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Joe W. Gray
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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. Medical Imaging: 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. Medical Imaging: 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. Medical Imaging: 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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