No more non-model species: the promise of next generation sequencing for comparative immunology.

[1]  Antoine Flahault,et al.  Climate change and infectious diseases , 2016, Public Health Reviews.

[2]  C. Gallardo‐Escárate,et al.  Identification of immune-related SNPs in the transcriptome of Mytilus chilensis through high-throughput sequencing. , 2013, Fish & shellfish immunology.

[3]  Joanne Trgovcich,et al.  Dual Analysis of the Murine Cytomegalovirus and Host Cell Transcriptomes Reveal New Aspects of the Virus-Host Cell Interface , 2013, PLoS pathogens.

[4]  Kirsty Minton.  Immune regulation: Long non-coding RNAs in the immune system , 2013, Nature Reviews Immunology.

[5]  F. Citarella,et al.  Dynamic Nature of Noncoding RNA Regulation of Adaptive Immune Response , 2013, International journal of molecular sciences.

[6]  Daniel R. Caffrey,et al.  A Long Noncoding RNA Mediates Both Activation and Repression of Immune Response Genes , 2013, Science.

[7]  C. Grunau,et al.  Schistosoma mansoni Mucin Gene (SmPoMuc) Expression: Epigenetic Control to Shape Adaptation to a New Host , 2013, PLoS pathogens.

[8]  A. Carvajal,et al.  Single nucleotide polymorphisms in immunity-related genes and their association with mastitis in Chilean dairy cattle. , 2013, Genetics and molecular research : GMR.

[9]  P. Wade,et al.  Epigenetics and the adaptive immune response. , 2013, Molecular aspects of medicine.

[10]  M. Reichelt,et al.  5-methyl-cytosine and 5-hydroxy-methyl-cytosine in the genome of Biomphalaria glabrata, a snail intermediate host of Schistosoma mansoni , 2013, Parasites & Vectors.

[11]  S. Adamo,et al.  Are all eggs created equal? Food availability and the fitness trade-off between reproduction and immunity , 2013 .

[12]  Graham M. Hughes,et al.  Using Illumina next generation sequencing technologies to sequence multigene families in de novo species , 2013, Molecular ecology resources.

[13]  Xinshu Xiao,et al.  Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants. , 2013, RNA.

[14]  D. Allemand,et al.  Genes Related to Ion-Transport and Energy Production Are Upregulated in Response to CO2-Driven pH Decrease in Corals: New Insights from Transcriptome Analysis , 2013, PloS one.

[15]  J. Allienne,et al.  Biomphalysin, a New β Pore-forming Toxin Involved in Biomphalaria glabrata Immune Defense against Schistosoma mansoni , 2013, PLoS pathogens.

[16]  Guangliang Yin,et al.  Whole-genome DNA methylation in skin lesions from patients with psoriasis vulgaris. , 2013, Journal of autoimmunity.

[17]  A. Vilcinskas,et al.  Expansion of the antimicrobial peptide repertoire in the invasive ladybird Harmonia axyridis , 2013, Proceedings of the Royal Society B: Biological Sciences.

[18]  P. Khaitovich,et al.  Birth and expression evolution of mammalian microRNA genes , 2013, Genome research.

[19]  M. Chilvers,et al.  Rapid transcriptome characterization and parsing of sequences in a non-model host-pathogen interaction; pea-Sclerotinia sclerotiorum , 2012, BMC Genomics.

[20]  David S. Schneider,et al.  Where does innate immunity stop and adaptive immunity begin? , 2012, Cell host & microbe.

[21]  R. Chandra,et al.  Anopheles NF-κB-regulated splicing factors direct pathogen-specific repertoires of the hypervariable pattern recognition receptor AgDscam. , 2012, Cell host & microbe.

[22]  A. Westermann,et al.  Dual RNA-seq of pathogen and host , 2012, Nature Reviews Microbiology.

[23]  E. Loker,et al.  Compatibility polymorphism in snail/schistosome interactions: From field to theory to molecular mechanisms. , 2012, Developmental and comparative immunology.

[24]  P. De Vita,et al.  Alternative splicing: enhancing ability to cope with stress via transcriptome plasticity. , 2012, Plant science : an international journal of experimental plant biology.

[25]  N. Weng,et al.  The molecular basis of the memory T cell response: differential gene expression and its epigenetic regulation , 2012, Nature Reviews Immunology.

[26]  Ruslan Medzhitov,et al.  Disease Tolerance as a Defense Strategy , 2012, Science.

[27]  Wenwei Zhang,et al.  Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome , 2012, Nature Biotechnology.

[28]  W. Potts,et al.  Experimental viral evolution to specific host MHC genotypes reveals fitness and virulence trade-offs in alternative MHC types , 2012, Proceedings of the National Academy of Sciences.

[29]  C. Eizaguirre,et al.  Rapid and adaptive evolution of MHC genes under parasite selection in experimental vertebrate populations , 2012, Nature Communications.

[30]  M. Ychou,et al.  A large-scale candidate gene approach identifies SNPs in SOD2 and IL13 as predictive markers of response to preoperative chemoradiation in rectal cancer , 2011, The Pharmacogenomics Journal.

[31]  S. Roberts,et al.  Is There a Relationship between DNA Methylation and Phenotypic Plasticity in Invertebrates? , 2011, Front. Physio..

[32]  Lenwood S. Heath,et al.  ClaMS: A Classifier for Metagenomic Sequences , 2011, Standards in genomic sciences.

[33]  D. Ferrandon,et al.  Le printemps de l’immunité innée couronné à Stockholm - Prix Nobel de Médecine 2011 : Bruce A. Beutler, Jules A. Hoffmann et Ralph M. Steinman , 2011 .

[34]  A. Heddi,et al.  Antimicrobial Peptides Keep Insect Endosymbionts Under Control , 2011, Science.

[35]  Xiongfei Xu,et al.  The microRNA miR-29 controls innate and adaptive immune responses to intracellular bacterial infection by targeting interferon-γ , 2011, Nature Immunology.

[36]  L. Smith,et al.  Invertebrate immune diversity. , 2011, Developmental and comparative immunology.

[37]  A. Fujiyama,et al.  Using the Acropora digitifera genome to understand coral responses to environmental change , 2011, Nature.

[38]  S. Leib,et al.  SNPs in DNA repair genes associated to meningitis and host immune response. , 2011, Mutation research.

[39]  Leon N. Schulte,et al.  Analysis of the host microRNA response to Salmonella uncovers the control of major cytokines by the let‐7 family , 2011, The EMBO journal.

[40]  Arun K. Ramani,et al.  Genome-wide analysis of alternative splicing in Caenorhabditis elegans. , 2011, Genome research.

[41]  J. Derisi,et al.  RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts , 2011, Nucleic acids research.

[42]  Johan T den Dunnen,et al.  New methods for next generation sequencing based microRNA expression profiling , 2010, BMC Genomics.

[43]  Frédéric Delsuc,et al.  Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate , 2010, Science.

[44]  M. Meyerson,et al.  A novel totivirus and piscine reovirus (PRV) in Atlantic salmon (Salmo salar) with cardiomyopathy syndrome (CMS) , 2010, Virology Journal.

[45]  S. Forêt,et al.  The Honey Bee Epigenomes: Differential Methylation of Brain DNA in Queens and Workers , 2010, PLoS biology.

[46]  R. Vierkant,et al.  Associations between SNPs in candidate immune-relevant genes and rubella antibody levels: a multigenic assessment , 2010, BMC Immunology.

[47]  S. Roberts,et al.  DNA methylation patterns provide insight into epigenetic regulation in the Pacific oyster (Crassostrea gigas) , 2010, BMC Genomics.

[48]  Todd H. Oakley,et al.  The Amphimedon queenslandica genome and the evolution of animal complexity , 2010, Nature.

[49]  L. David,et al.  SNP discovery and development of genetic markers for mapping innate immune response genes in common carp (Cyprinus carpio). , 2010, Fish & shellfish immunology.

[50]  C. Zang,et al.  Discrete roles of STAT4 and STAT6 transcription factors in tuning epigenetic modifications and transcription during T helper cell differentiation. , 2010, Immunity.

[51]  David B Goldstein,et al.  Screening the human exome: a comparison of whole genome and whole transcriptome sequencing , 2010, Genome Biology.

[52]  Alok Bhattacharya,et al.  Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood , 2010, BMC Genomics.

[53]  Benjamin M. Wheeler,et al.  The dynamic genome of Hydra , 2010, Nature.

[54]  L. Feuk,et al.  Global and unbiased detection of splice junctions from RNA-seq data , 2010, Genome Biology.

[55]  Chia-Lin Wei,et al.  Dynamic changes in the human methylome during differentiation. , 2010, Genome research.

[56]  Kevin D Lafferty,et al.  The ecology of climate change and infectious diseases. , 2010, Ecology.

[57]  Dawei Li,et al.  The sequence and de novo assembly of the giant panda genome , 2010, Nature.

[58]  Katherine M. Buckley,et al.  Highly diversified innate receptor systems and new forms of animal immunity. , 2010, Seminars in immunology.

[59]  H. Bovenhuis,et al.  Across-line SNP association study of innate and adaptive immune response in laying hens. , 2010, Animal genetics.

[60]  G. Weinstock,et al.  A SNP discovery method to assess variant allele probability from next-generation resequencing data. , 2010, Genome research.

[61]  Gene W. Yeo,et al.  Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans , 2010, Nature Structural &Molecular Biology.

[62]  Dawei Li,et al.  The sequence and de novo assembly of the giant panda genome , 2010, Nature.

[63]  David Serre,et al.  MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome , 2009, Nucleic acids research.

[64]  Jie Lv,et al.  HHMD: the human histone modification database , 2009, Nucleic Acids Res..

[65]  R. Holt,et al.  Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. , 2009, Genome research.

[66]  Ken Chen,et al.  VarScan: variant detection in massively parallel sequencing of individual and pooled samples , 2009, Bioinform..

[67]  D. Allemand,et al.  Comprehensive EST analysis of the symbiotic sea anemone, Anemonia viridis , 2009, BMC Genomics.

[68]  M. Goodisman,et al.  DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera , 2009, Proceedings of the National Academy of Sciences.

[69]  Kristina M Smith,et al.  Native chromatin immunoprecipitation (N-ChIP) and ChIP-Seq of Schistosoma mansoni: Critical experimental parameters. , 2009, Molecular and biochemical parasitology.

[70]  K. Zhao,et al.  Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq , 2009, Nucleic acids research.

[71]  Huanming Yang,et al.  SNP detection for massively parallel whole-genome resequencing. , 2009, Genome research.

[72]  P. Taberlet,et al.  New generation sequencers as a tool for genotyping of highly polymorphic multilocus MHC system , 2009, Molecular ecology resources.

[73]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[74]  L. Smith,et al.  Highly Variable Immune-Response Proteins (185/333) from the Sea Urchin, Strongylocentrotus purpuratus: Proteomic Analysis Identifies Diversity within and between Individuals1 , 2009, The Journal of Immunology.

[75]  Gene W. Yeo,et al.  An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells , 2009, Nature Structural &Molecular Biology.

[76]  B. Chen,et al.  Dscam and DSCAM: complex genes in simple animals, complex animals yet simple genes. , 2009, Genes & development.

[77]  Joachim Kurtz,et al.  Introduction. Ecological immunology , 2009, Philosophical Transactions of the Royal Society B: Biological Sciences.

[78]  B. Frey,et al.  Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing , 2008, Nature Genetics.

[79]  R. Durbin,et al.  Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P

, 2022 .

[80]  S. Reynolds,et al.  Immune function keeps endosymbionts under control , 2008, Journal of biology.

[81]  Eric T. Wang,et al.  Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.

[82]  V. Moulton,et al.  Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. , 2008, Genome research.

[83]  Hanlee P. Ji,et al.  Next-generation DNA sequencing , 2008, Nature Biotechnology.

[84]  W. L. Ruzzo,et al.  MicroRNA Discovery and Profiling in Human Embryonic Stem Cells by Deep Sequencing of Small RNA Libraries , 2008, Stem cells.

[85]  M. Marra,et al.  Applications of next-generation sequencing technologies in functional genomics. , 2008, Genomics.

[86]  Navin Elango,et al.  DNA methylation and structural and functional bimodality of vertebrate promoters. , 2008, Molecular biology and evolution.

[87]  C. S. Sullivan.  New roles for large and small viral RNAs in evading host defences , 2008, Nature Reviews Genetics.

[88]  K. Morris,et al.  The Dscam homologue of the crustacean Daphnia is diversified by alternative splicing like in insects. , 2008, Molecular biology and evolution.

[89]  A. Xu,et al.  Genomic analysis of the immune gene repertoire of amphioxus reveals extraordinary innate complexity and diversity. , 2008, Genome research.

[90]  R. Durbin,et al.  A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis , 2008, Nature Biotechnology.

[91]  Robert J. Moore,et al.  A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. , 2008, Genome research.

[92]  J. Rast,et al.  Marine Invertebrate Genome Sequences and Our Evolving Understanding of Animal Immunity , 2008, The Biological Bulletin.

[93]  E. Loker,et al.  Expression profiling and binding properties of fibrinogen-related proteins (FREPs), plasma proteins from the schistosome snail host Biomphalaria glabrata , 2008, Innate immunity.

[94]  M. Mindrinos,et al.  SNP discovery and molecular evolution in Anopheles gambiae, with special emphasis on innate immune system , 2008, BMC Genomics.

[95]  J. Marden,et al.  Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing , 2008, Molecular ecology.

[96]  V. Kunin,et al.  CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea , 2008, Nature Reviews Microbiology.

[97]  Gabor T. Marth,et al.  Pyrobayes: an improved base caller for SNP discovery in pyrosequences , 2008, Nature Methods.

[98]  Matthew E Hudson,et al.  Sequencing breakthroughs for genomic ecology and evolutionary biology , 2008, Molecular ecology resources.

[99]  Matthew E Hudson,et al.  Wasp Gene Expression Supports an Evolutionary Link Between Maternal Behavior and Eusociality , 2007, Science.

[100]  T. Bosch,et al.  The evolution of immunity: a low-life perspective. , 2007, Trends in immunology.

[101]  P. Cossart,et al.  Histone modifications induced by a family of bacterial toxins , 2007, Proceedings of the National Academy of Sciences.

[102]  Olivier Voinnet,et al.  Antiviral Immunity Directed by Small RNAs , 2007, Cell.

[103]  Nicholas H. Putnam,et al.  Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization , 2007, Science.

[104]  F. Jiggins,et al.  The age and evolution of an antiviral resistance mutation in Drosophila melanogaster , 2007, Proceedings of the Royal Society B: Biological Sciences.

[105]  Adrian Bird,et al.  CpG methylation is targeted to transcription units in an invertebrate genome. , 2007, Genome research.

[106]  David J. Miller,et al.  The innate immune repertoire in Cnidaria - ancestral complexity and stochastic gene loss , 2007, Genome Biology.

[107]  Qun Pan,et al.  Global analysis of alternative splicing during T-cell activation. , 2007, RNA.

[108]  D. Campbell-Lendrum,et al.  Global climate change: implications for international public health policy. , 2007, Bulletin of the World Health Organization.

[109]  Katherine M. Buckley,et al.  Distinctive expression patterns of 185/333 genes in the purple sea urchin, Strongylocentrotus purpuratus: an unexpectedly diverse family of transcripts in response to LPS, β-1,3-glucan, and dsRNA , 2007, BMC Molecular Biology.

[110]  Jonathan P. Bollback,et al.  The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing , 2007, PloS one.

[111]  Katherine M. Buckley,et al.  The immune gene repertoire encoded in the purple sea urchin genome. , 2006, Developmental biology.

[112]  J. Rast,et al.  Genomic Insights into the Immune System of the Sea Urchin , 2006, Science.

[113]  D. Baltimore,et al.  NF-κB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses , 2006, Proceedings of the National Academy of Sciences.

[114]  H. Taylor,et al.  AgDscam, a Hypervariable Immunoglobulin Domain-Containing Receptor of the Anopheles gambiae Innate Immune System , 2006, PLoS biology.

[115]  F. Ausubel.  Are innate immune signaling pathways in plants and animals conserved? , 2005, Nature Immunology.

[116]  M. Kondo,et al.  Extensive Diversity of Ig-Superfamily Proteins in the Immune System of Insects , 2005, Science.

[117]  L. Smith,et al.  Macroarray analysis of coelomocyte gene expression in response to LPS in the sea urchin. Identification of unexpected immune diversity in an invertebrate. , 2005, Physiological genomics.

[118]  Kristen W. Lynch,et al.  Consequences of regulated pre-mRNA splicing in the immune system , 2004, Nature Reviews Immunology.

[119]  E. Loker,et al.  Representation of an immune responsive gene family encoding fibrinogen-related proteins in the freshwater mollusc Biomphalaria glabrata, an intermediate host for Schistosoma mansoni. , 2004, Gene.

[120]  Sue Kong,et al.  Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system , 2004, BMC Genomics.

[121]  A. Emery,et al.  THE MITOCHONDRIAL GENOME OF BIOMPHALARIA GLABRATA (GASTROPODA: BASOMMATOPHORA), INTERMEDIATE HOST OF SCHISTOSOMA MANSONI* , 2004, The Journal of parasitology.

[122]  T. Kepler,et al.  Invertebrate immune systems – not homogeneous, not simple, not well understood , 2004, Immunological reviews.

[123]  R. Saint,et al.  EST Analysis of the Cnidarian Acropora millepora Reveals Extensive Gene Loss and Rapid Sequence Divergence in the Model Invertebrates , 2003, Current Biology.

[124]  Thomas E. Royce,et al.  Distribution of NF-κB-binding sites across human chromosome 22 , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[125]  B. Turner,et al.  Immunoprecipitation of native chromatin: NChIP. , 2003, Methods.

[126]  R. Gaynor,et al.  Histone H3 phosphorylation by IKK-α is critical for cytokine-induced gene expression , 2003, Nature.

[127]  E. Loker,et al.  The FREP gene family in the snail Biomphalaria glabrata: additional members, and evidence consistent with alternative splicing and FREP retrosequences. Fibrinogen-related proteins. , 2003, Developmental and comparative immunology.

[128]  N. Burdin,et al.  How Microarrays Can Improve Our Understanding of Immune Responses and Vaccine Development , 2002, Annals of the New York Academy of Sciences.

[129]  P. Gross,et al.  Diversity of the penaeidin antimicrobial peptides in two shrimp species , 2002, Immunogenetics.

[130]  R. Ostfeld,et al.  Climate Warming and Disease Risks for Terrestrial and Marine Biota , 2002, Science.

[131]  S. Eddy.  Non–coding RNA genes and the modern RNA world , 2001, Nature Reviews Genetics.

[132]  Paul T. Spellman,et al.  Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[133]  P. Hraber,et al.  On the species of origin: diagnosing the source of symbiotic transcripts , 2001, Genome Biology.

[134]  Christopher J. Lee,et al.  Genome-wide detection of alternative splicing in expressed sequences of human genes , 2001, Nucleic Acids Res..

[135]  Albert Jeltsch,et al.  DNA of Drosophila melanogaster contains 5‐methylcytosine , 2000, The EMBO journal.

[136]  J. Patz,et al.  Effects of environmental change on emerging parasitic diseases. , 2000, International journal for parasitology.

[137]  J. C. Clemens,et al.  Drosophila Dscam Is an Axon Guidance Receptor Exhibiting Extraordinary Molecular Diversity , 2000, Cell.

[138]  Stephen M. Mount,et al.  The genome sequence of Drosophila melanogaster. , 2000, Science.

[139]  Gabor T. Marth,et al.  A general approach to single-nucleotide polymorphism discovery , 1999, Nature Genetics.

[140]  Eva Jablonka,et al.  The Role of DNA Methylation in Invertebrates: Developmental Regulation or Genome Defense? , 1998 .

[141]  M. Tomita,et al.  CpG distribution patterns in methylated and non-methylated species. , 1997, Gene.

[142]  R. Miller,et al.  A family of fibrinogen-related proteins that precipitates parasite-derived molecules is produced by an invertebrate after infection. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[143]  B. Sheldon,et al.  Ecological immunology: costly parasite defences and trade-offs in evolutionary ecology. , 1996, Trends in ecology & evolution.

[144]  V. J. Simpson,et al.  Caenorhabditis elegans DNA does not contain 5-methylcytosine at any time during development or aging. , 1986, Nucleic acids research.

[145]  A. Bird,et al.  Methylated and unmethylated DNA compartments in the sea urchin genome , 1979, Cell.

[146]  L. Rather,et al.  Lectures on the Comparative Pathology of Inflammation , 1970, Medical History.

[147]  N. Gay,et al.  University of Birmingham Toll-6 and Toll-7 function as neurotrophin receptors in the Drosophila melanogaster CNS , 2013 .

[148]  B. A. Stout,et al.  Differential transcriptomic responses of Biomphalaria glabrata (Gastropoda, Mollusca) to bacteria and metazoan parasites, Schistosoma mansoni and Echinostoma paraensei (Digenea, Platyhelminthes). , 2010, Molecular immunology.

[149]  A. Rai,et al.  Immune response biomarker profiling application on ProtoArray protein microarrays. , 2010, Methods in molecular biology.

[150]  Matthew Mort,et al.  Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. , 2009, Genome research.

[151]  B. Degnan,et al.  An ancient and variable mannose-binding lectin from the coral Acropora millepora binds both pathogens and symbionts. , 2008, Developmental and comparative immunology.

[152]  T. Wood,et al.  Toll-like receptor genes (TLRs) from Capitella capitata and Helobdella robusta (Annelida). , 2008, Developmental and comparative immunology.

[153]  J. G. Patton,et al.  Alternative splicing is an efficient mechanism for the generation of protein diversity: contractile protein genes as a model system. , 1991, Advances in enzyme regulation.

[154]  E. Cooper.  Why developmental and comparative immunology , 1977 .