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Results: 1 to 20 of 38

1.

PuFFIN - a parameter-free method to build nucleosome maps from paired-end reads.

Polishko A, Bunnik EM, Le Roch KG, Lonardi S.

BMC Bioinformatics. 2014;15 Suppl 9:S11. doi: 10.1186/1471-2105-15-S9-S11. Epub 2014 Sep 10.

PMID:
25252810
[PubMed - in process]
Free PMC Article
2.

DNA-encoded nucleosome occupancy is associated with transcription levels in the human malaria parasite Plasmodium falciparum.

Bunnik EM, Polishko A, Prudhomme J, Ponts N, Gill SS, Lonardi S, Le Roch KG.

BMC Genomics. 2014 May 8;15:347. doi: 10.1186/1471-2164-15-347.

PMID:
24885191
[PubMed - in process]
Free PMC Article
3.

Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression.

Ay F, Bunnik EM, Varoquaux N, Bol SM, Prudhomme J, Vert JP, Noble WS, Le Roch KG.

Genome Res. 2014 Jun;24(6):974-88. doi: 10.1101/gr.169417.113. Epub 2014 Mar 26.

PMID:
24671853
[PubMed - in process]
4.

An Introduction to Functional Genomics and Systems Biology.

Bunnik EM, Le Roch KG.

Adv Wound Care (New Rochelle). 2013 Nov;2(9):490-498.

PMID:
24527360
[PubMed]
Free PMC Article
5.

The ubiquitin system: an essential component to unlocking the secrets of malaria parasite biology.

Hamilton MJ, Lee M, Le Roch KG.

Mol Biosyst. 2014 Apr;10(4):715-23. doi: 10.1039/c3mb70506d. Epub 2014 Jan 30.

PMID:
24481176
[PubMed - in process]
6.

Genome-wide mapping of DNA methylation in the human malaria parasite Plasmodium falciparum.

Ponts N, Fu L, Harris EY, Zhang J, Chung DW, Cervantes MC, Prudhomme J, Atanasova-Penichon V, Zehraoui E, Bunnik EM, Rodrigues EM, Lonardi S, Hicks GR, Wang Y, Le Roch KG.

Cell Host Microbe. 2013 Dec 11;14(6):696-706. doi: 10.1016/j.chom.2013.11.007.

PMID:
24331467
[PubMed - indexed for MEDLINE]
7.

The multifunctional autophagy pathway in the human malaria parasite, Plasmodium falciparum.

Cervantes S, Bunnik EM, Saraf A, Conner CM, Escalante A, Sardiu ME, Ponts N, Prudhomme J, Florens L, Le Roch KG.

Autophagy. 2014 Jan;10(1):80-92. doi: 10.4161/auto.26743. Epub 2013 Nov 11.

PMID:
24275162
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum.

Bunnik EM, Chung DW, Hamilton M, Ponts N, Saraf A, Prudhomme J, Florens L, Le Roch KG.

Genome Biol. 2013 Nov 22;14(11):R128. doi: 10.1186/gb-2013-14-11-r128.

PMID:
24267660
[PubMed - in process]
Free PMC Article
9.

The E3 ubiquitin ligase XIAP restricts Anaplasma phagocytophilum colonization of Ixodes scapularis ticks.

Severo MS, Choy A, Stephens KD, Sakhon OS, Chen G, Chung DW, Le Roch KG, Blaha G, Pedra JH.

J Infect Dis. 2013 Dec 1;208(11):1830-40. doi: 10.1093/infdis/jit380. Epub 2013 Jul 29.

PMID:
23901084
[PubMed - indexed for MEDLINE]
10.

An apicoplast localized ubiquitylation system is required for the import of nuclear-encoded plastid proteins.

Agrawal S, Chung DW, Ponts N, van Dooren GG, Prudhomme J, Brooks CF, Rodrigues EM, Tan JC, Ferdig MT, Striepen B, Le Roch KG.

PLoS Pathog. 2013;9(6):e1003426. doi: 10.1371/journal.ppat.1003426. Epub 2013 Jun 13.

PMID:
23785288
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Recent advances in malaria drug discovery.

Biamonte MA, Wanner J, Le Roch KG.

Bioorg Med Chem Lett. 2013 May 15;23(10):2829-43. doi: 10.1016/j.bmcl.2013.03.067. Epub 2013 Mar 27. Review.

PMID:
23587422
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Characterization of the ubiquitylating components of the human malaria parasite's protein degradation pathway.

Chung DW, Ponts N, Prudhomme J, Rodrigues EM, Le Roch KG.

PLoS One. 2012;7(8):e43477. doi: 10.1371/journal.pone.0043477. Epub 2012 Aug 17.

PMID:
22912882
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

NORMAL: accurate nucleosome positioning using a modified Gaussian mixture model.

Polishko A, Ponts N, Le Roch KG, Lonardi S.

Bioinformatics. 2012 Jun 15;28(12):i242-9. doi: 10.1093/bioinformatics/bts206.

PMID:
22689767
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Strand-specific RNA-seq applied to malaria samples.

Ponts N, Chung DW, Le Roch KG.

Methods Mol Biol. 2012;883:59-73. doi: 10.1007/978-1-61779-839-9_4.

PMID:
22589124
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

BRAT-BW: efficient and accurate mapping of bisulfite-treated reads.

Harris EY, Ponts N, Le Roch KG, Lonardi S.

Bioinformatics. 2012 Jul 1;28(13):1795-6. doi: 10.1093/bioinformatics/bts264. Epub 2012 May 3.

PMID:
22563065
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

High content live cell imaging for the discovery of new antimalarial marine natural products.

Cervantes S, Stout PE, Prudhomme J, Engel S, Bruton M, Cervantes M, Carter D, Tae-Chang Y, Hay ME, Aalbersberg W, Kubanek J, Le Roch KG.

BMC Infect Dis. 2012 Jan 3;12:1. doi: 10.1186/1471-2334-12-1.

PMID:
22214291
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Chromatin-driven de novo discovery of DNA binding motifs in the human malaria parasite.

Harris EY, Ponts N, Le Roch KG, Lonardi S.

BMC Genomics. 2011 Dec 13;12:601. doi: 10.1186/1471-2164-12-601.

PMID:
22165844
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Exploratory analysis of genomic segmentations with Segtools.

Buske OJ, Hoffman MM, Ponts N, Le Roch KG, Noble WS.

BMC Bioinformatics. 2011 Oct 26;12:415. doi: 10.1186/1471-2105-12-415.

PMID:
22029426
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Genomics and integrated systems biology in Plasmodium falciparum: a path to malaria control and eradication.

Le Roch KG, Chung DW, Ponts N.

Parasite Immunol. 2012 Feb-Mar;34(2-3):50-60. doi: 10.1111/j.1365-3024.2011.01340.x. Review.

PMID:
21995286
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Unraveling the ubiquitome of the human malaria parasite.

Ponts N, Saraf A, Chung DW, Harris A, Prudhomme J, Washburn MP, Florens L, Le Roch KG.

J Biol Chem. 2011 Nov 18;286(46):40320-30. doi: 10.1074/jbc.M111.238790. Epub 2011 Sep 19.

PMID:
21930698
[PubMed - indexed for MEDLINE]
Free PMC Article

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