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Marquita Ellis

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Marquita Ellis Ph.D.
Interim Computer Science Postdoctoral Fellow
Phone: 510-495-2431
Marquita Ellis is an interim postdoctoral researcher at LBNL, working with the CLaSS and Exabiome groups. Her doctoral research, with Katherine Yelick at UC Berkeley, focused on parallelizing irregular applications for distributed memory scalability with case studies from genomics.  Before completing her Ph.D. at Berkeley, she conducted research on concurrent data structures and transactional memory systems with Maurice Herlihy at Brown University, where she received her bachelor’s and master’s degrees in Computer Science.
  

Journal Articles

Katherine Yelick, Aydın Buluç, Muaaz Awan, Ariful Azad, Benjamin Brock, Rob Egan, Saliya Ekanayake, Marquita Ellis, Evangelos Georganas, Giulia Guidi, Steven Hofmeyr, Oguz Selvitopi, Cristina Teodoropol, Leonid Oliker, "The parallelism motifs of genomic data analysis", Philosophical Transactions of The Royal Society A: Mathematical, Physical and Engineering Sciences, 2020,

Giulia Guidi, Marquita Ellis, Daniel Rokhsar, Katherine Yelick, Aydın Buluç, "BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper (Preprint)", Submitted, 2018, doi: https://doi.org/10.1101/464420

Conference Papers

Alberto Zeni, Giulia Guidi, Marquita Ellis, Nan Ding, Marco D. Santambrogio, Steven Hofmeyr, Aydın Buluç, Leonid Oliker, Katherine Yelick, "LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment", 34th IEEE International Parallel and Distributed Processing Symposium (IPDPS20), 2020,

Marquita Ellis, Giulia Guidi, Aydın Buluç, Leonid Oliker, Katherine Yelick, "diBELLA: Distributed Long Read to Long Read Alignment", 48th International Conference on Parallel Processing (ICPP), June 25, 2019,

M Ellis, E Georganas, R Egan, S Hofmeyr, A Buluç, B Cook, L Oliker, K Yelick, "Performance characterization of de novo genome assembly on leading parallel systems", Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2017, 10417 LN:79--91, doi: 10.1007/978-3-319-64203-1_6

E Georganas, M Ellis, R Egan, S Hofmeyr, A Buluç, B Cook, L Oliker, K Yelick, "MerBench: PGAS benchmarks for high performance genome assembly", Proceedings of PAW 2017: 2nd Annual PGAS Applications Workshop - Held in conjunction with SC 2017: The International Conference for High Performance Computing, Networking, Storage and Analysis, 2017, 2017-Jan:1--4, doi: 10.1145/3144779.3169109