Joe W. Gray

38 papers A 1B 1C 4Journal 19Unranked 13
YearRankTypeTitle / Venue / Authors
2023 J jnl
3D multiplexed tissue imaging reconstruction and optimized region of interest (ROI) selection through deep learning model of channels embedding.
Frontiers Bioinform.
Erik A. Burlingame, Luke Ternes, Jia-Ren Lin, Yu-An Chen, Eun Na Kim, Joe W. Gray, Young Hwan Chang
2023 J jnl
Efficient semi-supervised semantic segmentation of electron microscopy cancer images with sparse annotations.
Frontiers Bioinform.
Lucas Pagano, Guillaume Thibault, Walid Bousselham, Jessica L. Riesterer, Xubo Song, Joe W. Gray
2023 J jnl
Segmentation of cellular ultrastructures on sparsely labeled 3D electron microscopy images using deep learning.
Frontiers Bioinform.
Archana Machireddy, Guillaume Thibault, Kevin G. Loftis, Kevin Stoltz, Cecilia E. Bueno, Hannah R. Smith, Jessica L. Riesterer, Joe W. Gray, Xubo Song
2022 J jnl
Computational multiplex panel reduction to maximize information retention in breast cancer tissue microarrays.
PLoS Comput. Biol.
Luke Ternes, Jia-Ren Lin, Yu-An Chen, Joe W. Gray, Young Hwan Chang
2022 A conf
Efficient Self-Ensemble for Semantic Segmentation.
BMVC
Walid Bousselham, Guillaume Thibault, Lucas Pagano, Archana Machireddy, Joe W. Gray, Young Hwan Chang, Xubo Song
2021 J jnl
Efficient Self-Ensemble Framework for Semantic Segmentation.
CoRR
Walid Bousselham, Guillaume Thibault, Lucas Pagano, Archana Machireddy, Joe W. Gray, Young Hwan Chang, Xubo Song
2020 — conf
Activation vs. Organization: Prognostic Implications of T and B Cell Features of the PDAC Microenvironment.
ISMCO
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
2019 B conf
Variational autoencoding tissue response to microenvironment perturbation.
Image Processing
Geoffrey F. Schau, Guillaume Thibault, Mark A. Dane, Joe W. Gray, Laura M. Heiser, Young Hwan Chang
2019 — conf
cmIF: A Python Library for Scalable Multiplex Imaging Pipelines.
ISMCO
Jennifer Eng, Elmar Bucher, Elliot Gray, Lydia Grace Campbell, Guillaume Thibault, Laura Heiser, Summer Gibbs, Joe W. Gray, Koei Chin, Young Hwan Chang
2018 — conf
SHIFT: speedy histopathological-to-immunofluorescent translation of whole slide images using conditional generative adversarial networks.
Digital Pathology
Erik A. Burlingame, Adam A. Margolin, Joe W. Gray, Young Hwan Chang
2017 — conf
Breast cancer histopathology image analysis pipeline for tumor purity estimation.
ISBI
Vahid Azimi, Young Hwan Chang, Guillaume Thibault, Jaclyn Smith, Takahiro Tsujikawa, Benjamin Kukull, Bradden Jensen, Christopher Corless, Adam A. Margolin, Joe W. Gray
2017 — conf
Deep learning based Nucleus Classification in pancreas histological images.
EMBC
Young Hwan Chang, Guillaume Thibault, Owen Madin, Vahid Azimi, Cole Meyers, Brett Johnson, Jason Link, Adam A. Margolin, Joe W. Gray
2017 — conf
Integrative analysis on histopathological image for identifying cellular heterogeneity.
Digital Pathology
Young Hwan Chang, Guillaume Thibault, Brett Johnson, Adam A. Margolin, Joe W. Gray
2017 — conf
Multiplexed immunohistochemistry image analysis using sparse coding.
EMBC
Young Hwan Chang, Takahiro Tsujikawa, Adam A. Margolin, Lisa M. Coussens, Joe W. Gray
2016 — conf
Quantitative analysis of histological tissue image based on cytological profiles and spatial statistics.
EMBC
Young Hwan Chang, Guillaume Thibault, Vahid Azimi, Brett Johnson, Danielle Jorgens, Jason Link, Adam A. Margolin, Joe W. Gray
2016 J jnl
Reconstruction of Gene Regulatory Networks Based on Repairing Sparse Low-Rank Matrices.
IEEE ACM Trans. Comput. Biol. Bioinform.
Young Hwan Chang, Roel Dobbe, Palak Bhushan, Joe W. Gray, Claire J. Tomlin
2015 C conf
Heterogeneity in cancer dynamics: A convex formulation to dissect dynamic trajectories and infer LTV models of networked systems.
ACC
Roel Dobbe, Young Hwan Chang, James Korkola, Joe W. Gray, Claire J. Tomlin
2015 — conf
Retrieving common dynamics of gene regulatory networks under various perturbations.
CDC
Young Hwan Chang, Roel Dobbe, Palak Bhushan, Joe W. Gray, Claire J. Tomlin
2014 J jnl
Causal network inference using biochemical kinetics.
Bioinform.
Chris J. Oates, Frank Dondelinger, Nora Bayani, James Korkola, Joe W. Gray, Sach Mukherjee
2014 J jnl
Exact reconstruction of gene regulatory networks using compressive sensing.
BMC Bioinform.
Young Hwan Chang, Joe W. Gray, Claire J. Tomlin
2013 — conf
Adaptive H-Extrema for Automatic Immunogold Particle Detection.
CIARP (2)
Guillaume Thibault, Kristiina Iljin, Christopher Arthur, Izhak Shafran, Joe W. Gray
2013 J jnl
Invariant Delineation of Nuclear Architecture in Glioblastoma Multiforme for Clinical and Molecular Association.
IEEE Trans. Medical Imaging
Hang Chang, Ju Han, Alexander Borowsky, Leandro A. Loss, Joe W. Gray, Paul T. Spellman, Bahram Parvin
2012 J jnl
Bayesian Inference of Signaling Network Topology in a Cancer Cell Line.
Bioinform.
Steven M. Hill, Yiling Lu, Jennifer Molina, Laura Heiser, Paul T. Spellman, Terence P. Speed, Joe W. Gray, Gordon B. Mills, Sach Mukherjee
2012 J jnl
Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology.
BMC Bioinform.
Steven M. Hill, Richard M. Neve, Nora Bayani, Wen-Lin Kuo, Safiyyah Ziyad, Paul T. Spellman, Joe W. Gray, Sach Mukherjee
2012 — conf
Learning invariant features of tumor signatures.
ISBI
Quoc V. Le, Ju Han, Joe W. Gray, Paul T. Spellman, Alexander Borowsky, Bahram Parvin
2012 J jnl
Optimization-based Inference for Temporally Evolving Networks with Applications in Biology.
J. Comput. Biol.
Young Hwan Chang, Joe W. Gray, Claire J. Tomlin
2011 — conf
Comparison of sparse coding and kernel methods for histopathological classification of gliobastoma multiforme.
ISBI
Ju Han, Hang Chang, Leandro A. Loss, Kai Zhang, Frederick L. Baehner, Joe W. Gray, Paul T. Spellman, Bahram Parvin
2011 J jnl
Morphometic analysis of TCGA glioblastoma multiforme.
BMC Bioinform.
Hang Chang, Gerald Fontenay, Ju Han, Ge Cong, Frederick L. Baehner, Joe W. Gray, Paul T. Spellman, Bahram Parvin
2011 C conf
Optimization-based inference for temporally evolving Boolean networks with applications in biology.
ACC
Young Hwan Chang, Joe W. Gray, Claire J. Tomlin
2010 C conf
An ODE model for the HER2/3-AKT signaling pathway in cancers that overexpress HER2.
ACC
Solomon Itani, Joe W. Gray, Claire J. Tomlin
2010 J jnl
Linking Changes in Epithelial Morphogenesis to Cancer Mutations Using Computational Modeling.
PLoS Comput. Biol.
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
2010 J jnl
Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture.
PLoS Comput. Biol.
Ju Han, Hang Chang, Orsi Giricz, Genee Y. Lee, Frederick L. Baehner, Joe W. Gray, Mina J. Bissell, Paraic A. Kenny, Bahram Parvin
2010 J jnl
Prediction of epigenetically regulated genes in breast cancer cell lines.
BMC Bioinform.
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
2010 J jnl
Sparse multitask regression for identifying common mechanism of response to therapeutic targets.
Bioinform.
Kai Zhang, Joe W. Gray, Bahram Parvin
2009 J jnl
A Primer on Regression Methods for Decoding
PLoS Comput. Biol.
Debopriya Das, Matteo Pellegrini, Joe W. Gray
2009 — conf
Morphometric Subtyping for a Panel of Breast Cancer Cell Lines.
ISBI
Ju Han, Hang Chang, Gerald Fontenay, Nicholas J. Wang, Joe W. Gray, Bahram Parvin
2009 J jnl
Sparse combinatorial inference with an application in cancer biology.
Bioinform.
Sach Mukherjee, Steven Pelech, Richard M. Neve, Wen-Lin Kuo, Safiyyah Ziyad, Paul T. Spellman, Joe W. Gray, Terence P. Speed
2007 C conf
Spectral Decomposition of Signaling Networks.
CIBCB
Bahram Parvin, Nirmalya Ghosh, Laura Heiser, Merrill Knapp, Carolyn L. Talcott, Keith Laderoute, Joe W. Gray, Paul T. Spellman