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RESOURCE: Computational Analysis of Plasmodium falciparum Metabolism: Organizing Genomic Information to Facilitate Drug Discovery
- Iwei Yeh,
- Theodor Hanekamp,
- Sophia Tsoka,
- Peter D. Karp,
- and Russ B. Altman
Genome Res. May 2004 14: 917-924; Published in Advance April 12, 2004, doi:10.1101/gr.2050304
...falciparum. Biochem. J. 363 : 833 -838. ↵ Overbeek, R., Larsen, N., Pusch, G.D., D'Souza, M., Selkov Jr., E., Kyrpides, N., Fonstein, M., Maltsev, N., and Selkov, E. 2000 . WIT: Integrated system for high-throughput sequence analysis and metabolic reconstruction. Nucleic Acids Res. 28 : 123 -125. ↵ Shuto, S...
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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
..., colored de Bruijn graphs from short-read data for all samples, align long-read–derived haplotypes and multiple reference data sources to restore graph connectivity information, and call variants using graph path-finding algorithms and a model for simultaneous alignment and recombination. We validate...
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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...-read sequencing allows for high-throughput characterization of the locus, and efforts are underway to gather germline diversity across human populations (Rodriguez et al. 2020). However, although this strategy yields highly accurate reads, it does not contiguously resolve the entirety of the locus and may miss...
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Method: Variant antigen repertoires in Trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs
- Sara Silva Pereira,
- Aitor Casas-Sánchez,
- Lee R. Haines,
- Moses Ogugo,
- Kihara Absolomon,
- Mandy Sanders,
- Steve Kemp,
- Álvaro Acosta-Serrano,
- Harry Noyes,
- Matthew Berriman,
- and Andrew P. Jackson
Genome Res. September 2018 28: 1383-1394; Published in Advance July 13, 2018, doi:10.1101/gr.234146.118
...natural infections and sequential laboratory tsetse transmissions of the same parasite clone (Barry et al. 1983). In P. falciparum, the var gene expression radically changes following a single mosquito passage (Bachmann et al. 2016). In Plasmodium chabaudi, vector passaging not only alters cir (chabaudi...
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Method: Genome-scale identification of cellular pathways required for cell surface recognition
- Sumana Sharma,
- S. Josefin Bartholdson,
- Amalie C.M. Couch,
- Kosuke Yusa,
- and Gavin J. Wright
Genome Res. September 2018 28: 1372-1382; Published in Advance June 18, 2018, doi:10.1101/gr.231183.117
...involves expressing the entire ectodomain of a receptor as a soluble recombinant protein. The ectodomains are usually purposefully oligomerized so that they can be used as highly avid probes to identify binding partners by expression cloning or biochemical purifications (Wright et al. 2010). More recently...
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Research: Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements
- Luisa Berná,
- Pablo Marquez,
- Andrés Cabrera,
- Gonzalo Greif,
- María E. Francia,
- and Carlos Robello
Genome Res. May 2021 31: 823-833; Published in Advance April 27, 2021, doi:10.1101/gr.262832.120
...characterization of four novel Neospora caninum strains. Parasitol Res 118: 3535–3542. doi:10.1007/s00436-019-06474-9 ↵Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA. 2012. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics...
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Method: Paired-end sequencing of Fosmid libraries by Illumina
- Louise J.S. Williams,
- Diana G. Tabbaa,
- Na Li,
- Aaron M. Berlin,
- Terrance P. Shea,
- Iain MacCallum,
- Michael S. Lawrence,
- Yotam Drier,
- Gad Getz,
- Sarah K. Young,
- David B. Jaffe,
- Chad Nusbaum,
- and Andreas Gnirke
Genome Res. November 2012 22: 2241-2249; Published in Advance July 16, 2012, doi:10.1101/gr.138925.112
...into the cloned insert. (D) The insert is cleaved at the two translated nicks as well as at nicks originating at any BbvCI sites within the genomic DNA sequence. (E) Fragments are circularized by intramolecular ligation. (F ) Recircularized vector molecules serve as templates for inverse PCR with full...
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REPORT: Sequence and Analysis of Chromosome I of the Amitochondriate Intracellular Parasite Encephalitozoon cuniculi (Microspora)
- Pierre Peyret,
- Michael D. Katinka,
- Simone Duprat,
- Francis Duffieux,
- Valérie Barbe,
- Martin Barbazanges,
- Jean Weissenbach,
- William Saurin,
- and Christian P. Vivarès
Genome Res. February 1, 2001 11: 198-207; doi:10.1101/gr.164301
...for cloning. The repetitive elements are composed of alternate G(A or G)GCCT(C or T)CT, GAGCCTTGTTT, and GAGACGCAGTGTTGCCAGGATG. In the pBAM recombinant library (genomic DNA digested by Cvi JI, see Methods), ∼0.1% of the clones exhibited the same repeats but none were found in the pBAC library (genomic DNA...
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LETTER: Characterizing Embryonic Gene Expression Patterns in the Mouse Using Nonredundant Sequence-Based Selection
- Rita Sousa-Nunes,
- Amer Ahmed Rana,
- Ross Kettleborough,
- Joshua M. Brickman,
- Melanie Clements,
- Alistair Forrest,
- Sean Grimmond,
- Philip Avner,
- James C. Smith,
- Sally L. Dunwoodie,
- and Rosa S.P. Beddington
Genome Res. December 2003 13: 2609-2620; Published in Advance January 1, 2003, doi:10.1101/gr.1362303
...., and Herrmann, B.G. 2000 . Large-scale screen for genes controlling mammalian embryogenesis, using high-throughput gene expression analysis in mouse embryos. Mech. Dev. 98 : 77 -94. ↵ Niehrs, C. and Pollet, N. 1999 . Synexpression groups in eukaryotes. Nature 402 : 483 -487. ↵ Nishinakamura, R., Matsumoto, Y...
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INSIGHT/OUTLOOK: The Beautifully Simple but Intriguingly Complex World of Small Genomes
- Sandra W. Clifton and
- Bruce A. Roe
Genome Res. April 1, 1998 8: 331-333; doi:10.1101/gr.8.4.331
...in recombination or gene expression, or they could be genes of unknown function. Partial genomic sequence data also are useful as the available data from the Neisseria gonorrhoeae reveals putative restriction/modification genes that subsequently were cloned and tested. Two of the putative genes were active in vivo...

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