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Structures and bioactivities of dihydrochalcones from Metrodorea stipularis.

Burger MC, Fernandes JB, da Silva MF, Escalante A, Prudhomme J, Le Roch KG, Izidoro MA, Vieira PC.

J Nat Prod. 2014 Nov 26;77(11):2418-22. doi: 10.1021/np500453x. Epub 2014 Nov 6.


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.


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.


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.


An Introduction to Functional Genomics and Systems Biology.

Bunnik EM, Le Roch KG.

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


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. Review.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.

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