J. Spouge

发表

Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins.

C. DeLisi, H. Margalit, J. Cornette, 1987, Journal of molecular biology.

Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae.

R. J. Cho, M. Campbell, T. Wolfsberg, 1999, Genome research.

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.

Thomas L. Madden, T. Madden, S. Altschul, 2001, Nucleic acids research.

Speeding up dynamic programming algorithms for finding optimal lattice paths

J. Spouge, 1989 .

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

J. Spouge, M. Frith, Yonil Park, 2008, Nucleic acids research.

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

John L. Spouge, Maricel G. Kann, Hyrum D. Carroll, 2010, Bioinform..

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

S. Bryant, J. Spouge, M. Kann, 2007, Nucleic acids research.

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

Z. Weng, J. Spouge, M. Frith, 2002, Nucleic acids research.

Lineage-specific gene expansions in bacterial and archaeal genomes.

E V Koonin, E. Koonin, Y. Wolf, 2001, Genome research.

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

John L. Spouge, Conrad L. Schoch, Vincent Robert, 2012, Proceedings of the National Academy of Sciences.

A DNA barcode for land plants

W. John Kress, Sujeevan Ratnasingham, John L. Spouge, 2009, Proceedings of the National Academy of Sciences.

Finite-size corrections to Poisson approximations of rare events in renewal processes

John L. Spouge, J. Spouge, 2001, Journal of Applied Probability.

Long-range percolation in one-dimension

J. Spouge, 1984 .

Statistical analysis of over-represented words in human promoter sequences.

D. Landsman, J. Spouge, L. Mariño-Ramírez, 2004, Nucleic acids research.

Finding functional sequence elements by multiple local alignment.

Z. Weng, J. Spouge, M. Frith, 2004, Nucleic acids research.

Computation of the gamma, digamma, and trigamma functions

J. Spouge, 1994 .

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

D. Landsman, J. Spouge, L. Mariño-Ramírez, 2009, Methods in molecular biology.

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

D. Landsman, J. Spouge, O. Bodenreider, 2009, Methods in molecular biology.

CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

J. Spouge, F. Nitsche, J. Pawlowski, 2012, PLoS biology.

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

Yonil Park, John L Spouge, Sergey Sheetlin, 2009, Annals of statistics.

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

John L. Spouge, Yonil Park, Sergey Sheetlin, 2005, Nucleic acids research.

Towards a unified paradigm for sequence-based identification of fungi [Review]

J. Spouge, 2016 .

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

Olivier Bodenreider, John L. Spouge, David Landsman, 2008, Nucleic acids research.

Markov Additive Processes and Repeats in Sequences

J. Spouge, 2007, Journal of Applied Probability.

Least Squares Isotonic Regression in Two Dimensions

H. Wan, W. J. Wilbur, J. Spouge, 2003 .

Hemolysis Pathways during Storage of Erythrocytes and Inter-Donor Variability in Erythrocyte Morphology

J. Spouge, G. Brenner-Weiss, K. Melzak, 2020, Transfusion Medicine and Hemotherapy.

Empirical Null Estimation using Discrete Mixture Distributions and its Application to Protein Domain Data

Maricel Kann, Thomas A. Peterson, Johan Lim, 2016, 1608.07204.

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

J. Spouge, Mileidy W. Gonzalez, J. Ziegelbauer, 2020, Algorithms Mol. Biol..

The practical evaluation of DNA barcode efficacy.

J. Spouge, L. Mariño-Ramírez, 2012, Methods in molecular biology.

DNA BARCODING IN LAND PLANTS: DEVELOPING STANDARDS TO QUANTIFY AND MAXIMIZE SUCCESS.

Alissa M. Resch, W. Kress, J. Spouge, 2008, Taxon.

Analytic solutions to Smoluchowski's coagulation equation: a combinatorial interpretation

J. Spouge, 1985 .

Frameshift alignment: statistics and post-genomic applications

Martin C. Frith, John L. Spouge, Yonil Park, 2014, Bioinform..

Sequence Alignment Statistics

J. Spouge, 2010 .

Blocking of human immunodeficiency virus infection depends on cell density and viral stock age

J. Spouge, M. Dembo, P. Nara, 1991, Journal of virology.

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

J. Spouge, Vruj Patel, 2020, PloS one.

Fungi in Thailand: A Case Study of the Efficacy of an ITS Barcode for Automatically Identifying Species within the Annulohypoxylon and Hypoxylon Genera

J. Spouge, C. Phosri, N. Suwannasai, 2013, PloS one.

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

J. Spouge, Yonil Park, S. Sheetlin, 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.

Path reversal, islands, and the gapped alignment of random sequences

J. Spouge, 2004 .

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

J. Spouge, 2019, Theoretical population biology.

Statistical analysis of sparse infection data and its implications for retroviral treatment trials in primates.

J. Spouge, 1992, Proceedings of the National Academy of Sciences of the United States of America.

Novel FFT Techniques for Sequence Analysis

J. Spouge, S. Rajasekaran, Xioming Jin, 2003 .

T cell multideterminant regions in the human immunodeficiency virus envelope: toward overcoming the problem of major histocompatibility complex restriction.

C. DeLisi, H. Margalit, J. Cornette, 1989, International immunology.

Changes in the Plasticity of HIV-1 Nef RNA during the Evolution of the North American Epidemic

J. Spouge, Mileidy W. Gonzalez, Amirhossein Manzourolajdad, 2016, PloS one.

Finite-size corrections to Poisson approximations in general renewal-success processes

J. Spouge, 2005 .

A cytopathic infectivity assay of human immunodeficiency virus type 1 in human primary macrophages.

J. Spouge, P. Nara, M. Merges, 1996, Journal of virological methods.

Multideterminant regions of the HIV-1 envelope with sites seen by murine and human helper T cells: circumventing the MHC restriction problem

C. DeLisi, J. Cornette, K. Cease, 1990 .

Protein Antigenic Structures Recognized by T Cells; Potential Applications to Vaccine Design

C. DeLisi, H. Margalit, J. Cornette, 1987, Immunological reviews.

Domain analysis of symbionts and hosts (DASH) in a genome-wide survey of pathogenic human viruses

J. Spouge, Mileidy W. Gonzalez, 2013, BMC Research Notes.

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

J. Spouge, J. Foulke, Mileidy W. Gonzalez, 2017, Proceedings of the National Academy of Sciences.

How to optimally sample a sequence for rapid analysis

J. Spouge, M. Frith, Jim Shaw, 2022, bioRxiv.

Inequalities on the Overshoot beyond a Boundary for Independent Summands with Differing Distributions.

J. Spouge, 2007, Statistics & probability letters.

AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes.

E V Koonin, A. F. Neuwald, E. Koonin, 1999, Genome research.

This special issue includes a selection of papers presented at the 2nd IEEE International Conference. Introduction.

Sanguthevar Rajasekaran, Ion Mandoiu, Mihai Pop, 2014, International Journal of Bioinformatics Research and Applications.

Statistics in Immunology and Biochemistry : An Application to T Cell Antigenic Sites

J. Spouge, J. Berzofsky, 2018 .

Domain analysis of symbionts and hosts (DASH) in a genome-wide survey of pathogenic human viruses

J. Spouge, Mileidy W. Gonzalez, 2013, BMC Research Notes.

How to optimally sample a sequence for rapid analysis

J. Spouge, M. Frith, Jim Shaw, 2022, bioRxiv.

New finite-size correction for local alignment score distributions

Thomas L. Madden, T. Madden, J. Spouge, 2012, BMC Research Notes.

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

J. Spouge, 2021, PloS one.

Solutions and critical times for the monodisperse coagulation equation when aij=A + B(i + j) + Cij

J. Spouge, J L Spouge, 1983 .

The Efficient Computation of Position-Specific Match Scores with the Fast Fourier Transform

Sanguthevar Rajasekaran, John L. Spouge, X. Jin, 2002, J. Comput. Biol..

10 – The Role of MHC and Amphipathic Structures in T Cell Recognition: Features Determining Immunodominance

C. DeLisi, H. Margalit, J. Cornette, 1988 .

A New Method for Estimating Species Age Supports the Coexistence of Malaria Parasites and Their Mammalian Hosts

David G. Harris, Joana C. Silva, J. Spouge, 2015, Molecular biology and evolution.

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

J. Spouge, Mileidy W. Gonzalez, J. Ziegelbauer, 2018, Proceedings of the National Academy of Sciences.

Within a sample from a population, the distribution of the number of descendants of a subsample's most recent common ancestor.

John L Spouge, J. Spouge, 2014, Theoretical population biology.

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

David Landsman, Leonardo Mariño-Ramírez, John L. Spouge, 2016, BMC Bioinformatics.

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 Sheetlin, 2014, Int. J. Bioinform. Res. Appl..

Assembly , Operation , and Disassembly of Protein Complexes : A Class of Chaperone-Like ATPases Associated with the + AAA

A. F. Neuwald, E. Koonin, L. Aravind, 1999 .

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

Kannan Tharakaraman, John L. Spouge, David Landsman, 2006, BMC Bioinformatics.

Accelerated convergence and robust asymptotic regression of the Gumbel scale parameter for gapped sequence alignment

John L. Spouge, Yonil Park, J. Spouge, 2005 .

Factors underlying spontaneous inactivation and susceptibility to neutralization of human immunodeficiency virus.

J. L. Raina, J. Spouge, J. Moore, 1992, Virology.

HIV requires multiple gp120 molecules for CD4-mediated infection

J. Spouge, M. Dembo, P. Nara, 1990, Nature.

Prediction of immunodominant helper T cell antigenic sites from the primary sequence.

J L Cornette, C. DeLisi, H. Margalit, 1987, Journal of immunology.

Viral multiplicity of attachment and its implications for human immunodeficiency virus therapies

J. Spouge, 1994, Journal of virology.

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

Martin C. Frith, John L. Spouge, Yonil Park, 2015, Bioinform..

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

J. Spouge, Mileidy W. Gonzalez, G. Lewis, 2015, Journal of Virology.

Structural prediction of RNA switches using conditional base-pair probabilities

J. Spouge, Amirhossein Manzourolajdad, 2019, PloS one.

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

David Landsman, Kannan Tharakaraman, John L. Spouge, 2005, ISMB.

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

John L. Spouge, Yonil Park, J. Spouge, 2002, Bioinform..

Coalescent: an open-science framework for importance sampling in coalescent theory

Susanta Tewari, John L. Spouge, J. Spouge, 2015, PeerJ.

Analytic results for quantifying HIV infectivity

J. Spouge, M. Dembo, S. Layne, 1989 .

Alignment-free genome comparison enables accurate geographic sourcing of white oak DNA

David L. Erickson, Fengzhu Sun, J. Spouge, 2018, BMC Genomics.

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

Nak-Kyeong Kim, Kannan Tharakaraman, Leonardo Mariño-Ramírez, 2008, BMC Bioinformatics.

Strong conformational propensities enhance T cell antigenicity.

C DeLisi, J L Cornette, H. Guy, 1987, Journal of immunology.

Quantifying the infectivity of human immunodeficiency virus.

J. Spouge, M. Dembo, M Dembo, 1989, Proceedings of the National Academy of Sciences of the United States of America.

Increasing stability with complexity in a system composed of unstable subsystems

John L. Spouge, J. Spouge, 1986 .

Conserved fragments of transposable elements in intergenic regions: evidence for widespread recruitment of MIR- and L2-derived sequences within the mouse and human genomes.

David G. Harris, J. Spouge, S. Shabalina, 2003, Genetical research.

Measuring HIV infectivity

J. Spouge, M. Dembo, S. Layne, 1989 .

Random Graph Problems in Polymer Chemistry

J. Spouge, 1985 .

Analytic results for finite systems of ringed flory polymers

J. Spouge, 1984 .

The combinatorics and extreme value statistics of protein threading

A. Marchler-Bauer, S. Bryant, J. Spouge, 1999 .

NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data

J. Spouge, Nak-Kyeong Kim, R. Jayatillake, 2013, BMC Genomics.

Recent SIV-Macaque Trials: A Reassessment of Immune Priming and Varying Infectability in Repeated Low-dose Challenge Studies

J. Spouge, 2021, bioRxiv.

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

J. Spouge, Mileidy W. Gonzalez, A. Devico, 2017, Retrovirology.

Human plasma enhances the infectivity of primary human immunodeficiency virus type 1 isolates in peripheral blood mononuclear cells and monocyte-derived macrophages

J. Spouge, P. Nara, W. Tsai, 1995, Journal of virology.

Increase of Primary HIV‐1 Production in Human Peripheral Blood Mononuclear Cells by Intermittent Medium Replenishment

J. Spouge, Suh-Chin Wu, P. Nara, 1998, Biotechnology progress.

SINGLE-PARTICLE SURVIVAL IN PARALLEL GATED TRAPPING

J. Spouge, 1997 .

STOCHASTICALLY GATED CHEMICAL REACTIONS

J. Spouge, 1997 .

Measurement of a Barcode’s Accuracy in Identifying Species

John L. Spouge, J. Spouge, 2016 .

Empirical null estimation using zero‐inflated discrete mixture distributions and its application to protein domain data

Maricel Kann, Thomas A. Peterson, Johan Lim, 2018, Biometrics.

Equilibrium polymer size distributions

J. Spouge, 1983 .

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

Nak-Kyeong Kim, Kannan Tharakaraman, John L. Spouge, 2006, Bioinform..

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

D. Landsman, J. Spouge, L. Mariño-Ramírez, 2016, BMC Bioinformatics.

MultiDomainBenchmark: a multi-domain query and subject database suite

J. Spouge, Mileidy W. Gonzalez, Hyrum D. Carroll, 2019, BMC Bioinformatics.

Estimating age-stratified transmission and reproduction numbers during the early exponential phase of an epidemic: A case study with COVID-19 data

J. Spouge, Z. Stanke, 2023, Epidemics.

HIV-1 infection kinetics in tissue cultures.

R I Shrager, J. Spouge, D. Dimitrov, 1996, Mathematical biosciences.

The ruzzo-tompa algorithm can find the maximal paths in weighted, directed graphs on a one-dimensional lattice

Leonardo Mariño-Ramírez, John L. Spouge, Sergey Sheetlin, 2012, 2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS).

MultiDomainBenchmark: a multi-domain query and subject database suite

John L. Spouge, Hyrum D. Carroll, Mileidy Gonzalez, 2019, BMC Bioinformatics.

A closed formula relevant to 'Theory of local k-mer selection with applications to long-read alignment' by Jim Shaw and Yun William Yu

J. Spouge, 2022, Bioinform..

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

John L Spouge, David L. Erickson, María P Martín, 2020, PloS one.

Exact solutions for a diffusion-reaction process in one dimension.

J. Spouge, Spouge, 1988, Physical review letters.

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

J. Spouge, Kannan Tharakaraman, Nak-Kyeong Kim, 2006, Bioinform..

Equilibrium ring formation in polymer solutions

J. Spouge, 1986 .

Coagulation and the total weight-fraction over a threshold size☆

J. Spouge, G. I. Bell, 1986 .

An existence theorem for the discrete coagulation-fragmentation equations

J. Spouge, Y. B, N. L. Spottge, 1984, Mathematical Proceedings of the Cambridge Philosophical Society.

A branching-process solution of the polydisperse coagulation equation

John L. Spouge, J. Spouge, 1984, Advances in Applied Probability.

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

J. Spouge, Mileidy W. Gonzalez, G. Lewis, 2015, Journal of Virology.

The size distribution for theAgRBf−g Model of polymerization

J. Spouge, 1983 .

therapies. virus implications for human immunodeficiency Viral multiplicity of attachment and its

J. Spouge, 2013 .

Viral Multiplicity ofAttachment andItsImplications for HumanImmunodeficiency Virus Therapies

J. Spouge, 1994 .

Cross-linking of Identical Particles by Multiple Ligand-Types

John L. Spouge, J. Spouge, 1985 .

An existence theorem for the discrete coagulation–fragmentation equations

John L. Spouge, J. Spouge, 1984, Mathematical Proceedings of the Cambridge Philosophical Society.

Exact solutions for diffusion-reaction processes in one dimension. II. Spatial distributions

J. Spouge, 1988 .

Solutions and critical times for the polydisperse coagulation equation when a(x,y)=A+B(x+y)+Cxy

J. Spouge, 1983 .

Ancestry-attenuated effects of socioeconomic deprivation on type 2 diabetes disparities in the All of Us cohort

J. Spouge, Shivam Sharma, I. Jordan, 2023, BMC Global and Public Health.

Ancestry-attenuated effects of socioeconomic deprivation on type 2 diabetes disparities in the All of Us cohort

J. Spouge, Shivam Sharma, I. Jordan, 2023, Research square.

Exact solutions for random coagulation processes

M. Schreckenberg, J. Spouge, M. Schreckenberg, 1985 .

Increasing Representativeness in the All of Us Cohort Using Inverse Probability Weighting

J. Spouge, Shivam Sharma, Leonardo Mariño-Ramírez, 2024, medRxiv.