BLAMM: BLAS-based algorithm for finding position weight matrix occurrences in DNA sequences on CPUs and GPUs

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Fast motif matching revisited: high-order PWMs, SNPs and indels

(2016) Janne H. Korhonen et al.   BIOINFORMATICS

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Parallel Position Weight Matrices algorithms

(2010) Mathieu Giraud et al.   PARALLEL COMPUTING

MOODS: fast search for position weight matrix matches in DNA sequences

(2009) J. Korhonen et al.   BIOINFORMATICS

Finding Significant Matches of Position Weight Matrices in Linear Time

(2009) Cinzia Pizzi et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Anatomy of high-performance matrix multiplication

(2008) Kazushige Goto et al.   ACM TRANSACTIONS ON MATHEMATICAL SOFTWARE

Pseudocounts for transcription factor binding sites

(2008) Keishin Nishida et al.   NUCLEIC ACIDS RESEARCH

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger et al.   NUCLEIC ACIDS RESEARCH

Fast profile matching algorithms — A survey

(2008) Cinzia Pizzi et al.   THEORETICAL COMPUTER SCIENCE