On the Computational Power of a Continuous-Space Optical Model of Computation. - Thomas J. Naughton; Damien Woods (MCU, 2001)

Distributed Java Platform with Programmable MIMD Capabilities. - Thomas M. Keane; Richard Allen; Thomas J. Naughton; James O. McInerney; John Waldron (FIDJI, 2002)

Emulation of an unconventional model of computation in Java. - Aidan J. Delaney; Thomas J. Naughton (PPPJ/IRE, 2002)

Distributed computing for DNA analysis. - Thomas M. Keane; Richard Allen; Thomas J. Naughton; James O. McInerney; John Waldron (PPPJ/IRE, 2002)

Multi-tiered distributed computing platform. - Andrew J. Page; Thomas M. Keane; Richard Allen; Thomas J. Naughton; John Waldron (PPPJ, 2003)

Adaptive Scheduling across a Distributed Computation Platform. - Andrew J. Page; Thomas M. Keane; Thomas J. Naughton (ISPDC/HeteroPar, 2004)

A High-Throughput Bioinformatics Distributed Computing Platform. - Thomas M. Keane; Andrew J. Page; James O. McInerney; Thomas J. Naughton (CBMS, 2005)

OSCAR Meta-Package System. - John Mugler; Thomas J. Naughton; Stephen L. Scott (HPCS, 2005)

Bioinformatics on a Heterogeneous Java Distributed System. - Andrew J. Page; Thomas M. Keane; Thomas J. Naughton (IPDPS, 2005)

Dynamic Task Scheduling using Genetic Algorithms for Heterogeneous Distributed Computing. - Andrew J. Page; Thomas J. Naughton (IPDPS, 2005)

Framework for Task Scheduling in Heterogeneous Distributed Computing Using Genetic Algorithms. - Andrew J. Page; Thomas J. Naughton (Artif. Intell. Rev., 2005)

DSEARCH: sensitive database searching using distributed computing. - Thomas M. Keane; Thomas J. Naughton (Bioinform., 2005)

DPRml: distributed phylogeny reconstruction by maximum likelihood. - Thomas M. Keane; Thomas J. Naughton; Simon A. A. Travers; James O. McInerney; Grace P. McCormack (Bioinform., 2005)

An optical model of computation. - Damien Woods; Thomas J. Naughton (Theor. Comput. Sci., 2005)

A Component-Based Approach to Improving the Modularity of OSCAR. - Geoffroy Vallée; Thomas J. Naughton; Stephen L. Scott; Jeffrey M. Squyres; Erich Focht (HPCS, 2006)

Distributed Monte Carlo simulation of light transportation in tissue. - Andrew J. Page; Shirley Coyle; Thomas M. Keane; Thomas J. Naughton; Charles Markham; Tomás E. Ward (IPDPS, 2006)

OSCAR - OSCAR community meeting. - Stephen L. Scott; Thomas J. Naughton; Geoffroy Vallée (SC, 2006)

Building Large Phylogenetic Trees on Coarse-Grained Parallel Machines. - Thomas M. Keane; Andrew J. Page; Thomas J. Naughton; Simon A. A. Travers; James O. McInerney (Algorithmica, 2006)

Three-Dimensional Imaging and Processing Using Computational Holographic Imaging. - Yann Frauel; Thomas J. Naughton; Osamu Matoba; Enrique Tajahuerce-Romera; Bahram Javidi (Proc. IEEE, 2006)

System management software for virtual environments. - Geoffroy Vallée; Thomas J. Naughton; Stephen L. Scott (Conf. Computing Frontiers, 2007)

Evaluation of fault-tolerant policies using simulation. - Anand Tikotekar; Geoffroy Vallée; Thomas J. Naughton; Stephen L. Scott; Chokchai Leangsuksun (CLUSTER, 2007)

Design and Implementation of a Menu Based OSCAR Command Line Interface. - Wesley Bland; Thomas J. Naughton; Geoffroy Vallée; Stephen L. Scott (HPCS, 2007)

Automatic Testing Tool for OSCAR Using System-level Virtualization. - Geoffroy Vallée; Thomas J. Naughton; Wesley Bland; Stephen L. Scott (HPCS, 2007)

MultiPhyl: a high-throughput phylogenomics webserver using distributed computing. - Thomas M. Keane; Thomas J. Naughton; James O. McInerney (Nucleic Acids Res., 2007)

Histogram Approaches for Lossy Compression of Digital Holograms of Three-Dimensional Objects. - Alison E. Shortt; Thomas J. Naughton; Bahram Javidi (IEEE Trans. Image Process., 2007)

A Framework for Proactive Fault Tolerance. - Geoffroy Vallée; Kulathep Charoenpornwattana; Christian Engelmann; Anand Tikotekar; Chokchai Leangsuksun; Thomas J. Naughton; Stephen L. Scott (ARES, 2008)

An Analysis of HPC Benchmarks in Virtual Machine Environments. - Anand Tikotekar; Geoffroy Vallée; Thomas J. Naughton; Hong Ong; Christian Engelmann; Stephen L. Scott (Euro-Par Workshops, 2008)

Effects of virtualization on a scientific application running a hyperspectral radiative transfer code on virtual machines. - Anand Tikotekar; Geoffroy Vallée; Thomas J. Naughton; Hong Ong; Christian Engelmann; Stephen L. Scott; Anthony M. Filippi (HPCVirt@EuroSys, 2008)

Proposal for Modifications to the OSCAR Architecture to Address Challenges in Distributed System Management. - Geoffroy Vallée; Thomas J. Naughton; Stephen L. Scott (HPCS, 2008)

Parallel and Sequential Optical Computing. - Damien Woods; Thomas J. Naughton (OSC, 2008)

System-Level Virtualization for High Performance Computing. - Geoffroy Vallée; Thomas J. Naughton; Christian Engelmann; Hong Ong; Stephen L. Scott (PDP, 2008)

Virtual System Environments. - Geoffroy Vallée; Thomas J. Naughton; Hong Ong; Anand Tikotekar; Christian Engelmann; Wesley Bland; Ferrol Aderholdt; Stephen L. Scott (SVM, 2008)

Implementations of a Model of Physical Sorting. - Niall Murphy; Thomas J. Naughton; Damien Woods; Beverley Henley; Kieran McDermott; Elaine Duffy; Peter J. M. Van Der Burgt; Niamh Woods (Int. J. Unconv. Comput., 2008)

Scheduling in a dynamic heterogeneous distributed system using estimation error. - Andrew J. Page; Thomas M. Keane; Thomas J. Naughton (J. Parallel Distributed Comput., 2008)

Performance comparison of two virtual machine scenarios using an HPC application: a case study using molecular dynamics simulations. - Anand Tikotekar; Hong Ong; Sadaf R. Alam; Geoffroy Vallée; Thomas J. Naughton; Christian Engelmann; Stephen L. Scott (HPCVirt@EuroSys, 2009)

Proactive Fault Tolerance Using Preemptive Migration. - Christian Engelmann; Geoffroy Vallée; Thomas J. Naughton; Stephen L. Scott (PDP, 2009)

A tunable holistic resiliency approach for high-performance computing systems. - Stephen L. Scott; Christian Engelmann; Geoffroy Vallée; Thomas J. Naughton; Anand Tikotekar; George Ostrouchov; Chokchai Leangsuksun; Nichamon Naksinehaboon; Raja Nassar; Mihaela Paun; Frank Mueller 001; Chao Wang 056; et al. (PPoPP, 2009)

Optical computing. - Damien Woods; Thomas J. Naughton (Appl. Math. Comput., 2009)

Optical Computing. - Thomas J. Naughton; Damien Woods (Encyclopedia of Complexity and Systems Science, 2009)

Loadable Hypervisor Modules. - Thomas J. Naughton; Geoffroy Vallée; Stephen L. Scott; Ferrol Aderholdt (HICSS, 2010)

System-level virtualization research at Oak Ridge National Laboratory. - Stephen L. Scott; Geoffroy Vallée; Thomas J. Naughton; Anand Tikotekar; Christian Engelmann; Hong Ong (Future Gener. Comput. Syst., 2010)

Multi-heuristic dynamic task allocation using genetic algorithms in a heterogeneous distributed system. - Andrew J. Page; Thomas M. Keane; Thomas J. Naughton (J. Parallel Distributed Comput., 2010)

A Case for Virtual Machine Based Fault Injection in a High-Performance Computing Environment. - Thomas J. Naughton; Geoffroy Vallée; Christian Engelmann; Stephen L. Scott (Euro-Par Workshops (1), 2011)

5th Workshop on System-Level Virtualization for High Performance Computing (HPCVirt 2011). - Stephen L. Scott; Geoffroy Vallée; Thomas J. Naughton (Euro-Par Workshops (1), 2011)

Realization of User Level Fault Tolerant Policy Management through a Holistic Approach for Fault Correlation. - Byung H. Park; Thomas J. Naughton; Pratul K. Agarwal; David E. Bernholdt; Al Geist; Jennifer L. Tippens (POLICY, 2011)

A Log-Scaling Fault Tolerant Agreement Algorithm for a Fault Tolerant MPI. - Joshua Hursey; Thomas J. Naughton; Geoffroy Vallée; Richard L. Graham (EuroMPI, 2011)

Heterotic Computing Examples with Optics, Bacteria, and Chemicals. - Susan Stepney; Samson Abramsky; Matthias Bechmann; Jerzy Gorecki; Viv Kendon; Thomas J. Naughton; Mario J. Pérez-Jiménez; Francisco José Romero-Campero; Angelika Sebald (UCNC, 2012)

Architecture for the next generation system management tools. - Jérôme Gallard; Adrien Lebre; Christine Morin; Thomas J. Naughton; Stephen L. Scott; Geoffroy Vallée (Future Gener. Comput. Syst., 2012)

Using Performance Tools to Support Experiments in HPC Resilience. - Thomas J. Naughton; Swen Böhm; Christian Engelmann; Geoffroy Vallée (Euro-Par Workshops, 2013)

A Runtime Environment for Supporting Research in Resilient HPC System Software & Tools. - Geoffroy Vallée; Thomas J. Naughton; Swen Böhm; Christian Engelmann (CANDAR, 2013)

Toward a Performance/Resilience Tool for Hardware/Software Co-design of High-Performance Computing Systems. - Christian Engelmann; Thomas J. Naughton (ICPP, 2013)

Efficient Checkpointing of Virtual Machines Using Virtual Machine Introspection. - Ferrol Aderholdt; Fang Han; Stephen L. Scott; Thomas J. Naughton (CCGRID, 2014)

Improving the Performance of the Extreme-Scale Simulator. - Christian Engelmann; Thomas J. Naughton (DS-RT, 2014)

What Is the Right Balance for Performance and Isolation with Virtualization in HPC? - Thomas J. Naughton; Garry Smith; Christian Engelmann; Geoffroy Vallée; Ferrol Aderholdt; Stephen L. Scott (Euro-Par Workshops (1), 2014)

Supporting the Development of Resilient Message Passing Applications Using Simulation. - Thomas J. Naughton; Christian Engelmann; Geoffroy Vallée; Swen Böhm (PDP, 2014)

Towards a resilience investigation framework for high performance computing. - Thomas J. Naughton (2014)

Scalable and Fault Tolerant Failure Detection and Consensus. - Amogh Katti; Giuseppe Di Fatta; Thomas J. Naughton; Christian Engelmann (EuroMPI, 2015)

STCI: Scalable RunTime Component Infrastructure. - Geoffroy Vallée; David E. Bernholdt; Swen Böhm; Thomas J. Naughton (EuroMPI, 2015)

A Cooperative Approach to Virtual Machine Based Fault Injection. - Thomas J. Naughton; Christian Engelmann; Geoffroy Vallée; Ferrol Aderholdt; Stephen L. Scott (Euro-Par Workshops, 2016)

Adding Fault Tolerance to NPB Benchmarks Using ULFM. - Zachary W. Parchman; Geoffroy Vallée; Thomas J. Naughton; Christian Engelmann; David E. Bernholdt; Stephen L. Scott (FTXS@HPDC, 2016)

A new deadlock resolution protocol and message matching algorithm for the extreme-scale simulator. - Christian Engelmann; Thomas J. Naughton (Concurr. Comput. Pract. Exp., 2016)

Preemptive Resource Management for Dynamically Arriving Tasks in an Oversubscribed Heterogeneous Computing System. - Dylan Machovec; Sudeep Pasricha; Anthony A. Maciejewski; Howard Jay Siegel; Gregory A. Koenig; Michael Wright; Marcia Hilton; Rajendra Rambharos; Thomas J. Naughton; Neena Imam (IPDPS Workshops, 2017)

Balancing Performance and Portability with Containers in HPC: An OpenSHMEM Example. - Thomas J. Naughton; Lawrence Sorrillo; Adam Simpson; Neena Imam (OpenSHMEM, 2017)

Her2 Challenge Contest: A Detailed Assessment of Automated Her2 Scoring Algorithms in Whole Slide Images of Breast Cancer Tissues. - Talha Qaiser; Abhik Mukherjee; Chaitanya Reddy Pb; Sai Dileep Munugoti; Vamsi Tallam; Tomi Pitkäaho; Taina Lehtimäki; Thomas J. Naughton; Matt Berseth; Aníbal Pedraza; Ramakrishnan Mukundan; Matthew Smith 007; et al. (CoRR, 2017)

Wireless Holographic Image Communications Relying on Unequal Error Protected Bitplanes. - Yongkai Huo; Péter Tamás Kovács; Thomas J. Naughton; Lajos Hanzo (IEEE Trans. Veh. Technol., 2017)

A comparison of Amazon Web Services and Microsoft Azure cloud platforms for high performance computing. - Charlotte Kotas; Thomas J. Naughton; Neena Imam (ICCE, 2018)

Oak Ridge OpenSHMEM Benchmark Suite. - Thomas J. Naughton; Ferrol Aderholdt; Matthew B. Baker; Swaroop Pophale; Manjunath Gorentla Venkata; Neena Imam (OpenSHMEM, 2018)

Epidemic failure detection and consensus for extreme parallelism. - Amogh Katti; Giuseppe Di Fatta; Thomas J. Naughton; Christian Engelmann (Int. J. High Perform. Comput. Appl., 2018)

Characterizing the Performance of Executing Many-tasks on Summit. - Matteo Turilli; André Merzky; Thomas J. Naughton; Wael R. Elwasif; Shantenu Jha (IPDRM@SC, 2019)

Software Framework for Federated Science Instruments. - Thomas J. Naughton; Seth Hitefield; Lawrence Sorrillo; Nageswara S. V. Rao; James Kohl; Wael R. Elwasif; Jean-Christophe Bilheux; Hassina Z. Bilheux; Swen Boehm; Jason Kincl; Satyabrata Sen; Neena Imam (SMC, 2020)

Application health monitoring for extreme-scale resiliency using cooperative fault management. - Pratul K. Agarwal; Thomas J. Naughton; Byung H. Park; David E. Bernholdt; Joshua Hursey; Al Geist (Concurr. Comput. Pract. Exp., 2020)

A survey of MPI usage in the US exascale computing project. - David E. Bernholdt; Swen Boehm; George Bosilca; Manjunath Gorentla Venkata; Ryan E. Grant; Thomas J. Naughton; Howard Pritchard; Martin Schulz 001; Geoffroy R. Vallée (Concurr. Comput. Pract. Exp., 2020)

Virtual Framework for Development and Testing of Federation Software Stack. - Anees Al-Najjar; Nageswara S. V. Rao; Neena Imam; Thomas J. Naughton; Seth Hitefield; Lawrence Sorrillo; James Kohl; Wael R. Elwasif; Jean-Christophe Bilheux; Hassina Z. Bilheux; Swen Boehm; Jason Kincl (LCN, 2021)

VFSIE - Development and Testing Framework for Federated Science Instruments. - Anees Al-Najjar; Nageswara S. V. Rao; Neena Imam; Thomas J. Naughton; Seth Hitefield; Lawrence Sorrillo; James Kohl; Wael R. Elwasif; Jean-Christophe Bilheux; Hassina Z. Bilheux; Swen Boehm; Jason Kincl (CoRR, 2021)

Bebras-inspired Computational Thinking Primary School Resources Co-created by Computer Science Academics and Teachers. - Taina Lehtimäki; Rosemary Monahan; Aidan Mooney; Kevin Casey; Thomas J. Naughton (ITiCSE (1), 2022)

RADICAL-Pilot and PMIx/PRRTE: Executing Heterogeneous Workloads at Large Scale on Partitioned HPC Resources. - Mikhail Titov; Matteo Turilli; André Merzky; Thomas J. Naughton; Wael R. Elwasif; Shantenu Jha (JSSPP, 2022)

Towards a Standard Process Management Infrastructure for Workflows Using Python. - Wael R. Elwasif; Thomas J. Naughton; Matthew B. Baker (PDCAT, 2022)

The INTERSECT Open Federated Architecture for the Laboratory of the Future. - Christian Engelmann; Olga A. Kuchar; Swen Boehm; Michael J. Brim; Thomas J. Naughton; Suhas Somnath; Scott Atchley; Jack Lange; Ben Mintz; Elke Arenholz (SMC, 2022)

Emulation Framework for Distributed Large-Scale Systems Integration. - Neena Imam; Nageswara S. V. Rao; Anees Al-Najjar; Thomas J. Naughton; Seth Hitefield (SysCon, 2022)

A computational thinking module for secondary students and pre-service teachers using Bebras-style tasks. - Taina Lehtimäki; James Hamm; Aidan Mooney; Kevin Casey; Rosemary Monahan; Thomas J. Naughton (UKICER, 2022)

A Computational Thinking Obstacle Course Based on Bebras Tasks for K-12 Schools. - Taina Lehtimäki; Rosemary Monahan; Aidan Mooney; Kevin Casey; Thomas J. Naughton (ITiCSE (1), 2023)

Computational Thinking Resources Inspired by Bebras. - Taina Lehtimäki; Rosemary Monahan; Aidan Mooney; Kevin Casey; Thomas J. Naughton (ITiCSE (2), 2023)

A Framework for Integrating Quantum Simulation and High Performance Computing. - Amir Shehata; Thomas J. Naughton; In-Saeng Suh (QCE, 2024)

Integrating Quantum Computing with High-Performance Computing: A Streamlined Approach. - Amir Shehata; Thomas J. Naughton; In-Saeng Suh (QCE, 2024)

Towards Sustainable Post-Exascale Leadership Computing. - Woong Shin; James B. White; Wael R. Elwasif; Rafael Ferreira da Silva; Christopher Zimmer 001; Bronson Messer; Reuben D. Budiardja; Antigoni Georgiadou; Verónica Melesse Vergara; Jack Lange; Matthias Maiterth; Tim Osborne; et al. (SC Workshops, 2024)

Bringing HPE Slingshot 11 support to Open MPI. - Amir Shehata; Thomas J. Naughton; David E. Bernholdt; Howard Pritchard (Concurr. Comput. Pract. Exp., 2024)

Teaching Computational Thinking Through Active Games: Insights from Teacher Training. - Taina Lehtimäki; Eddie Costello; Kevin Casey; Aidan Mooney; Rosemary Monahan; Thomas J. Naughton (ISSEP, 2025)

Building a Software Stack for Quantum-HPC Integration. - Amir Shehata; Peter Groszkowski; Thomas J. Naughton; Muralikrishnan Gopalakrishnan Meena; Elaine Wong; Daniel Claudino; Rafael Ferreira da Silva; Thomas Beck (CoRR, 2025)

Bridging paradigms: Designing for HPC-Quantum convergence. - Amir Shehata; Peter Groszkowski; Thomas J. Naughton; Muralikrishnan Gopalakrishnan Meena; Elaine Wong; Daniel Claudino; Rafael Ferreira da Silva; Thomas Beck (Future Gener. Comput. Syst., 2026)