76 - Lu XM., Batugedara G., Lee M., Prudhomme J., Bunnik E., Le Roch KG. Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum. Nucleic Acids Research. 2017 May 22;  doi:10.1093/nar/gkx464.

75 - Daub ME, Prudhomme J, Ben Mamoun C, Le Roch KG, Vanderwal CD. Antimalarial Properties of Simplified Kalihinol Analogues. ACS Med Chem Lett. 2017 Feb 16;8(3):355-360. doi: 10.1021/acsmedchemlett.7b00013.

74 - Batugedara G., Lu XM., Bunnik EM. and Le Roch KG. The role of chromatin structure in gene regulation of the human malaria parasite. Trends in Parasitology.  2017 Jan 5. pii: S1471-4922(16)30226-4. doi: 10.1016/j.pt.2016.12.004.

73- Bunnik EM, Batugedara G., Saraf A., Prudhomme J., Florens L., and Le Roch KG. The mRNA-bound proteome in the human malaria parasite Plasmodium falciparum. Genome Biology.  2016 Jul 5;17(1):147. doi: 10.1186/s13059-016-1014-0. PMID: 27381095.

 

72- Saraf  S., Cervantes S., Bunnik EM., Ponts N., Sardiu ME., Chung DWD., Prudhomme J., Wen K., Varberg JM., Washburn MP., Florens L., and Le Roch KG.  Dynamic and combinatorial landscape of histone modifications during the malaria parasite cell cycle. J Proteome Res. 2016 J Proteome Res. 2016 Aug 5;15(8):2787-801. doi: 10.1021/acs.jproteome.6b00366. Epub 2016 Jun 24. PMID:27291344.

 

71- Klionsky DJ et al., Guidelines for the use and interpretation of assays for monitoring autophagy Autophagy. 2016 Jan 2;12(1):1-222. PMID: 26799652.

 

70- Nieves K, Prudhomme J, Le Roch KG, Franzblau SG, Rodríguez AD. Natural product-based synthesis of novel anti-infective isothiocyanate - and isoselenocyanate-functionalized amphilectane diterpenes. Bioorg. Med Chem Lett. 2015 Dec 22. PMID: 26748697

 

69- Lu XM, Bunnik EM, Pokhriyal N, Nasseri S, Lonardi S, Analysis of nucleosome positioning landscapes enables gene discovery in the human malaria parasite Plasmodium falciparum. Le Roch KG. BMC Genomics. 2015 Nov 25;16(1):1005. PMID: 26607328.

 

68- Aviles, E. Prudhomme, J., Le Roch, K. and Rodriguez, A.. Structures, semisyntheses, and absolute configurations of the antiplasmodial a-substituted b-lactam monamphilectines B and C from the sponge Svenzea flava. Tetrahedron, 2015 Jan 21;71(3):487-494..

 

67- Bunnik EM. and Le Roch KG. PfAlba1: master regulator of translation in the malaria parasite. Genome Biology 2015, October 8, 16:221.

 

66- Avilés E, Prudhomme J, Le Roch KG, Franzblau SG, Chandrasena K, Mayer AM, Rodríguez AD. Synthesis and preliminary biological evaluation of a small library of hybrid compounds based on Ugi isocyanide multicomponent reactions with a marine natural product scaffold. Bioorg Med Chem Lett. 2015 Sep 15. pii: S0960-894X(15)30070-6.

 

65- Daub ME, Prudhomme J, Le Roch K, Vanderwal CD. Synthesis and potent antimalarial activity of kalihinol B. J Am Chem Soc. 2015 Apr 22;137(15):4912-5.

 

64 - Ay F., Bunnik EM., Varoquaux N., Vert JP., Stafford Noble W., Le Roch KG.  Multiple dimensions of gene regulation in the malaria parasite Plasmodium falciparum. Bioessays. 2015 Feb;37(2):182-94.

 

63- De Melo Burger, M; Fernandes, JB; da Silva, M.F.; Escalante, A.; Prudhomme, J.; Le Roch, K.; Izidoro, M. and Vieira P.C.. Structures and Bioactivities of New Dihydrochalcones from Metrodorea stipularis Mart. (Rutaceae)" J Nat Prod. 2014 Nov 26;77(11):2418-22.

 

62- Russell K., Cheng CH., Bizzaro J.W., Ponts N., Emes, R.D. , Le Roch KG. Marx K.A. and Horrocks P.. Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites. BMC Genomics. 2014 Oct 3;15(1):848.

 

61- Polishko A., Bunnik EM., Le Roch K., Lonardi S. PuFFIN - A Parameter-free Method to Build Nucleosome Maps from Paired-end Reads BMC Bioinformatics, 2014, September 10, 15:S11.

 

60- Bunnik EM., Polishko A., Prudhomme J., Ponts N., Gill SS., Lonardi S. and Le Roch KG. DNA-encoded nucleosome occupancy regulates transcriptional levels in the human malaria parasite Plasmodium falciparum. BMC Genomics. 2014 May 8;15:347.

 

59 - Ay F., Bunnik EM., Varoquaux N., Bol SM., Prudhomme J., Vert JP., Stafford Noble W., Le Roch KG. The three-dimensional model of the P. falciparum genome reveals the role of genome architecture in regulating gene expression. Genome Res. 2014 Jun;24(6):974-88.

 

58 - Hamilton MJ., Lee M., and Le Roch KG. The ubiquitin system:  an essential component to unlocking the secrets of malaria parasite biology.  Molecular BioSystems. 2014 Jan 30.

 

57 - Bunnik EM., Chung DW, Hamilton M., Ponts N., Prudhomme J., and Le Roch KG. Polysome Profiling reveals Translational Control of Gene Expression 1 in the Human Malaria Parasite Plasmodium falciparum. Genome Biol. 2013 Nov 22;14(11):R128.

 

56 – Ponts N., Fu L., Harris EY., Zhang J., Chung DW, Cervantes MC., Prudhomme J., Atanasova-Penichon V., Zehraoui E., Bunnik E., Rodrigues EM., Lonardi S, Hicks GR., Wang Y and Le Roch KG. Genome-scale discovery of DNA methylations in the human malaria parasite. Cell Host & Microbe 2013 – Dec 11; 14 – 6(696-706).

 

55 - Bunnik EM. and Le Roch KG. An introduction to functional genomics and systems biology. Advances in Wound Care. 2013 Nov;2(9):490-498.

 

54 – Cervantes S., Bunnik EM., Saraf S., Conner CM., Escalante E., Sardiu ME, Ponts N., Prudhomme J., Florens L., and Le Roch KG. The multifunctional autophagy pathway in the human malaria parasite, Plasmodium falciparum. Autophagy. 2013 Nov 11;10(1).

 

53 -  Teasdale M., Prudhomme, J., Torres M., Braley M.; Cervantes S., Bhatia S., La Clair J., Le Roch K. †, and Kubanek J. Pharmacokinetics, metabolism, and in vivo efficacy of the antimalarial natural product bromophycolide A. ACS Medicinal Chemistry Letters 2013. Oct 10;4(10):989-993. † Contributed equally to this work, Co-corresponding Authors.

 

52 - Zafrir Ilan E, Torres MR., Prudhomme J., Le Roch K., Jensen PR., and Fenical W. Farnesides A and B, Sesquiterpenoid Nucleoside Ethers from a Marine-Derived Streptomyces sp., strain CNT-372 from Fiji. J Nat Prod. 2013 Sep 27;76(9):1815-8. doi: 10.1021/np400351t.

 

51 – Agrawal S., Chung DWD., Ponts N., Van Dooren GG., Prudhomme J., , Brooks CF., Rodrigues EM., Tan JC., Ferdig MT., Striepen B., and Le Roch KG. An apicoplast localized ubiquitylation system is required for the import of nuclear-encoded plastid proteins.  PLoS Pathogen. 2013 Jun;9(6):e1003426. doi: 10.1371/journal.ppat.1003426.

 

50 - Biamonte MA., Wanner J and Le Roch KG. Recent advances in malaria drug discovery. Bioorg Med Chem Lett. 2013 May 15;23(10):2829-43. doi: 10.1016/j.bmcl.2013.03.067.

 

49 – Severo SM., Choy A., Stephens KD., Sakhon OS., Chen G., Chung DD., Le Roch KG , Blaha G. and Pedra JHF.  The E3 Ubiquitin Ligase XIAP Restricts Anaplasma phagocytophilum Colonization of Ixodes scapularis Ticks. J Infect Dis. 2013 Jul 29.

 

48 - Teasdale, M.E., Shearer, T.L., Engel, S., Alexander, T.S., Fairchild, C.R., Prudhomme, J., Torres, M., Le Roch, K., Aalbersberg, W., Hay, M., Kubanek, J. Bromophycoic acids: Bioactive natural products from a Fijian red alga Callophycus sp. The Journal of Organic Chemistry. J Org Chem. 2012 Sep 21;77(18):8000-6.

 

47 - Chung, D., Ponts, N., Prudhomme, J., Rodrigues, E., Le Roch, K.  Characterization of the ubiquitylating components of the human malaria parasite's protein degradation pathway. PLoS One. 2012;7(8):e43477. doi: 10.1371/journal.pone.0043477. Epub 2012 Aug 17.

 

46 - Ponts N.,  Chung DW. and Le Roch K.. Strand-specific RNA-seq in malaria samples.  RNA Abundance Analysis: Methods and Protocols. Humana Press. Springer Science.  Methods Mol Biol. 2012; 883:59-73.

 

45 - Polishko A, Ponts N, Le Roch KG, Lonardi S NOrMAL: Accurate Nucleosome Positioning using a Modified Gaussian Mixture Model. Bioinformatics. 2012 Jun 15;28(12):i242-9.

 

44 - Harris EY, Ponts N, Le Roch KG, Lonardi S. BRAT-BW: Efficient and accurate mapping of bisulfite-treated reads. Bioinformatics. 2012 Jul 1;28(13):1795-6. Epub 2012 May 3.

 

43 - Le Roch K.G, Chung DW. and Ponts N. Genomics and Integrated Systems Biology in Plasmodium falciparum: A Path to Malaria Control and Eradication.  Parasite Immunol. 2012 Feb-Mar;34(2-3):50-60.

 

42 - Cervantes S., Stout E. P., Prudhomme J., Engel S., Burton M., Cervantes M., Carter D., Chang Y.T, Hay M.E., Aalbersberg W., Kubanek J. and Le Roch KG.  High Content Live Cell Imaging Evaluation for the Discovery of New Antimalarial Natural Products. BMC Infect Dis. 2012 Jan 3;12:1.

 

41- Harris E., Ponts N., Levchuk A., Le Roch K. †  and Lonardi S. Chromatin-driven de novo discovery of DNA binding motifs in the human malaria parasite. 2011 BMC Genomics. Dec 13;12:601. † Contributed equally to this work.

 

40- Buske OJ, Hoffman MM, Ponts, Le Roch KG and Noble WS. Exploratory analysis of genomic segmentations with Segtools. BMC Bioinformatics. 2011 Oct 26;12:415.

 

39- Ponts, N., Saraf, A., Chung, D.K., Harris, A., Prudhomme J., Washburn M. P., Florens L., Le Roch K.G..  Unraveling the Human Malaria Parasite’s Ubiquitome. J. Biol. Chem. 2011 Nov 18;286(46):40320-30.

 

38 - Stout EP, Cervantes S, Prudhomme J, France S, La Clair JJ, Le Roch KG  and Kubanek J.  Bromophycolide A targets heme crystallization in the human malaria parasite Plasmodium falciparum. ChemMedChem. 2011 Jul 5. doi: 10.1002/cmdc.201100252. † Contributed equally to this work.

 

37 - Stout EP, Prudhomme J, Le Roch K, Aalbersberg W, Hay ME, Kubanek J.  Unusual antimalarial meroditerpenes from tropical red macroalgae. Bioorg Med Chem Lett. 2010 Oct 1;20(19):5662-5.

 

36 - Ponts N., Harris E.Y, Lonardi S and Le Roch K.G. Nucleosome occupancy at transcription start sites in the human malaria parasite: a hard-wired evolution of virulence? Infect Genet Evol. 2011. 11(4):716-24. doi: 10.1016/j.meegid.2010.08.002.

 

35 - Halbert J., Ayong L., Equinet L., Le Roch K., Hardy M., Goldring D., Reininger L., Waters N., Chakrabarti D. and Doerig C.. Pfcrk-3, an essential transcriptional CDK-related protein kinase of the human malaria parasite Plasmodium falciparum. Eukaryot Cell.  2010 Jun; 9(6):952-9.

 

34 - Lin AS.,Stout EP., Prudhomme P., Le Roch K, Fairchild CR., Franzblau FG., Aalbersberg W., Hay ME., and Kubanek J.  Bioactive Bromophycolides R-U from the Fijian Red Alga Callophycus serratus. J. Nat. Prod.  2010, 73, 275–278.

 

33 - Chung DW and Le Roch KG. Targeting the Plasmodium ubiquitin/proteasome system with anti-malarial drugs: promises for the future. Infect Disord Drug Targets. 2010 Jun; 10(3):158-64.

 

32 - Harris E., Ponts N., Levchuk A., Le Roch K. and Lonardi S. BRAT: bisulfite-treated reads analysis tool. Bioinformatics. 2010 Feb 15; 26(4):572-3.

 

31 - Ponts N., Harris RY., Prudhomme J., Wick I., Eckhardt C., Hicks G., Hardiman G., Lonardi S. and Le Roch KG. . Nucleosome Landscape and Control of Transcription in the Human Malaria Parasite. Genome Res. 2010 Feb;20(2):228-38.

 

30 - Lane AM., Mular L., Drenkard EJ., Shearer TL., Engel S., Fredericq S., Fairchild CR., Prudhomme J., Le Roch K., Hay ME, Aalbersberg W. and Kubanek J. Ecological leads for natural product discovery: Novel sesquiterpene hydroquinones from the red macroalga Peyssonnelia sp. 2010, Tetrahedron.

 

29 - Chung DW, Ponts N, Cervantes S and Le Roch KG. Post-translational modifications in Plasmodium: more than you think! Mol Biochem Parasitol. 2009 Dec;168(2):123-34.

 

28 - Cervantes S, Prudhomme J, Carter D, Gopi KG, Li Q, Chang YT and Le Roch KG: High-content live cell imaging with RNA probes: advancements in high-throughput antimalarial drug discovery. BMC Cell Biol, 2009 10:45.   Highly Accessed manuscript.

 

27 - Lane AL, Stout EP, Lin AS, Prudhomme J, Le Roch K, Fairchild CR, Franzblau SG, Hay ME, Aalbersberg W, Kubanek J: Antimalarial bromophycolides J-Q from the Fijian red alga Callophycus serratus. J Org Chem, 2009 74(7):2736-2742.

 

26 - Stout PE, Hasemeyer A, Lane AL, Davenport T, Engel S, Hay ME, Fairchild CR, Prudhomme J, Le Roch K, Aalbersberg W. and Kubanek J. Antibacterial Neurymenolides from the Fijian Red Alga Neurymenia fraxinifolia. (2009) Org Lett. Jan 1;11(1):225-8.

25 - Jiang RW, Haya ME, Fairchildc CR, Prudhomme J, Le Roch K., Aalbersberge W and Kubanek J. Antineoplastic unsaturated fatty acids from Fijian macroalgae. (2008) Phytochemistry. Oct; 69(13):2495-500.

 

24 - Prudhomme J, McDaniel E, Ponts N, Bertani S, Fenical W, Jensen P, and Le Roch K.  Marine actinomycetes: a new source of compounds against the human malaria parasite. PLoS ONE 2008 3: e2335. Interview and Media highlights in Science Express.

 

23 - Ponts N, Yang J, Chung DW, Prudhomme J, Girke T and Le Roch K. Deciphering the ubiquitin-mediated pathway in apicomplexan parasites: a potential strategy to interfere with parasite virulence. PLoS ONE 2008 3: e2386.

 

22 - Le Roch KG, Johnson JR, Ahiboh H, Chung DW, Prudhomme J., Plouffe D., Henson K., Zhou Y, Witola W., Yates JR, Ben Mamoun C., Winzeler EA and Vial H. et al. A systematic approach to understand the mechanism of action of the bisthiazolium compound T4 on the human malaria parasite, Plasmodium falciparum. BMC Genomics, 2008 9(1):513.

 

21 - Young JA, Johnson JR, Benner C, Yan SF, Chen K, Le Roch K, Zhou Y and Winzeler EA. In silico discovery of transcription regulatory elements in Plasmodium falciparum. BMC Genomics, 2008 9:70.

 

20 - Kato N, Sakata T, Breton G, Le Roch KG, Nagle A, Andersen C., Bursulaya B., Henson K, Johnson J, Kota Kumar A, Marr F, Mason D, McNamara C, Plouffe D., Ramachandran V, Spooner M, Tuntland T, Zhou Y, Peters EP, Chatterjee A, Schultz PG, Ward GA, Gray N, Harper J. and Winzeler EA. Gene expression signatures and small-molecule compounds link a protein kinase to Plasmodium falciparum motility. Nat Chem Biol 2008 4(6):347-56

 

19 - Lane AL, Stout EP, Hay ME, Prusak AC, Hardcastle K, Fairchild CR, Franzblau CG, Le Roch K, Prudhomme J, Aalbersberg w, and Kubanek J. Callophycoic Acids and Callophycols from the Fijian Red Alga Callophycus serratus. J Org Chem, 2007 72 (19):7343-51.

 

18 - Gunasekera AM, Myrick A, Le Roch K, Winzeler AE and Wirth DF. Plasmodium falciparum: Genome wide perturbations in transcript profiles among mixed stage cultures after chloroquine treatment. Exp Parasitol, 2007  87-92.

 

17 - Gunasekera AM, Myrick A, Militello KT, Sims JS, Dong CK, Le Roch K, Winzeler AE and Wirth DF. Regulatory motifs uncovered among gene expression clusters in Plasmodium falciparum. Mol Biochem Parasitol, 2007 153 (1).

 

16 - Deitsch K, Duraisingh M, Dzikowski R, Gunasekera A, Khan S, Le Roch K, Llinas M, Mair G., Shock J, Roos D., Sim J, Wiegand R. and Winzeler EA.  Mechanisms of gene regulation in Plasmodium. Am J Trop Med Hyg 2007 77: 201-208.

 

15 - Daily JP, Scanfeld D, Pochet N, Le Roch K, Plouffe D, Kamal M, Sarr O, Mboup S, Ndir S,  Wypij D, Levasseur K, Thomas E, Tamayo P, Dong C, Zhou Y, Lander ES, Ndiaye D, Wirth D, Winzeler EA, Mesirov JP and Regev A. Distinct physiological states of Plasmodium falciparum in malaria-infected patients. Nature 2007 450: 1091-1095. † Contributed equally to this work.

 

14 - Kidgell C, Volkman SK, Daily J, Borevitz JO, Plouffe D, Zhou Y, Johnson JR, Le Roch K, Sarr O, Ndir O, Mboup S, Batalov S, Wirth W andWinzeler EA. A systematic map of genetic variation in Plasmodium falciparum. PLoS Pathog 2006 2: e57.

 

13 - Young J., Fivelman Q., Blair P., De la Vega P., Le Roch KG, Zhou Y., Carucci DJ., Baker D., Winzeler E.  The Plasmodium falciparum sexual development transcriptome: A microarray analysis using ontology-based pattern identification. Mol Biochem Parasitol. 2005 Sep;143(1):67-79.

 

12 - Daily J., Le Roch KG., Sarr O., Ndiaye D., Lukens A., Zhou Y., Ndir O., Mboup M., Sultan A., Winzeler E., Wirth DF.  In vivo transcriptome of Plasmodium falciparum reveals overexpression of transcripts that encode surface proteins. J. Infect Dis. 2005 Apr 1;191(7):1196-203.

 

11 - Le Roch KG, Johnson J., Florens L., Zhou Y., Santrosyan A., Grainger M., Yan F, Williamson K., Holder A., Carucci D., Yates, III JR, and Winzeler EA. Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res. 2004 Nov; 14(11):2308-18

 

10 - Daily JP, Le Roch KG, Sarr O, Fang X, Zhou Y, Ndir O, Mboup S, Sultan A, Winzeler EA, Wirth DF.  In vivo transcriptional profiling of P. falciparum. Malar J. 2004 Aug 5;3 (1):30.

 

9 - T.Y. Sam-Yellowe, L. Florens, J. R. Johnson, T. Wang, K. G. Le Roch, Y. Zhou, S. Batalov, J. A. Drazba, D.J. Carucci, E. A. Winzeler and J. R. Yates III.  A plasmodium gene family encoding Maurer’s cleft membrane proteins: Structural properties and expression profiling. Genome Res. 2004 Jun;14 (6):1052-9.)

 

8 - Le Roch KG., Zhou Y., Blair P., Grainger M., Moch KJ, Haynes DJ, De la Vega P, Holder A., Batalov S., Carucci DJ and Winzeler AE. Discovery of gene function by expression profiling of the malaria parasite lifecycle. Science, 2003 September 12;301: 1503-1508.

 

7 - Merckx A.*, Le Roch K*, Nivez MP, Alano P., Gutierrez G., Nebreda A., Goldrin D., Patterson S., Chakrabarti D.  and Doerig C.. Novel cyclin-related proteins of the human malaria parasite Plasmodium falciparum . J Biol Chem, July 17, 2003. * Equal contribution to this work.

 

6 - Le Roch KG., Zhou Y., Batalov S., and Winzeler E. Monitoring the chromosome 2 intraerythrocytic transcriptome of Plasmodium falciparum using oligonucleotide arrays American journal of tropical Medicine and Hygiene. 2002. 67(3), 233-243.

 

5 - Volkmann, S., Hartl, D., Wirth, D., Nielson, K.,Choi M., Batalov, S., Zhou, Y., Plouffe D.,  Le Roch, K. G., Abagyan R and Winzeler, E. Excess Polymorphisms in Genes for Membrane Proteins in Plasmodium falciparum. Science, 2002 Oct 4;298(5591):216-218

 

4 - Li Z, Le Roch K, Geyer JA, Woodard CL, Prigge ST, Koh J, Doerig C, Waters NC. Influence of human p16(INK4) and p21(CIP1) on the in vitro activity of recombinant Plasmodium falciparum cyclin-dependent protein kinases. Biochem. Biophys. Res. Commun. 2001 Nov 16;288(5):1207-11.

 

3 - Dorin D, Le Roch K, Sallicandro P, Alano P, Parzy D, Poullet P, Meijer L, Doerig C. Pfnek-1, a NIMA-related kinase from the human malaria parasite Plasmodium falciparum. Biochemical properties and possible involvement in MAPK regulation. Eur. J. Biochem. 2001 May;268(9):2600-8.

2 - Knockaert M, Gray N, Damiens E, Chang YT, Grellier P, Grant K, Fergusson D, Mottram J, Soete M, Dubremetz JF, Le Roch K, Doerig C, Schultz P, Meijer L. Intracellular targets of cyclin-dependent kinase inhibitors: identification by affinity chromatography using immobilised inhibitors. Chem. Biol. 2000 Jun ; 7(6):411-22.

 

1 - Le Roch K, Sestier C, Dorin D, Waters N, Kappes B, Chakrabarti D, Meijer L, Doerig C.  Activation of a Plasmodium falciparum cdc2-related kinase by heterologous p25 and cyclin H. Functional characterization of a P. falciparum cyclin homologue. J. Biol. Chem. 2000 Mar 24;275(12):8952-8.