Searching journal content for articles similar to Pizzi and Frontali 11 (2): 218.

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  1. 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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  2. INSIGHT/OUTLOOK: Low-Complexity Regions in Plasmodium Proteins: In Search of a Function
    • Luciano Brocchieri
    Genome Res. February 1, 2001 11: 195-197; doi:10.1101/gr.176401
    ...In a new window Figure 1. Partial alignment of the ookinete adhesive protein between the Plasmodium falciparum (PLAFA) and the rodent malaria agent Plasmodium berghei (PLABE) sequences, showing two low-complexity elements (lower case, unaligned) between regions of alignment (upper case). The first region...
  3. 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
    ...to the equivalent 18S/28S rRNA Chr 1 pileups. Regions with pileups on inner portions of Chr 5, 7, and 8 are low complexity regions composed by tandem repeats (Supplemental Table S8). In Chr 5, we have one uncharacterized protein (CPATCC_0023030), full of tandem repeats and good RNA-seq support for its expression...
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  4. 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
    ...% of the . These sequences were searched for similarity against the other Plasmodium s using WU-BLASTN ( http://blast.wustl.edu/ ) with dust and seg low-complexity filters. Only hits with a length ≥50 bp and with at least 70% identity were further processed. BLAST-matches were mapped back at the P. falciparum and merged...
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  5. LETTER: Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion
    • Nuno L. Barbosa-Morais,
    • Maria Carmo-Fonseca,
    • and Samuel Aparício
    Genome Res. January 2006 16: 66-77; Published in Advance December 12, 2005, doi:10.1101/gr.3936206
    ...(Mmus), chicken (Ggal), Fugu (Frub), Ciona (Cint), fruit fly (Dmel), C. elegans (Cele), Arabidopsis (Atha), and Plasmodium (Pfal) (for simplicity only one rodent, one teleost, and one insect are shown). Amino-acid positions of each domain within the protein are also indicated in the domain...
  6. LETTER: Functional insights from the distribution and role of homopeptide repeat-containing proteins
    • Noel G. Faux,
    • Stephen P. Bottomley,
    • Arthur M. Lesk,
    • James A. Irving,
    • John R. Morrison,
    • Maria Garcia de la Banda,
    • and James C. Whisstock
    Genome Res. April 2005 15: 537-551; doi:10.1101/gr.3096505
    ...highlight several interesting anomalies. Drosophila melanogaster possesses an overabundance of poly-Q RCPs, >3.5-fold more than that of Homo sapiens and sixfold more than another insect, the mosquito Anopheles gambiae ( Fig. 3B ). In contrast, poly-Q repeats are extremely rare in Plasmodium falciparum...
  7. Method: Detection of simple and complex de novo mutations with multiple reference sequences
    • Kiran V. Garimella,
    • Zamin Iqbal,
    • Michael A. Krause,
    • Susana Campino,
    • Mihir Kekre,
    • Eleanor Drury,
    • Dominic Kwiatkowski,
    • Juliana M. Sá,
    • Thomas E. Wellems,
    • and Gil McVean
    Genome Res. August 2020 30: 1154-1169; Published in Advance August 19, 2020, doi:10.1101/gr.255505.119
    ...and evaluate the approach using extensive simulations and use it to characterize the rate and spectrum of de novo mutation events in 119 progeny from four Plasmodium falciparum experimental crosses, using long-read data on the parents to inform reconstructions of the progeny and to detect several known...
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  8. Research: Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals
    • Ulrike Böhme,
    • Thomas D. Otto,
    • James A. Cotton,
    • Sascha Steinbiss,
    • Mandy Sanders,
    • Samuel O. Oyola,
    • Antoine Nicot,
    • Sylvain Gandon,
    • Kailash P. Patra,
    • Colin Herd,
    • Ellen Bushell,
    • Katarzyna K. Modrzynska,
    • Oliver Billker,
    • Joseph M. Vinetz,
    • Ana Rivero,
    • Chris I. Newbold,
    • and Matthew Berriman
    Genome Res. April 2018 28: 547-560; Published in Advance March 2, 2018, doi:10.1101/gr.218123.116
    ...1 and SURFIN families, respectively. Next, we searched for those predicted motifs in all predicted proteins (excluding low-complexity regions) of the 11 sequenced Plasmodium species and visualized the results as a binary occurrence matrix (Supplemental Fig. S14B). Although some proteins share...
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  9. Method: Quantitative insertion-site sequencing (QIseq) for high throughput phenotyping of transposon mutants
    • Iraad F. Bronner,
    • Thomas D. Otto,
    • Min Zhang,
    • Kenneth Udenze,
    • Chengqi Wang,
    • Michael A. Quail,
    • Rays H.Y. Jiang,
    • John H. Adams,
    • and Julian C. Rayner
    Genome Res. July 2016 26: 980-989; Published in Advance May 10, 2016, doi:10.1101/gr.200279.115
    ...Bac mutants in the human malaria parasite Plasmodium falciparum but should be applicable to many other eukaryotic genomes. QIseq proved accurate, confirming known sites in >100 mutants, and sensitive, identifying and monitoring sites over a >10,000-fold dynamic range of sequence counts. Applying QIseq...
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  10. Letter: Nucleosome landscape and control of transcription in the human malaria parasite
    • Nadia Ponts,
    • Elena Y. Harris,
    • Jacques Prudhomme,
    • Ivan Wick,
    • Colleen Eckhardt-Ludka,
    • Glenn R. Hicks,
    • Gary Hardiman,
    • Stefano Lonardi,
    • and Karine G. Le Roch
    Genome Res. February 2010 20: 228-238; Published in Advance January 6, 2010, doi:10.1101/gr.101063.109
    .....org Nucleosome positioning in Plasmodium protein-free DNA than histone-bound regions and can be accessed by any type of DNA-binding proteins during most of the erythrocytic cycle, especially at the trophozoite and early schizont stages (18–30 hpi). We verified that this abundance of protein-free regions...
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