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2020 – today
- 2023
[j18]Erik A. 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. Frontiers Bioinform. 3 (2023)- [j17]Archana Machireddy, Guillaume Thibault, Kevin G. Loftis, Kevin Stoltz, Cecilia E. Bueno, Hannah R. Smith, Jessica L. Riesterer, Joe W. Gray, Xubo Song:
Segmentation of cellular ultrastructures on sparsely labeled 3D electron microscopy images using deep learning. Frontiers Bioinform. 3 (2023) - [j16]Lucas Pagano, Guillaume Thibault, Walid Bousselham, Jessica L. Riesterer, Xubo Song, Joe W. Gray:
Efficient semi-supervised semantic segmentation of electron microscopy cancer images with sparse annotations. Frontiers Bioinform. 3 (2023) - 2022
- [j15]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. PLoS Comput. Biol. 18(9): 1010505 (2022) - [c19]Walid Bousselham, Guillaume Thibault, Lucas Pagano, Archana Machireddy, Joe W. Gray, Young Hwan Chang, Xubo Song:
Efficient Self-Ensemble for Semantic Segmentation. BMVC 2022: 892 - 2021
- [i1]Walid Bousselham, Guillaume Thibault, Lucas Pagano, Archana Machireddy, Joe W. Gray, Young Hwan Chang, Xubo Song:
Efficient Self-Ensemble Framework for Semantic Segmentation. CoRR abs/2111.13280 (2021) - 2020
- [c18]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. ISMCO 2020: 44-55
2010 – 2019
- 2019
- [c17]Jennifer Eng, Elmar Bucher, Elliot Gray, Lydia Grace Campbell, Guillaume Thibault, Laura Heiser, Summer Gibbs, Joe W. Gray, Koei Chin, Young Hwan Chang:
cmIF: A Python Library for Scalable Multiplex Imaging Pipelines. ISMCO 2019: 37-43 - [c16]Geoffrey F. Schau, Guillaume Thibault, Mark A. Dane, Joe W. Gray, Laura M. Heiser, Young Hwan Chang:
Variational autoencoding tissue response to microenvironment perturbation. Image Processing 2019: 109491M - 2018
- [c15]Erik A. 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. Digital Pathology 2018: 1058105 - 2017
- [c14]Young Hwan Chang, Guillaume Thibault, Owen Madin, Vahid Azimi, Cole Meyers, Brett Johnson, Jason Link, Adam A. Margolin, Joe W. Gray:
Deep learning based Nucleus Classification in pancreas histological images. EMBC 2017: 672-675 - [c13]Young Hwan Chang, Takahiro Tsujikawa, Adam A. Margolin, Lisa M. Coussens, Joe W. Gray:
Multiplexed immunohistochemistry image analysis using sparse coding. EMBC 2017: 4046-4049 - [c12]Vahid Azimi, Young Hwan Chang, Guillaume Thibault, Jaclyn Smith, Takahiro Tsujikawa, Benjamin Kukull, Bradden Jensen, Christopher Corless, Adam A. Margolin, Joe W. Gray:
Breast cancer histopathology image analysis pipeline for tumor purity estimation. ISBI 2017: 1137-1140 - [c11]Young Hwan Chang, Guillaume Thibault, Brett Johnson, Adam A. Margolin, Joe W. Gray:
Integrative analysis on histopathological image for identifying cellular heterogeneity. Digital Pathology 2017: 101400T - 2016
- [j14]Young Hwan Chang, Roel Dobbe, Palak Bhushan, Joe W. Gray, Claire J. Tomlin:
Reconstruction of Gene Regulatory Networks Based on Repairing Sparse Low-Rank Matrices. IEEE ACM Trans. Comput. Biol. Bioinform. 13(4): 767-777 (2016) - [c10]Young Hwan Chang, Guillaume Thibault, Vahid Azimi, Brett Johnson, Danielle Jorgens, Jason Link, Adam A. Margolin, Joe W. Gray:
Quantitative analysis of histological tissue image based on cytological profiles and spatial statistics. EMBC 2016: 1175-1178 - 2015
- [c9]Roel Dobbe, Young Hwan Chang, James Korkola, Joe W. Gray, Claire J. Tomlin:
Heterogeneity in cancer dynamics: A convex formulation to dissect dynamic trajectories and infer LTV models of networked systems. ACC 2015: 4398-4403 - [c8]Young Hwan Chang, Roel Dobbe, Palak Bhushan, Joe W. Gray, Claire J. Tomlin:
Retrieving common dynamics of gene regulatory networks under various perturbations. CDC 2015: 2531-2536 - 2014
- [j13]Chris J. Oates, Frank Dondelinger, Nora Bayani, James Korkola, Joe W. Gray, Sach Mukherjee:
Causal network inference using biochemical kinetics. Bioinform. 30(17): 468-474 (2014) - [j12]Young Hwan Chang, Joe W. Gray, Claire J. Tomlin:
Exact reconstruction of gene regulatory networks using compressive sensing. BMC Bioinform. 15: 400 (2014) - 2013
- [j11]Hang Chang, Ju Han, Alexander Borowsky, Leandro A. Loss, Joe W. Gray, Paul T. Spellman, Bahram Parvin:
Invariant Delineation of Nuclear Architecture in Glioblastoma Multiforme for Clinical and Molecular Association. IEEE Trans. Medical Imaging 32(4): 670-682 (2013) - [c7]Guillaume Thibault, Kristiina Iljin, Christopher Arthur, Izhak Shafran, Joe W. Gray:
Adaptive H-Extrema for Automatic Immunogold Particle Detection. CIARP (2) 2013: 238-245 - 2012
- [j10]Steven M. Hill, Yiling Lu, Jennifer Molina, Laura Heiser, Paul T. Spellman, Terence P. Speed, Joe W. Gray, Gordon B. Mills, Sach Mukherjee:
Bayesian Inference of Signaling Network Topology in a Cancer Cell Line. Bioinform. 28(21): 2804-2810 (2012) - [j9]Steven M. Hill, Richard M. Neve, Nora Bayani, Wen-Lin Kuo, Safiyyah Ziyad, Paul T. Spellman, Joe W. Gray, Sach Mukherjee:
Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology. BMC Bioinform. 13: 94 (2012) - [j8]Young Hwan Chang, Joe W. Gray, Claire J. Tomlin:
Optimization-based Inference for Temporally Evolving Networks with Applications in Biology. J. Comput. Biol. 19(12): 1307-1323 (2012) - [c6]Quoc V. Le, Ju Han, Joe W. Gray, Paul T. Spellman, Alexander Borowsky, Bahram Parvin:
Learning invariant features of tumor signatures. ISBI 2012: 302-305 - 2011
- [j7]Hang Chang, Gerald Fontenay, Ju Han, Ge Cong, Frederick L. Baehner, Joe W. Gray, Paul T. Spellman, Bahram Parvin:
Morphometic analysis of TCGA glioblastoma multiforme. BMC Bioinform. 12: 484 (2011) - [c5]Young Hwan Chang, Joe W. Gray, Claire J. Tomlin:
Optimization-based inference for temporally evolving Boolean networks with applications in biology. ACC 2011: 4129-4134 - [c4]Ju Han, Hang Chang, Leandro A. Loss, Kai Zhang, Frederick L. Baehner, Joe W. Gray, Paul T. Spellman, Bahram Parvin:
Comparison of sparse coding and kernel methods for histopathological classification of gliobastoma multiforme. ISBI 2011: 711-714 - 2010
- [j6]Kai Zhang, Joe W. Gray, Bahram Parvin:
Sparse multitask regression for identifying common mechanism of response to therapeutic targets. Bioinform. 26(12): 97-105 (2010) - [j5]Leandro A. Loss, Anguraj Sadanandam, Steffen Durinck, Shivani Nautiya, Diane Flaucher, Victoria E. H. Carlton, Martin Moorhead, Yontao Lu, Joe W. Gray, Malek Faham, Paul T. Spellman, Bahram Parvin:
Prediction of epigenetically regulated genes in breast cancer cell lines. BMC Bioinform. 11: 305 (2010) - [j4]Ju Han, Hang Chang, Orsi Giricz, Genee Y. Lee, Frederick L. Baehner, Joe W. Gray, Mina J. Bissell, Paraic A. Kenny, Bahram Parvin:
Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture. PLoS Comput. Biol. 6(2) (2010) - [j3]Katarzyna A. Rejniak, Shizhen E. Wang, Nicole S. Bryce, Hang Chang, Bahram Parvin, Jerome Jourquin, Lourdes Estrada, Joe W. Gray, Carlos L. Arteaga, Alissa M. Weaver, Vito Quaranta, Alexander R. A. Anderson:
Linking Changes in Epithelial Morphogenesis to Cancer Mutations Using Computational Modeling. PLoS Comput. Biol. 6(8) (2010) - [c3]Solomon Itani, Joe W. Gray, Claire J. Tomlin:
An ODE model for the HER2/3-AKT signaling pathway in cancers that overexpress HER2. ACC 2010: 1235-1241
2000 – 2009
- 2009
- [j2]Sach Mukherjee, Steven Pelech, Richard M. Neve, Wen-Lin Kuo, Safiyyah Ziyad, Paul T. Spellman, Joe W. Gray, Terence P. Speed:
Sparse combinatorial inference with an application in cancer biology. Bioinform. 25(2): 265-271 (2009) - [j1]Debopriya Das, Matteo Pellegrini, Joe W. Gray:
A Primer on Regression Methods for Decoding cis-Regulatory Logic. PLoS Comput. Biol. 5(1) (2009) - [c2]Ju Han, Hang Chang, Gerald Fontenay, Nicholas J. Wang, Joe W. Gray, Bahram Parvin:
Morphometric Subtyping for a Panel of Breast Cancer Cell Lines. ISBI 2009: 791-794 - 2007
- [c1]Bahram Parvin, Nirmalya Ghosh, Laura Heiser, Merrill Knapp, Carolyn L. Talcott, Keith Laderoute, Joe W. Gray, Paul T. Spellman:
Spectral Decomposition of Signaling Networks. CIBCB 2007: 76-81
Coauthor Index
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