Searching journal content for articles similar to Jing et al. 9 (2): 175.

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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
    ..., the human malaria parasite, Plasmodium falciparum, is incapable of pyrimidine salvage for mRNA biogenesis. To capture cellular mRNA dynamics during Plasmodium development, we engineered parasites that can salvage pyrimidines through the expression of a single bifunctional yeast fusion gene, cytosine...
  2. 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...
    OPEN ACCESS ARTICLE
  3. 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...
  4. Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
    • Rodrigo P. Baptista,
    • Yiran Li,
    • Adam Sateriale,
    • Mandy J. Sanders,
    • Karen L. Brooks,
    • Alan Tracey,
    • Brendan R.E. Ansell,
    • Aaron R. Jex,
    • Garrett W. Cooper,
    • Ethan D. Smith,
    • Rui Xiao,
    • Jennifer E. Dumaine,
    • Peter Georgeson,
    • Bernard J. Pope,
    • Matthew Berriman,
    • Boris Striepen,
    • James A. Cotton,
    • and Jessica C. Kissinger
    Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
    ...Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions Rodrigo P. Baptista1,2, Yiran Li2, Adam Sateriale3, Mandy J. Sanders4, Karen L. Brooks4, Alan...
    OPEN ACCESS ARTICLE
  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. Research: Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains
    • Sergey V. Ulianov,
    • Ekaterina E. Khrameeva,
    • Alexey A. Gavrilov,
    • Ilya M. Flyamer,
    • Pavel Kos,
    • Elena A. Mikhaleva,
    • Aleksey A. Penin,
    • Maria D. Logacheva,
    • Maxim V. Imakaev,
    • Alexander Chertovich,
    • Mikhail S. Gelfand,
    • Yuri Y. Shevelyov,
    • and Sergey V. Razin
    Genome Res. January 2016 26: 70-84; Published in Advance October 30, 2015, doi:10.1101/gr.196006.115
    ...Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains Sergey V. Ulianov 1 , 2 , 12 , Ekaterina E. Khrameeva 3 , 4 , 12 , Alexey A. Gavrilov 1 , Ilya M. Flyamer 1 , 2 , Pavel...
  7. 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...
  8. LETTER: Low-Complexity Regions in Plasmodium falciparum Proteins
    • Elisabetta Pizzi and
    • Clara Frontali
    Genome Res. February 1, 2001 11: 218-229; Published in Advance January 18, 2001, doi:10.1101/gr.152201
    ...by multiple-alignment procedures when sequences of bona fide homologs are available. Amino acid preferences are fairly uniform in the set of hydrophilic low-complexity segments identified in the two P. falciparum chromosomes sequenced, as well as in sequenced genes from Plasmodium berghei , but differ from...
  9. 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
    ...recently by Chakrabarti et al. (2007) . Interestingly, this study has provided independent evidence for the expression of the chromosome-internal, var gene-associated, novel structured ncRNA family in P. falciparum described previously. Plasmodium s vary significantly in their GC-content (from 20% in P...
    OPEN ACCESS ARTICLE
  10. 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
    ...its complex life cycle, but the corresponding regulatory mechanisms are incompletely understood. To study the relationship between architecture and gene regulation in Plasmodium, we assayed the architecture of P. falciparum at three time points during its erythrocytic (asexual) cycle. Using chromosome...
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