Joe W. Gray

Publication Activity (10 Years)

Years Active: 2007-2023
Publications (10 Years): 16

Top Topics

Semantic Segmentation

Electron Microscopy

Gene Regulatory

Top Venues

Frontiers Bioinform.

Medical Imaging: Digital Pathology

Publications

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)
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)
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)
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) (2022)
Walid Bousselham, Guillaume Thibault, Lucas Pagano, Archana Machireddy, Joe W. Gray, Young Hwan Chang, Xubo Song
Efficient Self-Ensemble for Semantic Segmentation. BMVC (2022)
Walid Bousselham, Guillaume Thibault, Lucas Pagano, Archana Machireddy, Joe W. Gray, Young Hwan Chang, Xubo Song
Efficient Self-Ensemble Framework for Semantic Segmentation. CoRR (2021)
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)
Geoffrey F. Schau, Guillaume Thibault, Mark A. Dane, Joe W. Gray, Laura M. Heiser, Young Hwan Chang
Variational autoencoding tissue response to microenvironment perturbation. Medical Imaging: Image Processing (2019)
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)
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. Medical Imaging: Digital Pathology (2018)
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)
Young Hwan Chang, Guillaume Thibault, Brett Johnson, Adam A. Margolin, Joe W. Gray
Integrative analysis on histopathological image for identifying cellular heterogeneity. Medical Imaging: Digital Pathology (2017)
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)
Young Hwan Chang, Takahiro Tsujikawa, Adam A. Margolin, Lisa M. Coussens, Joe W. Gray
Multiplexed immunohistochemistry image analysis using sparse coding. EMBC (2017)
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)
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) (2016)
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)
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)
Young Hwan Chang, Joe W. Gray, Claire J. Tomlin
Exact reconstruction of gene regulatory networks using compressive sensing. BMC Bioinform. 15 (2014)
Chris J. Oates, Frank Dondelinger, Nora Bayani, James Korkola, Joe W. Gray, Sach Mukherjee
Causal network inference using biochemical kinetics. Bioinform. 30 (17) (2014)
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) (2013)
Guillaume Thibault, Kristiina Iljin, Christopher Arthur, Izhak Shafran, Joe W. Gray
Adaptive H-Extrema for Automatic Immunogold Particle Detection. CIARP (2) (2013)
Quoc V. Le, Ju Han, Joe W. Gray, Paul T. Spellman, Alexander Borowsky, Bahram Parvin
Learning invariant features of tumor signatures. ISBI (2012)
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 (2012)
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) (2012)
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) (2012)
Young Hwan Chang, Joe W. Gray, Claire J. Tomlin
Optimization-based inference for temporally evolving Boolean networks with applications in biology. ACC (2011)
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 (2011)
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)
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 (2010)
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)
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)
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)
Kai Zhang, Joe W. Gray, Bahram Parvin
Sparse multitask regression for identifying common mechanism of response to therapeutic targets. Bioinform. 26 (12) (2010)
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)
Debopriya Das, Matteo Pellegrini, Joe W. Gray
-Regulatory Logic. PLoS Comput. Biol. 5 (1) (2009)
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) (2009)
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)