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Items: 1 to 20 of 51

1.

DNA structural features of eukaryotic TATA-containing and TATA-less promoters.

Yella VR, Bansal M.

FEBS Open Bio. 2017 Feb 16;7(3):324-334. doi: 10.1002/2211-5463.12166. eCollection 2017 Mar.

2.

TSSPlant: a new tool for prediction of plant Pol II promoters.

Shahmuradov IA, Umarov RK, Solovyev VV.

Nucleic Acids Res. 2017 May 5;45(8):e65. doi: 10.1093/nar/gkw1353.

3.

Structural features of DNA that determine RNA polymerase II core promoter.

Il'icheva IA, Khodikov MV, Poptsova MS, Nechipurenko DY, Nechipurenko YD, Grokhovsky SL.

BMC Genomics. 2016 Nov 25;17(1):973.

4.

Selection processes in simple sequence repeats suggest a correlation with their genomic location: insights from a fungal model system.

Gonthier P, Sillo F, Lagostina E, Roccotelli A, Cacciola OS, Stenlid J, Garbelotto M.

BMC Genomics. 2015 Dec 29;16:1107. doi: 10.1186/s12864-015-2274-x.

5.

The impact of sequence length and number of sequences on promoter prediction performance.

Carvalho SG, Guerra-Sá R, de C Merschmann LH.

BMC Bioinformatics. 2015;16 Suppl 19:S5. doi: 10.1186/1471-2105-16-S19-S5. Epub 2015 Dec 16.

6.

Genome-wide analysis of transcription factor binding sites and their characteristic DNA structures.

Dai Z, Guo D, Dai X, Xiong Y.

BMC Genomics. 2015;16 Suppl 3:S8. doi: 10.1186/1471-2164-16-S3-S8. Epub 2015 Jan 29.

7.

The pattern of DNA cleavage intensity around indels.

Chen W, Zhang L.

Sci Rep. 2015 Feb 9;5:8333. doi: 10.1038/srep08333.

8.

iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition.

Lin H, Deng EZ, Ding H, Chen W, Chou KC.

Nucleic Acids Res. 2014 Dec 1;42(21):12961-72. doi: 10.1093/nar/gku1019. Epub 2014 Oct 31.

9.

iSS-PseDNC: identifying splicing sites using pseudo dinucleotide composition.

Chen W, Feng PM, Lin H, Chou KC.

Biomed Res Int. 2014;2014:623149. doi: 10.1155/2014/623149. Epub 2014 May 21.

10.

Rule-based knowledge acquisition method for promoter prediction in human and Drosophila species.

Huang WL, Tung CW, Liaw C, Huang HL, Ho SY.

ScientificWorldJournal. 2014;2014:327306. doi: 10.1155/2014/327306. Epub 2014 Jan 29.

11.

Genome-wide analysis of promoters: clustering by alignment and analysis of regular patterns.

Pettinato L, Calistri E, Di Patti F, Livi R, Luccioli S.

PLoS One. 2014 Jan 22;9(1):e85260. doi: 10.1371/journal.pone.0085260. eCollection 2014.

12.

Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots.

Kumari S, Ware D.

PLoS One. 2013 Oct 29;8(10):e79011. doi: 10.1371/journal.pone.0079011. eCollection 2013.

13.

DNA methylation patterns facilitate the identification of microRNA transcription start sites: a brain-specific study.

Bhadra T, Bhattacharyya M, Feuerbach L, Lengauer T, Bandyopadhyay S.

PLoS One. 2013 Jun 24;8(6):e66722. doi: 10.1371/journal.pone.0066722. Print 2013. Erratum in: PLoS One. 2013;8(12). doi:10.1371/annotation/dd8f4acc-3859-46e2-9136-20b6b4d08d21.

14.

Unravelling the hidden DNA structural/physical code provides novel insights on promoter location.

Durán E, Djebali S, González S, Flores O, Mercader JM, Guigó R, Torrents D, Soler-López M, Orozco M.

Nucleic Acids Res. 2013 Aug;41(15):7220-30. doi: 10.1093/nar/gkt511. Epub 2013 Jun 12.

15.

A composite method based on formal grammar and DNA structural features in detecting human polymerase II promoter region.

Datta S, Mukhopadhyay S.

PLoS One. 2013;8(2):e54843. doi: 10.1371/journal.pone.0054843. Epub 2013 Feb 20.

16.

Novel core promoter elements in the oomycete pathogen Phytophthora infestans and their influence on expression detected by genome-wide analysis.

Roy S, Poidevin L, Jiang T, Judelson HS.

BMC Genomics. 2013 Feb 16;14:106. doi: 10.1186/1471-2164-14-106.

17.

Identification of regulatory regions of bidirectional genes in cervical cancer.

Wang G, Qi K, Zhao Y, Li Y, Juan L, Teng M, Li L, Liu Y, Wang Y.

BMC Med Genomics. 2013;6 Suppl 1:S5. doi: 10.1186/1755-8794-6-S1-S5. Epub 2013 Jan 23.

18.

iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition.

Chen W, Feng PM, Lin H, Chou KC.

Nucleic Acids Res. 2013 Apr 1;41(6):e68. doi: 10.1093/nar/gks1450. Epub 2013 Jan 8.

19.

The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology.

Wang D, Xia Y, Li X, Hou L, Yu J.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1199-205. doi: 10.1093/nar/gks1225. Epub 2012 Nov 28.

20.

DNA structural properties in the classification of genomic transcription regulation elements.

Meysman P, Marchal K, Engelen K.

Bioinform Biol Insights. 2012;6:155-68. doi: 10.4137/BBI.S9426. Epub 2012 Jul 2.

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