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Items: 1 to 50 of 73


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

Patel V, Spouge JL.

PLoS One. 2020 Jan 10;15(1):e0227127. doi: 10.1371/journal.pone.0227127. eCollection 2020.


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

Manzourolajdad A, Spouge JL.

PLoS One. 2019 Jun 12;14(6):e0217625. doi: 10.1371/journal.pone.0217625. eCollection 2019.


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

Spouge JL.

Theor Popul Biol. 2019 Jun;127:7-15. doi: 10.1016/j.tpb.2019.03.001. Epub 2019 Mar 12.


MultiDomainBenchmark: a multi-domain query and subject database suite.

Carroll HD, Spouge JL, Gonzalez M.

BMC Bioinformatics. 2019 Feb 14;20(1):77. doi: 10.1186/s12859-019-2660-5.


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

Tang K, Ren J, Cronn R, Erickson DL, Milligan BG, Parker-Forney M, Spouge JL, Sun F.

BMC Genomics. 2018 Dec 10;19(1):896. doi: 10.1186/s12864-018-5253-1.


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

Tagawa T, Gao S, Koparde VN, Gonzalez M, Spouge JL, Serquiña AP, Lurain K, Ramaswami R, Uldrick TS, Yarchoan R, Ziegelbauer JM.

Proc Natl Acad Sci U S A. 2018 Dec 11;115(50):12805-12810. doi: 10.1073/pnas.1816183115. Epub 2018 Nov 19.


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

Mengistu M, Tang AH, Foulke JS Jr, Blanpied TA, Gonzalez MW, Spouge JL, Gallo RC, Lewis GK, DeVico AL.

Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):E9893-E9902. doi: 10.1073/pnas.1705074114. Epub 2017 Oct 30.


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

Gauran IIM, Park J, Lim J, Park D, Zylstra J, Peterson T, Kann M, Spouge JL.

Biometrics. 2018 Jun;74(2):458-471. doi: 10.1111/biom.12779. Epub 2017 Sep 22.


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

Gonzalez M, DeVico AL, Spouge JL.

Retrovirology. 2017 Feb 24;14(1):13. doi: 10.1186/s12977-016-0326-1.


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

Acevedo-Luna N, Mariño-Ramírez L, Halbert A, Hansen U, Landsman D, Spouge JL.

BMC Bioinformatics. 2016 Nov 21;17(1):479.


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

Manzourolajdad A, Gonzalez M, Spouge JL.

PLoS One. 2016 Sep 29;11(9):e0163688. doi: 10.1371/journal.pone.0163688. eCollection 2016.


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

Sheetlin S, Park Y, Frith MC, Spouge JL.

Bioinformatics. 2016 Jan 15;32(2):304-5. doi: 10.1093/bioinformatics/btv575. Epub 2015 Oct 1.


Improving Retrieval Efficacy of Homology Searches Using the False Discovery Rate.

Carroll HD, Williams AC, Davis AG, Spouge JL.

IEEE/ACM Trans Comput Biol Bioinform. 2015 May-Jun;12(3):531-7. doi: 10.1109/TCBB.2014.2366112.


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

Tewari S, Spouge JL.

PeerJ. 2015 Aug 18;3:e1203. doi: 10.7717/peerj.1203. eCollection 2015.


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

Mandoiu I, Pop M, Rajasekaran S, Spouge JL.

Int J Bioinform Res Appl. 2014;10(4-5):341-4. No abstract available.


A new method for estimating species age supports the coexistence of malaria parasites and their Mammalian hosts.

Silva JC, Egan A, Arze C, Spouge JL, Harris DG.

Mol Biol Evol. 2015 May;32(5):1354-64. doi: 10.1093/molbev/msv005. Epub 2015 Jan 13.


Frameshift alignment: statistics and post-genomic applications.

Sheetlin SL, Park Y, Frith MC, Spouge JL.

Bioinformatics. 2014 Dec 15;30(24):3575-82. doi: 10.1093/bioinformatics/btu576. Epub 2014 Aug 28.


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

Spouge JL, Mariño-Ramírez L, Sheetlin SL.

Int J Bioinform Res Appl. 2014;10(4-5):384-408. doi: 10.1504/IJBRA.2014.062991.


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

Spouge JL.

Theor Popul Biol. 2014 Mar;92:51-4. doi: 10.1016/j.tpb.2013.11.004. Epub 2013 Dec 7.


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

Kim NK, Jayatillake RV, Spouge JL.

BMC Genomics. 2013 May 25;14:349. doi: 10.1186/1471-2164-14-349.


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

Gonzalez MW, Spouge JL.

BMC Res Notes. 2013 May 24;6:209. doi: 10.1186/1756-0500-6-209.


Fungi in Thailand: a case study of the efficacy of an ITS barcode for automatically identifying species within the Annulohypoxylon and Hypoxylon genera.

Suwannasai N, Martín MP, Phosri C, Sihanonth P, Whalley AJ, Spouge JL.

PLoS One. 2013;8(2):e54529. doi: 10.1371/journal.pone.0054529. Epub 2013 Feb 4.


CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms.

Pawlowski J, Audic S, Adl S, Bass D, Belbahri L, Berney C, Bowser SS, Cepicka I, Decelle J, Dunthorn M, Fiore-Donno AM, Gile GH, Holzmann M, Jahn R, Jirků M, Keeling PJ, Kostka M, Kudryavtsev A, Lara E, Lukeš J, Mann DG, Mitchell EA, Nitsche F, Romeralo M, Saunders GW, Simpson AG, Smirnov AV, Spouge JL, Stern RF, Stoeck T, Zimmermann J, Schindel D, de Vargas C.

PLoS Biol. 2012;10(11):e1001419. doi: 10.1371/journal.pbio.1001419. Epub 2012 Nov 6. No abstract available.


Coalescent: an open-source and scalable framework for exact calculations in coalescent theory.

Tewari S, Spouge JL.

BMC Bioinformatics. 2012 Oct 3;13:257. doi: 10.1186/1471-2105-13-257.


New finite-size correction for local alignment score distributions.

Park Y, Sheetlin S, Ma N, Madden TL, Spouge JL.

BMC Res Notes. 2012 Jun 12;5:286. doi: 10.1186/1756-0500-5-286.


The practical evaluation of DNA barcode efficacy.

Spouge JL, Mariño-Ramírez L.

Methods Mol Biol. 2012;858:365-77. doi: 10.1007/978-1-61779-591-6_17.


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

Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W; Fungal Barcoding Consortium; Fungal Barcoding Consortium Author List.

Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):6241-6. doi: 10.1073/pnas.1117018109. Epub 2012 Mar 27.


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

Sheetlin S, Park Y, Spouge JL.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Sep;84(3 Pt 1):031914. Epub 2011 Sep 13.


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

Carroll HD, Kann MG, Sheetlin SL, Spouge JL.

Bioinformatics. 2010 Jul 15;26(14):1708-13. doi: 10.1093/bioinformatics/btq270. Epub 2010 May 26.


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

Mariño-Ramírez L, Tharakaraman K, Spouge JL, Landsman D.

Methods Mol Biol. 2009;537:263-76. doi: 10.1007/978-1-59745-251-9_13.


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

Frith MC, Park Y, Sheetlin SL, Spouge JL.

Nucleic Acids Res. 2008 Oct;36(18):5863-71. doi: 10.1093/nar/gkn579. Epub 2008 Sep 16.


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

Kim NK, Tharakaraman K, Mariño-Ramírez L, Spouge JL.

BMC Bioinformatics. 2008 Jun 4;9:262. doi: 10.1186/1471-2105-9-262.


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

Tharakaraman K, Bodenreider O, Landsman D, Spouge JL, Mariño-Ramírez L.

Nucleic Acids Res. 2008 May;36(8):2777-86. doi: 10.1093/nar/gkn137. Epub 2008 Mar 26.


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

Kann MG, Sheetlin SL, Park Y, Bryant SH, Spouge JL.

Nucleic Acids Res. 2007;35(14):4678-85. Epub 2007 Jun 27.


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

Kim NK, Tharakaraman K, Spouge JL.

Bioinformatics. 2006 Dec 1;22(23):2870-5. Epub 2006 Oct 26.


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

Tharakaraman K, Mariño-Ramírez L, Sheetlin SL, Landsman D, Spouge JL.

BMC Bioinformatics. 2006 Sep 8;7:408.


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

Sheetlin S, Park Y, Spouge JL.

Nucleic Acids Res. 2005 Sep 6;33(15):4987-94. Print 2005.


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

Tharakaraman K, Mariño-Ramírez L, Sheetlin S, Landsman D, Spouge JL.

Bioinformatics. 2005 Jun;21 Suppl 1:i440-8.


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

Mariño-Ramírez L, Spouge JL, Kanga GC, Landsman D.

Nucleic Acids Res. 2004 Feb 12;32(3):949-58. Print 2004. Erratum in: Nucleic Acids Res. 2004 Dec;32(22):6718. Nucleic Acids Res. 2004 Nov 8;32(19):5972.


Finding functional sequence elements by multiple local alignment.

Frith MC, Hansen U, Spouge JL, Weng Z.

Nucleic Acids Res. 2004 Jan 2;32(1):189-200. Print 2004.


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

Park Y, Spouge JL.

Bioinformatics. 2002 Sep;18(9):1236-42.


The efficient computation of position-specific match scores with the fast fourier transform.

Rajasekaran S, Jin X, Spouge JL.

J Comput Biol. 2002;9(1):23-33.


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

Schäffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF.

Nucleic Acids Res. 2001 Jul 15;29(14):2994-3005. Review.


Lineage-specific gene expansions in bacterial and archaeal genomes.

Jordan IK, Makarova KS, Spouge JL, Wolf YI, Koonin EV.

Genome Res. 2001 Apr;11(4):555-65.


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

Wolfsberg TG, Gabrielian AE, Campbell MJ, Cho RJ, Spouge JL, Landsman D.

Genome Res. 1999 Aug;9(8):775-92.

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