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Results: 1 to 20 of 55

1.

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):384-408. doi: 10.1504/IJBRA.2014.062991.

PMID:
24989859
[PubMed - in process]
2.

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.

PMID:
24321308
[PubMed - in process]
Free Article
3.

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.

PMID:
23706083
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
23706066
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
23390499
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
23139639
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
23033878
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
22691307
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
22684965
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
22454494
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
22060410
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
20505002
[PubMed - indexed for MEDLINE]
Free PMC Article
13.
14.

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.

PMID:
19378149
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
18796526
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
18533028
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
18367472
[PubMed - indexed for MEDLINE]
Free PMC Article
18.
19.

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.

PMID:
17596268
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
17068091
[PubMed - indexed for MEDLINE]
Free Article

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