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Items: 1 to 20 of 72

1.

Effect of PCR extension temperature on high-throughput sequencing.

López-Barragán MJ, Quiñones M, Cui K, Lemieux J, Zhao K, Su XZ.

Mol Biochem Parasitol. 2011 Mar;176(1):64-7. doi: 10.1016/j.molbiopara.2010.11.013. Epub 2010 Nov 26.

2.

Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.

Oyola SO, Otto TD, Gu Y, Maslen G, Manske M, Campino S, Turner DJ, Macinnis B, Kwiatkowski DP, Swerdlow HP, Quail MA.

BMC Genomics. 2012 Jan 3;13:1. doi: 10.1186/1471-2164-13-1.

3.

Optimized whole-genome amplification strategy for extremely AT-biased template.

Oyola SO, Manske M, Campino S, Claessens A, Hamilton WL, Kekre M, Drury E, Mead D, Gu Y, Miles A, MacInnis B, Newbold C, Berriman M, Kwiatkowski DP.

DNA Res. 2014 Dec;21(6):661-71. doi: 10.1093/dnares/dsu028. Epub 2014 Sep 19.

4.

Linear amplification for deep sequencing.

Hoeijmakers WA, Bártfai R, Françoijs KJ, Stunnenberg HG.

Nat Protoc. 2011 Jun 23;6(7):1026-36. doi: 10.1038/nprot.2011.345.

PMID:
21720315
5.

Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray.

Jiang H, Yi M, Mu J, Zhang L, Ivens A, Klimczak LJ, Huyen Y, Stephens RM, Su XZ.

BMC Genomics. 2008 Aug 25;9:398. doi: 10.1186/1471-2164-9-398.

6.

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries.

Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, Russ C, Jaffe DB, Nusbaum C, Gnirke A.

Genome Biol. 2011;12(2):R18. doi: 10.1186/gb-2011-12-2-r18. Epub 2011 Feb 21.

7.

Detection of Genomic Polymorphism in Plasmodium falciparum using an arbitrarily primed PCR assay.

Rojas MO, De-Castro J, Mariño G, Wasserman M.

J Eukaryot Microbiol. 1996 Jul-Aug;43(4):323-6.

PMID:
8768436
8.

Analysis of the compositional biases in Plasmodium falciparum genome and proteome using Arabidopsis thaliana as a reference.

Bastien O, Lespinats S, Roy S, Métayer K, Fertil B, Codani JJ, Maréchal E.

Gene. 2004 Jul 21;336(2):163-73.

PMID:
15246528
9.

Microarray-based comparative genomic analyses of the human malaria parasite Plasmodium falciparum using Affymetrix arrays.

Carret CK, Horrocks P, Konfortov B, Winzeler E, Qureshi M, Newbold C, Ivens A.

Mol Biochem Parasitol. 2005 Dec;144(2):177-86. Epub 2005 Sep 8.

PMID:
16174539
10.

The evolution of genomic GC content undergoes a rapid reversal within the genus Plasmodium.

Nikbakht H, Xia X, Hickey DA.

Genome. 2014 Sep;57(9):507-11. doi: 10.1139/gen-2014-0158. Epub 2015 Jan 9.

11.

Reduced extension temperatures required for PCR amplification of extremely A+T-rich DNA.

Su XZ, Wu Y, Sifri CD, Wellems TE.

Nucleic Acids Res. 1996 Apr 15;24(8):1574-5. No abstract available.

12.

Thermal asymmetric interlaced PCR amplification of YAC insert end fragments for chromosome walking in Plasmodium falciparum and other A/T-rich genomes.

Foster JM, Christodoulou Z, Cowan GM, Newbold CI.

Biotechniques. 1999 Aug;27(2):240, 244, 246. No abstract available.

PMID:
10457822
13.

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.

Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y.

BMC Genomics. 2012 Jul 24;13:341. doi: 10.1186/1471-2164-13-341.

14.

An effective method to purify Plasmodium falciparum DNA directly from clinical blood samples for whole genome high-throughput sequencing.

Auburn S, Campino S, Clark TG, Djimde AA, Zongo I, Pinches R, Manske M, Mangano V, Alcock D, Anastasi E, Maslen G, Macinnis B, Rockett K, Modiano D, Newbold CI, Doumbo OK, Ouédraogo JB, Kwiatkowski DP.

PLoS One. 2011;6(7):e22213. doi: 10.1371/journal.pone.0022213. Epub 2011 Jul 18.

15.

Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum.

Gardner MJ, Tettelin H, Carucci DJ, Cummings LM, Aravind L, Koonin EV, Shallom S, Mason T, Yu K, Fujii C, Pederson J, Shen K, Jing J, Aston C, Lai Z, Schwartz DC, Pertea M, Salzberg S, Zhou L, Sutton GG, Clayton R, White O, Smith HO, Fraser CM, Adams MD, Venter JC, Hoffman SL.

Science. 1998 Nov 6;282(5391):1126-32. Erratum in: Science 1998 Dec 4;282(5395):1827.

16.

PCR-based gene synthesis as an efficient approach for expression of the A+T-rich malaria genome.

Withers-Martinez C, Carpenter EP, Hackett F, Ely B, Sajid M, Grainger M, Blackman MJ.

Protein Eng. 1999 Dec;12(12):1113-20.

PMID:
10611405
17.

A screen for conserved sequences with biased base composition identifies noncoding RNAs in the A-T rich genome of Plasmodium falciparum.

Upadhyay R, Bawankar P, Malhotra D, Patankar S.

Mol Biochem Parasitol. 2005 Dec;144(2):149-58. Epub 2005 Sep 9.

PMID:
16183147
18.

Proteome composition in Plasmodium falciparum: higher usage of GC-rich nonsynonymous codons in highly expressed genes.

Chanda I, Pan A, Dutta C.

J Mol Evol. 2005 Oct;61(4):513-23. Epub 2005 Jul 21.

PMID:
16044241
20.

Nucleosome occupancy at transcription start sites in the human malaria parasite: a hard-wired evolution of virulence?

Ponts N, Harris EY, Lonardi S, Le Roch KG.

Infect Genet Evol. 2011 Jun;11(4):716-24. doi: 10.1016/j.meegid.2010.08.002. Epub 2010 Aug 11.

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