Author details

Full Name

John L Spouge

Affiliation

ORCID

Career Start Year

1982

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36702468	How to optimally sample a sequence for rapid analysis.	Bioinformatics	2023
38045036	Ancestry-attenuated effects of socioeconomic deprivation on type 2 diabetes disparities in the cohort.		2023
37595401	Estimating age-stratified transmission and reproduction numbers during the early exponential phase of an epidemic: A case study with COVID-19 data.		2023
37790565	Ancestry-attenuated effects of socioeconomic deprivation on type 2 diabetes disparities in the All of Us cohort.		2023
36063041	A closed formula relevant to 'Theory of local k-mer selection with applications to long-read alignment' by Jim Shaw and Yun William Yu.		2022
33708051	Hemolysis Pathways during Storage of Erythrocytes and Inter-Donor Variability in Erythrocyte Morphology.	Transfusion Medicine and Hemotherapy	2021
34255772	A comprehensive estimation of country-level basic reproduction numbers R0 for COVID-19: Regime regression can automatically estimate the end of the exponential phase in epidemic data.	PLoS ONE	2021
33826666	Correction: Figures of merit and statistics for detecting faulty species identification with DNA barcodes: A case study in Ramaria and related fungal genera.	PLoS ONE	2021
32968428	A linear-time algorithm that avoids inverses and computes Jackknife (leave-one-out) products like convolutions or other operators in commutative semigroups.	Algorithms for Molecular Biology	2020
31923263	Estimating the basic reproduction number of a pathogen in a single host when only a single founder successfully infects.	PLoS ONE	2020
32813726	Figures of merit and statistics for detecting faulty species identification with DNA barcodes: A case study in Ramaria and related fungal genera.	PLoS ONE	2020
30764761	MultiDomainBenchmark: a multi-domain query and subject database suite.	BMC Bioinformatics	2019
31188853	Structural prediction of RNA switches using conditional base-pair probabilities.	PLoS ONE	2019
30876864	An accurate approximation for the expected site frequency spectrum in a Galton-Watson process under an infinite sites mutation model.	Theoretical Population Biology	2019
30526482	Alignment-free genome comparison enables accurate geographic sourcing of white oak DNA.	BMC Genomics	2018
28940296	Empirical null estimation using zero-inflated discrete mixture distributions and its application to protein domain data.	Biometrics	2018
30455306	Discovery of Kaposi's sarcoma herpesvirus-encoded circular RNAs and a human antiviral circular RNA.	Proceedings of the National Academy of Sciences of the United States of America	2018
28231858	Conserved signatures indicate HIV-1 transmission is under strong selection and thus is not a "stochastic" process.	Retrovirology	2017
29087304	Patterns of conserved gp120 epitope presentation on attached HIV-1 virions.	Proceedings of the National Academy of Sciences of the United States of America	2017
27871221	Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules.	BMC Bioinformatics	2016
26428291	ALP & FALP: C++ libraries for pairwise local alignment E-values.	Bioinformatics	2016
27685447	Changes in the Plasticity of HIV-1 Nef RNA during the Evolution of the North American Epidemic.	PLoS ONE	2016
26312189	Coalescent: an open-science framework for importance sampling in coalescent theory.	PeerJ	2015
25589738	A new method for estimating species age supports the coexistence of malaria parasites and their Mammalian hosts.	Mol Biol Evol	2015
25589663	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.	Journal of Virology	2015
26357264	Improving Retrieval Efficacy of Homology Searches Using the False Discovery Rate.	IEEE/ACM Transactions on Computational Biology and Bioinformatics	2015
25172925	Frameshift alignment: statistics and post-genomic applications.	Bioinformatics	2014
25715438	This special issue includes a selection of papers presented at the 2nd IEEE International Conference. Introduction.	International Journal of Bioinformatics Research and Applications	2014
24321308	Within a sample from a population, the distribution of the number of descendants of a subsample's most recent common ancestor.	Theoretical Population Biology	2014
24989859	Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps.	International Journal of Bioinformatics Research and Applications	2014
23706066	Domain analysis of symbionts and hosts (DASH) in a genome-wide survey of pathogenic human viruses.	BMC Research Notes	2013
23390499	Fungi in Thailand: a case study of the efficacy of an ITS barcode for automatically identifying species within the Annulohypoxylon and Hypoxylon genera.	PLoS ONE	2013
23706083	NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data.	BMC Genomics	2013
23033878	Coalescent: an open-source and scalable framework for exact calculations in coalescent theory.	BMC Bioinformatics	2012
22691307	New finite-size correction for local alignment score distributions.	BMC Research Notes	2012
22684965	The practical evaluation of DNA barcode efficacy.	Methods in Molecular Biology	2012
22454494	Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.	Proc Natl Acad Sci U S A	2012
23139639	CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms.	PLoS Biology	2012
22060410	Objective method for estimating asymptotic parameters, with an application to sequence alignment.		2011
20505002	Threshold Average Precision (TAP-k): a measure of retrieval designed for bioinformatics.	Bioinformatics	2010
20148197	ESTIMATING THE GUMBEL SCALE PARAMETER FOR LOCAL ALIGNMENT OF RANDOM SEQUENCES BY IMPORTANCE SAMPLING WITH STOPPING TIMES.	Annals of Statistics	2009
19381547	Identification of cis-regulatory elements in gene co-expression networks using A-GLAM.	Methods Mol Biol	2009
19378149	Promoter analysis: gene regulatory motif identification with A-GLAM.	Methods in Molecular Biology	2009
18533028	Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites.	BMC Bioinformatics	2008
19779570	DNA BARCODING IN LAND PLANTS: DEVELOPING STANDARDS TO QUANTIFY AND MAXIMIZE SUCCESS.	Taxon	2008
18796526	The whole alignment and nothing but the alignment: the problem of spurious alignment flanks.	Nucleic Acids Res	2008
18367472	The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.	Nucleic Acids Res	2008
17596268	The identification of complete domains within protein sequences using accurate E-values for semi-global alignment.	Nucleic Acids Res	2007
19461943	Inequalities on the Overshoot beyond a Boundary for Independent Summands with Differing Distributions.	Statistics and Probability Letters	2007
16961919	Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements.	BMC Bioinformatics	2006