Publications

2020

PersGNN: Applying Topological Data Analysis and Geometric Deep Learning to Structure-Based Protein Function Prediction, Nicolas Swenson, Aditi S Krishnapriyan, Aydin Buluc, Dmitriy Morozov, Katherine Yelick, arXiv preprint arXiv:2010.16027, 2020/10/30. (To appear, NeurIPS Workshop.)

Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly, Giulia Guidi, Oguz Selvitopi, Marquita Ellis, Leonid Oliker, Kathering Yelick, Aydin Buluc, arXiv:2010.10055, 2020.

10 Years Later: Cloud Computing is Closing the Performance Gap, Giulia Guidi, Marquita Ellis, Aydin Buluc, Katherine Yelick, David Culler, 2020/11/2, arXiv preprint arXiv:2011.00656.

Reducing Communication in Graph Neural Network Training, Alok Tripathy, Katherine Yelick, Aydin Buluc, Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC20), November 2020. arXiv preprint arXiv:2005.033002020Q. To appear.

Distributed many-to-many protein sequence alignment using sparse matrices, Oguz Selvitopi, Saliya Ekanayake, Giulia Guidi, Georgios Pavlopoulos, Ariful Azad, and Aydin Buluç, Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC20), November 2020. arXiv preprint arXiv:2009.1446732020. To appear.

Communication-Avoiding and Memory-Constrained Sparse Matrix-Matrix Multiplication at Extreme Scale, Md Taufique Hussain, Oguz Selvitopi, Aydin Buluç, Ariful Azad, October 2020, arXiv preprint arXiv:2010.085262020.

ADEPT: a domain independent sequence alignment strategy for GPU architectures, Muaaz Awan, Jack Deslippe, Aydin Buluc, Oguz Selvitopi, Steven Hofmeyr, Leonid Oliker, Katherine Yelick, BMC Bioinformatics 21 (1), 1-29, September 2020.

Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridumand its diploid progenitors, Sean P. Gordon, Bruno Contreras-Moreira, Joshua J. Levy, Armin Djamei, Angelika Czedik-Eysenberg, Virginia S. Tartaglio, Adam Session, Joel Martin, Amy Cartwright, Andrew Katz, Vasanth R. Singan, Eugene Goltsman, Kerrie Barry, Vinh Ha Dinh-Thi, Boulos Chalhoub, Antonio Diaz-Perez, Ruben Sancho, Joanna Lusinska, Elzbieta Wolny, Candida Nibau, John H. Doonan, Luis A. J. Mur, Chris Plott, Jerry Jenkins, Samuel P. Hazen, Scott J. Lee, Shengqiang Shu, David Goodstein, Daniel Rokhsar, Jeremy Schmutz, Robert Hasterok, Pilar Catalan, John P. Vogel, Nature Communications, 11 (3670) July 2020.

Optimizing high performance Markov clustering for pre-exascale architectures. Oguz Selvitopi, Md Taufique Hussain, Ariful Azad, and Aydin Buluç. In Proceedings of the International Parallel and Distributed Processing Symposium, May 2020.

Parallelizing Irregular Applications for Distributed Memory Scalability: Case Studies from Genomics. Marquita Ellis, (Committee: Katherine A. Yelick, James Demmel, Aydin Buluç, and Daniel Rokhsar). PhD dissertation, University of California, Berkeley, May 2020.

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment, Alberto Zeni, Giulia Guidi, Marquita Ellis, Nan Ding, Marco D Santambrogio, Steven Hofmeyr, Aydın Buluç, Leonid Oliker, Katherine Yelick, 2020.

GPU accelerated partial order multiple sequence alignment for long reads self-correction, Francesco Peverelli, Lorenzo Di Tucci, Marco D Santambrogio, Nan Ding, Steven Hofmeyr, Aydın Buluç, Leonid Oliker, Katherine Yelick, 2020/1/1, bioRxiv2020.

BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper, Giulia Guidi, Marquita Ellis, Daniel Rokhsar, Katherine Yelick, Aydın Buluç, 2020/1/1, bioRxiv2020. doi: https://doi.org/10.1101/464420.

Terabase-scale metagenome coassembly with MetaHipMer, Steven Hofmeyr, Rob Egan, Evangelos Georganas, Alex C. Copeland, Robert Riley, Alicia Clum, Emiley Eloe-Fadrosh, Simon Roux, Eugene Goltsman, Aydın Buluç, Daniel Rokhsar, Leonid Oliker, Katherine Yelick, Scientific reports, Nature Publishing Group (10:1), pp. 1-11. July 1, 2020.

Parallel algorithms for finding connected components using linear algebra, Yongzhe Zhang, Ariful Azad, and Aydin Buluç, Journal of Parallel and Distributed Computing, April 2020.

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

2019

RDMA vs. RPC for implementing distributed data structures, Benjamin A Brock, Yuxin Chen, Jiakun Yan, John Owens, Aydın Buluç, Katherine Yelick, 2019/11/18, 2019 IEEE/ACM 9th Workshop on Irregular Applications: Architectures and Algorithms (IA3) at SC19, Pages 17-22.

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. DOI 10.1145/3337821.3337919

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.

2018

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.

2017

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.

2016

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

2015

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