Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks. - Jong Min Lee 002; Erwin P. Gianchandani; James A. Eddy; Jason A. Papin (PLoS Comput. Biol., 2008)

Biological Data Integration and Model Building. - James A. Eddy; Nathan D. Price 001 (Encyclopedia of Complexity and Systems Science, 2009)

Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC). - James A. Eddy; Leroy E. Hood; Nathan D. Price 001; Donald Geman (PLoS Comput. Biol., 2010)

Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup. - Andrew T. Magis; John C. Earls; Youn-Hee Ko; James A. Eddy; Nathan D. Price 001 (Bioinform., 2011)

Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. - Caroline B. Milne; James A. Eddy; Ravali Raju; Soroush Ardekani; Pan-Jun Kim; Ryan S. Senger; Yong-Su Jin; Hans P. Blaschek; Nathan D. Price 001 (BMC Syst. Biol., 2011)

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. - Yuliang Wang; James A. Eddy; Nathan D. Price 001 (BMC Syst. Biol., 2012)

AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures. - John C. Earls; James A. Eddy; Cory C. Funk; Youn-Hee Ko; Andrew T. Magis; Nathan D. Price 001 (BMC Bioinform., 2013)

The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification. - Ujjwal Baid; Satyam Ghodasara; Michel Bilello; Suyash Mohan; Evan Calabrese; Errol Colak; Keyvan Farahani; Jayashree Kalpathy-Cramer; Felipe C. Kitamura; Sarthak Pati; Luciano M. Prevedello; Jeffrey D. Rudie; et al. (CoRR, 2021)

Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database. - Ashley Clayton; Mialy M. DeFelice; Brynn Zalmanek; Jay Hodgson; Caroline Morin; Stockard Simon; Julie A. Bletz; James A. Eddy; Milen Nikolov; Jineta Banerjee; Kalyan C. Vinnakota; Marco Marasca; et al. (Database J. Biol. Databases Curation, 2022)

The NLP Sandbox: an efficient model-to-data system to enable federated and unbiased evaluation of clinical NLP models. - Yao Yan; Thomas Yu; Kathleen Muenzen; Sijia Liu 002; Connor Boyle; George Koslowski; Jiaxin Zheng; Nicholas J. Dobbins; Clement Essien; Hongfang Liu; Larsson Omberg; Meliha Yestigen; et al. (CoRR, 2022)

The ASNR-MICCAI Brain Tumor Segmentation (BraTS) Challenge 2023: Intracranial Meningioma. - Dominic LaBella; Maruf Adewole; Michelle Alonso-Basanta; Talissa Altes; Syed Muhammad Anwar; Ujjwal Baid; Timothy Bergquist; Radhika Bhalerao; Sully F. Chen; Verena Chung; Gian Marco Conte; Farouk Dako; et al. (CoRR, 2023)

The Brain Tumor Segmentation (BraTS) Challenge 2023: Local Synthesis of Healthy Brain Tissue via Inpainting. - Florian Kofler; Felix Meissen; Felix Steinbauer; Robert Graf; Eva Oswald; Ezequiel de la Rosa; Hongwei Bran Li; Ujjwal Baid; Florian A. Hölzl; Özgün Turgut; Izabela Horvath; Diana Waldmannstetter; et al. (CoRR, 2023)

The Brain Tumor Segmentation (BraTS) Challenge 2023: Brain MR Image Synthesis for Tumor Segmentation (BraSyn). - Hongwei Bran Li; Gian Marco Conte; Syed Muhammad Anwar; Florian Kofler; Koen Van Leemput; Marie Piraud; Ivan Ezhov; Felix Meissen; Maruf Adewole; Anastasia Janas; Anahita Fathi Kazerooni; Dominic LaBella; et al. (CoRR, 2023)

The Brain Tumor Segmentation (BraTS) Challenge 2023: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs). - Anahita Fathi Kazerooni; Nastaran Khalili; Xinyang Liu; Debanjan Haldar; Zhifan Jiang; Syed Muhammad Anwar; Jake Albrecht; Maruf Adewole; Udunna Anazodo; Hannah Anderson; Sina Bagheri; Ujjwal Baid; et al. (CoRR, 2023)

The Brain Tumor Segmentation (BraTS) Challenge 2023: Glioma Segmentation in Sub-Saharan Africa Patient Population (BraTS-Africa). - Maruf Adewole; Jeffrey D. Rudie; Anu Gbadamosi; Oluyemisi Toyobo; Raymond Confidence; Dong Zhang 009; Olubukola Omidiji; Rachel Akinola; Mohammad Abba Suwaid; Adaobi Emegoakor; Nancy Ojo; Kenneth Aguh; et al. (CoRR, 2023)

Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful? - Awan Afiaz; Andrey Ivanov; John Chamberlin; David Hanauer; Candace Savonen; Mary J. Goldman; Martin Morgan; Michael Reich; Alexander Getka; Aaron Holmes; Sarthak Pati; Dan Knight; et al. (CoRR, 2023)

Federated benchmarking of medical artificial intelligence with MedPerf. - Alexandros Karargyris; Renato Umeton; Micah J. Sheller; Alejandro Aristizabal; Johnu George; Anna Wuest; Sarthak Pati; Hasan Kassem; Maximilian Zenk; Ujjwal Baid; Prakash Narayana Moorthy; Alexander Chowdhury; et al. (Nat. Mac. Intell., 2023)

The Brain Tumor Segmentation in Pediatrics (BraTS-PEDs) Challenge: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs). - Anahita Fathi Kazerooni; Nastaran Khalili; Deep Gandhi; Xinyang Liu; Zhifan Jiang; Syed Muhammed Anwar; Jake Albrecht; Maruf Adewole; Udunna Anazodo; Hannah Anderson; Sina Bagheri; Ujjwal Baid; et al. (CoRR, 2024)

Analysis of the BraTS 2023 Intracranial Meningioma Segmentation Challenge. - Dominic LaBella; Ujjwal Baid; Omaditya Khanna; Shan McBurney-Lin; Ryan McLean; Pierre Nedelec; Arif Rashid; Nourel Hoda Tahon; Talissa Altes; Radhika Bhalerao; Yaseen Dhemesh; Devon Godfrey; et al. (CoRR, 2024)

BraTS-PEDs: Results of the Multi-Consortium International Pediatric Brain Tumor Segmentation Challenge 2023. - Anahita Fathi Kazerooni; Nastaran Khalili; Xinyang Liu; Debanjan Haldar; Zhifan Jiang; Anna Zapaishchykova; Julija Pavaine; Lubdha M. Shah; Blaise V. Jones; Nakul Sheth; Sanjay P. Prabhu; Aaron S. McAllister; et al. (CoRR, 2024)