text:
a heterotrophic protist engulfed and retained a cyanobacterium in its cytoplasm. Once successfully established, this plastid spread into other protist lineages through eukaryote-eukaryote (secondary and tertiary) endosymbioses. This process of serial cell capture and enslavement explains the diversity of photosynthetic eukaryotes. Recent genomic and phylogenomic approaches have significantly clarified plastid genome evolution, the movement of endosymbiont genes to the "host" nuclear genome (endosymbiotic gene transfer), and plastid spread throughout the eukaryotic tree of life. Here we review these aspects of plastid evolution with a focus on understanding early events in plastid endosymbiosis.},
author = {Reyes-Prieto, Adrian and Weber, Andreas P M and Bhattacharya, Debashish},
doi = {10.1146/annurev.genet.41.110306.130134},
file = {:home/fin/Documents/papers/mendeley/Reyes-Prieto, Weber, Bhattacharya\_2007\_The origin and establishment of the plastid in algae and plants.\_Annual review of genetics.pdf:pdf},
isbn = {0066-4197 (Print)$\backslash$n0066-4197 (Linking)},
issn = {0066-4197},
journal = {Annu. Rev. Genet.},
keywords = {cyanobacterium,endosymbiosis,endosymbiotic gene transfer,organelle,protein import,solute transporter},
pages = {147--168},
pmid = {17600460},
title = {{The origin and establishment of the plastid in algae and plants.}},
volume = {41},
year = {2007}
}
@article{Niess1982,
author = {Niess, D\"{o}rte and Reisser, Werner and Wiessner, Wolfgang},
doi = {10.1007/BF00393320},
file = {:home/fin/Documents/papers/mendeley/Niess, Reisser, Wiessner\_1982\_Photobehaviour of Paramecium bursaria infected with different symbiotic and aposymbiotic species of Chlore.pdf:pdf},
issn = {00320935},
journal = {Planta},
keywords = {Chlorella,Endosymbiosis,Infection,Paramecium bursaria,Photobehaviour},
pages = {475--480},
title = {{Photobehaviour of Paramecium bursaria infected with different symbiotic and aposymbiotic species of Chlorella}},
volume = {156},
year = {1982}
}
@article{Katoh2013,
author = {Katoh, K. and Standley, D. M.},
doi = {10.1093/molbev/mst010},
file = {:home/fin/Documents/papers/mendeley/Katoh, Standley\_2013\_MAFFT Multiple Sequence Alignment Software Version 7 Improvements in Performance and Usability\_Molecular Biology an.pdf:pdf},
issn = {0737-4038},
journal = {Mol. Biol. Evol.},
keywords = {metagemone,multiple sequence alignment,parallel processing,progressive alignment,protein structure},
number = {4},
pages = {772--780},
title = {{MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability}},
url = {http://mbe.oxfordjournals.org/cgi/doi/10.1093/molbev/mst010},
volume = {30},
year = {2013}
}
@incollection{Gortz1988,
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {Gortz, Hans-dieter},
booktitle = {Paramecium},
chapter = {22},
doi = {10.1017/CBO9781107415324.004},
editor = {Gortz, Hans-dieter},
eprint = {arXiv:1011.1669v3},
file = {:home/fin/Documents/papers/mendeley/Gortz\_1988\_Endocytobiosis\_Paramecium.pdf:pdf},
isbn = {9788578110796},
issn = {1098-6596},
keywords = {Gortz1988},
pages = {393--405},
pmid = {25246403},
publisher = {Springer-Verlag New York},
title = {{Endocytobiosis}},
year = {1988}
}
@article{Arnaiz2011a,
abstract = {ParameciumDB is a community model organism database built with the GMOD toolkit to integrate the genome and biology of the ciliate Paramecium tetraurelia. Over the last four years, post-genomic data from proteome and transcriptome studies has been incorporated along with predicted orthologs in 33 species, annotations from the community and publications from the scientific literature. Available tools include BioMart for complex queries, GBrowse2 for genome browsing, the Apollo genome editor for expert curation of gene models, a Blast server, a motif finder, and a wiki for protocols, nomenclature guidelines and other documentation. In-house tools have been developed for ontology browsing and evaluation of off-target RNAi matches. Now ready for next-generation deep sequencing data and the genomes of other Paramecium species, this open-access resource is available at http://paramecium.cgm.cnrs-gif.fr.},
author = {Arnaiz, Olivier and Sperling, Linda},
doi = {10.1093/nar/gkq918},
file = {:home/fin/Documents/papers/mendeley/Arnaiz, Sperling\_2011\_ParameciumDB in 2011 New tools and new data for functional and comparative genomics of the model ciliate Parame(2).pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$n0305-1048 (Linking)},
issn = {03051048},
journal = {Nucleic Acids Res.},
number = {October 2010},
pages = {632--636},
pmid = {20952411},
title = {{ParameciumDB in 2011: New tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia}},
volume = {39},
year = {2011}
}
@article{Darriba2012,
abstract = {The statistical selection of best-fit models of nucleotide substitution$\backslash$nis routine in the phylogenetic analysis of DNA sequence alignments1.$\backslash$nWith the advent of next-generation sequencing technologies, most$\backslash$nresearchers are moving from phylogenetics to phylogenomics, in which$\backslash$nlarge sequence alignments typically include hundreds or thousands$\backslash$nof loci. Phylogenetic resources\ldots},
author = {Darriba, Diego and Taboada, Guillermo L and Doallo, Ram\'{o}n and Posada, David},
doi = {10.1038/nmeth.2109},
file = {:home/fin/Documents/papers/mendeley/Darriba et al.\_2012\_jModelTest 2 more models, new heuristics and parallel computing\_Nature Methods.pdf:pdf},
isbn = {1548-7091},
issn = {1548-7091},
journal = {Nat. Methods},
number = {8},
pages = {772--772},
pmid = {22847109},
publisher = {Nature Publishing Group},
title = {{jModelTest 2: more models, new heuristics and parallel computing}},
url = {http://dx.doi.org/10.1038/nmeth.2109},
volume = {9},
year = {2012}
}
@article{Keeling2004a,
abstract = {By synthesizing data from individual gene phylogenies, large concatenated gene trees, and other kinds of molecular, morphological, and biochemical markers, we begin to see the broad outlines of a global phylogenetic tree of eukaryotes. This tree is apparently composed of five large assemblages, or ''supergroups.'' Plants and algae, or more generally eukaryotes with plastids (the photosynthetic organelle of plants and algae and their nonphotosynthetic derivatives) are scattered among four of the five supergroups. This is because plastids have had a complex evolutionary history involving several endosymbiotic events that have led to their transmission from one group to another. Here, the history of the plastid and of its various hosts is reviewed with particular attention to the number and nature of the endosymbiotic events that led to the current distribution of plastids. There is accumulating evidence to support a single primary origin of plastids from a cyanobacterium (with one intriguing possible exception in the little-studied amoeba Paulinella), followed by the diversification of glaucophytes, red and green algae, with plants evolving from green algae. Following this, some of these algae were themselves involved in secondary endosymbiotic events. The best current evidence indicates that two independent secondary endosymbioses involving green algae gave rise to euglenids and chlorarachniophytes, whereas a single endosymbiosis with a red algae gave rise to the chromalveolates, a diverse group including cryptomonads, haptophytes, heterokonts, and alveolates. Dinoflagellates (alveolates) have since taken up other algae in serial secondary and tertiary endosymbioses, raising a number of controversies over the origin of their plastids, and by extension, the recently discovered cryptic plastid of the closely related apicomplexan parasites. To understand an evolutionary process fully, it is important to understand the phylogenetic relationships among the organ-isms in which that process is manifested. Accordingly, our interpretation of the history of photosynthesis has been strong-ly influenced by changes in our understanding of the tree of life and, in particular, the tree of eukaryotes. Early attempts to reconstruct an evolutionary tree of eu-karyotes were based on morphological and biochemical sim-ilarities. These were highly successful at identifying many ma-jor groups of related organisms, but not as successful at iden-tifying the relationships between these large groups (Bruger-olle and Taylor, 1977). This is due in part to the fact that the majority of eukaryotic diversity lies in the microbial world (protists and algae), in which morphological characters uniting a particular group are often obvious, but characters for be-tween-group comparisons are less easy to come by. Certain highly conserved characters, such as features of mitochondrial ultrastructure (Taylor, 1978), were useful in extending our un-derstanding of large-scale relationships, but for some time the overall tree of eukaryotes resembled more a bush with a hand-ful of broken branches than it did a tree. The introduction of molecular data to phylogenetic analyses held great promise to solve this problem by providing a seem-ingly limitless supply of unambiguously comparable amino acid and nucleotide characters. The first large-scale molecular analyses based on small subunit ribosomal RNA (SSU rRNA) yielded a fully resolved tree, integrating microbial diversity and placing the plants, animals, and fungi in the context of their microbial cousins (Sogin, 1991). While some relation-ships on the rRNA tree were arguable (Hasegawa et al., 1993), overall it was the accepted model of eukaryotic evolution, and 1 Manuscript received},
author = {Keeling, Patrick J},
doi = {10.3732/ajb.91.10.1481},
file = {:home/fin/Documents/papers/mendeley/Keeling\_2004\_Diversity and Evolutionary History of Plastids and Their Hosts the Tree of Eukaryotes\_American Journal of Botany.pdf:pdf},
isbn = {0002-9122},
issn = {0002-9122, 1537-2197},
journal = {Am. J. Bot.},
keywords = {algae,endosymbiosis,phylogeny,plastid,tree of eukaryotes},
number = {10},
pages = {1481--1493},
pmid = {21652304},
title = {{Diversity and Evolutionary History of Plastids and Their Hosts the Tree of Eukaryotes}},
volume = {91},
year = {2004}
}
@article{Champenois2014,
author = {Champenois, Jennifer and Marfaing, H\'{e}l\`{e}ne and Pierre, Ronan},
doi = {10.1007/s10811-014-0431-2},
file = {:home/fin/Documents/papers/mendeley/Champenois, Marfaing, Pierre\_2014\_Review of the taxonomic revision of Chlorella and consequences for its food uses in Europe\_Journal of.pdf:pdf},
issn = {0921-8971},
journal = {J. Appl. Phycol.},
keywords = {chlorophyceae,food supplements,microalgae,novel food regulation,systematics},
pages = {1845--1851},
title = {{Review of the taxonomic revision of Chlorella and consequences for its food uses in Europe}},
url = {http://link.springer.com/10.1007/s10811-014-0431-2},
year = {2014}
}
@article{Sauer1989,
abstract = {The cDNA coding for the inducible H+/hexose cotransporter of Chlorella kessleri has been cloned and sequenced. It was isolated by differential screening of a cDNA library prepared from glucose-induced cells. The increase in expression of the gene correlates quantitatively with the increase in uptake activity due to induction; it is not expressed in a hexose transport mutant. An open reading frame allows for a membrane protein of 533 amino acids with a relative molecular mass of 57 kDa. This protein is highly homologous to the human and rat glucose transporters catalyzing facilitated diffusion and to the bacterial H+/pentose cotransporters. It is not related to the H+/lactose cotransporter of E. colli and to the mammalian Na+/glucose cotransporter.},
author = {Sauer, N. and Tanner, W.},
file = {:home/fin/Documents/papers/mendeley/Sauer, Tanner\_1989\_The Hexose Carrier from Chlorella. cDNA cloning of a eucaryotic H Cotransporter\_FEBS Letters.pdf:pdf},
issn = {0014-5793},
journal = {FEBS Lett.},
keywords = {Base Sequence,Blotting,Chlorella,Chlorella: genetics,Cloning,DNA,DNA: genetics,Genes,Messenger,Messenger: genetics,Molecular,Molecular Sequence Data,Molecular Weight,Monosaccharide Transport Proteins,Monosaccharide Transport Proteins: genetics,Plant,RNA,Southern},
number = {1},
pages = {43--6},
pmid = {2599110},
title = {{The Hexose Carrier from Chlorella. cDNA cloning of a eucaryotic H+ Cotransporter}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/2599110},
volume = {259},
year = {1989}
}
@article{Koonin2014,
author = {Koonin, Eugene V},
doi = {10.1073/pnas.1418789111},
file = {:home/fin/Documents/papers/mendeley/Koonin\_2014\_Horizontal transfer beyond genes.\_Proceedings of the National Academy of Sciences of the United States of America.pdf:pdf},
issn = {1091-6490},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
month = oct,
number = {45},
pages = {15865--15866},
pmid = {25359214},
title = {{Horizontal transfer beyond genes.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25359214},
volume = {111},
year = {2014}
}
@article{Fujishima2012,
abstract = {Paramecium species are extremely valuable organisms to enable experiments for the reestablishment of endosymbiosis. This is investigated in two different systems, the first with Paramecium caudatum and the endonuclear symbiotic bacterium Holospora species. Although most endosymbiotic bacteria cannot grow outside the host cell as a result of their reduced genome size, Holospora species can maintain their infectivity for a limited time. We found that an 89-kDa periplasmic protein has an important function for Holospora's invasion into the target nucleus, and that Holospora alters the host gene expression; the host thereby acquires resistance against various stresses. The second system is the symbiosis between P. bursaria and symbiotic Chlorella. Alga-free P. bursaria and the algae retain the ability to grow without a partner. Consequently, endosymbiosis between the aposymbiotic host cells and the symbiotic algae can be reestablished easily by mixing them. We now found four checkpoints for the reestablishment of the endosymbiosis between P. bursaria and the algae. The findings in the two systems provide excellent opportunities for us to elucidate not only infection processes but also to assess the associations leading to eukaryotic cell evolution. This paper summarizes recent progresses on reestablishment of the primary and the secondary endosymbiosis in Paramecium.},
author = {Fujishima, Masahiro and Kodama, Yuuki},
doi = {10.1016/j.ejop.2011.10.002},
file = {:home/fin/Documents/papers/mendeley/Fujishima, Kodama\_2012\_Endosymbionts in paramecium.\_European Journal of Protistology.pdf:pdf},
issn = {1618-0429},
journal = {Eur. J. Protistol.},
keywords = {Chlorella,Chlorella: physiology,Holosporaceae,Holosporaceae: physiology,Host-Pathogen Interactions,Paramecium,Paramecium: microbiology,Symbiosis},
month = may,
number = {2},
pages = {124--37},
pmid = {22153895},
publisher = {Elsevier GmbH},
title = {{Endosymbionts in paramecium.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22153895},
volume = {48},
year = {2012}
}
@article{Buchheim2011,
abstract = {BACKGROUND: Chloroplast-encoded genes (matK and rbcL) have been formally proposed for use in DNA barcoding efforts targeting embryophytes. Extending such a protocol to chlorophytan green algae, though, is fraught with problems including non homology (matK) and heterogeneity that prevents the creation of a universal PCR toolkit (rbcL). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta. METHODOLOGY/PRINCIPAL FINDINGS: Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses. CONCLUSIONS/SIGNIFICANCE: Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages.},
author = {Buchheim, Mark a and Keller, Alexander and Koetschan, Christian and F\"{o}rster, Frank and Merget, Benjamin and Wolf, Matthias},
doi = {10.1371/journal.pone.0016931},
file = {:home/fin/Documents/papers/mendeley/Buchheim et al.\_2011\_Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics towards an automated reconstruction o.pdf:pdf},
issn = {1932-6203},
journal = {PLoS One},
keywords = {Automation,Base Sequence,Chlorophyta,Chlorophyta: classification,Chlorophyta: genetics,DNA Barcoding,Phylogeny,RNA,Ribosomal,Ribosomal: genetics,Taxonomic,Taxonomic: methods},
month = jan,
number = {2},
pages = {e16931},
pmid = {21347329},
title = {{Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3037400\&tool=pmcentrez\&rendertype=abstract},
volume = {6},
year = {2011}
}
@article{Kumar1996,
abstract = {A stepwise algorithm for reconstructing minimum evolution (ME) trees from evolutionary distance data is proposed. In each step, a taxon that potentially has a neighbor (another taxon connected to it with a single interior node) is first chosen and then its true neighbor searched iteratively. For m taxa, at most (m-1)!/2 trees are examined and the tree with the minimum sum of branch lengths (S) is chosen as the final tree. This algorithm provides simple strategies for restricting the tree space searched and allows us to implement efficient ways of dynamically computing the ordinary least squares estimates of S for the topologies examined. Using computer simulation, we found that the efficiency of the ME method in recovering the correct tree is similar to that of the neighbor-joining method (Saitou and Nei 1987). A more exhaustive search is unlikely to improve the efficiency of the ME method in finding the correct tree because the correct tree is almost always included in the tree space searched with this stepwise algorithm. The new algorithm finds trees for which S values may not be significantly different from that of the ME tree if the correct tree contains very small interior branches or if the pairwise distance estimates have large sampling errors. These topologies form a set of plausible alternatives to the ME tree and can be compared with each other using statistical tests based on the minimum evolution principle. The new algorithm makes it possible to use the ME method for large data sets.},
author = {Kumar, S},
file = {:home/fin/Documents/papers/mendeley/Kumar\_1996\_A stepwise algorithm for finding minimum evolution trees.\_Molecular biology and evolution.pdf:pdf},
issn = {0737-4038},
journal = {Mol. Biol. Evol.},
keywords = {distance method,ing,phylogeny},
number = {4},
pages = {584--593},
pmid = {8882501},
title = {{A stepwise algorithm for finding minimum evolution trees.}},
volume = {13},
year = {1996}
}
@article{Sato2011,
abstract = {Protistan species belonging to the phylum Apicomplexa have a non-photosynthetic secondary plastid-the apicoplast. Although its tiny genome and even the entire nuclear genome has been sequenced for several organisms bearing the organelle, the reason for its existence remains largely obscure. Some of the functions of the apicoplast, including housekeeping ones, are significantly different from those of other plastids, possibly due to the organelle's unique symbiotic origin.},
author = {Sato, Shigeharu},
doi = {10.1007/s00018-011-0646-1},
file = {:home/fin/Documents/papers/mendeley/Sato\_2011\_The apicomplexan plastid and its evolution\_Cellular and Molecular Life Sciences.pdf:pdf},
isbn = {1420-9071 (Electronic)$\backslash$n1420-682X (Linking)},
issn = {1420682X},
journal = {Cell. Mol. Life Sci.},
keywords = {Apicomplexa,Evolution,Housekeeping functions,Plastid,Symbiosis},
pages = {1285--1296},
pmid = {21380560},
title = {{The apicomplexan plastid and its evolution}},
volume = {68},
year = {2011}
}
@article{Martinez2014,
author = {Martinez, J. and Longdon, B. and Bauer, S. and Chan, Yuk-Sang and Miller, W. J. and Bourtzis, K and Teixeira, L and Jiggins, Francis M.},
doi = {10.1371/journal.ppat.1004369},
file = {:home/fin/Documents/papers/mendeley/Martinez et al.\_2014\_Symbionts commonly provide broad spectrum resistance to viruses in insects a comparative analysis of Wolbachia stra.pdf:pdf},
issn = {15537374},
journal = {PLoS Pathog.},
number = {9},
pmid = {25233341},
title = {{Symbionts commonly provide broad spectrum resistance to viruses in insects: a comparative analysis of Wolbachia strains}},
volume = {In press},
year = {2014}
}
@article{Lasken2007,
abstract = {Single microbial cells can now be sequenced using DNA amplified by the Multiple Displacement Amplification (MDA) reaction. The few femtograms of DNA in a bacterium are amplified into micrograms of high molecular weight DNA suitable for DNA library construction and Sanger sequencing. The MDA-generated DNA also performs well when used directly as template for pyrosequencing by the 454 Life Sciences method. While MDA from single cells loses some of the genomic sequence, this approach will greatly accelerate the pace of sequencing from uncultured microbes. The genetically linked sequences from single cells are also a powerful tool to be used in guiding genomic assembly of shotgun sequences of multiple organisms from environmental DNA extracts (metagenomic sequences). ?? 2007 Elsevier Ltd. All rights reserved.},
author = {Lasken, Roger S.},
doi = {10.1016/j.mib.2007.08.005},
file = {:home/fin/Documents/papers/mendeley/Lasken\_2007\_Single-cell genomic sequencing using Multiple Displacement Amplification\_Current Opinion in Microbiology.pdf:pdf},
isbn = {1369-5274},
issn = {13695274},
journal = {Curr. Opin. Microbiol.},
pages = {510--516},
pmid = {17923430},
title = {{Single-cell genomic sequencing using Multiple Displacement Amplification}},
volume = {10},
year = {2007}
}
@article{Atkinson2005,
abstract = {In The Descent of Man (1871), Darwin observed "curious parallels" between the processes of biological and linguistic evolution. These parallels mean that evolutionary biologists and historical linguists seek answers to similar questions and face similar problems. As a result, the theory and methodology of the two disciplines have evolved in remarkably similar ways. In addition to Darwin's curious parallels of process, there are a number of equally curious parallels and connections between the development of methods in biology and historical linguistics. Here we briefly review the parallels between biological and linguistic evolution and contrast the historical development of phylogenetic methods in the two disciplines. We then look at a number of recent studies that have applied phylogenetic methods to language data and outline some current problems shared by the two fields.},
author = {Atkinson, Quentin D and Gray, Russell D},
doi = {10.1080/10635150590950317},
file = {:home/fin/Documents/papers/mendeley/Atkinson, Gray\_2005\_Curious parallels and curious connections--phylogenetic thinking in biology and historical linguistics.\_Systematic b.pdf:pdf},
isbn = {10635157},
issn = {1063-5157},
journal = {Syst. Biol.},
number = {4},
pages = {513--526},
pmid = {16051587},
title = {{Curious parallels and curious connections--phylogenetic thinking in biology and historical linguistics.}},
volume = {54},
year = {2005}
}
@article{Ohkawa2011,
abstract = {Single-cell green paramecia (Paramecium bursaria) is a swimming vehicle that carries several hundred cells of endo-symbiotic green algae. Here, a novel model for endo-symbiosis, prepared by introducing and maintaining the cells of cyanobacterium (Synechocystis spp. PCC 6803) in the apo-symbiotic cells of P. bursaria is described.},
author = {Ohkawa, Hiroshi and Hashimoto, Naoko and Furukawa, Shunsuke and Kadono, Takashi and Kawano, Tomonori},
doi = {10.4161/psb.6.6.15239},
file = {:home/fin/Documents/papers/mendeley/Ohkawa et al.\_2011\_Forced symbiosis between Synechocystis spp. PCC 6803 and apo-symbiotic Paramecium bursaria as an experimental model f.pdf:pdf},
isbn = {1559-2324 (Electronic)$\backslash$r1559-2316 (Linking)},
issn = {1559-2316},
journal = {Plant Signal. Behav.},
keywords = {cyanobacteria,diagostic pcr,escherichia coli,evolution,food vacuole,green paramecia},
number = {July 2015},
pages = {773--776},
pmid = {21494093},
title = {{Forced symbiosis between Synechocystis spp. PCC 6803 and apo-symbiotic Paramecium bursaria as an experimental model for evolutionary emergence of primitive photosynthetic eukaryotes}},
volume = {6},
year = {2011}
}
@article{Rockwell2014,
author = {Rockwell, Nathan C. and Lagarias, J. C. and Bhattacharya, Debashish},
doi = {10.3389/fevo.2014.00066},
file = {:home/fin/Documents/papers/mendeley/Rockwell, Lagarias, Bhattacharya\_2014\_Primary endosymbiosis and the evolution of light and oxygen sensing in photosynthetic eukaryotes\_F.pdf:pdf},
issn = {2296-701X},
journal = {Front. Ecol. Evol.},
keywords = {algal evolution,algal evolution, Archaeplastida, phytochrome, ferr,archaeplastida,ferredoxin-depending bilin reductase,it,phagotrophy,phytochrome,primary,primary endosymbiosis,s complicated,the story of plastid},
number = {October},
pages = {1--13},
title = {{Primary endosymbiosis and the evolution of light and oxygen sensing in photosynthetic eukaryotes}},
url = {http://journal.frontiersin.org/article/10.3389/fevo.2014.00066/abstract},
volume = {2},
year = {2014}
}
@article{Brennecke2013,
abstract = {Single-cell RNA-seq can yield valuable insights about the variability within a population of seemingly homogeneous cells. We developed a quantitative statistical method to distinguish true biological variability from the high levels of technical noise in single-cell experiments. Our approach quantifies the statistical significance of observed cell-to-cell variability in expression strength on a gene-by-gene basis. We validate our approach using two independent data sets from Arabidopsis thaliana and Mus musculus.},
author = {Brennecke, Philip and Anders, Simon and Kim, Jong Kyoung and Kołodziejczyk, Aleksandra a and Zhang, Xiuwei and Proserpio, Valentina and Baying, Bianka and Benes, Vladimir and Teichmann, Sarah a and Marioni, John C and Heisler, Marcus G},
doi = {10.1038/nmeth.2645},
file = {:home/fin/Documents/papers/mendeley/Brennecke et al.\_2013\_Accounting for technical noise in single-cell RNA-seq experiments.\_Nature methods.pdf:pdf},
isbn = {0000000000},
issn = {1548-7105},
journal = {Nat. Methods},
keywords = {RNA,RNA: methods,Sequence Analysis,Single-Cell Analysis},
number = {11},
pages = {1093--5},
pmid = {24056876},
title = {{Accounting for technical noise in single-cell RNA-seq experiments.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24056876},
volume = {10},
year = {2013}
}
@article{Kodama2010,
author = {Kodama, Y and Fujishima, M},
file = {:home/fin/Documents/papers/mendeley/Kodama, Fujishima\_2010\_Induction of secondary symbiosis between the ciliate Paramecium and the green alga Chlorella\_Current Research, Te.pdf:pdf},
journal = {Curr. Res. Technol. Educ. Top. Appl. Microbiol. Microb. Biotechnol.},
keywords = {chlorella,evolution,infection,paramecium,perialgal vacuole membrane,secondary endosymbiosis},
pages = {95--102},
title = {{Induction of secondary symbiosis between the ciliate Paramecium and the green alga Chlorella}},
year = {2010}
}
@article{Auer2010,
abstract = {Next-generation sequencing technologies are quickly becoming the preferred approach for characterizing and quantifying entire genomes. Even though data produced from these technologies are proving to be the most informative of any thus far, very little attention has been paid to fundamental design aspects of data collection and analysis, namely sampling, randomization, replication, and blocking. We discuss these concepts in an RNA sequencing framework. Using simulations we demonstrate the benefits of collecting replicated RNA sequencing data according to well known statistical designs that partition the sources of biological and technical variation. Examples of these designs and their corresponding models are presented with the goal of testing differential expression.},
author = {Auer, Paul L and Doerge, R W},
doi = {10.1534/genetics.110.114983},
file = {:home/fin/Documents/papers/mendeley/Auer, Doerge\_2010\_Statistical design and analysis of RNA sequencing data.\_Genetics.pdf:pdf},
issn = {1943-2631},
journal = {Genetics},
keywords = {Base Sequence,Clinical Laboratory Techniques,Research Design},
month = jun,
number = {2},
pages = {405--16},
pmid = {20439781},
title = {{Statistical design and analysis of RNA sequencing data.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2881125\&tool=pmcentrez\&rendertype=abstract},
volume = {185},
year = {2010}
}
@article{Thomas2003a,
author = {Thomas, P. D.},
doi = {10.1093/nar/gkg115},
file = {:home/fin/Documents/papers/mendeley/Thomas\_2003\_PANTHER a browsable database of gene products organized by biological function, using curated protein family and subfamily c.pdf:pdf},
issn = {13624962},
journal = {Nucleic Acids Res.},
number = {1},
pages = {334--341},
title = {{PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkg115},
volume = {31},
year = {2003}
}
@article{Emanuelsson2007,
author = {Emanuelsson, Olof and Brunak, S\o ren and von Heijne, Gunnar and Nielsen, Henrik},
doi = {10.1038/nprot.2007.131},
file = {:home/fin/Documents/papers/mendeley/Emanuelsson et al.\_2007\_Locating proteins in the cell using TargetP, SignalP and related tools\_Nature Protocols.pdf:pdf},
issn = {1754-2189},
journal = {Nat. Protoc.},
number = {4},
pages = {953--971},
title = {{Locating proteins in the cell using TargetP, SignalP and related tools}},
url = {http://www.nature.com/doifinder/10.1038/nprot.2007.131},
volume = {2},
year = {2007}
}
@article{Kato2009b,
author = {Kato, Yutaka and Imamura, Nobutaka},
file = {:home/fin/Documents/papers/mendeley/Kato, Imamura\_2009\_Amino acid transport systems of Japanese Paramecium symbiont F36-ZK\_Symbiosis.pdf:pdf},
journal = {Symbiosis},
keywords = {amino acid transport,chlorella,paramecium bursaria},
pages = {99--107},
title = {{Amino acid transport systems of Japanese Paramecium symbiont F36-ZK}},
year = {2009}
}
@article{Ozsolak2009,
abstract = {Our understanding of human biology and disease is ultimately dependent on a complete understanding of the genome and its functions. The recent application of microarray and sequencing technologies to transcriptomics has changed the simplistic view of transcriptomes to a more complicated view of genome-wide transcription where a large fraction of transcripts emanates from unannotated parts of genomes, and underlined our limited knowledge of the dynamic state of transcription. Most of this broad body of knowledge was obtained indirectly because current transcriptome analysis methods typically require RNA to be converted to complementary DNA (cDNA) before measurements, even though the cDNA synthesis step introduces multiple biases and artefacts that interfere with both the proper characterization and quantification of transcripts. Furthermore, cDNA synthesis is not particularly suitable for the analysis of short, degraded and/or small quantity RNA samples. Here we report direct single molecule RNA sequencing without prior conversion of RNA to cDNA. We applied this technology to sequence femtomole quantities of poly(A)(+) Saccharomyces cerevisiae RNA using a surface coated with poly(dT) oligonucleotides to capture the RNAs at their natural poly(A) tails and initiate sequencing by synthesis. We observed transcript 3' end heterogeneity and polyadenylated small nucleolar RNAs. This study provides a path to high-throughput and low-cost direct RNA sequencing and achieving the ultimate goal of a comprehensive and bias-free understanding of transcriptomes.},
author = {Ozsolak, Fatih and Platt, Adam R and Jones, Dan R and Reifenberger, Jeffrey G and Sass, Lauryn E and McInerney, Peter and Thompson, John F and Bowers, Jayson and Jarosz, Mirna and Milos, Patrice M},
doi = {10.1038/nature08390},
file = {:home/fin/Documents/papers/mendeley/Ozsolak et al.\_2009\_Direct RNA sequencing\_Nature.pdf:pdf},
isbn = {1476-4687; 0028-0836},
issn = {0028-0836},
journal = {Nature},
number = {7265},
pages = {814--818},
pmid = {19776739},
publisher = {Nature Publishing Group},
title = {{Direct RNA sequencing}},
url = {http://dx.doi.org/10.1038/nature08390},
volume = {461},
year = {2009}
}
@article{Crespi2008,
abstract = {The symbiotic interaction between Rhizobium bacteria and legume plants leads to the induction of a new developmental program: the formation of nitrogen-fixing root nodules. Nodulation is triggered by specific bacterial signals, the Nod factors, and integrates plant developmental regulatory pathways to reactivate differentiated cortical cells. This results in the formation of a de novo meristem, corresponding to a plant stem cell niche. Recent data have shown a crucial function of the phytohormone cytokinin and its signaling pathway in nodule initiation. Activation of either cytokinin or components of the Nod factor signaling pathway leads to spontaneous induction of the nodule organogenesis program. These genetic analyses have been complemented with genomic studies of transcriptional networks activated during early nodulation. Transcriptional and posttranscriptional regulation, notably involving transcription factors and microRNAs, fine-tune the dynamic equilibrium between proliferating meristematic and differentiated nitrogen-fixing cells. The recent identification of these regulatory mechanisms has helped elucidate nodule organogenesis and the agriculturally relevant process of symbiotic nitrogen fixation and extended our understanding of how differentiated root cells acquire developmental plasticity to form a new organ.},
author = {Crespi, Martin and Frugier, Florian},
doi = {10.1126/scisignal.149re11},
file = {:home/fin/Documents/papers/mendeley/Crespi, Frugier\_2008\_De novo organ formation from differentiated cells root nodule organogenesis.\_Science signaling.pdf:pdf},
isbn = {1937-9145 (Electronic)},
issn = {1937-9145},
journal = {Sci. Signal.},
number = {49},
pages = {re11},
pmid = {19066400},
title = {{De novo organ formation from differentiated cells: root nodule organogenesis.}},
volume = {1},
year = {2008}
}
@article{Iwatsuki1988,
author = {Iwatsuki, K and Naitoh, Y},
file = {:home/fin/Documents/papers/mendeley/Iwatsuki, Naitoh\_1988\_Behavioural responses to light in Paramecium bursaria in relation to its symbiotic green alga Chlorella\_Journal of.pdf:pdf},
journal = {J. Exp. Biol.},
pages = {43--60},
title = {{Behavioural responses to light in Paramecium bursaria in relation to its symbiotic green alga Chlorella}},
url = {http://jeb.biologists.org/content/134/1/43.short},
volume = {60},
year = {1988}
}
@article{Sanger1975,
abstract = {A simple and rapid method for determining nucleotide sequences in single-stranded DNA by primed synthesis with DNA polymerase is described. It depends on the use of Escherichia coli DNA polymerase I and DNA polymerase from bacteriophage T4 under conditions of different limiting nucleoside triphosphates and concurrent fractionation of the products according to size by ionophoresis on acrylamide gels. The method was used to determine two sequences in bacteriophage $\phi$X174 DNA using the synthetic decanucleotide A-G-A-A-A-T-A-A-A-A and a restriction enzyme digestion product as primers.},
author = {Sanger, F and Coulson, A R},
doi = {10.1016/0022-2836(75)90213-2},
file = {:home/fin/Documents/papers/mendeley/Sanger, Coulson\_1975\_A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase.\_Journal of molecular biolo.pdf:pdf},
isbn = {0022-2836 (Print) 0022-2836 (Linking)},
issn = {00222836},
journal = {J. Mol. Biol.},
pages = {441--448},
pmid = {1100841},
title = {{A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase.}},
volume = {94},
year = {1975}
}
@article{Le2008,
abstract = {Amino acid replacement matrices are an essential basis of protein phylogenetics. They are used to compute substitution probabilities along phylogeny branches and thus the likelihood of the data. They are also essential in protein alignment. A number of replacement matrices and methods to estimate these matrices from protein alignments have been proposed since the seminal work of Dayhoff et al. (1972). An important advance was achieved by Whelan and Goldman (2001) and their WAG matrix, thanks to an efficient maximum likelihood estimation approach that accounts for the phylogenies of sequences within each training alignment. We further refine this method by incorporating the variability of evolutionary rates across sites in the matrix estimation and using a much larger and diverse database than BRKALN, which was used to estimate WAG. To estimate our new matrix (called LG after the authors), we use an adaptation of the XRATE software and 3,912 alignments from Pfam, comprising approximately 50,000 sequences and approximately 6.5 million residues overall. To evaluate the LG performance, we use an independent sample consisting of 59 alignments from TreeBase and randomly divide Pfam alignments into 3,412 training and 500 test alignments. The comparison with WAG and JTT shows a clear likelihood improvement. With TreeBase, we find that 1) the average Akaike information criterion gain per site is 0.25 and 0.42, when compared with WAG and JTT, respectively; 2) LG is significantly better than WAG for 38 alignments (among 59), and significantly worse with 2 alignments only; and 3) tree topologies inferred with LG, WAG, and JTT frequently differ, indicating that using LG impacts not only the likelihood value but also the output tree. Results with the test alignments from Pfam are analogous. LG and a PHYML implementation can be downloaded from http://atgc.lirmm.fr/LG.},
author = {Le, Si Quang and Gascuel, Olivier},
doi = {10.1093/molbev/msn067},
file = {:home/fin/Documents/papers/mendeley/Le, Gascuel\_2008\_An improved general amino acid replacement matrix\_Molecular Biology and Evolution.pdf:pdf},
isbn = {1537-1719 (Electronic)$\backslash$n0737-4038 (Linking)},
issn = {07374038},
journal = {Mol. Biol. Evol.},
keywords = {Amino acid substitutions,JTT,Maximum likelihood estimations,Phylogenetic inference,Replacement matrices,WAG},
number = {7},
pages = {1307--1320},
pmid = {18367465},
title = {{An improved general amino acid replacement matrix}},
volume = {25},
year = {2008}
}
@article{Felsenstein1985,
author = {Felsenstein, Joseph},
file = {:home/fin/Documents/papers/mendeley/Felsenstein\_1985\_Confidence Limits on Phylogenies An Approach Using the Bootstrap\_Evolution.pdf:pdf},
journal = {Evolution (N. Y).},
number = {4},
pages = {783--791},
title = {{Confidence Limits on Phylogenies: An Approach Using the Bootstrap}},
volume = {39},
year = {1985}
}
@article{DelCampo2014,
author = {del Campo, Javier and Sieracki, Michael E and Molestina, Robert and Keeling, Patrick and Massana, Ramon and Ruiz-Trillo, I\~{n}aki},
file = {:home/fin/Documents/papers/mendeley/del Campo et al.\_2014\_The others our biased perspective of eukaryotic genomes\_Trends in Ecology \& Evolution.pdf:pdf},
journal = {Trends Ecol. Evol.},
number = {5},
pages = {252--259},
title = {{The others: our biased perspective of eukaryotic genomes}},
volume = {29},
year = {2014}
}
@article{Shih2013,
abstract = {Chloroplasts and mitochondria descended from bacterial ancestors, but the dating of these primary endosymbiosis events remains very uncertain, despite their importance for our understanding of the evolution of both bacteria and eukaryotes. All phylogenetic dating in the Proterozoic and before is difficult: Significant debates surround potential fossil calibration points based on the interpretation of the Precambrian microbial fossil record, and strict molecular clock methods cannot be expected to yield accurate dates over such vast timescales because of strong heterogeneity in rates. Even with more sophisticated relaxed-clock analyses, nodes that are distant from fossil calibrations will have a very high uncertainty in dating. However, endosymbiosis events and gene duplications provide some additional information that has never been exploited in dating; namely, that certain nodes on a gene tree must represent the same events, and thus must have the same or very similar dates, even if the exact date is uncertain. We devised techniques to exploit this information: cross-calibration, in which node date calibrations are reused across a phylogeny, and cross-bracing, in which node date calibrations are formally linked in a hierarchical Bayesian model. We apply these methods to proteins with ancient duplications that have remained associated and originated from plastid and mitochondrial endosymbionts: the $\alpha$ and $\beta$ subunits of ATP synthase and its relatives, and the elongation factor thermo unstable. The methods yield reductions in dating uncertainty of 14-26\% while only using date calibrations derived from phylogenetically unambiguous Phanerozoic fossils of multicellular plants and animals. Our results suggest that primary plastid endosymbiosis occurred ∼900 Mya and mitochondrial endosymbiosis occurred ∼1,200 Mya.},
author = {Shih, Patrick M and Matzke, Nicholas J},
doi = {10.1073/pnas.1305813110},
file = {:home/fin/Documents/papers/mendeley/Shih, Matzke\_2013\_Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATP.pdf:pdf},
issn = {1091-6490},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
keywords = {Adenosine Triphosphatases,Adenosine Triphosphatases: classification,Adenosine Triphosphatases: metabolism,Calibration,Phylogeny,Symbiosis},
number = {30},
pages = {12355--60},
pmid = {23776247},
title = {{Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3725117\&tool=pmcentrez\&rendertype=abstract},
volume = {110},
year = {2013}
}
@article{Bachvaroff2011,
abstract = {Dinoflagellates and apicomplexans are a strongly supported monophyletic group in rDNA phylogenies, although this phylogeny is not without controversy, particularly between the two groups. Here we use concatenated protein-coding genes from expressed sequence tags or genomic data to construct phylogenies including "typical" dinophycean dinoflagellates, a parasitic syndinian dinoflagellate, Amoebophrya sp., and two related species, Oxyrrhis marina, and Perkinsus marinus. Seventeen genes encoding proteins associated with the ribosome were selected for phylogenetic analysis. The dataset was limited for the most part by data availability from the dinoflagellates. Forty-five taxa from four major lineages were used: the heterokont outgroup, ciliates, dinoflagellates, and apicomplexans. Amoebophrya sp. was included in this phylogeny as a sole representative of the enigmatic marine alveolate or syndinian lineage. The atypical dinoflagellate O. marina, usually excluded from rDNA analyses due to long branches, was also included. The resulting phylogenies were well supported in concatenated analyses with only a few unstable or weakly supported branches; most features were consistent when different lineages were pruned from the tree or different genes were concatenated. The least stable branches involved the placement of Cryptosporidium spp. within the Apicomplexa and the relationships between P. marinus, Amoebophrya sp., and O. marina. Both bootstrap and approximately unbiased test results confirmed that P. marinus, Amoebophrya sp., O. marina, and the remaining dinoflagellates form a monophyletic lineage to the exclusion of Apicomplexa.},
author = {Bachvaroff, Tsvetan R and Handy, Sara M and Place, Allen R and Delwiche, Charles F},
doi = {10.1111/j.1550-7408.2011.00555.x},
file = {:home/fin/Documents/papers/mendeley/Bachvaroff et al.\_2011\_Alveolate phylogeny inferred using concatenated ribosomal proteins.\_The Journal of Eukaryotic Microbiology.pdf:pdf},
issn = {1550-7408},
journal = {J. Eukaryot. Microbiol.},
keywords = {Alveolata,Alveolata: classification,Alveolata: genetics,Computational Biology,Computational Biology: methods,Expressed Sequence Tags,Genome,Phylogeny,Protozoan,Ribosomal Proteins,Ribosomal Proteins: genetics},
number = {3},
pages = {223--33},
pmid = {21518081},
title = {{Alveolate phylogeny inferred using concatenated ribosomal proteins.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21518081},
volume = {58},
year = {2011}
}
@article{Hirner2006,
author = {Hirner, a.},
doi = {10.1105/tpc.106.041012},
file = {:home/fin/Documents/papers/mendeley/Hirner\_2006\_Arabidopsis LHT1 Is a High-Affinity Transporter for Cellular Amino Acid Uptake in Both Root Epidermis and Leaf Mesophyll\_the.pdf:pdf},
issn = {1040-4651},
journal = {Plant Cell Online},
number = {August},
pages = {1931--1946},
title = {{Arabidopsis LHT1 Is a High-Affinity Transporter for Cellular Amino Acid Uptake in Both Root Epidermis and Leaf Mesophyll}},
url = {http://www.plantcell.org/cgi/doi/10.1105/tpc.106.041012},
volume = {18},
year = {2006}
}
@article{Legin2014,
abstract = {Multi-elemental, isotope selective nano-scale secondary ion mass spectrometry (NanoSIMS) combined with confocal laser-scanning microscopy was used to characterize the subcellular distribution of 15N-labeled cisplatin in human colon cancer cells. These analyses indicated predominant cisplatin colocalisation with sulfur-rich structures in both the nucleus and cytoplasm. Furthermore, colocalisation of platinum with phosphorus-rich chromatin regions was observed, which is consistent with its binding affinity to DNA as the generally accepted crucial target of the drug. Application of 15N-labeled cisplatin and subsequent measurement of the nitrogen isotopic composition and determination of the relative intensities of platinum and nitrogen associated secondary ion signals in different cellular compartments with NanoSIMS suggested partial dissociation of Pt-N bonds during the accumulation process, in particular within nucleoli at elevated cisplatin concentrations. This finding raises the question as to whether the observed intracellular dissociation of the drug has implications for the mechanism of action of cisplatin. Within the cytoplasm, platinum mainly accumulated in acidic organelles, as demonstrated by a direct combination of specific fluorescent staining, confocal laser scanning microscopy and NanoSIMS. Different processing of platinum drugs in acidic organelles might be relevant for their detoxification, as well as for their mode of action.},
author = {Legin, Anton a. and Schintlmeister, Arno and Jakupec, Michael a. and Galanski, Markus and Lichtscheidl, Irene and Wagner, Michael and Keppler, Bernhard K.},
doi = {10.1039/c3sc53426j},
file = {:home/fin/Documents/papers/mendeley/Legin et al.\_2014\_NanoSIMS combined with fluorescence microscopy as a tool for subcellular imaging of isotopically labeled platinum-base.pdf:pdf},
isbn = {2041-6520},
issn = {2041-6520},
journal = {Chem. Sci.},
pages = {3135},
title = {{NanoSIMS combined with fluorescence microscopy as a tool for subcellular imaging of isotopically labeled platinum-based anticancer drugs}},
url = {http://xlink.rsc.org/?DOI=c3sc53426j},
volume = {5},
year = {2014}
}
@article{Kiefer2013,
author = {Chalker, Douglas L and Meyer, E. and Mochizuki, Kazufumi},
doi = {10.1016/j.mrfmmm.2008.07.014},
file = {:home/fin/Documents/papers/mendeley/Chalker, Meyer, Mochizuki\_2013\_Epigenetics of ciliates\_Cold Spring Harbour Prespectives on Epigenetics.pdf:pdf},
journal = {Cold Spring Harb. Prespectives Epigenetics},
pages = {a017764},
title = {{Epigenetics of ciliates}},
volume = {5},
year = {2013}
}
@article{Minin2003,
author = {Minin, Vladimir and Abdo, Zaid and Joyce, Paul and Sullivan, Jack},
doi = {10.1080/10635150390235494},
file = {:home/fin/Documents/papers/mendeley/Minin et al.\_2003\_Performance-Based Selection of Likelihood Models for Phylogeny Estimation\_Systematic Biology.pdf:pdf},
issn = {1063-5157},
journal = {Syst. Biol.},
number = {5},
pages = {674--683},
title = {{Performance-Based Selection of Likelihood Models for Phylogeny Estimation}},
url = {http://sysbio.oxfordjournals.org/cgi/doi/10.1080/10635150390235494},
volume = {52},
year = {2003}
}
@article{Weiberg2013,
abstract = {Botrytis cinerea, the causative agent of gray mold disease, is an aggressive fungal pathogen that infects more than 200 plant species. Here, we show that some B. cinerea small RNAs (Bc-sRNAs) can silence Arabidopsis and tomato genes involved in immunity. These Bc-sRNAs hijack the host RNA interference (RNAi) machinery by binding to Arabidopsis Argonaute 1 (AGO1) and selectively silencing host immunity genes. The Arabidopsis ago1 mutant exhibits reduced susceptibility to B. cinerea, and the B. cinerea dcl1 dcl2 double mutant that can no longer produce these Bc-sRNAs displays reduced pathogenicity on Arabidopsis and tomato. Thus, this fungal pathogen transfers "virulent" sRNA effectors into host plant cells to suppress host immunity and achieve infection, which demonstrates a naturally occurring cross-kingdom RNAi as an advanced virulence mechanism.},
author = {Weiberg, Arne and Wang, Ming and Lin, Feng-Mao and Zhao, Hongwei and Zhang, Zhihong and Kaloshian, Isgouhi and Huang, Hsien-Da and Jin, Hailing},
doi = {10.1126/science.1239705},
file = {:home/fin/Documents/papers/mendeley/Weiberg et al.\_2013\_Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways.\_Science (New York, N.Y.).pdf:pdf},
isbn = {0036-8075, 1095-9203},
issn = {1095-9203},
journal = {Science},
keywords = {Arabidopsis,Arabidopsis Proteins,Arabidopsis Proteins: genetics,Arabidopsis: genetics,Arabidopsis: immunology,Arabidopsis: microbiology,Argonaute Proteins,Argonaute Proteins: genetics,Botrytis,Botrytis: genetics,Botrytis: pathogenicity,Gene Expression Regulation, Plant,Host-Pathogen Interactions,Host-Pathogen Interactions: genetics,Host-Pathogen Interactions: immunology,Lycopersicon esculentum,Lycopersicon esculentum: genetics,Lycopersicon esculentum: immunology,Lycopersicon esculentum: microbiology,Mutation,Plant Diseases,Plant Diseases: genetics,Plant Diseases: immunology,Plant Diseases: microbiology,RNA Interference,RNA, Fungal,RNA, Fungal: genetics,RNA, Small Interfering,RNA, Small Interfering: genetics,Virulence,Virulence: genetics},
number = {October},
pages = {118--23},
pmid = {24092744},
title = {{Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24092744},
volume = {342},
year = {2013}
}
@article{DeWever2009,
abstract = {Recent data revealed that metazoans such as mites and springtails have persisted in Antarctica throughout several glacial-interglacial cycles, which contradicts the existing paradigm that terrestrial life was wiped out by successive glacial events and that the current inhabitants are recent colonizers. We used molecular phylogenetic techniques to study Antarctic microchlorophyte strains isolated from lacustrine habitats from maritime and continental Antarctica. The 14 distinct chlorophycean and trebouxiophycean lineages observed point to a wide phylogenetic diversity of apparently endemic Antarctic lineages at different taxonomic levels. This supports the hypothesis that long-term survival took place in glacial refugia, resulting in a specific Antarctic flora. The majority of the lineages have estimated ages between 17 and 84 Ma and probably diverged from their closest relatives around the time of the opening of Drake Passage (30-45 Ma), while some lineages with longer branch lengths have estimated ages that precede the break-up of Gondwana. The variation in branch length and estimated age points to several independent but rare colonization events.},
author = {{De Wever}, Aaike and Leliaert, Frederik and Verleyen, Elie and Vanormelingen, Pieter and {Van der Gucht}, Katleen and Hodgson, Dominic a and Sabbe, Koen and Vyverman, Wim},
doi = {10.1098/rspb.2009.0994},
file = {:home/fin/Documents/papers/mendeley/De Wever et al.\_2009\_Hidden levels of phylodiversity in Antarctic green algae further evidence for the existence of glacial refugia.\_Pro.pdf:pdf},
issn = {0962-8452},
journal = {Proc. Biol. Sci.},
keywords = {Antarctic Regions,Biodiversity,DNA, Plant,DNA, Plant: genetics,Ecosystem,Eukaryota,Eukaryota: genetics,Eukaryota: physiology,Evolution, Molecular,Ice Cover,Phylogeny},
month = oct,
number = {1673},
pages = {3591--9},
pmid = {19625320},
title = {{Hidden levels of phylodiversity in Antarctic green algae: further evidence for the existence of glacial refugia.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2817313\&tool=pmcentrez\&rendertype=abstract},
volume = {276},
year = {2009}
}
@article{Kessler1990,
author = {Kessler, E and Huss, V A R},
doi = {10.1111/j.1438-8677.1990.tb00139.x},
issn = {1438-8677},
journal = {Bot. Acta},
keywords = {Acanthocystis,Biochemical taxonomy,Chlorella,Paramecium,classification,inorganic nitrogen sources,symbiosis,vitamin B12 requirement},
month = may,
number = {2},
pages = {140--142},
publisher = {Blackwell Publishing Ltd},
title = {{Biochemical Taxonomy of Symbiotic Chlorella Strains from Paramecium and Acanthocystis*}},
url = {http://dx.doi.org/10.1111/j.1438-8677.1990.tb00139.x},
volume = {103},
year = {1990}
}
@article{Peng2012,
abstract = {MOTIVATION: Next-generation sequencing allows us to sequence reads from a microbial environment using single-cell sequencing or metagenomic sequencing technologies. However, both technologies suffer from the problem that sequencing depth of different regions of a genome or genomes from different species are highly uneven. Most existing genome assemblers usually have an assumption that sequencing depths are even. These assemblers fail to construct correct long contigs.$\backslash$n$\backslash$nRESULTS: We introduce the IDBA-UD algorithm that is based on the de Bruijn graph approach for assembling reads from single-cell sequencing or metagenomic sequencing technologies with uneven sequencing depths. Several non-trivial techniques have been employed to tackle the problems. Instead of using a simple threshold, we use multiple depthrelative thresholds to remove erroneous k-mers in both low-depth and high-depth regions. The technique of local assembly with paired-end information is used to solve the branch problem of low-depth short repeat regions. To speed up the process, an error correction step is conducted to correct reads of high-depth regions that can be aligned to highconfident contigs. Comparison of the performances of IDBA-UD and existing assemblers (Velvet, Velvet-SC, SOAPdenovo and Meta-IDBA) for different datasets, shows that IDBA-UD can reconstruct longer contigs with higher accuracy.$\backslash$n$\backslash$nAVAILABILITY: The IDBA-UD toolkit is available at our website http://www.cs.hku.hk/\~{}alse/idba\_ud},
author = {Peng, Yu and Leung, Henry C M and Yiu, S M and Chin, Francis Y L},
doi = {10.1093/bioinformatics/bts174},
file = {:home/fin/Documents/papers/mendeley/Peng et al.\_2012\_IDBA-UD a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.\_Bioinformatics (O.pdf:pdf},
isbn = {1367-4811 (Electronic)$\backslash$n1367-4803 (Linking)},
issn = {1367-4811},
journal = {Bioinformatics},
keywords = {Algorithms,Bacteria,Bacteria: genetics,Genome,High-Throughput Nucleotide Sequencing,Metagenomics,Metagenomics: methods,Sequence Analysis, DNA,Sequence Analysis, DNA: methods,Single-Cell Analysis,Single-Cell Analysis: methods},
number = {11},
pages = {1420--8},
pmid = {22495754},
title = {{IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22495754},
volume = {28},
year = {2012}
}
@article{Bininda-Emonds2004,
abstract = {Supertrees result from combining many smaller, overlapping phylogenetic trees into a single, more comprehensive tree. As such, supertree construction is probably as old as the field of systematics itself, and remains our only way of visualizing the Tree of Life as a whole. Over the past decade, supertree construction has gained a more formal, objective footing, and has become an area of active theoretical and practical research. Here, I review the history of the supertree approach, focusing mainly on its current implementation. The supertrees of today represent some of the largest, complete phylogenies available for many groups, but are not without their critics. I conclude by arguing that the ever-growing molecular revolution will result in supertree construction taking on a new role and implementation in the future for analyzing large DNA sequence matrices as part of a divide-and-conquer phylogenetic approach.},
author = {Bininda-Emonds, O. R P},
doi = {10.1016/j.tree.2004.03.015},
file = {:home/fin/Documents/papers/mendeley/Bininda-Emonds\_2004\_The evolution of supertrees\_Trends in Ecology and Evolution.pdf:pdf},
isbn = {0169-5347 (Print)},
issn = {01695347},
journal = {Trends Ecol. Evol.},
number = {6},
pages = {315--322},
pmid = {16701277},
title = {{The evolution of supertrees}},
volume = {19},
year = {2004}
}
@article{Eggensperger2013,
author = {Eggensperger, Katharina and Feurer, Matthias and Hutter, Frank},
file = {:home/fin/Documents/papers/mendeley/Eggensperger, Feurer, Hutter\_2013\_Towards an empirical foundation for assessing bayesian optimization of hyperparameters\_\ldots Bayesian.pdf:pdf},
journal = {\ldots Bayesian Optim. \ldots},
pages = {1--5},
title = {{Towards an empirical foundation for assessing bayesian optimization of hyperparameters}},
url = {http://automl.org/papers/13-BayesOpt\_EmpiricalFoundation.pdf},
year = {2013}
}
@article{Mistry2013,
author = {Mistry, J. and Finn, R. D. and Eddy, S. R. and Bateman, a. and Punta, M.},
doi = {10.1093/nar/gkt263},
file = {:home/fin/Documents/papers/mendeley/Mistry et al.\_2013\_Challenges in homology search HMMER3 and convergent evolution of coiled-coil regions\_Nucleic Acids Research.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {12},
pages = {e121--e121},
title = {{Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkt263},
volume = {41},
year = {2013}
}
@article{Blanc2012,
abstract = {BACKGROUND: Little is known about the mechanisms of adaptation of life to the extreme environmental conditions encountered in polar regions. Here we present the genome sequence of a unicellular green alga from the division chlorophyta, Coccomyxa subellipsoidea C-169, which we will hereafter refer to as C-169. This is the first eukaryotic microorganism from a polar environment to have its genome sequenced.$\backslash$n$\backslash$nRESULTS: The 48.8 Mb genome contained in 20 chromosomes exhibits significant synteny conservation with the chromosomes of its relatives Chlorella variabilis and Chlamydomonas reinhardtii. The order of the genes is highly reshuffled within synteny blocks, suggesting that intra-chromosomal rearrangements were more prevalent than inter-chromosomal rearrangements. Remarkably, Zepp retrotransposons occur in clusters of nested elements with strictly one cluster per chromosome probably residing at the centromere. Several protein families overrepresented in C. subellipsoidae include proteins involved in lipid metabolism, transporters, cellulose synthases and short alcohol dehydrogenases. Conversely, C-169 lacks proteins that exist in all other sequenced chlorophytes, including components of the glycosyl phosphatidyl inositol anchoring system, pyruvate phosphate dikinase and the photosystem 1 reaction center subunit N (PsaN).$\backslash$n$\backslash$nCONCLUSIONS: We suggest that some of these gene losses and gains could have contributed to adaptation to low temperatures. Comparison of these genomic features with the adaptive strategies of psychrophilic microbes suggests that prokaryotes and eukaryotes followed comparable evolutionary routes to adapt to cold environments.},
author = {Blanc, Guillaume and Agarkova, Irina and Grimwood, Jane and Kuo, Alan and Brueggeman, Andrew and Dunigan, David D and Gurnon, James and Ladunga, Istvan and Lindquist, Erika and Lucas, Susan and Pangilinan, Jasmyn and Pr\"{o}schold, Thomas and Salamov, Asaf and Schmutz, Jeremy and Weeks, Donald and Yamada, Takashi and Lomsadze, Alexandre and Borodovsky, Mark and Claverie, Jean-Michel and Grigoriev, Igor V and {Van Etten}, James L},
doi = {10.1186/gb-2012-13-5-r39},
file = {:home/fin/Documents/papers/mendeley/Blanc et al.\_2012\_The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation\_Genome Biology.pdf:pdf},
isbn = {1465-6906},
issn = {1465-6906},
journal = {Genome Biol.},
number = {5},
pages = {R39},
pmid = {22630137},
publisher = {BioMed Central Ltd},
title = {{The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation}},
url = {http://genomebiology.com/2012/13/5/R39},
volume = {13},
year = {2012}
}
@article{Tautenhahn2012,
abstract = {Recently, interest in untargeted metabolomics has become prevalent in the general scientific community among an increasing number of investigators. The majority of these investigators, however, do not have the bioinformatic expertise that has been required to process metabolomic data by using command-line driven software programs. Here we introduce a novel platform to process untargeted metabolomic data that uses an intuitive graphical interface and does not require installation or technical expertise. This platform, called XCMS Online, is a web-based version of the widely used XCMS software that allows users to easily upload and process liquid chromatography/mass spectrometry data with only a few mouse clicks. XCMS Online provides a solution for the complete untargeted metabolomic workflow including feature detection, retention time correction, alignment, annotation, statistical analysis, and data visualization. Results can be browsed online in an interactive, customizable table showing statistics, chromatograms, and putative METLIN identities for each metabolite. Additionally, all results and images can be downloaded as zip files for offline analysis and publication. XCMS Online is available at https://xcmsonline.scripps.edu.},
author = {Tautenhahn, Ralf and Patti, Gary J and Rinehart, Duane and Siuzdak, Gary},
doi = {10.1021/ac300698c},
file = {:home/fin/Documents/papers/mendeley/Tautenhahn et al.\_2012\_XCMS Online a web-based platform to process untargeted metabolomic data.\_Analytical chemistry.pdf:pdf},
isbn = {0003-2700},
issn = {1520-6882},
journal = {Anal. Chem.},
keywords = {Automatic Data Processing,Automatic Data Processing: methods,Chromatography, Liquid,Chromatography, Liquid: statistics \& numerical dat,Humans,Internet,Mass Spectrometry,Mass Spectrometry: statistics \& numerical data,Metabolomics,Plants,Software},
pages = {5035--9},
pmid = {22533540},
title = {{XCMS Online: a web-based platform to process untargeted metabolomic data.}},
url = {http://dx.doi.org/10.1021/ac300698c},
volume = {84},
year = {2012}
}
@article{LeCun1998,
abstract = {Multilayer neural networks trained with the back-propagation
algorithm constitute the best example of a successful gradient based
learning technique. Given an appropriate network architecture,
gradient-based learning algorithms can be used to synthesize a complex
decision surface that can classify high-dimensional patterns, such as
handwritten characters, with minimal preprocessing. This paper reviews
various methods applied to handwritten character recognition and
compares them on a standard handwritten digit recognition task.
Convolutional neural networks, which are specifically designed to deal
with the variability of 2D shapes, are shown to outperform all other
techniques. Real-life document recognition systems are composed of
multiple modules including field extraction, segmentation recognition,
and language modeling. A new learning paradigm, called graph transformer
networks (GTN), allows such multimodule systems to be trained globally
using gradient-based methods so as to minimize an overall performance
measure. Two systems for online handwriting recognition are described.
Experiments demonstrate the advantage of global training, and the
flexibility of graph transformer networks. A graph transformer network
for reading a bank cheque is also described. It uses convolutional
neural network character recognizers combined with global training
techniques to provide record accuracy on business and personal cheques.
It is deployed commercially and reads several million cheques per day
},
author = {LeCun, Yann and Bottou, L\'{e}on and Bengio, Yoshua and Haffner, Patrick},
doi = {10.1109/5.726791},
file = {:home/fin/Documents/papers/mendeley/LeCun et al.\_1998\_Gradient-based learning applied to document recognition\_Proceedings of the IEEE.pdf:pdf},
isbn = {0018-9219},
issn = {00189219},
journal = {Proc. IEEE},
keywords = {Convolutional neural networks,Document recognition,Finite state transducers,Gradient-based learning,Graph transformer networks,Machine learning,Neural networks,Optical character recognition (OCR)},
pages = {2278--2323},
pmid = {15823584},
title = {{Gradient-based learning applied to document recognition}},
volume = {86},
year = {1998}
}
@article{Saier2009,
author = {Saier, M. H. and Yen, M. R. and Noto, K. and Tamang, D. G. and Elkan, C.},
doi = {10.1093/nar/gkn862},
file = {:home/fin/Documents/papers/mendeley/Saier et al.\_2009\_The Transporter Classification Database recent advances\_Nucleic Acids Research.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {November 2008},
pages = {D274--D278},
title = {{The Transporter Classification Database: recent advances}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkn862},
volume = {37},
year = {2009}
}
@article{Katoh2002,
abstract = {A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.},
author = {Katoh, Kazutaka and Misawa, Kazuharu and Kuma, Kei-ichi and Miyata, Takashi},
doi = {10.1093/nar/gkf436},
file = {:home/fin/Documents/papers/mendeley/Katoh et al.\_2002\_MAFFT a novel method for rapid multiple sequence alignment based on fast Fourier transform.\_Nucleic acids research.pdf:pdf},
isbn = {1362-4962 (Electronic)},
issn = {1362-4962},
journal = {Nucleic Acids Res.},
number = {14},
pages = {3059--3066},
pmid = {12136088},
title = {{MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.}},
volume = {30},
year = {2002}
}
@article{Wichterman1948,
author = {Wichterman, R.},
file = {:home/fin/Documents/papers/mendeley/Wichterman\_1948\_The Biological Effects of X-Rays on Mating Types and Conjugation of Paramecium Bursaria\_Biological Bulletin.pdf:pdf},
journal = {Biol. Bull.},
number = {2},
pages = {113--127},
title = {{The Biological Effects of X-Rays on Mating Types and Conjugation of Paramecium Bursaria}},
volume = {94},
year = {1948}
}
@article{Helber2011,
abstract = {For more than 400 million years, plants have maintained a mutualistic symbiosis with arbuscular mycorrhizal (AM) fungi. This evolutionary success can be traced to the role of these fungi in providing plants with mineral nutrients, particularly phosphate. In return, photosynthates are given to the fungus, which support its obligate biotrophic lifestyle. Although the mechanisms involved in phosphate transfer have been extensively studied, less is known about the reciprocal transfer of carbon. Here, we present the high-affinity Monosaccharide Transporter2 (MST2) from Glomus sp with a broad substrate spectrum that functions at several symbiotic root locations. Plant cell wall sugars can efficiently outcompete the Glc uptake capacity of MST2, suggesting they can serve as alternative carbon sources. MST2 expression closely correlates with that of the mycorrhiza-specific Phosphate Transporter4 (PT4). Furthermore, reduction of MST2 expression using host-induced gene silencing resulted in impaired mycorrhiza formation, malformed arbuscules, and reduced PT4 expression. These findings highlight the symbiotic role of MST2 and support the hypothesis that the exchange of carbon for phosphate is tightly linked. Unexpectedly, we found that the external mycelium of AM fungi is able to take up sugars in a proton-dependent manner. These results imply that the sugar uptake system operating in this symbiosis is more complex than previously anticipated.},
author = {Helber, N. and Wippel, K. and Sauer, N. and Schaarschmidt, S. and Hause, B. and Requena, N.},
doi = {10.1105/tpc.111.089813},
file = {:home/fin/Documents/papers/mendeley/Helber et al.\_2011\_A Versatile Monosaccharide Transporter That Operates in the Arbuscular Mycorrhizal Fungus Glomus sp Is Crucial for th.pdf:pdf},
isbn = {1040-4651},
issn = {1040-4651},
journal = {Plant Cell},
number = {October},
pages = {3812--3823},
pmid = {21972259},
title = {{A Versatile Monosaccharide Transporter That Operates in the Arbuscular Mycorrhizal Fungus Glomus sp Is Crucial for the Symbiotic Relationship with Plants}},
volume = {23},
year = {2011}
}
@article{Schulz2012,
abstract = {MOTIVATION: High-throughput sequencing has made the analysis of new model organisms more affordable. Although assembling a new genome can still be costly and difficult, it is possible to use RNA-seq to sequence mRNA. In the absence of a known genome, it is necessary to assemble these sequences de novo, taking into account possible alternative isoforms and the dynamic range of expression values. RESULTS: We present a software package named Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms. It achieves this by using an array of hash lengths, a dynamic filtering of noise, a robust resolution of alternative splicing events and the efficient merging of multiple assemblies. It was tested on human and mouse RNA-seq data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome assemblers. AVAILABILITY AND IMPLEMENTATION: Oases is freely available under the GPL license at www.ebi.ac.uk/\~{}zerbino/oases/.},
author = {Schulz, Marcel H and Zerbino, Daniel R and Vingron, Martin and Birney, Ewan},
doi = {10.1093/bioinformatics/bts094},
file = {:home/fin/Documents/papers/mendeley/Schulz et al.\_2012\_Oases robust de novo RNA-seq assembly across the dynamic range of expression levels.\_Bioinformatics.pdf:pdf},
issn = {1367-4811},
journal = {Bioinformatics},
keywords = {Algorithms,Alternative Splicing,Animals,Gene Expression Profiling,High-Throughput Nucleotide Sequencing,High-Throughput Nucleotide Sequencing: methods,Humans,Messenger,Messenger: genetics,Mice,RNA,RNA: methods,Sequence Analysis,Software},
month = apr,
number = {8},
pages = {1086--92},
pmid = {22368243},
title = {{Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3324515\&tool=pmcentrez\&rendertype=abstract},
volume = {28},
year = {2012}
}
@article{Kodama2014c,
author = {Kodama, Yuuki and Fujishima, Masahiro},
doi = {10.1111/1574-6941.12448},
file = {:home/fin/Documents/papers/mendeley/Kodama, Fujishima\_2014\_Symbiotic Chlorella variabilis incubated under constant dark conditions for 24 hours loses the ability to avoid dige.:},
issn = {01686496},
journal = {FEMS Microbiol. Ecol.},
keywords = {chlorella spp,digestion,endosymbiosis,lysosome,paramecium bursaria},
pages = {946--955},
title = {{Symbiotic Chlorella variabilis incubated under constant dark conditions for 24 hours loses the ability to avoid digestion by host lysosomal enzymes in digestive vacuoles of host ciliate Paramecium bursaria}},
url = {http://femsec.oxfordjournals.org/cgi/doi/10.1111/1574-6941.12448},
volume = {90},
year = {2014}
}
@article{Zhang2014,
author = {Zhang, Qingpeng and Pell, Jason and Canino-Koning, Rosangela and Howe, Adina Chuang and Brown, C. Titus},
doi = {10.1371/journal.pone.0101271},
file = {:home/fin/Documents/papers/mendeley/Zhang et al.\_2014\_These Are Not the K-mers You Are Looking For Efficient Online K-mer Counting Using a Probabilistic Data Structure\_PLoS.pdf:pdf},
issn = {1932-6203},
journal = {PLoS One},
number = {7},
pages = {e101271},
title = {{These Are Not the K-mers You Are Looking For: Efficient Online K-mer Counting Using a Probabilistic Data Structure}},
url = {http://dx.plos.org/10.1371/journal.pone.0101271},
volume = {9},
year = {2014}
}
@misc{ISO2009,
abstract = {ISO 80000-2:2009 gives general information about mathematical signs and symbols, their meanings, verbal equivalents and applications. The recommendations in ISO 80000-2:2009 are intended mainly for use in the natural sciences and technology, but also apply to other areas where mathematics is used.},
author = {{ISO International Standard}},
file = {:home/fin/Documents/papers/mendeley/ISO International Standard\_2009\_Quantities and units -- Part 2 Mathematical signs and symbols to be used in the natural sciences and tec.pdf:pdf},
title = {{Quantities and units -- Part 2: Mathematical signs and symbols to be used in the natural sciences and technology}},
year = {2009}
}
@misc{SeqtkGitHub,
author = {Li, Heng},
booktitle = {GitHub},
title = {{Seqtk}},
url = {https://github.com/lh3/seqtk/},
urldate = {2014-10-10},
year = {2015}
}
@misc{Dayhoff1978,
author = {Dayhoff, M and Schwartz, R and Orcutt, B},
booktitle = {Atlas Protein Seq. Struct.},
doi = {10.1.1.145.4315},
file = {:home/fin/Documents/papers/mendeley/Dayhoff, Schwartz, Orcutt\_1978\_A Model of Evolutionary Change in Proteins\_Atlas of Protein Sequence and Structure.pdf:pdf},
isbn = {0912466073},
issn = {17494613},
pages = {345--352},
title = {{A Model of Evolutionary Change in Proteins}},
year = {1978}
}
@misc{Nederbragt2013,
author = {Nederbragt, Alexander J.},
doi = {10.6084/m9.figshare.100940},
title = {{Developments in Next-Generation Sequencing Technologies}},
url = {http://dx.doi.org/10.6084/m9.figshare.100940},
year = {2013}
}
@article{Waterhouse2001,
abstract = {Gene silencing was perceived initially as an unpredictable and inconvenient side effect of introducing transgenes into plants. It now seems that it is the consequence of accidentally triggering the plant's adaptive defence mechanism against viruses and transposable elements. This recently discovered mechanism, although mechanistically different, has a number of parallels with the immune system of mammals.},
author = {Waterhouse, P M and Wang, M B and Lough, T},
doi = {10.1038/35081168},
file = {:home/fin/Documents/papers/mendeley/Waterhouse, Wang, Lough\_2001\_Gene silencing as an adaptive defence against viruses.\_Nature.pdf:pdf},
isbn = {0028-0836},
issn = {0028-0836},
journal = {Nature},
keywords = {Animals,Antisense,DNA Transposable Elements,Gene Expression Regulation,Gene Silencing,Methylation,Plant,Plant Diseases,Plant Diseases: genetics,Plant Diseases: virology,Plant Viruses,Plant Viruses: physiology,Plants,Plants: immunology,Plants: virology,RNA,Ribonucleases,Ribonucleases: metabolism,Small Interfering,Viral,Viral: metabolism},
pages = {834--42},
pmid = {11459066},
title = {{Gene silencing as an adaptive defence against viruses.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11459066},
volume = {411},
year = {2001}
}
@article{Huber2002,
author = {Huber, Harald and Hohn, Michael J and Rachel, Reinhard and Fuchs, Tanja},
file = {:home/fin/Documents/papers/mendeley/Huber et al.\_2002\_A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont\_Nature.pdf:pdf},
journal = {Nature},
number = {May},
pages = {63--67},
title = {{A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont}},
volume = {417},
year = {2002}
}
@article{Kodama2008,
abstract = {Cycloheximide is known to inhibit preferentially protein synthesis of symbiotic Chlorella of the ciliate Paramecium bursaria, but to hardly host protein synthesis. Treatment of algae-bearing Paramecium cells with cycloheximide induces synchronous swelling of all perialgal vacuoles that are localized immediately beneath the host's cell membrane. In this study, the space between the symbiotic algal cell wall and the perialgal vacuole membrane widened to about 25 times its normal width 24 h after treatment with cycloheximide. Then, the vacuoles detached from beneath the host's cell membrane, were condensed and stained with Gomori's solution, and the algae in the vacuoles were digested. Although this phenomenon is induced only under a fluorescent light condition, and not under a constant dark condition, this phenomenon was not induced in paramecia treated with cycloheximide in the light in the presence of the photosynthesis inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea. These results indicate that algal proteins synthesized in the presence of algal photosynthesis serve some important function to prevent expansion of the perialgal vacuole and to maintain the ability of the perialgal vacuole membrane to protect itself from host lysosomal fusion.},
author = {Kodama, Yuuki and Fujishima, Masahiro},
doi = {10.1016/j.protis.2008.02.005},
file = {:home/fin/Documents/papers/mendeley/Kodama, Fujishima\_2008\_Cycloheximide induces synchronous swelling of perialgal vacuoles enclosing symbiotic Chlorella vulgaris and diges.pdf:pdf},
isbn = {1434-4610},
issn = {1434-4610},
journal = {Protist},
keywords = {Acid Phosphatase,Acid Phosphatase: metabolism,Algal Proteins,Algal Proteins: metabolism,Animals,Cell Count,Chlorella vulgaris,Chlorella vulgaris: drug effects,Chlorella vulgaris: physiology,Chlorella vulgaris: radiation effects,Cycloheximide,Cycloheximide: pharmacology,Digestion,Light,Lysosomes,Lysosomes: drug effects,Lysosomes: physiology,Paramecium,Paramecium: drug effects,Paramecium: physiology,Paramecium: radiation effects,Photosynthesis,Photosynthesis: drug effects,Protein Synthesis Inhibitors,Protein Synthesis Inhibitors: pharmacology,Symbiosis,Vacuoles,Vacuoles: drug effects,Vacuoles: physiology},
number = {May},
pages = {483--94},
pmid = {18479967},
title = {{Cycloheximide induces synchronous swelling of perialgal vacuoles enclosing symbiotic Chlorella vulgaris and digestion of the algae in the ciliate Paramecium bursaria.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18479967},
volume = {159},
year = {2008}
}
@article{Bouhouche2011,
author = {Bouhouche, K. and Gout, J.-F. and Kapusta, a. and Betermier, M. and Meyer, E.},
doi = {10.1093/nar/gkq1283},
file = {:home/fin/Documents/papers/mendeley/Bouhouche et al.\_2011\_Functional specialization of Piwi proteins in Paramecium tetraurelia from post-transcriptional gene silencing to g.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {10},
pages = {4249--4264},
title = {{Functional specialization of Piwi proteins in Paramecium tetraurelia from post-transcriptional gene silencing to genome remodelling}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkq1283},
volume = {39},
year = {2011}
}
@article{Arp2007,
author = {Arp, a J and Childress, J J and Arp, a J and Childress, J J and Childress, J J and Fisher, C R and Girguis, P R and Childress, J J and Akashi, H and Gojobori, T and Rau, G H and Hedges, J I and Rau, G H and Fisher, C R and Brooks, J M},
file = {:home/fin/Documents/papers/mendeley/Arp et al.\_2007\_Amplified Silencing\_Unknown.pdf:pdf},
number = {January},
pages = {199--200},
title = {{Amplified Silencing}},
volume = {315},
year = {2007}
}
@article{Schatz1996,
author = {Schatz, G. and Dobberstein, B.},
file = {:home/fin/Documents/papers/mendeley/Schatz, Dobberstein\_1996\_Common Principles of Protein Translocation Across Membranes\_Science.pdf:pdf},
journal = {Science (80-. ).},
number = {5255},
pages = {1519--1526},
title = {{Common Principles of Protein Translocation Across Membranes}},
volume = {271},
year = {1996}
}
@article{Liang2013,
author = {Liang, Hongwei and Zen, Ke and Zhang, Junfeng and Zhang, Chen-Yu and Chen, Xi},
doi = {10.4161/rna.23663},
file = {:home/fin/Documents/papers/mendeley/Liang et al.\_2013\_New roles for microRNAs in cross-species communication\_RNA Biology.pdf:pdf},
issn = {1547-6286},
journal = {RNA Biol.},
keywords = {be transmitted from one,between different,communication or signal interference,cross-species communication,even in a cross-kingdom,facilitating cross-,ldlrap1,malaria parasite,manner,microrna,mir-451,mir168a,species,species to another,talk,the identification of,virus},
number = {December},
pages = {367--370},
title = {{New roles for microRNAs in cross-species communication}},
url = {http://www.tandfonline.com/doi/abs/10.4161/rna.23663},
volume = {10},
year = {2013}
}
@article{McCutchan1988,
abstract = {We have determined the complete sequence of two structurally distinct 18S ribosomal RNA genes from the malarial parasite Plasmodium falcipar'dm. S1 nuclease analyses demonstrate that only one of the genes is represented in stable rRNA populations isolated from blood-stage parasites. Comparisons of homologous rRNA genes from Plasmodium berghei and P. faiciparum reveal that they are identical at 86\% of their positions. From comparisons of the Plasmodium genes to that of humans, it was possible to design genus-specific as well as species-specific oligonucleotide probes that can be used to distinguish the parasite 18S ribosomal RNA from that of its host. The utilization of these probes as diagnostic reagents is discussed.},
author = {McCutchan, Thomas F. and de la Cruz, Vidal F. and Lal, Altaf A. and Gunderson, John H. and Elwood, Hille J. and Sogin, Mitchell L},
file = {:home/fin/Documents/papers/mendeley/McCutchan et al.\_1988\_Primary sequences of two small subunit ribosomal RNA genes from Plasmodium falciparum\_Molecular and Biochemical Pa.pdf:pdf},
isbn = {0374-9096 (Print)$\backslash$r0374-9096 (Linking)},
issn = {0374-9096},
journal = {Mol. Biochem. Parasitol.},
keywords = {Animals,Antimalarials,Antimalarials: pharmacology,Antimalarials: therapeutic use,Canada,Canada: ethnology,Chloroquine,Chloroquine: pharmacology,Doxycycline,Doxycycline: therapeutic use,Drug Resistance,Erythrocytes,Erythrocytes: parasitology,Falciparum,Falciparum: diagnosis,Falciparum: prevention \& control,Falciparum: therapy,Humans,Malaria,Male,Mefloquine,Mefloquine: therapeutic use,Middle Aged,Mozambique,Parasitemia,Parasitemia: parasitology,Plasmodium falciparum,Plasmodium falciparum: drug effects,Plasmodium falciparum: isolation \& purification,Quinine,Quinine: therapeutic use,Recurrence,Recurrence: prevention \& control,Travel,Turkey},
pages = {63--68},
pmid = {17205701},
title = {{Primary sequences of two small subunit ribosomal RNA genes from Plasmodium falciparum}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17205701},
volume = {28},
year = {1988}
}
@article{KodamaNRA2012b,
author = {Kodama, Y. and Shumway, M. and Leinonen, R.},
doi = {10.1093/nar/gkr854},
file = {:home/fin/Documents/papers/mendeley/Kodama, Shumway, Leinonen\_2012\_The sequence read archive explosive growth of sequencing data\_Nucleic Acids Research.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {October 2011},
pages = {D54--D56},
title = {{The sequence read archive: explosive growth of sequencing data}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkr854},
volume = {40},
year = {2012}
}
@inproceedings{Siegel1959,
author = {Siegel, R W and Karakashian, S J},
booktitle = {Anat. Rec.},
number = {3},
organization = {WILEY-LISS DIV JOHN WILEY \& SONS INC, 605 THIRD AVE, NEW YORK, NY 10158-0012},
pages = {639},
title = {{Dissociation and restoration of endocellular symbiosis in Paramecium-Bursaria}},
volume = {134},
year = {1959}
}
@article{Earl2011,
abstract = {Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from http://www.assemblathon.org/.},
author = {Earl, Dent and Bradnam, Keith and {St. John}, John and Darling, Aaron and Lin, Dawei and Fass, Joseph and Yu, Hung On Ken and Buffalo, Vince and Zerbino, Daniel R. and Diekhans, Mark and Nguyen, Ngan and Ariyaratne, Pramila Nuwantha and Sung, Wing Kin and Ning, Zemin and Haimel, Matthias and Simpson, Jared T. and Fonseca, Nuno a. and Birol, Inan\c{c} and Docking, T. Roderick and Ho, Isaac Y. and Rokhsar, Daniel S. and Chikhi, Rayan and Lavenier, Dominique and Chapuis, Guillaume and Naquin, Delphine and Maillet, Nicolas and Schatz, Michael C. and Kelley, David R. and Phillippy, Adam M. and Koren, Sergey and Yang, Shiaw Pyng and Wu, Wei and Chou, Wen Chi and Srivastava, Anuj and Shaw, Timothy I. and Ruby, J. Graham and Skewes-Cox, Peter and Betegon, Miguel and Dimon, Michelle T. and Solovyev, Victor and Seledtsov, Igor and Kosarev, Petr and Vorobyev, Denis and Ramirez-Gonzalez, Ricardo and Leggett, Richard and MacLean, Dan and Xia, Fangfang and Luo, Ruibang and Li, Zhenyu and Xie, Yinlong and Liu, Binghang and Gnerre, Sante and MacCallum, Iain and Przybylski, Dariusz and Ribeiro, Filipe J. and Sharpe, Ted and Hall, Giles and Kersey, Paul J. and Durbin, Richard and Jackman, Shaun D. and Chapman, Jarrod a. and Huang, Xiaoqiu and DeRisi, Joseph L. and Caccamo, Mario and Li, Yingrui and Jaffe, David B. and Green, Richard E. and Haussler, David and Korf, Ian and Paten, Benedict},
doi = {10.1101/gr.126599.111},
file = {:home/fin/Documents/papers/mendeley/Earl et al.\_2011\_Assemblathon 1 A competitive assessment of de novo short read assembly methods\_Genome Research.pdf:pdf},
isbn = {1549-5469 (Electronic) 1088-9051 (Linking)},
issn = {10889051},
journal = {Genome Res.},
pages = {2224--2241},
pmid = {21926179},
title = {{Assemblathon 1: A competitive assessment of de novo short read assembly methods}},
volume = {21},
year = {2011}
}
@article{mlpack2013,
author = {Curtin, Ryan R and Cline, James R and Slagle, Neil P and March, William B and Ram, P and Mehta, Nishant A and Gray, Alexander G},
journal = {J. Mach. Learn. Res.},
pages = {801--805},
title = {{MLPACK: A Scalable C++ Machine Learning Library}},
volume = {14},
year = {2013}
}
@article{Tange2011a,
address = {Frederiksberg, Denmark},
author = {Tange, O},
journal = {;login USENIX Mag.},
month = feb,
number = {1},
pages = {42--47},
title = {{GNU Parallel - The Command-Line Power Tool}},
url = {http://www.gnu.org/s/parallel},
volume = {36},
year = {2011}
}
@article{Palmer2010,
abstract = {BACKGROUND: With the rapid expansion of DNA sequencing databases, it is now feasible to identify relevant information from prior sequencing projects and completed genomes and apply it to de novo sequencing of new organisms. As an example, this paper demonstrates how such extra information can be used to improve de novo assemblies by augmenting the overlapping step. Finding all pairs of overlapping reads is a key task in many genome assemblers, and to this end, highly efficient algorithms have been developed to find alignments in large collections of sequences. It is well known that due to repeated sequences, many aligned pairs of reads nevertheless do not overlap. But no overlapping algorithm to date takes a rigorous approach to separating aligned but non-overlapping read pairs from true overlaps. RESULTS: We present an approach that extends the Minimus assembler by a data driven step to classify overlaps as true or false prior to contig construction. We trained several different classification models within the Weka framework using various statistics derived from overlaps of reads available from prior sequencing projects. These statistics included percent mismatch and k-mer frequencies within the overlaps as well as a comparative genomics score derived from mapping reads to multiple reference genomes. We show that in real whole-genome sequencing data from the E. coli and S. aureus genomes, by providing a curated set of overlaps to the contigging phase of the assembler, we nearly doubled the median contig length (N50) without sacrificing coverage of the genome or increasing the number of mis-assemblies. CONCLUSIONS: Machine learning methods that use comparative and non-comparative features to classify overlaps as true or false can be used to improve the quality of a sequence assembly.},
author = {Palmer, Lance E and Dejori, Mathaeus and Bolanos, Randall and Fasulo, Daniel},
doi = {10.1186/1471-2105-11-33},
file = {:home/fin/Documents/papers/mendeley/Palmer et al.\_2010\_Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction.\_BMC bioin.pdf:pdf},
isbn = {1471-2105 (Electronic)$\backslash$n1471-2105 (Linking)},
issn = {1471-2105},
journal = {BMC Bioinformatics},
pages = {33},
pmid = {20078885},
title = {{Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction.}},
volume = {11},
year = {2010}
}
@article{Cuvelier2010,
author = {Cuvelier, M. L. and Allen, a. E. and Monier, a. and McCrow, J. P. and Messie, M. and Tringe, S. G. and Woyke, T. and Welsh, R. M. and Ishoey, T. and Lee, J.-H. and Binder, B. J. and DuPont, C. L. and Latasa, M. and Guigand, C. and Buck, K. R. and Hilton, J. and Thiagarajan, M. and Caler, E. and Read, B. and Lasken, R. S. and Chavez, F. P. and Worden, a. Z.},
doi = {10.1073/pnas.1001665107},
file = {:home/fin/Documents/papers/mendeley/Cuvelier et al.\_2010\_Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton\_Proceedings of the Nati.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
number = {33},
pages = {14679--14684},
title = {{Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton}},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1001665107},
volume = {107},
year = {2010}
}
@article{Doring2008,
author = {D\"{o}ring, Andreas and Weese, David and Rausch, Tobias and Reinert, Knut},
doi = {10.1186/1471-2105-9-11},
file = {:home/fin/Documents/papers/mendeley/D\"{o}ring et al.\_2008\_SeqAn An efficient, generic C library for sequence analysis\_BMC Bioinformatics.pdf:pdf},
issn = {1471-2105},
journal = {BMC Bioinformatics},
pages = {11},
title = {{SeqAn An efficient, generic C++ library for sequence analysis}},
url = {http://www.biomedcentral.com/1471-2105/9/11},
volume = {9},
year = {2008}
}
@article{Fama2000,
abstract = {The coenocytic green alga Caulerpa racemosa colonized the Mediterranean some time after the opening of the Suez Canal in 1869. For most of the past century it has remained confined to the southeastern Mediterranean, but over the past several years the species has been reported in abundance along the western coasts of Italy, Sardinia and the Marseille area of southern France. Whether this constitutes a natural range expansion or a possible new introduction is under discussion. The purpose of this study was to establish the ITS signatures of populations inside and outside the Mediterranean. ITS1 sequences were compared among 78 clones from 21 individuals representing 11 populations of C. racemosa, collected from the Western Mediterranean, the Canary Islands, Panama and Western Australia. Intraindividual polymorphism of ITS1 was found to be as high or higher than inter-individual polymorphism across all samples tested. Polymorphism parsimony analysis, which takes into account intra-individual variation, revealed strong separation between individuals from Panama, Fuerteventura (Canary Is.) and the Mediterranean. In contrast, none of the six Mediterranean populations could be distinguished from one another. In addition, individuals and their clones collected from Perth (Australia) and Gran Canaria were spread throughout the Mediterranean clade. Possible reasons for the lack of homogenization of ITS arrays in C. racemosa under the mechanisms of concerted evolution and implications for phylogeographic interpretation are discussed and compared with Caulerpa taxifolia.},
author = {Fama, P and Olsen, J L and Stam, W T and Procaccini, G},
doi = {10.1080/09670260010001735951},
file = {:home/fin/Documents/papers/mendeley/Fama et al.\_2000\_High levels of intra- and inter-individual polymorphism in the rDNA ITS1 of Caulerpa racemosa (Chlorophyta)\_European Jo.pdf:pdf},
isbn = {0967-0262},
issn = {0967-0262},
journal = {Eur. J. Phycol.},
keywords = {Algae,Biogeography,Concerted Evolution,Drive,Mediterranean Sea,Nuclear Ribosomal Dna,Origin,Phylogeny,Taxifolia,Transcribed Spacer Sequences},
number = {December},
pages = {349--356},
pmid = {4879679},
title = {{High levels of intra- and inter-individual polymorphism in the rDNA ITS1 of Caulerpa racemosa (Chlorophyta)}},
volume = {35},
year = {2000}
}
@article{Murray2012,
author = {Murray, Shauna a. and Patterson, David J. and Thessen, Anne E.},
doi = {10.1016/j.tree.2012.08.011},
file = {:home/fin/Documents/papers/mendeley/Murray, Patterson, Thessen\_2012\_Transcriptomics and microbial eukaryote diversity A way forward\_Trends in Ecology and Evolution.pdf:pdf},
isbn = {0169-5347},
issn = {01695347},
journal = {Trends Ecol. Evol.},
number = {12},
pages = {651--652},
pmid = {22940223},
publisher = {Elsevier Ltd},
title = {{Transcriptomics and microbial eukaryote diversity: A way forward}},
url = {http://dx.doi.org/10.1016/j.tree.2012.08.011},
volume = {27},
year = {2012}
}
@article{Kawahara2012,
abstract = {A filamentous fungus, Magnaporthe oryzae, is a causal agent of rice blast disease, which is one of the most serious diseases affecting cultivated rice, Oryza sativa. However, the molecular mechanisms underlying both rice defense and fungal attack are not yet fully understood. Extensive past studies have characterized many infection-responsive genes in the pathogen and host plant, separately. To understand the plant-pathogen interaction comprehensively, it is valuable to monitor the gene expression profiles of both interacting organisms simultaneously in the same infected plant tissue. Although the host-pathogen interaction during the initial infection stage is important for the establishment of infection, the detection of fungal gene expression in infected leaves at the stage has been difficult because very few numbers of fungal cells are present. Using the emerging RNA-Seq technique, which has a wide dynamic range for expression analyses, we analyzed the mixed transcriptome of rice and blast fungus in infected leaves at 24 hours post-inoculation, which is the point when the primary infection hyphae penetrate leaf epidermal cells. We demonstrated that our method detected the gene expression of both the host plant and pathogen simultaneously in the same infected leaf blades in natural infection conditions without any artificial treatments. The upregulation of 240 fungal transcripts encoding putative secreted proteins was observed, suggesting that these candidates of fungal effector genes may play important roles in initial infection processes. The upregulation of transcripts encoding glycosyl hydrolases, cutinases and LysM domain-containing proteins were observed in the blast fungus, whereas pathogenesis-related and phytoalexin biosynthetic genes were upregulated in rice. Furthermore, more drastic changes in expression were observed in the incompatible interactions compared with the compatible ones in both rice and blast fungus at this stage. Our mixed transcriptome analysis is useful for the simultaneous elucidation of the tactics of host plant defense and pathogen attack.},
author = {Kawahara, Yoshihiro and Oono, Youko and Kanamori, Hiroyuki and Matsumoto, Takashi and Itoh, Takeshi and Minami, Eiichi},
doi = {10.1371/journal.pone.0049423},
file = {:home/fin/Documents/papers/mendeley/Kawahara et al.\_2012\_Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction.\_PloS one.pdf:pdf},
isbn = {1932-6203 (Electronic)$\backslash$r1932-6203 (Linking)},
issn = {1932-6203},
journal = {PLoS One},
keywords = {Gene Expression Profiling,Gene Expression Regulation, Plant,Genes, Fungal,Genes, Fungal: genetics,Genes, Plant,Genes, Plant: genetics,Host-Pathogen Interactions,Host-Pathogen Interactions: genetics,Magnaporthe,Magnaporthe: genetics,Magnaporthe: physiology,Molecular Sequence Annotation,Oryza sativa,Oryza sativa: genetics,Oryza sativa: immunology,Oryza sativa: microbiology,Plant Diseases,Plant Diseases: genetics,Plant Diseases: microbiology,Plant Leaves,Plant Leaves: genetics,Plant Leaves: microbiology,RNA, Fungal,RNA, Fungal: genetics,Real-Time Polymerase Chain Reaction,Reproducibility of Results,Sequence Analysis, RNA,Sequence Analysis, RNA: methods,Transcriptome,Transcriptome: genetics,Up-Regulation,Up-Regulation: genetics},
number = {11},
pages = {e49423},
pmid = {23139845},
title = {{Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction.}},
url = {http://dx.plos.org/10.1371/journal.pone.0049423},
volume = {7},
year = {2012}
}
@article{Lipson2009,
abstract = {We present single-molecule sequencing digital gene expression (smsDGE), a high-throughput, amplification-free method for accurate quantification of the full range of cellular polyadenylated RNA transcripts using a Helicos Genetic Analysis system. smsDGE involves a reverse-transcription and polyA-tailing sample preparation procedure followed by sequencing that generates a single read per transcript. We applied smsDGE to the transcriptome of Saccharomyces cerevisiae strain DBY746, using 6 of the available 50 channels in a single sequencing run, yielding on average 12 million aligned reads per channel. Using spiked-in RNA, accurate quantitative measurements were obtained over four orders of magnitude. High correlation was demonstrated across independent flow-cell channels, instrument runs and sample preparations. Transcript counting in smsDGE is highly efficient due to the representation of each transcript molecule by a single read. This efficiency, coupled with the high throughput enabled by the single-molecule sequencing platform, provides an alternative method for expression profiling.},
author = {Lipson, Doron and Raz, Tal and Kieu, Alix and Jones, Daniel R and Giladi, Eldar and Thayer, Edward and Thompson, John F and Letovsky, Stan and Milos, Patrice and Causey, Marie},
doi = {10.1038/nbt.1551},
file = {:home/fin/Documents/papers/mendeley/Lipson et al.\_2009\_Quantification of the yeast transcriptome by single-molecule sequencing.\_Nature biotechnology.pdf:pdf},
isbn = {1546-1696 (Electronic)$\backslash$r1087-0156 (Linking)},
issn = {1087-0156},
journal = {Nat. Biotechnol.},
number = {7},
pages = {652--658},
pmid = {19581875},
title = {{Quantification of the yeast transcriptome by single-molecule sequencing.}},
volume = {27},
year = {2009}
}
@article{Stiller2014,
author = {Stiller, John W and Schreiber, John and Yue, Jipei and Guo, Hui and Ding, Qin and Huang, Jinling},
doi = {10.1038/ncomms6764},
file = {:home/fin/Documents/papers/mendeley/Stiller et al.\_2014\_The evolution of photosynthesis in chromist algae through serial endosymbioses\_Nature Communications.pdf:pdf},
journal = {Nat. Commun.},
pages = {1--7},
publisher = {Nature Publishing Group},
title = {{The evolution of photosynthesis in chromist algae through serial endosymbioses}},
url = {http://dx.doi.org/10.1038/ncomms6764},
volume = {5},
year = {2014}
}
@article{Jennings1939,
author = {Jennings, H S},
file = {:home/fin/Documents/papers/mendeley/Jennings\_1939\_Genetics of Paramecium Bursaria. I. Mating Types and Groups, Their Interrelations and Distribution Mating Behavior and Sel.pdf:pdf},
journal = {Genetics},
number = {March},
pages = {202--233},
pmid = {17246919},
title = {{Genetics of Paramecium Bursaria. I. Mating Types and Groups, Their Interrelations and Distribution; Mating Behavior and Self Sterility.}},
volume = {24},
year = {1939}
}
@article{Pak2007,
author = {Pak, Julia and Fire, Andrew},
file = {:home/fin/Documents/papers/mendeley/Pak, Fire\_2007\_Distinct Populations of Primary and Secondary Effectors During RNAi in C. elegans\_Science.pdf:pdf},
journal = {Science (80-. ).},
pages = {241--244},
title = {{Distinct Populations of Primary and Secondary Effectors During RNAi in C. elegans}},
volume = {315},
year = {2007}
}
@article{Sims2014,
abstract = {SUMMARY: Computational genomics seeks to draw biological inferences from genomic datasets, often by integrating and contextualizing next-generation sequencing data. CGAT provides an extensive suite of tools designed to assist in the analysis of genome scale data from a range of standard file formats. The toolkit enables filtering, comparison, conversion, summarization and annotation of genomic intervals, gene sets and sequences. The tools can both be run from the Unix command line and installed into visual workflow builders, such as Galaxy. AVAILABILITY: The toolkit is freely available from http://github.com/CGATOxford/cgat CONTACT: andreas.heger@dpag.ox.ac.uk.},
author = {Sims, David and Ilott, Nicholas E. and Sansom, Stephen N. and Sudbery, Ian M. and Johnson, Jethro S. and Fawcett, Katherine a. and Berlanga-Taylor, Antonio J. and Luna-Valero, Sebastian and Ponting, Chris P. and Heger, Andreas},
doi = {10.1093/bioinformatics/btt756},
file = {:home/fin/Documents/papers/mendeley/Sims et al.\_2014\_CGAT Computational genomics analysis toolkit\_Bioinformatics.pdf:pdf},
isbn = {1367-4811 (Electronic)$\backslash$r1367-4803 (Linking)},
issn = {14602059},
journal = {Bioinformatics},
number = {9},
pages = {1290--1291},
pmid = {24395753},
title = {{CGAT: Computational genomics analysis toolkit}},
volume = {30},
year = {2014}
}
@incollection{Quinlan2014,
author = {Quinlan, Aaron R},
booktitle = {Curr. Protoc. Bioinforma.},
doi = {10.1002/0471250953.bi1112s47},
isbn = {9780471250951},
keywords = {bioinformatics,genome analysis,genome features,genome intervals,genomics},
publisher = {John Wiley \& Sons, Inc.},
title = {{BEDTools: The Swiss-Army Tool for Genome Feature Analysis}},
url = {http://dx.doi.org/10.1002/0471250953.bi1112s47},
year = {2014}
}
@article{Schwarz1978,
abstract = {The problem of selecting one of a number of models of different dimensions is treated by finding its Bayes solution, and evaluating the leading terms of its asymptotic expansion. These terms are a valid large-sample criterion beyond the Bayesian context, since they do not depend on the a priori distribution.},
author = {Schwarz, Gideon},
doi = {10.1214/aos/1176344136},
file = {:home/fin/Documents/papers/mendeley/Schwarz\_1978\_Estimating the dimension of a model\_The Annals of Statistics.pdf:pdf},
isbn = {0780394224},
issn = {0090-5364},
journal = {Ann. Stat.},
pages = {461--464},
pmid = {2958889},
title = {{Estimating the dimension of a model}},
url = {http://projecteuclid.org/euclid.aos/1176344136},
volume = {6},
year = {1978}
}
@article{scikit-learn,
author = {Pedregosa, F and Varoquaux, G and Gramfort, A and Michel, V and Thirion, B and Grisel, O and Blondel, M and Prettenhofer, P and Weiss, R and Dubourg, V and Vanderplas, J and Passos, A and Cournapeau, D and Brucher, M and Perrot, M and Duchesnay, E},
journal = {J. Mach. Learn. Res.},
pages = {2825--2830},
title = {{Scikit-learn: Machine Learning in \{P\}ython}},
volume = {12},
year = {2011}
}
@article{Ren2009,
abstract = {Supermatrix and supertree methods are two strategies advocated for phylogenetic analysis of sequence data from multiple gene loci, especially when some species are missing at some loci. The supermatrix method concatenates sequences from multiple genes into a data supermatrix for phylogenetic analysis, and ignores differences in evolutionary dynamics among the genes. The supertree method analyzes each gene separately and assembles the subtrees estimated from individual genes into a supertree for all species. Most algorithms suggested for supertree construction lack statistical justifications and ignore uncertainties in the subtrees. Instead of supermatrix or supertree, we advocate the use of likelihood function to combine data from multiple genes while accommodating their differences in the evolutionary process. This combines the strengths of the supermatrix and supertree methods while avoiding their drawbacks. We conduct computer simulation to evaluate the performance of the supermatrix, supertree, and maximum likelihood methods applied to two phylogenetic problems: molecular-clock dating of species divergences and reconstruction of species phylogenies. The results confirm the theoretical superiority of the likelihood method. Supertree or separate analyses of data of multiple genes may be useful in revealing the characteristics of the evolutionary process of multiple gene loci, and the information may be used to formulate realistic models for combined analysis of all genes by likelihood. ?? 2008 Elsevier B.V. All rights reserved.},
author = {Ren, Fengrong and Tanaka, Hiroshi and Yang, Ziheng},
doi = {10.1016/j.gene.2008.04.002},
file = {:home/fin/Documents/papers/mendeley/Ren, Tanaka, Yang\_2009\_A likelihood look at the supermatrix-supertree controversy\_Gene.pdf:pdf},
isbn = {0378-1119},
issn = {03781119},
journal = {Gene},
keywords = {Bayesian,Combined analysis,Likelihood,Likelihood supertree,Supermatrix,Supertree},
number = {1-2},
pages = {119--125},
pmid = {18502054},
publisher = {Elsevier B.V.},
title = {{A likelihood look at the supermatrix-supertree controversy}},
url = {http://dx.doi.org/10.1016/j.gene.2008.04.002},
volume = {441},
year = {2009}
}
@article{Vitter1985,
abstract = {We introduce fast algorithms for selecting a random sample of n records without replacement from a pool of N records, where the value of N is unknown beforehand. The main result of the paper is the design and analysis of Algorithm Z; it does the sampling in one pass using constant space and in O ( n (1 + log( N/n ))) expected time, which is optimum, up to a constant factor. Several optimizations are studied that collectively improve the speed of the naive version of the algorithm by an order of magnitude. We give an efficient Pascal-like implementation that incorporates these modifications and that is suitable for general use. Theoretical and empirical results indicate that Algorithm Z outperforms current methods by a significant margin.},
author = {Vitter, Jeffrey S.},
doi = {10.1145/3147.3165},
file = {:home/fin/Documents/papers/mendeley/Vitter\_1985\_Random Sampling with a Reservoir\_ACM Transactions on Mathematical Software.pdf:pdf},
issn = {00983500},
journal = {ACM Trans. Math. Softw.},
number = {1},
pages = {37--57},
title = {{Random Sampling with a Reservoir}},
volume = {11},
year = {1985}
}
@article{Bhattacharya2007,
abstract = {What factors drove the transformation of the cyanobacterial progenitor of plastids (e.g. chloroplasts) from endosymbiont to bona fide organelle? This question lies at the heart of organelle genesis because, whereas intracellular endosymbionts are widespread in both unicellular and multicellular eukaryotes (e.g. rhizobial bacteria, Chlorella cells in ciliates, Buchnera in aphids), only two canonical eukaryotic organelles of endosymbiotic origin are recognized, the plastids of algae and plants and the mitochondrion. Emerging data on (1) the discovery of non-canonical plastid protein targeting, (2) the recent origin of a cyanobacterial-derived organelle in the filose amoeba Paulinella chromatophora, and (3) the extraordinarily reduced genomes of psyllid bacterial endosymbionts begin to blur the distinction between endosymbiont and organelle. Here we discuss the use of these terms in light of new data in order to highlight the unique aspects of plastids and mitochondria and underscore their central role in eukaryotic evolution.},
author = {Bhattacharya, Debashish and Archibald, John M and Weber, Andreas P M and Reyes-Prieto, Adrian},
doi = {10.1002/bies.20671},
file = {:home/fin/Documents/papers/mendeley/Bhattacharya et al.\_2007\_How do endosymbionts become organelles Understanding early events in plastid evolution.\_BioEssays news and rev.pdf:pdf},
isbn = {0265-9247 (Print)},
issn = {0265-9247},
journal = {Bioessays},
keywords = {Biological,Evolution,Models,Plant Proteins,Plant Proteins: chemistry,Plastids,Plastids: physiology,Protein Transport,Symbiosis},
pages = {1239--46},
pmid = {18027391},
title = {{How do endosymbionts become organelles? Understanding early events in plastid evolution.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18027391},
volume = {29},
year = {2007}
}
@article{Swan2013,
abstract = {Planktonic bacteria dominate surface ocean biomass and influence global biog