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Items: 1 to 20 of 115

1.

Computational pan-genomics: status, promises and challenges.

Computational Pan-Genomics Consortium.

Brief Bioinform. 2018 Jan 1;19(1):118-135. doi: 10.1093/bib/bbw089. Review.

2.

PanTools: representation, storage and exploration of pan-genomic data.

Sheikhizadeh S, Schranz ME, Akdel M, de Ridder D, Smit S.

Bioinformatics. 2016 Sep 1;32(17):i487-i493. doi: 10.1093/bioinformatics/btw455.

PMID:
27587666
3.

Pan-Genome Storage and Analysis Techniques.

Zekic T, Holley G, Stoye J.

Methods Mol Biol. 2018;1704:29-53. doi: 10.1007/978-1-4939-7463-4_2. Review.

PMID:
29277862
4.

seq-seq-pan: building a computational pan-genome data structure on whole genome alignment.

Jandrasits C, Dabrowski PW, Fuchs S, Renard BY.

BMC Genomics. 2018 Jan 15;19(1):47. doi: 10.1186/s12864-017-4401-3.

5.

Pan-Tetris: an interactive visualisation for Pan-genomes.

Hennig A, Bernhardt J, Nieselt K.

BMC Bioinformatics. 2015;16 Suppl 11:S3. doi: 10.1186/1471-2105-16-S11-S3. Epub 2015 Aug 13.

6.

Ten years of pan-genome analyses.

Vernikos G, Medini D, Riley DR, Tettelin H.

Curr Opin Microbiol. 2015 Feb;23:148-54. doi: 10.1016/j.mib.2014.11.016. Epub 2014 Dec 5. Review.

PMID:
25483351
7.

Building a pan-genome reference for a population.

Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B.

J Comput Biol. 2015 May;22(5):387-401. doi: 10.1089/cmb.2014.0146. Epub 2015 Jan 7.

8.

A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies.

Thakur S, Guttman DS.

BMC Bioinformatics. 2016 Jun 30;17(1):260. doi: 10.1186/s12859-016-1142-2.

9.

RPAN: rice pan-genome browser for ∼3000 rice genomes.

Sun C, Hu Z, Zheng T, Lu K, Zhao Y, Wang W, Shi J, Wang C, Lu J, Zhang D, Li Z, Wei C.

Nucleic Acids Res. 2017 Jan 25;45(2):597-605. doi: 10.1093/nar/gkw958. Epub 2016 Dec 10.

10.

PanWeb: A web interface for pan-genomic analysis.

Pantoja Y, Pinheiro K, Veras A, Araújo F, Lopes de Sousa A, Guimarães LC, Silva A, Ramos RTJ.

PLoS One. 2017 May 24;12(5):e0178154. doi: 10.1371/journal.pone.0178154. eCollection 2017.

11.

PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes.

Clarke TH, Brinkac LM, Inman JM, Sutton G, Fouts DE.

BMC Bioinformatics. 2018 Jun 27;19(1):246. doi: 10.1186/s12859-018-2250-y.

12.

Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes.

Grytten I, Rand KD, Nederbragt AJ, Storvik GO, Glad IK, Sandve GK.

PLoS Comput Biol. 2019 Feb 19;15(2):e1006731. doi: 10.1371/journal.pcbi.1006731. eCollection 2019 Feb.

13.

Promoting synergistic research and education in genomics and bioinformatics.

Yang JY, Yang MQ, Zhu MM, Arabnia HR, Deng Y.

BMC Genomics. 2008;9 Suppl 1:I1. doi: 10.1186/1471-2164-9-S1-I1. Review.

14.

Coordinates and intervals in graph-based reference genomes.

Rand KD, Grytten I, Nederbragt AJ, Storvik GO, Glad IK, Sandve GK.

BMC Bioinformatics. 2017 May 18;18(1):263. doi: 10.1186/s12859-017-1678-9.

15.

PILER: identification and classification of genomic repeats.

Edgar RC, Myers EW.

Bioinformatics. 2005 Jun;21 Suppl 1:i152-8.

PMID:
15961452
16.

Genome assembly reborn: recent computational challenges.

Pop M.

Brief Bioinform. 2009 Jul;10(4):354-66. doi: 10.1093/bib/bbp026. Epub 2009 May 29.

17.

Computational analysis of alternative splicing in plant genomes.

Song QA, Catlin NS, Brad Barbazuk W, Li S.

Gene. 2019 Feb 15;685:186-195. doi: 10.1016/j.gene.2018.10.026. Epub 2018 Oct 12. Review.

PMID:
30321657
18.

micropan: an R-package for microbial pan-genomics.

Snipen L, Liland KH.

BMC Bioinformatics. 2015 Mar 12;16:79. doi: 10.1186/s12859-015-0517-0.

19.

Bioinformatics software for biologists in the genomics era.

Kumar S, Dudley J.

Bioinformatics. 2007 Jul 15;23(14):1713-7. Epub 2007 May 7.

PMID:
17485425
20.

A dictionary based informational genome analysis.

Castellini A, Franco G, Manca V.

BMC Genomics. 2012 Sep 17;13:485. doi: 10.1186/1471-2164-13-485.

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