text:
relationships among whales to the results of a Bremer support sensitivity analysis and of a recently developed application of RASA theory to the question of putative outgroup taxon plesiomorphy content.},
author = {Milinkovitch, M C and Lyons-Weiler, J},
doi = {10.1006/mpev.1998.0503},
file = {:home/fin/Documents/papers/mendeley/Milinkovitch, Lyons-Weiler\_1998\_Finding optimal ingroup topologies and convexities when the choice of outgroups is not obvious.\_Molecula.pdf:pdf},
issn = {1055-7903},
journal = {Mol. Phylogenet. Evol.},
keywords = {bremer support,convexity,molecular,outgroup rooting,rasa,sensitivity analysis,topology},
number = {3},
pages = {348--357},
pmid = {9667982},
title = {{Finding optimal ingroup topologies and convexities when the choice of outgroups is not obvious.}},
volume = {9},
year = {1998}
}
@article{Sana2008,
abstract = {In an effort to simplify and streamline compound identification from metabolomics data generated by liquid chromatography time-of-flight mass spectrometry, we have created software for constructing Personalized Metabolite Databases with content from over 15,000 compounds pulled from the public METLIN database (http://metlin.scripps.edu/). Moreover, we have added extra functionalities to the database that (a) permit the addition of user-defined retention times as an orthogonal searchable parameter to complement accurate mass data; and (b) allow interfacing to separate software, a Molecular Formula Generator (MFG), that facilitates reliable interpretation of any database matches from the accurate mass spectral data. To test the utility of this identification strategy, we added retention times to a subset of masses in this database, representing a mixture of 78 synthetic urine standards. The synthetic mixture was analyzed and screened against this METLIN urine database, resulting in 46 accurate mass and retention time matches. Human urine samples were subsequently analyzed under the same analytical conditions and screened against this database. A total of 1387 ions were detected in human urine; 16 of these ions matched both accurate mass and retention time parameters for the 78 urine standards in the database. Another 374 had only an accurate mass match to the database, with 163 of those masses also having the highest MFG score. Furthermore, MFG calculated a formula for a further 849 ions that had no match to the database. Taken together, these results suggest that the METLIN Personal Metabolite database and MFG software offer a robust strategy for confirming the formula of database matches. In the event of no database match, it also suggests possible formulas that may be helpful in interpreting the experimental results.},
author = {Sana, Theodore R and Roark, Joseph C and Li, Xiangdong and Waddell, Keith and Fischer, Steven M},
file = {:home/fin/Documents/papers/mendeley/Sana et al.\_2008\_Molecular formula and METLIN Personal Metabolite Database matching applied to the identification of compounds generated.pdf:pdf},
journal = {J. Biomol. Tech.},
pages = {258--266},
title = {{Molecular formula and METLIN Personal Metabolite Database matching applied to the identification of compounds generated by LC/TOF-MS.}},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed\&id=19137116\&retmode=ref\&cmd=prlinks papers3://publication/uuid/D7F177D8-BEB4-420F-BF56-4C3864212D47},
volume = {19},
year = {2008}
}
@article{Brent2007,
abstract = {Computational prediction of gene structure is crucial for interpreting genomic sequences. But how do the algorithms involved work and how accurate are they?},
author = {Brent, Michael R},
doi = {10.1038/nbt0807-883},
file = {:home/fin/Documents/papers/mendeley/Brent\_2007\_How does eukaryotic gene prediction work\_Nature biotechnology.pdf:pdf},
isbn = {1087-0156 (Print)},
issn = {1087-0156},
journal = {Nat. Biotechnol.},
number = {8},
pages = {883--885},
pmid = {17687368},
title = {{How does eukaryotic gene prediction work?}},
volume = {25},
year = {2007}
}
@article{Sievers2011,
abstract = {Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.},
author = {Sievers, Fabian and Wilm, Andreas and Dineen, David and Gibson, Toby J and Karplus, Kevin and Li, Weizhong and Lopez, Rodrigo and McWilliam, Hamish and Remmert, Michael and S\"{o}ding, Johannes and Thompson, Julie D and Higgins, Desmond G},
doi = {10.1038/msb.2011.75},
file = {:home/fin/Documents/papers/mendeley/Sievers et al.\_2011\_Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega\_Molecular Systems.pdf:pdf},
isbn = {1744-4292 (Electronic)$\backslash$r1744-4292 (Linking)},
issn = {1744-4292},
journal = {Mol. Syst. Biol.},
keywords = {bioinformatics,hidden markov models,multiple sequence alignment},
number = {539},
pmid = {21988835},
title = {{Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega}},
volume = {7},
year = {2011}
}
@article{Martin1998b,
abstract = {Organelle genome reduction and its impact on plant cells is summarized with examples of gene transfer to the nucleus from both plastids and mitochondria. Factors which may influence the immediate fate of genes that become transferred to the nucleus and factors which may help to determine whether such transfer events become genetically fixed are considered.},
author = {Martin, W. and Herrmann, R. G.},
doi = {10.1104/pp.118.1.9},
file = {:home/fin/Documents/papers/mendeley/Martin, Herrmann\_1998\_Gene Transfer from Organelles to the Nucleus How Much, What Happens, and Why\_Plant physiology.pdf:pdf},
isbn = {0032-0889},
issn = {1532-2548},
journal = {Plant Physiol.},
number = {1},
pages = {9--17},
pmid = {9733521},
title = {{Gene Transfer from Organelles to the Nucleus: How Much, What Happens, and Why?}},
volume = {118},
year = {1998}
}
@article{Schwartz1976,
author = {Schwartz, Robert M and Dayhoff, Margaret O},
file = {:home/fin/Documents/papers/mendeley/Schwartz, Dayhoff\_1976\_Origins of Prokaryotes, Eukaryotes, Mitochondria, and Chloroplasts\_Science.pdf:pdf},
journal = {Science (80-. ).},
number = {January},
pages = {395--403},
title = {{Origins of Prokaryotes, Eukaryotes, Mitochondria, and Chloroplasts}},
volume = {199},
year = {1976}
}
@article{Rost2004,
author = {Rost, B. and Yachdav, G. and Liu, J.},
doi = {10.1093/nar/gkh377},
file = {:home/fin/Documents/papers/mendeley/Rost, Yachdav, Liu\_2004\_The PredictProtein server\_Nucleic Acids Research.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
pages = {W321--W326},
title = {{The PredictProtein server}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkh377},
volume = {32},
year = {2004}
}
@article{Molnar2014,
author = {Molnar, M. and Ilie, L.},
doi = {10.1093/bib/bbu029},
file = {:home/fin/Documents/papers/mendeley/Molnar, Ilie\_2014\_Correcting Illumina data\_Briefings in Bioinformatics.pdf:pdf},
issn = {1467-5463},
journal = {Brief. Bioinform.},
keywords = {coverage breadth,coverage depth,dna sequencing,error correction,illumina data},
title = {{Correcting Illumina data}},
url = {http://bib.oxfordjournals.org/cgi/doi/10.1093/bib/bbu029},
year = {2014}
}
@article{Guarnieri2011,
abstract = {Biofuels derived from algal lipids represent an opportunity to dramatically impact the global energy demand for transportation fuels. Systems biology analyses of oleaginous algae could greatly accelerate the commercialization of algal-derived biofuels by elucidating the key components involved in lipid productivity and leading to the initiation of hypothesis-driven strain-improvement strategies. However, higher-level systems biology analyses, such as transcriptomics and proteomics, are highly dependent upon available genomic sequence data, and the lack of these data has hindered the pursuit of such analyses for many oleaginous microalgae. In order to examine the triacylglycerol biosynthetic pathway in the unsequenced oleaginous microalga, Chlorella vulgaris, we have established a strategy with which to bypass the necessity for genomic sequence information by using the transcriptome as a guide. Our results indicate an upregulation of both fatty acid and triacylglycerol biosynthetic machinery under oil-accumulating conditions, and demonstrate the utility of a de novo assembled transcriptome as a search model for proteomic analysis of an unsequenced microalga.},
author = {Guarnieri, Michael T. and Nag, Ambarish and Smolinski, Sharon L. and Darzins, Al and Seibert, Michael and Pienkos, Philip T.},
doi = {10.1371/journal.pone.0025851},
file = {:home/fin/Documents/papers/mendeley/Guarnieri et al.\_2011\_Examination of triacylglycerol biosynthetic pathways via de novo transcriptomic and proteomic analyses in an unseq.pdf:pdf},
isbn = {1932-6203},
issn = {19326203},
journal = {PLoS One},
number = {10},
pmid = {22043295},
title = {{Examination of triacylglycerol biosynthetic pathways via de novo transcriptomic and proteomic analyses in an unsequenced microalga}},
volume = {6},
year = {2011}
}
@article{Blanc2010,
abstract = {Chlorella variabilis NC64A, a unicellular photosynthetic green alga (Trebouxiophyceae), is an intracellular photobiont of Paramecium bursaria and a model system for studying virus/algal interactions. We sequenced its 46-Mb nuclear genome, revealing an expansion of protein families that could have participated in adaptation to symbiosis. NC64A exhibits variations in GC content across its genome that correlate with global expression level, average intron size, and codon usage bias. Although Chlorella species have been assumed to be asexual and nonmotile, the NC64A genome encodes all the known meiosis-specific proteins and a subset of proteins found in flagella. We hypothesize that Chlorella might have retained a flagella-derived structure that could be involved in sexual reproduction. Furthermore, a survey of phytohormone pathways in chlorophyte algae identified algal orthologs of Arabidopsis thaliana genes involved in hormone biosynthesis and signaling, suggesting that these functions were established prior to the evolution of land plants. We show that the ability of Chlorella to produce chitinous cell walls likely resulted from the capture of metabolic genes by horizontal gene transfer from algal viruses, prokaryotes, or fungi. Analysis of the NC64A genome substantially advances our understanding of the green lineage evolution, including the genomic interplay with viruses and symbiosis between eukaryotes.},
author = {Blanc, Guillaume and Duncan, Garry and Agarkova, Irina and Borodovsky, Mark and Gurnon, James and Kuo, Alan and Lindquist, Erika and Lucas, Susan and Pangilinan, Jasmyn and Polle, Juergen and Salamov, Asaf and Terry, Astrid and Yamada, Takashi and Dunigan, David D and Grigoriev, Igor V and Claverie, Jean-Michel and {Van Etten}, James L},
doi = {10.1105/tpc.110.076406},
file = {:home/fin/Documents/papers/mendeley/Blanc et al.\_2010\_The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex..pdf:pdf},
issn = {1532-298X},
journal = {Plant Cell},
keywords = {Base Composition,Cell Wall,Cell Wall: metabolism,Chlorella,Chlorella: genetics,Chlorella: virology,DNA, Plant,DNA, Plant: genetics,Evolution, Molecular,Expressed Sequence Tags,Flagella,Flagella: genetics,Genome, Plant,Molecular Sequence Data,Multigene Family,Plant Growth Regulators,Plant Growth Regulators: genetics,Repetitive Sequences, Nucleic Acid,Reproduction,Sequence Analysis, DNA,Symbiosis},
month = sep,
number = {9},
pages = {2943--55},
pmid = {20852019},
title = {{The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2965543\&tool=pmcentrez\&rendertype=abstract},
volume = {22},
year = {2010}
}
@article{Alvarez-Loayza2011,
abstract = {Pathogens are hypothesized to play an important role in the maintenance of tropical forest plant species richness. Notably, species richness may be promoted by incomplete filling of niche space due interactions of host populations with their pathogens. A potentially important group of pathogens are endophytic fungi, which asymptomatically colonize plants and are diverse and abundant in tropical ecosystems. Endophytes may alter competitive abilities of host individuals and improve host fitness under stress, but may also become pathogenic. Little is known of the impacts of endophytes on niche-space filling of their hosts.Here we evaluate how a widespread fungal endophyte infecting a common tropical palm influences its recruitment and survival in natural ecosystems, and whether this impact is modulated by the abiotic environment, potentially constraining host niche-space filling. Iriartea deltoidea dominates many wet lowland Neotropical forests. Diplodia mutila is a common asymptomatic endophyte in mature plants; however, it causes disease in some seedlings. We investigated the effects of light availability on D. mutila disease expression.We found I. deltoidea seedlings to preferentially occur under shady conditions. Correspondingly, we also found that high light triggers endophyte pathogenicity, while low light favors endosymbiotic development, constraining recruitment of endophyte-infested seedlings to shaded understory by reducing seedling survival in direct light. Pathogenicity of D. mutila under high light is proposed to result from light-induced production of H(2)O(2) by the fungus, triggering hypersensitivity, cell death, and tissue necrosis in the palm. This is the first study to demonstrate that endophytes respond to abiotic factors to influence plant distributions in natural ecosystems; and the first to identify light as a factor influencing where an endophyte is placed on the endosymbiont-pathogen continuum. Our findings show that pathogens can indeed constrain niche-space filling of otherwise successful tropical plant species, providing unoccupied niche space for other species.},
author = {\'{A}lvarez-Loayza, Patricia and White, James F. and Torres, M\'{o}nica S. and Balslev, Henrik and Kristiansen, Thea and Svenning, Jens Christian and Gil, Nathalie},
doi = {10.1371/journal.pone.0016386},
file = {:home/fin/Documents/papers/mendeley/\'{A}lvarez-Loayza et al.\_2011\_Light converts endosymbiotic fungus to pathogen, influencing seedling survival and niche-space filling of a.pdf:pdf},
isbn = {1932-6203; 1932-6203},
issn = {19326203},
journal = {PLoS One},
number = {1},
pmid = {21305008},
title = {{Light converts endosymbiotic fungus to pathogen, influencing seedling survival and niche-space filling of a common tropical tree, Iriartea deltoidea}},
volume = {6},
year = {2011}
}
@article{Smith1981,
abstract = {The identification of maximally homologous subsequences among sets of long sequences is an important problem in molecular sequence analysis. The problem is straightforward only if one restricts consideration to contiguous subsequences (segments) containing no internal deletions or insertions. The more general problem has its solution in an extension of sequence metrics (Sellers 1974; Waterman et al., 1976) developed to measure the minimum number of “events” required to convert one sequence into another. These developments in the modern sequence analysis began with the heuristic homology algorithm of Needleman \& Wunsch (1970) which first introduced an iterative matrix method of calculation. Numerous other heuristic algorithms have been suggested including those of Fitch (1966) and Dayhoff (1969). More mathemat- ically rigorous algorithms were suggested by Sankoff (1972), Reichert et al. (1973) and Beyer et al. (1979) but these were generally not biologically satisfying or interpretable. Success came with Sellers (1974) development of a true metric measure of the distance between sequences. This metric was later generalized by Waterman et al. (1976) to include deletions/insertions of arbitrary length. This metric represents the minimum number of “mutational events” required to convert one sequence into another. It is of interest to note that Smith et al. (1980) have recently shown that under some conditions the generalized Sellers metric is equivalent to the original homology algorithm of Needleman \& Wunsch (1970). In this letter we extend the above ideas to find a pair of segments, one from each of two long sequences, such that there is no other pair of segments with greater similarity (homology). The similarity measure used here allows for arbitrary length deletions and insertions.},
author = {Smith, T. and Waterman, M.},
doi = {10.1016/0022-2836(81)90087-5},
file = {:home/fin/Documents/papers/mendeley/Smith, Waterman\_1981\_Identification of common molecular subsequences\_Journal of Molecular Biology.pdf:pdf},
isbn = {0022-2836},
issn = {00222836},
journal = {J. Mol. Biol.},
pages = {195--197},
pmid = {7265238},
title = {{Identification of common molecular subsequences}},
url = {http://dx.doi.org/10.1016/0022-2836(81)90087-5},
volume = {147},
year = {1981}
}
@article{Summerer2009,
abstract = {We assessed the photoprotective role of symbiotic Chlorella in the ciliate Paramecium bursaria by comparing their sensitivity to UV radiation (UVR) with Chlorella-reduced and Chlorella-free (aposymbiotic) cell lines of the same species. Aposymbiotic P. bursaria had significantly higher mortality than the symbiotic cell lines when exposed to UVR. To elucidate the protection mechanism, we assessed the algal distribution within the ciliate using thin-sections and transmission electron microscopy and estimated the screening factor by Chlorella based on an optical model. These analyses evidenced a substantial screening factor ranging, from 59.2\% to 93.2\% (320nm) for regular algal distribution. This screening efficiency reached up to approximately 100\% when Chlorella algae were dislocated to the posterior region of the ciliate. The dislocation was observed in symbiotic ciliates only under exposure to UV plus photosynthetically active radiation (PAR) or to high PAR levels. Moreover, under exposure to UVB radiation and high PAR, symbiotic P. bursaria aggregated into dense spots. This behavior could represent an efficient avoidance strategy not yet described for ciliates. Analyses of the intact symbiosis and their algal symbionts for UV-screening compounds (mycosporine-like amino acids and sporopollenin) proved negative. Overall, our results show that photoprotection in this ciliate symbiosis represents an additional advantage to the hitherto postulated nutritional benefits.},
author = {Summerer, Monika and Sonntag, Bettina and H\"{o}rtnagl, Paul and Sommaruga, Ruben},
doi = {10.1016/j.protis.2008.11.005},
file = {:home/fin/Documents/papers/mendeley/Summerer et al.\_2009\_Symbiotic ciliates receive protection against UV damage from their algae a test with Paramecium bursaria and Chlore.pdf:pdf},
issn = {1618-0941},
journal = {Protist},
keywords = {Animals,Chlorella,Chlorella: physiology,Chlorella: ultrastructure,Microscopy, Electron, Transmission,Paramecium,Paramecium: physiology,Paramecium: radiation effects,Paramecium: ultrastructure,Symbiosis,Ultraviolet Rays},
month = may,
number = {2},
pages = {233--43},
pmid = {19195930},
title = {{Symbiotic ciliates receive protection against UV damage from their algae: a test with Paramecium bursaria and Chlorella.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19195930},
volume = {160},
year = {2009}
}
@article{Brightwell2004,
abstract = {We show that the problem of counting the number of Eulerian circuits in an undirected graph is complete for the class P.},
archivePrefix = {arXiv},
arxivId = {cs/0405067},
author = {Brightwell, Graham R and Winkler, Peter},
eprint = {0405067},
file = {:home/fin/Documents/papers/mendeley/Brightwell, Winkler\_2004\_Note on Counting Eulerian Circuits\_Symposium A Quarterly Journal In Modern Foreign Literatures.pdf:pdf},
journal = {Symp. A Q. J. Mod. Foreign Lit.},
pages = {1--7},
primaryClass = {cs},
title = {{Note on Counting Eulerian Circuits}},
url = {http://arxiv.org/abs/cs/0405067},
year = {2004}
}
@article{Yashchenko2012,
abstract = {Paramecium bursaria Chlorella viruses were observed by applying transmission electron microscopy in the native symbiotic system Paramecium bursaria (Ciliophora, Oligohymenophorea) and the green algae Chlorella (Chlorellaceae, Trebouxiophyceae). Virus particles were abundant and localized in the ciliary pits of the cortex and in the buccal cavity of P. bursaria. This was shown for two types of the symbiotic systems associated with two types of Chlorella viruses - Pbi or NC64A. A novel quantitative stereological approach was applied to test whether virus particles were distributed randomly on the Paramecium surface or preferentially occupied certain zones. The ability of the virus to form an association with the ciliate was investigated experimentally; virus particles were mixed with P. bursaria or with symbiont-free species P. caudatum. Our results confirmed that in the freshwater ecosystems two types of P. bursaria -Chlorella symbiotic systems exist, those without Chlorella viruses and those associated with a large amount of the viruses. The fate of Chlorella virus particles at the Paramecium surface was determined based on obtained statistical data and taking into account ciliate feeding currents and cortical reorganization during cell division. A life cycle of the viruses in the complete symbiotic system is proposed.},
author = {Yashchenko, Varvara V and Gavrilova, Olga V and Rautian, Maria S and Jakobsen, Kjetill S},
doi = {10.1016/j.ejop.2011.05.002},
file = {:home/fin/Documents/papers/mendeley/Yashchenko et al.\_2012\_Association of Paramecium bursaria Chlorella viruses with Paramecium bursaria cells ultrastructural studies.\_Euro.pdf:pdf},
issn = {1618-0429},
journal = {Eur. J. Protistol.},
keywords = {Chlorella,Chlorella: virology,Electron,Microscopy,Paramecium,Paramecium: parasitology,Paramecium: ultrastructure,Paramecium: virology,Transmission,Virion,Virion: physiology,Virion: ultrastructure,Virus Attachment},
month = may,
number = {2},
pages = {149--59},
pmid = {21700436},
publisher = {Elsevier GmbH},
title = {{Association of Paramecium bursaria Chlorella viruses with Paramecium bursaria cells: ultrastructural studies.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21700436},
volume = {48},
year = {2012}
}
@article{Mockler2005,
abstract = {DNA microarrays are a well-established technology for measuring gene expression levels. Microarrays designed for this purpose use relatively few probes for each gene and are biased toward known and predicted gene structures. Recently, high-density oligonucleotide-based whole-genome microarrays have emerged as a preferred platform for genomic analysis beyond simple gene expression profiling. Potential uses for such whole-genome arrays include empirical annotation of the transcriptome, chromatin-immunoprecipitation-chip studies, analysis of alternative splicing, characterization of the methylome (the methylation state of the genome), polymorphism discovery and genotyping, comparative genome hybridization, and genome resequencing. Here we review different whole-genome microarray designs and applications of this technology to obtain a wide variety of genomic scale information. ?? 2004 Elsevier Inc. All rights reserved.},
author = {Mockler, Todd C. and Ecker, Joseph R.},
doi = {10.1016/j.ygeno.2004.10.005},
file = {:home/fin/Documents/papers/mendeley/Mockler, Ecker\_2005\_Applications of DNA tiling arrays for whole-genome analysis\_Genomics.pdf:pdf},
isbn = {0888-7543},
issn = {08887543},
journal = {Genomics},
pages = {1--15},
pmid = {15607417},
title = {{Applications of DNA tiling arrays for whole-genome analysis}},
volume = {85},
year = {2005}
}
@article{Gurevich2013a,
abstract = {SUMMARY: Limitations of genome sequencing techniques have led to dozens of assembly algorithms, none of which is perfect. A number of methods for comparing assemblers have been developed, but none is yet a recognized benchmark. Further, most existing methods for comparing assemblies are only applicable to new assemblies of finished genomes; the problem of evaluating assemblies of previously unsequenced species has not been adequately considered. Here, we present QUAST-a quality assessment tool for evaluating and comparing genome assemblies. This tool improves on leading assembly comparison software with new ideas and quality metrics. QUAST can evaluate assemblies both with a reference genome, as well as without a reference. QUAST produces many reports, summary tables and plots to help scientists in their research and in their publications. In this study, we used QUAST to compare several genome assemblers on three datasets. QUAST tables and plots for all of them are available in the Supplementary Material, and interactive versions of these reports are on the QUAST website.$\backslash$n$\backslash$nAVAILABILITY: http://bioinf.spbau.ru/quast .$\backslash$n$\backslash$nSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
author = {Gurevich, Alexey and Saveliev, Vladislav and Vyahhi, Nikolay and Tesler, Glenn},
doi = {10.1093/bioinformatics/btt086},
file = {:home/fin/Documents/papers/mendeley/Gurevich et al.\_2013\_QUAST Quality assessment tool for genome assemblies\_Bioinformatics.pdf:pdf},
isbn = {1367-4811 (Electronic)$\backslash$r1367-4803 (Linking)},
issn = {13674803},
journal = {Bioinformatics},
number = {8},
pages = {1072--1075},
pmid = {23422339},
title = {{QUAST: Quality assessment tool for genome assemblies}},
volume = {29},
year = {2013}
}
@article{Fujishima2005,
abstract = {Holospora obtusa is a macronucleus-specific bacterium of the ciliate Paramecium caudatum. Three types of P. caudatum cells (H. obtusa-free cells, cells bearing the reproductive form of H. obtusa and cells bearing the predominantly infectious form of H. obtusa) cultured at 25??C were transferred to 4, 10, 25, 35 and 40??C and their swimming velocities were measured by taking photomicrographs with two-second exposures. The H. obtusa-free cells almost ceased swimming at both 4 and 40??C, while cells bearing the reproductive form and those bearing the predominantly infectious form actively swam even at these temperatures. These results show that the host cell can acquire heat-shock resistance when infected by H. obtusa in the macronucleus. This is the first evidence to show that the endonuclear symbiont Holospora contributes to maintain the ciliary movement of the host even at temperatures unsuitable for the host growth. ?? 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.},
author = {Fujishima, Masahiro and Kawai, Miki and Yamamoto, Ryu},
doi = {10.1016/j.femsle.2004.11.053},
file = {:home/fin/Documents/papers/mendeley/Fujishima, Kawai, Yamamoto\_2005\_Paramecium caudatum acquires heat-shock resistance in ciliary movement by infection with the endonuclear.pdf:pdf},
isbn = {0378-1097 (Print)$\backslash$n0378-1097 (Linking)},
issn = {03781097},
journal = {FEMS Microbiol. Lett.},
keywords = {Ciliary movement,Endonuclear symbiotic bacterium,Heat-shock resistance,Holospora obtusa,Infection,Paramecium caudatum,Swimming velocity},
pages = {101--105},
pmid = {15668007},
title = {{Paramecium caudatum acquires heat-shock resistance in ciliary movement by infection with the endonuclear symbiotic bacterium Holospora obtusa}},
volume = {243},
year = {2005}
}
@article{Grigoriev2011,
abstract = {The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. The JGI Genome Portal (http://genome.jgi.doe.gov) provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. We describe here the general organization of the Genome Portal and the most recent addition, MycoCosm (http://jgi.doe.gov/fungi), a new integrated fungal genomics resource.},
author = {Grigoriev, Igor V and Nordberg, Henrik and Shabalov, Igor and Aerts, Andrea and Cantor, Mike and Goodstein, David and Kuo, Alan and Minovitsky, Simon and Nikitin, Roman and Ohm, Robin a and Otillar, Robert and Poliakov, Alex and Ratnere, Igor and Riley, Robert and Smirnova, Tatyana and Rokhsar, Daniel and Dubchak, Inna},
doi = {10.1093/nar/gkr947},
file = {:home/fin/Documents/papers/mendeley/Grigoriev et al.\_2011\_P@JGI-DOE@The Genome Portal of the Department of Energy Joint Genome Institute.\_Nucleic acids research.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic Acids Res.},
number = {November 2011},
pages = {1--7},
pmid = {22110030},
title = {{P@JGI-DOE@The Genome Portal of the Department of Energy Joint Genome Institute.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22110030},
volume = {40},
year = {2011}
}
@article{Kodama2011,
abstract = {Each symbiotic Chlorella of the ciliate Paramecium bursaria is enclosed in a perialgal vacuole membrane derived from the host digestive vacuole membrane. Alga-free paramecia and symbiotic algae can grow independently. Mixing them experimentally can cause reinfection. Earlier, we reported that the symbiotic algae appear to push the host trichocysts aside to become fixed beneath the host cell cortex during the algal reinfection process. Indirect immunofluorescence microscopy with a monoclonal antibody against the trichocysts demonstrates that the trichocysts change their locality to form algal attachment sites and decrease their density beneath the host cell cortex through algal reinfection. Transmission electron microscopy to detect acid phosphatase activity showed that some trichocysts near the host cell cortex are digested by the host lysosomal fusion during algal reinfection. Removal of algae from the host cell using cycloheximide recovers the trichocyst's arrangement and number near the host cell cortex. These results indicate that symbiotic algae compete for their attachment sites with preexisting trichocysts and that the algae have the ability to ensure algal attachment sites beneath the host cell cortex.},
annote = {fixed algae can't localise therefore active metabolic process},
author = {Kodama, Yuuki and Fujishima, Masahiro},
doi = {10.1007/s00709-010-0175-z},
file = {:home/fin/Documents/papers/mendeley/Kodama, Fujishima\_2011\_Endosymbiosis of Chlorella species to the ciliate Paramecium bursaria alters the distribution of the host's trich.pdf:pdf},
issn = {1615-6102},
journal = {Protoplasma},
keywords = {Chlorella,Chlorella: drug effects,Chlorella: physiology,Cycloheximide,Cycloheximide: pharmacology,Fluorescence,Microscopy,Paramecium,Paramecium: cytology,Paramecium: physiology,Symbiosis},
month = apr,
pages = {325--337},
pmid = {20582727},
title = {{Endosymbiosis of Chlorella species to the ciliate Paramecium bursaria alters the distribution of the host's trichocysts beneath the host cell cortex}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20582727},
volume = {248},
year = {2011}
}
@article{Eddy1995,
abstract = {A simulated annealing method is described for training hidden Markov models and producing multiple sequence alignments from initially unaligned protein or DNA sequences. Simulated annealing in turn uses a dynamic programming algorithm for correctly sampling suboptimal multiple alignments according to their probability and a Boltzmann temperature factor. The quality of simulated annealing alignments is evaluated on structural alignments of ten different protein families, and compared to the performance of other HMMtr aining methods and the ClnstalW program. Simulated annealing is better able to find near-global optima in the multiple alignment probability landscape than the other tested HMMtra ining methods. Neither ClustalW nor simulated annealing produce consistently better alignments compared to each other. Examinationo f the specific cases in which ClustalW outperforms simulated annealing, and vice versa, provides insight into the strengths and weaknesses of current hidden Markov model approaches.},
author = {Eddy, Sean R},
file = {:home/fin/Documents/papers/mendeley/Eddy\_1995\_Multiple alignment using hidden Markov model\_Intelligent Systems for Molecular Biology.pdf:pdf},
journal = {Intell. Syst. Mol. Biol.},
pages = {114--120},
pmid = {7584426},
title = {{Multiple alignment using hidden Markov model}},
volume = {ISMB-95},
year = {1995}
}
@article{Wang1994,
abstract = {We study the computational complexity of two popular problems in multiple sequence alignment: multiple alignment with SP-score and multiple tree alignment. It is shown that the first problem is NP-complete and the second is MAX SNP-hard. The complexity of tree alignment with a given phylogeny is also considered.},
author = {Wang, L and Jiang, T},
doi = {dx.doi.org/10.1089/cmb.1994.1.337},
file = {:home/fin/Documents/papers/mendeley/Wang, Jiang\_1994\_On the complexity of multiple sequence alignment.\_Journal of computational biology.pdf:pdf},
issn = {1066-5277},
journal = {J. Comput. Biol.},
keywords = {approxi-,computational complexity,evolutionary tree,multiple sequence alignment,sp-score},
pages = {337--348},
pmid = {8790475},
title = {{On the complexity of multiple sequence alignment.}},
volume = {1},
year = {1994}
}
@article{Gunderson1987,
abstract = {The phylogenetic relationships among the chlorophyte Chlamydomonas reinhardtii, the chrysophyte Ochromonas danica, and the oomycete Achyla bisexualis were explored by comparing the sequences of their small-subunit ribosomal RNA coding regions. Comparisons of similarity values or inspection of phylogenetic trees constructed by distance matrix methods reveal a very close relationship between oomycetes and chrysophytes. The separation of chrysophytes from chlorophytes is comparable to that of plants from animals, and both separations are far antedated by the divergence of a number of other protist groups.},
author = {Gunderson, J H and Elwood, H and Ingold, a and Kindle, K and Sogin, M L},
doi = {10.1073/pnas.84.16.5823},
file = {:home/fin/Documents/papers/mendeley/Gunderson et al.\_1987\_Phylogenetic relationships between chlorophytes, chrysophytes, and oomycetes\_Proc Natl Acad Sci U S A.pdf:pdf},
isbn = {0027-8424 (Print)$\backslash$n0027-8424 (Linking)},
issn = {0027-8424},
journal = {Proc Natl Acad Sci U S A},
keywords = {*Phylogeny,Animals,Base Sequence,Chlamydomonas/*genetics,Chytridiomycota/*genetics,Eukaryota/*genetics,Oomycetes/*genetics,Phaeophyta/*genetics,RNA, Ribosomal/analysis,Species Specificity},
number = {August},
pages = {5823--5827},
pmid = {3475703},
title = {{Phylogenetic relationships between chlorophytes, chrysophytes, and oomycetes}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/3475703},
volume = {84},
year = {1987}
}
@article{Berger1986,
author = {Berger, James D},
file = {:home/fin/Documents/papers/mendeley/Berger\_1986\_Autogamy Cell Cycle Stage-specific in Paramecium Commitment to Meiosis\_Experimental Cell Research.pdf:pdf},
journal = {Exp. Cell Res.},
pages = {475--485},
title = {{Autogamy Cell Cycle Stage-specific in Paramecium Commitment to Meiosis}},
volume = {166},
year = {1986}
}
@article{Yoon2011,
abstract = {Whole-genome shotgun sequence data from three individual cells isolated from seawater, followed by analysis of ribosomal DNA, indicated that the cells represented three divergent clades of picobiliphytes. In contrast with the recent description of this phylum, we found no evidence of plastid DNA nor of nuclear-encoded plastid-targeted proteins, which suggests that these picobiliphytes are heterotrophs. Genome data from one cell were dominated by sequences from a widespread single-stranded DNA virus. This virus was absent from the other two cells, both of which contained non-eukaryote DNA derived from marine Bacteroidetes and large DNA viruses. By using shotgun sequencing of uncultured marine picobiliphytes, we revealed the distinct interactions of individual cells.},
author = {Yoon, Hwan Su and Price, Dana C and Stepanauskas, Ramunas and Rajah, Veeran D and Sieracki, Michael E and Wilson, William H and Yang, Eun Chan and Duffy, Siobain and Bhattacharya, Debashish},
doi = {10.1126/science.1203163},
file = {:home/fin/Documents/papers/mendeley/Yoon et al.\_2011\_Single-cell genomics reveals organismal interactions in uncultivated marine protists.\_Science (New York, N.Y.).pdf:pdf},
isbn = {0036-8075},
issn = {0036-8075},
journal = {Science},
number = {6030},
pages = {714--717},
pmid = {21551060},
title = {{Single-cell genomics reveals organismal interactions in uncultivated marine protists.}},
volume = {332},
year = {2011}
}
@incollection{Kato2009a,
author = {Kato, Yutaka and Imamura, Nobutaka},
booktitle = {Endosymbionts in Paramecium},
chapter = {3},
doi = {10.1007/978-3-540-92677-1},
editor = {Fujishima, Masahiro},
file = {:home/fin/Documents/papers/mendeley/Kato, Imamura\_2009\_Metabolic Control Between the Symbiotic Chlorella and the Host Paramecium\_Endosymbionts in Paramecium.pdf:pdf},
isbn = {978-3-540-92676-4},
pages = {57--82},
publisher = {Springer},
series = {Microbiology Monographs},
title = {{Metabolic Control Between the Symbiotic Chlorella and the Host Paramecium}},
url = {http://link.springer.com/10.1007/978-3-540-92677-1},
volume = {12},
year = {2009}
}
@article{Movahedi2014,
abstract = {As the vast majority of all microbes are unculturable, single-cell sequencing has become a significant method to gain insight into microbial physiology. Single-cell sequencing methods, currently powered by multiple displacement genome amplification (MDA), have passed important milestones such as finishing and closing the genome of a prokaryote. However, the quality and reliability of genome assemblies from single cells are still unsatisfactory due to uneven coverage depth and the absence of scattered chunks of the genome in the final collection of reads caused by MDA bias. In this work, our new algorithm Hybrid De novo Assembler (HyDA) demonstrates the power of co-assembly of multiple single-cell genomic data sets through significant improvement of the assembly quality in terms of predicted functional elements and length statistics. Co-assemblies contain significantly more base pairs and protein coding genes, cover more subsystems, and consist of longer contigs compared to individual assemblies by the same algorithm as well as state-of-the-art single-cell assemblers SPAdes and IDBA-UD. Hybrid De novo Assembler (HyDA) is also able to avoid chimeric assemblies by detecting and separating shared and exclusive pieces of sequence for input data sets. By replacing one deep single-cell sequencing experiment with a few single-cell sequencing experiments of lower depth, the co-assembly method can hedge against the risk of failure and loss of the sample, without significantly increasing sequencing cost. Application of the single-cell co-assembler HyDA to the study of three uncultured members of an alkane-degrading methanogenic community validated the usefulness of the co-assembly concept.},
author = {Movahedi, N. S. and Taghavi, Z. and Embree, M. and Nagarajan, H. and Zengler, K. and Chitsaz, H.},
doi = {10.1101/002972},
file = {:home/fin/Documents/papers/mendeley/Movahedi et al.\_2014\_Efficient synergistic single-cell genome assembly\_bioRxiv.pdf:pdf},
journal = {bioRxiv},
title = {{Efficient synergistic single-cell genome assembly}},
url = {http://biorxiv.org/content/early/2014/02/24/002972.abstract},
year = {2014}
}
@article{Eck1966,
author = {Eck, Richard V and Dayhoff, Margaret O},
publisher = {National Biomedical Research Foundation, Silver Spring},
title = {{Atlas of Protein Sequence and Structure}},
year = {1966}
}
@article{Corliss1974,
author = {Corliss, John O},
file = {:home/fin/Documents/papers/mendeley/Corliss\_1974\_The changing world of ciliate systematics historical analysis of past efforts and a newly proposed phylogenetic scheme of c.pdf:pdf},
journal = {Syst. Zool.},
pages = {91--138},
title = {{The changing world of ciliate systematics: historical analysis of past efforts and a newly proposed phylogenetic scheme of classification for the protistan phylum ciliophora}},
volume = {23},
year = {1974}
}
@article{Hortnagl2007a,
abstract = {We tested the hypothesis that photo-oxidative stress is greater in symbiotic representatives of the freshwater ciliate Paramecium bursaria than in aposymbiotic (i.e., without Chlorella) ones. The level of oxidative stress was determined by assessing reactive oxygen species (ROS) with two fluorescent probes (hydroethidine and dihydrorhodamine123) by flow cytometry in exponential and stationary growth phases of both strains. Photo-oxidative stress was assessed in the laboratory after exposure of the ciliates to photosynthetically active radiation (PAR: 400-700 nm) and PAR+ultraviolet radiation (UVR: 280-400 nm). Additionally, both strains were screened for their antioxidant defenses by measuring the activity of the enzymes catalase, superoxide dismutase (SOD), and glutathione reductase. The results showed that aposymbiotic ciliates had higher levels of PAR-induced oxidative stress than symbiotic ones. Significant differences in PAR-induced oxidative stress were also found in both strains when comparing exponential and stationary growth phases with generally higher values in the former. After exposure to UVR, aposymbiotic ciliates in the stationary phase had the highest levels of ROS despite an increase in SOD activity. By contrast, exposure to UVR decreased catalase activity in both strains. Overall, our results suggest that in this ciliate symbiosis, the presence of symbionts minimizes photo-oxidative stress. This work represents the first assessment of photo-oxidative stress in an algal-ciliate mutualistic symbiosis.},
author = {H\"{o}rtnagl, Paul H and Sommaruga, Ruben},
doi = {10.1039/b703119j},
file = {:home/fin/Documents/papers/mendeley/H\"{o}rtnagl, Sommaruga\_2007\_Photo-oxidative stress in symbiotic and aposymbiotic strains of the ciliate Paramecium bursaria.\_Photochemi(2).pdf:pdf},
isbn = {1474-905X (Print)},
issn = {1474-905X},
journal = {Photochem. Photobiol. Sci.},
number = {8},
pages = {842--847},
pmid = {17668113},
title = {{Photo-oxidative stress in symbiotic and aposymbiotic strains of the ciliate Paramecium bursaria.}},
volume = {6},
year = {2007}
}
@article{Coleman2003,
abstract = {The internal transcribed spacer (ITS) region of the nuclear rDNA cistrons is one of the more frequently utilized regions for phylogenetic analyses at the genus and species levels. It has proven valuable for phylogenetic reconstruction of species and genus relationships, using comparisons of primary sequence. Although potential transcript secondary structure homology is often utilized to aid alignment in comparisons of ribosomal gene sequences, such consideration has rarely been applied to ITS primarily because secondary structures for its transcript were not available. Here, we describe the value of applying ITS2 RNA transcript secondary structure information to improve alignments, which then allows comparisons at even deeper taxonomic levels. The evolutionarily conserved subportions of ITS2, apparently necessary for positioning of the multimolecular transcript processing machinery, also provide material for distinguishing evolutionarily rare events, 'Compensatory Base Changes' in the relatively conserved regions, that might be useful in recognizing how arbitrary are the assignments of classical taxonomic ranks in disparate groups of eukaryotes. This relatively short and easily sequenced region of DNA - ITS2 - has yet to be fully exploited in phylogenetics.},
author = {Coleman, Annette W.},
doi = {10.1016/S0168-9525(03)00118-5},
file = {:home/fin/Documents/papers/mendeley/Coleman\_2003\_ITS2 is a double-edged tool for eukaryote evolutionary comparisons\_Trends in Genetics.pdf:pdf},
isbn = {0168-9525},
issn = {01689525},
journal = {Trends Genet.},
number = {7},
pages = {370--375},
pmid = {12850441},
title = {{ITS2 is a double-edged tool for eukaryote evolutionary comparisons}},
volume = {19},
year = {2003}
}
@article{Schulz2014,
abstract = {Amoebae serve as hosts for various intracellular bacteria, including human pathogens. These microbes are able to overcome amoebal defense mechanisms and successfully establish a niche for replication, which is usually the cytoplasm. Here, we report on the discovery of a bacterial symbiont that is located inside the nucleus of its Hartmannella sp. host. This symbiont, tentatively named 'Candidatus Nucleicultrix amoebiphila', is only moderately related to known bacteria (∼90\% 16S and 23S rRNA sequence similarity) and member of a novel clade of protist symbionts affiliated with the Rickettsiales and Rhodospirillales. Screening of 16S rRNA amplicon data sets revealed a broad distribution of these bacteria in freshwater and soil habitats. 'Candidatus Nucleicultrix amoebiphila' traffics within 6 h post infection to the host nucleus. Maximum infection levels are reached after 96-120 h, at which time point the nucleus is pronouncedly enlarged and filled with bacteria. Transmission of the symbionts occurs vertically upon host cell division but may also occur horizontally through host cell lysis. Although we observed no impact on the fitness of the original Hartmannella sp. host, the bacteria are rather lytic for Acanthamoeba castellanii. Intranuclear symbiosis is an exceptional phenomenon, and amoebae represent an ideal model system to further investigate evolution and underlying molecular mechanisms of these unique microbial associations.The ISME Journal advance online publication, 6 February 2014; doi:10.1038/ismej.2014.5.},
author = {Schulz, Frederik and Lagkouvardos, Ilias and Wascher, Florian and Aistleitner, Karin and Kostanj\v{s}ek, Rok and Horn, Matthias},
doi = {10.1038/ismej.2014.5},
file = {:home/fin/Documents/papers/mendeley/Schulz et al.\_2014\_Life in an unusual intracellular niche a bacterial symbiont infecting the nucleus of amoebae.\_The ISME journal.pdf:pdf},
issn = {1751-7370},
journal = {ISME J.},
keywords = {acanthamoeba,endonuclear,hartmannella,nucleus,rickettsia,symbiosis},
pages = {1634--1644},
pmid = {24500618},
title = {{Life in an unusual intracellular niche: a bacterial symbiont infecting the nucleus of amoebae.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24500618},
year = {2014}
}
@article{Hoshina2004,
abstract = {Endosymbiotic green algae of Japanese Paramecium bursaria were phylogenetically analyzed based on DNA sequences from the ribosomal DNA operon (18S rDNA, ITS1, 5.8S rDNA, and ITS2). Phylogenetic trees constructed using 18S rDNA sequences showed that the symbionts belong to the Chlorella sensu stricto (Trebouxiophyceae) group. They are genetically closer to the C. vulgaris Beijerinck group than to C. kessleri Fott et Nov\'{a}kov\'{a} as proposed previously. Branching order in C. vulgaris group was unresolved in 18S rDNA trees. Compared heterogeneities of 18S rDNA, ITS1, 5.8S r, and ITS2 among symbionts and two Chlorella species, indicated that the ITS2 region (and probably also ITS1) is better able to resolve phylogenetic problems in such closely related taxa. All six symbiotic sequences obtained here (approximately 4000-bp sequences of 18S rDNA, ITS1, 5.8S rDNA, and ITS2) were completely identical in each, strongly suggesting a common origin.},
author = {Hoshina, R and Kamako, S-I and Imamura, N},
doi = {10.1055/s-2004-820888},
file = {:home/fin/Documents/papers/mendeley/Hoshina, Kamako, Imamura\_2004\_Phylogenetic position of endosymbiotic green algae in Paramecium bursaria Ehrenberg from Japan.\_Plant biol.pdf:pdf},
isbn = {2004820888},
issn = {1435-8603},
journal = {Plant Biol. (Stuttg).},
keywords = {Animals,Base Sequence,Chlorella,Chlorella: classification,Chlorella: genetics,Chlorella: isolation \& purification,DNA, Ribosomal,DNA, Ribosomal Spacer,DNA, Ribosomal Spacer: genetics,DNA, Ribosomal: genetics,Japan,Paramecium,Paramecium: isolation \& purification,Phylogeny,Symbiosis},
month = jul,
number = {4},
pages = {447--53},
pmid = {15248128},
title = {{Phylogenetic position of endosymbiotic green algae in Paramecium bursaria Ehrenberg from Japan.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15248128},
volume = {6},
year = {2004}
}
@article{Mohr2012,
author = {Mohr, Stephanie E. and Perrimon, Norbert},
doi = {10.1002/wrna.110},
file = {:home/fin/Documents/papers/mendeley/Mohr, Perrimon\_2012\_RNAi screening new approaches, understandings, and organisms\_Wiley Interdisciplinary Reviews RNA.pdf:pdf},
issn = {17577004},
journal = {Wiley Interdiscip. Rev. RNA},
number = {April},
pages = {145--158},
title = {{RNAi screening: new approaches, understandings, and organisms}},
url = {http://doi.wiley.com/10.1002/wrna.110},
volume = {3},
year = {2012}
}
@article{Ellegaard2013,
abstract = {The importance of host-specialization to speciation processes in obligate host-associated bacteria is well known, as is also the ability of recombination to generate cohesion in bacterial populations. However, whether divergent strains of highly recombining intracellular bacteria, such as Wolbachia, can maintain their genetic distinctness when infecting the same host is not known. We first developed a protocol for the genome sequencing of uncultivable endosymbionts. Using this method, we have sequenced the complete genomes of the Wolbachia strains wHa and wNo, which occur as natural double infections in Drosophila simulans populations on the Seychelles and in New Caledonia. Taxonomically, wHa belong to supergroup A and wNo to supergroup B. A comparative genomics study including additional strains supported the supergroup classification scheme and revealed 24 and 33 group-specific genes, putatively involved in host-adaptation processes. Recombination frequencies were high for strains of the same supergroup despite different host-preference patterns, leading to genomic cohesion. The inferred recombination fragments for strains of different supergroups were of short sizes, and the genomes of the co-infecting Wolbachia strains wHa and wNo were not more similar to each other and did not share more genes than other A- and B-group strains that infect different hosts. We conclude that Wolbachia strains of supergroup A and B represent genetically distinct clades, and that strains of different supergroups can co-exist in the same arthropod host without converging into the same species. This suggests that the supergroups are irreversibly separated and that barriers other than host-specialization are able to maintain distinct clades in recombining endosymbiont populations. Acquiring a good knowledge of the barriers to genetic exchange in Wolbachia will advance our understanding of how endosymbiont communities are constructed from vertically and horizontally transmitted genes.},
author = {Ellegaard, Kirsten Maren and Klasson, Lisa and N\"{a}slund, Kristina and Bourtzis, Kostas and Andersson, Siv G E},
doi = {10.1371/journal.pgen.1003381},
file = {:home/fin/Documents/papers/mendeley/Ellegaard et al.\_2013\_Comparative genomics of Wolbachia and the bacterial species concept.\_PLoS genetics.pdf:pdf},
isbn = {1553-7404},
issn = {1553-7404},
journal = {PLoS Genet.},
keywords = {Animals,Drosophila,Drosophila: genetics,Drosophila: microbiology,Genome, Bacterial,Genomics,New Caledonia,Phylogeny,Recombination, Genetic,Sequence Analysis, DNA,Seychelles,Species Specificity,Symbiosis,Symbiosis: genetics,Symbiosis: physiology,Wolbachia,Wolbachia: genetics,Wolbachia: physiology},
number = {4},
pages = {e1003381},
pmid = {23593012},
title = {{Comparative genomics of Wolbachia and the bacterial species concept.}},
url = {http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003381},
volume = {9},
year = {2013}
}
@article{Bashan2015,
author = {Bashan, Yoav and Lopez, Blanca R. and Huss, Volker a. R. and Amavizca, Edgar and De-Bashan, Luz E.},
doi = {10.1007/s10811-015-0571-z},
file = {:home/fin/Documents/papers/mendeley/Bashan et al.\_2015\_Chlorella sorokiniana (formerly C. vulgaris) UTEX 2714, a non-thermotolerant microalga useful for biotechnological ap.pdf:pdf},
issn = {0921-8971},
journal = {J. Appl. Phycol.},
keywords = {1964,2011,article,chlorella,electronic supplementary material the,horst vierheilig,of csic,online version of this,reference strains,rhizae researcher dr,spain,spanish mycor-,systematics,the german,this study is dedicated,to the memory of},
title = {{Chlorella sorokiniana (formerly C. vulgaris) UTEX 2714, a non-thermotolerant microalga useful for biotechnological applications and as a reference strain}},
url = {http://link.springer.com/10.1007/s10811-015-0571-z},
year = {2015}
}
@article{Li2014,
author = {Li, Bo and Fillmore, Nathanael and Bai, Yongsheng and Collins, Mike and Thomson, James a and Stewart, Ron and Dewey, Colin N},
doi = {10.1186/s13059-014-0553-5},
file = {:home/fin/Documents/papers/mendeley/Li et al.\_2014\_Evaluation of de novo transcriptome assemblies from RNA-Seq data\_Genome Biology.pdf:pdf},
journal = {Genome Biol.},
number = {553},
pages = {1--21},
title = {{Evaluation of de novo transcriptome assemblies from RNA-Seq data}},
volume = {15},
year = {2014}
}
@article{Luo2012,
abstract = {BACKGROUND: There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions.$\backslash$n$\backslash$nFINDINGS: To overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome.$\backslash$n$\backslash$nCONCLUSIONS: Benchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were \~{}20.9 kbp and \~{}22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16\% to 93.91\%, and memory consumption was \~{}2/3 lower during the point of largest memory consumption.},
author = {Luo, Ruibang and Liu, Binghang and Xie, Yinlong and Li, Zhenyu and Huang, Weihua and Yuan, Jianying and He, Guangzhu and Chen, Yanxiang and Pan, Qi and Liu, Yunjie and Tang, Jingbo and Wu, Gengxiong and Zhang, Hao and Shi, Yujian and Liu, Yong and Yu, Chang and Wang, Bo and Lu, Yao and Han, Changlei and Cheung, David W and Yiu, Siu-Ming and Peng, Shaoliang and Xiaoqian, Zhu and Liu, Guangming and Liao, Xiangke and Li, Yingrui and Yang, Huanming and Wang, Jian and Lam, Tak-Wah and Wang, Jun},
doi = {10.1186/2047-217X-1-18},
file = {:home/fin/Documents/papers/mendeley/Luo et al.\_2012\_SOAPdenovo2 an empirically improved memory-efficient short-read de novo assembler.\_GigaScience.pdf:pdf},
isbn = {2047-217X (Electronic)$\backslash$n2047-217X (Linking)},
issn = {2047-217X},
journal = {Gigascience},
keywords = {assembly,contig,error correction,gap-filling,genome,scaffold},
pages = {18},
pmid = {23587118},
title = {{SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.}},
url = {http://www.gigasciencejournal.com/content/1/1/18},
volume = {1},
year = {2012}
}
@article{Jeanfils1993,
abstract = {Growth and nitrate uptake were studied on free-living and immobilized Chlorella vulgaris cells cultivated in medium containing different nitrate concentrations. First, the effect of nitrate concentrations on growth indicated that cells can live in the presence of high concentrations as high as 97 mM. Although no le- thal effect on cells was observed such concentration a slow down in growth and a decrease in biom- ass produced was observed. The rate of nitrate uptake increased with the nitrate concentration in the medium. The maximum uptake rate was reached in first days of culture in both free-living and immo- bilized cells. The rate dropped more rapidly for cells growing in 2 mM nitrate than for cells growing in higher nitrate concentration. The maximum rate was very much the same for free-living and immobi- lized and was within the order of 0.45 to 0.57 /ug NO3 h-' 10 -6 cells. Immobilization modified the changes of nitrate uptake rate for concentration higher than 2 mM.},
author = {Jeanfils, J. and Canisius, M-F. and Burlion, N.},
doi = {10.1007/BF02186240},
file = {:home/fin/Documents/papers/mendeley/Jeanfils, Canisius, Burlion\_1993\_Effect of high nitrate concentrations on growth and nitrate uptake by free-living and immobilized Chlor.pdf:pdf},
issn = {0921-8971},
journal = {J. Appl. Phycol.},
keywords = {alginate bead,chlorella vulgaris,growth,immobilized cells,nitrate uptake},
pages = {369--374},
title = {{Effect of high nitrate concentrations on growth and nitrate uptake by free-living and immobilized Chlorella vulgaris cells}},
url = {http://www.springerlink.com/index/10.1007/BF02186240},
volume = {5},
year = {1993}
}
@article{Cohen1957,
author = {Cohen, G N and Monod, J},
file = {:home/fin/Documents/papers/mendeley/Cohen, Monod\_1957\_Bacterial permeases\_Bacteriol Rev.pdf:pdf},
isbn = {0005-3678 (Print)},
issn = {0005-3678},
journal = {Bacteriol Rev},
keywords = {BACTERIA/metabolism,Bacteria/ metabolism,Enzymes,Osmosis,Osmosis and permeability,Permeability},
pages = {169--194},
pmid = {13471457},
title = {{Bacterial permeases}},
volume = {21},
year = {1957}
}
@article{Vorobyev2009,
author = {Vorobyev, Konstantin and Andronov, Evgeny and Skoblo, Inna and Migunova, Alexandra and Kvitko, Konstantin},
file = {:home/fin/Documents/papers/mendeley/Vorobyev et al.\_2009\_An atypical Chlorella symbiont from Paramecium bursaria\_Protistology.pdf:pdf},
journal = {Protistology},
keywords = {18s rrna gene,abbreviations,chlorella,group i intron,paramecium bursaria,paramecium bursaria chlorella virus,pbcv},
number = {1},
pages = {39--44},
title = {{An atypical Chlorella symbiont from Paramecium bursaria}},
volume = {6},
year = {2009}
}
@article{Poretsky2005,
abstract = {We analyzed gene expression in marine and freshwater bacterioplankton communities by the direct retrieval and analysis of microbial transcripts. Environmental mRNA, obtained from total RNA by subtractive hybrid- ization of rRNA, was reverse transcribed, amplified with random primers, and cloned. Approximately 400 clones were analyzed, of which80\% were unambiguously mRNA derived. mRNAs appeared to be from diverse taxonomic groups, including both Bacteria (mainly - and -Proteobacteria) and Archaea (mainly Euryarcha- eota). Many transcripts could be linked to environmentally important processes such as sulfur oxidation (soxA), assimilation of C1 compounds (fdh1B), and acquisition of nitrogen via polyamine degradation (aphA). Environmental transcriptomics is a means of exploring functional gene expression within natural microbial communities without bias toward known sequences, and provides a new approach for obtaining community- specific variants of key functional genes.},
author = {Poretsky, Rachel S and Bano, Nasreen and Buchan, Alison and Kleikemper, Jutta and Pickering, Maria and Pate, Whitney M and Moran, Mary Ann and Hollibaugh, James T and Lecleir, Gary},
doi = {10.1128/AEM.71.7.4121},
file = {:home/fin/Documents/papers/mendeley/Poretsky et al.\_2005\_Analysis of Microbial Gene Transcripts in Environmental Samples\_Applied and environmental microbiology.pdf:pdf},
journal = {Appl. Environ. Microbiol.},
number = {7},
pages = {4121--4126},
title = {{Analysis of Microbial Gene Transcripts in Environmental Samples}},
volume = {71},
year = {2005}
}
@article{Keller2005,
author = {Keller, Lani C. and Romijn, Edwin P. and Zamora, Ivan and Yates, John R. and Marshall, Wallace F.},
doi = {10.1016/j.cub.2005.05.024},
file = {:home/fin/Documents/papers/mendeley/Keller et al.\_2005\_Proteomic Analysis of Isolated Chlamydomonas Centrioles Reveals Orthologs of Ciliary-Disease Genes\_Current Biology.pdf:pdf},
issn = {09609822},
journal = {Curr. Biol.},
pages = {1090--1098},
title = {{Proteomic Analysis of Isolated Chlamydomonas Centrioles Reveals Orthologs of Ciliary-Disease Genes}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0960982205005130},
volume = {15},
year = {2005}
}
@article{Yule1903a,
author = {Yule, Gu},
doi = {10.1093/biomet/2.2.121},
file = {:home/fin/Documents/papers/mendeley/Yule\_1903\_Notes on the theory of association of attributes in statistics\_Biometrika.pdf:pdf},
isbn = {0006-3444},
issn = {0006-3444},
journal = {Biometrika},
number = {2},
pages = {121--134},
title = {{Notes on the theory of association of attributes in statistics}},
url = {http://books.google.com/books?hl=en\&lr=\&id=qwkCAAAAYAAJ\&oi=fnd\&pg=PA121\&dq=Notes+on+the+Theory+of+Association+of+Attributes+in+Statistics\&ots=tlZ3rmeTkq\&sig=CoO4\_oGyotMfY1SUTaIMpqc0ztU},
volume = {2},
year = {1903}
}
@article{Suzuki2015,
author = {Suzuki, S. and Kakuta, M. and Ishida, T. and Akiyama, Y.},
doi = {10.1093/bioinformatics/btu780},
file = {:home/fin/Documents/papers/mendeley/Suzuki et al.\_2015\_Faster sequence homology searches by clustering subsequences\_Bioinformatics.pdf:pdf},
issn = {1367-4803},
journal = {Bioinformatics},
number = {November 2014},
pages = {1183--1190},
title = {{Faster sequence homology searches by clustering subsequences}},
url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btu780},
volume = {31},
year = {2015}
}
@article{Jiggins2013,
abstract = {Circadian timekeeping in plants increases photosynthesis and productivity. There are circadian oscillations in the abundance of many chloroplast-encoded transcripts, but it is not known how the circadian clock regulates chloroplast transcription or the photosynthetic apparatus. We show that, in Arabidopsis, nuclear-encoded SIGMA FACTOR5 (SIG5) controls circadian rhythms of transcription of several chloroplast genes, revealing one pathway by which the nuclear-encoded circadian oscillator controls rhythms of chloroplast gene expression. We also show that SIG5 mediates the circadian gating of light input to a chloroplast-encoded gene. We have identified an evolutionarily conserved mechanism that communicates circadian timing information between organelles with distinct genetic systems and have established a new level of integration between eukaryotic circadian clocks and organelles of endosymbiotic origin.},
author = {Jiggins, C D and Hirschmann, R J and Bundey, R a and Insel, P a and Crossland, J P and Pool, J E and Kassner, V a and Aquadro, C F and Carroll, S B and Swinehart, J and Kingsley, E P and Jensen, J D and Hoekstra, H E and Larson, J G and Manceau, M and Wiley, C D and Stephens, M and Duhl, D M J and Millar, S E and Miller, K a and Barsh, G S and Hernandez, R D and Williamson, S H and Bustamante, C D and Kim, Y and Hartl, D L and Parsch, J and Goncalves, G and Chupasko, J and Kay, E and Kingsley, E and Demboski, J and Foundation, Science and Agency, Projects and Fellowship, Postdoctoral and Commission, Parks},
file = {:home/fin/Documents/papers/mendeley/Jiggins et al.\_2013\_Circadian Control of Chloroplast\_Nature.pdf:pdf},
journal = {Nature},
number = {March},
pages = {1316--1319},
title = {{Circadian Control of Chloroplast}},
volume = {339},
year = {2013}
}
@article{Abrams1987,
author = {Abrams, P.a.},
file = {:home/fin/Documents/papers/mendeley/Abrams\_1987\_On classifying intractions between populations\_Oecologia.pdf:pdf},
journal = {Oecologia},
keywords = {competition,interaction,mutualism,predation},
pages = {272--281},
title = {{On classifying intractions between populations}},
volume = {73},
year = {1987}
}
@book{Mitchell1997,
author = {Mitchell, Tom E},
pages = {2},
publisher = {McGraw Hill},
title = {{Machine Learning}},
year = {1997}
}
@article{Saier2006,
abstract = {The Transporter Classification Database (TCDB) is a web accessible, curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from a variety of living organisms. TCDB is a curated repository for factual information compiled from >10,000 references, encompassing approximately 3000 representative transporters and putative transporters, classified into >400 families. The transporter classification (TC) system is an International Union of Biochemistry and Molecular Biology approved system of nomenclature for transport protein classification. TCDB is freely accessible at http://www.tcdb.org. The web interface provides several different methods for accessing the data, including step-by-step access to hierarchical classification, direct search by sequence or TC number and full-text searching. The functional ontology that underlies the database structure facilitates powerful query searches that yield valuable data in a quick and easy way. The TCDB website also offers several tools specifically designed for analyzing the unique characteristics of transport proteins. TCDB not only provides curated information and a tool for classifying newly identified membrane proteins, but also serves as a genome transporter-annotation tool.},
author = {Saier, Milton H and Tran, Can V and Barabote, Ravi D},
doi = {10.1093/nar/gkj001},
file = {:home/fin/Documents/papers/mendeley/Saier, Tran, Barabote\_2006\_TCDB the Transporter Classification Database for membrane transport protein analyses and information.\_Nucleic.pdf:pdf},
isbn = {1362-4962 (Electronic)},
issn = {1362-4962},
journal = {Nucleic Acids Res.},
pages = {D181--D186},
pmid = {16381841},
title = {{TCDB: the Transporter Classification Database for membrane transport protein analyses and information.}},
volume = {34},
year = {2006}
}
@incollection{Tanner1974,
author = {Tanner, W and Haass, D and Decker, M and Loos, E and Komor, B and Komor, E},
booktitle = {Membr. Transp. Plants SE  - 28},
doi = {10.1007/978-3-642-65986-7\_28},
editor = {Zimmermann, Ulrich and Dainty, Jack},
isbn = {978-3-642-65988-1},
language = {English},
pages = {202--208},
publisher = {Springer Berlin Heidelberg},
title = {{Active Hexose Transport in Chlorella vulgaris}},
url = {http://dx.doi.org/10.1007/978-3-642-65986-7\_28},
year = {1974}
}
@article{Yang2013a,
author = {Yang, X. and Chockalingam, S. P. and Aluru, S.},
doi = {10.1093/bib/bbs015},
file = {:home/fin/Documents/papers/mendeley/Yang, Chockalingam, Aluru\_2013\_A survey of error-correction methods for next-generation sequencing\_Briefings in Bioinformatics(2).pdf:pdf},
issn = {1467-5463},
journal = {Brief. Bioinform.},
keywords = {error correction,next-generation sequencing,sequence analysis},
number = {1},
pages = {56--66},
title = {{A survey of error-correction methods for next-generation sequencing}},
url = {http://bib.oxfordjournals.org/cgi/doi/10.1093/bib/bbs015},
volume = {14},
year = {2013}
}
@article{Gao2014,
author = {Gao, Chunfang and Wang, Yun and Shen, Yue and Yan, Dong and He, Xi and Dai, Junbiao and Wu, Qingyu},
doi = {10.1186/1471-2164-15-582},
file = {:home/fin/Documents/papers/mendeley/Gao et al.\_2014\_Oil accumulation mechanisms of the oleaginous microalga Chlorella protothecoides revealed through its genome, transcript.pdf:pdf},
issn = {1471-2164},
journal = {BMC Genomics},
keywords = {chlorella protothecoides,cn,correspondence,edu,genome sequence,hexose-proton,jbdai,lipid,microalgae,oil accumulation,proteomic,qingyu,symporter,transcriptome,tsinghua},
pages = {582},
title = {{Oil accumulation mechanisms of the oleaginous microalga Chlorella protothecoides revealed through its genome, transcriptomes, and proteomes}},
url = {http://www.biomedcentral.com/1471-2164/15/582},
volume = {15},
year = {2014}
}
@article{Hodges2011,
author = {Hodges, Matthew E and Wickstead, Bill and Gull, Keith and Langdale, Jane a},
doi = {10.1186/1471-2229-11-185},
file = {:home/fin/Documents/papers/mendeley/Hodges et al.\_2011\_Conservation of ciliary proteins in plants with no cilia\_BMC Plant Biology.pdf:pdf},
issn = {1471-2229},
journal = {BMC Plant Biol.},
keywords = {basal body,centriole,cilia,evolution,flagella,land plants},
number = {1},
pages = {185},
publisher = {BioMed Central Ltd},
title = {{Conservation of ciliary proteins in plants with no cilia}},
url = {http://www.biomedcentral.com/1471-2229/11/185},
volume = {11},
year = {2011}
}
@article{MacManes2014,
abstract = {The widespread and rapid adoption of high-throughput sequencing technologies has afforded researchers the opportunity to gain a deep understanding of genome level processes that underlie evolutionary change, and perhaps more importantly, the links between genotype and phenotype. In particular, researchers interested in functional biology and adaptation have used these technologies to sequence mRNA transcriptomes of specific tissues, which in turn are often compared to other tissues, or other individuals with different phenotypes. While these techniques are extremely powerful, careful attention to data quality is required. In particular, because high-throughput sequencing is more error-prone than traditional Sanger sequencing, quality trimming of sequence reads should be an important step in all data processing pipelines. While several software packages for quality trimming exist, no general guidelines for the specifics of trimming have been developed. Here, using empirically derived sequence data, I provide general recommendations regarding the optimal strength of trimming, specifically in mRNA-Seq studies. Although very aggressive quality trimming is common, this study suggests that a more gentle trimming, specifically of those nucleotides whose Phred score <2 or <5, is optimal for most studies across a wide variety of metrics.},
author = {MacManes, Matthew D.},
doi = {10.3389/fgene.2014.00013},
file = {:home/fin/Documents/papers/mendeley/MacManes\_2014\_On the optimal trimming of high-throughput mRNA sequence data\_Frontiers in Genetics.pdf:pdf},
isbn = {1664-8021 (Electronic)$\backslash$r1664-8021 (Linking)},
issn = {16648021},
journal = {Front. Genet.},
keywords = {Assembly error,Illumina,Quality control,Quality trimming,Rnaseq},
number = {January},
pages = {1--7},
pmid = {24567737},
title = {{On the optimal trimming of high-throughput mRNA sequence data}},
volume = {5},
year = {2014}
}
@article{Henikoff1992,
abstract = {Methods for alignment of protein sequences typically measure similarity by using a substitution matrix with scores for all possible exchanges of one amino acid with another. The most widely used matrices are based on the Dayhoff model of evolutionary rates. Using a different approach, we have derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins. This led to marked improvements in alignments and in searches using queries from each of the groups.},
author = {Henikoff, S and Henikoff, J G},
doi = {10.1073/pnas.89.22.10915},
file = {:home/fin/Documents/papers/mendeley/Henikoff, Henikoff\_1992\_Amino acid substitution matrices from protein blocks.\_Proceedings of the National Academy of Sciences of the Uni.pdf:pdf},
isbn = {0027-8424 (Print)},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
number = {November},
pages = {10915--10919},
pmid = {1438297},
title = {{Amino acid substitution matrices from protein blocks.}},
volume = {89},
year = {1992}
}
@incollection{Leung2014,
author = {Leung, HenryC.M. and Yiu, S M and Chin, FrancisY.L.},
booktitle = {Res. Comput. Mol. Biol. SE  - 12},
doi = {10.1007/978-3-319-05269-4\_12},
editor = {Sharan, Roded},
isbn = {978-3-319-05268-7},
keywords = {assembling,metatranscriptomic reads,next-generation sequencing,protein sequence alignment},
language = {English},
pages = {160--172},
publisher = {Springer International Publishing},
series = {Lecture Notes in Computer Science},
title = {{IDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Information}},
url = {http://dx.doi.org/10.1007/978-3-319-05269-4\_12},
volume = {8394},
year = {2014}
}
@article{Ketting2011,
abstract = {Small non-coding RNAs, through association with Argonaute protein family members, have a variety of functions during the development of an organism. Although there is increased mechanistic understanding of the RNA interference (RNAi) pathways surrounding these small RNAs, how their effects are modulated by subcellular compartmentalization and cross-pathway functional interactions is only beginning to be explored. This review examines the current understanding of these aspects of RNAi pathways and the biological functions of these pathways. © 2011 Elsevier Inc.},
author = {Ketting, Ren\'{e} F.},
doi = {10.1016/j.devcel.2011.01.012},
file = {:home/fin/Documents/papers/mendeley/Ketting\_2011\_The Many Faces of RNAi\_Developmental Cell.pdf:pdf},
isbn = {1878-1551 (Electronic) 1534-5807 (Linking)},
issn = {15345807},
journal = {Dev. Cell},
pages = {148--161},
pmid = {21316584},
title = {{The Many Faces of RNAi}},
volume = {20},
year = {2011}
}
@article{Tautenhahn2012a,
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Tautenhahn, Ralf and Cho, Kevin and Uritboonthai, Winnie and Zhu, Zhengjiang and Patti, Gary J and Siuzdak, Gary},
doi = {10.1038/nbt.2348},
eprint = {NIHMS150003},
file = {:home/fin/Documents/papers/mendeley/Tautenhahn et al.\_2012\_An accelerated workflow for untargeted metabolomics using the METLIN database.\_Nat Biotechnol.pdf:pdf},
isbn = {1546-1696},
issn = {1087-0156},
journal = {Nat Biotechnol},
keywords = {Alpha,Database Management Systems,Databases, Factual,Humans,Metabolomics,Tandem Mass Spectrometry,research support, n.i.h., extramural,research support, non-u.s. gov't,research support, u.s. gov't, non-p.h.s.},
number = {9},
pages = {826--828},
pmid = {22965049},
title = {{An accelerated workflow for untargeted metabolomics using the METLIN database.}},
volume = {30},
year = {2012}
}
@manual{Wickham2014,
annote = {R package version 0.3.0.2},
author = {Wickham, Hadley and Francois, Romain},
title = {{dplyr: A Grammar of Data Manipulation}},
url = {http://cran.r-project.org/package=dplyr},
year = {2014}
}
@article{Korfhage2015,
author = {Korfhage, Christian and Fricke, Evelyn and Meier, Andreas},
doi = {10.1002/0471142727.mb0720s111},
file = {:home/fin/Documents/papers/mendeley/Korfhage, Fricke, Meier\_2015\_Whole-Transcriptome Amplification of Single Cells for Next-Generation Sequencing\_Current Protocols in Molec.pdf:pdf},
isbn = {0471142727},
journal = {Curr. Protoc. Mol. Biol.},
keywords = {2015,a,and meier,article,c,cell r next-generation sequencing,e,fricke,how to cite this,korfhage,ngs,r cancer r whole,r gene regulation,transcriptome amplification,transcriptome analysis r single,whole-transcriptome,wta},
number = {July},
pages = {7.20.1--7.20.19},
title = {{Whole-Transcriptome Amplification of Single Cells for Next-Generation Sequencing}},
url = {http://doi.wiley.com/10.1002/0471142727.mb0720s111},
year = {2015}
}
@article{Geurts2006,
author = {Geurts, Pierre and Ernst, Damien and Wehenkel, Louis},
doi = {10.1007/s10994-006-6226-1},
file = {:home/fin/Documents/papers/mendeley/Geurts, Ernst, Wehenkel\_2006\_Extremely randomized trees\_Machine Learning.pdf:pdf},
issn = {0885-6125},
journal = {Mach. Learn.},
keywords = {bias,cut-point randomization,decision and regression trees,ensemble methods,kernel-based models,supervised learning,variance tradeoff},
number = {October 2005},
pages = {3--42},
title = {{Extremely randomized trees}},
url = {http://link.springer.com/10.1007/s10994-006-6226-1},
volume = {63},
year = {2006}
}
@article{Kodama2012,
abstract = {Cells of the ciliate Paramecium bursaria harbor symbiotic Chlorella spp. in their cytoplasm. To establish endosymbiosis with alga-free P. bursaria, symbiotic algae must leave the digestive vacuole (DV) to appear in the cytoplasm by budding of the DV membrane. This budding was induced not only by intact algae but also by boiled or fixed algae. However, this budding was not induced when food bacteria or India ink were ingested into the DVs. These results raise the possibility that P. bursaria can recognize sizes of the contents in the DVs. To elucidate this possibility, microbeads with various diameters were mixed with alga-free P. bursaria and traced their fate. Microbeads with 0.20$\mu$m diameter did not induce budding of the DVs. Microbeads with 0.80$\mu$m diameter produced DVs of 5-10$\mu$m diameter at 3min after mixing; then the DVs fragmented and became vacuoles of 2-5$\mu$m diameter until 3h after mixing. Each microbead with a diameter larger than 3.00$\mu$m induced budding similarly to symbiotic Chlorella. These observations reveal that induction of DV budding depends on the size of the contents in the DVs. Dynasore, a dynamin inhibitor, greatly inhibited DV budding, suggesting that dynamin might be involved in DV budding.},
author = {Kodama, Yuuki and Fujishima, Masahiro},
doi = {10.1016/j.protis.2011.10.004},
file = {:home/fin/Documents/papers/mendeley/Kodama, Fujishima\_2012\_Characteristics of the digestive vacuole membrane of the alga-bearing ciliate Paramecium bursaria.\_Protist.pdf:pdf},
issn = {1618-0941},
journal = {Protist},
keywords = {Chlorella,Chlorella: physiology,Chlorella: ultrastructure,Intracellular Membranes,Intracellular Membranes: ultrastructure,Paramecium,Paramecium: microbiology,Paramecium: physiology,Paramecium: ultrastructure,Symbiosis,Vacuoles,Vacuoles: microbiology,Vacuoles: physiology,Vacuoles: ultrastructure},
month = jul,
number = {4},
pages = {658--70},
pmid = {22177452},
publisher = {Elsevier GmbH.},
title = {{Characteristics of the digestive vacuole membrane of the alga-bearing ciliate Paramecium bursaria.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22177452},
volume = {163},
year = {2012}
}
@article{Hoshina2013,
author = {Hoshina, Ryo and Fujiwara, Yuko},
doi = {10.1111/pre.12010},
file = {:home/fin/Documents/papers/mendeley/Hoshina, Fujiwara\_2013\_Molecular characterization of Chlorella cultures of the National Institute for Environmental Studies culture coll.pdf:pdf},
issn = {13220829},
journal = {Phycol. Res.},
keywords = {chlorella,didymogenes,group i intron,internal transcribed spacer 2,micractinium,species},
month = apr,
number = {2},
pages = {124--132},
title = {{Molecular characterization of Chlorella cultures of the National Institute for Environmental Studies culture collection with description of Micractinium inermum sp. nov., Didymogenes sphaerica sp. nov., and Didymogenes soliella sp. nov. (Chlorellaceae, Tr}},
url = {http://doi.wiley.com/10.1111/pre.12010},
volume = {61},
year = {2013}
}
@article{Lineberger1980,
abstract = {Differential cryoprotection is afforded to chloroplast thylakoids against freeze-induced uncoupling of cyclic photophosphorylation by equimolar concentrations of glucose, sucrose, and raffinose. This differential protective effect appears to be due to nonideal activity-concentration profiles exhibited by the sugars during freezing. When cryoprotection is analyzed as a function of the mole fraction of NaCl to which the membranes are exposed during freezing, the pattern of protection to cyclic photophosphorylation and its component reactions is not dependent upon the chemical identity of the protective solute. Cryoprotective efficiency of glucose, sucrose, and raffinose can be accounted for by proposing an activity dependent alteration in the freezing environment rather than specific solute-membrane interactions.},
author = {Lineberger, R D},
doi = {10.1104/pp.65.2.298},
file = {:home/fin/Documents/papers/mendeley/Lineberger\_1980\_Cryoprotection by glucose, sucrose, and raffinose to chloroplast thylakoids.\_Plant physiology.pdf:pdf},
issn = {0032-0889},
journal = {Plant Physiol.},
pages = {298--304},
pmid = {16661177},
title = {{Cryoprotection by glucose, sucrose, and raffinose to chloroplast thylakoids.}},
volume = {65},
year = {1980}
}
@article{Mathews2004,
abstract = {A dynamic programming algorithm for prediction of RNA secondary structure has been revised to accommodate folding constraints determined by chemical modification and to include free energy increments for coaxial stacking of helices when they are either adjacent or separated by a single mismatch. Furthermore, free energy parameters are revised to account for recent experimental results for terminal mismatches and hairpin, bulge, internal, and multibranch loops. To demonstrate the applicability of this method, in vivo modification was performed on 5S rRNA in both Escherichia coli and Candida albicans with 1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate, dimethyl sulfate, and kethoxal. The percentage of known base pairs in the predicted structure increased from 26.3\% to 86.8\% for the E. coli sequence by using modification constraints. For C. albicans, the accuracy remained 87.5\% both with and without modification data. On average, for these sequences and a set of 14 sequences with known secondary structure and chemical modification data taken from the literature, accuracy improves from 67\% to 76\%. This enhancement primarily reflects improvement for three sequences that are predicted with <40\% accuracy on the basis of energetics alone. For these sequences, inclusion of chemical modification constraints improves the average accuracy from 28\% to 78\%. For the 11 sequences with <6\% pseudoknotted base pairs, structures predicted with constraints from chemical modification contain on average 84\% of known canonical base pairs.},
author = {Mathews, David H and Disney, Matthew D and Childs, Jessica L and Schroeder, Susan J and Zuker, Michael and Turner, Douglas H},
doi = {10.1073/pnas.0401799101},
file = {:home/fin/Documents/papers/mendeley/Mathews et al.\_2004\_Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary.pdf:pdf},
isbn = {0027-8424 (Print)$\backslash$n0027-8424 (Linking)},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
number = {19},
pages = {7287--7292},
pmid = {15123812},
title = {{Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.}},
volume = {101},
year = {2004}
}
@article{Shi2005,
author = {Shi, D.-Q.},
doi = {10.1105/tpc.105.033563},
file = {:home/fin/Documents/papers/mendeley/Shi\_2005\_SLOW WALKER1, Essential for Gametogenesis in Arabidopsis, Encodes a WD40 Protein Involved in 18S Ribosomal RNA Biogenesis\_the P.pdf:pdf},
issn = {1040-4651},
journal = {Plant Cell Online},
keywords = {agronomy,beijing 100094,biochemistry,c state key laboratory,california 95616,china,china agricultural university,college of biological sciences,d plant biology and,davis,ek life sciences laboratory,life sciences addition 1002,national university of singapore,of plant physiology and,singapore 117604,university of california},
number = {August},
pages = {2340--2354},
title = {{SLOW WALKER1, Essential for Gametogenesis in Arabidopsis, Encodes a WD40 Protein Involved in 18S Ribosomal RNA Biogenesis}},
url = {http://www.plantcell.org/cgi/doi/10.1105/tpc.105.033563},
volume = {17},
year = {2005}
}
@inproceedings{Wichterman1946,
author = {Wichterman, R},
booktitle = {Anat. Rec.},
number = {3},
organization = {WILEY-LISS DIV JOHN WILEY \& SONS INC, 605 THIRD AVE, NEW YORK, NY 10158-0012},
pages = {381--382},
title = {{TIME RELATIONSHIPS OF THE NUCLEAR BEHAVIOR IN THE CONJUGATION OF GREEN AND COLORLESS PARAMECIUM-BURSARIA}},
volume = {94},
year = {1946}
}
@article{Leemis2008,
author = {Leemis, Lawrence M and McQueston, Jacquelyn T},
doi = {10.1198/000313008X270448},
file = {:home/fin/Documents/papers/mendeley/Leemis, McQueston\_2008\_Univariate Distribution Relationships\_The American Statistician.pdf:pdf},
issn = {0003-1305},
journal = {Am. Stat.},
keywords = {asymptotic relationships,distribution proper-,limiting distributions,stochastic parameters,ties,transforma-},
month = feb,
number = {1},
pages = {45--53},
title = {{Univariate Distribution Relationships}},
url = {http://www.tandfonline.com/doi/abs/10.1198/000313008X270448},
volume = {62},
year = {2008}
}
@article{Emanuelsson2000,
abstract = {A neural network-based tool, TargetP, for large-scale subcellular location prediction of newly identified proteins has been developed. Using N-terminal sequence information only, it discriminates between proteins destined for the mitochondrion, the chloroplast, the secretory pathway, and "other" localizations with a success rate of 85\% (plant) or 90\% (non-plant) on redundancy-reduced test sets. From a TargetP analysis of the recently sequenced Arabidopsis thaliana chromosomes 2 and 4 and the Ensembl Homo sapiens protein set, we estimate that 10\% of all plant proteins are mitochondrial and 14\% chloroplastic, and that the abundance of secretory proteins, in both Arabidopsis and Homo, is around 10\%. TargetP also predicts cleavage sites with levels of correctly predicted sites ranging from approximately 40\% to 50\% (chloroplastic and mitochondrial presequences) to above 70\% (secretory signal peptides). TargetP is available as a web-server at http://www.cbs.dtu.dk/services/TargetP/.},
author = {Emanuelsson, O and Nielsen, H and Brunak, S and von Heijne, G},
doi = {10.1006/jmbi.2000.3903},
file = {:home/fin/Documents/papers/mendeley/Emanuelsson et al.\_2000\_Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.\_Journal of Molecu.pdf:pdf},
issn = {0022-2836},
journal = {J. Mol. Biol.},
keywords = {Amino Acid Sequence,Arabidopsis,Biological Transport,Chloroplasts,Chloroplasts: chemistry,Chloroplasts: metabolism,Cytoplasm,Cytoplasm: chemistry,Cytoplasm: metabolism,Databases,Factual,Humans,Internet,Mitochondria,Mitochondria: chemistry,Mitochondria: metabolism,Molecular Sequence Data,Neural Networks (Computer),Nuclear Proteins,Nuclear Proteins: chemistry,Nuclear Proteins: genetics,Nuclear Proteins: metabolism,Plant Proteins,Plant Proteins: chemistry,Plant Proteins: genetics,Plant Proteins: metabolism,Plant Proteins: secretion,Post-Translational,Protein Processing,Protein Sorting Signals,Protein Sorting Signals: chemistry,Protein Sorting Signals: physiology,Proteins,Proteins: chemistry,Proteins: genetics,Proteins: metabolism,Proteins: secretion,Reproducibility of Results,Sensitivity and Specificity,Software},
month = jul,
number = {4},
pages = {1005--16},
pmid = {10891285},
title = {{Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10891285},
volume = {300},
year = {2000}
}
@article{Vogt1992,
author = {Vogt, G.},
doi = {10.1007/BF01403722},
file = {:home/fin/Documents/papers/mendeley/Vogt\_1992\_Enclosure of bacteria by the rough endoplasmic reticulum of shrimp hepatopancreas cells\_Protoplasma.pdf:pdf},
issn = {0033183X},
journal = {Protoplasma},
keywords = {Bacteria,Endocytobiosis,Endoplasmic reticulum,Hepatopancreas,Palaemon elegans,Peribacterial compartment},
pages = {89--96},
title = {{Enclosure of bacteria by the rough endoplasmic reticulum of shrimp hepatopancreas cells}},
volume = {171},
year = {1992}
}
@article{Stern2012,
abstract = {BACKGROUND: DNA barcoding offers an efficient way to determine species identification and to measure biodiversity. For dinoflagellates, an ancient alveolate group of about 2000 described extant species, DNA barcoding studies have revealed large amounts of unrecognized species diversity, most of which is not represented in culture collections. To date, two mitochondrial gene markers, Cytochrome Oxidase I (COI) and Cytochrome b oxidase (COB), have been used to assess DNA barcoding in dinoflagellates, and both failed to amplify all taxa and suffered from low resolution. Nevertheless, both genes yielded many examples of morphospecies showing cryptic speciation and morphologically distinct named species being genetically similar, highlighting the need for a common marker. For example, a large number of cultured Symbiodinium strains have neither taxonomic identification, nor a common measure of diversity that can be used to compare this genus to other dinoflagellates.$\backslash$n$\backslash$nMETHODOLOGY/PRINCIPAL FINDINGS: The purpose of this study was to evaluate the Internal Transcribed Spacer units 1 and 2 (ITS) of the rDNA operon, as a high resolution marker for distinguishing species dinoflagellates in culture. In our study, from 78 different species, the ITS barcode clearly differentiated species from genera and could identify 96\% of strains to a known species or sub-genus grouping. 8.3\% showed evidence of being cryptic species. A quarter of strains identified had no previous species identification. The greatest levels of hidden biodiversity came from Scrippsiella and the Pfiesteriaceae family, whilst Heterocapsa strains showed a high level of mismatch to their given species name.$\backslash$n$\backslash$nCONCLUSIONS/SIGNIFICANCE: The ITS marker was successful in confirming species, revealing hidden diversity in culture collections. This marker, however, may have limited use for environmental barcoding due to paralogues, the potential for unidentifiable chimaeras and priming across taxa. In these cases ITS would serve well in combination with other markers or for specific taxon studies.},
author = {Stern, Rowena F and Andersen, Robert a and Jameson, Ian and K\"{u}pper, Frithjof C and Coffroth, Mary-Alice and Vaulot, Daniel and {Le Gall}, Florence and V\'{e}ron, Beno\^{\i}t and Brand, Jerry J and Skelton, Hayley and Kasai, Fumai and Lilly, Emily L and Keeling, Patrick J},
doi = {10.1371/journal.pone.0042780},
file = {:home/fin/Documents/papers/mendeley/Stern et al.\_2012\_Evaluating the ribosomal internal transcribed spacer (ITS) as a candidate dinoflagellate barcode marker.\_PloS one.pdf:pdf},
isbn = {1932-6203 (Electronic)$\backslash$r1932-6203 (Linking)},
issn = {1932-6203},
journal = {PLoS One},
keywords = {Animals,DNA Barcoding, Taxonomic,Dinoflagellida,Dinoflagellida: classification,Dinoflagellida: enzymology,Dinoflagellida: genetics,Electron Transport Complex IV,Electron Transport Complex IV: genetics,Genetic Markers,Phylogeny,Ribosomes,Ribosomes: metabolism},
number = {8},
pages = {e42780},
pmid = {22916158},
title = {{Evaluating the ribosomal internal transcribed spacer (ITS) as a candidate dinoflagellate barcode marker.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3420951\&tool=pmcentrez\&rendertype=abstract},
volume = {7},
year = {2012}
}
@article{Sapp2002,
abstract = {Constantin Merezhkowsky is celebrated today for his theory of symbiogenesis, postulated in the early decades of the twentieth century, particularly that chloroplasts were symbiotic cyanophytes (cyanobacteria). While biologists point singularly to what they see as his heroic achievement, its neglect and subsequent rediscovery, we introduce a broader and much more complex perspective on his science, his troubled life and career. We present a view of Merezhkowsky as zoologist, anthropologist, botanist, philosopher, and novelist. We explain the genesis of his theory of the origin of chloroplasts and of nucleus and cytoplasm as symbionts, as well as his depiction of the geo-chemical context of the origins and early evolution of life on earth. We also disclose his sordid social and political activities, his eugenics and racist writings, his paedophilia, and his metaphysics. Finally, we describe the context of his elaborate suicide in 1921.},
author = {Sapp, Jan and Carrapi\c{c}o, Francisco and Zolotonosov, Mikhail},
doi = {10.1080/03919710210001714493},
file = {:home/fin/Documents/papers/mendeley/Sapp, Carrapi\c{c}o, Zolotonosov\_2002\_Symbiogenesis the hidden face of Constantin Merezhkowsky.\_History and philosophy of the life sciences.pdf:pdf},
isbn = {0465043917},
issn = {0391-9714},
journal = {Hist. Philos. Life Sci.},
pages = {413--440},
pmid = {15045832},
title = {{Symbiogenesis: the hidden face of Constantin Merezhkowsky.}},
volume = {24},
year = {2002}
}
@article{Krasileva2013,
abstract = {BACKGROUND: The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs.$\backslash$n$\backslash$nRESULTS: A total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96\% of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22\% relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7\% of SNPs analyzed are correctly separated by phasing.$\backslash$n$\backslash$nCONCLUSIONS: Our study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies.},
archivePrefix = {arXiv},
arxivId = {arXiv:1305.6760},
author = {Krasileva, Ksenia V and Buffalo, Vince and Bailey, Paul and Pearce, Stephen and Ayling, Sarah and Tabbita, Facundo and Soria, Marcelo and Wang, Shichen and Akhunov, Eduard and Uauy, Cristobal and Dubcovsky, Jorge},
doi = {10.1186/gb-2013-14-6-r66},
eprint = {arXiv:1305.6760},
file = {:home/fin/Documents/papers/mendeley/Krasileva et al.\_2013\_Separating homeologs by phasing in the tetraploid wheat transcriptome.\_Genome biology.pdf:pdf},
isbn = {1465-6914 (Electronic)$\backslash$r1465-6906 (Linking)},
issn = {1465-6914},
journal = {Genome Biol.},
keywords = {gene prediction,multiple k-mer assembly,phasing,polyploid,pseudogenes,transcriptome assembly,triticum turgidum,triticum urartu,wheat},
pages = {R66},
pmid = {23800085},
title = {{Separating homeologs by phasing in the tetraploid wheat transcriptome.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4053977\&tool=pmcentrez\&rendertype=abstract},
volume = {14},
year = {2013}
}
@article{Hoff2009,
abstract = {Metagenomic sequencing projects yield numerous sequencing reads of a diverse range of uncultivated and mostly yet unknown microorganisms. In many cases, these sequencing reads cannot be assembled into longer contigs. Thus, gene prediction tools that were originally developed for whole-genome analysis are not suitable for processing metagenomes. Orphelia is a program for predicting genes in short DNA sequences that is available through a web server application (http://orphelia.gobics.de). Orphelia utilizes prediction models that were created with machine learning techniques on the basis of a wide range of annotated genomes. In contrast to other methods for metagenomic gene prediction, Orphelia has fragment length-specific prediction models for the two most popular sequencing techniques in metagenomics, chain termination sequencing and pyrosequencing. These models ensure highly specific gene predictions.},
author = {Hoff, Katharina J and Lingner, Thomas and Meinicke, Peter and Tech, Maike},
doi = {10.1093/nar/gkp327},
file = {:home/fin/Documents/papers/mendeley/Hoff et al.\_2009\_Orphelia predicting genes in metagenomic sequencing reads.\_Nucleic acids research.pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$r0305-1048 (Linking)},
issn = {1362-4962},
journal = {Nucleic Acids Res.},
keywords = {Environmental Microbiology,Genes,Genomics,Internet,Open Reading Frames,Sequence Analysis, DNA,Software,User-Computer Interface},
number = {May},
pages = {W101--5},
pmid = {19429689},
title = {{Orphelia: predicting genes in metagenomic sequencing reads.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2703946\&tool=pmcentrez\&rendertype=abstract},
volume = {37},
year = {2009}
}
@article{Xu2014,
abstract = {High-throughput RNA sequencing (RNA-seq) has become an instrumental assay for the analysis of multiple aspects of an organism's transcriptome. Further, the analysis of a biological specimen's associated microbiome can also be performed using RNA-seq data and this application is gaining interest in the scientific community. There are many existing bioinformatics tools designed for analysis and visualization of transcriptome data. Despite the availability of an array of next generation sequencing (NGS) analysis tools, the analysis of RNA-seq data sets poses a challenge for many biomedical researchers who are not familiar with command-line tools. Here we present RNA CoMPASS, a comprehensive RNA-seq analysis pipeline for the simultaneous analysis of transcriptomes and metatranscriptomes from diverse biological specimens. RNA CoMPASS leverages existing tools and parallel computing technology to facilitate the analysis of even very large datasets. RNA CoMPASS has a web-based graphical user interface with intrinsic queuing to control a distributed computational pipeline. RNA CoMPASS was evaluated by analyzing RNA-seq data sets from 45 B-cell samples. Twenty-two of these samples were derived from lymphoblastoid cell lines (LCLs) generated by the infection of na\"{\i}ve B-cells with the Epstein Barr virus (EBV), while another 23 samples were derived from Burkitt's lymphomas (BL), some of which arose in part through infection with EBV. Appropriately, RNA CoMPASS identified EBV in all LCLs and in a fraction of the BLs. Cluster analysis of the human transcriptome component of the RNA CoMPASS output clearly separated the BLs (which have a germinal center-like phenotype) from the LCLs (which have a blast-like phenotype) with evidence of activated MYC signaling and lower interferon and NF-kB signaling in the BLs. Together, this analysis illustrates the utility of RNA CoMPASS in the simultaneous analysis of transcriptome and metatranscriptome data. RNA CoMPASS is freely available at http://rnacompass.sourceforge.net/.},
author = {Xu, Guorong and Strong, Michael J. and Lacey, Michelle R. and Baribault, Carl and Flemington, Erik K. and Taylor, Christopher M.},
doi = {10.1371/journal.pone.0089445},
file = {:home/fin/Documents/papers/mendeley/Xu et al.\_2014\_RNA CoMPASS A dual approach for pathogen and host\_PLoS ONE.pdf:pdf},
issn = {19326203},
journal = {PLoS One},
number = {2},
pmid = {24586784},
title = {{RNA CoMPASS: A dual approach for pathogen and host}},
volume = {9},
year = {2014}
}
@article{Kadono2004,
abstract = {Paramecium bursaria (green paramecium) possesses endosymbiotically growing chlorella-like green algae. An aposymbiotic cell line of P. bursaria (MBw-1) was prepared from the green MB-1 strain with the herbicide paraquat. The SA-2 clone of symbiotic algae was employed to reinfect MBw-1 cells and thus a regreened cell line (MBr-1) was obtained. The regreened paramecia were used to study the impact of the host's growth status on the life cycle of the symbiotic algae. Firstly, the relationship between the timing of algal propagation and the host cell division was investigated by counting the algal cells in single host cells during and after the host cell division and also in the stationary phase. Secondly, the changes in the endogenous chlorophyll level, DNA content, and cell size in the symbiotic algae were monitored by flow cytometry and fluorescence microscopy. The number of algae was shown to be doubled prior to or during the host cell division and the algal population in the two daughter cells is maintained at constant level until the host cell cycle reenters the cytokinesis, suggesting that algal propagation and cell cycle are dependent on the host's cell cycle. During the host's stationary growth, unicellular algal vegetatives with low chlorophyll content were dominant. In contrast, complexes of algal cells called sporangia (containing 1-4 autospores) were present in the logarithmically growing hosts, indicating that algal cell division leading to the formation of sporangia with multiple autospores is active in the dividing paramecia.},
author = {Kadono, T and Kawano, T and Hosoya, H and Kosaka, T},
doi = {10.1007/s00709-004-0046-6},
file = {:home/fin/Documents/papers/mendeley/Kadono et al.\_2004\_Flow cytometric studies of the host-regulated cell cycle in algae symbiotic with green paramecium.\_Protoplasma.pdf:pdf},
issn = {0033-183X},
journal = {Protoplasma},
keywords = {Animals,Cell Cycle,Cell Division,Cell Size,Chlorophyll,Chlorophyll: metabolism,DNA,DNA: metabolism,Eukaryota,Eukaryota: cytology,Eukaryota: genetics,Eukaryota: physiology,Flow Cytometry,Life Cycle Stages,Paramecium,Paramecium: growth \& development,Paramecium: microbiology,Symbiosis},
month = jun,
pages = {133--141},
pmid = {15221518},
title = {{Flow cytometric studies of the host-regulated cell cycle in algae symbiotic with green paramecium.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15221518},
volume = {223},
year = {2004}
}
@article{Lloyd1982,
abstract = {It has long been realized that in pulse-code modulation (PCM), with a given ensemble of signals to handle, the quantum values should be spaced more closely in the voltage regions where the signal amplitude is more likely to fall. It has been shown by Panter and Dite that, in the limit as the number of quanta becomes infinite, the asymptotic fractional density of quanta per unit voltage should vary as the one-third power of the probability density per unit voltage of signal amplitudes. In this paper the corresponding result for any finite number of quanta is derived; that is, necessary conditions are found that the quanta and associated quantization intervals of an optimum finite quantization scheme must satisfy. The optimization criterion used is that the average quantiza- tion noise power be a minimum. It is shown that the result obtained here goes over into the Panter and Dite result as the number of quanta become large. The optimum quantization schemes for 26 quanta, b = 1,2,...,7, are given numerically for Gaussian and for Laplacian distribution of signal amplitudes.},
author = {Lloyd, S.},
doi = {10.1109/TIT.1982.1056489},
file = {:home/fin/Documents/papers/mendeley/Lloyd\_1982\_Least squares quantization in PCM\_IEEE Transactions on Information Theory.pdf:pdf},
isbn = {00189448 (ISSN)},
issn = {0018-9448},
journal = {IEEE Trans. Inf. Theory},
number = {2},
pages = {129--137},
title = {{Least squares quantization in PCM}},
volume = {28},
year = {1982}
}
@article{Buchon2006,
abstract = {RNA silencing is a form of nucleic-acid-based immunity, targeting viruses and genomic repeated sequences. First documented in plants and invertebrate animals, this host defence has recently been identified in mammals. RNAi is viewed as a conserved ancient mechanism protecting genomes from nucleic acid invaders. However, these tamed sequences are known to occasionally escape this host surveillance and invade the genome of their host. This response is consistent with the overall idea that parasitic sequences compete with cells to systematically counter host defences. Using examples taken from the current literature, we illustrate the dynamic move-countermove game played between these two protagonists, the host cell and its parasitic sequences, and discuss the consequences of this game on genome stability.},
author = {Buchon, N and Vaury, C},
doi = {10.1038/sj.hdy.6800789},
file = {:home/fin/Documents/papers/mendeley/Buchon, Vaury\_2006\_RNAi a defensive RNA-silencing against viruses and transposable elements.\_Heredity.pdf:pdf},
isbn = {0018-067X (Print)$\backslash$n0018-067X (Linking)},
issn = {0018-067X},
journal = {Heredity (Edinb).},
keywords = {Animals,DNA Transposable Elements,Host-Parasite Interactions,Host-Parasite Interactions: genetics,RNA Interference,Viruses,Viruses: genetics,Viruses: pathogenicity},
pages = {195--202},
pmid = {16369574},
title = {{RNAi: a defensive RNA-silencing against viruses and transposable elements.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16369574},
volume = {96},
year = {2006}
}
@article{Nordberg2014,
author = {Nordberg, H. and Cantor, M. and Dusheyko, S. and Hua, S. and Poliakov, a. and Shabalov, I. and Smirnova, T. and Grigoriev, I. V. and Dubchak, I.},
doi = {10.1093/nar/gkt1069},
file = {:home/fin/Documents/papers/mendeley/Nordberg et al.\_2014\_The genome portal of the Department of Energy Joint Genome Institute 2014 updates\_Nucleic Acids Research.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {November 2013},
pages = {D26--D31},
title = {{The genome portal of the Department of Energy Joint Genome Institute: 2014 updates}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkt1069},
volume = {42},
year = {2014}
}
@article{Nielsen1997,
author = {Nielsen, Henrik and Engelbrecht, Jacob and Brunak, Soren and Heijne, Gunnar},
doi = {10.1093/protein/10.1.1},
file = {:home/fin/Documents/papers/mendeley/Nielsen et al.\_1997\_Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites\_Protein Engineer.pdf:pdf},
isbn = {0269-2139 (Print)$\backslash$r0269-2139 (Linking)},
issn = {0129-0657},
journal = {Protein Eng.},
keywords = {1991,and the dicotelydoneous plant,arabidopsis thaliana,brunak,brunak et al,cleavage sites,e and s,hebsgaard,in pre-mrna from humans,protein sorting,s,secretion,signal peptide,submitted},
number = {1},
pages = {1--6},
pmid = {9051728},
title = {{Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites}},
url = {C:$\backslash$Users$\backslash$Ivan\_2$\backslash$Documents$\backslash$ReadCube Media$\backslash$Protein 1997 Nielsen H.pdf http://dx.doi.org/10.1093/protein/10.1.1},
volume = {10},
year = {1997}
}
@article{Camoni2006,
abstract = {H(+)-ATPase, the key enzyme for the energization of ion and nutrient transport across the plasma membrane, is activated by phosphorylation-dependent 14-3-3 binding. Since the involvement of 14-3-3 proteins in sugar sensing-regulated processes has recently emerged, here we address the question as to whether sugar sensing plays a role in the regulation of H(+)-ATPase. The data reported here show that sugar depletion inhibits the association of 14-3-3 proteins with H(+)-ATPase by hampering phosphorylation of the 14-3-3 binding site of the enzyme. By using non-metabolizable disaccharides, we show that H(+)-ATPase regulation by 14-3-3 proteins can involve a specific sugar perception and transduction mechanism.},
author = {Camoni, Lorenzo and Marra, Mauro and Garufi, Alessandra and Visconti, Sabina and Aducci, Patrizia},
doi = {10.1093/pcp/pcj046},
file = {:home/fin/Documents/papers/mendeley/Camoni et al.\_2006\_The maize root plasma membrane H-ATPase is regulated by a sugar-induced transduction pathway\_Plant and Cell Physiolog.pdf:pdf},
issn = {00320781},
journal = {Plant Cell Physiol.},
keywords = {14-3-3 proteins,H+-ATPase,Signal transduction,Sugar sensing,Zea mays},
number = {6},
pages = {743--747},
pmid = {16614095},
title = {{The maize root plasma membrane H+-ATPase is regulated by a sugar-induced transduction pathway}},
volume = {47},
year = {2006}
}
@article{Marker2010,
abstract = {In many eukaryotes, RNA-dependent RNA polymerases (RdRPs) play key roles in the RNAi pathway. They have been implicated in the recognition and processing of aberrant transcripts triggering the process, and in amplification of the silencing response. We have tested the functions of RdRP genes from the ciliate Paramecium tetraurelia in experimentally induced and endogenous mechanisms of gene silencing. In this organism, RNAi can be triggered either by high-copy, truncated transgenes or by directly feeding cells with double-stranded RNA (dsRNA). Surprisingly, dsRNA-induced silencing depends on the putatively functional RDR1 and RDR2 genes, which are required for the accumulation of both primary siRNAs and a distinct class of small RNAs suggestive of secondary siRNAs. In contrast, a third gene with a highly divergent catalytic domain, RDR3, is required for siRNA accumulation when RNAi is triggered by truncated transgenes. Our data further implicate RDR3 in the accumulation of previously described endogenous siRNAs and in the regulation of the surface antigen gene family. While only one of these genes is normally expressed in any clonal cell line, the knockdown of RDR3 leads to co-expression of multiple antigens. These results provide evidence for a functional specialization of Paramecium RdRP genes in distinct RNAi pathways operating during vegetative growth.},
author = {Marker, Simone and {Le Mou\"{e}l}, Anne and Meyer, Eric and Simon, Martin},
doi = {10.1093/nar/gkq131},
file = {:home/fin/Documents/papers/mendeley/Marker et al.\_2010\_Distinct RNA-dependent RNA polymerases are required for RNAi triggered by double-stranded RNA versus truncated transg.pdf:pdf},
isbn = {0002476800},
issn = {03051048},
journal = {Nucleic Acids Res.},
number = {12},
pages = {4092--4107},
pmid = {20200046},
title = {{Distinct RNA-dependent RNA polymerases are required for RNAi triggered by double-stranded RNA versus truncated transgenes in Paramecium tetraurelia}},
volume = {38},
year = {2010}
}
@article{Bengtsson2005,
author = {Bengtsson, Martin and St\aa hlberg, Anders and Rorsman, Patrik and Kubista, Mikael},
doi = {10.1101/gr.3820805.4},
file = {:home/fin/Documents/papers/mendeley/Bengtsson et al.\_2005\_Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution.pdf:pdf},
pages = {1388--1392},
title = {{Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels}},
year = {2005}
}
@article{Berger1980,
author = {Berger, Jacques},
file = {:home/fin/Documents/papers/mendeley/Berger\_1980\_Feeding Behaviour of Didinium nasutum on Paramecium bursaria with Normal or Apochlor

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib