes

Chang, Y. H. & Tomlin, C., Jul 22 2014, 2014 European Control Conference, ECC 2014. Institute of Electrical and Electronics Engineers Inc., p. 1492-1497 6 p. 6862187

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

Genes
Convex optimization
Biological systems
Gene expression
Time series
2013
3 Citations (Scopus)

Low-rank representation of neural activity and detection of submovements

Chang, Y. H., Chen, M., Gowda, S., Overduin, S. A., Carmena, J. M. & Tomlin, C., 2013, Proceedings of the IEEE Conference on Decision and Control. Institute of Electrical and Electronics Engineers Inc., p. 2544-2549 6 p. 6760263

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

Principal component analysis
Principal Component Analysis
Random Projection
Signature
Low-rank Matrices
2012
10 Citations (Scopus)

Data-driven graph reconstruction using compressive sensing

Chang, Y. H. & Tomlin, C., 2012, Proceedings of the IEEE Conference on Decision and Control. p. 1035-1040 6 p. 6426447

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

Compressive Sensing
Data-driven
Time series
Pathway
Proteins

Modeling response of biological signal pathways using a hybrid boolean framework

Chang, Y. H. & Tomlin, C., 2012, ASME 2012 5th Annual Dynamic Systems and Control Conference Joint with the JSME 2012 11th Motion and Vibration Conference, DSCC 2012-MOVIC 2012. Vol. 1. p. 335-344 10 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Ordinary differential equations
Biological systems
Dynamical systems
Mathematical models
Feedback
4 Citations (Scopus)

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

Chang, Y. H., Gray, J. & Tomlin, C., Dec 1 2012, In : Journal of Computational Biology. 19, 12, p. 1307-1323 17 p.

Research output: Contribution to journalArticle

Genetic Network
Biological Networks
Biology
Research Design
Costs and Cost Analysis
2011
5 Citations (Scopus)

Biologically-inspired coordination of multiple UAVs using sliding mode control

Chang, Y. H., Tomlin, C. & Hedrick, K., 2011, Proceedings of the American Control Conference. p. 4123-4128 6 p. 5991252

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

Sliding mode control
Aircraft
Synchronization
Motion control
Controllers
6 Citations (Scopus)

Inference of temporally evolving network dynamics with applications in biological systems

Chang, Y. H. & Tomlin, C., 2011, Proceedings of the IEEE Conference on Decision and Control. p. 3706-3711 6 p. 6160849

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

Network Dynamics
Biological systems
Biological Systems
Pathway
Graph Model
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
2008
7 Citations (Scopus)

Balance control in whole body coordination framework for biped humanoid robot MAHRU-R

Chang, Y. H., Oh, Y., Kim, D. & Hong, S., 2008, Proceedings of the 17th IEEE International Symposium on Robot and Human Interactive Communication, RO-MAN. p. 401-406 6 p. 4600699

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

Vibration control
Robots
Controllers
MATLAB
Vibrations (mechanical)

Development of a foot mechanism for landing experiment

Cheon, S., Oh, Y., Chang, Y. H. & Park, Y., 2008, IFAC Proceedings Volumes (IFAC-PapersOnline). 1 PART 1 ed. Vol. 17.

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

Landing
Experiments
Robots
1 Citation (Scopus)

Vibration suppression and balance control for biped humanoid walking

Chang, Y. H., Oh, Y., Kim, D. & Hong, S., 2008, IFAC Proceedings Volumes (IFAC-PapersOnline). 1 PART 1 ed. Vol. 17.

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

Vibration control
Robots
Vibrations (mechanical)
Experiments
5 Citations (Scopus)

Walking pattern generation for humanoid robots with LQR and feedforward control method

Hong, S., Oh, Y., Chang, Y. H. & You, B. J., 2008, Proceedings - 34th Annual Conference of the IEEE Industrial Electronics Society, IECON 2008. p. 1698-1703 6 p. 4758209

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

Feedforward control
Robots
Controllers
Pendulums
Feedback
2007
13 Citations (Scopus)

An omni-directional walking pattern generation method for humanoid robots with quartic polynomials

Hong, S., Oh, Y., Chang, Y. H. & You, B. J., 2007, IEEE International Conference on Intelligent Robots and Systems. p. 4207-4213 7 p. 4399397

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

Trajectories
Polynomials
Robots
Pendulums
3 Citations (Scopus)

Online phase tracking of interferometric optical fiber sensors for vibration control

Chang, Y. H., Kim, D. H., Han, J. H. & Lee, I., Apr 2007, In : Journal of Intelligent Material Systems and Structures. 18, 4, p. 311-321 11 p.

Research output: Contribution to journalArticle

Fiber optic sensors
Vibration control
Interferometers
Sensors
Piezoelectric materials
2006
4 Citations (Scopus)

A patch-type smart self-sensing actuator

Chang, Y. H., Kim, D. H., Lee, I. & Han, J. H., Jun 1 2006, In : Smart Materials and Structures. 15, 3, p. 667-677 11 p.

Research output: Contribution to journalArticle

Actuators
actuators
Vibration control
feedback control
Feedback control