Theatre: A Novel Tool For The Comparative Investigation and Display of Evolutionary Diversity of Functional and Structural Features in DNA Sequences. - Yvonne J. K. Edwards; Martin C. Frith; Greg Elgar; Martin J. Bishop 002 (German Conference on Bioinformatics, 1998)

Detection of cis -element clusters in higher eukaryotic DNA. - Martin C. Frith; Ulla Hansen; Zhiping Weng (Bioinform., 2001)

SeqVISTA: a graphical tool for sequence feature visualization and comparison. - Zhenjun Hu; Martin C. Frith; Tianhua Niu; Zhiping Weng (BMC Bioinform., 2003)

Theatre: a software tool for detailed comparative analysis and visualization of genomic sequence. - Yvonne J. K. Edwards; Tim J. Carver; Tanya Vavouri; Martin C. Frith; Martin J. Bishop 002; Greg Elgar (Nucleic Acids Res., 2003)

Cluster-Buster: finding dense clusters of motifs in DNA sequences. - Martin C. Frith; Michael C. Li; Zhiping Weng (Nucleic Acids Res., 2003)

MotifViz: an analysis and visualization tool for motif discovery. - Yutao Fu; Martin C. Frith; Peter M. Haverty; Zhiping Weng (Nucleic Acids Res., 2004)

CARRIE web service: automated transcriptional regulatory network inference and interactive analysis. - Peter M. Haverty; Martin C. Frith; Zhiping Weng (Nucleic Acids Res., 2004)

Large-scale clustering of CAGE tag expression data. - Kazuro Shimokawa; Yuko Okamura-Oho; Takio Kurita; Martin C. Frith; Jun Kawai; Piero Carninci; Yoshihide Hayashizaki (BMC Bioinform., 2007)

Discovering Sequence Motifs with Arbitrary Insertions and Deletions. - Martin C. Frith; Neil F. W. Saunders; Bostjan Kobe; Timothy L. Bailey (PLoS Comput. Biol., 2008)

MEME SUITE: tools for motif discovery and searching. - Timothy L. Bailey; Mikael Bodén; Fabian A. Buske; Martin C. Frith; Charles E. Grant; Luca Clementi; Jingyuan Ren; Wilfred W. Li; William Stafford Noble (Nucleic Acids Res., 2009)

In search of true reads: A classification approach to next generation sequencing data selection. - Edward Wijaya; Jean-François Pessiot; Martin C. Frith; Wataru Fujibuchi; Kiyoshi Asai; Paul Horton (BIBM Workshops, 2010)

Parameters for accurate genome alignment. - Martin C. Frith; Michiaki Hamada; Paul Horton (BMC Bioinform., 2010)

Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection. - Michiaki Hamada; Edward Wijaya; Martin C. Frith; Kiyoshi Asai (Bioinform., 2011)

CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences. - Michiaki Hamada; Koichiro Yamada; Kengo Sato; Martin C. Frith; Kiyoshi Asai (Nucleic Acids Res., 2011)

Adding unaligned sequences into an existing alignment using MAFFT and LAST. - Kazutaka Katoh; Martin C. Frith (Bioinform., 2012)

RecountDB: a database of mapped and count corrected transcribed sequences. - Edward Wijaya; Martin C. Frith; Kiyoshi Asai; Paul Horton (Nucleic Acids Res., 2012)

An approximate Bayesian approach for mapping paired-end DNA reads to a reference genome. - Anish Man Singh Shrestha; Martin C. Frith (Bioinform., 2013)

A bioinformatician's guide to the forefront of suffix array construction algorithms. - Anish Man Singh Shrestha; Martin C. Frith; Paul Horton (Briefings Bioinform., 2014)

Frameshift alignment: statistics and post-genomic applications. - Sergey L. Sheetlin; Yonil Park; Martin C. Frith; John L. Spouge (Bioinform., 2014)

A promoter-level mammalian expression atlas. - Fantom Consortium; RIKEN PMII; RIKEN CLST (DGT); Alistair R. R. Forrest; Hideya Kawaji; Michael Rehli; J. Kenneth Baillie; Michiel J. L. de Hoon; Vanja Haberle; Timo Lassmann; Ivan V. Kulakovskiy; Marina Lizio; et al. (Nat., 2014)

A Genetic Algorithm for Motif Finding Based on Statistical Significance. - Josep Basha Gutierrez; Martin C. Frith; Kenta Nakai (IWBBIO (1), 2015)

ALP & FALP: C++ libraries for pairwise local alignment E-values. - Sergey Sheetlin; Yonil Park; Martin C. Frith; John L. Spouge (Bioinform., 2016)

Training alignment parameters for arbitrary sequencers with LAST-TRAIN. - Michiaki Hamada; Yukiteru Ono; Kiyoshi Asai; Martin C. Frith (Bioinform., 2017)

Variable-order sequence modeling improves bacterial strain discrimination for Ion Torrent DNA reads. - Thomas M. Poulsen; Martin C. Frith (BMC Bioinform., 2017)

A Simplified Description of Child Tables for Sequence Similarity Search. - Martin C. Frith; Anish Man Singh Shrestha (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

How sequence alignment scores correspond to probability models. - Martin C. Frith (Bioinform., 2020)

Minimally overlapping words for sequence similarity search. - Martin C. Frith; Laurent Noé; Gregory Kucherov (Bioinform., 2021)

Improved DNA-Versus-Protein Homology Search for Protein Fossils. - Yin Yao; Martin C. Frith (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

How to optimally sample a sequence for rapid analysis. - Martin C. Frith; Jim Shaw; John L. Spouge (Bioinform., 2023)

The Statistics of Parametrized Syncmers in a Simple Mutation Process Without Spurious Matches. - John L. Spouge; Pijush Das; Ye Chen; Martin C. Frith (J. Comput. Biol., 2024)

A Simple Way to Find Related Sequences with Position-Specific Probabilities. - Martin C. Frith (RECOMB-CG, 2025)

Probability-Based Sequence Comparison Finds the Oldest Ever Nuclear Mitochondrial DNA Segments in Mammalian Genomes. - Muyao Huang; Martin C. Frith (RECOMB-CG, 2025)