Analyzing Immunity in Non-model Insects Using De Novo Transcriptomics
暂无分享,去创建一个
[1] S. Cherry,et al. Immunity in Drosophila melanogaster — from microbial recognition to whole-organism physiology , 2014, Nature Reviews Immunology.
[2] Eva C. Winnebeck,et al. Why Does Insect RNA Look Degraded? , 2010, Journal of insect science.
[3] J. Hillyer. Insect immunology and hematopoiesis. , 2016, Developmental and comparative immunology.
[4] Charity W. Law,et al. voom: precision weights unlock linear model analysis tools for RNA-seq read counts , 2014, Genome Biology.
[5] N. Stork,et al. How Many Species of Insects and Other Terrestrial Arthropods Are There on Earth? , 2018, Annual review of entomology.
[6] J. Hoffmann,et al. The immune response of Drosophila , 2003, Nature.
[7] D. Haussler,et al. Hidden Markov models in computational biology. Applications to protein modeling. , 1993, Journal of molecular biology.
[8] Shefali Setia,et al. Insect Innate Immunity Database (IIID): An Annotation Tool for Identifying Immune Genes in Insect Genomes , 2012, PloS one.
[9] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[10] Paul Theodor Pyl,et al. HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.
[11] Silvio C. E. Tosatto,et al. The Pfam protein families database in 2019 , 2018, Nucleic Acids Res..
[12] Sean R. Eddy,et al. nhmmer: DNA homology search with profile HMMs , 2013, Bioinform..
[13] Simon C. Potter,et al. The EMBL-EBI search and sequence analysis tools APIs in 2019 , 2019, Nucleic Acids Res..
[14] B. Lemaître,et al. The host defense of Drosophila melanogaster. , 2007, Annual review of immunology.
[15] Robert M. Waterhouse,et al. Evolutionary Dynamics of Immune-Related Genes and Pathways in Disease-Vector Mosquitoes , 2007, Science.
[16] Colin N. Dewey,et al. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.
[17] N. Friedman,et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.
[18] Lior Pachter,et al. Near-optimal probabilistic RNA-seq quantification , 2016, Nature Biotechnology.
[19] Wei Shi,et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..
[20] Sean R. Eddy,et al. Profile hidden Markov models , 1998, Bioinform..
[21] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[22] Colin N. Dewey,et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis , 2013, Nature Protocols.
[23] M. Robinson,et al. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. , 2015, F1000Research.
[24] S. Reynolds,et al. Insect Infection and Immunity: Evolution Ecology and Mechanisms , 2009 .
[25] Barbara Milutinović,et al. Immune priming in arthropods: an update focusing on the red flour beetle. , 2016, Zoology.
[26] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[27] J. Hoffmann,et al. Drosophila innate immunity: an evolutionary perspective , 2002, Nature Immunology.
[28] James Leebens-Mack,et al. Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes , 2012, PloS one.
[29] L. Viljakainen. Evolutionary genetics of insect innate immunity , 2015, Briefings in functional genomics.
[30] S. Eddy,et al. Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions , 2013, Nucleic acids research.
[31] Mark D. Robinson,et al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..
[32] Rob Patro,et al. Salmon provides fast and bias-aware quantification of transcript expression , 2017, Nature Methods.