Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius

[1]  Michael C. Schatz,et al.  Metassembler: merging and optimizing de novo genome assemblies , 2015, bioRxiv.

[2]  Noah Alexander,et al.  Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics , 2015, Cell systems.

[3]  E. Vargo,et al.  Host association drives genetic divergence in the bed bug, Cimex lectularius , 2015, Molecular ecology.

[4]  Xun Xu,et al.  Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology , 2014, GigaScience.

[5]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[6]  M. Hattori,et al.  Evolutionary origin of insect–Wolbachia nutritional mutualism , 2014, Proceedings of the National Academy of Sciences.

[7]  M. Siddall,et al.  Pyrosequencing the salivary transcriptome of Haemadipsa interrupta (Annelida: Clitellata: Haemadipsidae): anticoagulant diversity and insight into the evolution of anticoagulation capabilities in leeches , 2014 .

[8]  Matthew Fraser,et al.  InterProScan 5: genome-scale protein function classification , 2014, Bioinform..

[9]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[10]  Nicholas H. Putnam,et al.  The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution , 2013, Science.

[11]  Melissa J. Landrum,et al.  RefSeq: an update on mammalian reference sequences , 2013, Nucleic Acids Res..

[12]  Evi X. Stavrou,et al.  Prolylcarboxypeptidase promotes angiogenesis and vascular repair. , 2013, Blood.

[13]  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.

[14]  I. Shagina,et al.  A digestive prolyl carboxypeptidase in Tenebrio molitor larvae. , 2013, Insect biochemistry and molecular biology.

[15]  Gabor T. Marth,et al.  Haplotype-based variant detection from short-read sequencing , 2012, 1207.3907.

[16]  P. Kwok,et al.  Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly , 2012, Nature Biotechnology.

[17]  J. Ribeiro,et al.  An insight into the sialotranscriptome of Triatoma matogrossensis, a kissing bug associated with fogo selvagem in South America. , 2012, The American journal of tropical medicine and hygiene.

[18]  M. Schatz,et al.  Hybrid error correction and de novo assembly of single-molecule sequencing reads , 2012, Nature Biotechnology.

[19]  C. Scheuring,et al.  Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research , 2012, Nature Protocols.

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

[21]  S. Brunak,et al.  SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.

[22]  C. Saisawang,et al.  Insect glutathione transferases , 2011, Drug metabolism reviews.

[23]  B. Slatko,et al.  Recombination in Wolbachia Endosymbionts of Filarial Nematodes? , 2011, Applied and Environmental Microbiology.

[24]  A. Gnirke,et al.  High-quality draft assemblies of mammalian genomes from massively parallel sequence data , 2010, Proceedings of the National Academy of Sciences.

[25]  Klaus Peter Schliep,et al.  phangorn: phylogenetic analysis in R , 2010, Bioinform..

[26]  Taylor J. Maxwell,et al.  Deep resequencing reveals excess rare recent variants consistent with explosive population growth , 2010, Nature communications.

[27]  Patrick J. Biggs,et al.  SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data , 2010, BMC Bioinformatics.

[28]  R. Guralnick,et al.  GeoPhylo: an online tool for developing visualizations of phylogenetic trees in geographic space , 2010 .

[29]  Federico Abascal,et al.  TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations , 2010, Nucleic Acids Res..

[30]  G. K. Davis,et al.  Genome Sequence of the Pea Aphid Acyrthosiphon pisum , 2010, PLoS biology.

[31]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[32]  Daniel J. Blankenberg,et al.  Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists , 2010, Current protocols in molecular biology.

[33]  T. Fukatsu,et al.  Wolbachia as a bacteriocyte-associated nutritional mutualist , 2009, Proceedings of the National Academy of Sciences.

[34]  Eric T. Wang,et al.  An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data , 2009, PLoS Comput. Biol..

[35]  R. Norton,et al.  The toxicogenomic multiverse: convergent recruitment of proteins into animal venoms. , 2009, Annual review of genomics and human genetics.

[36]  R. Kini,et al.  Molecular diversity of anticoagulants from haematophagous animals , 2009, Thrombosis and Haemostasis.

[37]  K. Reinhardt,et al.  Bacteriolytic Activity in the Ejaculate of an Insect , 2009, The American Naturalist.

[38]  Steven J. M. Jones,et al.  Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .

[39]  E. Feil,et al.  How Diverse Is the Genus Wolbachia? Multiple-Gene Sequencing Reveals a Putatively New Wolbachia Supergroup Recovered from Spider Mites (Acari: Tetranychidae) , 2008, Applied and Environmental Microbiology.

[40]  M. Borodovsky,et al.  Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. , 2008, Genome research.

[41]  Ernest K. Lee,et al.  Using whole genome presence/absence data to untangle function in 12 Drosophila genomes , 2008, Fly.

[42]  J. Werren,et al.  Wolbachia: master manipulators of invertebrate biology , 2008, Nature Reviews Microbiology.

[43]  M. Meselson,et al.  Massive Horizontal Gene Transfer in Bdelloid Rotifers , 2008, Science.

[44]  P. Hammerstein,et al.  How many species are infected with Wolbachia? – a statistical analysis of current data , 2008, FEMS microbiology letters.

[45]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[46]  Keith Bradnam,et al.  CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes , 2007, Bioinform..

[47]  Travis E. Oliphant,et al.  Python for Scientific Computing , 2007, Computing in Science & Engineering.

[48]  John D. Hunter,et al.  Matplotlib: A 2D Graphics Environment , 2007, Computing in Science & Engineering.

[49]  A. Loukas,et al.  Molecular cloning and characterization of Ac-MTP-2, an astacin-like metalloprotease released by adult Ancylostoma caninum. , 2007, Molecular and biochemical parasitology.

[50]  M. F. Potter,et al.  Insecticide Resistance in the Bed Bug: A Factor in the Pest’s Sudden Resurgence? , 2007, Journal of medical entomology.

[51]  Rob DeSalle,et al.  Systematic Biology , 2008 .

[52]  H. Harlan Bed Bugs 101: the Basics of Cimex lectularius. , 2006 .

[53]  J. Werren,et al.  Phylogeny of Wolbachia pipientis based on gltA, groEL and ftsZ gene sequences: clustering of arthropod and nematode symbionts in the F supergroup, and evidence for further diversity in the Wolbachia tree. , 2005, Microbiology.

[54]  M. Borodovsky,et al.  Gene identification in novel eukaryotic genomes by self-training algorithm , 2005, Nucleic acids research.

[55]  J. Jurka,et al.  Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.

[56]  Thomas D. Wu,et al.  GMAP: a genomic mapping and alignment program for mRNA and EST sequence , 2005, Bioinform..

[57]  T. Svoboda,et al.  Bed Bug Infestations in an Urban Environment , 2005, Emerging infectious diseases.

[58]  J. Andersen,et al.  The role of salivary lipocalins in blood feeding by Rhodnius prolixus. , 2005, Archives of insect biochemistry and physiology.

[59]  A. Schmaier,et al.  Recombinant prolylcarboxypeptidase activates plasma prekallikrein. , 2004, Blood.

[60]  Ian Korf,et al.  Gene finding in novel genomes , 2004, BMC Bioinformatics.

[61]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[62]  Korbinian Strimmer,et al.  APE: Analyses of Phylogenetics and Evolution in R language , 2004, Bioinform..

[63]  Mario Stanke,et al.  Gene prediction with a hidden Markov model and a new intron submodel , 2003, ECCB.

[64]  J. Ribeiro,et al.  Cloning of a salivary gland metalloprotease and characterization of gelatinase and fibrin(ogen)lytic activities in the saliva of the Lyme disease tick vector Ixodes scapularis. , 2003, Biochemical and biophysical research communications.

[65]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[66]  S. Whelan,et al.  A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. , 2001, Molecular biology and evolution.

[67]  A. Tanaka,et al.  Triapsin, an unusual activatable serine protease from the saliva of the hematophagous vector of Chagas' disease Triatoma infestans (Hemiptera: Reduviidae). , 2001, Insect biochemistry and molecular biology.

[68]  J. Gutiérrez,et al.  Snake venom metalloproteinases: their role in the pathogenesis of local tissue damage. , 2000, Biochimie.

[69]  P. Buckland,et al.  Cimex lectularius L., the common bed bug from Pharaonic Egypt , 1999, Antiquity.

[70]  A. Devonshire,et al.  Evidence that the E4 and FE4 esterase genes responsible for insecticide resistance in the aphid Myzus persicae (Sulzer) are part of a gene family. , 1998, The Biochemical journal.

[71]  C. Walsh,et al.  D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant. , 1997, Biochemistry.

[72]  Ziheng Yang Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods , 1994, Journal of Molecular Evolution.

[73]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[74]  J. Felsenstein CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[75]  K. Mellanby A Comparison of the Physiology of the Two Species of Bed-bug which Attack Man , 1935, Parasitology.

[76]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[77]  M. F. Potter,et al.  The History of Bed Bug Management— With Lessons from the Past , 2011 .

[78]  K. Reinhardt,et al.  Biology of the bed bugs (Cimicidae). , 2007, Annual review of entomology.

[79]  Ernest K. Lee,et al.  OrthologID : automation of genome-scale ortholog identification within a parsimony framework , 2006 .

[80]  A. Bain Irritating Intimates: The Archaeoentomology of Lice, Fleas, and Bedbugs , 2004 .

[81]  Randall T. Schuh,et al.  True bugs of the world (Hemiptera:Heteroptera) : classification and natural history , 1995 .

[82]  J. Ribeiro Role of saliva in blood-feeding by arthropods. , 1987, Annual review of entomology.

[83]  J. Busvine Insecticide-resistance in bed-bugs. , 1958, Bulletin of the World Health Organization.