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)

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)

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

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)

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)

Parallelizing Irregular Applications for Distributed Memory Scalability: Case Studies from Genomics. - Marquita May Ellis (2020)

BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper. - Giulia Guidi; Marquita Ellis; Daniel Rokhsar; Katherine A. Yelick; Aydin Buluç (ACDA, 2021)

Scaling Generalized N-Body Problems, A Case Study from Genomics. - Marquita Ellis; Aydin Buluç; Katherine A. Yelick (ICPP, 2021)

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)

Asynchrony versus bulk-synchrony for a generalized N-body problem from genomics. - Marquita Ellis; Aydin Buluç; Katherine A. Yelick (PPoPP, 2021)

10 Years Later: Cloud Computing is Closing the Performance Gap. - Giulia Guidi; Marquita Ellis; Aydin Buluç; Katherine A. Yelick; David E. Culler (ICPE (Companion), 2021)

Cloud-Bursting and Autoscaling for Python-Native Scientific Workflows Using Ray. - Tingkai Liu; Marquita Ellis; Carlos H. A. Costa; Claudia Misale; Sara Kokkila Schumacher; Jinwook Jung; Gi-Joon Nam; Volodymyr V. Kindratenko (ISC Workshops, 2023)

Automated Data Management and Learning-Based Scheduling for Ray-Based Hybrid HPC-Cloud Systems. - Tingkai Liu; Huili Tao; Yicheng Lu; Zhongbo Zhu; Marquita Ellis; Sara Kokkila Schumacher; Volodymyr V. Kindratenko (Euro-Par (1), 2024)

Toward Open Earth Science as Fast and Accessible as Natural Language. - Marquita Ellis; Iksha Gurung; Muthukumaran Ramasubramanian; Rahul Ramachandran (CoRR, 2025)