Searching journal content for articles similar to Le Roch et al. 14 (11): 2308.

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  1. Method: Capturing in vivo RNA transcriptional dynamics from the malaria parasite Plasmodium falciparum
    • Heather J. Painter,
    • Manuela Carrasquilla,
    • and Manuel Llinás
    Genome Res. June 2017 27: 1074-1086; Published in Advance April 17, 2017, doi:10.1101/gr.217356.116
    ...of the yeast FCU gene was PCR amplified from Plasmodium falciparum vector pCC1 (Maier et al. 2006) and cloned as a translational fusion into the unique BglII andXbaI sites of the pCBM-BSD-684 5′Pfs16-gfp vector (Eksi et al. 2008), placing the transcription of the fused gene under the control of a P. falciparum...
  2. Research: Interactive transcriptome analysis of malaria patients and infecting Plasmodium falciparum
    • Junya Yamagishi,
    • Anna Natori,
    • Mohammed E.M. Tolba,
    • Arthur E. Mongan,
    • Chihiro Sugimoto,
    • Toshiaki Katayama,
    • Shuichi Kawashima,
    • Wojciech Makalowski,
    • Ryuichiro Maeda,
    • Yuki Eshita,
    • Josef Tuda,
    • and Yutaka Suzuki
    Genome Res. September 2014 24: 1433-1444; Published in Advance August 4, 2014, doi:10.1101/gr.158980.113
    ...the transcriptomes of the human hosts and the infecting parasites affect one another. Here we report the RNA-seq analysis of 116 Indonesian patients infected with the malaria parasite Plasmodium falciparum (Pf). We extracted RNAs from their peripheral blood as a mixture of host and parasite transcripts and mapped...
  3. Resource: Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum
    • Alistair Miles,
    • Zamin Iqbal,
    • Paul Vauterin,
    • Richard Pearson,
    • Susana Campino,
    • Michel Theron,
    • Kelda Gould,
    • Daniel Mead,
    • Eleanor Drury,
    • John O'Brien,
    • Valentin Ruano Rubio,
    • Bronwyn MacInnis,
    • Jonathan Mwangi,
    • Upeka Samarakoon,
    • Lisa Ranford-Cartwright,
    • Michael Ferdig,
    • Karen Hayton,
    • Xin-zhuan Su,
    • Thomas Wellems,
    • Julian Rayner,
    • Gil McVean,
    • and Dominic Kwiatkowski
    Genome Res. September 2016 26: 1288-1299; Published in Advance August 16, 2016, doi:10.1101/gr.203711.115
    ...Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum Alistair Miles 1 , 2 , Zamin Iqbal 3 , Paul Vauterin 1 , Richard Pearson 1 , 2 , Susana Campino 2 , Michel Theron 2 , Kelda...
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  4. Research: Transcriptional variation in the malaria parasite Plasmodium falciparum
    • Núria Rovira-Graells,
    • Archna P. Gupta,
    • Evarist Planet,
    • Valerie M. Crowley,
    • Sachel Mok,
    • Lluís Ribas de Pouplana,
    • Peter R. Preiser,
    • Zbynek Bozdech,
    • and Alfred Cortés
    Genome Res. May 2012 22: 925-938; Published in Advance March 13, 2012, doi:10.1101/gr.129692.111
    ...Malaria genetic variation has been extensively characterized, but the level of epigenetic plasticity remains largely unexplored. Here we provide a comprehensive characterization of transcriptional variation in the most lethal malaria parasite, Plasmodium falciparum, based on highly accurate transcriptional...
  5. Research: Genome scanning of Amazonian Plasmodium falciparum shows subtelomeric instability and clindamycin-resistant parasites
    • Neekesh V. Dharia,
    • David Plouffe,
    • Selina E.R. Bopp,
    • Gonzalo E. González-Páez,
    • Carmen Lucas,
    • Carola Salas,
    • Valeria Soberon,
    • Badry Bursulaya,
    • Tadeusz J. Kochel,
    • David J. Bacon,
    • and Elizabeth A. Winzeler
    Genome Res. November 2010 20: 1534-1544; Published in Advance September 9, 2010, doi:10.1101/gr.105163.110
    ...Genome scanning of Amazonian Plasmodium falciparum shows subtelomeric instability and clindamycin-resistant parasites Neekesh V. Dharia 1 , David Plouffe 2 , Selina E.R. Bopp 1 , Gonzalo E. González-Páez 1 , Carmen Lucas 3 , Carola...
  6. LETTER: Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum
    • Tobias Mourier,
    • Celine Carret,
    • Sue Kyes,
    • Zoe Christodoulou,
    • Paul P. Gardner,
    • Daniel C. Jeffares,
    • Robert Pinches,
    • Bart Barrell,
    • Matt Berriman,
    • Sam Griffiths-Jones,
    • Alasdair Ivens,
    • Chris Newbold,
    • and Arnab Pain
    Genome Res. February 2008 18: 281-292; Published in Advance December 20, 2007, doi:10.1101/gr.6836108
    ...malaria Plasmodium falciparum is well documented ( Bozdech et al. 2003 ; Le Roch et al. 2004 ), analysis of the published sequence indicates a paucity of recognizable transcription factors and a lack of components for classical microRNA (miRNA)-mediated gene regulation ( Gardner et al. 2002 ; Aravind et...
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  7. Research: Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression
    • Ferhat Ay,
    • Evelien M. Bunnik,
    • Nelle Varoquaux,
    • Sebastiaan M. Bol,
    • Jacques Prudhomme,
    • Jean-Philippe Vert,
    • William Stafford Noble,
    • and Karine G. Le Roch
    Genome Res. June 2014 24: 974-988; Published in Advance March 26, 2014, doi:10.1101/gr.169417.113
    ...to participate in gene regulation through formation of specific chromatin loops that bring enhancers and enhancer-like elements in proximity to their target promoters. However, a global reorganization of the entire correlated with changes in transcriptional capacity, as described here for P. falciparum, has...
  8. RESOURCE: Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale
    • Shailesh V. Date and
    • Christian J. Stoeckert, Jr.
    Genome Res. April 2006 16: 542-549; Published in Advance March 6, 2006, doi:10.1101/gr.4573206
    ...Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale Protein function discovery in P. falciparum Shailesh V. Date 1 and Christian J. Stoeckert, Jr. Center for Bioinformatics, Department...
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  9. Method: Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories
    • Borislav Hrisimirov Hristov,
    • William Stafford Noble,
    • and Alessandro Bertero
    Genome Res. October 2024 34: 1610-1623; Published in Advance September 25, 2024, doi:10.1101/gr.278327.123
    ...: the Plasmodium falciparum var genes, the mouse olfactory receptor “Greek islands,” and the human RBM20 cardiac splicing factory. We then apply trans-C to systematically test the hypothesis that genes coregulated by the same trans-acting element (i.e., a transcription or splicing factor) colocalize in three...
  10. LETTER: A Plasmodium Gene Family Encoding Maurer's Cleft Membrane Proteins: Structural Properties and Expression Profiling
    • Tobili Y. Sam-Yellowe,
    • Laurence Florens,
    • Jeffrey R. Johnson,
    • Tongmin Wang,
    • Judith A. Drazba,
    • Karine G. Le Roch,
    • Yingyao Zhou,
    • Serge Batalov,
    • Daniel J. Carucci,
    • Elizabeth A. Winzeler,
    • and John R. Yates III
    Genome Res. June 2004 14: 1052-1059; Published in Advance May 12, 2004, doi:10.1101/gr.2126104
    ...a complex membrane network, which connects the parasitophorous vacuole to the host plasma membrane and is involved in protein transport and trafficking. We have identified a novel subtelomeric gene family in Plasmodium falciparum that encodes 11 transmembrane proteins localized to the Maurer's clefts...
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