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Method: Gene prediction in the immunoglobulin loci
- Vikram Sirupurapu,
- Yana Safonova,
- and Pavel A. Pevzner
Genome Res. June 2022 32: 1152-1169; Published in Advance May 11, 2022, doi:10.1101/gr.276676.122
...to the same selective pressure, for example, pressure driven by common pathogens. IGDetective also revealed extremely diverged V genes and a new family of evolutionary conserved V genes in bats with unusual noncanonical cysteines. Moreover, unlike all other previously reported antibodies, these cysteines...
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Method: A high-coverage artificial chromosome library for the genome-wide screening of drug-resistance genes in malaria parasites
- Shiroh Iwanaga,
- Izumi Kaneko,
- and Masao Yuda
Genome Res. May 2012 22: 985-992; Published in Advance March 16, 2012, doi:10.1101/gr.124164.111
...human malaria parasite Plasmodium vivax. Nature 455: 757–763. Culleton R, Martinelli A, Hunt P, Carter R. 2005. Linkage group selection: Rapid gene discovery in malaria parasites. Genome Res 15: 92–97. Deitsch K, Driskill C, Wellems T. 2001. Transformation of malaria parasites by the spontaneous uptake...
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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
...of this deletion in the Amazon suggests that widespread use of malaria rapid diagnostic tests that depend on HRP2 will result in missed diagnoses. Second, we show that a mutation in the apicoplast 23S rRNA correlates with a 100-fold increase in EC50 of clindamycin. Because it is relatively difficult to test...
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Research: Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection
- PingHsun Hsieh,
- Krishna R. Veeramah,
- Joseph Lachance,
- Sarah A. Tishkoff,
- Jeffrey D. Wall,
- Michael F. Hammer,
- and Ryan N. Gutenkunst
Genome Res. March 2016 26: 279-290; Published in Advance February 17, 2016, doi:10.1101/gr.192971.115
...) (Akaike 1974) and Bayesian information criteria (BIC) (Schwarz 1978) for model selection. Both AIC and BIC prefer the continuous asymmetric gene-flowmodel to the single-pulse gene flowmodel (Supplemental Table S2). As a second validation, we used patterns of linkage disequilibrium (LD) decay, information...
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LETTER: Cloning, Characterization, and Mapping of a Murine Promiscuous Chemokine Receptor Gene: Homolog of the Human Duffy Gene
- Hong Luo,
- Asok Chaudhuri,
- Kenneth R. Johnson,
- Kuldeep Neote,
- Valerie Zbrzezna,
- Yu He,
- and A. Oscar Pogo
Genome Res. September 1, 1997 7: 932-941; doi:10.1101/gr.7.9.932
...designed by use of the sequences of exon 2 of the mouse Dfy . Extaq (TaKaRa Biomedicals, Pan Vera Corp.) DNA polymerase was used in the 5′ and 3′ rapid amplification of cDNA ends (RACE) reactions. The 5′ and 3′ RACE fragments were inserted into pCR II vector, cloned, and sequenced. The full-length coding...
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Research: Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States
- Greta Bellinzona,
- Tiago Nardi,
- Michele Castelli,
- Gherard Batisti Biffignandi,
- Karim Adjou,
- Martha Betson,
- Yannick Blanchard,
- Ioana Bujila,
- Rachel Chalmers,
- Rebecca Davidson,
- Nicoletta D'Avino,
- Tuulia Enbom,
- Jacinto Gomes,
- Gregory Karadjian,
- Christian Klotz,
- Emma Östlund,
- Judith Plutzer,
- Ruska Rimhanen-Finne,
- Guy Robinson,
- Anna Rosa Sannella,
- Jacek Sroka,
- Christen Rune Stensvold,
- Karin Troell,
- Paolo Vatta,
- Barbora Zalewska,
- Claudio Bandi,
- Davide Sassera,
- and Simone M. Cacciò
Genome Res. June 2024 34: 877-887; Published in Advance July 8, 2024, doi:10.1101/gr.278830.123
...with gp60 molecular typing data that identified only IIa subtypes in U.S. isolates (Jann et al. 2022). A parallel could be drawn to the recent emergence and rapid spread of the C. hominis IfA12G1R5 subtype in Europe, Australia, and the United States (Braima et al. 2019; Huang et al. 2023; Peake et al...
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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
...-9806, USA; 10Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom Corresponding author: alistair.miles@well.ox.ac.uk Abstract The malaria parasite Plasmodium falciparum has a great capacity for evolutionary adaptation to evade host immunity...
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LETTER: Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization
- King-Hwa Ling,
- Marie-Adele Rajandream,
- Pierre Rivailler,
- Alasdair Ivens,
- Soon-Joo Yap,
- Alda M.B.N. Madeira,
- Karen Mungall,
- Karen Billington,
- Wai-Yan Yee,
- Alan T. Bankier,
- Fionnadh Carroll,
- Alan M. Durham,
- Nicholas Peters,
- Shu-San Loo,
- Mohd Noor Mat Isa,
- Jeniffer Novaes,
- Michael Quail,
- Rozita Rosli,
- Mariana Nor Shamsudin,
- Tiago J.P. Sobreira,
- Adrian R. Tivey,
- Siew-Fun Wai,
- Sarah White,
- Xikun Wu,
- Arnaud Kerhornou,
- Damer Blake,
- Rahmah Mohamed,
- Martin Shirley,
- Arthur Gruber,
- Matthew Berriman,
- Fiona Tomley,
- Paul H. Dear,
- and Kiew-Lian Wan
Genome Res. March 2007 17: 311-319; Published in Advance February 6, 2007, doi:10.1101/gr.5823007
...the long-range order of P- and R-segments. We are therefore confident that the segmentation found on Chr1 is typical of the remainder of the . We suspect that the unusual organization may serve to facilitate rapid evolution and diversification, a strategy of benefit to a parasite. Rearrangements within R...
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Research: Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance
- Tim Downing,
- Hideo Imamura,
- Saskia Decuypere,
- Taane G. Clark,
- Graham H. Coombs,
- James A. Cotton,
- James D. Hilley,
- Simonne de Doncker,
- Ilse Maes,
- Jeremy C. Mottram,
- Mike A. Quail,
- Suman Rijal,
- Mandy Sanders,
- Gabriele Schönian,
- Olivia Stark,
- Shyam Sundar,
- Manu Vanaerschot,
- Christiane Hertz-Fowler,
- Jean-Claude Dujardin,
- and Matthew Berriman
Genome Res. December 2011 21: 2143-2156; Published in Advance October 28, 2011, doi:10.1101/gr.123430.111
...; Supplemental Fig. S6). Detecting ancient and recent adaptive evolution in L. donovani L. donovani has been a parasite of humans for a long period of time, and so hostspecific selective processes are likely to have shaped its (Stevens et al. 2001; Simpson et al. 2006). Furthermore, genes are likely to show...
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Letter: The origins of apicomplexan sequence innovation
- James Wasmuth,
- Jennifer Daub,
- José Manuel Peregrín-Alvarez,
- Constance A.M. Finney,
- and John Parkinson
Genome Res. July 2009 19: 1202-1213; Published in Advance April 10, 2009, doi:10.1101/gr.083386.108
..., has allowed the parasite to expand its host range (Jakes et al. 2003). This leads to strong selection pressures, resulting in a rapid and extensive modification of the proteome and frequent speciation. Consistent with the data presented here, it is likely that many lineage-specific protein families...

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