Joe W. Gray

According to our database, Joe W. Gray authored at least 38 papers between 2007 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

Efficient semi-supervised semantic segmentation of electron microscopy cancer images with sparse annotations.

Lucas Pagano, Guillaume Thibault, Walid Bousselham, Jessica L. Riesterer, Xubo Song, Joe W. Gray

Frontiers Bioinform., May, 2023

Segmentation of cellular ultrastructures on sparsely labeled 3D electron microscopy images using deep learning.

Archana Machireddy, Guillaume Thibault, Kevin G. Loftis, Kevin Stoltz, Cecilia E. Bueno, Hannah R. Smith, Jessica L. Riesterer, Joe W. Gray, Xubo Song

Frontiers Bioinform., May, 2023

3D multiplexed tissue imaging reconstruction and optimized region of interest (ROI) selection through deep learning model of channels embedding.

Erik A. Burlingame, Luke Ternes, Jia-Ren Lin, Yu-An Chen, Eun Na Kim, Joe W. Gray, Young Hwan Chang

Frontiers Bioinform., May, 2023

2022

Computational multiplex panel reduction to maximize information retention in breast cancer tissue microarrays.

Luke Ternes, Jia-Ren Lin, Yu-An Chen, Joe W. Gray, Young Hwan Chang

PLoS Comput. Biol., September, 2022

Efficient Self-Ensemble for Semantic Segmentation.

Walid Bousselham, Guillaume Thibault, Lucas Pagano, Archana Machireddy, Joe W. Gray, Young Hwan Chang, Xubo Song

Proceedings of the 33rd British Machine Vision Conference 2022, 2022

2021

Efficient Self-Ensemble Framework for Semantic Segmentation.

Walid Bousselham, Guillaume Thibault, Lucas Pagano, Archana Machireddy, Joe W. Gray, Young Hwan Chang, Xubo Song

CoRR, 2021

2020

Activation vs. Organization: Prognostic Implications of T and B Cell Features of the PDAC Microenvironment.

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

Proceedings of the Mathematical and Computational Oncology, 2020

2019

Variational autoencoding tissue response to microenvironment perturbation.

Geoffrey F. Schau, Guillaume Thibault, Mark A. Dane, Joe W. Gray, Laura M. Heiser, Young Hwan Chang

Proceedings of the Medical Imaging 2019: Image Processing, 2019

cmIF: A Python Library for Scalable Multiplex Imaging Pipelines.

Jennifer Eng, Elmar Bucher, Elliot Gray, Lydia Grace Campbell, Guillaume Thibault, Laura Heiser, Summer Gibbs, Joe W. Gray, Koei Chin, Young Hwan Chang

Proceedings of the Mathematical and Computational Oncology - First International Symposium, 2019

2018

SHIFT: speedy histopathological-to-immunofluorescent translation of whole slide images using conditional generative adversarial networks.

Erik A. Burlingame, Adam A. Margolin, Joe W. Gray, Young Hwan Chang

Proceedings of the Medical Imaging 2018: Digital Pathology, 2018

2017

Integrative analysis on histopathological image for identifying cellular heterogeneity.

Young Hwan Chang, Guillaume Thibault, Brett Johnson, Adam A. Margolin, Joe W. Gray

Proceedings of the Medical Imaging 2017: Digital Pathology, 2017

Breast cancer histopathology image analysis pipeline for tumor purity estimation.

Vahid Azimi, Young Hwan Chang, Guillaume Thibault, Jaclyn Smith, Takahiro Tsujikawa, Benjamin Kukull, Bradden Jensen, Christopher Corless, Adam A. Margolin, Joe W. Gray

Proceedings of the 14th IEEE International Symposium on Biomedical Imaging, 2017

Multiplexed immunohistochemistry image analysis using sparse coding.

Young Hwan Chang, Takahiro Tsujikawa, Adam A. Margolin, Lisa M. Coussens, Joe W. Gray

Proceedings of the 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 2017

Deep learning based Nucleus Classification in pancreas histological images.

Young Hwan Chang, Guillaume Thibault, Owen Madin, Vahid Azimi, Cole Meyers, Brett Johnson, Jason Link, Adam A. Margolin, Joe W. Gray

Proceedings of the 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 2017

2016

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

Young Hwan Chang, Roel Dobbe, Palak Bhushan, Joe W. Gray, Claire J. Tomlin

IEEE ACM Trans. Comput. Biol. Bioinform., 2016

Quantitative analysis of histological tissue image based on cytological profiles and spatial statistics.

Young Hwan Chang, Guillaume Thibault, Vahid Azimi, Brett Johnson, Danielle Jorgens, Jason Link, Adam A. Margolin, Joe W. Gray

Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2016

2015

Retrieving common dynamics of gene regulatory networks under various perturbations.

Young Hwan Chang, Roel Dobbe, Palak Bhushan, Joe W. Gray, Claire J. Tomlin

Proceedings of the 54th IEEE Conference on Decision and Control, 2015

Heterogeneity in cancer dynamics: A convex formulation to dissect dynamic trajectories and infer LTV models of networked systems.

Roel Dobbe, Young Hwan Chang, James Korkola, Joe W. Gray, Claire J. Tomlin

Proceedings of the American Control Conference, 2015

2014

Exact reconstruction of gene regulatory networks using compressive sensing.

Young Hwan Chang, Joe W. Gray, Claire J. Tomlin

BMC Bioinform., 2014

Causal network inference using biochemical kinetics.

Chris J. Oates, Frank Dondelinger, Nora Bayani, James Korkola, Joe W. Gray, Sach Mukherjee

Bioinform., 2014

2013

Invariant Delineation of Nuclear Architecture in Glioblastoma Multiforme for Clinical and Molecular Association.

Hang Chang, Ju Han, Alexander Borowsky, Leandro A. Loss, Joe W. Gray, Paul T. Spellman, Bahram Parvin

IEEE Trans. Medical Imaging, 2013

Adaptive H-Extrema for Automatic Immunogold Particle Detection.

Guillaume Thibault, Kristiina Iljin, Christopher Arthur, Izhak Shafran, Joe W. Gray

Proceedings of the Progress in Pattern Recognition, Image Analysis, Computer Vision, and Applications, 2013

2012

Optimization-based Inference for Temporally Evolving Networks with Applications in Biology.

Young Hwan Chang, Joe W. Gray, Claire J. Tomlin

J. Comput. Biol., 2012

Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology.

Steven M. Hill, Richard M. Neve, Nora Bayani, Wen-Lin Kuo, Safiyyah Ziyad, Paul T. Spellman, Joe W. Gray, Sach Mukherjee

BMC Bioinform., 2012

Bayesian Inference of Signaling Network Topology in a Cancer Cell Line.

Steven M. Hill, Yiling Lu, Jennifer Molina, Laura Heiser, Paul T. Spellman, Terence P. Speed, Joe W. Gray, Gordon B. Mills, Sach Mukherjee

Bioinform., 2012

Learning invariant features of tumor signatures.

Quoc V. Le, Ju Han, Joe W. Gray, Paul T. Spellman, Alexander Borowsky, Bahram Parvin

Proceedings of the 9th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2012

2011

Morphometic analysis of TCGA glioblastoma multiforme.

Hang Chang, Gerald Fontenay, Ju Han, Ge Cong, Frederick L. Baehner, Joe W. Gray, Paul T. Spellman, Bahram Parvin

BMC Bioinform., 2011

Comparison of sparse coding and kernel methods for histopathological classification of gliobastoma multiforme.

Ju Han, Hang Chang, Leandro A. Loss, Kai Zhang, Frederick L. Baehner, Joe W. Gray, Paul T. Spellman, Bahram Parvin

Proceedings of the 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2011

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

Young Hwan Chang, Joe W. Gray, Claire J. Tomlin

Proceedings of the American Control Conference, 2011

2010

Linking Changes in Epithelial Morphogenesis to Cancer Mutations Using Computational Modeling.

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

PLoS Comput. Biol., 2010

Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture.

Ju Han, Hang Chang, Orsi Giricz, Genee Y. Lee, Frederick L. Baehner, Joe W. Gray, Mina J. Bissell, Paraic A. Kenny, Bahram Parvin

PLoS Comput. Biol., 2010

Prediction of epigenetically regulated genes in breast cancer cell lines.

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

BMC Bioinform., 2010

Sparse multitask regression for identifying common mechanism of response to therapeutic targets.

Kai Zhang, Joe W. Gray, Bahram Parvin

Bioinform., 2010

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

Solomon Itani, Joe W. Gray, Claire J. Tomlin

Proceedings of the American Control Conference, 2010

2009

A Primer on Regression Methods for Decoding <i>cis</i>-Regulatory Logic.

Debopriya Das, Matteo Pellegrini, Joe W. Gray

PLoS Comput. Biol., 2009

Sparse combinatorial inference with an application in cancer biology.

Sach Mukherjee, Steven Pelech, Richard M. Neve, Wen-Lin Kuo, Safiyyah Ziyad, Paul T. Spellman, Joe W. Gray, Terence P. Speed

Bioinform., 2009

Morphometric Subtyping for a Panel of Breast Cancer Cell Lines.

Ju Han, Hang Chang, Gerald Fontenay, Nicholas J. Wang, Joe W. Gray, Bahram Parvin

Proceedings of the 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Boston, MA, USA, June 28, 2009

2007

Spectral Decomposition of Signaling Networks.

Bahram Parvin, Nirmalya Ghosh, Laura Heiser, Merrill Knapp, Carolyn L. Talcott, Keith Laderoute, Joe W. Gray, Paul T. Spellman

Proceedings of the 2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2007