Parallel Implementation of an Adaptive Scheme for 3D Unstructured Grids on the SP2. - Leonid Oliker; Rupak Biswas; Roger C. Strawn (IRREGULAR, 1996)

Global Load Balancing with Parallel Mesh Adaption on Distributed-Memory Systems. - Rupak Biswas; Leonid Oliker; Andrew Sohn (SC, 1996)

Algorithms for Automatic Alignment of Arrays. - Siddhartha Chatterjee; John R. Gilbert; Leonid Oliker; Robert Schreiber; Thomas J. Sheffler (J. Parallel Distributed Comput., 1996)

Load balancing sequences of unstructured adaptive grids. - Rupak Biswas; Leonid Oliker (HiPC, 1997)

Load Balancing Unstructured Adaptive Grids for CFD Problems. - Rupak Biswas; Leonid Oliker (PP, 1997)

Efficient Load Balancing and Data Remapping for Adaptive Grid Calculations. - Leonid Oliker; Rupak Biswas (SPAA, 1997)

Performance Analysis and Portability of the PLUM Load Balancing System. - Leonid Oliker; Rupak Biswas; Harold N. Gabow (Euro-Par, 1998)

PLUM: Parallel Load Balancing for Adaptive Unstructured Meshes. - Leonid Oliker; Rupak Biswas (J. Parallel Distributed Comput., 1998)

Portable Parallel Programming for the Dynamic Load Balancing of Unstructured Grid Applications. - Rupak Biswas; Leonid Oliker; Sajal K. Das 001; Daniel J. Harvey (IPPS/SPDP, 1999)

Dynamic Load Balancing for Parallel Adaptive Unstructured Grid Computations. - Rupak Biswas; Leonid Oliker (PP, 1999)

Parallelization of a Dynamic Unstructured Application using Three Leading Paradigms. - Leonid Oliker; Rupak Biswas (SC, 1999)

Ordering Unstructured Meshes for Sparse Matrix Computations on Leading Parallel Systems. - Leonid Oliker; Xiaoye S. Li; Gerd Heber; Rupak Biswas (IPDPS Workshops, 2000)

System Utilization Benchmark on the Cray T3E and IBM SP. - Adrian T. Wong; Leonid Oliker; William T. C. Kramer; Teresa L. Kaltz; David H. Bailey (JSSPP, 2000)

ESP: A System Utilization Benchmark. - Adrian T. Wong; Leonid Oliker; William T. C. Kramer; Teresa L. Kaltz; David H. Bailey (SC, 2000)

Parallel tetrahedral mesh adaptation with dynamic load balancing. - Leonid Oliker; Rupak Biswas; Harold N. Gabow (Parallel Comput., 2000)

Parallelization of a Dynamic Unstructured Algorithm Using Three Leading Programming Paradigms. - Leonid Oliker; Rupak Biswas (IEEE Trans. Parallel Distributed Syst., 2000)

Message Passing Vs. Shared Address Space on a Clusters of SMPs. - Hongzhang Shan; Jaswinder Pal Singh; Leonid Oliker; Rupak Biswas (IPDPS, 2001)

Ordering Sparse Matrices for Cache-Based Systems. - Rupak Biswas; Leonid Oliker (PP, 2001)

Design Strategies for Irregularly Adapting Parallel Applications. - Leonid Oliker; Rupak Biswas; Hongzhang Shan; Jaswinder Pal Singh (PP, 2001)

Memory-Intensive Benchmarks: IRAM vs. Cache-Based Machines. - Brian R. Gaeke; Parry Husbands; Xiaoye S. Li; Leonid Oliker; Katherine A. Yelick; Rupak Biswas (IPDPS, 2002)

A Comparison of Three Programming Models for Adaptive Applications on the Origin2000. - Hongzhang Shan; Jaswinder Pal Singh; Leonid Oliker; Rupak Biswas (J. Parallel Distributed Comput., 2002)

Effects of Ordering Strategies and Programming Paradigms on Sparse Matrix Computations. - Leonid Oliker; Xiaoye S. Li; Parry Husbands; Rupak Biswas (SIAM Rev., 2002)

Performance Evaluation of Two Emerging Media Processors: VIRAM and Imagine. - Sourav Chatterji; Manikandan Narayanan; Jason Duell; Leonid Oliker (IPDPS, 2003)

Evaluation of Cache-based Superscalar and Cacheless Vector Architectures for Scientific Computations. - Leonid Oliker; Andrew Canning; Jonathan Carter 002; John Shalf; David Skinner; Stéphane Ethier; Rupak Biswas; M. Jahed Djomehri; Rob F. Van der Wijngaart (SC, 2003)

Job Superscheduler Architecture and Performance in Computational Grid Environments. - Hongzhang Shan; Leonid Oliker; Rupak Biswas (SC, 2003)

Message passing and shared address space parallelism on an SMP cluster. - Hongzhang Shan; Jaswinder Pal Singh; Leonid Oliker; Rupak Biswas (Parallel Comput., 2003)

Performance Characteristics of a Cosmology Package on Leading HPC Architectures. - Jonathan Carter 002; Julian Borrill; Leonid Oliker (HiPC, 2004)

Identifying Performance Bottlenecks on Modern Microarchitectures Using an Adaptable Probe. - Gorden Griem; Leonid Oliker; John Shalf; Katherine A. Yelick (IPDPS, 2004)

Scientific Computations on Modern Parallel Vector Systems. - Leonid Oliker; Andrew Canning; Jonathan Carter 002; John Shalf; Stéphane Ethier (SC, 2004)

A Performance Evaluation of the Cray X1 for Scientific Applications. - Leonid Oliker; Rupak Biswas; Julian Borrill; Andrew Canning; Jonathan Carter 002; M. Jahed Djomehri; Hongzhang Shan; David Skinner (VECPAR, 2004)

Impact of modern memory subsystems on cache optimizations for stencil computations. - Shoaib Kamil 001; Parry Husbands; Leonid Oliker; John Shalf; Katherine A. Yelick (Memory System Performance, 2005)

Integrated Performance Monitoring of a Cosmology Application on Leading HEC Platforms. - Julian Borrill; Jonathan Carter 002; Leonid Oliker; David Skinner; Rupak Biswas (ICPP, 2005)

Leading Computational Methods on Scalar and Vector HEC Platforms. - Leonid Oliker; Jonathan Carter 002; Michael F. Wehner; Andrew Canning; Stéphane Ethier; Arthur A. Mirin; David Parks; Patrick H. Worley; Shigemune Kitawaki; Yoshinori Tsuda (SC, 2005)

Analyzing Ultra-Scale Application Communication Requirements for a Reconfigurable Hybrid Interconnect. - John Shalf; Shoaib Kamil 001; Leonid Oliker; David Skinner (SC, 2005)

Performance evaluation of the SX-6 vector architecture for scientific computations. - Leonid Oliker; Andrew Canning; Jonathan Carter 002; John Shalf; David Skinner; Stéphane Ethier; Rupak Biswas; M. Jahed Djomehri; Rob F. Van der Wijngaart (Concurr. Pract. Exp., 2005)

Performance Evaluation and Modeling of Ultra-Scale Systems. - Leonid Oliker; Rupak Biswas; Rob F. Van der Wijngaart; David H. Bailey; Allan Snavely (Parallel Processing for Scientific Computing, 2006)

Implicit and explicit optimizations for stencil computations. - Shoaib Kamil 001; Kaushik Datta; Samuel Williams 001; Leonid Oliker; John Shalf; Katherine A. Yelick (Memory System Performance and Correctness, 2006)

Performance characteristics of an adaptive mesh refinement calculation on scalar and vector platforms. - Michael L. Welcome; Charles A. Rendleman; Leonid Oliker; Rupak Biswas (Conf. Computing Frontiers, 2006)

The potential of the cell processor for scientific computing. - Samuel Williams 001; John Shalf; Leonid Oliker; Shoaib Kamil 001; Parry Husbands; Katherine A. Yelick (Conf. Computing Frontiers, 2006)

Performance Evaluation of Scientific Applications on Modern Parallel Vector Systems. - Jonathan Carter 002; Leonid Oliker; John Shalf (VECPAR, 2006)

Reconfigurable hybrid interconnection for static and dynamic scientific applications. - Shoaib Kamil 001; Ali Pinar; Daniel K. Gunter; Michael Lijewski; Leonid Oliker; John Shalf (Conf. Computing Frontiers, 2007)

Scientific Application Performance on Candidate PetaScale Platforms. - Leonid Oliker; Andrew Canning; Jonathan Carter 002; Costin Iancu; Michael Lijewski; Shoaib Kamil 001; John Shalf; Hongzhang Shan; Erich Strohmaier; Stéphane Ethier; Tom Goodale (IPDPS, 2007)

Investigation of leading HPC I/O performance using a scientific-application derived benchmark. - Julian Borrill; Leonid Oliker; John Shalf; Hongzhang Shan (SC, 2007)

Scientific Computing Kernels on the Cell Processor. - Samuel Williams 001; John Shalf; Leonid Oliker; Shoaib Kamil 001; Parry Husbands; Katherine A. Yelick (Int. J. Parallel Program., 2007)

Lattice Boltzmann simulation optimization on leading multicore platforms. - Samuel Williams 001; Jonathan Carter 002; Leonid Oliker; John Shalf; Katherine A. Yelick (IPDPS, 2008)

Stencil computation optimization and auto-tuning on state-of-the-art multicore architectures. - Kaushik Datta; Mark Murphy; Vasily Volkov; Samuel Williams 001; Jonathan Carter 002; Leonid Oliker; David A. Patterson 001; John Shalf; Katherine A. Yelick (SC, 2008)

Large-scale gyrokinetic particle simulation of microturbulence in magnetically confined fusion plasmas. - Stéphane Ethier; William M. Tang; Robert Walkup; Leonid Oliker (IBM J. Res. Dev., 2008)

Preface. - Rupak Biswas; Leonid Oliker (Int. J. High Perform. Comput. Appl., 2008)

Scientific Application Performance On Leading Scalar and Vector Supercomputering Platforms. - Leonid Oliker; Andrew Canning; Jonathan Carter 002; John Shalf; Stéphane Ethier (Int. J. High Perform. Comput. Appl., 2008)

Towards Ultra-High Resolution Models of Climate and Weather. - Michael F. Wehner; Leonid Oliker; John Shalf (Int. J. High Perform. Comput. Appl., 2008)

Improving Memory Subsystem Performance Using ViVA: Virtual Vector Architecture. - Joseph Gebis; Leonid Oliker; John Shalf; Samuel Williams 001; Katherine A. Yelick (ARCS, 2009)

Green flash: Designing an energy efficient climate supercomputer. - Leonid Oliker (IPDPS, 2009)

Analysis of photonic networks for a chip multiprocessor using scientific applications. - Gilbert Hendry; Shoaib Kamil 001; Aleksandr Biberman; Johnnie Chan; Benjamin G. Lee; Marghoob Mohiyuddin; Ankit Jain; Keren Bergman; Luca P. Carloni; John Kubiatowicz; Leonid Oliker; John Shalf (NOCS, 2009)

Memory-efficient optimization of Gyrokinetic particle-to-grid interpolation for multicore processors. - Kamesh Madduri; Samuel Williams 001; Stéphane Ethier; Leonid Oliker; John Shalf; Erich Strohmaier; Katherine A. Yelick (SC, 2009)

A design methodology for domain-optimized power-efficient supercomputing. - Marghoob Mohiyuddin; Mark Murphy; Leonid Oliker; John Shalf; John Wawrzynek; Samuel Williams 001 (SC, 2009)

Energy-Efficient Computing for Extreme-Scale Science. - David Donofrio; Leonid Oliker; John Shalf; Michael F. Wehner; Chris Rowen; Jens Krueger; Shoaib Kamil 001; Marghoob Mohiyuddin (Computer, 2009)

Optimization of a lattice Boltzmann computation on state-of-the-art multicore platforms. - Samuel Williams 001; Jonathan Carter 002; Leonid Oliker; John Shalf; Katherine A. Yelick (J. Parallel Distributed Comput., 2009)

Revolutionary technologies for acceleration of emerging petascale applications. - Rupak Biswas; Leonid Oliker; Jeffrey S. Vetter (Parallel Comput., 2009)

HPC global file system performance analysis using a scientific-application derived benchmark. - Julian Borrill; Leonid Oliker; John Shalf; Hongzhang Shan; Andrew Uselton (Parallel Comput., 2009)

Optimization of sparse matrix-vector multiplication on emerging multicore platforms. - Samuel Williams 001; Leonid Oliker; Richard W. Vuduc; John Shalf; Katherine A. Yelick; James Demmel (Parallel Comput., 2009)

Optimization and Performance Modeling of Stencil Computations on Modern Microprocessors. - Kaushik Datta; Shoaib Kamil 001; Samuel Williams 001; Leonid Oliker; John Shalf; Katherine A. Yelick (SIAM Rev., 2009)

Auto-Tuning Stencil Computations on Multicore and Accelerators. - Kaushik Datta; Samuel Williams 001; Vasily Volkov; Jonathan Carter 002; Leonid Oliker; John Shalf; Katherine A. Yelick (Scientific Computing with Multicore and Accelerators, 2010)

Sparse Matrix-Vector Multiplication on Multicore and Accelerators. - Samuel Williams 001; Nathan Bell; Jee Whan Choi; Michael Garland; Leonid Oliker; Richard Vu (Scientific Computing with Multicore and Accelerators, 2010)

Silicon Nanophotonic Network-on-Chip Using TDM Arbitration. - Gilbert Hendry; Johnnie Chan; Shoaib Kamil 001; Leonid Oliker; John Shalf; Luca P. Carloni; Keren Bergman (Hot Interconnects, 2010)

Optimizing and tuning the fast multipole method for state-of-the-art multicore architectures. - Aparna Chandramowlishwaran; Samuel Williams 001; Leonid Oliker; Ilya Lashuk; George Biros; Richard W. Vuduc (IPDPS, 2010)

An auto-tuning framework for parallel multicore stencil computations. - Shoaib Kamil 001; Cy P. Chan; Leonid Oliker; John Shalf; Samuel Williams 001 (IPDPS, 2010)

Parallel I/O performance: From events to ensembles. - Andrew Uselton; Mark Howison; Nicholas J. Wright; David Skinner; Noel Keen; John Shalf; Karen L. Karavanic; Leonid Oliker (IPDPS, 2010)

Communication Requirements and Interconnect Optimization for High-End Scientific Applications. - Shoaib Kamil 001; Leonid Oliker; Ali Pinar; John Shalf (IEEE Trans. Parallel Distributed Syst., 2010)

Cosmic microwave background map-making at the petascale and beyond. - Rajesh Sudarsan; Julian Borrill; Christopher Cantalupo; Theodore Kisner; Kamesh Madduri; Leonid Oliker; Yili Zheng; Horst D. Simon (ICS, 2011)

Reduced-Bandwidth Multithreaded Algorithms for Sparse Matrix-Vector Multiplication. - Aydin Buluç; Samuel Williams 001; Leonid Oliker; James Demmel (IPDPS, 2011)

Hardware/software co-design for energy-efficient seismic modeling. - Jens Krueger; David Donofrio; John Shalf; Marghoob Mohiyuddin; Samuel Williams 001; Leonid Oliker; Franz-Josef Pfreundt (SC, 2011)

Gyrokinetic toroidal simulations on leading multi- and manycore HPC systems. - Kamesh Madduri; Khaled Z. Ibrahim; Samuel Williams 001; Eun-Jin Im; Stéphane Ethier; John Shalf; Leonid Oliker (SC, 2011)

Extracting ultra-scale Lattice Boltzmann performance via hierarchical and distributed auto-tuning. - Samuel Williams 001; Leonid Oliker; Jonathan Carter 002; John Shalf (SC, 2011)

Gyrokinetic particle-in-cell optimization on emerging multi- and manycore platforms. - Kamesh Madduri; Eun-Jin Im; Khaled Z. Ibrahim; Samuel Williams 001; Stéphane Ethier; Leonid Oliker (Parallel Comput., 2011)

Emerging programming paradigms for large-scale scientific computing. - Leonid Oliker; Rajesh Nishtala; Rupak Biswas (Parallel Comput., 2011)

Green Flash: Climate Machine (LBNL). - John Shalf; David Donofrio; Chris Rowen; Leonid Oliker; Michael F. Wehner (Encyclopedia of Parallel Computing, 2011)

High-performance analysis of filtered semantic graphs. - Aydin Buluç; Armando Fox; John R. Gilbert; Shoaib Kamil 001; Adam Lugowski; Leonid Oliker; Samuel Williams 001 (PACT, 2012)

Can Network-Offload Based Non-blocking Neighborhood MPI Collectives Improve Communication Overheads of Irregular Graph Algorithms? - Krishna Chaitanya Kandalla; Aydin Buluç; Hari Subramoni; Karen Tomko; Jérôme Vienne; Leonid Oliker; Dhabaleswar K. Panda 001 (CLUSTER Workshops, 2012)

Abstract: Advances in Gyrokinetic Particle in Cell Simulation for Fusion Plasmas to Extreme Scale. - Bei Wang 002; Stéphane Ethier; William M. Tang; Khaled Z. Ibrahim; Kamesh Madduri; Samuel W. Williams; Leonid Oliker; Timothy J. Williams (SC Companion, 2012)

Poster: Advances in Gyrokinetic Particle in Cell Simulation for Fusion Plasmas to Extreme Scale. - Bei Wang 002; Stéphane Ethier; William M. Tang; Khaled Z. Ibrahim; Kamesh Madduri; Samuel W. Williams; Leonid Oliker; Timothy J. Williams (SC Companion, 2012)

Optimization of geometric multigrid for emerging multi- and manycore processors. - Samuel Williams 001; Dhiraj D. Kalamkar; Amik Singh; Anand M. Deshpande; Brian van Straalen; Mikhail Smelyanskiy; Ann S. Almgren; Pradeep Dubey; John Shalf; Leonid Oliker (SC, 2012)

Optimization of Parallel Particle-to-Grid Interpolation on Leading Multicore Platforms. - Kamesh Madduri; Jimmy Su; Samuel Williams 001; Leonid Oliker; Stéphane Ethier; Katherine A. Yelick (IEEE Trans. Parallel Distributed Syst., 2012)

Compiler generation and autotuning of communication-avoiding operators for geometric multigrid. - Protonu Basu; Anand Venkat; Mary W. Hall; Samuel Williams 001; Brian van Straalen; Leonid Oliker (HiPC, 2013)

High-Productivity and High-Performance Analysis of Filtered Semantic Graphs. - Aydin Buluç; Erika Duriakova; Armando Fox; John R. Gilbert; Shoaib Kamil 001; Adam Lugowski; Leonid Oliker; Samuel Williams 001 (IPDPS, 2013)

Performance Tuning of Fock Matrix and Two-Electron Integral Calculations for NWChem on Leading HPC Platforms. - Hongzhang Shan; Brian Austin; Wibe de Jong; Leonid Oliker; Nicholas J. Wright; Edoardo Aprà (PMBS@SC, 2013)

Kinetic turbulence simulations at extreme scale on leadership-class systems. - Bei Wang 002; Stéphane Ethier; William M. Tang; Timothy J. Williams; Khaled Z. Ibrahim; Kamesh Madduri; Samuel Williams 001; Leonid Oliker (SC, 2013)

Analysis and optimization of gyrokinetic toroidal simulations on homogenous and heterogenous platforms. - Khaled Z. Ibrahim; Kamesh Madduri; Samuel Williams 001; Bei Wang 002; Stéphane Ethier; Leonid Oliker (Int. J. High Perform. Comput. Appl., 2013)

Introduction for Special Issue on Autotuning. - Leonid Oliker; Richard W. Vuduc (Int. J. High Perform. Comput. Appl., 2013)

Best paper awards: 26th international parallel and distributed processing symposium (IPDPS 2012). - Leonid Oliker; Katherine A. Yelick (J. Parallel Distributed Comput., 2013)

Efficient and accurate clustering for large-scale genetic mapping. - Veronika Strnadova; Aydin Buluç; Jarrod Chapman; John R. Gilbert; Joseph Gonzalez 001; Stefanie Jegelka; Daniel Rokhsar; Leonid Oliker (BIBM, 2014)

Parallel De Bruijn Graph Construction and Traversal for De Novo Genome Assembly. - Evangelos Georganas; Aydin Buluç; Jarrod Chapman; Leonid Oliker; Daniel Rokhsar; Katherine A. Yelick (SC, 2014)

Roofline Model Toolkit: A Practical Tool for Architectural and Program Analysis. - Yu Jung Lo; Samuel Williams 001; Brian van Straalen; Terry J. Ligocki; Matthew J. Cordery; Nicholas J. Wright; Mary W. Hall; Leonid Oliker (PMBS@SC, 2014)

Efficient data reduction for large-scale genetic mapping. - Veronika Strnadová-Neeley; Aydin Buluç; Jarrod Chapman; John R. Gilbert; Joseph Gonzalez 001; Leonid Oliker (BCB, 2015)

Parallel Performance Optimizations on Unstructured Mesh-based Simulations. - Abhinav Sarje; Sukhyun Song; Douglas Jacobsen; Kevin A. Huck; Jeffrey K. Hollingsworth; Allen D. Malony; Samuel Williams 001; Leonid Oliker (ICCS, 2015)

Compiler-Directed Transformation for Higher-Order Stencils. - Protonu Basu; Mary W. Hall; Samuel Williams 001; Brian van Straalen; Leonid Oliker; Phillip Colella (IPDPS, 2015)

merAligner: A Fully Parallel Sequence Aligner. - Evangelos Georganas; Aydin Buluç; Jarrod Chapman; Leonid Oliker; Daniel Rokhsar; Katherine A. Yelick (IPDPS, 2015)

Thread-level parallelization and optimization of NWChem for the Intel MIC architecture. - Hongzhang Shan; Samuel Williams 001; Wibe de Jong; Leonid Oliker (PMAM@PPoPP, 2015)

HipMer: an extreme-scale de novo genome assembler. - Evangelos Georganas; Aydin Buluç; Jarrod Chapman; Steven A. Hofmeyr; Chaitanya Aluru; Rob Egan; Leonid Oliker; Daniel Rokhsar; Katherine A. Yelick (SC, 2015)

Parallel processing of filtered queries in attributed semantic graphs. - Adam Lugowski; Shoaib Kamil 001; Aydin Buluç; Samuel Williams 001; Erika Duriakova; Leonid Oliker; Armando Fox; John R. Gilbert (J. Parallel Distributed Comput., 2015)

Special issue "Graph analysis for scientific discovery". - Aydin Buluç; Leonid Oliker; John R. Gilbert (Parallel Comput., 2015)

Communication-Avoiding Parallel Sparse-Dense Matrix-Matrix Multiplication. - Penporn Koanantakool; Ariful Azad; Aydin Buluç; Dmitriy Morozov; Sang-Yun Oh; Leonid Oliker; Katherine A. Yelick (IPDPS, 2016)

Evaluating and Optimizing the NERSC Workload on Knights Landing. - Taylor Barnes; Brandon Cook 001; Jack Deslippe; Douglas Doerfler; Brian Friesen; Yun (Helen) He; Thorsten Kurth; Tuomas Koskela; Mathieu Lobet; Tareq M. Malas; Leonid Oliker; Andrey Ovsyannikov; et al. (PMBS@SC, 2016)

Extreme scale plasma turbulence simulations on top supercomputers worldwide. - William M. Tang; Bei Wang 002; Stéphane Ethier; Grzegorz Kwasniewski; Torsten Hoefler; Khaled Z. Ibrahim; Kamesh Madduri; Samuel Williams 001; Leonid Oliker; Carlos Rosales-Fernandez; Timothy J. Williams (SC, 2016)

Applying the Roofline Performance Model to the Intel Xeon Phi Knights Landing Processor. - Douglas Doerfler; Jack Deslippe; Samuel Williams 001; Leonid Oliker; Brandon Cook 001; Thorsten Kurth; Mathieu Lobet; Tareq M. Malas; Jean-Luc Vay; Henri Vincenti (ISC Workshops, 2016)

LiRa: A New Likelihood-Based Similarity Score for Collaborative Filtering. - Veronika Strnadová-Neeley; Aydin Buluç; John R. Gilbert; Leonid Oliker; Weimin Ouyang (CoRR, 2016)

Performance Characterization of De Novo Genome Assembly on Leading Parallel Systems. - Marquita Ellis; Evangelos Georganas; Rob Egan; Steven A. Hofmeyr; Aydin Buluç; Brandon Cook 001; Leonid Oliker; Katherine A. Yelick (Euro-Par, 2017)

Performance analysis and optimization of the RAMPAGE metal alloy potential generation software. - Philip C. Roth; Hongzhang Shan; David Riegner; Nikolas Antolin; Sarat Sreepathi; Leonid Oliker; Samuel Williams 001; Shirley Moore; Wolfgang Windl (SEPS@SPLASH, 2017)

MerBench: PGAS Benchmarks for High Performance Genome Assembly. - Evangelos Georganas; Marquita Ellis; Rob Egan; Steven A. Hofmeyr; Aydin Buluç; Brandon Cook 001; Leonid Oliker; Katherine A. Yelick (PAW@SC, 2017)

Analyzing Performance of Selected NESAP Applications on the Cori HPC System. - Thorsten Kurth; William Arndt; Taylor Barnes; Brandon Cook 001; Jack Deslippe; Douglas Doerfler; Brian Friesen; Yun (Helen) He; Tuomas Koskela; Mathieu Lobet; Tareq M. Malas; Leonid Oliker; et al. (ISC Workshops, 2017)

Extreme-Scale De Novo Genome Assembly. - Evangelos Georganas; Steven A. Hofmeyr; Rob Egan; Aydin Buluç; Leonid Oliker; Daniel Rokhsar; Katherine A. Yelick (CoRR, 2017)

Communication-Avoiding Optimization Methods for Massive-Scale Graphical Model Structure Learning. - Penporn Koanantakool; Alnur Ali; Ariful Azad; Aydin Buluç; Dmitriy Morozov; Sang-Yun Oh; Leonid Oliker; Katherine A. Yelick (CoRR, 2017)

Compiler-based code generation and autotuning for geometric multigrid on GPU-accelerated supercomputers. - Protonu Basu; Samuel Williams 001; Brian van Straalen; Leonid Oliker; Phillip Colella; Mary W. Hall (Parallel Comput., 2017)

High-End Computing for Next-Generation Scientific Discovery. - Rupak Biswas; David Donofrio; Leonid Oliker (Parallel Comput., 2017)

Communication-Avoiding Optimization Methods for Distributed Massive-Scale Sparse Inverse Covariance Estimation. - Penporn Koanantakool; Alnur Ali; Ariful Azad; Aydin Buluç; Dmitriy Morozov; Leonid Oliker; Katherine A. Yelick; Sang-Yun Oh (AISTATS, 2018)

Roofline Scaling Trajectories: A Method for Parallel Application and Architectural Performance Analysis. - Khaled Z. Ibrahim; Samuel Williams 001; Leonid Oliker (HPCS, 2018)

Extreme scale de novo metagenome assembly. - Evangelos Georganas; Rob Egan; Steven A. Hofmeyr; Eugene Goltsman; Bill Arndt; Andrew Tritt; Aydin Buluç; Leonid Oliker; Katherine A. Yelick (SC, 2018)

A Novel Multi-level Integrated Roofline Model Approach for Performance Characterization. - Tuomas Koskela; Zakhar Matveev; Charlene Yang; Adetokunbo Adedoyin; Roman Belenov; Philippe Thierry; Zhengji Zhao; Rahulkumar Gayatri; Hongzhang Shan; Leonid Oliker; Jack Deslippe; Ron Green; et al. (ISC, 2018)

Performance Analysis of GPU Programming Models Using the Roofline Scaling Trajectories. - Khaled Z. Ibrahim; Samuel Williams 001; Leonid Oliker (Bench, 2019)

diBELLA: Distributed Long Read to Long Read Alignment. - Marquita Ellis; Giulia Guidi; Aydin Buluç; Leonid Oliker; Katherine A. Yelick (ICPP, 2019)

Modern gyrokinetic particle-in-cell simulation of fusion plasmas on top supercomputers. - Bei Wang 002; Stéphane Ethier; William M. Tang; Khaled Z. Ibrahim; Kamesh Madduri; Samuel Williams 001; Leonid Oliker (Int. J. High Perform. Comput. Appl., 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)

Performance Trade-offs in GPU Communication: A Study of Host and Device-initiated Approaches. - Taylor L. Groves; Ben Brock; Yuxin Chen; Khaled Z. Ibrahim; Lenny Oliker; Nicholas J. Wright; Samuel Williams 001; Katherine A. Yelick (PMBS@SC, 2020)

Timemory: Modular Performance Analysis for HPC. - Jonathan R. Madsen; Muaaz G. Awan; Hugo Brunie; Jack Deslippe; Rahulkumar Gayatri; Leonid Oliker; Yunsong Wang; Charlene Yang; Samuel Williams 001 (ISC, 2020)

ADEPT: a domain independent sequence alignment strategy for gpu architectures. - Muaaz G. Awan; Jack Deslippe; Aydin Buluç; Oguz Selvitopi; Steven A. Hofmeyr; Leonid Oliker; Katherine A. Yelick (BMC Bioinform., 2020)

The Parallelism Motifs of Genomic Data Analysis. - Katherine A. Yelick; Aydin Buluç; Muaaz G. Awan; Ariful Azad; Benjamin Brock; Rob Egan; Saliya Ekanayake; Marquita Ellis; Evangelos Georganas; Giulia Guidi; Steven A. Hofmeyr; Oguz Selvitopi; et al. (CoRR, 2020)

Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly. - Giulia Guidi; Oguz Selvitopi; Marquita Ellis; Leonid Oliker; Katherine A. Yelick; Aydin Buluç (IPDPS, 2021)

Distributed-Memory k-mer Counting on GPUs. - Israt Nisa; Prashant Pandey 001; Marquita Ellis; Leonid Oliker; Aydin Buluç; Katherine A. Yelick (IPDPS, 2021)

Architectural Requirements for Deep Learning Workloads in HPC Environments. - Khaled Z. Ibrahim; Tan Nguyen 001; Hai Ah Nam; Wahid Bhimji; Steven Farrell; Leonid Oliker; Michael Rowan; Nicholas J. Wright; Samuel Williams 001 (PMBS, 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)

Distributed-Memory Parallel Contig Generation for De Novo Long-Read Genome Assembly. - Giulia Guidi; Gabriel Raulet; Daniel Rokhsar; Leonid Oliker; Katherine A. Yelick; Aydin Buluç (ICPP, 2022)

Preprocessing Pipeline Optimization for Scientific Deep Learning Workloads. - Khaled Z. Ibrahim; Leonid Oliker (IPDPS, 2022)

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)

Extreme-Scale Many-against-Many Protein Similarity Search. - Oguz Selvitopi; Saliya Ekanayake; Giulia Guidi; Muaaz G. Awan; Georgios A. Pavlopoulos; Ariful Azad; Nikos Kyrpides; Leonid Oliker; Katherine A. Yelick; Aydin Buluç (SC, 2022)

Designing Efficient SIMD Kernels for High Performance Sequence Alignment. - Doru-Thom Popovici; Muaaz Gul Awan; Giulia Guidi; Rob Egan; Steven A. Hofmeyr; Leonid Oliker; Katherine A. Yelick (IPDPS Workshops, 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)

FTL: Transfer Learning Nonlinear Plasma Dynamic Transitions in Low Dimensional Embeddings via Deep Neural Networks. - Zhe Bai; Xishuo Wei; William Tang 002; Leonid Oliker; Zhihong Lin; Samuel Williams 001 (CoRR, 2024)

Exabiome: Advancing Microbial Science through Exascale Computing. - Steven A. Hofmeyr; Aydin Buluç; Robert Riley 002; Rob Egan; Oguz Selvitopi; Leonid Oliker; Katherine A. Yelick; Migun Shakya; Brett Youtsey; Ariful Azad (Comput. Sci. Eng., 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)

Transfer learning nonlinear plasma dynamic transitions in low dimensional embeddings via deep neural networks. - Zhe Bai; Xishuo Wei; William Tang 002; Leonid Oliker; Zhihong Lin; Samuel Williams 001 (Mach. Learn. Sci. Technol., 2025)

Spatio-temporal Fourier Transformer (StFT) for Long-term Dynamics Prediction. - Da Long; Shandian Zhe; Samuel Williams 001; Leonid Oliker; Zhe Bai (CoRR, 2025)