Spectral Decomposition of Signaling Networks. - Bahram Parvin; Nirmalya Ghosh; Laura Heiser; Merrill Knapp; Carolyn L. Talcott; Keith Laderoute; Joe W. Gray; Paul T. Spellman (CIBCB, 2007)

Morphometric Subtyping for a Panel of Breast Cancer Cell Lines. - Ju Han; Hang Chang; Gerald Fontenay; Nicholas J. Wang; Joe W. Gray; Bahram Parvin (ISBI, 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)

A Primer on Regression Methods for Decoding cis-Regulatory Logic. - Debopriya Das; Matteo Pellegrini; Joe W. Gray (PLoS Comput. Biol., 2009)

An ODE model for the HER2/3-AKT signaling pathway in cancers that overexpress HER2. - Solomon Itani; Joe W. Gray; Claire J. Tomlin (ACC, 2010)

Sparse multitask regression for identifying common mechanism of response to therapeutic targets. - Kai Zhang 001; Joe W. Gray; Bahram Parvin (Bioinform., 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)

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)

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)

Optimization-based inference for temporally evolving Boolean networks with applications in biology. - Young Hwan Chang; Joe W. Gray; Claire J. Tomlin (ACC, 2011)

Comparison of sparse coding and kernel methods for histopathological classification of gliobastoma multiforme. - Ju Han; Hang Chang; Leandro A. Loss; Kai Zhang 001; Frederick L. Baehner; Joe W. Gray; Paul T. Spellman; Bahram Parvin (ISBI, 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)

Learning invariant features of tumor signatures. - Quoc V. Le; Ju Han; Joe W. Gray; Paul T. Spellman; Alexander Borowsky; Bahram Parvin (ISBI, 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)

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)

Optimization-based Inference for Temporally Evolving Networks with Applications in Biology. - Young Hwan Chang; Joe W. Gray; Claire J. Tomlin (J. Comput. Biol., 2012)

Adaptive H-Extrema for Automatic Immunogold Particle Detection. - Guillaume Thibault; Kristiina Iljin; Christopher Arthur; Izhak Shafran; Joe W. Gray (CIARP (2), 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)

Causal network inference using biochemical kinetics. - Chris J. Oates; Frank Dondelinger; Nora Bayani; James Korkola; Joe W. Gray; Sach Mukherjee (Bioinform., 2014)

Exact reconstruction of gene regulatory networks using compressive sensing. - Young Hwan Chang; Joe W. Gray; Claire J. Tomlin (BMC Bioinform., 2014)

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 (ACC, 2015)

Retrieving common dynamics of gene regulatory networks under various perturbations. - Young Hwan Chang; Roel Dobbe; Palak Bhushan; Joe W. Gray; Claire J. Tomlin (CDC, 2015)

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 (EMBC, 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)

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 (EMBC, 2017)

Multiplexed immunohistochemistry image analysis using sparse coding. - Young Hwan Chang; Takahiro Tsujikawa; Adam A. Margolin; Lisa M. Coussens; Joe W. Gray (EMBC, 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 (ISBI, 2017)

Integrative analysis on histopathological image for identifying cellular heterogeneity. - Young Hwan Chang; Guillaume Thibault; Brett Johnson; Adam A. Margolin; Joe W. Gray (Digital Pathology, 2017)

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 (Digital Pathology, 2018)

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 (ISMCO, 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 (Image Processing, 2019)

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 (ISMCO, 2020)

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)

Efficient Self-Ensemble for Semantic Segmentation. - Walid Bousselham; Guillaume Thibault; Lucas Pagano; Archana Machireddy; Joe W. Gray; Young Hwan Chang; Xubo Song (BMVC, 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., 2022)

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., 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., 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., 2023)