Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis

[1]  C. O'kelly,et al.  Diversity and Evolution of Paramoeba spp. and their Kinetoplastid Endosymbionts , 2017, The Journal of eukaryotic microbiology.

[2]  P. Keeling,et al.  Morphological Identification and Single-Cell Genomics of Marine Diplonemids , 2016, Current Biology.

[3]  K. Gull,et al.  Cilium transition zone proteome reveals compartmentalization and differential dynamics of ciliopathy complexes , 2016, Proceedings of the National Academy of Sciences.

[4]  B. Curtis,et al.  Heme pathway evolution in kinetoplastid protists , 2016, BMC Evolutionary Biology.

[5]  C. Lowe,et al.  Shining a Light on Exploitative Host Control in a Photosynthetic Endosymbiosis , 2016, Current Biology.

[6]  Mark C. Field,et al.  Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism , 2016, Current Biology.

[7]  C. Lowe,et al.  Host control and nutrient trading in a photosynthetic symbiosis. , 2015, Journal of theoretical biology.

[8]  Minoru Kanehisa,et al.  KEGG as a reference resource for gene and protein annotation , 2015, Nucleic Acids Res..

[9]  H. Hashimi,et al.  Gene Loss and Error-Prone RNA Editing in the Mitochondrion of Perkinsela, an Endosymbiotic Kinetoplastid , 2015, mBio.

[10]  S. Kelly,et al.  OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy , 2015, Genome Biology.

[11]  A. Pandey,et al.  Comprehensive proteomics analysis of glycosomes from Leishmania donovani. , 2015, Omics : a journal of integrative biology.

[12]  N. Moran,et al.  Heritable symbiosis: The advantages and perils of an evolutionary rabbit hole , 2015, Proceedings of the National Academy of Sciences.

[13]  P. Michels,et al.  Evolution, dynamics and specialized functions of glycosomes in metabolism and development of trypanosomatids. , 2014, Current opinion in microbiology.

[14]  R. Orlando,et al.  Proteomic Analysis of the Acidocalcisome, an Organelle Conserved from Bacteria to Human Cells , 2014, PLoS pathogens.

[15]  S. Kelly,et al.  SLaP mapper: A webserver for identifying and quantifying spliced-leader addition and polyadenylation site usage in kinetoplastid genomes , 2014, Molecular and biochemical parasitology.

[16]  J. Lukeš,et al.  Evolution of parasitism in kinetoplastid flagellates. , 2014, Molecular and biochemical parasitology.

[17]  K. Hill,et al.  Motility and more: the flagellum of Trypanosoma brucei , 2014, Nature Reviews Microbiology.

[18]  Michael D. Urbaniak,et al.  High-Confidence Glycosome Proteome for Procyclic Form Trypanosoma brucei by Epitope-Tag Organelle Enrichment and SILAC Proteomics , 2014, Journal of proteome research.

[19]  Mark C. Field,et al.  The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants , 2014, PLoS genetics.

[20]  Paul Medvedev,et al.  Informed and automated k-mer size selection for genome assembly , 2013, Bioinform..

[21]  P. Keeling,et al.  The number, speed, and impact of plastid endosymbioses in eukaryotic evolution. , 2013, Annual review of plant biology.

[22]  William S Hancock,et al.  The proteome browser web portal. , 2013, Journal of proteome research.

[23]  J. Archibald,et al.  Treetrimmer: a method for phylogenetic dataset size reduction , 2013, BMC Research Notes.

[24]  F. Raymond,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Ray Meta: scalable de novo metagenome assembly and profiling , 2012 .

[25]  B. Warscheid,et al.  Mitochondrial Outer Membrane Proteome of Trypanosoma brucei Reveals Novel Factors Required to Maintain Mitochondrial Morphology* , 2012, Molecular & Cellular Proteomics.

[26]  M. Mann,et al.  Comparative Proteomics of Two Life Cycle Stages of Stable Isotope-labeled Trypanosoma brucei Reveals Novel Components of the Parasite's Host Adaptation Machinery* , 2012, Molecular & Cellular Proteomics.

[27]  T. Ochsenreiter,et al.  Proteome remodelling during development from blood to insect-form Trypanosoma brucei quantified by SILAC and mass spectrometry , 2012, BMC Genomics.

[28]  M. Fujishima,et al.  Cell division and density of symbiotic Chlorella variabilis of the ciliate Paramecium bursaria is controlled by the host's nutritional conditions during early infection process. , 2012, Environmental microbiology.

[29]  Michael A. J. Ferguson,et al.  Comparative SILAC Proteomic Analysis of Trypanosoma brucei Bloodstream and Procyclic Lifecycle Stages , 2012, PLoS ONE.

[30]  B. Nowak,et al.  In vitro cultured Neoparamoeba perurans causes amoebic gill disease in Atlantic salmon and fulfils Koch's postulates. , 2012, International journal for parasitology.

[31]  Y. Saeys,et al.  GenomeView: a next-generation genome browser , 2011, Nucleic acids research.

[32]  N. Moran,et al.  Extreme genome reduction in symbiotic bacteria , 2011, Nature Reviews Microbiology.

[33]  Sitao Wu,et al.  WebMGA: a customizable web server for fast metagenomic sequence analysis , 2011, BMC Genomics.

[34]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[35]  J. Lukeš,et al.  Genomic Characterization of Neoparamoeba pemaquidensis (Amoebozoa) and Its Kinetoplastid Endosymbiont , 2011, Eukaryotic Cell.

[36]  H. Rodger,et al.  A review of infectious gill disease in marine salmonid fish. , 2011, Journal of fish diseases.

[37]  M. Carrington,et al.  Identification of the meiotic life cycle stage of Trypanosoma brucei in the tsetse fly , 2011, Proceedings of the National Academy of Sciences.

[38]  Walter Pirovano,et al.  BIOINFORMATICS APPLICATIONS , 2022 .

[39]  K. Gull,et al.  Beyond 9+0: noncanonical axoneme structures characterize sensory cilia from protists to humans , 2010, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[40]  Sean R. Eddy,et al.  Hidden Markov model speed heuristic and iterative HMM search procedure , 2010, BMC Bioinformatics.

[41]  F. Silbermann,et al.  The ciliary pocket: an endocytic membrane domain at the base of primary and motile cilia , 2010, Journal of Cell Science.

[42]  M. E. Hodges,et al.  Reconstructing the evolutionary history of the centriole from protein components , 2010, Journal of Cell Science.

[43]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[44]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[45]  Eileen Kraemer,et al.  TriTrypDB: a functional genomic resource for the Trypanosomatidae , 2009, Nucleic Acids Res..

[46]  Mark C. Field,et al.  The trypanosome flagellar pocket , 2009, Nature Reviews Microbiology.

[47]  Toni Gabaldón,et al.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..

[48]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[49]  W. de Souza,et al.  Subcellular proteomics of Trypanosoma cruzi reservosomes , 2009, Proteomics.

[50]  Uzma Alam,et al.  Genomics and Evolution of Microbial Eukaryotes , 2009, The Yale Journal of Biology and Medicine.

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

[52]  I. Fiala,et al.  Neoparamoeba spp. and their eukaryotic endosymbionts similar to Perkinsela amoebae (Hollande, 1980): coevolution demonstrated by SSU rRNA gene phylogenies. , 2008, European journal of protistology.

[53]  J. Stevens.  Kinetoplastid phylogenetics, with special reference to the evolution of parasitic trypanosomes. , 2008, Parasite.

[54]  N. Young,et al.  Neoparamoeba perurans is a cosmopolitan aetiological agent of amoebic gill disease. , 2008, Diseases of aquatic organisms.

[55]  P. Legendre,et al.  Microheterogeneity and Coevolution: An Examination of rDNA Sequence Characteristics in Neoparamoeba pemaquidensis and Its Prokinetoplastid Endosymbiont , 2007, The Journal of eukaryotic microbiology.

[56]  J. Archibald,et al.  Novel Nucleomorph Genome Architecture in the Cryptomonad Genus Hemiselmis , 2006, The Journal of eukaryotic microbiology.

[57]  Alexandros Stamatakis,et al.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..

[58]  L. E. Lee,et al.  High yield and rapid growth of Neoparamoeba pemaquidensis in co-culture with a rainbow trout gill-derived cell line RTgill-W1. , 2006, Journal of fish diseases.

[59]  A. Simpson,et al.  The evolution and diversity of kinetoplastid flagellates. , 2006, Trends in parasitology.

[60]  K. Gull,et al.  Flagellar motility is required for the viability of the bloodstream trypanosome , 2006, Nature.

[61]  D. Rigden,et al.  Autophagy and Related processes in Trypanosomatids: Insights from Genomic and Bioinformatic Analyses , 2006, Autophagy.

[62]  Heather J Munden,et al.  The Genome of the Kinetoplastid Parasite, Leishmania major , 2005, Science.

[63]  Daniel Nilsson,et al.  Comparative Genomics of Trypanosomatid Parasitic Protozoa , 2005, Science.

[64]  David M. A. Martin,et al.  The Genome of the African Trypanosome Trypanosoma brucei , 2005, Science.

[65]  B. Nowak,et al.  Neoparamoeba branchiphila n. sp., and related species of the genus Neoparamoeba Page, 1987: morphological and molecular characterization of selected strains. , 2005, Journal of fish diseases.

[66]  D. Moreira,et al.  An updated view of kinetoplastid phylogeny using environmental sequences and a closer outgroup: proposal for a new classification of the class Kinetoplastea. , 2004, International journal of systematic and evolutionary microbiology.

[67]  H. Philippe,et al.  A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. , 2004, Molecular biology and evolution.

[68]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[69]  W. Martin,et al.  Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes , 2004, Nature Reviews Genetics.

[70]  A. Nylund,et al.  Ichthyobodo necator (Kinetoplastida)--a complex of sibling species. , 2004, Diseases of aquatic organisms.

[71]  F. C. Page.  Paramoeba: A Common Marine Genus , 1973, Hydrobiologia.

[72]  Jodie J. Yin,et al.  A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes , 2004, Genome Biology.

[73]  Michael P Barrett,et al.  The trypanosomiases , 2003, The Lancet.

[74]  Stephen M. Mount,et al.  Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. , 2003, Nucleic acids research.

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

[76]  J. Lukeš,et al.  Perkinsiella amoebae-like endosymbionts of Neoparamoeba spp., relatives of the kinetoplastid Ichthyobodo , 2003 .

[77]  J. Lukeš,et al.  Kinetoplast DNA Network: Evolution of an Improbable Structure , 2002, Eukaryotic Cell.

[78]  R. Litaker,et al.  Molecular Taxonomy of the Suborder Bodonina (Order Kinetoplastida), Including the Important Fish Parasite, Ichthyobodo necator , 2002, The Journal of eukaryotic microbiology.

[79]  A. Fairlamb,et al.  Metabolism and functions of trypanothione in the Kinetoplastida. , 1992, Annual review of microbiology.

[80]  K. Stuart,et al.  RNA editing in kinetoplastid protozoa , 1991, Current opinion in genetics & development.

[81]  M. Castagna,et al.  Ultrastructure of the Nebenkörper or "secondary nucleus" of the parasitic amoeba Paramoeba perniciosa (Amoebida, Paramoebidae). , 1971, Journal of invertebrate pathology.

[82]  F. C. Page.  Two New Species of Paramoeba from Maine , 1970 .

[83]  J. Thiery.  Mise en evidence des polysaccharides sur coupes fines en microscopie electronique , 1967 .