The Cancer Imaging Phenomics Toolkit (CaPTk): Technical Overview. - Sarthak Pati; Ashish Singh; Saima Rathore; Aimilia Gastounioti; Mark Bergman; Phuc Ngo; Sung Min Ha; Dimitrios Bounias; James Minock; Grayson Murphy; Hongming Li; Amit Bhattarai; et al. (BrainLes@MICCAI (2), 2019)

Skull-Stripping of Glioblastoma MRI Scans Using 3D Deep Learning. - Siddhesh P. Thakur; Jimit Doshi; Sarthak Pati; Sung Min Ha; Chiharu Sako; Sanjay N. Talbar; Uday Kulkarni; Christos Davatzikos; Güray Erus; Spyridon Bakas (BrainLes@MICCAI (1), 2019)

Estimating Glioblastoma Biophysical Growth Parameters Using Deep Learning Regression. - Sarthak Pati; Vaibhav Sharma; Heena Aslam; Siddhesh P. Thakur; Hamed Akbari; Andreas Mang; Shashank Subramanian; George Biros; Christos Davatzikos; Spyridon Bakas (BrainLes@MICCAI (1), 2020)

Brain extraction on MRI scans in presence of diffuse glioma: Multi-institutional performance evaluation of deep learning methods and robust modality-agnostic training. - Siddhesh P. Thakur; Jimit Doshi; Sarthak Pati; Saima Rathore; Chiharu Sako; Michel Bilello; Sung Min Ha; Gaurav Shukla; Adam E. Flanders; Aikaterini Kotrotsou; Mikhail Milchenko; Spencer Liem; et al. (NeuroImage, 2020)

Optimization of Deep Learning Based Brain Extraction in MRI for Low Resource Environments. - Siddhesh P. Thakur; Sarthak Pati; Ravi Panchumarthy; Deepthi Karkada; Junwen Wu; Dmitry Kurtaev; Chiharu Sako; Prashant Shah; Spyridon Bakas (BrainLes@MICCAI (1), 2021)

GaNDLF: A Generally Nuanced Deep Learning Framework for Scalable End-to-End Clinical Workflows in Medical Imaging. - Sarthak Pati; Siddhesh P. Thakur; Megh Bhalerao; Ujjwal Baid; Caleb M. Grenko; Brandon Edwards; Micah J. Sheller; Jose Agraz; Bhakti Baheti; Vishnu Bashyam; Parth Sharma; Babak Haghighi; et al. (CoRR, 2021)

Federated Learning for the Classification of Tumor Infiltrating Lymphocytes. - Ujjwal Baid; Sarthak Pati; Tahsin M. Kurç; Rajarsi Gupta 001; Erich Bremer; Shahira Abousamra; Siddhesh P. Thakur; Joel H. Saltz; Spyridon Bakas (CoRR, 2022)

Pan-Cancer Tumor Infiltrating Lymphocyte Detection based on Federated Learning. - Ujjwal Baid; Sarthak Pati; Tahsin M. Kurç; Rajarsi Gupta 001; Erich Bremer; Shahira Abousamra; Siddhesh P. Thakur; Joel H. Saltz; Spyridon Bakas (IEEE Big Data, 2024)

BraTS-Path Challenge: Assessing Heterogeneous Histopathologic Brain Tumor Sub-regions. - Spyridon Bakas; Siddhesh P. Thakur; Shahriar Faghani; Mana Moassefi; Ujjwal Baid; Verena Chung; Sarthak Pati; Shubham Innani; Bhakti Baheti; Jake Albrecht; Alexandros Karargyris; Hasan Kassem; et al. (CoRR, 2024)

Biochemical Prostate Cancer Recurrence Prediction: Thinking Fast & Slow. - Suhang You; Sanyukta Adap; Siddhesh P. Thakur; Bhakti Baheti; Spyridon Bakas (CoRR, 2024)

Optimization of deep learning models for inference in low resource environments. - Siddhesh P. Thakur; Sarthak Pati; Junwen Wu; Ravi Panchumarthy; Deepthi Karkada; Alexander Kozlov; Vasily Shamporov; Alexander Suslov; Daniil Lyakhov; Maksim Proshin; Prashant Shah; Dimitrios Makris 001; et al. (Comput. Biol. Medicine, 2025)

Skull stripping with purely synthetic data. - Jong Sung Park; Juhyung Ha; Siddhesh P. Thakur; Alexandra Badea; Spyridon Bakas; Eleftherios Garyfallidis (CoRR, 2025)