CESMTuner: An Auto-tuning Framework for the Community Earth System Model. - Nan Ding 006; Wei Xue 003; Xu Ji; Haoyu Xu; Zhenya Song (HPCC/CSS/ICESS, 2014)

Refactoring and optimizing the community atmosphere model (CAM) on the sunway taihulight supercomputer. - Haohuan Fu; Junfeng Liao; Wei Xue 003; Lanning Wang; Dexun Chen; Long Gu; Jinxiu Xu 001; Nan Ding 006; Xinliang Wang; Conghui He; Shizhen Xu; Yishuang Liang; et al. (SC, 2016)

Redesigning CAM-SE for peta-scale climate modeling performance and ultra-high resolution on Sunway TaihuLight. - Haohuan Fu; Junfeng Liao; Nan Ding 006; Xiaohui Duan; Lin Gan; Yishuang Liang; Xinliang Wang; Jinzhe Yang; Yan Zheng; Weiguo Liu; Lanning Wang; Guangwen Yang (SC, 2017)

An Instruction Roofline Model for GPUs. - Nan Ding 006; Samuel Williams 001 (PMBS@SC, 2019)

An automatic performance model-based scheduling tool for coupled climate system models. - Nan Ding 006; Wei Xue 003; Zhenya Song; Haohuan Fu; Shiming Xu; Weimin Zheng (J. Parallel Distributed Comput., 2019)

GPU accelerated partial order multiple sequence alignment for long reads self-correction. - Francesco Peverelli; Lorenzo Di Tucci; Marco D. Santambrogio; Nan Ding 006; Steven A. Hofmeyr; Aydin Buluç; Leonid Oliker; Katherine A. Yelick (IPDPS Workshops, 2020)

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment. - Alberto Zeni; Giulia Guidi; Marquita Ellis; Nan Ding 006; Marco D. Santambrogio; Steven A. Hofmeyr; Aydin Buluç; Leonid Oliker; Katherine A. Yelick (IPDPS, 2020)

Leveraging One-Sided Communication for Sparse Triangular Solvers. - Nan Ding 006; Samuel Williams 001; Yang Liu 179; Xiaoye S. Li (PP, 2020)

APMT: an automatic hardware counter-based performance modeling tool for HPC applications. - Nan Ding 006; Victor W. Lee; Wei Xue 003; Weimin Zheng (CCF Trans. High Perform. Comput., 2020)

A Message-Driven, Multi-GPU Parallel Sparse Triangular Solver. - Nan Ding 006; Yang Liu 179; Samuel Williams 001; Xiaoye S. Li (ACDA, 2021)

Evaluating Performance and Portability of a core bioinformatics kernel on multiple vendor GPUs. - Muhammad Haseeb; Nan Ding 006; Jack Deslippe; Muaaz Gul Awan (P3HPC@SC, 2021)

Accelerating large scale de novo metagenome assembly using GPUs. - Muaaz Gul Awan; Steven A. Hofmeyr; Rob Egan; Nan Ding 006; Aydin Buluç; Jack Deslippe; Leonid Oliker; Katherine A. Yelick (SC, 2021)

A Methodology for Evaluating Tightly-integrated and Disaggregated Accelerated Architectures. - Taylor L. Groves; Christopher S. Daley; Rahulkumar Gayatri; Hai Ah Nam; Nan Ding 006; Lenny Oliker; Nicholas J. Wright; Samuel Williams 001 (PMBS@SC, 2022)

Instruction Roofline: An insightful visual performance model for GPUs. - Nan Ding 006; Muaaz G. Awan; Samuel Williams 001 (Concurr. Comput. Pract. Exp., 2022)

Evaluating the Performance of One-sided Communication on CPUs and GPUs. - Nan Ding 006; Muhammad Haseeb; Taylor L. Groves; Samuel Williams 001 (SC Workshops, 2023)

Unified Communication Optimization Strategies for Sparse Triangular Solver on CPU and GPU Clusters. - Yang Liu 179; Nan Ding 006; Piyush Sao; Samuel Williams 001; Xiaoye Sherry Li (SC, 2023)

A Workflow Roofline Model for End-to-End Workflow Performance Analysis. - Nan Ding 006; Brian Austin; Yang Liu 179; Neil Mehta; Steven Farrell; Johannes P. Blaschke; Leonid Oliker; Hai Ah Nam; Nicholas J. Wright; Samuel Williams 001 (SC, 2024)

Performance Modeling and Analysis of a de Bruijn Graph Based Local Assembly Kernel on Multiple Vendor GPUs. - LeAnn M. Lindsey; Nan Ding 006; Jack Deslippe; Muaaz Awan (SC Workshops, 2024)

Evaluating the potential of disaggregated memory systems for HPC applications. - Nan Ding 006; Pieter Maris; Hai Ah Nam; Taylor L. Groves; Muaaz Gul Awan; LeAnn Lindsey; Christopher S. Daley; Oguz Selvitopi; Leonid Oliker; Nicholas J. Wright; Samuel Williams 001 (Concurr. Comput. Pract. Exp., 2024)

Maximizing Power-Constrained Supercomputing Throughput. - Nan Ding 006; Oscar Antepara; Zhengji Zhao; Brian Austin; Leonid Oliker; Nicholas J. Wright; Samuel Williams 001 (ISC, 2025)

Optimizing Nuclear Configuration Interaction Calculations on GPUs: A Comparative Performance Study of Programming Models. - Abdullah Alperen; Nan Ding 006; Khaled Z. Ibrahim; Pieter Maris; Leonid Oliker; Chao Yang 001; Hasan Metin Aktulga (ISC, 2025)