A parallel tiled and sparsified Four-Russians algorithm for Nussinov's RNA folding

VK Tchendji, FIK Youmbi, CT Djamegni… - … /ACM Transactions on …, 2022 - ieeexplore.ieee.org
To enable extensive research on the ribonucleic acid (RNA) molecule, predicting its spatial
structure stands as a much-valued research field. In this regard, Nussinov and Jacobson …

Taking RNA-RNA Interaction to Machine Peak

C Mondal, S Rajopadhye - IEEE Transactions on Parallel and …, 2024 - ieeexplore.ieee.org
RNA-RNA interactions (RRIs) are essential in many biological processes, including gene
transcription, translation, and localization. They play a critical role in diseases such as …

Accelerating the BPMax algorithm for RNA-RNA interaction

C Mondal, S Rajopadhye - 2021 IEEE International Parallel …, 2021 - ieeexplore.ieee.org
RNA-RNA interactions (RRI) play an important role in various biological processes such as
gene transcription, and are known to play a critical role in diseases such as cancer and …

3D Tiled Code Generation for Nussinov's Algorithm

W Bielecki, P Błaszyński, M Pałkowski - Applied Sciences, 2022 - mdpi.com
Current state-of-the-art parallel codes used to calculate the maximum number of pairs for a
given RNA sequence by means of Nussinov's algorithm do not allow for achieving speedup …

A tropical semiring multiple matrix-product library on GPUs:(not just) a step towards RNA-RNA interaction computations

B Gildemaster, P Ghalsasi… - 2020 IEEE International …, 2020 - ieeexplore.ieee.org
RNA-RNA interaction (RRI) is important in processes such as gene regulation, and certain
classes of RRI are known to play roles in various diseases including cancer and …

Efficient computation of RNA partition functions using McCaskill's algorithm

C Zhao, S Sahni - 2020 15th Conference on Computer Science …, 2020 - ieeexplore.ieee.org
We develop efficient single-and multi-core algorithms to compute partition functions for RNA
sequences. Our algorithms, which are based on McCaskill's algorithm, are benchmarked …

Graphical processing unit accelerated RNA substructure comparison and search engine

A Kumari - 2021 - search.proquest.com
Exponentially increasing Ribonucleic acid (RNA) secondary structure databases have
presented new challenges to researchers in the field and motivated the idea for fast …

RNA secondary structure prediction using AlphaZ

T Pathan - 2010 - search.proquest.com
Optimizing complex algorithms using conventional programming languages can be a
difficult task. The performance aspect of such implementations relies on the programmer and …

An Overview of Miscellaneous Applications of GPU Computing

S Stankovic, J Astola - 2012 - hgpu.org
In general, the GPU computing denotes computing over a GPU system consisting of a
graphics processing unit (GPU) and a central processing unit (CPU). Such systems are …