Zobrazeno 1 - 10
of 65
pro vyhledávání: '"Guidi, Giulia"'
Autor:
Li, Jiajie, Schmelzle, Jan-Niklas, Du, Yixiao, Heumos, Simon, Guarracino, Andrea, Guidi, Giulia, Prins, Pjotr, Garrison, Erik, Zhang, Zhiru
Computational Pangenomics is an emerging field that studies genetic variation using a graph structure encompassing multiple genomes. Visualizing pangenome graphs is vital for understanding genome diversity. Yet, handling large graphs can be challengi
Externí odkaz:
http://arxiv.org/abs/2409.00876
High-Performance Sorting-Based k-mer Counting in Distributed Memory with Flexible Hybrid Parallelism
Autor:
Li, Yifan, Guidi, Giulia
Publikováno v:
In The 53rd International Conference on Parallel Processing (ICPP 24), August 12-15, 2024, Gotland, Sweden
In generating large quantities of DNA data, high-throughput sequencing technologies require advanced bioinformatics infrastructures for efficient data analysis. k-mer counting, the process of quantifying the frequency of fixed-length k DNA subsequenc
Externí odkaz:
http://arxiv.org/abs/2407.07718
Dedicated accelerator hardware has become essential for processing AI-based workloads, leading to the rise of novel accelerator architectures. Furthermore, fundamental differences in memory architecture and parallelism have made these accelerators ta
Externí odkaz:
http://arxiv.org/abs/2304.08662
Autor:
Selvitopi, Oguz, Ekanayake, Saliya, Guidi, Giulia, Awan, Muaaz G., Pavlopoulos, Georgios A., Azad, Ariful, Kyrpides, Nikos, Oliker, Leonid, Yelick, Katherine, Buluç, Aydın
Publikováno v:
SC'22: Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, 2022
Similarity search is one of the most fundamental computations that are regularly performed on ever-increasing protein datasets. Scalability is of paramount importance for uncovering novel phenomena that occur at very large scales. We unleash the powe
Externí odkaz:
http://arxiv.org/abs/2303.01845
Autor:
Guidi, Giulia, Raulet, Gabriel, Rokhsar, Daniel, Oliker, Leonid, Yelick, Katherine, Buluc, Aydin
Publikováno v:
ICPP22, August 29-September 1, 2022, Bordeaux, France
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is increasing the
Externí odkaz:
http://arxiv.org/abs/2207.04350
Autor:
Garcia, Rolando, Guidi, Giulia
Coordination protocols help programmers of distributed systems reason about the effects of transactions on the state of the system, but they're not cheap. Coordination protocols may involve multiple rounds of communication, which can hurt system resp
Externí odkaz:
http://arxiv.org/abs/2109.08192
Publikováno v:
Companion of the 2021 ACM/SPEC International Conference on Performance Engineering (ICPE21 Companion)
Can cloud computing infrastructures provide HPC-competitive performance for scientific applications broadly? Despite prolific related literature, this question remains open. Answers are crucial for designing future systems and democratizing high-perf
Externí odkaz:
http://arxiv.org/abs/2011.00656
Autor:
Guidi, Giulia, Selvitopi, Oguz, Ellis, Marquita, Oliker, Leonid, Yelick, Katherine, Buluc, Aydin
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies overlapping seq
Externí odkaz:
http://arxiv.org/abs/2010.10055
Autor:
Selvitopi, Oguz, Ekanayake, Saliya, Guidi, Giulia, Pavlopoulos, Georgios, Azad, Ariful, Buluc, Aydin
Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation and gene location.
Externí odkaz:
http://arxiv.org/abs/2009.14467
Autor:
Zeni, Alberto, Guidi, Giulia, Ellis, Marquita, Ding, Nan, Santambrogio, Marco D., Hofmeyr, Steven, Buluç, Aydın, Oliker, Leonid, Yelick, Katherine
Publikováno v:
34th IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2020
Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for third-generation seq
Externí odkaz:
http://arxiv.org/abs/2002.05200