Molecular tools for studying the major malaria vector Anopheles funestus: improving the utility of the genome using a comparative poly(A) and Ribo-Zero RNAseq analysis

[1]  K. Paaijmans,et al.  Long-lasting insecticidal nets no longer effectively kill the highly resistant Anopheles funestus of southern Mozambique , 2015, Malaria Journal.

[2]  P. Hoen,et al.  Alternative mRNA transcription, processing, and translation: insights from RNA sequencing , 2015 .

[3]  Sandra Gesing,et al.  VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases , 2014, Nucleic Acids Res..

[4]  James E. Allen,et al.  Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes , 2014, Science.

[5]  J. Birungi,et al.  Widespread Pyrethroid and DDT Resistance in the Major Malaria Vector Anopheles funestus in East Africa Is Driven by Metabolic Resistance Mechanisms , 2014, PloS one.

[6]  R. Hunt,et al.  Insecticide resistance and role in malaria transmission of Anopheles funestus populations from Zambia and Zimbabwe , 2014, Parasites & Vectors.

[7]  N. Cuamba,et al.  The highly polymorphic CYP6M7 cytochrome P450 gene partners with the directionally selected CYP6P9a and CYP6P9b genes to expand the pyrethroid resistance front in the malaria vector Anopheles funestus in Africa , 2014, BMC Genomics.

[8]  H. Lehrach,et al.  Influence of RNA extraction methods and library selection schemes on RNA-seq data , 2014, BMC Genomics.

[9]  C. Perou,et al.  Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling , 2014, BMC Genomics.

[10]  Janet Hemingway,et al.  A single mutation in the GSTe2 gene allows tracking of metabolically based insecticide resistance in a major malaria vector , 2014, Genome Biology.

[11]  Susumu Goto,et al.  Data, information, knowledge and principle: back to metabolism in KEGG , 2013, Nucleic Acids Res..

[12]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[13]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[14]  M. Paine,et al.  Directionally selected cytochrome P450 alleles are driving the spread of pyrethroid resistance in the major malaria vector Anopheles funestus , 2012, Proceedings of the National Academy of Sciences.

[15]  Janet Hemingway,et al.  Impact of pyrethroid resistance on operational malaria control in Malawi , 2012, Proceedings of the National Academy of Sciences.

[16]  Zhengwei Zhu,et al.  CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..

[17]  Nadav S. Bar,et al.  Landscape of transcription in human cells , 2012, Nature.

[18]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[19]  Mark Yandell,et al.  MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects , 2011, BMC Bioinformatics.

[20]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[21]  N. Hall,et al.  A De Novo Expression Profiling of Anopheles funestus, Malaria Vector in Africa, Using 454 Pyrosequencing , 2011, PloS one.

[22]  Li Yang,et al.  Genomewide characterization of non-polyadenylated RNAs , 2011, Genome Biology.

[23]  Caroline W. Kabaria,et al.  The dominant Anopheles vectors of human malaria in Africa, Europe and the Middle East: occurrence data, distribution maps and bionomic précis , 2010, Parasites & Vectors.

[24]  Brian P. Lazzaro,et al.  De Novo Transcriptome Sequencing in Anopheles funestus Using Illumina RNA-Seq Technology , 2010, PloS one.

[25]  Songnian Hu,et al.  A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing. , 2010, Genomics.

[26]  Eva C. Winnebeck,et al.  Why Does Insect RNA Look Degraded? , 2010, Journal of insect science.

[27]  J. Morgan,et al.  Pyrethroid Resistance in an Anopheles funestus Population from Uganda , 2010, PloS one.

[28]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[29]  M. Robinson,et al.  A scaling normalization method for differential expression analysis of RNA-seq data , 2010, Genome Biology.

[30]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[31]  E. Wagner,et al.  Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail , 2008, Nature Reviews Genetics.

[32]  Sofia M. C. Robb,et al.  MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. , 2007, Genome research.

[33]  Mark D. Robinson,et al.  Moderated statistical tests for assessing differences in tag abundance , 2007, Bioinform..

[34]  T. Preiss,et al.  Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome. , 2007, RNA.

[35]  J. Krzywinski,et al.  Analysis of the complete mitochondrial DNA from Anopheles funestus: an improved dipteran mitochondrial genome annotation and a temporal dimension of mosquito evolution. , 2006, Molecular phylogenetics and evolution.

[36]  R. Hunt,et al.  Laboratory selection for and characteristics of pyrethroid resistance in the malaria vector Anopheles funestus , 2005, Medical and veterinary entomology.

[37]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[38]  Jian Wang,et al.  The Genome Sequence of the Malaria Mosquito Anopheles gambiae , 2002, Science.

[39]  Eric R. Ziegel,et al.  Generalized Linear Models , 2002, Technometrics.

[40]  D. Kell,et al.  The Kyoto Encyclopedia of Genes and Genomes—KEGG , 2000, Yeast.

[41]  M. Kühl,et al.  XB/U-cadherin mRNA contains cytoplasmic polyadenylation elements and is polyadenylated during oocyte maturation in Xenopus laevis. , 1995, Biochimica et biophysica acta.

[42]  T. D. Schneider,et al.  Sequence logos: a new way to display consensus sequences. , 1990, Nucleic acids research.

[43]  S. S. Wilks.  The Large-Sample Distribution of the Likelihood Ratio for Testing Composite Hypotheses , 1938 .

[44]  P. ’. ‘t Hoen,et al.  Alternative mRNA transcription, processing, and translation: insights from RNA sequencing. , 2015, Trends in genetics : TIG.

[45]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[46]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .