Publications

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

Giulia Guidi, Marquita Ellis, Daniel Rokhsar, Katherine Yelick, Aydın Buluç. BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper, 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.

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

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

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

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

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

Evangelos Georganas, Aydın Buluç, Jarrod Chapman, Steven Hofmeyr, Chaitanya Aluru, Rob Egan, Leonid Oliker, Daniel Rokhsar, and Katherine Yelick. 2015. HipMer: an extreme-scale de novo genome assembler. 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

Evangelos Georganas, Aydın Buluç, Jarrod Chapman, Leonid Oliker, Daniel Rokhsar and Katherine Yelick. merAligner: A Fully Parallel Sequence Aligner. 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