The parallelism motifs of genomic data analysis

End-to-End Differentiable Learning of Protein Structure

(2019) Mohammed AlQuraishi   Cell Systems

Performance optimization, modeling and analysis of sparse matrix-matrix products on multi-core and many-core processors

(2019) Yusuke Nagasaka et al.   PARALLEL COMPUTING

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Introducing difference recurrence relations for faster semi-global alignment of long sequences

(2018) Hajime Suzuki et al.   BMC BIOINFORMATICS

HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks

(2018) Ariful Azad et al.   NUCLEIC ACIDS RESEARCH

Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems

(2017) Tony Pan et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Efficient parallelization using rank convergence in dynamic programming algorithms

(2016) Saeed Maleki et al.   COMMUNICATIONS OF THE ACM

Apache Spark

(2016) Matei Zaharia et al.   COMMUNICATIONS OF THE ACM

Exploiting Multiple Levels of Parallelism in Sparse Matrix-Matrix Multiplication

(2016) Ariful Azad et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions

(2013) Yongchao Liu et al.   BMC BIOINFORMATICS

Parallel Sparse Matrix-Matrix Multiplication and Indexing: Implementation and Experiments

(2012) Aydin Buluç et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

The Combinatorial BLAS: design, implementation, and applications

(2011) Aydın Buluç et al.   INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics

Graph Clustering Via a Discrete Uncoupling Process

(2008) Stijn Van Dongen   SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS