Publications

Journal (J), (peer reviewed) Conference (C), Book Chapter(B), US Patent Applications and Issued Patents, Non-refereed Conference/Meeting (M)

    [Code]

• • Variational autoencoder (VAE) for MEMA image analysis: https://github.com/schaugf/ImageVA

  • Staining Unmixing and Normalization in Python: https://github.com/schaugf/HEnorm_python

  • Custom Software and Scripts for Nuclear Segmentation and Marker Quantification: https://ars.els-cdn.com/content/image/1-s2.0-S2211124718320503-mmc4.zip

  • SHIFT: https://gitlab.com/eburling/shift

  • cmIF: https://gitlab.com/engje/cmif 

  • Napari cmIF viewer: https://gitlab.com/eburling/napari-cmif-viewer

  • RESTORE: https://gitlab.com/Chang_Lab/cycif_int_norm

  • NEMO: https://github.com/schaugf/NEMO

  • CYCIF-Sankey: https://gitlab.com/eburling/cycif-sankey

  • MicePAN: https://github.com/GelatinFrogs/MicePan-Segmentation

  • Grapheno: https://gitlab.com/eburling/grapheno

  • ME-VAE: https://github.com/GelatinFrogs/ME-VAE_Architecture

Peer-Reviewed / Refereed Articles /BioRxiv(* equal contribution / # corresponding)

• (under review) 

  • J58. Cigdem Ak,  Zeynep Sayar,  Guillaume Thibault,  Erik Burlingame, Jenny Eng, Alex Chitsazan,  Andrew Adey,  Christopher Boniface,  Paul T Spellman,  George V Thomas,  Ryan Kopp,  Emek Demir,  Young Hwan Chang,  Vasilis Stavrinides,  Sebnem Ece Eksi, "Multiplex imaging of localized prostate tumors reveals changes in mast cell type composition and spatial organization of AR-positive cells in the tumor microenvironment" (bioRxiv)

  • J57. Prabhakaran, Sandhya, Clarence Yapp, Gregory J. Baker, Johanna Beyer, Young Hwan Chang, Allison L. Creason, Robert Krueger et al. "Addressing persistent challenges in digital image analysis of cancerous tissues" (bioRxiv)

  • J56. Zachary Sims*, Luke Strgar*, Dharani Thirumalaisamy, Robert Heussner, Guillaume Thibault, Young Hwan Chang#, "SEG: SEgmentation Evaluation in absence of Ground truth labels" (bioRxiv)

• 2024

  • J55. Zachary Sims, Gordon Mills, Young Hwan Chang#, "MIM-CyCIF: Masked Imaging Modeling for Enhancing Cyclic Immunofluorescence (CyCIF) with Panel Reduction and Imputation" (bioRxiv), Communications Biology (accepted)

  • J54. Riley M. Whalen, Ashley N. Anderson, Jocelyn A. Jones, Zachary Sims, Young Hwan Chang, Michel A. Nederlof, Summer L. Gibbs, Melissa H. Wong, Ultra-high content analyses of circulating and tumor-associated hybrid cells, Scientific Reports (accepted)

  • J53. Robert T. Heussner, Riley M. Whalen, Ashley Anderson, Heather Theison, Joseph Baik, Summer Gibbs, Melissa H. Wong, Young Hwan Chang#, "Quantitative image analysis pipeline for detecting circulating hybrid cells in immunofluorescence images with human-level accuracy" (bioRxiv), Cytometry: Part A (accepted)

  • J52. Femel, J., Booth, J.L., Asnaashari, T.G., Leachman, S.A., Tsujikawa, T., White, K.P., Chang, Y.H. and Lund, A.W., 2024. "Quantitative multiplex immunohistochemistry reveals inter-patient lymphovascular and immune heterogeneity in primary cutaneous melanoma", Frontiers Immunology.

  • C77. Zac Sims, Young Hwan Chang#, "A Masked Image Modeling Approach to CycIF Panel Reduction and Marker Imputation", 2024 GTC AI conference.

• 2023

  • J51. Erik Burlingame*, Luke Ternes*, Jia-Ren Lin, Yu-An Chen, Eun Na Kim, Joe W. Gray, Young Hwan Chang#, "3D multiplexed tissue imaging reconstruction and optimized region-of-interest (ROI) selection through deep learning model of channels embedding" (bioRxiv), Frontiers in Bioinformatics, section Computational BioImaging (Current advances of computational methods for tissue multiplexed imaging in research and diagnosis)

  • J50. Eun Na Kim*, Phyllis Zixuan Chen*, Dario Bressan, Monika Tripathi, Ahmad Miremadi, Massimilano di Pietro, Lisa M Coussens, Gregory J Hannon, Rebecca C Fitzgerald, Lizhe Zhuang#, Young Hwan Chang#, "Dual-modality imaging of immunofluorescence and imaging mass cytometry for whole slide imaging with accurate single-cell segmentation" (bioRxiv), Cell Reports Methods

  • J49. Zinab O Doha, Xiaoyan Wang, Nicholas Calistri, Jennifer Eng, Colin J Daniel, Luke Ternes, Eun Na Kim, Carl Pelz, Michael Munks, Courtney Betts, Nell Kirchberger, Sunjong Kwon, Elmar Bucher, Xi Li, Trent Waugh, Jennifer A Pietenpol, Melinda E Sanders, Gordon B Mills, Koei Chin, Young Hwan Chang, Lisa M Coussens, Joe W Gray, Laura Heiser, Rosalie C Sears, "A Novel Mouse Model that Recapitulates the Heterogeneity of Human Triple Negative Breast Cancer" (bioRxiv), Nature Communications

  • J48. Erin S. Stempinski, Lucas Pagano, Jessica L. Riesterer, Steven K. Adamou, Guillaume Thibault, Xubo Song, Young Hwan Chang, Claudia S. Lopes, "Automated large volume sample preparation for vEM", Methods in Cell Biology, 2023. Academic Press Inc.

  • J47. Copperman, J., Gross, S.M., Chang, Y.H., Heiser, L.M. and Zuckerman, D.M., 2023. Morphodynamical cell state description via live-cell imaging trajectory embedding. Communications Biology, 6(1), p.484.

  • J46. Steele, M.M., Jaiswal, A., Delclaux, I., Dryg, I.D., Hurugan, D., Femel, J., Son, S., du Bois, H., Hill, C., Leachman, S.A.,  Chang, Y.H., Coussens, L. M., Anandasabapathy, N., Lund, A.W., 2023. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology, 24(4), pp.664-675.

  • C76. Zac Sims, Young Hwan Chang#, "A Masked Image Modeling Approach to CycIF Panel Reduction and Marker Imputation", MLCB 2023 (Oral presentation)

    • Oral presentations were selected from the top 15% of all submitted 2-page and 8-page papers. 

  • C75. Erik Burlingame*, Luke Ternes*, Eun Na Kim, Joe W. Gray, Young Hwan Chang#, Multiplexed tissue imaging reconstruction and optimized region-of-interest (ROI) selection through deep learning model of channels embedding, AACR 2023

• 2022

  • J45. Luke Ternes, Jia-Ren Lin, Yu-An Chen, Joe W. Gray, Young Hwan Chang#, "Computational Multiplex Panel Reduction to Maximize Information Retention in Breast Cancer Tissue Microarrays" (bioRxiv), PLOS Computational Biology (link)

  • J44. Michael S. Parappilly, Yuki Chin, Riley M. Whalen, Ashley N. Anderson, Trinity L. Robinson, Luke Strgar, Thomas L. Sutton, Patrick Conley, Christopher Klocke, Summer L. Gibbs, Young Hwan Chang, Guanming Wu, Melissa H. Wong, Alison H. Skalet, Circulating Neoplastic-Immune Hybrid Cells Predict Metastatic Progression in Uveal Melanoma, Cancers, 2022, 14(19), 4617 

  • J43. Stahlberg, E.A., Abdel-Rahman, M.H., Aguilar, B., Asadpoure, A., Beckman, R.A., Borkon, L., Bryan, J.N., Cebulla, C.C., Chang, Y.H., Chatterjee, A. and Deng, J., Exploring Approaches for Predictive Cancer Patient Digital Twins: Opportunities for Collaboration and Innovation. Frontiers in Digital Health, p.191.

  • J42. Navid Mohammad Mirzaei, Zuzana Tatarova, Wenrui Hao, Navid Changizi, Alizera Asadpoure, Ioannis K. Zervantonakis, Yu Hu, Young Hwan Chang, Leili Shahriyari, "A PDE Model of Breast Tumor Progression in MMTV-PyMT Mice", Journal of Personalized Medicine, 12(5): 807 (link)

  • J41. Srinand Sundaram*, Eun Na Kim*, Georgina M. Jones, Shamilene Sivagnanam, Monika Tripathi, Ahmad Miremadi, Massimiliano Di Pietro, Lisa Coussens, Rebecca C. Fitzgerald, Young Hwan Chang# and Lizhe Zhuang#, Deciphering the immune complexity in esophageal adenocarcinoma and pre-cancerous lesions with sequential multiplex immunohistochemistry and sparse subspace clustering (SSC) approach. Frontiers in Immunology - Cancer Immunity and Immunotherapy (link)

  • J40. Luke Ternes, Mark Dane, Marilyne Labie, Gordon Mills, Joe Gray, Laura Heiser, Young Hwan Chang#, "A Multi-Encoder Variational AutoEncoder controls Multiple Transformational Features in Single Cell Image Analysis" (bioRxiv), Communications Biology (link)

  • J39. Navid Mohammad Mirzaei, Navid Changizi, Alireza Asadpoure, Sumeyye Su, Dilruba Sufia, Zuzana Tatarova, Ioannis K. Zervantonakis, Young Hwan Chang, Leili Shahriyari, "Investigating key cell types and molecules dynamics in  PyMT mice model of breast cancer through a mathematical model", PLOS Computational Biology, 18(3): e1009953 (link)

  • J38. Denis Schapiro, Clarence Yapp, Artem Sokolov, Sheila M. Reynolds, Yu-An Chen, Damir Sudar, Yubin Xie, Jeremy Muhlich, Raquel Arias-Camison, Sarah Arena, Adam J. Taylor, Milen Nikolov, Madison Tyler, Jia-Ren Lin, Erik Burlingame, Human Tumor Atlas Network, Young Hwan Chang, Samouil L. Farhi, Vésteinn Thorsson, Nithya Venkatamohan, Julia L. Drewes, Dana Pe’er, David A. Gutman, Markus D. Herrmann, Nils Gehlenborg, Peter Bankhead, Joseph T. Roland, John M. Herndon, Michael P. Snyder, Michael Angelo, Garry Nolan, Jason R. Swedlow, Nikolaus Schultz, Daniel T. Merrick, Sarah A. Mazzili, Ethan Cerami, Scott J. Rodig, Sandro Santagata & Peter K. Sorger, MITI minimum information guidelines for highly multiplexed tissue images, Nature Methods (link)

  • J37. Brett E. Johnson, Allison L. Creason, Jayne M. Stommel, Jamie Keck, Swapnil Parmar, Courtney B. Betts, Aurora Blucher, Christopher Boniface, Elmar Bucher, Erik Burlingame, Koei Chin, Jennifer Eng , Heidi S. Feiler, Annette Kolodzie , Ben Kong, Marilyne Labrie, Patrick Leyshock , Souraya Mitri, Janice Patterson, Jessica L. Riesterer, Shamilene Sivagnanam, Damir Sudar, Guillaume Thibault, Christina Zheng, Xiaolin Nan, Laura M. Heiser, Paul T. Spellman, George Thomas, Emek Demir, Young Hwan Chang, Lisa M. Coussens, Alexander R. Guimaraes, Christopher Corless, Jeremy Goecks, Raymond Bergan, Zahi Mitri, Gordon B. Mills, and Joe W. Gray, "An Omic and Multidimensional Spatial Atlas from Serial Biopsies of an Evolving Metastatic Breast Cancer" (bioRxiv), Cell Reports Medicine (link)

  • C74. Walid Bousselham, Guillaume Thibault, Lucas Pagano, Archana Machireddy, Joe Gray, Young Hwan Chang, Xubo Song, "Efficient Self-Ensemble for Semantic Segmentation", British Machine Vision Conference 2022 (accepted)

  • C73. Tina Ghodsi, Young Hwan Chang#, "Optimal drug treatment for reducing long-term drug resistance", the 61st IEEE Conference on Decision and Control, Dec 5-9 (accepted)

  • C72. Luke Ternes, Mark Dane, Marilyne Labie, Gordon Mills, Joe Gray, Laura Heiser, Young Hwan Chang#, "Extracting more biologically relevant features from multiplexed imaging with a Multi-Encoder Variational AutoEncoder (ME-VAE)", Image-based profiling workshop at the 2022 Pacific Symposium on Biocomputing conference, Jan 3-7 (selected as a lightning talk) (link)

• 2021

  • J36. CSBC/PS-ON Image Analysis Working Group, Juan Carlos Vizcarra,  Erik A Burlingame,  Clemens B Hug,  Yury Goltsev,  Brian S White,  Darren R Tyson,  Artem Sokolov, A community-based approach to image analysis of cells, tissues and tumors, Computerized Medical Imaging and Graphics (bioRxiv) (accepted)

  • J35. Kanako Yoshimura, Takahiro Tsujikawa, Junichi Mitsuda, Hiroshi Ogi, Sumiyo Saburi, Gaku Ohmura, Akihito Arai, Saya Shibata, Guillaume Thibault, Young Hwan Chang, Daniel R Clayburgh, Satoru Yasukawa, Aya Miyagawa-Hayashino, Eiichi Konishi, Kyoko Itoh, Lisa M Coussens, Shigeru Hirano, Spatial profiles of intratumoral PD-1+ helper T cells predict prognosis in head and neck squamous cell carcinoma, Frontiers in Immunology  (link)

  • J34. Mirzaei NM, Su S, Sofia D, Hegarty M, Abdel-Rahman MH, Asadpoure A, Cebulla C, Chang YH, Hao W, Jackson P, Lee AV, Stover DG, Tatarova Z, Zervantonakis I, Shahriyari L, Mathematical Model of Breast Tumors Progression Based on Their Immune Infiltration. Journal of Personalized Medicine (link)

  • J33. Marilyne Labrie, Allen Li, Allison Creason, Courtney Betts, Jamie Keck, Brett Johnson, Shamilene Sivagnanam, Christopher Boniface, Hongli Ma, Aurora Blucher, Young Hwan Chang, Koei Chin, Jacqueline Vuky, Alexander Guimaraes, Molly Downey, Jeong Youn Lim, Lina Gao, Kiara Siex, Swapnil Parmar, Annette Kolodzie, Paul Spellman, Jeremy Goecks, Lisa Coussens, Christopher Corless, Raymon Bergan, Joe Gray, Gordon Mills, Zahi Mitri, Multi-omics analysis of serial samples from metastatic TNBC patients on PARP inhibitor monotherapy provide insight into rational PARP inhibitor therapy combinations, npj Precision Oncology (medRxiv) (link)

  • J32. Dariush Fooladivanda*, Qie Hu*, Young Hwan Chang#, Secure Dynamic State Estimation for Cyber Security of AC Microgrids  (* equal contribution), Frontiers in Control Engineering, section Nonlinear Control (arxiv) https://doi.org/10.3389/fcteg.2021.734220

  • J31. Erik Ames Burlingame, Jennifer Eng, Guillaume Thibault, Koei Chin,  Joe W. Gray,  Young Hwan Chang#, "Toward reproducible, scalable, and robust data analysis across multiplex tissue imaging platforms" (bioRxiv), Cell Reports Methods 2021 Jul 23:100053.

  • J30. Matthew S. Dietz, Thomas L. Sutton, Brett S. Walker, Charles E. Gast, Luai Zarour, Sidharth K. Sengupta, John R. Swain, Jennifer Eng, Michael Parappilly, Kristen Limbach, Ariana Sattler, Erik Burlingame, Yuki Chin, Austin Gower, Jose L. Montoya Mira, Ajay Sapre, Yu-Jui Chiu, Daniel R. Clayburgh, SuEllen J. Pommier, Jeremy P. Cetnar, Jared M. Fischer, Jerry J. Jaboin, Seunggu J. Han, Kellie J. Nazemi, Rodney F. Pommier, Kevin G. Billingsley, Brett C. Sheppard, V. Liana Tsikitis, Alison H. Skalet, Skye C. Mayo, Charles D. Lopez, Joe W. Gray, Gordon B. Mills, Zahi Mitri, Young Hwan Chang, Koei Chin, Melissa H. Wong, "Relevance of Circulating Hybrid Cells as a Non-Invasive Biomarker for Myriad Solid Tumors", Scientific Reports, 11, 13630 (pdf)

  • C71. Tina Ghodsi Asnaashari, Young Hwan Chang#, Strategies to reduce long-term drug resistance by considering effects of  differential selective treatments, International Symposium on Mathematical and Computational Oncology

  • C70. Luke Ternes*, Ge Huang*, Christian Lanciault, Guillaume Thibault, Rachelle Riggers, Joe W. Gray, John Muschler#, Young Hwan Chang#, VISTA: VIsual Semantic Tissue Analysis for pancreatic disease quantification in murine cohorts, AACR Virtual Special Conference on Pancreatic Cancer on September 29-30

  • C69. Ternes L, Mark D, Marilyne L, Gordon M, Gray J, Heiser L, Chang YH#, ME-VAE: Multi-Encoder Variational AutoEncoder for Controlling Multiple Transformational Features in Single Cell Image Analysis, 29th Conference on Intelligent Systems for Molecular Biology and the 20th European Conference on Computational Biology (ISMB/ECCB 2021), MLCSB COSI: Machine Learning in Computational and Systems Biology, July 25-30, 2021 (virtual presentation).

• 2020

  • J29. Anne Trinh, Carlos R. Gil Del Alcazar, Sachet A. Shukla, Koei Chin, Young Hwan Chang, Guillaume Thibault , Jennifer Eng , Bojana Jovanović, C. Marcelo Aldaz , So Yeon Park , Joon Jeong , Catherine Wu, Joe Gray, Kornelia Polyak, "Genomic alterations during the in situ to invasive ductal breast carcinoma transition shaped by the immune system", Molecular Cancer Research (pdf)

  • J28. Luke Ternes*, Ge Huang*, Christian Lanciault, Guillaume Thibault, Rachelle Riggers, Joe W. Gray, John Muschler#, Young Hwan Chang#,"VISTA: VIsual Semantic Tissue Analysis for pancreatic disease quantification in murine cohorts" (bioRxiv) Scientific Reports (pdf)  

  • J27. Erik Burlingame, Mary McDonnell, Geoffrey F. Schau, Guillaume Thibault, Christian Lanciault, Terry Morgan, Brett Johnson, Christopher Corless, Joe Gray, Young Hwan Chang#,"SHIFT: Speedy Histological-to-ImmunoFluorescent Translation of a tumor signature enabled by deep learning” (bioRxiv), Scientific Reports (pdf)

  • J26. Orit Rozenblatt-Rosen, HTAN et al., "The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution", Cell (pdf) 

  • J25. Young Hwan Chang#, Koei Chin, Guillaume Thibault, Jennifer Eng, Erik Burlingame,  Joe W. Gray#, "RESTORE: Robust intEnSiTy nORmalization mEthod for multiplexed imaging" (bioRxiv), Communications Biology (pdf)

  • J24. Elizabeth Mitchell,  Sonali Jindal, Tiffany Chan,  Jayasri Narasimhan,  Shamilene Sivagnanam, Elliot  Gray,  Young Hwan Chang, Sheila Weinmann,  Pepper Schedin, "Loss of myoepithelial calponin-1 characterizes high risk ductal carcinoma in situ cases, which are further stratified by T cell composition", Molecular Carcinogenesis (special edition) [IF=3.411] (pdf) (cover)

  • J23. Geoffrey F. Schau, Erik A. Burlingame, Guillaume Thibault, Tauangtham Anekpuritanang, Ying Wang, Joe W. Gray, Christopher Corless, Young Hwan Chang#, "Predicting primary site of secondary liver cancer with a neural estimator of metastatic origin," J. Med. Imag. 7(1), 012706 (2020), doi: 10.1117/1.JMI.7.1.012706. 

  • C68. Luke Ternes, Joe W Gray, Laura Heiser, Young Hwan Chang#. "Feature controlled variational autoencoder to learn biologically meaningful features for single cell image analysis”, Workshop on Learning Meaningful Representations of Life (LMRL) at NeurIPS 2020, Dec 11 (accepted)

  • C67. Luke Ternes, Laura Heiser, Young Hwan Chang# "Feature Controlled Variational Autoencoder for Single Cell Image Analysis", the 15th Machine Learning in Computational Biology (MLCB) meeting, Nov 23-24 (accepted)

  • C66. Elliot Gray, Shannon Liudahl, Shamilene Sivagnanam, Courtney Betts, Jason Link, Dove Keith, Brett Sheppard, Rosalie Sears, Guillaume Thibault, Joe W. Gray, Lisa M. Coussens, Young Hwan Chang#, "Activation vs. Organization: Prognostic Implications of T and B cell Features of the PDAC Microenvironment", International Symposium on Mathematical and Computational Oncology (ISMCO'20) [Oral presentation] (accepted)

  • C65. Geoff Schau, Erik Burlingame, Young Hwan Chang, "DISSECT: DISentangle SharablE ConTent for Multimodal Integration and Crosswise-mapping", 59th IEEE Conference on Decision and Control (CDC) (bioRxiv) (accepted)

  • C64. Young Hwan Chang, Jeremy Linsley, Josh Lamstein, Jaslin Kalra, Irina Epstein, Mariya Barch, Kenneth Daily, Phil Synder, Laura Heiser, Steve Finkbeiner, "Single cell tracking based on Voronoi partition via stable matching", 59th IEEE Conference on Decision and Control (CDC) (bioRxiv) (accepted)

  • C63. Nathan McMahon, Allison Solanki, Jocelyn Jones, Sunjong Kwon, Young Hwan Chang, Koei Chin, Michel Nederlof, Joe Gray, and Summer L. Gibbs, "Fluorescent Imaging for In Situ Measurement of Drug Target Engagement and Cell Signaling Pathways", Microscopy Histopathology and Analytics 2020 Washington, DC United States 20–23 April 2020 (pdf)

  • C62. Luke Ternes, Guillaume Thibault, Joe W. Gray, Young Hwan Chang#,  "Iterative deep learning based segmentation on cyclic immunofluorescence imaging by using recursive refinement", IEEE International Symposium on Biomedical Imaging (ISBI'20), the Marriott Coralville, Iowa City, April 3 - 7, 2020 

  • C61. Vahid Azimi, Ngoc Tran, Guillaume Thibault, Young Hwan Chang, Eva Medvedova, Kevin R. Turner, Robert Christian, Philipp W. Raess, Automated Analysis of Plasma Cell Percentage and Light Chain Clonality in Bone Marrow Biopsy Whole Slide Images, USCAP 2020 Annual Meeting, Feb 29-March 5, 2020 

  • C60. McMahon, N.P., Solanki, A., Jones, J., Kwon, S., Chang, Y.H., Chin, K., Nederlof, M.A., Gray, J.W. and Gibbs, S.L., Fluorescent imaging technologies for in situ measurement of drug target engagement and cell signaling pathways. In Visualizing and Quantifying Drug Distribution in Tissue IV (Vol. 11219, p. 112190O). International Society for Optics and Photonics. Feb, 2020.(pdf)

  • M21. Young Hwan Chang, "Seeing More with Deep Learning in Biomedical Imaging", OHSU-PSU Machine Learning for Health workshop, June 19, 2020 (Virtual presentation)

  • M20. Luke Ternes, Ge Huang, Christian Lanciault, Guillaume Thibault, Rachelle Rigger, Joe W. Gray, John Muschler, and Young Hwan Chang, "VISTA: Virtual ImmunoSTAining for pancreatic disease quantification in murine cohorts", OHSU-PSU Machine Learning for Health workshop, June 19, 2020 (Virtual presentation)

  • M19. Geoffrey Schau, Hassan Ghani, Erik Burlingame,  Joe Gray, Chris Corless, and Young Hwan Chang, "Unsupervised Histological Feature Manifold Learning for Massively Parallel Whole Slide Annotation", OHSU-PSU Machine Learning for Health workshop, June 19, 2020 (Virtual presentation)

  • M18. Erik Burlingame, Jennifer Eng, Guillaume Thibault, Geoffrey Schau, Koei Chin, Joe W. Gray, and Young Hwan Chang, "Balanced learning of cell state representations" OHSU-PSU Machine Learning for Health workshop, June 19, 2020 (Virtual presentation) [Poster session award (2nd prize)]

  • M17. Elliot Gray, Shannon Liudahl, Shamilene Sivagnanam, Courtney Betts, Jason Link, Dove Keith, Brett Sheppard, Rosalie Sears, Guillaume Thibault, Joe W. Gray, Lisa M. Coussens, and Young Hwan Chang, "Elucidating intratumoral T and B cell functionality related to spatial metrics for pancreatic cancer patient stratification via interpretable machine learning", OHSU-PSU Machine Learning for Health workshop, June 19, 2020 (Virtual presentation) [Poster session award (2nd prize)]

• 2019

  • J22. Yerim Lee, Carey Phelps, Tao Huang, Barmak Mostofian, Lei Wu, Ying Zhang, Young Hwan Chang, Philip J. S. Stork, Joe W. Gray, Daniel M. Zuckerman, Xiaolin Nan, "High-throughput single-particle tracking reveals nested membrane nanodomain organization that dictates Ras diffusion and trafficking", eLife [IF=7.551] (pdf)

  • J21. Julia K. Doh, Young Hwan Chang, Caroline A. Enns, Claudia S. Lopez, Kimberly E. Beatty, "Imaging VIPER-labeled Cellular Proteins by Correlative Light and Electron Microscopy", Bio-protocol (pdf)

  • J20. Jennifer Eng, Guillaume Thibault, Shiuh-Wen Luoh, Joe W. Gray, Young Hwan Chang#, Koei Chin#, "Cyclic Multiplexed-Immunofluorescence (cmIF), A Highly Multiplexed Method for Single-cell Analysis", Biomarkers for Immunotherapy of Cancer (Series Title: Methods and Protocols), Vol 2055, ISBN:978-1-4939-9772-5 (pdf) [book chapter] 

  • J19.  Takahiro Tsujikawa*, Guillaume Thibault*, Vahid Azimi, Sam Sivagnanam, Grace Banik, Casey Means, Rie Kawashima, Daniel R. Clayburgh, Joe W. Gray, Lisa M. Coussens, Young Hwan Chang#, "Robust cell detection and segmentation for image cytometry reveal Th17 cell heterogeneity", Cytometry: Part A [IF=3.26] (pdf)

  • J18. Ellen M. Langer*, Brittany L. Allen-Petersen*, Shelby M. King, Nicholas D. Kendsersky, Megan A. Turnidge, Genevra M. Kuziel, Rachelle Riggers, Ravi Samatham, Taylor S. Amery, Steven L. Jacques, Brett C. Sheppard, James E. Korkola, John L. Muschler, Guillaume Thibault, Young Hwan Chang, Joe W. Gray, Sharon C. Presnell, Deborah G. Nguyen, Rosalie C. Sears, "Modeling tumor phenotypes in vitro with three-dimensional bioprinting", Cell Reports [IF=8.032] (pdf)

  • C59. Erik Burlingame, Jennifer Eng, Guillaume Thibault, Geoffrey Schau, Koei Chin, Joe W. Gray, Young Hwan Chang#, "Balanced learning of cell state representations", Learning Meaningful Representation of Life (NeurIPS 2019 Workshop) (accepted)

  • C58. Geoffrey F. Schau, Zeynep Sayar, Erik A. Burlingame, Jenny Eng Koei Chin, Ece Eksi, Joe W. Gray, Young Hwan Chang#, "Estimating Mutual Information Content of Biomedical Data Modalities through Self-Supervised Domain Translation in Prostate Cancer", Learning Meaningful Representation of Life (NeurIPS 2019 Workshop) (accepted)

  • C57. Jennifer Eng, Elmar Bucher, Elliot Gray, Lydia Grace Campbell, Guillaume Thibault, Summer Gibbs, Joe W Gray#,Koei Chin#, Young Hwan Chang#,  "cmIF: A python library for scalable multiplex imaging pipelines", the 1st International Symposium on Mathematical and Computational Oncology (ISMCO), Lake Tahoe, Oct 14-16, 2019 (selected for an oral presentation)

  • C56. Vahid Azimi, Ngoc Tran, Guillaume Thibaut, Young Hwan Chang, Eva Medvedova, Philipp W. Raess, An automated image analysis for plasma cell quantitation and multiple myeloma prognostication, Pathology Visions 2019, Oct 6-8, Orlando, FL (abstract)

  • C55. Luke Ternes, Caitlin Mills, Kartik Subramanian, Yunguan Wang, Clarence Yapp, Sean Gross, LINCS MCF10A Consortium, Joe Gray, Peter Sorger, Laura Heiser, Young Hwan Chang, "The temporal dynamics of ligand treated MCF10A cells using cyclic immunofluorescent imaging data”, BioImaging Informatics 2019, Allen Institute, Oct 2-4, 2019 (abstract) (link)

  • C54. J Linsley, YH Chang, L Heiser, J Kalra, J Lamstein, I Epstein, M Barch, K Daily, P Synder, D Linsley, S Finkbeiner, Automated single cell tracking for longitudinal imaging of neurodegeneration, BioImage Informatics 2019, Oct 2-4, 2019, Allen Institute (selected for an oral presentation [15 selected talks]) (link) (talk)

  • C53. Lizhe Zhuang, Young Hwan Chang, Srinand Sundaram, Sam Sivagnanam, Massimiliano Di Pietro, Lisa Coussens and Rebecca C. Fitzgerald, "Deciphering the immune complexity in oesophageal adenocarcinoma and pre-cancerous lesions with multiplex IHC and Sparse Coding approach", The Early Detection of Cancer Conference, Sept 24-26, Canary Center, Stanford

  • C52. Erik Burlingame, Mary McDonnell, Geoffrey F. Schau, Guillaume Thibault, Christian Lanciault, Terry Morgan, Brett Johnson, Christopher Corless, Joe Gray, Young Hwan Chang*, "SHIFT: deep learning-based inference of biomarker distribution in histopathology images with speedy histopathological-to-immunofluorescent translation", Frontier of AI-Assisted Care (FAC) Symposium, Sept 18-19, Stanford, https://med.stanford.edu/frontierofaicare.html

  • C51. Geoffrey F. Schau, Erik A. Burlingame, Guillaume Thibault, Tauangtham Anekpuritanang, Ying Wang, Joe W. Gray, Christopher Corless, Young Hwan Chang*, "Predicting Primary Site of Secondary Liver Cancer with a NeuralEstimator of Metastatic Origin (NEMO)", Frontier of AI-Assisted Care (FAC) Symposium, Sept 18-19, Stanford, https://med.stanford.edu/frontierofaicare.html

  • C50. Nathan McMahon, Jocelyn Jones, Allison Solanki, Jennifer Eng, Sunjong Kwon, Young Hwan Chang, Guillaume Thibault, Koei Chin, Michel Nederlof, Joe Gray, Summer L Gibbs, "Antibody Conjugated Oligonucleotides as a Platform for Cyclic Immunofluorescent Staining" Microscopy and Microanalysis 25 (S2), 1206-1207

  • C49. Ying Zhang, Kai Tao, Lei Wu, Yerim Lee, Young Hwan Chang, Xiaolin Nan, "Studying Ras Nanocluster Formation on the Cell Membrane with Correlative Superresolution and Electron Microscopies", Microscopy and Microanalysis 25 (S2), 1220-1221

  • C48. Guillaume Thibault, Jessica Riesterer, Kevin Stoltz, Kevin Loftis, Geoffrey Schau, Erin Stempinski, Claudia López, Young Hwan Chang, Joe W Gray, "Computer Vision Techniques for Cancerous Cells Analysis in FIB-SEM Images", Microscopy and Microanalysis 25 (S2), 1196-1197

  • C47. Julia K Doh, Jonathan D White, Hannah K Zane, Young Hwan Chang, Claudia S Lόpez, Caroline A Enns, Kimberly E Beatty, "VIPER: A Genetically-Encoded Tag for Fluorescence and Electron Microscopy", Microscopy and Microanalysis 25 (S2), 1204-1205

  • C46. Jennifer Eng, Elliot Gray, Lydia Grace Campbell, Guillaume Thibault, Koei Chin, Young Hwan Chang, Mitch Dowsett, Joe Gray, "Immune-tumor spatial architecture in breast cancer subtypes", 34th Congress of the International Society for Advancement of Cytometry (CYTO 2019), Vancouver, June 22-26, 2019 (abstract) [selected as a finalist for the CYTO student competition, Exceptional Student Award]

  • C45. Elliot Gray*, Jenny Eng*, Guillaume Thibault, Lydia Grace Cambell, Koei Chin, Young Hwan Chang, Joe W. Gray, "Prognostic value of spatial pattern analysis in breast cancer subtypes using cyclic immunofluorescence imaging", NCI MathOnc meeting, OHSU, May 13-14, 2019 (2-page) [selected as an oral presentation]

  • C44. Geoffrey F. Schau, Mark Dane, Guillaume Thibault, Rebecca L. Smith, Kaylyn Devlin, David Kilburn, Joe W. Gray, Jim Korkola, Laura Heiser, Young Hwan Chang, "Deep Learning Approach for Assessment of Microenvironment Signals on Phenotypic State of Triple Negative Breast Cancer", 31st International Association for Breast Cancer Research Conference (IABCR 2018), Egmond aan Zee, The Netherlands, April 15-18, 2019 (abstract)

  • C43. Geoffrey Schau, Mark Dane, Guillaume Thibault, Joe Gray, Laura Heiser, Young Hwan Chang#, "Variational Autoencoding Tissue Response to Microenvironment Perturbation" SPIE Medical Imaging Conference, San Diego, Feb 16-21, 2019 (Oral Presentation) (pdf)

  • C42. Nathan McMahon, Jocelyn Jones, Jennifer Eng, Sunjong Kwon, Young Hwan Chang, Guillaume Thibault, Koei Chin, Michel Nederlof, Joe Gray, Summer Gibbs, Antibody conjugated oligonucleotides as a platform for cyclic immunofluorescent staining, SPIE Photonics WEST BIOS, San Francisco, CA Feb 2-7, 2019 (pdf)

  • C41. Kevin G Loftis, Kevin Stoltz, Guillaume Thibault, Jessica L Riesterer, Young Hwan Chang, Joe Gray, "CNN based semi-supervised FIB-SEM image segmentation via propagation of learned information from a small subset of a single image stack", 2019 Quantitative BioImaging Conference, Rennes, France, January 9-11, 2019 (pdf) (abstract)

• 2018

  • J17. Julia K. Doh, Jonathan D. White, Hannah K. Zane, Young Hwan Chang, Claudia S. Lopez, Caroline A. Enns, Kimberly E. Beatty, "VIPER is a genetically encoded peptide tag for fluorescence and electron microscopy", PNAS [IF=9.504], 115 (51) 12961-12966 (pdf)[OHSU Paper of the Month, Jan 2019]

  • J16. Ryan S. Lane , Julia Femel , Alec Breazeale, Christopher P. Loo , Guillaume Thibault , Andy Kaempf , Motomi Mori , Takahiro Tsujikawa , Young Hwan Chang, Amanda W. Lund, "IFNγ-Activated Dermal Lymphatic Vessels Inhibit Cytotoxic T cells in Melanoma and Inflamed Skin", Journal of Experimental Medicine, vol. 215 no. 12. [IF=10.79] (pdf)

  • J15. Young Hwan Chang*, You Jeong Heo*, Junhun Cho*, Sang Yong Song, Jeeyun Lee and Kyoung-Mee Kim "Computational measurement of tumor immune microenvironment in gastric adenocarcinomas" Scientific Reports 8(pdf) [IF=4.122]

  • J14. Florian Rambow, Aljosja Rogiers, Oskar Marin-Bejar, Sara Aibar, Julia Femel, Michael Dewaele, Panagiotis Karras, Daniel Brown, Young Hwan Chang, Maria Debiec-Rychter, Carmen Adriaens, Enrico Radaelli, Pascal Wolter, Oliver Bechter, Adriano Piris, Dennie T. Frederick, Genevieve Boland, Keith T. Flaherty, Joost J. van den Oord, Thierry Voet, Stein Aerts, Amanda W. Lund & Jean-Christophe Marine, "Towards minimal residual disease-directed therapy in melanoma" Cell (pdf) [IF=31.398]

  • J13. Young Hwan Chang*,#, Qie Hu* and Claire Tomlin, “Secure estimation based Kalman Filter for cyber–physical systems against sensor attacks" Automatica, Volume 54 (2018), Issue 9 (September) (pdf) [IF=6.126]

  • J12. Junhun Cho*, Young Hwan Chang*, You Jeong Heo, Seungtae Kim, Nayoung KD Kim, Joon Oh Park, Won Ki Kang, Jeeyun Lee, Kyoung-Mee Kim, "Four distinct immune microenvironment subtypes in gastric adenocarcinoma with special reference to microsatellite instability" (* equal contribution) ESMO Open, 3(3), p.e000326. (pdf)

  • C40. Yerim Lee, Carey Phelps, Tao Huang, Barmak Mostofian, Young Hwan Chang, Daniel Zuckerman, and Xiaolin Nan "Quantification of Ras membrane diffusion and multimer formation in live cells", q-bio Conference (2018), June 26 - 29, 2018 Rice University Houston, Texas  (pdf) [1-page]

  • C39. Elliot Gray, Elizabeth Mitchell, Sonali Jindal, Pepper Schedin, Young Hwan Chang#, "A method for quantification of calponin expression in myoepithelial cells in immunohistochemical images of ductal carcinoma in situ", IEEE International Symposium on Biomedical Imaging (ISBI'18), Washington DC, April 4-7, 2018 (Accepted) [4-page] (pdf)

  • C38. Erik Burlingame, Adam A. Margolin, Joe W. Gray, Young Hwan Chang# "SHIFT: Speedy Histopathological-to-ImmunoFluorescent Translation of whole slide images using conditional generative adversarial networks" In Medical Imaging 2018: Digital Pathology (Vol. 10581, p. 1058105). International Society for Optics and Photonics., 10 - 15 February 2018 Houston, Texas United States (Accepted, Oral Presentation) [6-page] (pdf)

  • M17. Takahiro Tsujikawa, Guillaume Thibault, Young Hwan Chang, Edward El Rassi, Daniel R. Clayburgh, David Sauer, Akihito Arai, Molly F. Kulesz-Martin, Motomi Mori, Shigeru Hirano, Paul W. Flint, Lisa M. Coussens, "Intra-tumor immune heterogeneity is associated with prognosis of oropharyngeal head and neck squamous cell carcinoma", Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL (pdf)

  • M16. Sonali Jindal, Elizabeth Mitchell, Tiffany Chan, Jay Narasimhan, Elliot Gray, Young Hwan Chang, Sheila Weinmann, Pepper Schedin,"Multiplex Immunohistochemistry Provides Insight into Cross-Talk between Myoepithelial and Immune Cells in Ductal Carcinoma In Situ (DCIS) Progression", the 20th annual Breast Cancer Issues Conference, March 17, Portland OR (abstract)

  • M15. Jennifer Eng, Summer Gibbs, Michel Nederlof, Guillaume Thibault, Young Hwan Chang, Koei Chin, Joe Gray, " Development of cyclic multiplex immunofluorescence assay for quantitative spatial analysis in breast cancer", the 20th annual Breast Cancer Issues Conference, March 17, Portland OR (abstract)

  • M14. Sonali Jindal, Elizabeth Mitchell, Tiffany Chan, Jay Narasimhan, Elliot Gray, Young Hwan Chang, Sheila Weinmann, Pepper Schedin, "Multiplex Immunohistochemistry Provides Insight Into Cross-Talk Between Myoepithelial And Immune Cells In Ductal Carcinoma In Situ (DCIS) Progression", EXPERIMENTAL BIOLOGY 2018, April 21-25, San Diego Convention Center, San Diego (abstract)

  • M13. Jocelyn Jones, Koei Chin, Sunjong Kwon, Young Hwan Chang, Michel Nederlof, Joe Gray, Summer L. Gibbs, "Antibody-oligonucleotide based cyclic immunofluorescence facilitates highly multiplexed quantitative analysis for clinical histology" SPIE Photonics West, BIOS 2018 (abstract)

• 2017

  • J11. Qie Hu*, Dariush Fooladivanda*, Young Hwan Chang*, and Claire J. Tomlin "Secure State Estimation and Control for Cyber Security of the Nonlinear Power Systems" (*equal contribution), IEEE Transactions on Control of Network Systems (pdf), 2017

  • J10. Takahiro Tsujikawa, Sushil Kumar, Rohan N. Borkar, Vahid Azimi, Guillaume Thibault, Young Hwan Chang, Ariel Balter, Patrick Leyshock, Rie Kawashima, Gina Choe, Eric R. Lutz, Lei Zheng, Elizabeth M. Jaffee, Edward El Rassi, Daniel R. Clayburgh, Molly F. Kulesz-Martin, Adam A. Margolin, Motomi Mori, Joe W. Gray, Paul W. Flint, Lisa M. Coussens*, "Quantitative multiplex immunohistochemistry reveals myeloid-inflamed tumor-immune complexity associated with poor prognosis", Cell Reports, (pdf), 2017

  • C37. Young Hwan Chang*, Takahiro Tsujikawa*, Adam Margolin, Lisa M. Coussens and Joe W. Gray "Multiplexed Immunohistochemistry Image Analysis using Sparse Coding" (*equal contribution), In Engineering in Medicine and Biology Society (EMBC), 2017 39th Annual International Conference of the IEEE (pp. 4046-4049). IEEE.  (4 pages paper) (Oral Presentation) (pdf)

  • C36. Young Hwan Chang*, Guillaume THIBAULT*, Owen Madin, Vahid Azimi, Cole Meyers, Brett Johnson, Jason Link, Adam Margolin, Joe W. Gray, "Deep Learning based Nucleus Classification in Pancreas Histological Images" (*equal contribution) In Engineering in Medicine and Biology Society (EMBC), 2017 39th Annual International Conference of the IEEE (pp. 672-675). IEEE. (4 pages paper) (pdf)

  • C35. Koei Chin, Michel Nederlof, Young Hwan Chang, Summer Gibbs, Sunjong Kwon, Ting Zheng, Joe Gray, "Development of cyclic multicolor immunofluorescence assay and companion software for quantitative spatial analysis in HER-2 breast cancer" the 32nd Congress of the International Society for Advancement of Cytometry (CYTO2017) (Abstract)

  • C34. Young Hwan Chang*, Takahiro Tsujikawa*, Adam Margolin, Lisa M. Coussens, Joe W. Gray, "Sparse coding-based image cytometry for multiplexed Immunohistochemistry" the 32nd Congress of the International Society for Advancement of Cytometry (CYTO2017) (Oral Presentation)

  • C33. Gabriella Fiore*, Young Hwan Chang, Qie Hu, M. Domenica Di Benedetto and Claire Tomlin, "Secure state estimation for linear systems with sparse malicious packet drops", In American Control Conference (ACC), 2017 (pp. 1898-1903). IEEE., May 24-26, Seattle, WA (pdf)

  • C32. Qie Hu*, Dariush Fooladivanda*, Young Hwan Chang*, and Claire J. Tomlin "Secure state estimation for nonlinear power systems under cyber attacks" (*equal contribution), In American Control Conference (ACC), 2017 (pp. 2779-2784). IEEE., May 24-26, Seattle, WA (pdf)

  • C31. Vahid Azimi,  Young Hwan Chang*, Guillaume Thibault, Jaclyn Smith, Takahiro Tsujikawa, Ben Kukull,  Brad Jensen, Christopher Corless, Adam Margolin, Joe W. Gray, "Breast Cancer Histopathology Image Analysis Pipeline for Tumor Purity Estimation", In Biomedical Imaging (ISBI 2017), 2017 IEEE 14th International Symposium on (pp. 1137-1140). IEEE, April 18-21, Melbourne, Australia (pdf)

  • C30. Young Hwan Chang*, Guillaume Thibault, Brett Johnson, Adam Margolin, Joe W. Gray, "Integrative Analysis on Histopathological Image for Identifying Cellular Heterogeneity", In Medical Imaging 2017: Digital Pathology (Vol. 10140, p. 101400T). International Society for Optics and Photonics. doi:10.1117/12.2250428 (pdf)

  • M12. Junhun Cho, Young Hwan Chang, Hyunsik Bae, Kyoung-Mee Kim "Programmed Cell Death-Ligand 1 Expression in Microsatellite Instability-High Gastric Carcinomas", United States & Canadian Academy of Pathology (USCAP) Annual Meeting, Mar 4-10, 2017 San Antonio, Texas (Abstract) (pdf)

• 2016

  • J9. David Hayden, Young Hwan Chang, Jorge Goncalves, Claire Tomlin, "Sparse Network Identifiability via Compressed Sensing"  Automatica, Vol 52, Issue 5, 2016 (pdf)

  • J8. Young Hwan Chang, Roel Dobbe, Palak Bhushan, Joe W. Gray, Claire Tomlin, "Reconstruction of gene regulatory networks based on repairing sparse low-rank matrices" IEEE/ACM transactions on computational biology and bioinformatics, 13(4), pp.767-777. (pdf) 

  • C29. Young Hwan Chang*, Guillaume Thibault, Vahid Azimi, Brett Johnson, Danielle Jorgens, Jason Link, Adam Margolin, Joe W. Gray "Quantitative Analysis of Histological Tissue Image based on Cytological Profiles and Spatial Statistics" In Engineering in Medicine and Biology Society (EMBC), 2016 IEEE 38th Annual International Conference of the (pp. 1175-1178). IEEE. (pdf) 

  • C28. Young Hwan Chang, Patrick Foley, Vahid Azimi, Rohan Borkar, Jonathan Lefman, "Primer for Image Informatics for Precision Medicine" Humanitarian Technology 2016 Science, Systems and Global Impact, June 2016, Cambridge-Boston MA USA (pdf) 

    • Procedia Engineering Volume 159, 2016, Pages 58–65

  • C27. Qie Hu*, Young Hwan Chang*, Claire J. Tomlin, "Secure Estimation for Unmanned Aerial Vehicles (UAVs) against Adversarial Attacks" International Council of the Aeronautical Sciences (ICAS) 2016 (pdf) 

• 2015

  • J7. Gowda S, Overduin SA, Chen M, Chang Y­‐H, Tomlin CJ, Carmena JM, "Accelerating submovement decomposition with search space reduction heuristics" IEEE Transactions on Biomedical Engineering, 62(10), pp.2508-2515. (pdf) 

  • J6. Young Hwan Chang, James Korkola, Dhara N. Amin, Mark Moasser, Jose M. Carmena, Joe W. Gray and Claire J. Tomlin, "Disentangling Multidimensional Spatiotemporal Data into their Common and Aberrant Responses", PLoS ONE 10(4): e0121607, 2015 (pdf) 

  • C26. Palak Bhushan, Young Hwan Chang, Claire J. Tomlin, "Iterative Function Separation for Gene Regulatory Function Identification", In Decision and Control (CDC), 2015 IEEE 54th Annual Conference on (pp. 133-138). IEEE. (pdf) 

  • C25. Young Hwan Chang, Roel Dobbe, Palak Bhushan, Joe W. Gray, Claire Tomlin, "Retrieving Common Dynamics of Gene Regulatory Network under Various Perturbations", In Decision and Control (CDC), 2015 IEEE 54th Annual Conference on (pp. 2531-2536). IEEE. (pdf) 

  • C24. Roel Dobbe, Young Hwan Chang, Jim Korkola, Joe W. Gray, Claire Tomlin, "Heterogeneity in cancer dynamics: A convex formulation to dissect dynamic trajectories and infer LTV models of networked systems", In American Control Conference (ACC), 2015 (pp. 4398-4403). IEEE. (pdf)

• 2014

  • J5. Young Hwan Chang, Joe W. Gray and Claire Tomlin, "Exact Reconstruction of Gene Regulatory Networks using Compressive Sensing," BMC Bioinformatics 2014, 15:400 (pdf)

  • C23. Young Hwan Chang*, J. Lu*, M. Chen* , M. Tomizuka, J. Carmena, C. J. Tomlin, "Design of Neural Decoder by Sensory Prediction and Error Correction" (* equally contributed), Proceedings of the 53rd IEEE Conference on Decision and Control (CDC), Los Angeles 2014 (pdf)

  • C22. Young Hwan Chang, Roel Dobbe, Palak Bhushan, Joe W. Gray, Claire Tomlin, "Reconstruction of gene regulatory networks based on repairing sparse low-rank matrices", the Seventh Annual RECOMB/ISCB RSG Conference, Nov 9-14, San Diego 2014 (Accepted for oral presentation and invited to submit partner journals to publish in a Pubmed-indexed journal)  (link)

  • C21. Roel Dobbe, Young Hwan Chang, Jim Korkola, Joe W. Gray, Claire Tomlin, "An efficient algorithm to retrieve a dynamic model and heterogeneous treatment response in HER2+ breast cancer", International Conference on Systems Biology 2014 (pdf)

  • C20. Young Hwan Chang*, Mo Chen*, Maryam Shanechi, Jose Carmena and Claire Tomlin, "A Design of Neural Decoder by Reducing Discrepancy between Manual Control (MC) and Brain Control (BC)" (* equally contributed), In Control Conference (ECC), 2014 European (pp. 516-521). IEEE. (pdf)

  • C19. Young Hwan Chang, and Claire Tomlin, "Reconstruction of Gene Regulatory Networks with Hidden Node" In Control Conference (ECC), 2014 European (pp. 1492-1497). IEEE. (pdf)

• 2013

  • Doctoral Dissertation

    • Young Hwan Chang, "Towards a Systems Understanding in Biology: Data and Modeling." (Doctoral Dissertation, UC Berkeley pdf)

  • C18. Young Hwan Chang, Mo Chen, Simon A. Overduin, Suraj Gowda, Jose M Carmena and Claire Tomlin, "Low-rank Representation of Neural Activity and Detection of Submovements", Proceedings of the 52nd IEEE Conference on Decision and Control (CDC), Florence, Italy, 2013 (pdf)

• 2012

  • J4. Young Hwan Chang, Joe W Gray, and Claire Tomlin, "Optimization-based Inference for Temporally Evolving Networks with Applications in Biology," Journal of Computational Biology. 19(12): 1307-1323, 2012  (pdf)

  • C17. S.A. Overduin, Y.-H. Chang, S. Gowda, M. Chen, A.L. Orsborn, K. So, E. Bizzi, C. Tomlin, J.M. Carmena, "Detection of submovement primitives for neuroprosthetic motor control" Society for Neuroscience 2012 (pdf)

  • C16. Young Hwan Chang, and Claire Tomlin, "Data-driven Graph Reconstruction using Compressive Sensing" In Decision and Control (CDC), 2012 IEEE 51st Annual Conference on (pp. 1035-1040). IEEE. (pdf)

  • C15. Young Hwan Chang, and Claire Tomlin, "Modeling Response of Biological Signal Pathways using a Hybrid Boolean Framework" In ASME 2012 5th Annual Dynamic Systems and Control Conference joint with the JSME 2012 11th Motion and Vibration Conference (pp. 335-344). American Society of Mechanical Engineers. (pdf)

• 2011

  • C14. Young Hwan Chang, and Claire Tomlin, "Inference of Temporally Evolving Network Dynamics with Applications in Biological Systems" In Decision and Control and European Control Conference (CDC-ECC), 2011 50th IEEE Conference on (pp. 3706-3711). IEEE. (pdf)

  • C13. Young Hwan Chang, Joe W. Gray, Claire Tomlin, "Optimization-based Inference for Temporally Evolving Boolean Networks with Applications in Biology"  In American Control Conference (ACC), 2011 (pp. 4129-4134). IEEE. (pdf)

  • C12. Young Hwan Chang, Claire Tomlin, Karl Hedrick, "Biologically-inspired Coordination of Multiple UAVs using Sliding Mode Control."  In American Control Conference (ACC), 2011 (pp. 4123-4128). IEEE. (pdf)

• 2008

  • C11. Seokmin Hong, Yonghwan Oh, Young-Hwan Chang, Bum-Jae You, “Walking pattern generation for Humanoid robots with LQR and feedforward control method.” The 34th Annual Conference of the IEEE Industrial Electronics Society (IECON2008) (pdf)

  • C10. Young-Hwan Chang, Yonghwan Oh, Doik Kim, Seokmin Hong, “Balance Control in Whole Body Coordination Framework for Biped Humanoid Robot MAHRU-R,” RO-MAN 2008. (pdf)

  • C9. Seyoung Cheon, Yonghwan Oh, Young-Hwan Chang, Youngpil Park, “Development of a foot mechanism for landing experiment,” 17th IFAC World Congress 2008. (pdf)

  • C8. Ho-Lim Choi, Young-Hwan Chang, Yonghwan Oh, Jong-Tae Lim, “On robust position control of DC motors by ǫ-PID controller and its application to humanoid robot arms”, 17th IFAC World Congress 2008. (pdf)

  • C7. Young-Hwan Chang, Yonghwan Oh, Doik Kim, Seokmin Hong, “Vibration Suppression and Balance Control for Biped Humanoid Walking,” 17th IFAC World Congress 2008. (pdf)

• 2007

  • J3. Chang, Y.-H., Kim, D.-H., Han, J.-H., Lee, I., "On-line phase tracking of interferometric optical fiber sensor for vibration control," Journal of Intelligent Material Systems and Structures, Vol 18, pp 311-321, 2007. (pdf)

  • C6. Seokmin Hong, Yonghwan Oh, Young-Hwan Chang, Bum-Jae You, “An Omni-directional Walking Pattern Generation Method for Humanoid Robots with Quartic Polynomials,” IEEE International Conference on Intelligent Robots and Systems (IROS 2007), San Diego, Oct 2007 (pdf)

• 2006

  • J2. Chang, Y.-H., Kim, D.-H., Han, J.-H., Lee, I., "A patch-type smart self-sensing actuator," Smart Materials and Structures, Vol 15, No.3, pp 667-677. 2006 (pdf)

• 2005

  • J1. Kim, D.-H., Chang, Y.-H., Han, J.-H., Lee, I., "Optical phase estimation for patch-type EFPI sensor system and its application to flutter suppression," Smart Materials and Structures, Vol 14, No.4, pp 696-706. 2005 (pdf)

• 2004

  • C5. Han, J.-H., Chang, Y.-H., Kim, D.-H., Lee, I., "Patch-type self-sensing actuator using PZT and EFPI for vibration control," 9th International Conference on New Actuators (ACTUATOR2004), Bremen, Germany, 2004. 6 (pdf)

  • C4. J. -H. Han, L. -H. Kang, Y. -H. Chang, D. -H. Kim, "Active vibration control using self-sensing actuator,” 4th International Symposium on Advanced Fluid Information and Transdisciplinary Fluid Integration, Japan, 2004. 3 (pdf)

  • C3. Chang, Y.-H., Kim, D.-H., Han, J.-H., Lee, I., “On-line Phase Tracking of EFPI Sensor and Fuzzy Logic Vibration Control,” International Workshop on Advanced Smart Materials and Smart Structures Technology, Hawaii, USA, January 12-14, 2004 (link)

• 2003

  • C2. Kim, J.-Y., Chang, Y.-H., Kim, E.-G., Lee I.-C., Kang, H.-G., Park. C. "The Image Interpretation Module Development for Daejeon, Korea," The 24th Asian conference on Remote Sensing & 2003 International Symposium on Remote Sensing, Busan Exhibition and Convention Center (BEXCO), Busan, Korea, November 3-7, 2003

  • C1. Kim. D.-H., Chang, Y.-H., Han, J.-H. Lee, I., "Active Control of Flow-Induced Vibration Using Piezoelectric Actuation and Neural-Networks," The 32nd  International Congress and Exposition on Noise Control Engineering, Jeju International Convention Center, Seogwipo, Korea, August 25-28, 2003 (pdf)

• Book Chapter

  • B2. Young Hwan Chang, Claire J. Tomlin, Network Identification Methods, Handbook of Mathematical Methods in Cancer Biology, NCI (submitted) (pdf)

  • B1. Seokmin Hong, Yonghwan Oh, Young-Hwan Chang, Bum-Jae You, “A Walking Pattern Generation Method for Humanoid Robots Using Least Square Method and Quartic Polynomial.” Humanoid Robots, ISBN 978-953-7619-44-2, Hard cover, 388 pages, Publisher: InTechPublication date: January 2009 (pdf)

• Meeting

  • M11. Vahid Azimi,  Young Hwan Chang*, Guillaume Thibault, Jaclyn Smith, Takahiro Tsujikawa, Ben Kukull,  Brad Jensen, Christopher Corless, Adam Margolin, Joe W. Gray, "Automated Calculation of Tumor Purity from Histopathology Specimens using Supervised Machine Learning", ACP Internal Medicine Meeting 2017, San Diego, CA, San Diego Convention Center, March 30 - April 1, 2017

  • M10. Young Hwan Chang, "Quantitative image analysis of cell-to-cell heterogeneity", NCI OHSU Tumor Heterogeneity Workshop, Oct 31, 2015

  • M9. Young Hwan Chang*, Qie Hu*, Claire Tomlin, "Secure Estimation for Cyber-Physical Systems against Adversarial Attacks," (Poster) Swarm Lab Retreat (June 4-5, 2015)

  • M8. Young Hwan Chang, Margaret Chapman, Roel Dobbe, Palak Bhushan, Joe W. Gray, Claire Tomlin, "Reconstruction of gene regulatory networks based on repairing sparse low-rank matrices," (Poster) Stanford Center for Systems Biology (2nd Annual Center Meeting, May 29, 2015)

  • M7. Roel Dobbe, Young Hwan Chang, Stephan Xiahuan Liu, Jim Korkola, Laura Heiser, Joe W. Gray, Claire Tomlin, "Leveraging novel methods for high-dimensional data analysis and system identification in cancer biology"  ICBP/PSOC Math Meeting, February 26-28, Tampa Florida

  • M6. Young Hwan Chang, Jim Korkola, Dhara N. Amin, Mark Moasser, Joe W. Gray, Claire J. Tomlin, “Denovo Data-driven Network Identification and Disentanglement of Heterogeneous Data into their Common and Aberrant Responses ,” (Poster) Stanford Center for Systems Biology (1st Annual Center Meeting, May 27, 2014)

  • M3.  Young Hwan Chang, and Claire Tomlin, "Optimization-based Inference for Temporally Evolving Networks with Applications in Biology" Integrative Cancer Biology Program  Steering Committee Meeting, New York, Sep 14-16, 2011 (Poster) 

  • M2. Young Hwan Chang, and Claire Tomlin, "Optimization-based Inference for Temporally Evolving Networks with Applications in Biology" Bay Area Physical Science-Oncology Center, PSOC 2nd Annual Site Visit, Stanley Hall, UC Berkeley. Aug 22, 2011 (Poster)

  • M1.  Young Hwan Chang, Joe W. Gray, Claire Tomlin, "Optimization-based Inference for temporal evolving biological (Boolean) Network with application of HER2 overexpressed breast cancer" NCI ICBP Mathematical Modeling Meeting 2010  (Poster)

    • Technical Report UCB/EECS-2010-133 (pdf)

  • M5. NCI's ICBP PI Meeting, Embassy Suits, San Francisco Airport Waterfront in Burlingame, CA, May 7-9, 2012

    • • Young Hwan Chang, and Claire Tomlin, "Data-driven Graph Reconstruction using Compressive Sensing" (Poster) 

  • M4. NSF EFRI Grantees Conference, Key Bridge Marriott, Arlingon, VA, Mar 7-9, 2012   

• U.S AND INTERNATIONAL PATENT APPLICATIONS AND ISSUED PATENTS

  • 3. Seokmin Hong, Yonghwan Oh, Young-Hwan Chang, Doik Kim, Bum-Jae You, "Method of generating a walking pattern for a humanoid robot," US8126594 B2 (pdf)

  • 2. Young-Hwan Chang, Yonghwan Oh, Doik Kim, Youngjin Choi, Bum-Jae You, “Apparatus and method for balancing and damping control in whole body coordination framework for biped humanoid robot,” US8447429 B2 (pdf)

  • 1. Lee, I., Han, J.-H., Kim, D.-H., Chang, Y.-H., "Patch-type Extrinsic Fabry-Perot Interferometric fiber optic sensor and realtime structural vibration monitoring method using the same," US7076122 B2 (pdf)

• DOMESTIC JOURNAL (KOREA)

  • 1. Chang, Y.-H., Kim. D.-H., Han, J.-H. Lee, I., “On-line Phase Tracking of Patch Type EFPI Sensor and  uzzy Logic Vibration Control,” Journal of the Korean Society for Noise and Vibration engineering, Vol 14, No. 8, pp726-733, 2004.8

• DOMESTIC CONFERENCE (KOREA)

  • 1. Young-Hwan Chang, Do-Hyung Kim, Seung-Man Yang, Ki-Yeon Park, Keun-Ho Rew and In Lee, "PPF/Adaptive PPF Control of Vortex-induced Vibration of Composite Beam with Rigid Cylinder," The Korean Society for Composite Materials Conference, Korean Air Gimhae Plants pp. 147-150. 2002. 10.

  • 2. Ki-Yeon Park, Do-Hyung Kim, Seung-Man Yang, Young-Hwan Chang, Won-Ho Shin and In Lee, “Subsonic Flutter Experiment of Composite Flat Plate,” The Korean Society for Aeronautical and Space Science Conference, Phoenix Park, pp. 246-249, 2002. 11

  • 3. Do-Hyung Kim, Young-Hwan Chang, Jae-Heung Han and In Lee, “Vibration Control of a Composite Plate with attached FBG sensor,” The Korean Society for Composite Materials Conference, Hoseo University pp. 14-17, 2003. 4

  • 4. Jae-Heung Han, Young-Hwan Chang, Do-Hyung Kim, and In Lee, “On-line Phase Tracking of Patch Type EFPI Sensor and Fuzzy Logic Vibration Control,” Journal of the Korean Society for Noise and Vibration engineering Conference, Gyeongju TEMF Hotel, pp. 568-574, 2004. 5

• DOMESTIC PATENT APPLICATIONS AND ISSUED PATENTS

  • 1. In Lee, Jae-Heung Han, Do-Hyung Kim, Young-Hwan Chang, "Patch-type Extrinsic Fabry-Perot Interferometric fiber optic sensor and realtime structural vibration monitoring method using the same," Patent Number (Korea) 0507839 (2005.08.03)

  • 2. In Lee, Jae-Heung Han, Do-Hyung Kim, Young-Hwan Chang, "Self-sensing actuator utilizing optical fiber and piezoelectric materials and operating method of the same," Patent Number (Korea) 0533323 (2005.11.28)

  • 3. Young-Hwan Chang, “System for Monitoring Quantity of Abrasion of Noncontact Brake Pad," Patent Number (Korea) 0534285 (2005.12.01)

  • 4. Young-Hwan Chang, “Tire strain monitoring system," Patent Number (Korea) 0579972 (2006.05.08)

  • 5. Young-Hwan Chang, “Active Balance Control method and system for shimmy improvement," Publication Number (Korea) 10-2004-0081008

  • 6. Young-Hwan Chang, “System that control head lamp-device reacting in the speed for automobile," Publication Number (Korea) 10-2004-0106645

  • 7. Young-Hwan Chang, “Cross Bar Structure of Suspension System for Automobile," Publication Number (Korea) 10-2005-0038038

  • 8. Young-Hwan Chang, “An active suspension for vehicle and a controlling method thereof," Publication Number (Korea) 10-2005-0060625

  • 9. Young-Hwan Chang, “Tire Pressure Monitoring System using time delay," Publication Number (Korea) 10-2005-0067390

  • 10. Young-Hwan Chang, “Defrost method of vehicle glass," Publication Number (Korea) 10-2007-0114903

  • 11. Young-Hwan Chang, Yonghwan Oh, Doik Kim, YoungJin Choi, Bum-Jae You, “Apparatus and method for balancing and damping control in whole body coordination framework for biped humanoid robot,” Publication Number (Korea) 10-2007-0132416