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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.


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.

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