Publications

The Parallelism Motifs of Genomic Data Analysis. 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, and Leonid Oliker, Philosophical Transactions of the Royal Society A, 2020, 378:20190394. doi: 10.1098/rsta.2019.0394

Exascale Applications: Skin in the Game. Francis Alexander, Ann Almgren, John Bell, Amitava Bhattacharjee, Jacqueline Chen, Phil Colella, David Daniel, Jack DeSlippe, Lori Diachin, Erik Draeger, Anshu Dubey, Thom Dunning, Thomas Evans, Ian Foster, Marianne Francois, Tim Germann, Mark Gordon, Salman Habib, Mahantesh Halappanavar, Steven Hamilton,William Hart, Zhenyu (Henry) Huang, Aimee Hungerford, Daniel Kasen, Paul R. C. Kent, Tzanio Kolev, Douglas B. Kothe, Andreas Kronfeld, Ye Luo, Paul Mackenzie, David McCallen, Bronson Messer, Sue Mniszewski, Chris Oehmen, AmedeoPerazzo, Danny Perez, David Richards,William J. Rider, Rob Rieben, Kenneth Roche, Andrew Siege, Michael Sprague, Carl Steefel, Rick Stevens, Madhava Syamlal, Mark Taylor, John Turner, Jean-Luc Vay, Artur F. Voter, Theresa L.Windus, and Katherine Yelick, Philosophical Transactions of the Royal Society A, 2020, 378:20190056. doi: 10.1098/rsta.2019.0056

diBELLA: Distributed Long Read to Long Read Alignment. Marquita Ellis, Giulia Guidi, Aydin Buluc, Leonid Oliker, and Katherine Yelick, International Conference on Parallel Processing, Kyoto, Japan, August 5-8, 2019.

BCL: A Cross-Platform Distributed Data Structures Library. Benjamin Brock, Aydin Buluc, and Katherine Yelick, International Conference on Parallel Processing, Kyoto, Japan, August 5-8, 2019.

Extreme Scale De Novo Metagenome Assembly. Evangelos Georganas, Steven Hofmeyr, Leonid Oliker, Rob Egan, Daniel Rokhsar, Aydin Buluc, Katherine Yelick.International Conference for High Performance Computing, Networking, Storage and Analysis (“Supercomputing”, SC’18), Dallas, Texas, November 2018. Best Paper Finalist.

BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper. Giulia Guidi, Marquita Ellis, Daniel Rokhsar, Katherine Yelick, Aydın Buluç. bioRxiv:464420, November 7, 2018. Presented as a poster at the 3rd Annual Northern California Computational Biology Symposium (NCCB) on October 6, 2018 in San Francisco. Also a poster presentation at the Biological Data Science meeting in Cold Spring Harbor Laboratory, New York on November 7-10, 2018.

HipMCL: A high-performance parallel implementation of the Markov clustering algorithm for large-scale networks. Ariful Azad, Georgios A. Pavlopoulos, Christos A. Ouzounis, Nikos C. Kyrpides, and Aydin Buluc. Nucleic Acids Research (NAR), Vol. 46, No. 6, April 6, 2018.

Extreme-Scale De Novo Genome Assembly. Evangelos Georganas, Steven Hofmeyr, Leonid Oliker, Rob Egan, Daniel Rokhsar, Aydin Buluc, Katherine Yelick. Exascale Scientific Applications: Scalability and Performance Portability, CRC Press, November 13, 2017.

MerBench: PGAS Benchmarks for High Performance Genome Assembly. Evangelos Georganas, Marquita Ellis, Rob Egan, Steven Hofmeyr, Aydin Buluç, Brandon Cook, Leonid Oliker, Katherine Yelick, Proceedings of the Second Annual PGAS Applications Workshop (at SC'17), November 12, 2017.

Performance characterization of de novo genome assembly on leading parallel systems. Marquita Ellis, Evangelos Georganas, Rob Egan, Steven Hofmeyr, Aydin Buluc, Brandon Cook, Leonid Oliker, and Katherine Yelick. In EuroPar - International European Conference on Parallel and Distributed Computing, 2017.

Scalable Parallel Algorithms for Genome Analysis. Evangelos Georganas. PhD thesis, EECS Department, University of California, Berkeley, August 2016.

HipMer: an extreme-scale de novo genome assembler. Evangelos Georganas, Aydın Buluç, Jarrod Chapman, Steven Hofmeyr, Chaitanya Aluru, Rob Egan, Leonid Oliker, Daniel Rokhsar, and Katherine Yelick. 2015. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC '15). ACM, New York, NY, USA, , Article 14 , 11 pages. DOI: https://doi.org/10.1145/2807591.2807664

merAligner: A Fully Parallel Sequence Aligner. Evangelos Georganas, Aydın Buluç, Jarrod Chapman, Leonid Oliker, Daniel Rokhsar and Katherine Yelick. 29th IEEE International Parallel & Distributed Processing Symposium (IPDPS 2015), Hyderabad, INDIA, May 2015. DOI: https://doi.org/10.1109/IPDPS.2015.96

Evangelos Georganas, Aydin Buluç, Jarrod Chapman, Leonid Oliker, Daniel Rokhsar, and Katherine Yelick. 2014. Parallel de bruijn graph construction and traversal for de novo genome assembly. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC '14). IEEE Press, Piscataway, NJ, USA, 437-448. DOI: http://dx.doi.org/10.1109/SC.2014.41