text:
eochemical processes, but remain poorly characterized owing to difficulties in cultivation. Using large-scale single cell genomics, we obtained insight into the genome content and biogeography of many bacterial lineages inhabiting the surface ocean. We found that, compared with existing cultures, natural bacterioplankton have smaller genomes, fewer gene duplications, and are depleted in guanine and cytosine, noncoding nucleotides, and genes encoding transcription, signal transduction, and noncytoplasmic proteins. These findings provide strong evidence that genome streamlining and oligotrophy are prevalent features among diverse, free-living bacterioplankton, whereas existing laboratory cultures consist primarily of copiotrophs. The apparent ubiquity of metabolic specialization and mixotrophy, as predicted from single cell genomes, also may contribute to the difficulty in bacterioplankton cultivation. Using metagenome fragment recruitment against single cell genomes, we show that the global distribution of surface ocean bacterioplankton correlates with temperature and latitude and is not limited by dispersal at the time scales required for nucleotide substitution to exceed the current operational definition of bacterial species. Single cell genomes with highly similar small subunit rRNA gene sequences exhibited significant genomic and biogeographic variability, highlighting challenges in the interpretation of individual gene surveys and metagenome assemblies in environmental microbiology. Our study demonstrates the utility of single cell genomics for gaining an improved understanding of the composition and dynamics of natural microbial assemblages.},
author = {Swan, Brandon K and Tupper, Ben and Sczyrba, Alexander and Lauro, Federico M and Martinez-Garcia, Manuel and Gonz\'{a}lez, Jos\'{e} M and Luo, Haiwei and Wright, Jody J and Landry, Zachary C and Hanson, Niels W and Thompson, Brian P and Poulton, Nicole J and Schwientek, Patrick and Acinas, Silvia G and Giovannoni, Stephen J and Moran, Mary Ann and Hallam, Steven J and Cavicchioli, Ricardo and Woyke, Tanja and Stepanauskas, Ramunas},
doi = {10.1073/pnas.1304246110},
file = {:home/fin/Documents/papers/mendeley/Swan et al.\_2013\_Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean.\_Proceedings of th.pdf:pdf},
isbn = {2236347030},
issn = {1091-6490},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
keywords = {Bacteria,Bacteria: classification,Bacteria: genetics,Genome, Bacterial,Geography,Marine Biology,Oceans and Seas,Plankton,Plankton: classification,Plankton: genetics,Water Microbiology},
number = {28},
pages = {11463--8},
pmid = {23801761},
title = {{Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3710821\&tool=pmcentrez\&rendertype=abstract},
volume = {110},
year = {2013}
}
@article{Bankevich2012,
abstract = {The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.},
author = {Bankevich, Anton and Nurk, Sergey and Antipov, Dmitry and Gurevich, Alexey a. and Dvorkin, Mikhail and Kulikov, Alexander S. and Lesin, Valery M. and Nikolenko, Sergey I. and Pham, Son and Prjibelski, Andrey D. and Pyshkin, Alexey V. and Sirotkin, Alexander V. and Vyahhi, Nikolay and Tesler, Glenn and Alekseyev, Max a. and Pevzner, Pavel a.},
doi = {10.1089/cmb.2012.0021},
file = {:home/fin/Documents/papers/mendeley/Bankevich et al.\_2012\_SPAdes A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing\_Journal of Computational Bio.pdf:pdf},
isbn = {1066-5277},
issn = {1066-5277},
journal = {J. Comput. Biol.},
keywords = {assembly,bacteria,de bruijn graph,sequencing,single cell},
number = {5},
pages = {455--477},
pmid = {22506599},
title = {{SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing}},
volume = {19},
year = {2012}
}
@article{Bachmann2013,
author = {Bachmann, H. and Fischlechner, M. and Rabbers, I. and Barfa, N. and {Branco dos Santos}, F. and Molenaar, D. and Teusink, B.},
doi = {10.1073/pnas.1308523110},
file = {:home/fin/Documents/papers/mendeley/Bachmann et al.\_2013\_Availability of public goods shapes the evolution of competing metabolic strategies\_Proceedings of the National Aca.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
number = {35},
pages = {14302--14307},
title = {{Availability of public goods shapes the evolution of competing metabolic strategies}},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1308523110},
volume = {110},
year = {2013}
}
@article{Capella-Gutierrez2009,
abstract = {SUMMARY: Multiple sequence alignments are central to many areas of bioinformatics. It has been shown that the removal of poorly aligned regions from an alignment increases the quality of subsequent analyses. Such an alignment trimming phase is complicated in large-scale phylogenetic analyses that deal with thousands of alignments. Here, we present trimAl, a tool for automated alignment trimming, which is especially suited for large-scale phylogenetic analyses. trimAl can consider several parameters, alone or in multiple combinations, for selecting the most reliable positions in the alignment. These include the proportion of sequences with a gap, the level of amino acid similarity and, if several alignments for the same set of sequences are provided, the level of consistency across different alignments. Moreover, trimAl can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized. AVAILABILITY: trimAl has been written in C++, it is portable to all platforms. trimAl is freely available for download (http://trimal.cgenomics.org) and can be used online through the Phylemon web server (http://phylemon2.bioinfo.cipf.es/). Supplementary Material is available at http://trimal.cgenomics.org/publications.},
author = {Capella-Guti\'{e}rrez, Salvador and Silla-Mart\'{\i}nez, Jos\'{e} M. and Gabald\'{o}n, Toni},
doi = {10.1093/bioinformatics/btp348},
file = {:home/fin/Documents/papers/mendeley/Capella-Guti\'{e}rrez, Silla-Mart\'{\i}nez, Gabald\'{o}n\_2009\_trimAl A tool for automated alignment trimming in large-scale phylogenetic analyses\_.pdf:pdf},
isbn = {1367-4803},
issn = {13674803},
journal = {Bioinformatics},
number = {15},
pages = {1972--1973},
pmid = {19505945},
title = {{trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses}},
volume = {25},
year = {2009}
}
@article{Chun1963,
author = {Chun, Edward H.L. and Vaughan, Maurice H. and Rich, Alexander},
doi = {10.1016/S0022-2836(63)80042-X},
file = {:home/fin/Documents/papers/mendeley/Chun, Vaughan, Rich\_1963\_The isolation and characterization of DNA associated with chloroplast preparations\_Journal of Molecular Biology.pdf:pdf},
issn = {00222836},
journal = {J. Mol. Biol.},
month = aug,
number = {2},
pages = {130--141},
publisher = {Academic Press Inc. (London) Ltd.},
title = {{The isolation and characterization of DNA associated with chloroplast preparations}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S002228366380042X},
volume = {7},
year = {1963}
}
@article{Douglas1986,
author = {Douglas, a E; Huss V a R},
doi = {10.1007/BF00413031},
file = {:home/fin/Documents/papers/mendeley/Douglas\_1986\_On the characteristics and taxonomic position of symbiotic Chlorella\_Arch Microbiol.pdf:pdf},
issn = {2180-4303},
journal = {Arch Microbiol},
keywords = {chlorella - symbiosis -,coelenterates,genus chlorella have been,green algae of the,identified in,release - sporopollenin,sponges,symbiosis with protozoa,taxonomy - maltose,turbellaria},
pages = {80--84},
title = {{On the characteristics and taxonomic position of symbiotic Chlorella}},
volume = {145},
year = {1986}
}
@article{Heeg2015,
author = {Heeg, Jaqueline S. and Wolf, Matthias},
doi = {10.1016/j.plgene.2015.08.001},
file = {:home/fin/Documents/papers/mendeley/Heeg, Wolf\_2015\_ITS2 and 18S rDNA sequence-structure phylogeny of Chlorella and allies (Chlorophyta, Trebouxiophyceae, Chlorellaceae)\_Pl.pdf:pdf},
issn = {23524073},
journal = {Plant Gene},
keywords = {Barcoding,ITS2,Internal transcribed spacer,Maximum likelihood,RRNA,Secondary structure,Sequence-structure alignment},
pages = {20--28},
publisher = {The Authors},
title = {{ITS2 and 18S rDNA sequence-structure phylogeny of Chlorella and allies (Chlorophyta, Trebouxiophyceae, Chlorellaceae)}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S2352407315000207},
volume = {4},
year = {2015}
}
@article{Margulies2005,
abstract = {The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99\% or better accuracy, in one four-hour run. To achieve an approximately 100-fold increase in throughput over current Sanger sequencing technology, we have developed an emulsion method for DNA amplification and an instrument for sequencing by synthesis using a pyrosequencing protocol optimized for solid support and picolitre-scale volumes. Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96\% coverage at 99.96\% accuracy in one run of the machine.},
author = {Margulies, Marcel and Egholm, Michael and Altman, William E and Attiya, Said and Bader, Joel S and Bemben, Lisa a and Berka, Jan and Braverman, Michael S and Chen, Yi-Ju and Chen, Zhoutao and Dewell, Scott B and Du, Lei and Fierro, Joseph M and Gomes, Xavier V and Godwin, Brian C and He, Wen and Helgesen, Scott and Ho, Chun Heen and Irzyk, Gerard P and Jando, Szilveszter C and Alenquer, Maria L I and Jarvie, Thomas P and Jirage, Kshama B and Kim, Jong-Bum and Knight, James R and Lanza, Janna R and Leamon, John H and Lefkowitz, Steven M and Lei, Ming and Li, Jing and Lohman, Kenton L and Lu, Hong and Makhijani, Vinod B and McDade, Keith E and McKenna, Michael P and Myers, Eugene W and Nickerson, Elizabeth and Nobile, John R and Plant, Ramona and Puc, Bernard P and Ronan, Michael T and Roth, George T and Sarkis, Gary J and Simons, Jan Fredrik and Simpson, John W and Srinivasan, Maithreyan and Tartaro, Karrie R and Tomasz, Alexander and Vogt, Kari a and Volkmer, Greg a and Wang, Shally H and Wang, Yong and Weiner, Michael P and Yu, Pengguang and Begley, Richard F and Rothberg, Jonathan M},
doi = {10.1038/nature04726},
file = {:home/fin/Documents/papers/mendeley/Margulies et al.\_2005\_Genome Sequencing in Microfabricated High-density Picolitre Reactors\_Nature.pdf:pdf},
isbn = {1476-4687 (Electronic)},
issn = {0028-0836},
journal = {Nature},
number = {September},
pages = {376--380},
pmid = {16056220},
title = {{Genome Sequencing in Microfabricated High-density Picolitre Reactors}},
volume = {437},
year = {2005}
}
@article{Shabalina2008,
author = {Shabalina, Svetlana A. and Koonin, Eugene V.},
doi = {10.1016/j.tree.2008.06.005.Origins},
file = {:home/fin/Documents/papers/mendeley/Shabalina, Koonin\_2008\_Origins and evolution of eukaryotic RNA interference\_Trends in Ecology \& Evolution.pdf:pdf},
isbn = {0302121838},
journal = {Trends Ecol. Evol.},
keywords = {aging,atm,autophagic cell death,autophagy,c,calorie restriction,cancer,diabetic nephropathy,dietary restriction,elegans,epigenetic modifications,genotoxic stress,germ cells,germline development,germline removal,germline sex determination,glp-1 notch signaling,hsf1,hyperglycemia,igf signaling,insulin,insulin resistance,insulin signaling,introduction to aging,kinase,longevity,meiotic entry,metabolic memory,microarray,mitochondria,mitochondrial respiration,nrf2,obesity,oxidative stress,p53,pre-mrna,proliferation,proteotoxicity,prp-17,sirt1,sirtuins,skn-1,splicing,tor signaling,vrk-1},
number = {10},
pages = {578--587},
title = {{Origins and evolution of eukaryotic RNA interference}},
volume = {23},
year = {2008}
}
@article{Fonseca2012,
abstract = {MOTIVATION: A ubiquitous and fundamental step in high-throughput sequencing analysis is the alignment (mapping) of the generated reads to a reference sequence. To accomplish this task, numerous software tools have been proposed. Determining the mappers that are most suitable for a specific application is not trivial. RESULTS: This survey focuses on classifying mappers through a wide number of characteristics. The goal is to allow practitioners to compare the mappers more easily and find those that are most suitable for their specific problem.},
author = {Fonseca, Nuno a. and Rung, Johan and Brazma, Alvis and Marioni, John C.},
doi = {10.1093/bioinformatics/bts605},
file = {:home/fin/Documents/papers/mendeley/Fonseca et al.\_2012\_Tools for mapping high-throughput sequencing data\_Bioinformatics.pdf:pdf},
isbn = {1367-4811 (Electronic)$\backslash$r1367-4803 (Linking)},
issn = {13674803},
journal = {Bioinformatics},
number = {24},
pages = {3169--3177},
pmid = {23060614},
title = {{Tools for mapping high-throughput sequencing data}},
volume = {28},
year = {2012}
}
@article{Hansen2010,
abstract = {Generation of cDNA using random hexamer priming induces biases in the nucleotide composition at the beginning of transcriptome sequencing reads from the Illumina Genome Analyzer. The bias is independent of organism and laboratory and impacts the uniformity of the reads along the transcriptome. We provide a read count reweighting scheme, based on the nucleotide frequencies of the reads, that mitigates the impact of the bias.},
author = {Hansen, Kasper D. and Brenner, Steven E. and Dudoit, Sandrine},
doi = {10.1093/nar/gkq224},
file = {:home/fin/Documents/papers/mendeley/Hansen, Brenner, Dudoit\_2010\_Biases in Illumina transcriptome sequencing caused by random hexamer priming\_Nucleic Acids Research.pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$r0305-1048 (Linking)},
issn = {03051048},
journal = {Nucleic Acids Res.},
number = {12},
pages = {1--7},
pmid = {20395217},
title = {{Biases in Illumina transcriptome sequencing caused by random hexamer priming}},
volume = {38},
year = {2010}
}
@article{Prescott1994,
abstract = {Ciliates contain two types of nuclei: a micronucleus and a macronucleus. The micronucleus serves as the germ line nucleus but does not express its genes. The macronucleus provides the nuclear RNA for vegetative growth. Mating cells exchange haploid micronuclei, and a new macronucleus develops from a new diploid micronucleus. The old macronucleus is destroyed. This conversion consists of amplification, elimination, fragmentation, and splicing of DNA sequences on a massive scale. Fragmentation produces subchromosomal molecules in Tetrahymena and Paramecium cells and much smaller, gene-sized molecules in hypotrichous ciliates to which telomere sequences are added. These molecules are then amplified, some to higher copy numbers than others. rDNA is differentially amplified to thousands of copies per macronucleus. Eliminated sequences include transposonlike elements and sequences called internal eliminated sequences that interrupt gene coding regions in the micronuclear genome. Some, perhaps all, of these are excised as circular molecules and destroyed. In at least some hypotrichs, segments of some micronuclear genes are scrambled in a nonfunctional order and are recorded during macronuclear development. Vegetatively growing ciliates appear to possess a mechanism for adjusting copy numbers of individual genes, which corrects gene imbalances resulting from random distribution of DNA molecules during amitosis of the macronucleus. Other distinctive features of ciliate DNA include an altered use of the conventional stop codons.},
author = {Prescott, D M},
doi = {10.1016/0022-2836(72)90095-2},
file = {:home/fin/Documents/papers/mendeley/Prescott\_1994\_The DNA of ciliated protozoa.\_Microbiological reviews.pdf:pdf},
isbn = {0146-0749 (Print)
0146-0749 (Linking)},
issn = {00222836},
journal = {Microbiol. Rev.},
number = {2},
pages = {233--267},
pmid = {8078435},
title = {{The DNA of ciliated protozoa.}},
volume = {58},
year = {1994}
}
@article{Sanz-Luque2015,
author = {Sanz-Luque, Emanuel and Chamizo-Ampudia, Alejandro and Llamas, Angel and Galvan, Aurora and Fernandez, Emilio},
doi = {10.3389/fpls.2015.00899},
file = {:home/fin/Documents/papers/mendeley/Sanz-Luque et al.\_2015\_Understanding nitrate assimilation and its regulation in microalgae\_Frontiers in Plant Science.pdf:pdf},
issn = {1664-462X},
journal = {Front. Plant Sci.},
keywords = {green algae,nitrate,nitrate assimilation,nitrate assimilation, nitrate/nitrite uptake, gree,nitric oxide,nitrite uptake,nitrogen metabolism},
number = {October},
title = {{Understanding nitrate assimilation and its regulation in microalgae}},
url = {http://journal.frontiersin.org/article/10.3389/fpls.2015.00899},
volume = {6},
year = {2015}
}
@article{Arnaiz2007,
abstract = {ParameciumDB (http://paramecium.cgm.cnrs-gif.fr) is a new model organism database associated with the genome sequencing project of the unicellular eukaryote Paramecium tetraurelia. Built with the core components of the Generic Model Organism Database (GMOD) project, ParameciumDB currently contains the genome sequence and annotations, linked to available genetic data including the Gif Paramecium stock collection. It is thus possible to navigate between sequences and stocks via the genes and alleles. Phenotypes, of mutant strains and of knockdowns obtained by RNA interference, are captured using controlled vocabularies according to the Entity-Attribute-Value model. ParameciumDB currently supports browsing of phenotypes, alleles and stocks as well as querying of sequence features (genes, UniProt matches, InterPro domains, Gene Ontology terms) and of genetic data (phenotypes, stocks, RNA interference experiments). Forms allow submission of RNA interference data and some bioinformatics services are available. Future ParameciumDB development plans include coordination of human curation of the near 40 000 gene models by members of the research community.},
author = {Arnaiz, Olivier and Cain, Scott and Cohen, Jean and Sperling, Linda},
doi = {10.1093/nar/gkl777},
file = {:home/fin/Documents/papers/mendeley/Arnaiz et al.\_2007\_ParameciumDB A community resource that integrates the Paramecium tetraurelia genome sequence with genetic data\_Nuclei.pdf:pdf},
isbn = {0305-1048},
issn = {03051048},
journal = {Nucleic Acids Res.},
number = {November 2006},
pages = {439--444},
pmid = {17142227},
title = {{ParameciumDB: A community resource that integrates the Paramecium tetraurelia genome sequence with genetic data}},
volume = {35},
year = {2007}
}
@article{Christa2014,
abstract = {Several sacoglossan sea slugs (Plakobranchoidea) feed upon plastids of large unicellular algae. Four species--called long-term retention (LtR) species--are known to sequester ingested plastids within specialized cells of the digestive gland. There, the stolen plastids (kleptoplasts) remain photosynthetically active for several months, during which time LtR species can survive without additional food uptake. Kleptoplast longevity has long been puzzling, because the slugs do not sequester algal nuclei that could support photosystem maintenance. It is widely assumed that the slugs survive starvation by means of kleptoplast photosynthesis, yet direct evidence to support that view is lacking. We show that two LtR plakobranchids, Elysia timida and Plakobranchus ocellatus, incorporate (14)CO2 into acid-stable products 60- and 64-fold more rapidly in the light than in the dark, respectively. Despite this light-dependent CO2 fixation ability, light is, surprisingly, not essential for the slugs to survive starvation. LtR animals survived several months of starvation (i) in complete darkness and (ii) in the light in the presence of the photosynthesis inhibitor monolinuron, all while not losing weight faster than the control animals. Contrary to current views, sacoglossan kleptoplasts seem to be slowly digested food reserves, not a source of solar power.},
author = {Christa, Gregor and Zimorski, Verena and Woehle, Christian and Tielens, Aloysius G M and W\"{a}gele, Heike and Martin, William F and Gould, Sven B},
doi = {10.1098/rspb.2013.2493},
file = {:home/fin/Documents/papers/mendeley/Christa et al.\_2013\_Plastid-bearing sea slugs fix CO2 in the light but do not require photosynthesis to survive.\_Proceedings. Biological.pdf:pdf},
issn = {1471-2954},
journal = {Proc. Biol. Sci.},
keywords = {biochemistry,evolution,plant science},
number = {20132493},
pmid = {24258718},
title = {{Plastid-bearing sea slugs fix CO2 in the light but do not require photosynthesis to survive.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24258718},
volume = {281},
year = {2013}
}
@article{Martin1999a,
author = {Martin, William and Kowallik, Klaus},
doi = {10.1080/09670269910001736342},
file = {:home/fin/Documents/papers/mendeley/Martin, Kowallik\_1999\_Annotated English translation of Mereschkowsky's 1905 paper ‘\"{U}ber Natur und Ursprung der Chromatophoren im Pf.pdf:pdf},
issn = {0967-0262},
journal = {Eur. J. Phycol.},
month = aug,
number = {3},
pages = {287--295},
title = {{Annotated English translation of Mereschkowsky's 1905 paper ‘\"{U}ber Natur und Ursprung der Chromatophoren im Pflanzenreiche’}},
url = {http://www.tandfonline.com/doi/abs/10.1080/09670269910001736342},
volume = {34},
year = {1999}
}
@article{Domingos2012,
abstract = {MACHINE LEARNING SYSTEMS automatically learn programs from data. This is often a very attractive alternative to manually constructing them, and in the last decade the use of machine learning has spread rapidly throughout computer science and beyond. Machine learning is used in Web search, spam filters, recommender systems, ad placement, credit scoring, fraud detection, stock trading, drug design, and many other applications. A recent report from the McKinsey Global Institute asserts that machine learning (a.k.a. data mining or predictive analytics) will be the driver of the next big wave of innovation. Several fine textbooks are available to interested practitioners and researchers (for example, Mitchell and Witten et al.). However, much of the “folk knowledge” that is needed to successfully develop machine learning applications is not readily available in them. As a result, many machine learning projects take much longer than necessary or wind up producing less-than-ideal results. Yet much of this folk knowledge is fairly easy to communicate. This is the purpose of this article.},
author = {Domingos, Pedro},
doi = {10.1145/2347736.2347755},
file = {:home/fin/Documents/papers/mendeley/Domingos\_2012\_A few useful things to know about machine learning\_Communications of the ACM.pdf:pdf},
isbn = {0001-0782},
issn = {00010782},
journal = {Commun. ACM},
pages = {78},
title = {{A few useful things to know about machine learning}},
volume = {55},
year = {2012}
}
@article{Mayer1999,
author = {Mayer, Kimberly M and Forney, James D},
file = {:home/fin/Documents/papers/mendeley/Mayer, Forney\_1999\_A Mutation in the Flanking 5'-TA-3' Dinucleotide Prevents Excision of an Internal Eliminated Sequence From the Parame.pdf:pdf},
journal = {Genetics},
pages = {597--604},
title = {{A Mutation in the Flanking 5'-TA-3' Dinucleotide Prevents Excision of an Internal Eliminated Sequence From the Paramecium tetraurelia Genome}},
volume = {151},
year = {1999}
}
@article{Beisson2010b,
author = {Beisson, Janine and B\'{e}termier, Mireille and Br\'{e}, M. H. and Cohen, Jean and Duharcourt, Sandra and Duret, Laurent and Kung, Ching and Malinsky, Sophie and Meyer, Eric and Preer, John R. and Sperling, Linda},
doi = {10.1101/pdb.prot5364},
file = {:home/fin/Documents/papers/mendeley/Beisson et al.\_2010\_DNA microinjection into the macronucleus of paramecium\_Cold Spring Harbor Protocols.pdf:pdf},
issn = {15596095},
journal = {Cold Spring Harb. Protoc.},
number = {1},
pages = {1--4},
pmid = {20150123},
title = {{DNA microinjection into the macronucleus of paramecium}},
volume = {5},
year = {2010}
}
@article{Jeon1978,
abstract = {A strain of Amoeba proteus has lost its ability to survive at temperatures above 26 degrees C as a result of becoming dependent on endosymbiotic bacteria that are psychrophile-like. The observed temperature sensitivity develops in fewer than 200 host cell generations (18 months of culture) after the host cells are experimentally infected with the symbionts.},
author = {Jeon, K W and Ahn, T I},
doi = {10.1126/science.202.4368.635},
file = {:home/fin/Documents/papers/mendeley/Jeon, Ahn\_1978\_Temperature sensitivity a cell character determined by obligate endosymbionts in amoebas.\_Science (New York, N.Y.).pdf:pdf},
issn = {0036-8075},
journal = {Science},
number = {November},
pages = {635--637},
pmid = {17754039},
title = {{Temperature sensitivity: a cell character determined by obligate endosymbionts in amoebas.}},
volume = {202},
year = {1978}
}
@article{Goodstein2012,
author = {Goodstein, D. M. and Shu, S. and Howson, R. and Neupane, R. and Hayes, R. D. and Fazo, J. and Mitros, T. and Dirks, W. and Hellsten, U. and Putnam, N. and Rokhsar, D. S.},
doi = {10.1093/nar/gkr944},
file = {:home/fin/Documents/papers/mendeley/Goodstein et al.\_2012\_Phytozome a comparative platform for green plant genomics\_Nucleic Acids Research.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {November 2011},
pages = {D1178--D1186},
title = {{Phytozome: a comparative platform for green plant genomics}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkr944},
volume = {40},
year = {2012}
}
@article{Ogata1999,
abstract = {Kyoto Encyclopedia of Genes and Genomes (KEGG) is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules. The major component of KEGG is the PATHWAY database that consists of graphical diagrams of biochemical pathways including most of the known metabolic pathways and some of the known regulatory pathways. The pathway information is also represented by the ortholog group tables summarizing orthologous and paralogous gene groups among different organisms. KEGG maintains the GENES database for the gene catalogs of all organisms with complete genomes and selected organisms with partial genomes, which are continuously re-annotated, as well as the LIGAND database for chemical compounds and enzymes. Each gene catalog is associated with the graphical genome map for chromosomal locations that is represented by Java applet. In addition to the data collection efforts, KEGG develops and provides various computational tools, such as for reconstructing biochemical pathways from the complete genome sequence and for predicting gene regulatory networks from the gene expression profiles. The KEGG databases are daily updated and made freely available (http://www.genome.ad.jp/kegg/).},
author = {Ogata, Hiroyuki and Goto, Susumu and Sato, Kazushige and Fujibuchi, Wataru and Bono, Hidemasa and Kanehisa, Minoru and Goto, Susumu and Ogata, Hiroyuki and Goto, Susumu and Sato, Kazushige and Fujibuchi, Wataru and Bono, Hidemasa and Kanehisa, Minoru and Goto, Susumu},
doi = {10.1093/nar/27.1.29},
file = {:home/fin/Documents/papers/mendeley/Ogata et al.\_1999\_KEGG Kyoto encyclopedia of genes and genomes\_Nucleic Acids Research.pdf:pdf},
isbn = {0305-1048 (Print)$\backslash$r0305-1048 (Linking)},
issn = {03051048},
journal = {Nucleic Acids Res.},
number = {1},
pages = {27--30},
pmid = {9847135},
title = {{KEGG: Kyoto encyclopedia of genes and genomes}},
volume = {27},
year = {1999}
}
@article{Russell2013,
author = {Russell, C. W. and Bouvaine, S. and Newell, P. D. and Douglas, a. E.},
doi = {10.1128/AEM.01543-13},
file = {:home/fin/Documents/papers/mendeley/Russell et al.\_2013\_Shared Metabolic Pathways in a Coevolved Insect-Bacterial Symbiosis\_Applied and Environmental Microbiology.pdf:pdf},
issn = {0099-2240},
journal = {Appl. Environ. Microbiol.},
number = {19},
pages = {6117--6123},
title = {{Shared Metabolic Pathways in a Coevolved Insect-Bacterial Symbiosis}},
url = {http://aem.asm.org/cgi/doi/10.1128/AEM.01543-13},
volume = {79},
year = {2013}
}
@article{Keeling2010,
abstract = {Plastids and mitochondria each arose from a single endosymbiotic event and share many similarities in how they were reduced and integrated with their host. However, the subsequent evolution of the two organelles could hardly be more different: mitochondria are a stable fixture of eukaryotic cells that are neither lost nor shuffled between lineages, whereas plastid evolution has been a complex mix of movement, loss and replacement. Molecular data from the past decade have substantially untangled this complex history, and we now know that plastids are derived from a single endosymbiotic event in the ancestor of glaucophytes, red algae and green algae (including plants). The plastids of both red algae and green algae were subsequently transferred to other lineages by secondary endosymbiosis. Green algal plastids were taken up by euglenids and chlorarachniophytes, as well as one small group of dinoflagellates. Red algae appear to have been taken up only once, giving rise to a diverse group called chromalveolates. Additional layers of complexity come from plastid loss, which has happened at least once and probably many times, and replacement. Plastid loss is difficult to prove, and cryptic, non-photosynthetic plastids are being found in many non-photosynthetic lineages. In other cases, photosynthetic lineages are now understood to have evolved from ancestors with a plastid of different origin, so an ancestral plastid has been replaced with a new one. Such replacement has taken place in several dinoflagellates (by tertiary endosymbiosis with other chromalveolates or serial secondary endosymbiosis with a green alga), and apparently also in two rhizarian lineages: chlorarachniophytes and Paulinella (which appear to have evolved from chromalveolate ancestors). The many twists and turns of plastid evolution each represent major evolutionary transitions, and each offers a glimpse into how genomes evolve and how cells integrate through gene transfers and protein trafficking.},
author = {Keeling, Patrick J},
doi = {10.1098/rstb.2009.0103},
file = {:home/fin/Documents/papers/mendeley/Keeling\_2010\_The endosymbiotic origin, diversification and fate of plastids.\_Philosophical transactions of the Royal Society of London..pdf:pdf},
isbn = {1471-2970 (Electronic)$\backslash$r0962-8436 (Linking)},
issn = {0962-8436},
journal = {Philos. Trans. R. Soc. Lond. B. Biol. Sci.},
keywords = {1,a single event,algae,endosymbiosis,endosymbiosis has played many,evolution,of global significance,phylogeny,plastids,protist,roles in the evolution,the origin of plastids},
pages = {729--748},
pmid = {20124341},
title = {{The endosymbiotic origin, diversification and fate of plastids.}},
volume = {365},
year = {2010}
}
@article{Tautenhahn2008,
author = {Tautenhahn, Ralf and Bottcher, Christoph and Neumann, Steffen},
doi = {10.1186/1471-2105-9-504},
file = {:home/fin/Documents/papers/mendeley/Tautenhahn, Bottcher, Neumann\_2008\_Highly sensitive feature detection for high resolution LCMS\_BMC Bioinformatics.pdf:pdf},
issn = {1471-2105},
journal = {BMC Bioinformatics},
pages = {504},
title = {{Highly sensitive feature detection for high resolution LC/MS}},
url = {http://www.biomedcentral.com/1471-2105/9/504},
volume = {9},
year = {2008}
}
@article{Kajitani2014,
abstract = {Although many de novo genome assembly projects have recently been conducted using high-throughput sequencers, assembling highly heterozygous diploid genomes is a substantial challenge due to the increased complexity of the de Bruijn graph structure predominantly used. To address the increasing demand for sequencing of nonmodel and/or wild-type samples, in most cases inbred lines or fosmid-based hierarchical sequencing methods are used to overcome such problems. However, these methods are costly and time consuming, forfeiting the advantages of massive parallel sequencing. Here, we describe a novel de novo assembler, Platanus, that can effectively manage high-throughput data from heterozygous samples. Platanus assembles DNA fragments (reads) into contigs by constructing de Bruijn graphs with automatically optimized k-mer sizes followed by the scaffolding of contigs based on paired-end information. The complicated graph structures that result from the heterozygosity are simplified during not only the contig assembly step but also the scaffolding step. We evaluated the assembly results on eukaryotic samples with various levels of heterozygosity. Compared with other assemblers, Platanus yields assembly results that have a larger scaffold NG50 length without any accompanying loss of accuracy in both simulated and real data. In addition, Platanus recorded the largest scaffold NG50 values for two of the three low-heterozygosity species used in the de novo assembly contest, Assemblathon 2. Platanus therefore provides a novel and efficient approach for the assembly of gigabase-sized highly heterozygous genomes and is an attractive alternative to the existing assemblers designed for genomes of lower heterozygosity.},
author = {Kajitani, Rei and Toshimoto, Kouta and Noguchi, Hideki and Toyoda, Atsushi and Ogura, Yoshitoshi and Okuno, Miki and Yabana, Mitsuru and Harada, Masayuki and Nagayasu, Eiji and Maruyama, Haruhiko and Kohara, Yuji and Fujiyama, Asao and Hayashi, Tetsuya and Itoh, Takehiko},
doi = {10.1101/gr.170720.113},
file = {:home/fin/Documents/papers/mendeley/Kajitani et al.\_2014\_Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads\_Genome Research.pdf:pdf},
issn = {15495469},
journal = {Genome Res.},
pages = {1384--1395},
pmid = {24755901},
title = {{Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads}},
volume = {24},
year = {2014}
}
@article{Tsiatis2010,
abstract = {Mutations in codons 12 and 13 of the KRAS oncogene are relatively common in colorectal and lung adenocarcinomas. Recent data indicate that these mutations result in resistance to anti-epidermal growth factor receptor therapy. Therefore, we assessed Sanger sequencing, pyrosequencing, and melting curve analysis for the detection of KRAS codon 12/13 mutations in formalin-fixed paraffin-embedded samples, including 58 primary and 42 metastatic colorectal adenocarcinomas, 63 primary and 17 metastatic lung adenocarcinomas, and 20 normal colon samples. Of 180 tumor samples, 62.2\% were KRAS mutant positive, and 37.8\% were negative. Melting curve analysis yielded no false positive or false negative results, but had 10\% equivocal calls. Melting curve analysis also resulted in 4 cases with melting curves inconsistent with either wild-type or codon 12/13 mutations. These patterns were generated from samples with double mutants in codons 12/13 and with mutations outside of codons 12/13. Pyrosequencing yielded no false positive or false negative results as well. However, two samples from one patient yielded a pyrogram that was flagged as abnormal, but the mutation subtype could not be determined. Finally, using an electronic cutoff of 10\%, Sanger sequencing showed 11.1\% false positives and 6.1\% false negatives. In our hands, the limit of detection for Sanger sequencing, pyrosequencing, and melting curve analysis was approximately 15 to 20\%, 5\%, and 10\% mutant alleles, respectively.},
author = {Tsiatis, Athanasios C and Norris-Kirby, Alexis and Rich, Roy G and Hafez, Michael J and Gocke, Christopher D and Eshleman, James R and Murphy, Kathleen M},
doi = {10.2353/jmoldx.2010.090188},
file = {:home/fin/Documents/papers/mendeley/Tsiatis et al.\_2010\_Comparison of Sanger sequencing, pyrosequencing, and melting curve analysis for the detection of KRAS mutations diag.pdf:pdf},
isbn = {1943-7811 (Electronic)$\backslash$r1525-1578 (Linking)},
issn = {15251578},
journal = {J. Mol. Diagn.},
number = {4},
pages = {425--432},
pmid = {20431034},
publisher = {American Society for Investigative Pathology and Association for Molecular Pathology},
title = {{Comparison of Sanger sequencing, pyrosequencing, and melting curve analysis for the detection of KRAS mutations: diagnostic and clinical implications.}},
url = {http://dx.doi.org/10.2353/jmoldx.2010.090188},
volume = {12},
year = {2010}
}
@article{Yoon2004,
abstract = {The appearance of photosynthetic eukaryotes (algae and plants) dramatically altered the Earth's ecosystem, making possible all vertebrate life on land, including humans. Dating algal origin is, however, frustrated by a meager fossil record. We generated a plastid multi-gene phylogeny with Bayesian inference and then used maximum likelihood molecular clock methods to estimate algal divergence times. The plastid tree was used as a surrogate for algal host evolution because of recent phylogenetic evidence supporting the vertical ancestry of the plastid in the red, green, and glaucophyte algae. Nodes in the plastid tree were constrained with six reliable fossil dates and a maximum age of 3,500 MYA based on the earliest known eubacterial fossil. Our analyses support an ancient (late Paleoproterozoic) origin of photosynthetic eukaryotes with the primary endosymbiosis that gave rise to the first alga having occurred after the split of the Plantae (i.e., red, green, and glaucophyte algae plus land plants) from the opisthokonts sometime before 1,558 MYA. The split of the red and green algae is calculated to have occurred about 1,500 MYA, and the putative single red algal secondary endosymbiosis that gave rise to the plastid in the cryptophyte, haptophyte, and stramenopile algae (chromists) occurred about 1,300 MYA. These dates, which are consistent with fossil evidence for putative marine algae (i.e., acritarchs) from the early Mesoproterozoic (1,500 MYA) and with a major eukaryotic diversification in the very late Mesoproterozoic and Neoproterozoic, provide a molecular timeline for understanding algal evolution.},
author = {Yoon, Hwan Su and Hackett, Jeremiah D. and Ciniglia, Claudia and Pinto, Gabriele and Bhattacharya, Debashish},
doi = {10.1093/molbev/msh075},
file = {:home/fin/Documents/papers/mendeley/Yoon et al.\_2004\_A Molecular Timeline for the Origin of Photosynthetic Eukaryotes\_Molecular Biology and Evolution.pdf:pdf},
isbn = {0737-4038 (Print)$\backslash$r0737-4038 (Linking)},
issn = {07374038},
journal = {Mol. Biol. Evol.},
keywords = {Algal origin,Divergence time estimates,Fossil record,Molecular clock,Plastid},
number = {5},
pages = {809--818},
pmid = {14963099},
title = {{A Molecular Timeline for the Origin of Photosynthetic Eukaryotes}},
volume = {21},
year = {2004}
}
@article{Rousseeuw1987,
abstract = {A new graphical display is proposed for partitioning techniques. Each cluster is represented by a so-called silhouette, which is based on the comparison of its tightness and separation. This silhouette shows which objects lie well within their cluster, and which ones are merely somewhere in between clusters. The entire clustering is displayed by combining the silhouettes into a single plot, allowing an appreciation of the relative quality of the clusters and an overview of the data configuration. The average silhouette width provides an evaluation of clustering validity, and might be used to select an ‘appropriate’ number of clusters.},
archivePrefix = {arXiv},
arxivId = {z0024},
author = {Rousseeuw, Peter J.},
doi = {10.1016/0377-0427(87)90125-7},
eprint = {z0024},
file = {:home/fin/Documents/papers/mendeley/Rousseeuw\_1987\_Silhouettes A graphical aid to the interpretation and validation of cluster analysis\_Journal of Computational and Applied.pdf:pdf},
isbn = {03770427},
issn = {03770427},
journal = {J. Comput. Appl. Math.},
keywords = {Graphical display,classification,cluster analysis,clustering validity},
pages = {53--65},
pmid = {19382406},
title = {{Silhouettes: A graphical aid to the interpretation and validation of cluster analysis}},
url = {http://www.sciencedirect.com/science/article/pii/0377042787901257},
volume = {20},
year = {1987}
}
@article{Maxam1977,
abstract = {DNA can be sequenced by a chemical procedure that breaks a terminally labeled DNA molecule partially at each repetition of a base. The lengths of the labeled fragments then identify the positions of that base. We describe reactions that cleave DNA preferentially at guanines, at adenines, at cytosines and thymines equally, and at cytosines alone. When the products of these four reactions are resolved by size, by electrophoresis on a polyacrylamide gel, the DNA sequence can be read from the pattern of radioactive bands. The technique will permit sequencing of at least 100 bases from the point of labeling.},
author = {Maxam, a M and Gilbert, W},
doi = {10.1073/pnas.74.2.560},
file = {:home/fin/Documents/papers/mendeley/Maxam, Gilbert\_1977\_A new method for sequencing DNA.\_Proceedings of the National Academy of Sciences of the United States of America.pdf:pdf},
isbn = {0027-8424 (Print)$\backslash$r0027-8424 (Linking)},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
number = {2},
pages = {560--564},
pmid = {265521},
title = {{A new method for sequencing DNA.}},
volume = {74},
year = {1977}
}
@article{Nurk2013,
abstract = {Recent advances in single-cell genomics provide an alternative to largely gene-centric metagenomics studies, enabling whole-genome sequencing of uncultivated bacteria. However, single-cell assembly projects are challenging due to (i) the highly nonuniform read coverage and (ii) a greatly elevated number of chimeric reads and read pairs. While recently developed single-cell assemblers have addressed the former challenge, methods for assembling highly chimeric reads remain poorly explored. We present algorithms for identifying chimeric edges and resolving complex bulges in de Bruijn graphs, which significantly improve single-cell assemblies. We further describe applications of the single-cell assembler SPAdes to a new approach for capturing and sequencing "microbial dark matter" that forms small pools of randomly selected single cells (called a mini-metagenome) and further sequences all genomes from the mini-metagenome at once. On single-cell bacterial datasets, SPAdes improves on the recently developed E+V-SC and IDBA-UD assemblers specifically designed for single-cell sequencing. For standard (cultivated monostrain) datasets, SPAdes also improves on A5, ABySS, CLC, EULER-SR, Ray, SOAPdenovo, and Velvet. Thus, recently developed single-cell assemblers not only enable single-cell sequencing, but also improve on conventional assemblers on their own turf. SPAdes is available for free online download under a GPLv2 license.},
author = {Nurk, Sergey and Bankevich, Anton and Antipov, Dmitry and Gurevich, Alexey a and Korobeynikov, Anton and Lapidus, Alla and Prjibelski, Andrey D and Pyshkin, Alexey and Sirotkin, Alexander and Sirotkin, Yakov and Stepanauskas, Ramunas and Clingenpeel, Scott R and Woyke, Tanja and McLean, Jeffrey S and Lasken, Roger and Tesler, Glenn and Alekseyev, Max a and Pevzner, Pavel a},
doi = {10.1089/cmb.2013.0084},
file = {:home/fin/Documents/papers/mendeley/Nurk et al.\_2013\_Assembling single-cell genomes and mini-metagenomes from chimeric MDA products.\_Journal of computational biology a jou.pdf:pdf},
isbn = {1557-8666 (Electronic)$\backslash$r1066-5277 (Linking)},
issn = {1557-8666},
journal = {J. Comput. Biol.},
keywords = {Algorithms,Base Composition,Computational Biology,Contig Mapping,Contig Mapping: methods,DNA, Bacterial,DNA, Bacterial: genetics,DNA, Concatenated,DNA, Concatenated: genetics,Escherichia coli,Escherichia coli: genetics,Gene Library,Genome, Bacterial,High-Throughput Nucleotide Sequencing,Nucleic Acid Amplification Techniques,Pedobacter,Pedobacter: genetics,Prochlorococcus,Prochlorococcus: genetics,Sequence Analysis, DNA,Single-Cell Analysis},
number = {10},
pages = {714--37},
pmid = {24093227},
title = {{Assembling single-cell genomes and mini-metagenomes from chimeric MDA products.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3791033\&tool=pmcentrez\&rendertype=abstract},
volume = {20},
year = {2013}
}
@article{Harris2004,
abstract = {The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.},
author = {Harris, M a and Clark, J and Ireland, a and Lomax, J and Ashburner, M and Foulger, R and Eilbeck, K and Lewis, S and Marshall, B and Mungall, C and Richter, J and Rubin, G M and Blake, J a and Bult, C and Dolan, M and Drabkin, H and Eppig, J T and Hill, D P and Ni, L and Ringwald, M and Balakrishnan, R and Cherry, J M and Christie, K R and Costanzo, M C and Dwight, S S and Engel, S and Fisk, D G and Hirschman, J E and Hong, E L and Nash, R S and Sethuraman, a and Theesfeld, C L and Botstein, D and Dolinski, K and Feierbach, B and Berardini, T and Mundodi, S and Rhee, S Y and Apweiler, R and Barrell, D and Camon, E and Dimmer, E and Lee, V and Chisholm, R and Gaudet, P and Kibbe, W and Kishore, R and Schwarz, E M and Sternberg, P and Gwinn, M and Hannick, L and Wortman, J and Berriman, M and Wood, V and de la Cruz, N and Tonellato, P and Jaiswal, P and Seigfried, T and White, R},
doi = {10.1093/nar/gkh036},
file = {:home/fin/Documents/papers/mendeley/Harris et al.\_2004\_The Gene Ontology (GO) database and informatics resource.\_Nucleic acids research.pdf:pdf},
isbn = {1362-4962 (Electronic)},
issn = {1362-4962},
journal = {Nucleic Acids Res.},
pages = {D258--D261},
pmid = {14681407},
title = {{The Gene Ontology (GO) database and informatics resource.}},
volume = {32},
year = {2004}
}
@article{Parfrey2011,
abstract = {Although macroscopic plants, animals, and fungi are the most familiar eukaryotes, the bulk of eukaryotic diversity is microbial. Elucidating the timing of diversification among the more than 70 lineages is key to understanding the evolution of eukaryotes. Here, we use taxon-rich multigene data combined with diverse fossils and a relaxed molecular clock framework to estimate the timing of the last common ancestor of extant eukaryotes and the divergence of major clades. Overall, these analyses suggest that the last common ancestor lived between 1866 and 1679 Ma, consistent with the earliest microfossils interpreted with confidence as eukaryotic. During this interval, the Earth's surface differed markedly from today; for example, the oceans were incompletely ventilated, with ferruginous and, after about 1800 Ma, sulfidic water masses commonly lying beneath moderately oxygenated surface waters. Our time estimates also indicate that the major clades of eukaryotes diverged before 1000 Ma, with most or all probably diverging before 1200 Ma. Fossils, however, suggest that diversity within major extant clades expanded later, beginning about 800 Ma, when the oceans began their transition to a more modern chemical state. In combination, paleontological and molecular approaches indicate that long stems preceded diversification in the major eukaryotic lineages.},
author = {Parfrey, Laura Wegener and Lahr, Daniel J G and Knoll, Andrew H and Katz, Laura a},
doi = {10.1073/pnas.1110633108},
file = {:home/fin/Documents/papers/mendeley/Parfrey et al.\_2011\_Estimating the timing of early eukaryotic diversification with multigene molecular clocks.\_Proceedings of the Nation.pdf:pdf},
isbn = {1091-6490 (Electronic)$\backslash$r0027-8424 (Linking)},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
number = {33},
pages = {13624--13629},
pmid = {21810989},
title = {{Estimating the timing of early eukaryotic diversification with multigene molecular clocks.}},
volume = {108},
year = {2011}
}
@article{Preston1996,
abstract = {Archaea, one of the three major domains of extant life, was thought to comprise predominantly microorganisms that inhabit extreme environments, inhospitable to most Eucarya and Bacteria. However, molecular phylogenetic surveys of native microbial assemblages are beginning to indicate that the evolutionary and physiological diversity of Archaea is far greater than previously supposed. We report here the discovery and preliminary characterization of a marine archaeon that inhabits the tissues of a temperate water sponge. The association was specific, with a single crenarchaeal phylotype inhabiting a single sponge host species. To our knowledge, this partnership represents the first described symbiosis involving Crenarchaeota. The symbiotic archaeon grows well at temperatures of 10 degrees C, over 60 degrees C below the growth temperature optimum of any cultivated species of Crenarchaeota. Archaea have been generally characterized as microorganisms that inhabit relatively circumscribed niches, largely high-temperature anaerobic environments. In contrast, data from molecular phylogenetic surveys, including this report, suggest that some crenarchaeotes have diversified considerably and are found in a wide variety of lifestyles and habitats. We present here the identification and initial description of Cenarchaeum symbiosum gen. nov., sp. nov., a symbiotic archaeon closely related to other nonthermophilic crenarchaeotes that inhabit diverse marine and terrestrial environments.},
author = {Preston, C M and Wu, K Y and Molinski, T F and DeLong, E F},
doi = {10.1073/pnas.93.13.6241},
file = {:home/fin/Documents/papers/mendeley/Preston et al.\_1996\_A psychrophilic crenarchaeon inhabits a marine sponge Cenarchaeum symbiosum gen. nov., sp. nov.\_Proceedings of the N.pdf:pdf},
isbn = {0027-8424 (Print)$\backslash$n0027-8424 (Linking)},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
number = {June},
pages = {6241--6246},
pmid = {8692799},
title = {{A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov.}},
volume = {93},
year = {1996}
}
@article{Crusoe2015,
author = {Crusoe, Michael R. and Alameldin, Hussien F. and Awad, Sherine and Boucher, Elmar and Caldwell, Adam and Cartwright, Reed and Charbonneau, Amanda and Constantinides, Bede and Edvenson, Greg and Fay, Scott and Fenton, Jacob and Fenzl, Thomas and Fish, Jordan and Garcia-Gutierrez, Leonor and Garland, Phillip and Gluck, Jonathan and Gonz\'{a}lez, Iv\'{a}n and Guermond, Sarah and Guo, Jiarong and Gupta, Aditi and Herr, Joshua R. and Howe, Adina and Hyer, Alex and H\"{a}rpfer, Andreas and Irber, Luiz and Kidd, Rhys and Lin, David and Lippi, Justin and Mansour, Tamer and McA'Nulty, Pamela and McDonald, Eric and Mizzi, Jessica and Murray, Kevin D. and Nahum, Joshua R. and Nanlohy, Kaben and Nederbragt, Alexander Johan and Ortiz-Zuazaga, Humberto and Ory, Jeramia and Pell, Jason and Pepe-Ranney, Charles and Russ, Zachary N. and Schwarz, Erich and Scott, Camille and Seaman, Josiah and Sievert, Scott and Simpson, Jared and Skennerton, Connor T. and Spencer, James and Srinivasan, Ramakrishnan and Standage, Daniel and Stapleton, James a. and Steinman, Susan R. and Stein, Joe and Taylor, Benjamin and Trimble, Will and Wiencko, Heather L. and Wright, Michael and Wyss, Brian and Zhang, Qingpeng and Zyme, En and Brown, C. Titus},
doi = {10.12688/f1000research.6924.1},
file = {:home/fin/Documents/papers/mendeley/Crusoe et al.\_2015\_The khmer software package enabling efficient nucleotide sequence analysis\_F1000Research.pdf:pdf},
issn = {2046-1402},
journal = {F1000Research},
pages = {1--9},
title = {{The khmer software package: enabling efficient nucleotide sequence analysis}},
url = {http://f1000research.com/articles/4-900/v1},
year = {2015}
}
@article{Pedrioli2004,
author = {Pedrioli, Patrick G a and Eng, Jimmy K and Hubley, Robert and Vogelzang, Mathijs and Deutsch, Eric W and Raught, Brian and Pratt, Brian and Nilsson, Erik and Angeletti, Ruth H and Apweiler, Rolf and Cheung, Kei and Costello, Catherine E and Hermjakob, Henning and Huang, Sequin and Julian, Randall K and Kapp, Eugene and McComb, Mark E and Oliver, Stephen G and Omenn, Gilbert and Paton, Norman W and Simpson, Richard and Smith, Richard and Taylor, Chris F and Zhu, Weimin and Aebersold, Ruedi},
doi = {10.1038/nbt1031},
file = {:home/fin/Documents/papers/mendeley/Pedrioli et al.\_2004\_A common open representation of mass spectrometry data and its application to proteomics research\_Nature Biotechnol.pdf:pdf},
issn = {1087-0156},
journal = {Nat. Biotechnol.},
number = {11},
pages = {1459--1466},
title = {{A common open representation of mass spectrometry data and its application to proteomics research}},
url = {http://www.nature.com/doifinder/10.1038/nbt1031},
volume = {22},
year = {2004}
}
@article{Karkar2015a,
abstract = {The origin of oxygenic photosynthesis in the Archaeplastida common ancestor was foundational for the evolution of multicellular life. It is very likely that the primary endosymbiosis that explains plastid origin relied initially on the establishment of a metabolic connection between the host cell and captured cyanobacterium. We posit that these connections were derived primarily from existing host-derived components. To test this idea, we used phylogenomic and network analysis to infer the phylogenetic origin and evolutionary history of 37 validated plastid innermost membrane (permeome) metabolite transporters from the model plant Arabidopsis thaliana. Our results show that 57\% of these transporter genes are of eukaryotic origin and that the captured cyanobacterium made a relatively minor (albeit important) contribution to the process. We also tested the hypothesis that the bacterium-derived hexose-phosphate transporter UhpC might have been the primordial sugar transporter in the Archaeplastida ancestor. Bioinformatic and protein localization studies demonstrate that this protein in the extremophilic red algae Galdieria sulphuraria and Cyanidioschyzon merolae are plastid targeted. Given this protein is also localized in plastids in the glaucophyte alga Cyanophora paradoxa, we suggest it played a crucial role in early plastid endosymbiosis by connecting the endosymbiont and host carbon storage networks. In summary, our work significantly advances understanding of plastid integration and favors a host-centric view of endosymbiosis. Under this view, nuclear genes of either eukaryotic or bacterial (noncyanobacterial) origin provided key elements of the toolkit needed for establishing metabolic connections in the primordial Archaeplastida lineage.},
author = {Karkar, Slim and Facchinelli, Fabio and Price, Dana C. and Weber, Andreas P. M. and Bhattacharya, Debashish},
doi = {10.1073/pnas.1421375112},
file = {:home/fin/Documents/papers/mendeley/Karkar et al.\_2015\_Metabolic connectivity as a driver of host and endosymbiont integration.\_Proceedings of the National Academy of Scien.pdf:pdf},
issn = {1091-6490},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
pages = {201421375},
pmid = {25825767},
title = {{Metabolic connectivity as a driver of host and endosymbiont integration.}},
url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1421375112$\backslash$nhttp://www.ncbi.nlm.nih.gov/pubmed/25825767},
year = {2015}
}
@article{Ashburner2000,
abstract = {Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.},
archivePrefix = {arXiv},
arxivId = {10614036},
author = {Ashburner, M and Ball, C a and Blake, J a and Botstein, D and Butler, H and Cherry, J M and Davis, a P and Dolinski, K and Dwight, S S and Eppig, J T and Harris, M a and Hill, D P and Issel-Tarver, L and Kasarskis, a and Lewis, S and Matese, J C and Richardson, J E and Ringwald, M and Rubin, G M and Sherlock, G},
doi = {10.1038/75556},
eprint = {10614036},
file = {:home/fin/Documents/papers/mendeley/Ashburner et al.\_2000\_Gene ontology tool for the unification of biology.\_Nature genetics.pdf:pdf},
isbn = {1023909812},
issn = {1061-4036},
journal = {Nat. Genet.},
number = {may},
pages = {25--29},
pmid = {10802651},
title = {{Gene ontology: tool for the unification of biology.}},
volume = {25},
year = {2000}
}
@article{Fire1998,
abstract = {Experimental introduction of RNA into cells can be used in certain biological systems to interfere with the function of an endogenous gene. Such effects have been proposed to result from a simple antisense mechanism that depends on hybridization between the injected RNA and endogenous messenger RNA transcripts. RNA interference has been used in the nematode Caenorhabditis elegans to manipulate gene expression. Here we investigate the requirements for structure and delivery of the interfering RNA. To our surprise, we found that double-stranded RNA was substantially more effective at producing interference than was either strand individually. After injection into adult animals, purified single strands had at most a modest effect, whereas double-stranded mixtures caused potent and specific interference. The effects of this interference were evident in both the injected animals and their progeny. Only a few molecules of injected double-stranded RNA were required per affected cell, arguing against stochiometric interference with endogenous mRNA and suggesting that there could be a catalytic or amplification component in the interference process.},
archivePrefix = {arXiv},
arxivId = {physics/9810036},
author = {Fire, a and Xu, S and Montgomery, M K and Kostas, S a and Driver, S E and Mello, C C},
doi = {10.1038/35888 [doi]},
eprint = {9810036},
file = {:home/fin/Documents/papers/mendeley/Fire et al.\_1998\_Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans\_Nature.pdf:pdf},
isbn = {0028-0836 (Print)$\backslash$r0028-0836 (Linking)},
issn = {0028-0836},
journal = {Nature},
keywords = {Animals,Caenorhabditis elegans Proteins,Caenorhabditis elegans/drug effects/ genetics,Calmodulin-Binding Proteins/genetics,Gene Expression Regulation/ drug effects,Genes, Helminth,Helminth Proteins/genetics,Muscle Proteins/genetics,Phenotype,RNA, Antisense/pharmacology,RNA, Double-Stranded/ pharmacology},
number = {February},
pages = {806--811},
pmid = {9486653},
primaryClass = {physics},
title = {{Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans}},
url = {http://www.nature.com/nature/journal/v391/n6669/pdf/391806a0.pdf},
volume = {391},
year = {1998}
}
@article{Kies1979,
author = {Kies, L. and Kremer, B. P.},
doi = {10.1007/BF00368819},
file = {:home/fin/Documents/papers/mendeley/Kies, Kremer\_1979\_Function of cyanelles in the thecamoeba Paulinella chromatophora\_Naturwissenschaften.pdf:pdf},
issn = {00281042},
journal = {Naturwissenschaften},
pages = {578--579},
title = {{Function of cyanelles in the thecamoeba Paulinella chromatophora}},
volume = {66},
year = {1979}
}
@article{Nishihara1998,
annote = {Main paper for culturing paramecium without chlorella},
author = {Nishihara, N and Horiike, S and Takahashi, T and Kosaka, T and Shigenaka, Y and Hosoya, H},
file = {:home/fin/Documents/papers/mendeley/Nishihara et al.\_1998\_Cloning and characterization of endosymbiotic algae isolated from Paramecium bursaria\_Protoplasma.pdf:pdf},
journal = {Protoplasma},
keywords = {chlorella sp,endosymbiosis,infection,paramecium},
pages = {91--99},
title = {{Cloning and characterization of endosymbiotic algae isolated from Paramecium bursaria}},
volume = {203},
year = {1998}
}
@article{Xie2014,
abstract = {MOTIVATION: Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. Owing to the rapid increase in throughputs and decrease in costs of next- generation sequencing, RNA-Seq in particular has become the method of choice. However, the very short reads (e.g. 2 × 90 bp paired ends) from next generation sequencing makes de novo assembly to recover complete or full-length transcript sequences an algorithmic challenge. RESULTS: Here, we present SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse. Using as our benchmarks the known transcripts from these well-annotated genomes (sequenced a decade ago), we assessed how SOAPdenovo-Trans and two other popular transcriptome assemblers handled such practical issues as alternative splicing and variable expression levels. Our conclusion is that SOAPdenovo-Trans provides higher contiguity, lower redundancy and faster execution. Availability and implementation: Source code and user manual are available at http://sourceforge.net/projects/soapdenovotrans/. CONTACT: xieyl@genomics.cn or bgi-soap@googlegroups.com Supplementary information: Supplementary data are available at Bioinformatics online.},
archivePrefix = {arXiv},
arxivId = {1305.6760},
author = {Xie, Yinlong and Wu, Gengxiong and Tang, Jingbo and Luo, Ruibang and Patterson, Jordan and Liu, Shanlin and Huang, Weihua and He, Guangzhu and Gu, Shengchang and Li, Shengkang and Zhou, Xin and Lam, Tak Wah and Li, Yingrui and Xu, Xun and Wong, Gane Ka Shu and Wang, Jun},
doi = {10.1093/bioinformatics/btu077},
eprint = {1305.6760},
file = {:home/fin/Documents/papers/mendeley/Xie et al.\_2014\_SOAPdenovo-Trans De novo transcriptome assembly with short RNA-Seq reads\_Bioinformatics.pdf:pdf},
isbn = {1367-4811 (Electronic)
1367-4803 (Linking)},
issn = {14602059},
journal = {Bioinformatics},
number = {12},
pages = {1660--1666},
pmid = {24532719},
title = {{SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads}},
volume = {30},
year = {2014}
}
@article{Ender2010,
author = {Ender, C. and Meister, G.},
doi = {10.1242/jcs.055210},
file = {:home/fin/Documents/papers/mendeley/Ender, Meister\_2010\_Argonaute proteins at a glance\_Journal of Cell Science.pdf:pdf},
issn = {0021-9533},
journal = {J. Cell Sci.},
pages = {1819--1823},
title = {{Argonaute proteins at a glance}},
url = {http://jcs.biologists.org/cgi/doi/10.1242/jcs.055210},
volume = {123},
year = {2010}
}
@article{Stegle2015,
author = {Stegle, Oliver and Teichmann, S.A and Marionii, John C.},
doi = {10.1038/nrg3833},
file = {:home/fin/Documents/papers/mendeley/Stegle, Teichmann, Marionii\_2015\_Computational and analytical challenges in single-cell transcriptomics\_Nature Reviews Genetics.pdf:pdf},
issn = {1471-0056},
journal = {Nat. Rev. Genet.},
number = {March},
pages = {133--145},
publisher = {Nature Publishing Group},
title = {{Computational and analytical challenges in single-cell transcriptomics}},
url = {http://dx.doi.org/10.1038/nrg3833},
volume = {16},
year = {2015}
}
@article{Caspi2007,
author = {Caspi, R. and Foerster, H. and Fulcher, C. a. and Kaipa, P. and Krummenacker, M. and Latendresse, M. and Paley, S. and Rhee, S. Y. and Shearer, a. G. and Tissier, C. and Walk, T. C. and Zhang, P. and Karp, P. D.},
doi = {10.1093/nar/gkm900},
file = {:home/fin/Documents/papers/mendeley/Caspi et al.\_2007\_The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of PathwayGenome Databases\_Nucleic Ac.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {October 2007},
pages = {D623--D631},
title = {{The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkm900},
volume = {36},
year = {2007}
}
@article{Wolpert1997,
abstract = {A framework is developed to explore the connection between
effective optimization algorithms and the problems they are solving. A
number of \&ldquo;no free lunch\&rdquo; (NFL) theorems are presented which
establish that for any algorithm, any elevated performance over one
class of problems is offset by performance over another class. These
theorems result in a geometric interpretation of what it means for an
algorithm to be well suited to an optimization problem. Applications of
the NFL theorems to information-theoretic aspects of optimization and
benchmark measures of performance are also presented. Other issues
addressed include time-varying optimization problems and a priori
\&ldquo;head-to-head\&rdquo; minimax distinctions between optimization
algorithms, distinctions that result despite the NFL theorems' enforcing
of a type of uniformity over all algorithms},
author = {Wolpert, David H. and Macready, William G.},
doi = {10.1109/4235.585893},
file = {:home/fin/Documents/papers/mendeley/Wolpert, Macready\_1997\_No free lunch theorems for optimization\_IEEE Transactions on Evolutionary Computation.pdf:pdf},
isbn = {1089778X},
issn = {1089778X},
journal = {IEEE Trans. Evol. Comput.},
keywords = {Evolutionary algorithms,Information theory,Optimization},
number = {1},
pages = {67--82},
pmid = {97063701362},
title = {{No free lunch theorems for optimization}},
volume = {1},
year = {1997}
}
@article{Weiberg2015,
abstract = {Humans, animals, and plants are constantly under attack from pathogens and pests, resulting in severe consequences on global human health and crop production. Small RNA (sRNA)-mediated RNA interference (RNAi) is a conserved regulatory mechanism that is involved in almost all eukaryotic cellular processes, including host immunity and pathogen virulence. Recent evidence supports the significant contribution of sRNAs and RNAi to the communication between hosts and some eukaryotic pathogens, pests, parasites, or symbiotic microorganisms. Mobile silencing signals-most likely sRNAs-are capable of translocating from the host to its interacting organism, and vice versa. In this review, we will provide an overview of sRNA communications between different kingdoms, with a primary focus on the advances in plant-pathogen interaction systems.},
author = {Weiberg, Arne and Bellinger, Marschal and Jin, Hailing},
doi = {10.1016/j.copbio.2014.12.025},
file = {:home/fin/Documents/papers/mendeley/Weiberg, Bellinger, Jin\_2015\_Conversations between kingdoms small RNAs.\_Current opinion in biotechnology.pdf:pdf},
issn = {1879-0429},
journal = {Curr. Opin. Biotechnol.},
month = jan,
pages = {207--215},
pmid = {25622136},
publisher = {Elsevier Ltd},
title = {{Conversations between kingdoms: small RNAs.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25622136},
volume = {32C},
year = {2015}
}
@article{Chitsaz2011,
abstract = {Whole genome amplification by the multiple displacement amplification (MDA) method allows sequencing of DNA from single cells of bacteria that cannot be cultured. Assembling a genome is challenging, however, because MDA generates highly nonuniform coverage of the genome. Here we describe an algorithm tailored for short-read data from single cells that improves assembly through the use of a progressively increasing coverage cutoff. Assembly of reads from single Escherichia coli and Staphylococcus aureus cells captures >91\% of genes within contigs, approaching the 95\% captured from an assembly based on many E. coli cells. We apply this method to assemble a genome from a single cell of an uncultivated SAR324 clade of Deltaproteobacteria, a cosmopolitan bacterial lineage in the global ocean. Metabolic reconstruction suggests that SAR324 is aerobic, motile and chemotaxic. Our approach enables acquisition of genome assemblies for individual uncultivated bacteria using only short reads, providing cell-specific genetic information absent from metagenomic studies.},
author = {Chitsaz, Hamidreza and Yee-Greenbaum, Joyclyn L and Tesler, Glenn and Lombardo, Mary-Jane and Dupont, Christopher L and Badger, Jonathan H and Novotny, Mark and Rusch, Douglas B and Fraser, Louise J and Gormley, Niall a and Schulz-Trieglaff, Ole and Smith, Geoffrey P and Evers, Dirk J and Pevzner, Pavel a and Lasken, Roger S},
doi = {10.1038/nbt.1966},
file = {:home/fin/Documents/papers/mendeley/Chitsaz et al.\_2011\_Efficient de novo assembly of single-cell bacterial genomes from short-read data sets\_Nature Biotechnology.pdf:pdf},
isbn = {1546-1696 (Electronic)$\backslash$r1087-0156 (Linking)},
issn = {1087-0156},
journal = {Nat. Biotechnol.},
number = {10},
pages = {915--921},
pmid = {21926975},
publisher = {Nature Publishing Group},
title = {{Efficient de novo assembly of single-cell bacterial genomes from short-read data sets}},
url = {http://dx.doi.org/10.1038/nbt.1966},
volume = {29},
year = {2011}
}
@misc{Tavare1986,
abstract = {Several data banks around the world are accumulating DNA sequences at a feverish rate, with tremendous potential for furthering our knowledge of how biological systems code and pass on information. The sophisticated mathematical analysis of that data is just beginning. The Eighteenth Annual Symposium on Some Mathematical Questions in Biology was held in conjunction with the Annual Meeting of the AAAS and brought together speakers knowledgeable in both biology and mathematics to discuss these developments and to emphasize the need for rigorous, efficient computational tools.These computational tools include biologically relevant definitions of sequence similarity and string matching algorithms. The solutions for some of these problems have great generality; the string matching methods first developed for biological sequences have now been applied to areas such as geology,linguistics, and speech recognition. There is a great potential here for creating of new mathematics to handle this growing data base, with new applications for many areas of mathematics, computer science, and statistics.},
author = {Tavare, S},
booktitle = {Am. Math. Soc. Lect. Math. Life Sci.},
file = {:home/fin/Documents/papers/mendeley/Tavare\_1986\_Some probabilistic and statistical problems in the analysis of DNA sequences\_American Mathematical Society Lectures on Mathe.pdf:pdf},
isbn = {0821811673},
keywords = {gtr,methods,model,molecular\_evolution,phylogenetics},
pages = {57--86},
title = {{Some probabilistic and statistical problems in the analysis of DNA sequences}},
url = {citeulike-article-id:4801403$\backslash$nhttp://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&amp$\backslash$npath=ASIN/0821811673},
volume = {17},
year = {1986}
}
@misc{Buffalo,
author = {Buffalo, Vince},
booktitle = {GitHub},
title = {{Scythe - A Bayesian Adapter Trimmer (Version 0.994 Beta)}},
url = {https://github.com/vsbuffalo/scythe},
urldate = {2015-04-20},
year = {2015}
}
@article{Chen1940,
author = {Chen, Tze-Tuan},
file = {:home/fin/Documents/papers/mendeley/Chen\_1940\_Polyploidy in Paramecium bursaria\_Genentics.pdf:pdf},
journal = {Genentics},
pages = {239--240},
title = {{Polyploidy in Paramecium bursaria}},
volume = {26},
year = {1940}
}
@article{Cavalli-Sforza1967,
abstract = {Page 1. Phylogenetic Analysis Models and Estimation Procedures LL CAVALLI-SFORZA AND AWF EDWARDS International Laboratory of Genetics and Biophysics, Naples, and Pavia Section, Istituto di Genetica, Universita di Pavia, Italy.},
author = {Cavalli-Sforza, L L and Edwards, a W F},
file = {:home/fin/Documents/papers/mendeley/Cavalli-Sforza, Edwards\_1967\_Phylogenetic analysis. Models and estimation procedures\_The American Journal of Human Genetics.pdf:pdf},
isbn = {0002-9297},
issn = {0002-9297},
journal = {Am. J. Hum. Genet.},
keywords = {biological evolution,blood group antigens,genetics,humans,models,population,statistics topic,theoretical},
number = {012},
pages = {233--257},
pmid = {6026583},
title = {{Phylogenetic analysis. Models and estimation procedures}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1706274\&tool=pmcentrez\&rendertype=abstract},
volume = {19},
year = {1967}
}
@article{Kato2006,
author = {Kato, Yutaka and Ueno, Seiko and Imamura, Nobutaka},
doi = {10.1016/j.plantsci.2005.09.018},
file = {:home/fin/Documents/papers/mendeley/Kato, Ueno, Imamura\_2006\_Studies on the nitrogen utilization of endosymbiotic algae isolated from Japanese Paramecium bursaria\_Plant Sci.pdf:pdf},
issn = {01689452},
journal = {Plant Sci.},
keywords = {chlorella,endosymbiont,nitrogen utilization,paramecium bursaria},
month = mar,
number = {3},
pages = {481--486},
title = {{Studies on the nitrogen utilization of endosymbiotic algae isolated from Japanese Paramecium bursaria}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0168945205003857},
volume = {170},
year = {2006}
}
@incollection{AubussonFleury2015,
abstract = {Abstract Paramecium is a single cell able to divide in its morphologically differentiated stage that has many cilia anchored at its cell surface. Many thousands of cilia are thus assembled in a short period of time during division to duplicate the cell pattern while the cell continues swimming. Most, but not all, of these sensory cilia are motile and involved in two main functions: prey capture and cell locomotion. These cilia display heterogeneity, both in their length and their biochemical properties. Thanks to these properties, as well as to the availability of many postgenomic tools and the possibility to follow the regrowth of cilia after deciliation, Paramecium offers a nice opportunity to study the assembly of the cilia, as well as the genesis of their diversity within a single cell. In this paper, after a brief survey of Paramecium morphology and cilia properties, we describe the tools and the protocols currently used for immunofluorescence, transmission electron microscopy, and ultrastructural immunocytochemistry to analyze cilia, with special recommendations to overcome the problem raised by cilium diversity.},
author = {Aubusson-Fleury, Anne and Cohen, Jean and Lemullois, Michel},
booktitle = {Methods in Cilia \& Flagella},
doi = {http://dx.doi.org/10.1016/bs.mcb.2014.12.007},
editor = {Basto, Renata and Marshall, Wallace F},
issn = {0091-679X},
keywords = {Basal body,Ciliates,Ciliogenesis,Cilium,Deciliation,Transition zone,Tubulin posttranslational modification},
pages = {457--485},
publisher = {Academic Press},
series = {Methods in Cell Biology},
title = {{Chapter 22 - Ciliary heterogeneity within a single cell: The Paramecium model}},
url = {http://www.sciencedirect.com/science/article/pii/S0091679X14000521},
volume = {127},
year = {2015}
}
@article{Camin1965,
abstract = {A method is described for reconstructing presumed cladistic evolutionary$\backslash$nsequences of recent organisms and its implications are discussed.$\backslash$nCharacters of the organisms to be studied are presented in a data$\backslash$nmatrix of the type employed in numerical taxonomy with the character$\backslash$nstates arrayed according to a presumed evolutionary sequence. The$\backslash$nreconstruction proceeds on the hypothesis that the minimum number$\backslash$nof evolutionary steps yields the correct cladogram. The method has$\backslash$nbeen programmed for computer processing.},
author = {Camin, Joseph H and Sokal, Robert R},
doi = {10.2307/2406441},
file = {:home/fin/Documents/papers/mendeley/Camin, Sokal\_1965\_A Method for deducing branching sequences in phylogeny\_Evolution.pdf:pdf},
issn = {0014-3820},
journal = {Evolution (N. Y).},
number = {3},
pages = {311--326},
title = {{A Method for deducing branching sequences in phylogeny}},
volume = {19},
year = {1965}
}
@article{Haft2003,
author = {Haft, D. H.},
doi = {10.1093/nar/gkg128},
file = {:home/fin/Documents/papers/mendeley/Haft\_2003\_The TIGRFAMs database of protein families\_Nucleic Acids Research.pdf:pdf},
issn = {13624962},
journal = {Nucleic Acids Res.},
number = {1},
pages = {371--373},
title = {{The TIGRFAMs database of protein families}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkg128},
volume = {31},
year = {2003}
}
@article{Boenigk2012,
abstract = {This paper summarises the Symposium 'Concepts in Protistology', during the VI European Congress of Protistology, Berlin, 25-29 July 2011. There is an increasing focus on cataloguing the number of species on earth, species barcoding initiatives, and the increasing need to reconcile molecular with morphological data in protists within a taxonomic framework. We identify several obstructions to defining species in protists, including the high incidence of asexuality, high levels of both morphological conservation and evolutionary convergence, high levels of genetic diversity that cannot so far be correlated with phenotypic characters, conflicting signals between both genetic and phenotypic taxonomic markers, and different requirements and challenges of species definition in different protist groups. We assert that there is no species 'category' for protists, and recommend that a working definition of species is clarified on a case-by-case basis. Thus, a consensus approach may emerge within protist groups, but any one approach is unlikely to encompass a wide phylogenetic range. However, as long as clarity of intent and method is maintained, the utility of the term 'species' in protists will also be maintained as a reproducible and convenient (if artificial) way of referring to particular lineages within a tightly defined context. ?? 2011 Elsevier GmbH.},
author = {Boenigk, Jens and Ereshefsky, Marc and Hoef-Emden, Kerstin and Mallet, James and Bass, David},
doi = {10.1016/j.ejop.2011.11.004},
file = {:home/fin/Documents/papers/mendeley/Boenigk et al.\_2012\_Concepts in protistology Species definitions and boundaries\_European Journal of Protistology.pdf:pdf},
isbn = {0932-4739},
issn = {09324739},
journal = {Eur. J. Protistol.},
keywords = {COI,ITS rDNA,OTU,Protist,SSU rDNA,Species concept},
number = {2},
pages = {96--102},
pmid = {22209540},
publisher = {Elsevier GmbH},
title = {{Concepts in protistology: Species definitions and boundaries}},
url = {http://dx.doi.org/10.1016/j.ejop.2011.11.004},
volume = {48},
year = {2012}
}
@article{Loudon2012,
abstract = {A recent study suggests that circadian clocks may have evolved at the time of the Great Oxidation Event 2.5 billion years ago in order to drive detoxification of reactive oxygen species. © 2012 Elsevier Ltd.},
author = {Loudon, Andrew S I},
doi = {10.1016/j.cub.2012.06.023},
file = {:home/fin/Documents/papers/mendeley/Loudon\_2012\_Circadian biology A 2.5 billion year old clock\_Current Biology.pdf:pdf},
isbn = {1879-0445 (Electronic)$\backslash$r0960-9822 (Linking)},
issn = {09609822},
journal = {Curr. Biol.},
number = {14},
pages = {570--571},
pmid = {22835791},
title = {{Circadian biology: A 2.5 billion year old clock}},
volume = {22},
year = {2012}
}
@article{Sullivan2005,
abstract = {Investigation into model selection has a long history in the statistical literature. As model-based approaches begin dominating systematic biology, increased attention has focused on how models should be selected for distance-based, likelihood, and Bayesian phylogenetics. Here, we review issues that render model-based approaches necessary, briefly review nucleotide-based models that attempt to capture relevant features of evolutionary processes, and review methods that have been applied to model selection in phylogenetics: likelihood-ratio tests, AIC, BIC, and performance-based approaches. CR - Copyright \&\#169; 2005 Annual Reviews},
author = {Sullivan, Jack and Joyce, Paul},
doi = {10.1146/annurev.ecolsys.36.102003.152633},
file = {:home/fin/Documents/papers/mendeley/Sullivan, Joyce\_2005\_Model Selection in Phylogenetics\_Annual Review of Ecology, Evolution, and Systematics.pdf:pdf},
isbn = {1543-592X},
issn = {1543-592X},
journal = {Annu. Rev. Ecol. Evol. Syst.},
keywords = {aic,bic,decision},
number = {May},
pages = {445--466},
title = {{Model Selection in Phylogenetics}},
volume = {36},
year = {2005}
}
@article{Summerer2008,
author = {Summerer, Monika and Sonntag, Bettina and Sommaruga, Ruben},
doi = {10.1111/j.1529-8817.2007.00455.x},
file = {:home/fin/Documents/papers/mendeley/Summerer, Sonntag, Sommaruga\_2008\_CILIATE-SYMBIONT SPECIFICITY OF FRESHWATER ENDOSYMBIOTIC iCHLORELLAi (TREBOUXIOPHYCEAE, CHLOROPHYTA)\_J.pdf:pdf},
issn = {00223646},
journal = {J. Phycol.},
pages = {77--84},
title = {{CILIATE-SYMBIONT SPECIFICITY OF FRESHWATER ENDOSYMBIOTIC <i>CHLORELLA</i> (TREBOUXIOPHYCEAE, CHLOROPHYTA)}},
url = {http://doi.wiley.com/10.1111/j.1529-8817.2007.00455.x},
volume = {44},
year = {2008}
}
@article{McAuley1986,
author = {McAuley, P.J.},
file = {:home/fin/Documents/papers/mendeley/McAuley\_1986\_Uptake of Amino Acids by Cultured and Freshly Isolated Symbiotic Chlorella\_New Phytologist.pdf:pdf},
journal = {New Phytol.},
keywords = {amino acid uptake,chlorella,green hydra,symbiosis},
pages = {415--427},
title = {{Uptake of Amino Acids by Cultured and Freshly Isolated Symbiotic Chlorella}},
volume = {104},
year = {1986}
}
@article{Goetz2012,
abstract = {A method for performing \{RNA-Seq\} on picograms of \{mRNA\} facilitates gene expression profiling of rare cells.},
author = {Goetz, Jillian J and Trimarchi, Jeffrey M},
doi = {10.1038/nbt.2325},
file = {:home/fin/Documents/papers/mendeley/Goetz, Trimarchi\_2012\_Transcriptome sequencing of single cells with Smart-Seq\_Nature Biotechnology.pdf:pdf},
isbn = {1087-0156},
issn = {1087-0156},
journal = {Nat. Biotechnol.},
number = {8},
pages = {763--765},
pmid = {22871714},
publisher = {Nature Publishing Group},
title = {{Transcriptome sequencing of single cells with Smart-Seq}},
url = {http://dx.doi.org/10.1038/nbt.2325},
volume = {30},
year = {2012}
}
@article{Johnson2011a,
abstract = {Many non-photosynthetic species of protists and metazoans are capable of hosting viable algal endosymbionts or their organelles through adaptations of phagocytic pathways. A form of mixotrophy combining phototrophy and heterotrophy, acquired phototrophy (AcPh) encompasses a suite of endosymbiotic and organelle retention interactions, that range from facultative to obligate. AcPh is a common phenomenon in aquatic ecosystems, with endosymbiotic associations generally more prevalent in nutrient poor environments, and organelle retention typically associated with more productive ones. All AcPhs benefit from enhanced growth due to access to photosynthetic products; however, the degree of metabolic integration and dependency in the host varies widely. AcPh is found in at least four of the major eukaryotic supergroups, and is the driving force in the evolution of secondary and tertiary plastid acquisitions. Mutualistic resource partitioning characterizes most algal endosymbiotic interactions, while organelle retention is a form of predation, characterized by nutrient flow (i.e., growth) in one direction. AcPh involves adaptations to recognize specific prey or endosymbionts and to house organelles or endosymbionts within the endomembrane system but free from digestion. In many cases, hosts depend upon AcPh for the production of essential nutrients, many of which remain obscure. The practice of AcPh has led to multiple independent secondary and tertiary plastid acquisition events among several eukaryote lineages, giving rise to the diverse array of algae found in modern aquatic ecosystems. This article highlights those AcPhs that are model research organisms for both metazoans and protists. Much of the basic biology of AcPhs remains enigmatic, particularly (1) which essential nutrients or factors make certain forms of AcPh obligatory, (2) how hosts regulate and manipulate endosymbionts or sequestered organelles, and (3) what genomic imprint, if any, AcPh leaves on non-photosynthetic host species.},
author = {Johnson, Matthew D.},
doi = {10.1007/s11120-010-9546-8},
file = {:home/fin/Documents/papers/mendeley/Johnson\_2011\_The acquisition of phototrophy Adaptive strategies of hosting endosymbionts and organelles\_Photosynthesis Research.pdf:pdf},
isbn = {0166-8595},
issn = {01668595},
journal = {Photosynth. Res.},
keywords = {Acquired phototrophy,Endosymbiosis,Karyoklepty,Kleptoplastidy,Mixotrophy},
number = {1},
pages = {117--132},
pmid = {20405214},
title = {{The acquisition of phototrophy: Adaptive strategies of hosting endosymbionts and organelles}},
volume = {107},
year = {2011}
}
@article{Smith-unna2015,
author = {Smith-unna, Richard and Boursnell, Chris and Patro, Rob and Hibberd, Julian M and Kelly, Steven},
file = {:home/fin/Documents/papers/mendeley/Smith-unna et al.\_2015\_TransRate reference free quality assessment of de-novo transcriptome assemblies\_bioRxiv preprintbioR.pdf:pdf},
journal = {bioRxiv Prepr.},
pages = {1--25},
title = {{TransRate: reference free quality assessment of de-novo transcriptome assemblies}},
volume = {June},
year = {2015}
}
@article{Wilcox1986,
author = {Wilcox, L. W.},
doi = {10.1007/BF01277000},
file = {:home/fin/Documents/papers/mendeley/Wilcox\_1986\_Prokaryotic endosymbionts in the chloroplast stroma of the dinoflagellate Woloszynskia pascheri\_Protoplasma.pdf:pdf},
issn = {0033183X},
journal = {Protoplasma},
keywords = {Dinoflagellate,Dinophyceae,Endosymbiosis,Pyrrophyta,Woloszynskia},
pages = {71--79},
title = {{Prokaryotic endosymbionts in the chloroplast stroma of the dinoflagellate Woloszynskia pascheri}},
volume = {135},
year = {1986}
}
@article{Schatz2012,
author = {Schatz, M C and Delcher, a L and Roberts, M and Marc\c{c}ais, G and Pop, M and Yorke, J a},
doi = {10.1101/gr.131383.111},
file = {:home/fin/Documents/papers/mendeley/Schatz et al.\_2012\_GAGE A critical evaluation of genome assemblies and assembly algorithms Steven L. Salzberg, Adam M. Phillippy, Alekse.pdf:pdf},
isbn = {1549-5469 (Electronic) 1088-9051 (Linking)},
issn = {1549-5469},
journal = {Genome Res.},
pages = {557--567},
pmid = {22147368},
title = {{GAGE: A critical evaluation of genome assemblies and assembly algorithms Steven L. Salzberg, Adam M. Phillippy, Aleksey Zimin, Daniela Puiu, Tanja Magoc, Sergey Koren, Todd J. Treangen}},
volume = {22},
year = {2012}
}
@article{Krienitz2004,
author = {Krienitz, L and Hegewald, H E and Hepperle, D and Huss, Volker a R and Rohr, T and Wolf, M},
file = {:home/fin/Documents/papers/mendeley/Krienitz et al.\_2004\_Phylogenetic Relationship of Chlorella and Parachlorella\_Phycologia.pdf:pdf},
journal = {Phycologia},
pages = {529--542},
title = {{Phylogenetic Relationship of Chlorella and Parachlorella}},
volume = {43},
year = {2004}
}
@article{Munoz-Merida2013,
abstract = {Olive breeding programmes are focused on selecting for traits as short juvenile period, plant architecture suited for mechanical harvest, or oil characteristics, including fatty acid composition, phenolic, and volatile compounds to suit new markets. Understanding the molecular basis of these characteristics and improving the efficiency of such breeding programmes require the development of genomic information and tools. However, despite its economic relevance, genomic information on olive or closely related species is still scarce. We have applied Sanger and 454 pyrosequencing technologies to generate close to 2 million reads from 12 cDNA libraries obtained from the Picual, Arbequina, and Lechin de Sevilla cultivars and seedlings from a segregating progeny of a Picual × Arbequina cross. The libraries include fruit mesocarp and seeds at three relevant developmental stages, young stems and leaves, active juvenile and adult buds as well as dormant buds, and juvenile and adult roots. The reads were assembled by library or tissue and then assembled together into 81 020 unigenes with an average size of 496 bases. Here, we report their assembly and their functional annotation.},
author = {Mu\~{n}oz-M\'{e}rida, Antonio and Gonz\'{a}lez-Plaza, Juan Jos\'{e} and Ca\~{n}ada, Andr\'{e}s and Blanco, Ana Mar\'{\i}a and Garc\'{\i}a-L\'{o}pez, Maria Del Carmen and Rodr\'{\i}guez, Jos\'{e} Manuel and Pedrola, Laia and Sicardo, M Dolores and Hern\'{a}ndez, M Luisa and {De la Rosa}, Ra\'{u}l and Belaj, Angjelina and Gil-Borja, Mayte and Luque, Francisco and Mart\'{\i}nez-Rivas, Jos\'{e} Manuel and Pisano, David G and Trelles, Oswaldo and Valpuesta, Victoriano and Beuz\'{o}n, Carmen R},
doi = {10.1093/dnares/dss036},
file = {:home/fin/Documents/papers/mendeley/Mu\~{n}oz-M\'{e}rida et al.\_2013\_De novo assembly and functional annotation of the olive (Olea europaea) transcriptome.\_DNA research.pdf:pdf},
issn = {1756-1663},
journal = {DNA Res.},
keywords = {Breeding,DNA,Databases,Expressed Sequence Tags,Fruit,Fruit: chemistry,Gene Library,Genetic,Genome,Molecular Sequence Annotation,Olea,Olea: genetics,Plant,Plant Oils,Plant Oils: chemistry,Seeds,Seeds: genetics,Sequence Analysis,Transcriptome},
number = {January},
pages = {93--108},
pmid = {23297299},
title = {{De novo assembly and functional annotation of the olive (Olea europaea) transcriptome.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3576661\&tool=pmcentrez\&rendertype=abstract},
volume = {20},
year = {2013}
}
@article{Richards2011c,
abstract = {Recently, $\alpha$-proteobacteria have been shown to possess virus-like gene transfer agents that facilitate high frequency gene transfer in natural environments between distantly related lineages. This system could have driven the genomic integration of the mitochondrial progenitor and its proto-eukaryote host and contributed to the evolutionary mosaic of genes seen in modern-day prokaryotic and eukaryotic genomes.},
author = {Richards, Thomas A and Archibald, John M},
doi = {10.1016/j.cub.2010.12.036},
file = {:home/fin/Documents/papers/mendeley/Richards, Archibald\_2011\_Cell evolution gene transfer agents and the origin of mitochondria.\_Current biology.pdf:pdf},
issn = {1879-0445},
journal = {Curr. Biol.},
keywords = {Alphaproteobacteria,Alphaproteobacteria: genetics,Biological Evolution,DNA Transposable Elements,Gene Transfer,Genetic,Horizontal,Mitochondria,Mitochondria: genetics,Models,Oceans and Seas,Phylogeny,Seawater,Seawater: microbiology},
month = feb,
number = {3},
pages = {R112--4},
pmid = {21300273},
publisher = {Elsevier Ltd},
title = {{Cell evolution: gene transfer agents and the origin of mitochondria.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21300273},
volume = {21},
year = {2011}
}
@article{Bosch2012,
abstract = {The Hydra holobiont involves at least three types of organisms that all share a long coevolutionary history and appear to depend on each other. Here I review how symbiotic algae and stably associated bacteria interact with the Hydra host and where in the tissue they are located. In particular I discuss the role of Toll-like receptor (TLR) signaling in maintaining Hydra's species-specific microbiota. I also discuss studies in Hydra viridis and its symbiotic Chlorella algae which indicate that the symbiotic algae are critically involved in the control of sexual differentiation in green Hydra. Finally, I review the state of "omics" in this tripartite association and the fact that the functioning of this holobiont is also a tale of several genomes.},
author = {Bosch, Thomas C G},
doi = {223/1/78 [pii]},
file = {:home/fin/Documents/papers/mendeley/Bosch\_2012\_What Hydra has to say about the role and origin of symbiotic interactions\_Biological Bulletin.pdf:pdf},
isbn = {1939-8697 (Electronic)$\backslash$r0006-3185 (Linking)},
issn = {00063185},
journal = {Biol. Bull.},
number = {August},
pages = {78--84},
pmid = {22983034},
title = {{What Hydra has to say about the role and origin of symbiotic interactions}},
volume = {223},
year = {2012}
}
@article{Zerbino2008,
abstract = {We have developed a new set of algorithms, collectively called "Velvet," to manipulate de Bruijn graphs for genomic sequence assembly. A de Bruijn graph is a compact representation based on short words (k-mers) that is ideal for high coverage, very short read (25-50 bp) data sets. Applying Velvet to very short reads and paired-ends information only, one can produce contigs of significant length, up to 50-kb N50 length in simulations of prokaryotic data and 3-kb N50 on simulated mammalian BACs. When applied to real Solexa data sets without read pairs, Velvet generated contigs of approximately 8 kb in a prokaryote and 2 kb in a mammalian BAC, in close agreement with our simulated results without read-pair information. Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies.},
archivePrefix = {arXiv},
arxivId = {arXiv:quant-ph/0209100},
author = {Zerbino, Daniel R and Birney, Ewan},
doi = {10.1101/gr.074492.107},
eprint = {0209100},
file = {:home/fin/Documents/papers/mendeley/Zerbino, Birney\_2008\_Velvet algorithms for de novo short read assembly using de Bruijn graphs.\_Genome research.pdf:pdf},
isbn = {1088-9051 (Print)$\backslash$r1088-9051 (Linking)},
issn = {1088-9051},
journal = {Genome Res.},
keywords = {Algorithms,Animals,Chromosomes, Artificial, Bacterial,Computational Biology,Computational Biology: methods,Computer Simulation,Genome, Bacterial,Genome, Human,Genomics,Humans,Mammals,Mammals: genetics,Sequence Analysis, DNA,Sequence Analysis, DNA: methods,Sequence Analysis, DNA: standards,Streptococcus,Streptococcus: genetics},
pages = {821--9},
pmid = {18349386},
primaryClass = {arXiv:quant-ph},
title = {{Velvet: algorithms for de novo short read assembly using de Bruijn graphs.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18349386},
volume = {18},
year = {2008}
}
@article{Tyra2007,
abstract = {BACKGROUND: It is generally accepted that a single primary endosymbiosis in the Plantae (red, green (including land plants), and glaucophyte algae) common ancestor gave rise to the ancestral photosynthetic organelle (plastid). Plastid establishment necessitated many steps, including the transfer and activation of endosymbiont genes that were relocated to the nuclear genome of the 'host' followed by import of the encoded proteins into the organelle. These innovations are, however, highly complex and could not have driven the initial formation of the endosymbiosis. We postulate that the re-targeting of existing host solute transporters to the plastid fore-runner was critical for the early success of the primary endosymbiosis, allowing the host to harvest endosymbiont primary production. RESULTS: We tested this model of transporter evolution by conducting a comprehensive analysis of the plastid permeome in Arabidopsis thaliana. Of 137 well-annotated transporter proteins that were initially considered, 83 that are broadly distributed in Plantae were submitted to phylogenetic analysis. Consistent with our hypothesis, we find that 58\% of Arabidopsis transporters, including all carbohydrate transporters, are of host origin, whereas only 12\% arose from the cyanobacterial endosymbiont. Four transporter genes are derived from a Chlamydia-like source, suggesting that establishment of the primary plastid likely involved contributions from at least two prokaryotic sources. CONCLUSION: Our results indicate that the existing plastid solute transport system shared by Plantae is derived primarily from host genes. Important contributions also came from the cyanobacterial endosymbiont and Chlamydia-like bacteria likely co-resident in the first algae.},
author = {Tyra, Heather M and Linka, Marc and Weber, Andreas P M and Bhattacharya, Debashish},
doi = {10.1186/gb-2007-8-10-r212},
file = {:home/fin/Documents/papers/mendeley/Tyra et al.\_2007\_Host origin of plastid solute transporters in the first photosynthetic eukaryotes.\_Genome biology.pdf:pdf},
isbn = {1465-6914 (Electronic)},
issn = {14656906},
journal = {Genome Biol.},
number = {10},
pages = {R212},
pmid = {17919328},
title = {{Host origin of plastid solute transporters in the first photosynthetic eukaryotes.}},
volume = {8},
year = {2007}
}
@article{Kanehisa2014,
author = {Kanehisa, M. and Goto, S. and Sato, Y. and Kawashima, M. and Furumichi, M. and Tanabe, M.},
doi = {10.1093/nar/gkt1076},
file = {:home/fin/Documents/papers/mendeley/Kanehisa et al.\_2014\_Data, information, knowledge and principle back to metabolism in KEGG\_Nucleic Acids Research.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {November 2013},
pages = {D199--D205},
title = {{Data, information, knowledge and principle: back to metabolism in KEGG}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkt1076},
volume = {42},
year = {2014}
}
@article{Nakasugi2014,
author = {Nakasugi, Kenlee and Crowhurst, Ross and Bally, Julia and Waterhouse, Peter},
doi = {10.1371/journal.pone.0091776},
file = {:home/fin/Documents/papers/mendeley/Nakasugi et al.\_2014\_Combining Transcriptome Assemblies from Multiple De Novo Assemblers in the Allo-Tetraploid Plant Nicotiana benthami.pdf:pdf},
issn = {1932-6203},
journal = {PLoS One},
number = {3},
pages = {e91776},
title = {{Combining Transcriptome Assemblies from Multiple De Novo Assemblers in the Allo-Tetraploid Plant Nicotiana benthamiana}},
url = {http://dx.plos.org/10.1371/journal.pone.0091776},
volume = {9},
year = {2014}
}
@inproceedings{Ng2002,
abstract = {Comparison of generative and discriminative classifiers is an ever-lasting topic. As an important contribution to this topic, based on their theoretical and empirical comparisons between the naive Bayes classifier and linear logistic regression, Ng and Jordan (NIPS 841-848, 2001) claimed that there exist two distinct regimes of performance between the generative and discriminative classifiers with regard to the training-set size. In this paper, our empirical and simulation studies, as a complement of their work, however, suggest that the existence of the two distinct regimes may not be so reliable. In addition, for real world datasets, so far there is no theoretically correct, general criterion for choosing between the discriminative and the generative approaches to classification of an observation x into a class y; the choice depends on the relative confidence we have in the correctness of the specification of either p(y vertical bar x) or p(x, y) for the data. This can be to some extent a demonstration of why Efron (J Am Stat Assoc 70(352):892-898, 1975) and O'Neill (J Am Stat Assoc 75(369):154-160, 1980) prefer normal-based linear discriminant analysis (LDA) when no model mis-specification occurs but other empirical studies may prefer linear logistic regression instead. Furthermore, we suggest that pairing of either LDA assuming a common diagonal covariance matrix (LDA-A) or the naive Bayes classifier and linear logistic regression may not be perfect, and hence it may not be reliable for any claim that was derived from the comparison between LDA-A or the naive Bayes classifier and linear logistic regression to be generalised to all generative and discriminative classifiers.},
archivePrefix = {arXiv},
arxivId = {http://dx.doi.org/10.1007/s11063-008-9088-7},
author = {Ng, Andrew Y. and Jordan, Michael I},
booktitle = {Adv. Neural Inf. Process. Syst. 14 (NIPS 2001)},
doi = {10.1007/s11063-008-9088-7},
editor = {Dietterich, T.G. and Becker, S. and Ghahramani, Z.},
eprint = {/dx.doi.org/10.1007/s11063-008-9088-7},
file = {:home/fin/Documents/papers/mendeley/Ng, Jordan\_2002\_On discriminative vs. generative classifiers A comparison of logistic regression and naive bayes\_Advances in Neural Info.pdf:pdf},
isbn = {1106300890},
issn = {13704621},
keywords = {Asymptotic relative efficiency,Discriminative classifiers,Generative classifiers,Logistic regression,Na??ve Bayes classifier,Normal-based discriminant analysis},
pages = {841--848},
primaryClass = {http:},
publisher = {MIT Press},
title = {{On discriminative vs. generative classifiers: A comparison of logistic regression and naive bayes}},
year = {2002}
}
@article{Marcais2011,
abstract = {Counting the number of occurrences of every k-mer (substring of length k) in a long string is a central subproblem in many applications, including genome assembly, error correction of sequencing reads, fast multiple sequence alignment and repeat detection. Recently, the deep sequence coverage generated by next-generation sequencing technologies has caused the amount of sequence to be processed during a genome project to grow rapidly, and has rendered current k-mer counting tools too slow and memory intensive. At the same time, large multicore computers have become commonplace in research facilities allowing for a new parallel computational paradigm.},
author = {Mar\c{c}ais, Guillaume and Kingsford, Carl},
doi = {10.1093/bioinformatics/btr011},
file = {:home/fin/Documents/papers/mendeley/Mar\c{c}ais, Kingsford\_2011\_A fast, lock-free approach for efficient parallel counting of occurrences of k-mers\_Bioinformatics.pdf:pdf},
isbn = {1367-4811 (Electronic)$\backslash$n1367-4803 (Linking)},
issn = {13674803},
journal = {Bioinformatics},
number = {6},
pages = {764--770},
pmid = {21217122},
title = {{A fast, lock-free approach for efficient parallel counting of occurrences of k-mers}},
volume = {27},
year = {2011}
}
@article{martin2011cutadapt,
author = {Martin, Marcel},
journal = {EMBnet. J.},
number = {1},
pages = {pp----10},
title = {{Cutadapt Removes Adapter Sequences from High-throughput Sequencing Reads}},
volume = {17},
year = {2011}
}
@article{Meister2004,
abstract = {Double-stranded RNA (dsRNA) is an important regulator of gene expression in many eukaryotes. It triggers different types of gene silencing that are collectively referred to as RNA silencing or RNA interference. A key step in known silencing pathways is the processing of dsRNAs into short RNA duplexes of characteristic size and structure. These short dsRNAs guide RNA silencing by specific and distinct mechanisms. Many components of the RNA silencing machinery still need to be identified and characterized, but a more complete understanding of the process is imminent.},
author = {Meister, Gunter and Tuschl, Thomas},
doi = {10.1038/nature02873},
file = {:home/fin/Documents/papers/mendeley/Meister, Tuschl\_2004\_Mechanisms of gene silencing by double-stranded RNA.\_Nature.pdf:pdf},
isbn = {1476-4687 (Electronic) 0028-0836 (Linking)},
issn = {0028-0836},
journal = {Nature},
number = {September},
pages = {343--349},
pmid = {15372041},
title = {{Mechanisms of gene silencing by double-stranded RNA.}},
volume = {431},
year = {2004}
}
@article{Jones2014,
abstract = {Varicella zoster virus (VZV) is the etiological agent of chickenpox and shingles, diseases characterized by epidermal skin blistering. Using a calcium-induced keratinocyte differentiation model we investigated the interaction between epidermal differentiation and VZV infection. RNA-seq analysis showed that VZV infection has a profound effect on differentiating keratinocytes, altering the normal process of epidermal gene expression to generate a signature that resembles patterns of gene expression seen in both heritable and acquired skin-blistering disorders. Further investigation by real-time PCR, protein analysis and electron microscopy revealed that VZV specifically reduced expression of specific suprabasal cytokeratins and desmosomal proteins, leading to disruption of epidermal structure and function. These changes were accompanied by an upregulation of kallikreins and serine proteases. Taken together VZV infection promotes blistering and desquamation of the epidermis, both of which are necessary to the viral spread and pathogenesis. At the same time, analysis of the viral transcriptome provided evidence that VZV gene expression was significantly increased following calcium treatment of keratinocytes. Using reporter viruses and immunohistochemistry we confirmed that VZV gene and protein expression in skin is linked with cellular differentiation. These studies highlight the intimate host-pathogen interaction following VZV infection of skin and provide insight into the mechanisms by which VZV remodels the epidermal environment to promote its own replication and spread.},
author = {Jones, Meleri and Dry, Inga R. and Frampton, Dan and Singh, Manuraj and Kanda, Ravinder K. and Yee, Michael B. and Kellam, Paul and Hollinshead, Michael and Kinchington, Paul R. and O'Toole, Edel a. and Breuer, Judith},
doi = {10.1371/journal.ppat.1003896},
file = {:home/fin/Documents/papers/mendeley/Jones et al.\_2014\_RNA-seq Analysis of Host and Viral Gene Expression Highlights Interaction between Varicella Zoster Virus and Keratinoc.pdf:pdf},
issn = {15537366},
journal = {PLoS Pathog.},
number = {1},
pmid = {24497829},
title = {{RNA-seq Analysis of Host and Viral Gene Expression Highlights Interaction between Varicella Zoster Virus and Keratinocyte Differentiation}},
volume = {10},
year = {2014}
}
@article{Arnaiz2010,
abstract = {The genome of Paramecium tetraurelia, a unicellular model that belongs to the ciliate phylum, has been shaped by at least 3 successive whole genome duplications (WGD). These dramatic events, which have also been documented in plants, animals and fungi, are resolved over evolutionary time by the loss of one duplicate for the majority of genes. Thanks to a low rate of large scale genome rearrangement in Paramecium, an unprecedented large number of gene duplicates of different ages have been identified, making this organism an outstanding model to investigate the evolutionary consequences of polyploidization. The most recent WGD, with 51\% of pre-duplication genes still in 2 copies, provides a snapshot of a phase of rapid gene loss that is not accessible in more ancient polyploids such as yeast.},
author = {Arnaiz, Olivier and Go\^{u}t, Jean-Fran\c{c}ois and B\'{e}termier, Mireille and Bouhouche, Khaled and Cohen, Jean and Duret, Laurent and Kapusta, Aur\'{e}lie and Meyer, Eric and Sperling, Linda},
doi = {10.1186/1471-2164-11-547},
file = {:home/fin/Documents/papers/mendeley/Arnaiz et al.\_2010\_Gene expression in a paleopolyploid a transcriptome resource for the ciliate Paramecium tetraurelia.\_BMC genomics.pdf:pdf},
isbn = {1471216411},
issn = {1471-2164},
journal = {BMC Genomics},
pages = {547},
pmid = {20932287},
title = {{Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia.}},
volume = {11},
year = {2010}
}
@article{Donaher2009,
abstract = {The cryptomonads are a group of unicellular algae that acquired photosynthesis through the engulfment of a red algal cell, a process called secondary endosymbiosis. Here, we present the complete plastid genome sequence of the secondarily nonphotosynthetic species Cryptomonas paramecium CCAP977/2a. The approximately 78 kilobase pair (Kbp) C. paramecium genome contains 82 predicted protein genes, 29 transfer RNA genes, and a single pseudogene (atpF). The C. paramecium plastid genome is approximately 50 Kbp smaller than those of the photosynthetic cryptomonads Guillardia theta and Rhodomonas salina; 71 genes present in the G. theta and/or R. salina plastid genomes are missing in C. paramecium. The pet, psa, and psb photosynthetic gene families are almost entirely absent. Interestingly, the ribosomal RNA operon, present as inverted repeats in most plastid genomes (including G. theta and R. salina), exists as a single copy in C. paramecium. The G + C content (38\%) is higher in C. paramecium than in other cryptomonad plastid genomes, and C. paramecium plastid genes are characterized by significantly different codon usage patterns and increased evolutionary rates. The content and structure of the C. paramecium plastid genome provides insight into the changes associated with recent loss of photosynthesis in a predominantly photosynthetic group of algae and reveals features shared with the plastid genomes of other secondarily nonphotosynthetic eukaryotes.},
author = {Donaher, Natalie and Tanifuji, Goro and Onodera, Naoko T and Malfatti, Stephanie a and Chain, Patrick S G and Hara, Yoshiaki and Archibald, John M},
doi = {10.1093/gbe/evp047},
file = {:home/fin/Documents/papers/mendeley/Donaher et al.\_2009\_The complete plastid genome sequence of the secondarily nonphotosynthetic alga Cryptomonas paramecium reduction, com.pdf:pdf},
issn = {1759-6653},
journal = {Genome Biol. Evol.},
keywords = {1,439,448,archibald,biol,ca,cryptomonads,dal,e-mail,evol,genome,genome reduction,john,photosyn-,plastids,secondary endosymbiosis,thesis},
pages = {439--448},
pmid = {20333213},
title = {{The complete plastid genome sequence of the secondarily nonphotosynthetic alga Cryptomonas paramecium: reduction, compaction, and accelerated

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib