List of works - John L Spouge

A linear-time algorithm that avoids inverses and computes Jackknife (leave-one-out) products like convolutions or other operators in commutative semigroups

scientific article published on 19 September 2020

ALP & FALP: C++ libraries for pairwise local alignment E-values

scientific article published on October 2015

Adding sequence context to a Markov background model improves the identification of regulatory elements

scientific article

Alignments anchored on genomic landmarks can aid in the identification of regulatory elements

scientific article published in June 2005

An accurate approximation for the expected site frequency spectrum in a Galton-Watson process under an infinite sites mutation model

scientific article published on 12 March 2019

Conserved molecular signatures in gp120 are associated with the genetic bottleneck during simian immunodeficiency virus (SIV), SIV-human immunodeficiency virus (SHIV), and HIV type 1 (HIV-1) transmission

scientific article

Conserved signatures indicate HIV-1 transmission is under strong selection and thus is not a "stochastic" process

scientific article

Discovery of Kaposi's sarcoma herpesvirus-encoded circular RNAs and a human antiviral circular RNA

article published in the Proceedings of the National Academy of Sciences of the United States of America

ESTIMATING THE GUMBEL SCALE PARAMETER FOR LOCAL ALIGNMENT OF RANDOM SEQUENCES BY IMPORTANCE SAMPLING WITH STOPPING TIMES

scientific article

Estimating the basic reproduction number of a pathogen in a single host when only a single founder successfully infects

scientific article published on 10 January 2020

Figures of merit and statistics for detecting faulty species identification with DNA barcodes: A case study in Ramaria and related fungal genera

scientific article published on 19 August 2020

Finding functional sequence elements by multiple local alignment

scientific article published on 02 January 2004

Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites

scientific article

Frameshift alignment: statistics and post-genomic applications

scientific article

Identification of cis-regulatory elements in gene co-expression networks using A-GLAM.

scientific article published on January 2009

Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules.

scientific article

New finite-size correction for local alignment score distributions ⬇️

scientific article published on June 12, 2012

Objective method for estimating asymptotic parameters, with an application to sequence alignment ⬇️

scientific article published on September 13, 2011

Patterns of conserved gp120 epitope presentation on attached HIV-1 virions

scientific article published on 30 October 2017

Promoter analysis: gene regulatory motif identification with A-GLAM.

scientific article

Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements

scientific article

Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps.

scientific article

Statistical analysis of over-represented words in human promoter sequences

scientific article

Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences

scientific article

Structural prediction of RNA switches using conditional base-pair probabilities.

scientific article published on 12 June 2019

The Gumbel pre-factor k for gapped local alignment can be estimated from simulations of global alignment

scientific article

The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site

scientific article

The correlation error and finite-size correction in an ungapped sequence alignment

scientific article

The identification of complete domains within protein sequences using accurate E-values for semi-global alignment

scientific article

The practical evaluation of DNA barcode efficacy

scientific article

The whole alignment and nothing but the alignment: the problem of spurious alignment flanks.

scientific article published on 16 September 2008

Threshold Average Precision (TAP-k): a measure of retrieval designed for bioinformatics

scientific article

List of works by John L Spouge

A linear-time algorithm that avoids inverses and computes Jackknife (leave-one-out) products like convolutions or other operators in commutative semigroups

ALP & FALP: C++ libraries for pairwise local alignment E-values

Adding sequence context to a Markov background model improves the identification of regulatory elements

Alignments anchored on genomic landmarks can aid in the identification of regulatory elements

An accurate approximation for the expected site frequency spectrum in a Galton-Watson process under an infinite sites mutation model

Conserved molecular signatures in gp120 are associated with the genetic bottleneck during simian immunodeficiency virus (SIV), SIV-human immunodeficiency virus (SHIV), and HIV type 1 (HIV-1) transmission

Conserved signatures indicate HIV-1 transmission is under strong selection and thus is not a "stochastic" process

Discovery of Kaposi's sarcoma herpesvirus-encoded circular RNAs and a human antiviral circular RNA

ESTIMATING THE GUMBEL SCALE PARAMETER FOR LOCAL ALIGNMENT OF RANDOM SEQUENCES BY IMPORTANCE SAMPLING WITH STOPPING TIMES

Estimating the basic reproduction number of a pathogen in a single host when only a single founder successfully infects

Figures of merit and statistics for detecting faulty species identification with DNA barcodes: A case study in Ramaria and related fungal genera

Finding functional sequence elements by multiple local alignment

Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites

Frameshift alignment: statistics and post-genomic applications

Identification of cis-regulatory elements in gene co-expression networks using A-GLAM.

Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules.

New finite-size correction for local alignment score distributions ⬇️

Objective method for estimating asymptotic parameters, with an application to sequence alignment ⬇️

Patterns of conserved gp120 epitope presentation on attached HIV-1 virions

Promoter analysis: gene regulatory motif identification with A-GLAM.

Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements

Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps.

Statistical analysis of over-represented words in human promoter sequences

Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences

Structural prediction of RNA switches using conditional base-pair probabilities.

The Gumbel pre-factor k for gapped local alignment can be estimated from simulations of global alignment

The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site

The correlation error and finite-size correction in an ungapped sequence alignment

The identification of complete domains within protein sequences using accurate E-values for semi-global alignment

The practical evaluation of DNA barcode efficacy

The whole alignment and nothing but the alignment: the problem of spurious alignment flanks.

Threshold Average Precision (TAP-k): a measure of retrieval designed for bioinformatics