John L. Spouge

Publication Activity (10 Years)

Years Active: 1991-2023
Publications (10 Years): 7

Top Topics

Transcription Factor Binding Sites

False Discovery Rate

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

Int. J. Bioinform. Res. Appl.

Publications

Martin C. Frith, Jim Shaw, John L. Spouge
How to optimally sample a sequence for rapid analysis. Bioinform. 39 (2) (2023)
John L. Spouge
A closed formula relevant to 'Theory of local k-mer selection with applications to long-read alignment' by Jim Shaw and Yun William Yu. Bioinform. 38 (20) (2022)
John L. Spouge, Joseph M. Ziegelbauer, Mileidy Gonzalez
A linear-time algorithm that avoids inverses and computes Jackknife (leave-one-out) products like convolutions or other operators in commutative semigroups. Algorithms Mol. Biol. 15 (1) (2020)
Hyrum D. Carroll, John L. Spouge, Mileidy Gonzalez
MultiDomainBenchmark: a multi-domain query and subject database suite. BMC Bioinform. 20 (1) (2019)
Natalia Acevedo-Luna, Leonardo Mariño-Ramírez, Armand Halbert, Ulla Hansen, David Landsman, John L. Spouge
Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules. BMC Bioinform. 17 (2016)
Sergey Sheetlin, Yonil Park, Martin C. Frith, John L. Spouge
-values. Bioinform. 32 (2) (2016)
Hyrum D. Carroll, Alex C. Williams, Anthony G. Davis, John L. Spouge
Improving Retrieval Efficacy of Homology Searches Using the False Discovery Rate. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (3) (2015)
Sergey L. Sheetlin, Yonil Park, Martin C. Frith, John L. Spouge
Frameshift alignment: statistics and post-genomic applications. Bioinform. 30 (24) (2014)
John L. Spouge, Leonardo Mariño-Ramírez, Sergey L. Sheetlin
Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps. Int. J. Bioinform. Res. Appl. 10 (4/5) (2014)
Hyrum D. Carroll, Alex C. Williams, Anthony G. Davis, John L. Spouge
False Discovery Rate for Homology Searches. BSB (2013)
John L. Spouge, Leonardo Mariño-Ramírez, Sergey Sheetlin
The ruzzo-tompa algorithm can find the maximal paths in weighted, directed graphs on a one-dimensional lattice. ICCABS (2012)
Susanta Tewari, John L. Spouge
Software: an open-source and scalable framework for exact calculations in coalescent theory. BMC Bioinform. 13 (2012)
Hyrum D. Carroll, Maricel G. Kann, Sergey Sheetlin, John L. Spouge
): a measure of retrieval designed for bioinformatics. Bioinform. 26 (14) (2010)
Nak-Kyeong Kim, Kannan Tharakaraman, Leonardo Mariño-Ramírez, John L. Spouge
Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites. BMC Bioinform. 9 (2008)
Kannan Tharakaraman, Leonardo Mariño-Ramírez, Sergey Sheetlin, David Landsman, John L. Spouge
Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements. BMC Bioinform. 7 (2006)
Nak-Kyeong Kim, Kannan Tharakaraman, John L. Spouge
Adding sequence context to a Markov background model improves the identification of regulatory elements. Bioinform. 22 (23) (2006)
Kannan Tharakaraman, Leonardo Mariño-Ramírez, Sergey Sheetlin, David Landsman, John L. Spouge
Alignments anchored on genomic landmarks can aid in the identification of regulatory elements. ISMB (Supplement of Bioinformatics) (2005)
Yonil Park, John L. Spouge
Searching for Multiple Words in a Markov Sequence. INFORMS J. Comput. 16 (4) (2004)
Sanguthevar Rajasekaran, X. Jin, John L. Spouge
The Efficient Computation of Position-Specific Match Scores with the Fast Fourier Transform. J. Comput. Biol. 9 (1) (2002)
Yonil Park, John L. Spouge
The correlation error and finite-size correction in an ungapped sequence alignment. Bioinform. 18 (9) (2002)
John L. Spouge
Fast optimal alignment. Comput. Appl. Biosci. 7 (1) (1991)