Fast optimal alignment. - John L. Spouge (Comput. Appl. Biosci., 1991)

The correlation error and finite-size correction in an ungapped sequence alignment. - Yonil Park; John L. Spouge (Bioinform., 2002)

The Efficient Computation of Position-Specific Match Scores with the Fast Fourier Transform. - Sanguthevar Rajasekaran; X. Jin; John L. Spouge (J. Comput. Biol., 2002)

Searching for Multiple Words in a Markov Sequence. - Yonil Park; John L. Spouge (INFORMS J. Comput., 2004)

Alignments anchored on genomic landmarks can aid in the identification of regulatory elements. - Kannan Tharakaraman; Leonardo Mariño-Ramírez; Sergey Sheetlin; David Landsman; John L. Spouge (ISMB (Supplement of Bioinformatics), 2005)

Adding sequence context to a Markov background model improves the identification of regulatory elements. - Nak-Kyeong Kim; Kannan Tharakaraman; John L. Spouge (Bioinform., 2006)

Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements. - Kannan Tharakaraman; Leonardo Mariño-Ramírez; Sergey Sheetlin; David Landsman; John L. Spouge (BMC Bioinform., 2006)

Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites. - Nak-Kyeong Kim; Kannan Tharakaraman; Leonardo Mariño-Ramírez; John L. Spouge (BMC Bioinform., 2008)

Threshold Average Precision (TAP-k): a measure of retrieval designed for bioinformatics. - Hyrum D. Carroll; Maricel G. Kann; Sergey Sheetlin; John L. Spouge (Bioinform., 2010)

The ruzzo-tompa algorithm can find the maximal paths in weighted, directed graphs on a one-dimensional lattice. - John L. Spouge; Leonardo Mariño-Ramírez; Sergey Sheetlin (ICCABS, 2012)

Software: an open-source and scalable framework for exact calculations in coalescent theory. - Susanta Tewari; John L. Spouge (BMC Bioinform., 2012)

False Discovery Rate for Homology Searches. - Hyrum D. Carroll; Alex C. Williams; Anthony G. Davis; John L. Spouge (BSB, 2013)

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

Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps. - John L. Spouge; Leonardo Mariño-Ramírez; Sergey L. Sheetlin (Int. J. Bioinform. Res. Appl., 2014)

Improving Retrieval Efficacy of Homology Searches Using the False Discovery Rate. - Hyrum D. Carroll; Alex C. Williams; Anthony G. Davis; John L. Spouge (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

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

Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules. - Natalia Acevedo-Luna; Leonardo Mariño-Ramírez; Armand Halbert; Ulla Hansen; David Landsman; John L. Spouge (BMC Bioinform., 2016)

MultiDomainBenchmark: a multi-domain query and subject database suite. - Hyrum D. Carroll; John L. Spouge; Mileidy Gonzalez (BMC Bioinform., 2019)

A linear-time algorithm that avoids inverses and computes Jackknife (leave-one-out) products like convolutions or other operators in commutative semigroups. - John L. Spouge; Joseph M. Ziegelbauer; Mileidy Gonzalez (Algorithms Mol. Biol., 2020)

A closed formula relevant to 'Theory of local k-mer selection with applications to long-read alignment' by Jim Shaw and Yun William Yu. - John L. Spouge (Bioinform., 2022)

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)

Landscape of racial and ethnic health disparities in the All of Us Research Program. - Vincent Lam; Shivam Sharma; John L. Spouge; I. King Jordan; Leonardo Mariño-Ramírez (Database J. Biol. Databases Curation, 2024)