A Predictor for Survival in Intermediate Grade Clear Cell Renal Cell Carcinoma. - Anupama Reddy; Angela Rose Brannon; Michael Seiler; Joseph Irgon; Börje Ljungberg; Hongjuan Zhao; James D. Brooks; Shridar Ganesan; W. Kimryn Rathmell; Gyan Bhanot (BIOCOMP, 2009)

Simulating market effects on boundedly rational agents in control of the dynamic dispatching of actors in network-based operations. - James D. Brooks; David Mendonça (WSC, 2013)

Model predictive building thermostatic controls of small-to-medium commercial buildings for optimal peak load reduction incorporating dynamic human comfort models: Algorithm and implementation. - Emrah Biyik; Sahika Genc; James D. Brooks (CCA, 2014)

Equity-effectiveness tradeoff in the allocation of flows in closed queueing networks. - James D. Brooks; David Mendonça (SysCon, 2014)

Collaborative Training Tools for Emergency Restoration of Critical Infrastructure Systems. - David Mendonça; Barbara Cutler; William A. Wallace; James D. Brooks (WorldCIST (1), 2014)

Linking Team Composition to Team Performance: An Application to Postdisaster Debris Removal Operations. - David Mendonça; James D. Brooks; Martha Grabowski (IEEE Trans. Hum. Mach. Syst., 2014)

Cloud-based model predictive building thermostatic controls of commercial buildings: Algorithm and implementation. - Emrah Biyik; James D. Brooks; Hullas Sehgal; Jigar Shah; Sahika Genc (ACC, 2015)

A Historical Analysis of the Field of OR/MS using Topic Models. - Christopher J. Gatti; James D. Brooks; Sarah G. Nurre (CoRR, 2015)

Estimating Computational Models of Dynamic Decision Making from Transactional Data. - James D. Brooks; David Mendonça; Xin Zhang 023; Martha Grabowski (GDN, 2016)

Allocation of flows in closed bipartite queueing networks. - James D. Brooks; Koushik Kar; David Mendonça (Eur. J. Oper. Res., 2016)

Scheduling distributed locomotives for optimal train handling. - Anup Menon; H. Kirk Mathews; James D. Brooks; Dan Dai; Brian N. Meyer (ACC, 2017)

Mining Electronic Health Records to Extract Patient-Centered Outcomes Following Prostate cancer Treatment. - Tina Hernandez-Boussard; Panayotis Kourdis; Wen-wai Yim; Rajendra Dulal; Douglas W. Blayney; James D. Brooks (AMIA, 2017)

A distributed simulator platform for rapid industrial user experience prototyping. - Roberto S. Silva Filho; Alexander K. Carroll; James D. Brooks (WSC, 2017)

An Automated Feature Engineering for Digital Rectal Examination Documentation using Natural Language Processing. - Selen Bozkurt; Jung Park In; Kathleen Mary Kan; Michelle Ferrari; Daniel L. Rubin; James D. Brooks; Tina Hernandez-Boussard (AMIA, 2018)

Identifying cases of metastatic prostate cancer using machine learning on electronic health records. - Martin G. Seneviratne; Juan M. Banda; James D. Brooks; Nigam Shah; Tina Hernandez-Boussard (AMIA, 2018)

Machine Learning Approaches for Extracting Stage from Pathology Reports in Prostate Cancer. - Raphael Lenain; Martin G. Seneviratne; Selen Bozkurt; Douglas W. Blayney; James D. Brooks; Tina Hernandez-Boussard (MedInfo, 2019)

Framework for the co-registration of MRI and histology images in prostate cancer patients with radical prostatectomy. - Mirabela Rusu; Christian Kunder; Richard E. Fan; Pejman Ghanouni; Robert B. West; Geoffrey A. Sonn; James D. Brooks (Image Processing, 2019)

Plexus Convolutional Neural Network (PlexusNet): A novel neural network architecture for histologic image analysis. - Okyaz Eminaga; Mahmoud Abbas; Christian Kunder; Andreas M. Loening; Jeanne Shen; James D. Brooks; Curtis P. Langlotz; Daniel L. Rubin (CoRR, 2019)

Deep Learning for Prostate Pathology. - Okyaz Eminaga; Yuri Tolkach; Christian Kunder; Mahmoud Abbas; Ryan Han; Rosalie Nolley; Axel Semjonow; Martin Boegemann; Sebastian Huss; Andreas M. Loening; Robert B. West; Geoffrey A. Sonn; et al. (CoRR, 2019)

Biologic and Prognostic Feature Scores from Whole-Slide Histology Images Using Deep Learning. - Okyaz Eminaga; Mahmoud Abbas; Yuri Tolkach; Rosalie Nolley; Christian Kunder; Axel Semjonow; Martin Boegemann; Andreas M. Loening; James D. Brooks; Daniel L. Rubin (CoRR, 2019)

Comparison of orthogonal NLP methods for clinical phenotyping and assessment of bone scan utilization among prostate cancer patients. - Jean Coquet; Selen Bozkurt; Kathleen M. Kan; Michelle Ferrari; Douglas W. Blayney; James D. Brooks; Tina Hernandez-Boussard (J. Biomed. Informatics, 2019)

Distinct Clusters of Patient reported outcome (PRO) trajectories among oncology patients receiving chemotherapy. - Selen Bozkurt; Amee D. Azad; Melih Yilmaz; James D. Brooks; Douglas W. Blayney; Tina Hernandez-Boussard (AMIA, 2020)

CorrSigNet: Learning CORRelated Prostate Cancer SIGnatures from Radiology and Pathology Images for Improved Computer Aided Diagnosis. - Indrani Bhattacharya; Arun Seetharaman; Wei Shao 008; Rewa Sood; Christian A. Kunder; Richard E. Fan; Simon John Christoph Soerensen; Jeffrey B. Wang; Pejman Ghanouni; Nikola C. Teslovich; James D. Brooks; Geoffrey A. Sonn; et al. (MICCAI (2), 2020)

Efficacy of Incentive Structures for Boundedly Rational Dispatchers in Large-Scale Queueing Networks. - James D. Brooks; David Mendonça; Xin Zhang 023 (IEEE Trans. Hum. Mach. Syst., 2020)

Weakly Supervised Registration of Prostate MRI and Histopathology Images. - Wei Shao 008; Indrani Bhattacharya; Simon John Christoph Soerensen; Christian A. Kunder; Jeffrey B. Wang; Richard E. Fan; Pejman Ghanouni; James D. Brooks; Geoffrey A. Sonn; Mirabela Rusu (MICCAI (4), 2021)

Bridging the gap between prostate radiology and pathology through machine learning. - Indrani Bhattacharya; David S. Lim; Han Lin Aung; Xingchen Liu; Arun Seetharaman; Christian A. Kunder; Wei Shao 008; Simon John Christoph Soerensen; Richard E. Fan; Pejman Ghanouni; Katherine J. To'o; James D. Brooks; et al. (CoRR, 2021)

ProsRegNet: A deep learning framework for registration of MRI and histopathology images of the prostate. - Wei Shao 008; Linda Banh; Christian A. Kunder; Richard E. Fan; Simon John Christoph Soerensen; Jeffrey B. Wang; Nikola C. Teslovich; Nikhil Madhuripan; Anugayathri Jawahar; Pejman Ghanouni; James D. Brooks; Geoffrey A. Sonn; et al. (Medical Image Anal., 2021)

3D Registration of pre-surgical prostate MRI and histopathology images via super-resolution volume reconstruction. - Rewa Sood; Wei Shao 008; Christian Kunder; Nikola C. Teslovich; Jeffrey B. Wang; Simon John Christoph Soerensen; Nikhil Madhuripan; Anugayathri Jawahar; James D. Brooks; Pejman Ghanouni; Richard E. Fan; Geoffrey A. Sonn; et al. (Medical Image Anal., 2021)

Correlated Feature Aggregation by Region Helps Distinguish Aggressive from Indolent Clear Cell Renal Cell Carcinoma Subtypes on CT. - Karin Stacke; Indrani Bhattacharya; Justin R. Tse; James D. Brooks; Geoffrey A. Sonn; Mirabela Rusu (CoRR, 2022)

Expanding the Secondary Use of Prostate Cancer Real World Data: Automated Classifiers for Clinical and Pathological Stage. - Selen Bozkurt; Christopher J. Magnani; Martin G. Seneviratne; James D. Brooks; Tina Hernandez-Boussard (Frontiers Digit. Health, 2022)

Selective identification and localization of indolent and aggressive prostate cancers via CorrSigNIA: an MRI-pathology correlation and deep learning framework. - Indrani Bhattacharya; Arun Seetharaman; Christian Kunder; Wei Shao 008; Leo C. Chen; Simon John Christoph Soerensen; Jeffrey B. Wang; Nikola C. Teslovich; Richard E. Fan; Pejman Ghanouni; James D. Brooks; Geoffrey A. Sonn; et al. (Medical Image Anal., 2022)

MIC-CUSP: Multimodal Image Correlations for Ultrasound-Based Prostate Cancer Detection. - Indrani Bhattacharya; Sulaiman Vesal; Hassan Jahanandish; Moonhyung Choi; Steve Ran Zhou; Zachary Kornberg; Elijah Richard Sommer; Richard E. Fan; James D. Brooks; Geoffrey A. Sonn; Mirabela Rusu (ASMUS@MICCAI, 2023)

Critical Evaluation of Artificial Intelligence as Digital Twin of Pathologist for Prostate Cancer Pathology. - Okyaz Eminaga; Mahmoud Abbas; Christian Kunder; Yuri Tolkach; Ryan Han; James D. Brooks; Rosalie Nolley; Axel Semjonow; Martin Boegemann; Robert B. West; Jin Long; Richard E. Fan; et al. (CoRR, 2023)

PlexusNet: A neural network architectural concept for medical image classification. - Okyaz Eminaga; Mahmoud Abbas; Jeanne Shen; Mark A. Laurie; James D. Brooks; Joseph C. Liao; Daniel L. Rubin (Comput. Biol. Medicine, 2023)

Deep learning-based automated pipeline for blood vessel detection and distribution analysis in multiplexed prostate cancer images. - Grigorios M. Karageorgos; Sanghee Cho; Elizabeth McDonough; Chrystal Chadwick; Soumya Ghose; Jonathan Owens; Kyeong Joo Jung; Raghu Machiraju; Robert West; James D. Brooks; Parag Mallick; Fiona Ginty (Frontiers Bioinform., 2023)

RAPHIA: A deep learning pipeline for the registration of MRI and whole-mount histopathology images of the prostate. - Wei Shao 008; Sulaiman Vesal; Simon J. C. Soerensen; Indrani Bhattacharya; Negar Golestani; Rikiya Yamashita; Christian A. Kunder; Richard E. Fan; Pejman Ghanouni; James D. Brooks; Geoffrey A. Sonn; Mirabela Rusu (Comput. Biol. Medicine, 2024)