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@article{Galvani2002,
abstract = {RNA interference can be induced very efficiently by feeding the ciliate Paramecium with bacteria engineered to express double-stranded RNA, opening the possibility of large-scale functional screening in this unicell.},
author = {Galvani, Ang\'{e}lique and Sperling, Linda},
file = {:home/fin/Documents/papers/mendeley/Galvani, Sperling\_2002\_RNA interference by feeding in Paramecium.\_Trends in Genetics.pdf:pdf},
issn = {0168-9525},
journal = {Trends Genet.},
keywords = {Animals,Double-Stranded,Double-Stranded: administration \& dosage,Double-Stranded: genetics,Gene Silencing,Paramecium,Paramecium: genetics,Phenotype,Protozoan,Protozoan: administration \& dosage,Protozoan: genetics,RNA, Double-Stranded,RNA, Double-Stranded: administration \& dosage,RNA, Double-Stranded: genetics,RNA, Protozoan,RNA, Protozoan: administration \& dosage,RNA, Protozoan: genetics},
month = jan,
number = {1},
pages = {11--2},
pmid = {11750689},
title = {{RNA interference by feeding in Paramecium.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11750689},
volume = {18},
year = {2002}
}
@article{Damaj2009,
abstract = {BACKGROUND: The sub-membranous skeleton of the ciliate Paramecium, the epiplasm, is composed of hundreds of epiplasmic scales centered on basal bodies, and presents a complex set of proteins, epiplasmins, which belong to a multigenic family. The repeated duplications observed in the P. tetraurelia genome present an interesting model of the organization and evolution of a multigenic family within a single cell.$\backslash$n$\backslash$nRESULTS: To study this multigenic family, we used phylogenetic, structural, and analytical transcriptional approaches. The phylogenetic method defines 5 groups of epiplasmins in the multigenic family. A refined analysis by Hydrophobic Cluster Analysis (HCA) identifies structural characteristics of 51 epiplasmins, defining five separate groups, and three classes. Depending on the sequential arrangement of their structural domains, the epiplasmins are defined as symmetric, asymmetric or atypical. The EST data aid in this classification, in the identification of putative regulating sequences such as TATA or CAAT boxes. When specific RNAi experiments were conducted using sequences from either symmetric or asymmetric classes, phenotypes were drastic. Local effects show either disrupted or ill-shaped epiplasmic scales. In either case, this results in aborted cell division. Using structural features, we show that 4 epiplasmins are also present in another ciliate, Tetrahymena thermophila. Their affiliation with the distinctive structural groups of Paramecium epiplasmins demonstrates an interspecific multigenic family.$\backslash$n$\backslash$nCONCLUSION: The epiplasmin multigenic family illustrates the history of genomic duplication in Paramecium. This study provides a framework which can guide functional analysis of epiplasmins, the major components of the membrane skeleton in ciliates. We show that this set of proteins handles an important developmental information in Paramecium since maintenance of epiplasm organization is crucial for cell morphogenesis.},
author = {Damaj, Raghida and Pomel, S\'{e}bastien and Bricheux, Genevi\`{e}ve and Coffe, G\'{e}rard and Vigu\`{e}s, Bernard and Ravet, Viviane and Bouchard, Philippe},
doi = {10.1186/1471-2148-9-125},
file = {:home/fin/Documents/papers/mendeley/Damaj et al.\_2009\_Cross-study analysis of genomic data defines the ciliate multigenic epiplasmin family strategies for functional analys.pdf:pdf},
isbn = {1471-2148 (Electronic)$\backslash$r1471-2148 (Linking)},
issn = {1471-2148},
journal = {BMC Evol. Biol.},
keywords = {Amino Acid Sequence,Animals,Cluster Analysis,Comparative Genomic Hybridization,DNA, Protozoan,DNA, Protozoan: genetics,Evolution, Molecular,Genetic,Genome, Protozoan,Molecular,Molecular Sequence Data,Multigene Family,Paramecium tetraurelia,Paramecium tetraurelia: genetics,Paramecium tetraurelia: metabolism,Phylogeny,Promoter Regions, Genetic,Protozoan,Protozoan Proteins,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Protozoan: genetics,Sequence Alignment,Sequence Analysis, DNA,Tetrahymena thermophila,Tetrahymena thermophila: genetics,Tetrahymena thermophila: metabolism},
pages = {125},
pmid = {19493334},
title = {{Cross-study analysis of genomic data defines the ciliate multigenic epiplasmin family: strategies for functional analysis in Paramecium tetraurelia.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2709106\&tool=pmcentrez\&rendertype=abstract},
volume = {9},
year = {2009}
}
@article{Dettmer2007,
abstract = {This review presents an overview of the dynamically developing field of mass spectrometry-based metabolomics. Metabolomics aims at the comprehensive and quantitative analysis of wide arrays of metabolites in biological samples. These numerous analytes have very diverse physico-chemical properties and occur at different abundance levels. Consequently, comprehensive metabolomics investigations are primarily a challenge for analytical chemistry and specifically mass spectrometry has vast potential as a tool for this type of investigation. Metabolomics require special approaches for sample preparation, separation, and mass spectrometric analysis. Current examples of those approaches are described in this review. It primarily focuses on metabolic fingerprinting, a technique that analyzes all detectable analytes in a given sample with subsequent classification of samples and identification of differentially expressed metabolites, which define the sample classes. To perform this complex task, data analysis tools, metabolite libraries, and databases are required. Therefore, recent advances in metabolomics bioinformatics are also discussed.},
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Dettmer, Katja and Aronov, Pavel a and Hammock, Bruce D},
doi = {10.1002/mas.20108},
eprint = {NIHMS150003},
file = {:home/fin/Documents/papers/mendeley/Dettmer, Aronov, Hammock\_2007\_Mass spectrometry-based metabolomics.\_Mass spectrometry reviews.pdf:pdf},
isbn = {0277-7037},
issn = {0277-7037},
journal = {Mass Spectrom. Rev.},
keywords = {Databases,Gene Expression Profiling,Gene Expression Profiling: methods,Information Storage and Retrieval,Information Storage and Retrieval: methods,Mass Spectrometry,Mass Spectrometry: methods,Peptide Mapping,Peptide Mapping: methods,Protein,Proteome,Proteome: analysis,Proteome: metabolism},
number = {1},
pages = {51--78},
pmid = {16921475},
title = {{Mass spectrometry-based metabolomics.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1904337\&tool=pmcentrez\&rendertype=abstract},
volume = {26},
year = {2007}
}
@article{Macaulay2014,
abstract = {Advances in whole-genome and whole-transcriptome amplification have permitted the sequencing of the minute amounts of DNA and RNA present in a single cell, offering a window into the extent and nature of genomic and transcriptomic heterogeneity which occurs in both normal development and disease. Single-cell approaches stand poised to revolutionise our capacity to understand the scale of genomic, epigenomic, and transcriptomic diversity that occurs during the lifetime of an individual organism. Here, we review the major technological and biological breakthroughs achieved, describe the remaining challenges to overcome, and provide a glimpse into the promise of recent and future developments.},
author = {Macaulay, Iain C. and Voet, Thierry},
doi = {10.1371/journal.pgen.1004126},
file = {:home/fin/Documents/papers/mendeley/Macaulay, Voet\_2014\_Single Cell Genomics Advances and Future Perspectives\_PLoS Genetics.pdf:pdf},
isbn = {1553-7404 (Electronic)$\backslash$r1553-7390 (Linking)},
issn = {15537390},
journal = {PLoS Genet.},
number = {1},
pmid = {24497842},
title = {{Single Cell Genomics: Advances and Future Perspectives}},
volume = {10},
year = {2014}
}
@incollection{Kandler1982,
author = {Kandler, O and Hopf, H},
booktitle = {Plant Carbohydrates I SE  - 8},
doi = {10.1007/978-3-642-68275-9\_8},
editor = {Loewus, FrankA. and Tanner, Widmar},
isbn = {978-3-642-68277-3},
language = {English},
pages = {348--383},
publisher = {Springer Berlin Heidelberg},
series = {Encyclopedia of Plant Physiology},
title = {{Oligosaccharides Based on Sucrose (Sucrosyl Oligosaccharides)}},
url = {http://dx.doi.org/10.1007/978-3-642-68275-9\_8},
volume = {13 / A},
year = {1982}
}
@article{Langmead2012,
abstract = {As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.},
author = {Langmead, Ben and Salzberg, Steven L},
doi = {10.1038/nmeth.1923},
file = {:home/fin/Documents/papers/mendeley/Langmead, Salzberg\_2012\_Fast gapped-read alignment with Bowtie 2.\_Nature Methods.pdf:pdf},
issn = {1548-7105},
journal = {Nat. Methods},
keywords = {Algorithms,Computational Biology,Computational Biology: methods,DNA,DNA: methods,Databases,Genetic,Genome,Human,Human: genetics,Humans,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis},
month = apr,
number = {4},
pages = {357--9},
pmid = {22388286},
title = {{Fast gapped-read alignment with Bowtie 2.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3322381\&tool=pmcentrez\&rendertype=abstract},
volume = {9},
year = {2012}
}
@article{Ruxton2006,
author = {Ruxton, G. D.},
doi = {10.1093/beheco/ark016},
file = {:home/fin/Documents/papers/mendeley/Ruxton\_2006\_The unequal variance t-test is an underused alternative to Student's t-test and the Mann-Whitney U test\_Behavioral Ecology.pdf:pdf},
issn = {1045-2249},
journal = {Behav. Ecol.},
number = {May},
pages = {688--690},
title = {{The unequal variance t-test is an underused alternative to Student's t-test and the Mann-Whitney U test}},
url = {http://www.beheco.oxfordjournals.org/cgi/doi/10.1093/beheco/ark016},
volume = {17},
year = {2006}
}
@article{Marker2014,
abstract = {In most eukaryotes, small RNA-mediated gene silencing pathways form complex interacting networks. In the ciliate Paramecium tetraurelia, at least two RNA interference (RNAi) mechanisms coexist, involving distinct but overlapping sets of protein factors and producing different types of short interfering RNAs (siRNAs). One is specifically triggered by high-copy transgenes, and the other by feeding cells with double-stranded RNA (dsRNA)-producing bacteria. In this study, we designed a forward genetic screen for mutants deficient in dsRNA-induced silencing, and a powerful method to identify the relevant mutations by whole-genome sequencing. We present a set of 47 mutant alleles for five genes, revealing two previously unknown RNAi factors: a novel Paramecium-specific protein (Pds1) and a Cid1-like nucleotidyl transferase. Analyses of allelic diversity distinguish non-essential and essential genes and suggest that the screen is saturated for non-essential, single-copy genes. We show that non-essential genes are specifically involved in dsRNA-induced RNAi while essential ones are also involved in transgene-induced RNAi. One of the latter, the RNA-dependent RNA polymerase RDR2, is further shown to be required for all known types of siRNAs, as well as for sexual reproduction. These results open the way for the dissection of the genetic complexity, interconnection, mechanisms and natural functions of RNAi pathways in P. tetraurelia.},
author = {Marker, Simone and Carradec, Quentin and Tanty, V\'{e}ronique and Arnaiz, Olivier and Meyer, Eric},
doi = {10.1093/nar/gku223},
file = {:home/fin/Documents/papers/mendeley/Marker et al.\_2014\_A forward genetic screen reveals essential and non-essential RNAi factors in Paramecium tetraurelia\_Nucleic Acids Res.pdf:pdf},
issn = {13624962},
journal = {Nucleic Acids Res.},
number = {11},
pages = {7268--7280},
pmid = {24860163},
title = {{A forward genetic screen reveals essential and non-essential RNAi factors in Paramecium tetraurelia}},
volume = {42},
year = {2014}
}
@article{Yao2005,
abstract = {Ciliated protozoan are unicellular eukaryotes. Most species in this diverse group display nuclear dualism, a special feature that supports both somatic and germline nuclei in the same cell. Probably due to this unique life style, they exhibit unusual nuclear characteristics that have intrigued researchers for decades. Among them are large-scale DNA rearrangements, which restructure the somatic genome to become drastically different from its germline origin. They resemble the classical phenomenon of chromatin diminution in some nematodes discovered more than a century ago. The mechanisms of such rearrangements, their biological roles, and their evolutionary origins have been difficult to understand. Recent studies have revealed a clear link to RNA interference, and begin to shed light on these issues. Using the simple ciliate Tetrahymena as a model, this chapter summarizes the physical characterization of these processes, describes recent findings that connect them to RNA interference, and discusses the details of their mechanisms, potential roles in genome defense, and possible occurrences in other organisms.},
author = {Yao, Meng-Chao and Chao, Ju-Lan},
doi = {10.1146/annurev.genet.39.073003.095906},
file = {:home/fin/Documents/papers/mendeley/Yao, Chao\_2005\_RNA-guided DNA deletion in Tetrahymena an RNAi-based mechanism for programmed genome rearrangements.\_Annual Review of Gen.pdf:pdf},
issn = {0066-4197},
journal = {Annu. Rev. Genet.},
keywords = {Animals,Chromatin,Chromatin: genetics,Chromatin: metabolism,Gene Rearrangement,Gene Rearrangement: genetics,Life Cycle Stages,RNA Interference,RNA Interference: physiology,Tetrahymena,Tetrahymena: genetics,Tetrahymena: growth \& development},
pages = {537--59},
pmid = {16285871},
title = {{RNA-guided DNA deletion in Tetrahymena: an RNAi-based mechanism for programmed genome rearrangements.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16285871},
volume = {39},
year = {2005}
}
@article{Maguire2014,
author = {Maguire, Finlay and Richards, Thomas A.},
doi = {10.1016/j.cub.2014.03.075},
file = {:home/fin/Documents/papers/mendeley/Maguire, Richards\_2014\_Organelle Evolution A Mosaic of ‘Mitochondrial’ Functions\_Current Biology.pdf:pdf},
issn = {09609822},
journal = {Curr. Biol.},
number = {11},
pages = {R518--R520},
publisher = {Elsevier},
title = {{Organelle Evolution: A Mosaic of ‘Mitochondrial’ Functions}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0960982214003972},
volume = {24},
year = {2014}
}
@manual{Allaire2014,
annote = {R package version 0.7.4},
author = {Allaire, J J and Horner, Jeffrey and Marti, Vicent and Porte, Natacha},
title = {{markdown: Markdown rendering for R}},
url = {http://cran.r-project.org/package=markdown},
year = {2014}
}
@article{Bradley1998,
abstract = {Practical approaches to clustering use an iterative procedure (e.g. K-Means, EM) which converges to one of numerous local minima. It is known that these iterative techniques are especially sensitive to initial starting conditions. We present a procedure for computing a refined starting condition from a given initial one that is based on an efficient technique for estimating the modes of a distribution. The refined initial starting condition allows the iterative algorithm to converge to a "better" local minimum. The procedure is applicable to a wide class of clustering algorithms for both discrete and continuous data. We demonstrate the application of this method to the popular K-Means clustering algorithm and show that refined inital starting points indeed lead to improved solutions. Refinement run time is considerably lower than the time required to cluster the full database. The method is scalable and can be coupled with a scalable clustering algorithm to address the large-scale clustering problems in data mining.},
author = {Bradley, Paul S and Bradley, P S},
file = {:home/fin/Documents/papers/mendeley/Bradley, Bradley\_1998\_Refining Initial Points for K-Means Clustering\_Microsoft Research.pdf:pdf},
isbn = {1558605568},
journal = {Microsoft Res.},
pages = {91--99},
title = {{Refining Initial Points for K-Means Clustering}},
year = {1998}
}
@article{Galluzzi2004,
author = {Galluzzi, Luca and Penna, Antonella and Bertozzini, Elena and Garc\'{e}s, Esther and Magnani, Mauro and Vila, Magda and Garce, Esther},
doi = {10.1128/AEM.70.2.1199},
file = {:home/fin/Documents/papers/mendeley/Galluzzi et al.\_2004\_Development of a Real-Time PCR Assay for Rapid Detection and Quantification of Alexandrium minutum ( a Dinoflagella.pdf:pdf},
journal = {Appl. Environ. Microbiol.},
number = {2},
pages = {1199--1206},
title = {{Development of a Real-Time PCR Assay for Rapid Detection and Quantification of Alexandrium minutum ( a Dinoflagellate ) Development of a Real-Time PCR Assay for Rapid Detection and Quantification of Alexandrium minutum ( a Dinoflagellate )}},
volume = {70},
year = {2004}
}
@article{Keeling2013,
abstract = {Plastids (chloroplasts) have long been recognized to have originated by endosymbiosis of a cyanobacterium, but their subsequent evolutionary history has proved complex because they have also moved between eukaryotes during additional rounds of secondary and tertiary endosymbioses. Much of this history has been revealed by genomic analyses, but some debates remain unresolved, in particular those relating to secondary red plastids of the chromalveolates, especially cryptomonads. Here, I examine several fundamental questions and assumptions about endosymbiosis and plastid evolution, including the number of endosymbiotic events needed to explain plastid diversity, whether the genetic contribution of the endosymbionts to the host genome goes far beyond plastid-targeted genes, and whether organelle origins are best viewed as a singular transition involving one symbiont or as a gradual transition involving a long line of transient food/symbionts. I also discuss a possible link between transporters and the evolution of protein targeting in organelle integration.},
author = {Keeling, Patrick J},
doi = {10.1146/annurev-arplant-050312-120144},
file = {:home/fin/Documents/papers/mendeley/Keeling\_2013\_The number, speed, and impact of plastid endosymbioses in eukaryotic evolution.\_Annual review of plant biology.pdf:pdf},
isbn = {1543-5008},
issn = {1545-2123},
journal = {Annu. Rev. Plant Biol.},
keywords = {Biological Evolution,Chloroplasts,Chloroplasts: genetics,Chloroplasts: metabolism,Cyanobacteria,Cyanobacteria: genetics,Eukaryota,Eukaryota: genetics,Plastids,Plastids: genetics,Plastids: metabolism,Protein Transport,Symbiosis},
pages = {583--607},
pmid = {23451781},
title = {{The number, speed, and impact of plastid endosymbioses in eukaryotic evolution.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23451781},
volume = {64},
year = {2013}
}
@inproceedings{el2013improved,
author = {{El Hadidi}, Mohamed and Ruscheweyh, Hans-Joachim and Huson, Daniel},
booktitle = {Jt. 21st Annu. Int. Conf. Intell. Syst. Mol. Biol. 12th Eur. Conf. Comput. Biol. 2013},
title = {{Improved metagenome analysis using MEGAN5}},
year = {2013}
}
@book{alberts2015molecular,
address = {New York, NY},
author = {Alberts, Bruce},
isbn = {9780815344322},
publisher = {Garland Science, Taylor and Francis Group},
title = {{Molecular biology of the cell}},
year = {2015}
}
@article{Puigbo2014,
abstract = {BACKGROUND: Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss. However, the actual rates of genome dynamics and relative contributions of different types of event across the diversity of prokaryotes are largely unknown, as are the sizes of microbial supergenomes, i.e. pools of genes that are accessible to the given microbial species.

RESULTS: We performed a comprehensive analysis of the genome dynamics in 35 groups (34 bacterial and one archaeal) of closely related microbial genomes using a phylogenetic birth-and-death maximum likelihood model to quantify the rates of gene family gain and loss, as well as expansion and reduction. The results show that loss of gene families dominates the evolution of prokaryotes, occurring at approximately three times the rate of gain. The rates of gene family expansion and reduction are typically seven and twenty times less than the gain and loss rates, respectively. Thus, the prevailing mode of evolution in bacteria and archaea is genome contraction, which is partially compensated by the gain of new gene families via horizontal gene transfer. However, the rates of gene family gain, loss, expansion and reduction vary within wide ranges, with the most stable genomes showing rates about 25 times lower than the most dynamic genomes. For many groups, the supergenome estimated from the fraction of repetitive gene family gains includes about tenfold more gene families than the typical genome in the group although some groups appear to have vast, 'open' supergenomes.

CONCLUSIONS: Reconstruction of evolution for groups of closely related bacteria and archaea reveals an extremely rapid and highly variable flux of genes in evolving microbial genomes, demonstrates that extensive gene loss and horizontal gene transfer leading to innovation are the two dominant evolutionary processes, and yields robust estimates of the supergenome size.},
author = {Puigb\`{o}, Pere and Lobkovsky, Alexander E and Kristensen, David M and Wolf, Yuri I and Koonin, Eugene V},
doi = {10.1186/s12915-014-0066-4},
file = {:home/fin/Documents/papers/mendeley/Puigb\`{o} et al.\_2014\_Genomes in turmoil quantification of genome dynamics in prokaryote supergenomes.\_BMC biology.pdf:pdf},
issn = {1741-7007},
journal = {BMC Biol.},
month = jan,
pages = {66},
pmid = {25141959},
title = {{Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4166000\&tool=pmcentrez\&rendertype=abstract},
volume = {12},
year = {2014}
}
@article{Karkar2015,
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 Scienc.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
pages = {201421375},
title = {{Metabolic connectivity as a driver of host and endosymbiont integration}},
url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1421375112},
year = {2015}
}
@article{Huson2007,
abstract = {Metagenomics is the study of the genomic content of a sample of organisms obtained from a common habitat using targeted or random sequencing. Goals include understanding the extent and role of microbial diversity. The taxonomical content of such a sample is usually estimated by comparison against sequence databases of known sequences. Most published studies use the analysis of paired-end reads, complete sequences of environmental fosmid and BAC clones, or environmental assemblies. Emerging sequencing-by-synthesis technologies with very high throughput are paving the way to low-cost random "shotgun" approaches. This paper introduces MEGAN, a new computer program that allows laptop analysis of large metagenomic data sets. In a preprocessing step, the set of DNA sequences is compared against databases of known sequences using BLAST or another comparison tool. MEGAN is then used to compute and explore the taxonomical content of the data set, employing the NCBI taxonomy to summarize and order the results. A simple lowest common ancestor algorithm assigns reads to taxa such that the taxonomical level of the assigned taxon reflects the level of conservation of the sequence. The software allows large data sets to be dissected without the need for assembly or the targeting of specific phylogenetic markers. It provides graphical and statistical output for comparing different data sets. The approach is applied to several data sets, including the Sargasso Sea data set, a recently published metagenomic data set sampled from a mammoth bone, and several complete microbial genomes. Also, simulations that evaluate the performance of the approach for different read lengths are presented.},
author = {Huson, Daniel H. and Auch, Alexander F. and Qi, Ji and Schuster, Stephan C.},
doi = {10.1101/gr.5969107},
file = {:home/fin/Documents/papers/mendeley/Huson et al.\_2007\_MEGAN analysis of metagenomic data\_Genome Research.pdf:pdf},
isbn = {1088-9051 (Print)},
issn = {10889051},
journal = {Genome Res.},
pages = {377--386},
pmid = {17255551},
title = {{MEGAN analysis of metagenomic data}},
volume = {17},
year = {2007}
}
@article{Bonetta2006,
author = {Bonetta, Laura},
doi = {10.1038/nmeth0206-141},
file = {:home/fin/Documents/papers/mendeley/Bonetta\_2006\_Genome sequencing in the fast lane\_Nature Methods.pdf:pdf},
issn = {1548-7091},
journal = {Nat. Methods},
number = {2},
pages = {141--147},
title = {{Genome sequencing in the fast lane}},
volume = {3},
year = {2006}
}
@article{Yanai-Balser2010,
abstract = {Paramecium bursaria chlorella virus 1 (PBCV-1), a member of the family Phycodnaviridae, is a large double-stranded DNA, plaque-forming virus that infects the unicellular green alga Chlorella sp. strain NC64A. The 330-kb PBCV-1 genome is predicted to encode 365 proteins and 11 tRNAs. To monitor global transcription during PBCV-1 replication, a microarray containing 50-mer probes to the PBCV-1 365 protein-encoding genes (CDSs) was constructed. Competitive hybridization experiments were conducted by using cDNAs from poly(A)-containing RNAs obtained from cells at seven time points after virus infection. The results led to the following conclusions: (i) the PBCV-1 replication cycle is temporally programmed and regulated; (ii) 360 (99\%) of the arrayed PBCV-1 CDSs were expressed at some time in the virus life cycle in the laboratory; (iii) 227 (62\%) of the CDSs were expressed before virus DNA synthesis begins; (iv) these 227 CDSs were grouped into two classes: 127 transcripts disappeared prior to initiation of virus DNA synthesis (considered early), and 100 transcripts were still detected after virus DNA synthesis begins (considered early/late); (v) 133 (36\%) of the CDSs were expressed after virus DNA synthesis begins (considered late); and (vi) expression of most late CDSs is inhibited by adding the DNA replication inhibitor, aphidicolin, prior to virus infection. This study provides the first comprehensive evaluation of virus gene expression during the PBCV-1 life cycle.},
author = {Yanai-Balser, Giane M and Duncan, Garry a and Eudy, James D and Wang, Dong and Li, Xiao and Agarkova, Irina V and Dunigan, David D and {Van Etten}, James L},
doi = {10.1128/JVI.01698-09},
file = {:home/fin/Documents/papers/mendeley/Yanai-Balser et al.\_2010\_Microarray analysis of Paramecium bursaria chlorella virus 1 transcription.\_Journal of virology.pdf:pdf},
isbn = {1098-5514 (Electronic)$\backslash$r0022-538X (Linking)},
issn = {0022-538X},
journal = {J. Virol.},
number = {1},
pages = {532--542},
pmid = {19828609},
title = {{Microarray analysis of Paramecium bursaria chlorella virus 1 transcription.}},
volume = {84},
year = {2010}
}
@article{Valentine2012,
abstract = {UNLABELLED: $\backslash$n$\backslash$nBACKGROUND: Changes in genes coding for ciliary proteins contribute to complex human syndromes called ciliopathies, such as Bardet-Biedl Syndrome (BBS). We used the model organism Paramecium to focus on ciliary ion channels that affect the beat form and sensory function of motile cilia and evaluate the effects of perturbing BBS proteins on these channels.$\backslash$n$\backslash$nMETHODS: We used immunoprecipitations and mass spectrometry to explore whether Paramecium proteins interact as in mammalian cells. We used RNA interference (RNAi) and swimming behavior assays to examine the effects of BBS depletion on ciliary ion channels that control ciliary beating. Combining RNA interference and epitope tagging, we examined the effects of BBS depletion of BBS 7, 8 and 9 on the location of three channels and a chemoreceptor in cilia.$\backslash$n$\backslash$nRESULTS: We found 10 orthologs of 8 BBS genes in P. tetraurelia. BBS1, 2, 4, 5, 7, 8 and 9 co-immunoprecipitate. While RNAi reduction of BBS 7 and 9 gene products caused loss and shortening of cilia, RNAi for all BBS genes except BBS2 affected patterns of ciliary motility that are governed by ciliary ion channels. Swimming behavior assays pointed to loss of ciliary K+ channel function. Combining RNAi and epitope tagged ciliary proteins we demonstrated that a calcium activated K+ channel was no longer located in the cilia upon depletion of BBS 7, 8 or 9, consistent with the cells' swimming behavior. The TRPP channel PKD2 was also lost from the cilia. In contrast, the ciliary voltage gated calcium channel was unaffected by BBS depletion, consistent with behavioral assays. The ciliary location of a chemoreceptor for folate was similarly unperturbed by the depletion of BBS 7, 8 or 9.$\backslash$n$\backslash$nCONCLUSIONS: The co-immunoprecipitation of BBS 1,2,4,5,7,8, and 9 suggests a complex of BBS proteins. RNAi for BBS 7, 8 or 9 gene products causes the selective loss of K+ and PKD2 channels from the cilia while the critical voltage gated calcium channel and a peripheral receptor protein remain undisturbed. These channels govern ciliary beating and sensory function. Importantly, in P. tetraurelia we can combine studies of ciliopathy protein function with behavior and location and control of ciliary channels.},
author = {Valentine, Megan Smith and Rajendran, Anbazhagan and Yano, Junji and Weeraratne, S Dilhan and Beisson, Janine and Cohen, Jean and Koll, France and {Van Houten}, Judith},
doi = {10.1186/2046-2530-1-16},
file = {:home/fin/Documents/papers/mendeley/Valentine et al.\_2012\_Paramecium BBS genes are key to presence of channels in Cilia.\_Cilia.pdf:pdf},
issn = {2046-2530},
journal = {Cilia},
number = {1},
pages = {16},
pmid = {23351336},
publisher = {Cilia},
title = {{Paramecium BBS genes are key to presence of channels in Cilia.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3556005\&tool=pmcentrez\&rendertype=abstract},
volume = {1},
year = {2012}
}
@article{Baudry2009,
abstract = {Programmed genome rearrangements drive functional gene assembly in ciliates during the development of the somatic macronucleus. The elimination of germline sequences is directed by noncoding RNAs and is initiated by DNA double-strand breaks, but the enzymes responsible for DNA cleavage have not been identified. We show here that PiggyMac (Pgm), a domesticated piggyBac transposase, is required for these rearrangements in Paramecium tetraurelia. A GFP-Pgm fusion localizes in developing macronuclei, where rearrangements take place, and RNAi-mediated silencing of PGM abolishes DNA cleavage. This is the first in vivo evidence suggesting an essential endonucleolytic function of a domesticated piggyBac transposase.},
author = {Baudry, C\'{e}line and Malinsky, Sophie and Restituito, Matthieu and Kapusta, Aur\'{e}lie and Rosa, Sarah and Meyer, Eric and B\'{e}termier, Mireille},
doi = {10.1101/gad.547309},
file = {:home/fin/Documents/papers/mendeley/Baudry et al.\_2009\_PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium.pdf:pdf},
isbn = {1549-5477 (Electronic)$\backslash$r0890-9369 (Linking)},
issn = {08909369},
journal = {Genes Dev.},
keywords = {Chromosome fragmentation,IES excision,Oligohymenophorean ciliates,Transposase domestication},
pages = {2478--2483},
pmid = {19884254},
title = {{PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium tetraurelia}},
volume = {23},
year = {2009}
}
@article{Arnaiz2011,
abstract = {ParameciumDB is a community model organism database built with the GMOD toolkit to integrate the genome and biology of the ciliate Paramecium tetraurelia. Over the last four years, post-genomic data from proteome and transcriptome studies has been incorporated along with predicted orthologs in 33 species, annotations from the community and publications from the scientific literature. Available tools include BioMart for complex queries, GBrowse2 for genome browsing, the Apollo genome editor for expert curation of gene models, a Blast server, a motif finder, and a wiki for protocols, nomenclature guidelines and other documentation. In-house tools have been developed for ontology browsing and evaluation of off-target RNAi matches. Now ready for next-generation deep sequencing data and the genomes of other Paramecium species, this open-access resource is available at http://paramecium.cgm.cnrs-gif.fr.},
author = {Arnaiz, Olivier and Sperling, Linda},
doi = {10.1093/nar/gkq918},
file = {:home/fin/Documents/papers/mendeley/Arnaiz, Sperling\_2011\_ParameciumDB in 2011 New tools and new data for functional and comparative genomics of the model ciliate Parameciu.pdf:pdf},
issn = {03051048},
journal = {Nucleic Acids Res.},
number = {October 2010},
pages = {632--636},
pmid = {20952411},
title = {{ParameciumDB in 2011: New tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia}},
volume = {39},
year = {2011}
}
@article{Edgar2004a,
abstract = {We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.},
author = {Edgar, Robert C.},
doi = {10.1093/nar/gkh340},
file = {:home/fin/Documents/papers/mendeley/Edgar\_2004\_MUSCLE Multiple sequence alignment with high accuracy and high throughput\_Nucleic Acids Research.pdf:pdf},
isbn = {0305-1048},
issn = {03051048},
journal = {Nucleic Acids Res.},
number = {5},
pages = {1792--1797},
pmid = {15034147},
title = {{MUSCLE: Multiple sequence alignment with high accuracy and high throughput}},
volume = {32},
year = {2004}
}
@article{McFadden2014,
abstract = {Recent progress in understanding the origins of plastids from endosymbiotic cyanobacteria is reviewed. Establishing when during geological time the endosymbiosis occurred remains elusive, but progress has been made in defining the cyanobacterial lineage most closely related to plastids, and some mechanistic insight into the possible existence of cryptic endosymbioses perhaps involving Chlamydia-like infections of the host have also been presented. The phylogenetic affinities of the host remain obscure. The existence of a second lineage of primary plastids in euglyphid amoebae has now been confirmed, but the quasipermanent acquisition of plastids by animals has been shown to be more ephemeral than initially suspected. A new understanding of how plastids have been integrated into their hosts by transfer of photosynthate, by endosymbiotic gene transfer and repatriation of gene products back to the endosymbiont, and by regulation of endosymbiont division is presented in context.},
author = {McFadden, Geoffrey I},
doi = {10.1101/cshperspect.a016105},
file = {:home/fin/Documents/papers/mendeley/McFadden\_2014\_Origin and evolution of plastids and photosynthesis in eukaryotes.\_Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harb. Perspect. Biol.},
pages = {a016105},
pmid = {24691960},
title = {{Origin and evolution of plastids and photosynthesis in eukaryotes.}},
url = {http://cshperspectives.cshlp.org/content/6/4/a016105.short?rss=1},
volume = {6},
year = {2014}
}
@article{Archibald2005,
author = {Archibald, John},
doi = {10.1080/15216540500167732},
file = {:home/fin/Documents/papers/mendeley/Archibald\_2005\_Jumping Genes and Shrinking Genomes – Probing the Evolution of Eukaryotic Photosynthesis with Genomics\_IUBMB Life (Inte.pdf:pdf},
isbn = {1521654050016},
issn = {1521-6543},
journal = {IUBMB Life (International Union Biochem. Mol. Biol. Life)},
keywords = {algae,chloroplasts,endosymbiosis,evolution,gene transfer,genomics,plastids},
number = {August},
pages = {539--547},
title = {{Jumping Genes and Shrinking Genomes – Probing the Evolution of Eukaryotic Photosynthesis with Genomics}},
url = {http://doi.wiley.com/10.1080/15216540500167732},
volume = {57},
year = {2005}
}
@article{Hochreiter1997,
author = {Hochreiter, Sepp and Schmidhuber, Jurgen},
doi = {10.1162/neco.1997.9.8.1735},
file = {:home/fin/Documents/papers/mendeley/Hochreiter, Schmidhuber\_1997\_Long short-term memory\_Neural Computation.pdf:pdf},
isbn = {08997667 (ISSN)},
issn = {0899-7667},
journal = {Neural Comput.},
number = {8},
pages = {1--32},
pmid = {9377276},
title = {{Long short-term memory}},
volume = {9},
year = {1997}
}
@article{Stoecker2009,
abstract = {Acquisition of phototrophy is widely distributed in the eukaryotic tree of life and can involve algal endosymbiosis or plastid retention from green or red origins. Species with acquired phototrophy are important components of diversity in aquatic ecosystems, but there are major differences in host and algal taxa involved and in niches of protists with acquired phototrophy in marine and freshwater ecosystems. Organisms that carry out acquired phototrophy are usually mixotrophs, but the degree to which they depend on phototrophy is variable. Evidence suggests that 'excess carbon' provided by acquired phototrophy has been important in supporting major evolutionary innovations that are crucial to the current ecological roles of these protists in aquatic ecosystems. Acquired phototrophy occurs primarily among radiolaria, foraminifera, ciliates and dinoflagellates, but is most ecologically important among the first three. Acquired phototrophy in foraminifera and radiolaria is crucial to their contributions to carbonate, silicate, strontium, and carbon flux in subtropical and tropical oceans. Planktonic ciliates with algal kleptoplastids are important in marine and fresh waters, whereas ciliates with green algal endosymbionts are mostly important in freshwaters. The phototrophic ciliate Myrionecta rubra can be a major primary producer in coastal ecosystems. Our knowledge of how acquired phototrophy influences trophic dynamics and biogeochemical cycles is rudimentary; we need to go beyond traditional concepts of 'plant' and 'animal' functions to progress in our understanding of aquatic microbial ecology. This is a rich area for exploration using a combination of classical and molecular techniques, laboratory and field research, and physiological and ecosystem modeling. © Inter-Research 2009.},
author = {Stoecker, Diane K. and Johnson, Matthew D. and {De Vargas}, Colomban and Not, Fabrice},
doi = {10.3354/ame01340},
file = {:home/fin/Documents/papers/mendeley/Stoecker et al.\_2009\_Acquired phototrophy in aquatic protists\_Aquatic Microbial Ecology.pdf:pdf},
isbn = {0948-3055},
issn = {09483055},
journal = {Aquat. Microb. Ecol.},
keywords = {Ciliates,Dinoflagellates,Endosymbiosis,Foraminifera,Karyoklepty,Kleptoplastidy,Mixotrophy,Myrionecta rubra,Radiolaria},
number = {December},
pages = {279--310},
title = {{Acquired phototrophy in aquatic protists}},
volume = {57},
year = {2009}
}
@article{Leliaert2012,
author = {Leliaert, Frederik and Smith, David R. and Moreau, Herv\'{e} and Herron, Matthew D. and Verbruggen, Heroen and Delwiche, Charles F. and {De Clerck}, Olivier},
doi = {10.1080/07352689.2011.615705},
file = {:home/fin/Documents/papers/mendeley/Leliaert et al.\_2012\_Phylogeny and Molecular Evolution of the Green Algae\_Critical Reviews in Plant Sciences.pdf:pdf},
issn = {0735-2689},
journal = {CRC. Crit. Rev. Plant Sci.},
month = jan,
number = {1},
pages = {1--46},
title = {{Phylogeny and Molecular Evolution of the Green Algae}},
url = {http://www.tandfonline.com/doi/abs/10.1080/07352689.2011.615705},
volume = {31},
year = {2012}
}
@article{Guindon2010,
abstract = {PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.},
author = {Guindon, St\'{e}phane and Dufayard, Jean-Fran\c{c}ois and Lefort, Vincent and Anisimova, Maria and Hordijk, Wim and Gascuel, Olivier},
doi = {10.1093/sysbio/syq010},
file = {:home/fin/Documents/papers/mendeley/Guindon et al.\_2010\_New algorithms and methods to estimate maximum-likelihood phylogenies assessing the performance of PhyML 3.0.\_System.pdf:pdf},
issn = {1076-836X},
journal = {Syst. Biol.},
keywords = {Algorithms,Classification,Classification: methods,Likelihood Functions,Phylogeny,Software},
month = may,
number = {3},
pages = {307--21},
pmid = {20525638},
title = {{New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20525638},
volume = {59},
year = {2010}
}
@article{Quail2012,
abstract = {BACKGROUND: Next generation sequencing (NGS) technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three major new sequencing platforms having been released in 2011: Ion Torrent's PGM, Pacific Biosciences' RS and the Illumina MiSeq. Here we compare the results obtained with those platforms to the performance of the Illumina HiSeq, the current market leader. In order to compare these platforms, and get sufficient coverage depth to allow meaningful analysis, we have sequenced a set of 4 microbial genomes with mean GC content ranging from 19.3 to 67.7\%. Together, these represent a comprehensive range of genome content. Here we report our analysis of that sequence data in terms of coverage distribution, bias, GC distribution, variant detection and accuracy.

RESULTS: Sequence generated by Ion Torrent, MiSeq and Pacific Biosciences technologies displays near perfect coverage behaviour on GC-rich, neutral and moderately AT-rich genomes, but a profound bias was observed upon sequencing the extremely AT-rich genome of Plasmodium falciparum on the PGM, resulting in no coverage for approximately 30\% of the genome. We analysed the ability to call variants from each platform and found that we could call slightly more variants from Ion Torrent data compared to MiSeq data, but at the expense of a higher false positive rate. Variant calling from Pacific Biosciences data was possible but higher coverage depth was required. Context specific errors were observed in both PGM and MiSeq data, but not in that from the Pacific Biosciences platform.

CONCLUSIONS: All three fast turnaround sequencers evaluated here were able to generate usable sequence. However there are key differences between the quality of that data and the applications it will support.},
author = {Quail, Michael a and Smith, Miriam and Coupland, Paul and Otto, Thomas D and Harris, Simon R and Connor, Thomas R and Bertoni, Anna and Swerdlow, Harold P and Gu, Yong},
doi = {10.1186/1471-2164-13-341},
file = {:home/fin/Documents/papers/mendeley/Quail et al.\_2012\_A tale of three next generation sequencing platforms comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq.pdf:pdf},
issn = {1471-2164},
journal = {BMC Genomics},
keywords = {Base Composition,Base Composition: genetics,Base Sequence,Bordetella pertussis,Bordetella pertussis: genetics,Databases, Genetic,Gene Library,Genome, Bacterial,Genome, Bacterial: genetics,Genome, Protozoan,Genome, Protozoan: genetics,Nucleotide Motifs,Nucleotide Motifs: genetics,Plasmodium falciparum,Plasmodium falciparum: genetics,Polymorphism, Single Nucleotide,Polymorphism, Single Nucleotide: genetics,Sequence Analysis, DNA,Sequence Analysis, DNA: instrumentation,Sequence Analysis, DNA: methods,Staphylococcus aureus,Staphylococcus aureus: genetics},
month = jan,
number = {1},
pages = {341},
pmid = {22827831},
publisher = {BMC Genomics},
title = {{A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3431227\&tool=pmcentrez\&rendertype=abstract},
volume = {13},
year = {2012}
}
@article{Wisecaver2014,
abstract = {Fungi contain a remarkable range of metabolic pathways, sometimes encoded by gene clusters, enabling them to digest most organic matter and synthesize an array of potent small molecules. Although metabolism is fundamental to the fungal lifestyle, we still know little about how major evolutionary processes, such as gene duplication (GD) and horizontal gene transfer (HGT), have interacted with clustered and non-clustered fungal metabolic pathways to give rise to this metabolic versatility. We examined the synteny and evolutionary history of 247,202 fungal genes encoding enzymes that catalyze 875 distinct metabolic reactions from 130 pathways in 208 diverse genomes. We found that gene clustering varied greatly with respect to metabolic category and lineage; for example, clustered genes in Saccharomycotina yeasts were overrepresented in nucleotide metabolism, whereas clustered genes in Pezizomycotina were more common in lipid and amino acid metabolism. The effects of both GD and HGT were more pronounced in clustered genes than in their non-clustered counterparts and were differentially distributed across fungal lineages; specifically, GD, which was an order of magnitude more abundant than HGT, was most frequently observed in Agaricomycetes, whereas HGT was much more prevalent in Pezizomycotina. The effect of HGT in some Pezizomycotina was particularly strong; for example, we identified 111 HGT events associated with the 15 Aspergillus genomes, which sharply contrasts with the 60 HGT events detected for the 48 genomes from the entire Saccharomycotina subphylum. Finally, the impact of GD within a metabolic category was typically consistent across all fungal lineages, whereas the impact of HGT was variable. These results indicate that GD is the dominant process underlying fungal metabolic diversity, whereas HGT is episodic and acts in a category- or lineage-specific manner. Both processes have a greater impact on clustered genes, suggesting that metabolic gene clusters represent hotspots for the generation of fungal metabolic diversity.},
author = {Wisecaver, Jennifer H and Slot, Jason C and Rokas, Antonis},
doi = {10.1371/journal.pgen.1004816},
file = {:home/fin/Documents/papers/mendeley/Wisecaver, Slot, Rokas\_2014\_The Evolution of Fungal Metabolic Pathways.\_PLoS genetics.pdf:pdf},
issn = {1553-7404},
journal = {PLoS Genet.},
month = dec,
number = {12},
pages = {e1004816},
pmid = {25474404},
title = {{The Evolution of Fungal Metabolic Pathways.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25474404},
volume = {10},
year = {2014}
}
@article{Huelsenbeck1997,
author = {Huelsenbeck, J P and Crandall, K a},
file = {:home/fin/Documents/papers/mendeley/Huelsenbeck, Crandall\_1997\_Phylogeny estimation and hypothesis testing using maximum likelihood\_Ann. Rev. Ecol. Syst.pdf:pdf},
journal = {Ann. Rev. Ecol. Syst.},
keywords = {LRT,ML,hypothesis testing,maximum likelihood,model selection,molecular clock,phylogenetics,review},
number = {May},
pages = {437--466},
title = {{Phylogeny estimation and hypothesis testing using maximum likelihood}},
volume = {28},
year = {1997}
}
@article{Tonooka2007,
author = {Tonooka, Yuki and Watanabe, Tsuyoshi},
doi = {10.1111/j.1744-7410.2007.00099.x},
file = {:home/fin/Documents/papers/mendeley/Tonooka, Watanabe\_2007\_Genetics of the relationship between the ciliate Paramecium bursaria and its symbiotic algae\_Invertebrate Biology.pdf:pdf},
issn = {10778306},
journal = {Invertebr. Biol.},
month = dec,
number = {4},
pages = {287--294},
title = {{Genetics of the relationship between the ciliate Paramecium bursaria and its symbiotic algae}},
url = {http://doi.wiley.com/10.1111/j.1744-7410.2007.00099.x},
volume = {126},
year = {2007}
}
@misc{Neuhauser2014,
author = {Neuhauser, Sigrid},
title = {{Personal Communication}},
year = {2014}
}
@article{Schultz2009,
author = {Schultz, J\"{o}rg and Wolf, Matthias},
doi = {10.1016/j.ympev.2009.01.008},
file = {:home/fin/Documents/papers/mendeley/Schultz, Wolf\_2009\_ITS2 sequence–structure analysis in phylogenetics A how-to manual for molecular systematics\_Molecular Phylogenetics.pdf:pdf},
issn = {10557903},
journal = {Mol. Phylogenet. Evol.},
keywords = {internal transcribed spacer 2},
number = {2},
pages = {520--523},
publisher = {Elsevier Inc.},
title = {{ITS2 sequence–structure analysis in phylogenetics: A how-to manual for molecular systematics}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790309000104},
volume = {52},
year = {2009}
}
@article{Liu2012a,
author = {Liu, B. and Yuan, J. and Yiu, S.-M. and Li, Z. and Xie, Y. and Chen, Y. and Shi, Y. and Zhang, H. and Li, Y. and Lam, T.-W. and Luo, R.},
doi = {10.1093/bioinformatics/bts563},
file = {:home/fin/Documents/papers/mendeley/Liu et al.\_2012\_COPE an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly\_Bioinformatics.pdf:pdf},
issn = {1367-4803},
journal = {Bioinformatics},
number = {22},
pages = {2870--2874},
title = {{COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly}},
url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/bts563},
volume = {28},
year = {2012}
}
@article{Boser1992,
abstract = {A training algorithm that maximizes the margin  between the training patterns and the decision  boundary is presented. The technique  is applicable to a wide variety of classifiaction  functions, including Perceptrons, polynomials,  and Radial Basis Functions. The effective  number of parameters is adjusted automatically  to match the complexity of the problem.  The solution is expressed as a linear combination  of supporting patterns. These are the  subset of training patterns that are closest to  the decision boundary. Bounds on the generalization  performance based on the leave-one-out  method and the VC-dimension are given. Experimental  results on optical character recognition  problems demonstrate the good generalization  obtained when compared with other  learning algorithms.  1 INTRODUCTION  Good generalization performance of pattern classifiers is achieved when the capacity of the classification function is matched to the size of the training set. Classifiers with a large numb...},
author = {Boser, Bernhard E. and Guyon, Isabelle M. and Vapnik, Vladimir N.},
doi = {10.1.1.21.3818},
file = {:home/fin/Documents/papers/mendeley/Boser, Guyon, Vapnik\_1992\_A Training Algorithm for Optimal Margin Classifiers\_Proceedings of the 5th Annual ACM Workshop on Computationa.pdf:pdf},
isbn = {089791497X},
issn = {0-89791-497-X},
journal = {Proc. 5th Annu. ACM Work. Comput. Learn. Theory},
pages = {144--152},
title = {{A Training Algorithm for Optimal Margin Classifiers}},
url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.21.3818},
year = {1992}
}
@article{Nowack2011,
abstract = {Paulinella chromatophora is a cercozoan amoeba that contains "chromatophores," which are photosynthetic inclusions of cyanobacterial origin. The recent discovery that chromatophores evolved independently of plastids, underwent major genome reduction, and transferred at least two genes to the host nucleus has highlighted P. chromatophora as a model to infer early steps in the evolution of photosynthetic organelles. However, owing to the paucity of nuclear genome sequence data, the extent of endosymbiotic gene transfer (EGT) and host symbiont regulation are currently unknown. A combination of 454 and Illumina next generation sequencing enabled us to generate a comprehensive reference transcriptome data set for P. chromatophora on which we mapped short Illumina cDNA reads generated from cultures from the dark and light phases of a diel cycle. Combined with extensive phylogenetic analyses of the deduced protein sequences, these data revealed that 1) about 0.3-0.8\% of the nuclear genes were obtained by EGT compared with 11-14\% in the Plantae, 2) transferred genes show a distinct bias in that many encode small proteins involved in photosynthesis and photoacclimation, 3) host cells established control over expression of transferred genes, and 4) not only EGT, but to a minor extent also horizontal gene transfer from organisms that presumably served as food sources, helped to shape the nuclear genome of P. chromatophora. The identification of a significant number of transferred genes involved in photosynthesis and photoacclimation of thylakoid membranes as well as the observed transcriptional regulation of these genes strongly implies import of the encoded gene products into chromatophores, a feature previously thought to be restricted to canonical organelles. Thus, a possible mechanism by which P. chromatophora exerts control over the performance of its newly acquired photosynthetic organelle may involve controlling the expression of nuclear-encoded chromatophore-targeted regulatory components of the thylakoid membranes.},
author = {Nowack, Eva C M and Vogel, Heiko and Groth, Marco and Grossman, Arthur R. and Melkonian, Michael and Gl\"{o}ckner, Gernot},
doi = {10.1093/molbev/msq209},
file = {:home/fin/Documents/papers/mendeley/Nowack et al.\_2011\_Endosymbiotic gene transfer and transcriptional regulation of transferred genes in Paulinella chromatophora\_Molecular.pdf:pdf},
isbn = {1537-1719 (Electronic)$\backslash$r0737-4038 (Linking)},
issn = {07374038},
journal = {Mol. Biol. Evol.},
keywords = {Paulinella chromatophora,endosymbiotic gene transfer,evolution,photosynthetic organelle,transcriptome},
number = {1},
pages = {407--422},
pmid = {20702568},
title = {{Endosymbiotic gene transfer and transcriptional regulation of transferred genes in Paulinella chromatophora}},
volume = {28},
year = {2011}
}
@article{Taguchi2012,
author = {Taguchi, K and Hirota, S and Nakayama, H and Kunugihara, D and Mihara, Y},
doi = {10.1088/1742-6596/352/1/012040},
file = {:home/fin/Documents/papers/mendeley/Taguchi et al.\_2012\_Optical Manipulation of Symbiotic Chlorella in Paramecium Bursaria Using a Fiber Axicon Microlens\_Journal of Physics.pdf:pdf},
issn = {1742-6596},
journal = {J. Phys. Conf. Ser.},
month = mar,
pages = {012040},
title = {{Optical Manipulation of Symbiotic Chlorella in Paramecium Bursaria Using a Fiber Axicon Microlens}},
url = {http://stacks.iop.org/1742-6596/352/i=1/a=012040?key=crossref.3268f4ce7eda2f07070103d227f03b0f},
volume = {352},
year = {2012}
}
@article{Phadke2009,
author = {Phadke, Sujal S. and Zufall, Rebecca a.},
doi = {10.1111/j.1095-8312.2009.01250.x},
file = {:home/fin/Documents/papers/mendeley/Phadke, Zufall\_2009\_Rapid diversification of mating systems in ciliates\_Biological Journal of the Linnean Society.pdf:pdf},
issn = {00244066},
journal = {Biol. J. Linn. Soc.},
keywords = {Euplotes,Evolution,Inheritance,Mating types,Paramecium,Tetraymena},
pages = {187--197},
title = {{Rapid diversification of mating systems in ciliates}},
volume = {98},
year = {2009}
}
@article{Harper1989,
author = {Harper, David S and Jahn, Carolyn L},
file = {:home/fin/Documents/papers/mendeley/Harper, Jahn\_1989\_Differential use of termination codons in ciliated protozoa\_Proceedings of the National Academy of Science, USA.pdf:pdf},
journal = {Proc. Natl. Acad. Sci. USA},
number = {May},
pages = {3252--3256},
title = {{Differential use of termination codons in ciliated protozoa}},
volume = {86},
year = {1989}
}
@article{Keller2008,
abstract = {BACKGROUND: Within Chlorophyceae the ITS2 secondary structure shows an unbranched helix I, except for the 'Hydrodictyon' and the 'Scenedesmus' clade having a ramified first helix. The latter two are classified within the Sphaeropleales, characterised by directly opposed basal bodies in their flagellar apparatuses (DO-group). Previous studies could not resolve the taxonomic position of the 'Sphaeroplea' clade within the Chlorophyceae without ambiguity and two pivotal questions remain open: (1) Is the DO-group monophyletic and (2) is a branched helix I an apomorphic feature of the DO-group? In the present study we analysed the secondary structure of three newly obtained ITS2 sequences classified within the 'Sphaeroplea' clade and resolved sphaeroplealean relationships by applying different phylogenetic approaches based on a combined sequence-structure alignment. RESULTS: The newly obtained ITS2 sequences of Ankyra judayi, Atractomorpha porcata and Sphaeroplea annulina of the 'Sphaeroplea' clade do not show any branching in the secondary structure of their helix I. All applied phylogenetic methods highly support the 'Sphaeroplea' clade as a sister group to the 'core Sphaeropleales'. Thus, the DO-group is monophyletic. Furthermore, based on characteristics in the sequence-structure alignment one is able to distinguish distinct lineages within the green algae. CONCLUSION: In green algae, a branched helix I in the secondary structure of the ITS2 evolves past the 'Sphaeroplea' clade. A branched helix I is an apomorph characteristic within the monophyletic DO-group. Our results corroborate the fundamental relevance of including the secondary structure in sequence analysis and phylogenetics.},
author = {Keller, Alexander and Schleicher, Tina and F\"{o}rster, Frank and Ruderisch, Benjamin and Dandekar, Thomas and M\"{u}ller, Tobias and Wolf, Matthias},
doi = {10.1186/1471-2148-8-218},
file = {:home/fin/Documents/papers/mendeley/Keller et al.\_2008\_ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales).\_BMC evolutionary biology.pdf:pdf},
isbn = {1471-2148 (Electronic)$\backslash$n1471-2148 (Linking)},
issn = {1471-2148},
journal = {BMC Evol. Biol.},
pages = {218},
pmid = {18655698},
title = {{ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales).}},
volume = {8},
year = {2008}
}
@article{Lapointe1994,
author = {Lapointe, Fran\c{c}ois-joseph and Kirsch, John A. W. and Bleiwiess, R.},
file = {:home/fin/Documents/papers/mendeley/Lapointe, Kirsch, Bleiwiess\_1994\_Jackknifing of Weighted Trees Validation of Phylogenies Reconstructed from Distance Matrices\_Molecular.pdf:pdf},
journal = {Mol. Phylogenet. Evol.},
number = {3},
pages = {256--267},
title = {{Jackknifing of Weighted Trees: Validation of Phylogenies Reconstructed from Distance Matrices}},
volume = {3},
year = {1994}
}
@article{Eckert1990,
abstract = {We have determined the fidelity of in vitro DNA synthesis catalyzed at high temperature by the DNA polymerase from the thermophilic bacterium Thermus aquaticus. Using a DNA substrate that contains a 3'-OH terminal mismatch, we demonstrate that the purified polymerase lacks detectable exonucleolytic proofreading activity. The fidelity of the Taq polymerase was measured by two assays which score errors produced during in vitro DNA synthesis of the lacZ alpha complementation gene in M13mp2 DNA. In both assays, the Taq polymerase produces single-base substitution errors at a rate of 1 for each 9000 nucleotides polymerized. Frameshift errors are also produced, at a frequency of 1/41,000. These results are discussed in relation to the effects of high temperature on fidelity and the use of the Taq DNA polymerase as a reagent for the in vitro amplification of DNA by the polymerase chain reaction.},
author = {Eckert, K.A. and Kunkel, T.A.},
doi = {10.1021/bi00416a027},
file = {:home/fin/Documents/papers/mendeley/Eckert, Kunkel\_1990\_High fidelity DNA synthesis by the Thermus aquaticus polymerase\_Biochemistry.pdf:pdf},
isbn = {0305-1048 (Print)$\backslash$n0305-1048 (Linking)},
issn = {0305-1048},
journal = {Biochemistry},
number = {13},
pages = {3739--3744},
pmid = {2847780},
title = {{High fidelity DNA synthesis by the Thermus aquaticus polymerase}},
volume = {18},
year = {1990}
}
@article{Buchfink2015,
author = {Buchfink, Benjamin and Xie, Chao and Huson, Daniel H.},
doi = {10.1038/nmeth.3176},
file = {:home/fin/Documents/papers/mendeley/Buchfink, Xie, Huson\_2015\_Fast and Sensitive Protein Alignment using DIAMOND\_Under Review.pdf:pdf},
isbn = {1548-7091},
issn = {15487105},
journal = {Under Rev.},
number = {1},
pmid = {25402007},
title = {{Fast and Sensitive Protein Alignment using DIAMOND}},
volume = {12},
year = {2015}
}
@article{Medvedev2011,
abstract = {The continuing improvements to high-throughput sequencing (HTS) platforms have begun to unfold a myriad of new applications. As a result, error correction of sequencing reads remains an important problem. Though several tools do an excellent job of correcting datasets where the reads are sampled close to uniformly, the problem of correcting reads coming from drastically non-uniform datasets, such as those from single-cell sequencing, remains open.},
author = {Medvedev, Paul and Scott, Eric and Kakaradov, Boyko and Pevzner, Pavel},
doi = {10.1093/bioinformatics/btr208},
file = {:home/fin/Documents/papers/mendeley/Medvedev et al.\_2011\_Error correction of high-throughput sequencing datasets with non-uniform coverage\_Bioinformatics.pdf:pdf},
isbn = {1367-4811 (Electronic)$\backslash$r1367-4803 (Linking)},
issn = {13674803},
journal = {Bioinformatics},
pages = {137--141},
pmid = {21685062},
title = {{Error correction of high-throughput sequencing datasets with non-uniform coverage}},
volume = {27},
year = {2011}
}
@article{Sandberg2014,
abstract = {Recent technical advances have enabled RNA sequencing (RNA-seq) in single cells. Exploratory studies have already led to insights into the dynamics of differentiation, cellular responses to stimulation and the stochastic nature of transcription. We are entering an era of single-cell transcriptomics that holds promise to substantially impact biology and medicine.},
author = {Sandberg, Rickard},
doi = {10.1038/nmeth.2764},
file = {:home/fin/Documents/papers/mendeley/Sandberg\_2014\_Entering the era of single-cell transcriptomics in biology and medicine\_Nature methods.pdf:pdf},
isbn = {1548-7091$\backslash$r1548-7105},
issn = {1548-7091},
journal = {Nat. Methods},
number = {1},
pages = {22--24},
pmid = {24524133},
publisher = {Nature Publishing Group},
title = {{Entering the era of single-cell transcriptomics in biology and medicine}},
url = {http://www.nature.com/doifinder/10.1038/nmeth.2764$\backslash$nhttp://www.nature.com/nmeth/journal/v11/n1/nmeth.2764/metrics/},
volume = {11},
year = {2014}
}
@article{Trapnell2011,
abstract = {High-throughput mRNA sequencing (RNA-Seq) promises simultaneous transcript discovery and abundance estimation. However, this would require algorithms that are not restricted by prior gene annotations and that account for alternative transcription and splicing. Here we introduce such algorithms in an open-source software program called Cufflinks. To test Cufflinks, we sequenced and analyzed >430 million paired 75-bp RNA-Seq reads from a mouse myoblast cell line over a differentiation time series. We detected 13,692 known transcripts and 3,724 previously unannotated ones, 62\% of which are supported by independent expression data or by homologous genes in other species. Over the time series, 330 genes showed complete switches in the dominant transcription start site (TSS) or splice isoform, and we observed more subtle shifts in 1,304 other genes. These results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation.},
author = {Trapnell, Cole and Williams, Brian a and Pertea, Geo and Mortazavi, Ali and Kwan, Gordon and van Baren, Marijke J and Salzberg, Steven L and Wold, Barbara J and Pachter, Lior},
doi = {10.1038/nbt.1621.Transcript},
file = {:home/fin/Documents/papers/mendeley/Trapnell et al.\_2011\_Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among.pdf:pdf},
isbn = {1546-1696 (Electronic)$\backslash$n1087-0156 (Linking)},
issn = {1546-1696},
journal = {Nat. Biotechnol.},
keywords = {Algorithms,Animals,Cell Differentiation,Cell Differentiation: genetics,Cell Line,Gene Expression Profiling,Gene Expression Profiling: methods,Genome,Messenger,Messenger: analysis,Messenger: genetics,Messenger: metabolism,Mice,Oligonucleotide Array Sequence Analysis,Oligonucleotide Array Sequence Analysis: methods,Protein Isoforms,Protein Isoforms: genetics,Protein Isoforms: metabolism,Proto-Oncogene Proteins c-myc,Proto-Oncogene Proteins c-myc: genetics,Proto-Oncogene Proteins c-myc: metabolism,RNA,RNA: methods,Sequence Analysis,Software},
number = {5},
pages = {511--515},
pmid = {20436464},
title = {{Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3146043\&tool=pmcentrez\&rendertype=abstract},
volume = {28},
year = {2011}
}
@article{Robertson2010,
abstract = {We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads from an adult mouse liver poly(A) RNA library, we identified known, new and alternative structures in expressed transcripts, and achieved high sensitivity and specificity relative to reference-based assembly methods.},
author = {Robertson, Gordon and Schein, Jacqueline and Chiu, Readman and Corbett, Richard and Field, Matthew and Jackman, Shaun D and Mungall, Karen and Lee, Sam and Okada, Hisanaga Mark and Qian, Jenny Q and Griffith, Malachi and Raymond, Anthony and Thiessen, Nina and Cezard, Timothee and Butterfield, Yaron S and Newsome, Richard and Chan, Simon K and She, Rong and Varhol, Richard and Kamoh, Baljit and Prabhu, Anna-Liisa and Tam, Angela and Zhao, YongJun and Moore, Richard a and Hirst, Martin and Marra, Marco a and Jones, Steven J M and Hoodless, Pamela a and Birol, Inanc},
doi = {10.1038/nmeth.1517},
file = {:home/fin/Documents/papers/mendeley/Robertson et al.\_2010\_De novo assembly and analysis of RNA-seq data.\_Nature methods.pdf:pdf},
isbn = {1548-7105 (Electronic)$\backslash$r1548-7091 (Linking)},
issn = {1548-7091},
journal = {Nat. Methods},
number = {11},
pages = {909--912},
pmid = {20935650},
title = {{De novo assembly and analysis of RNA-seq data.}},
volume = {7},
year = {2010}
}
@article{Kapaun1995,
abstract = {The stable amino-sugar fraction of the cell wall of the symbiotic Chlorella strain Pbi (Chlorophyceae) was isolated and investigated by sugar analysis, infra-red spectroscopy, lectin binding, enzymatic degradation, X-ray diffraction and electron microscopy. The results indicate the existence of a glycosaminoglycan which can be regarded as a chitin-like glycan. This carbohydrate structure is unusual for algae and reported here for the first time in unicellular chlorophycean algae.},
author = {Kapaun, Edwin and Reisser, Werner},
doi = {10.1007/BF00191563},
file = {:home/fin/Documents/papers/mendeley/Kapaun, Reisser\_1995\_A chitin-like glycan in the cell wall of a Chlorella sp. (Chlorococcales, Chlorophyceae)\_Planta.pdf:pdf},
isbn = {0032-0935},
issn = {00320935},
journal = {Planta},
keywords = {Amino sugar,Cell wall,Chitin,Chitosan,Chlorella,Chlorophyceae},
pages = {577--582},
title = {{A chitin-like glycan in the cell wall of a Chlorella sp. (Chlorococcales, Chlorophyceae)}},
volume = {197},
year = {1995}
}
@article{Goldman1987,
author = {Goldman, Nick},
file = {:home/fin/Documents/papers/mendeley/Goldman\_1987\_Statistical Tests of Models of DNA Substitution\_Journal of molecular evolution.pdf:pdf},
journal = {J. Mol. Evol.},
keywords = {evolutionary models - -,hypothesis testing,likelihood inference - -,maximum,molecular,phylogenetic inference - -,sta-,tistical testing - -},
pages = {182--198},
title = {{Statistical Tests of Models of DNA Substitution}},
volume = {36},
year = {1987}
}
@article{Bateman2002,
abstract = {Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/, in France at http://pfam.jouy.inra.fr/ and in the US at http://pfam.wustl.edu/. The latest version (6.6) of Pfam contains 3071 families, which match 69\% of proteins in SWISS-PROT 39 and TrEMBL 14. Structural data, where available, have been utilised to ensure that Pfam families correspond with structural domains, and to improve domain-based annotation. Predictions of non-domain regions are now also included. In addition to secondary structure, Pfam multiple sequence alignments now contain active site residue mark-up. New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource.},
author = {Bateman, a.},
doi = {10.1093/nar/30.1.276},
file = {:home/fin/Documents/papers/mendeley/Bateman\_2002\_The Pfam Protein Families Database\_Nucleic Acids Research.pdf:pdf},
isbn = {0305-1048},
issn = {13624962},
journal = {Nucleic Acids Res.},
keywords = {Animals,Binding Sites,Computer Graphics,Databases, Protein,Evolution, Molecular,Genome,Humans,Information Storage and Retrieval,Internet,Macromolecular Substances,Markov Chains,Phylogeny,Protein Structure, Secondary,Protein Structure, Tertiary,Proteins,Proteins: chemistry,Proteins: genetics,Proteins: physiology,Sequence Alignment},
number = {1},
pages = {276--280},
pmid = {11752314},
title = {{The Pfam Protein Families Database}},
url = {http://nar.oxfordjournals.org/content/30/1/276.abstract},
volume = {30},
year = {2002}
}
@article{Leung2008,
abstract = {Symbiotic associations are not only ubiquitous in nature, but they also play fun- damental roles in ecology and evolution. This paper discusses symbiosis with regards to the fit- ness costs and benefits conferred to the organisms involved in such interactions, and how the varying nature of these costs and benefits impinges on the way these associations are labelled. Focusing on recent research as examples, we discuss the influence of environmental factors, ontogenetic and evolutionary time, and the symbionts life history traits on the interaction dynamics of symbiotic associations, and argue that symbiotic interactions are highly plastic across circumstances and timescales. We conclude that many symbioses do not fit neatly into the traditional categories of mutualism, commensalism, or parasitism, and urge caution when using such labels to describe biotic interactions.},
author = {Leung, T. L F and Poulin, R.},
file = {:home/fin/Documents/papers/mendeley/Leung, Poulin\_2008\_Parasitism, commensalism, and mutualism Exploring the many shades of symbioses\_Vie et Milieu.pdf:pdf},
isbn = {0240-8759},
issn = {02408759},
journal = {Vie Milieu},
keywords = {Cheaters,Evolution,Mutualism,Parasitism,State-dependent strategies,Symbiosis,Transmission},
number = {2},
pages = {107--115},
title = {{Parasitism, commensalism, and mutualism: Exploring the many shades of symbioses}},
volume = {58},
year = {2008}
}
@article{opencv_library,
author = {Bradski, G},
journal = {Dr. Dobb's J. Softw. Tools},
keywords = {bibtex-import},
title = {{OpenCV library}},
year = {2000}
}
@article{Hirakawa2012,
abstract = {Most plastid proteins are encoded by their nuclear genomes and need to be targeted across multiple envelope membranes. In vascular plants, the translocons at the outer and inner envelope membranes of chloroplasts (TOC and TIC, respectively) facilitate transport across the two plastid membranes. In contrast, several algal groups harbor more complex plastids, the so-called secondary plastids, which are surrounded by three or four membranes, but the plastid protein import machinery (in particular, how proteins cross the membrane corresponding to the secondary endosymbiont plasma membrane) remains unexplored in many of these algae. To reconstruct the putative protein import machinery of a secondary plastid, we used the chlorarachniophyte alga Bigelowiella natans, whose plastid is bounded by four membranes and still possesses a relict nucleus of a green algal endosymbiont (the nucleomorph) in the intermembrane space. We identified nine homologs of plant-like TOC/TIC components in the recently sequenced B. natans nuclear genome, adding to the two that remain in the nucleomorph genome (B. natans TOC75 [BnTOC75] and BnTIC20). All of these proteins were predicted to be localized to the plastid and might function in the inner two membranes. We also show that the homologs of a protein, Der1, that is known to mediate transport across the second membrane in the several lineages with secondary plastids of red algal origin is not associated with plastid protein targeting in B. natans. How plastid proteins cross this membrane remains a mystery, but it is clear that the protein transport machinery of chlorarachniophyte plastids differs from that of red algal secondary plastids.},
author = {Hirakawa, Yoshihisa and Burki, Fabien and Keeling, Patrick J.},
doi = {10.1128/EC.05264-11},
file = {:home/fin/Documents/papers/mendeley/Hirakawa, Burki, Keeling\_2012\_Genome-based reconstruction of the protein import machinery in the secondary plastid of a chlorarachniophy.pdf:pdf},
isbn = {1535-9778},
issn = {15359778},
journal = {Eukaryot. Cell},
pages = {324--333},
pmid = {22267775},
title = {{Genome-based reconstruction of the protein import machinery in the secondary plastid of a chlorarachniophyte alga}},
volume = {11},
year = {2012}
}
@article{Ozsolak2011,
abstract = {Methods for in-depth genome-wide characterization of transcriptomes and quantification of transcript levels using various microarray and next-generation sequencing technologies have emerged as valuable tools for understanding cellular physiology and human disease biology and have begun to be utilized in various clinical diagnostic applications. Current methods, however, typically require RNA to be converted to complementary DNA prior to measurements. This step has been shown to introduce many biases and artifacts. In order to best characterize the 'true' transcriptome, the single-molecule direct RNA sequencing (DRS) technology was developed. This review focuses on the underlying principles behind the DRS, sample preparation steps, and the current and novel avenues of research and applications DRS offers.},
author = {Ozsolak, Fatih and Milos, Patrice M.},
doi = {10.1002/wrna.84.Single-molecule},
file = {:home/fin/Documents/papers/mendeley/Ozsolak, Milos\_2011\_Single-molecule direct RNA sequencing without cDNA synthesis\_Wiley Interdiscip Rev RNA.pdf:pdf},
issn = {1757-7012},
journal = {Wiley Interdiscip Rev RNA},
number = {4},
pages = {565--570},
pmid = {21957044},
title = {{Single-molecule direct RNA sequencing without cDNA synthesis}},
volume = {2},
year = {2011}
}
@article{Muscatine1967a,
abstract = {1.1. Soluble extracellular products of symbiotic algae (zoochlorellae) from Paramecium bursaria, Spongilla sp. and a mutant Chlorohydra viridissima were identified after photosynthesis in the presence of NaHC14O3 and compared to the products of ten strains of free-living algae.2.2. All of the symbiotic strains liberated soluble maltose principally or glucose to the extent of 5·4–86·7 per cent of their total photosynthate. All of the free-living strains liberated 0·4–7·6 per cent of their total photosynthate principally as glycolic acid.3.3. Liberation of soluble carbohydrate by symbiotic algae from fresh-water representatives of three animal phyla and by lichen algae is viewed as an adaptation to symbiosis.},
author = {Muscatine, Leonard and Karakashian, Stephen J. and Karakashian, Marlene W.},
doi = {10.1016/0010-406X(67)90720-7},
file = {:home/fin/Documents/papers/mendeley/Muscatine, Karakashian, Karakashian\_1967\_Soluble extracellular products of algae symbiotic with a ciliate, a sponge and a mutant hydra\_C.pdf:pdf},
issn = {0010406X},
journal = {Comp. Biochem. Physiol.},
pages = {1--12},
title = {{Soluble extracellular products of algae symbiotic with a ciliate, a sponge and a mutant hydra}},
url = {http://www.sciencedirect.com/science/article/pii/0010406X67907207},
volume = {20},
year = {1967}
}
@incollection{Sonneborn1970,
author = {Sonneborn, T. M.},
booktitle = {Methods Cell Biol.},
chapter = {12},
doi = {10.1016/S0091-679X(08)61758-6},
file = {:home/fin/Documents/papers/mendeley/Sonneborn\_1970\_Methods in Paramecium Research\_Methods in Cell Biology.pdf:pdf},
issn = {0091679X},
pages = {241--339},
title = {{Methods in Paramecium Research}},
volume = {4},
year = {1970}
}
@article{Ledergerber2011,
author = {Ledergerber, C. and Dessimoz, C.},
doi = {10.1093/bib/bbq077},
file = {:home/fin/Documents/papers/mendeley/Ledergerber, Dessimoz\_2011\_Base-calling for next-generation sequencing platforms\_Briefings in Bioinformatics.pdf:pdf},
issn = {1467-5463},
journal = {Brief. Bioinform.},
keywords = {454,base-calling,bustard,deep sequencing,illumina,next generation sequencing,roche,solexa},
number = {5},
pages = {489--497},
title = {{Base-calling for next-generation sequencing platforms}},
url = {http://bib.oxfordjournals.org/cgi/doi/10.1093/bib/bbq077},
volume = {12},
year = {2011}
}
@article{Smith1985,
author = {Smith, Lloyd M and Fung, Steven and Hunkapiller, Michael W and Hunkapiller, Tim J and Hood, Leroy E},
file = {:home/fin/Documents/papers/mendeley/Smith et al.\_1985\_The Synthesis of Oligonucleotides Containing an Alipathic Amino Group at the 5' Terminus Synthesis of Fluorescent DNA.pdf:pdf},
journal = {Nucleic Acids Res.},
number = {7},
pages = {2399--2412},
title = {{The Synthesis of Oligonucleotides Containing an Alipathic Amino Group at the 5' Terminus: Synthesis of Fluorescent DNA Primers for use in DNA Sequence Analysis}},
volume = {13},
year = {1985}
}
@article{Stamatakis2014,
author = {Stamatakis, a.},
doi = {10.1093/bioinformatics/btu033},
file = {:home/fin/Documents/papers/mendeley/Stamatakis\_2014\_RAxML version 8 a tool for phylogenetic analysis and post-analysis of large phylogenies\_Bioinformatics.pdf:pdf},
issn = {1367-4803},
journal = {Bioinformatics},
number = {9},
pages = {1312--1313},
title = {{RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies}},
url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btu033},
volume = {30},
year = {2014}
}
@article{Karkashian1965a,
author = {Karkashian, S.J. and Karkashian, M.W.},
file = {:home/fin/Documents/papers/mendeley/Karkashian, Karkashian\_1965\_Evolution and Symbiosis in the Genus Chlorella and Related Algae\_Evolution(2).pdf:pdf},
journal = {Evolution (N. Y).},
number = {3},
pages = {368--377},
title = {{Evolution and Symbiosis in the Genus Chlorella and Related Algae}},
volume = {19},
year = {1965}
}
@article{Reyes-Prieto2008,
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Reyes-Prieto, Adrian and Moustafa, A. and Bhattacharya, Debashish},
doi = {10.1016/j.biotechadv.2011.08.021.Secreted},
eprint = {NIHMS150003},
file = {:home/fin/Documents/papers/mendeley/Reyes-Prieto, Moustafa, Bhattacharya\_2008\_Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic\_Cur.pdf:pdf},
isbn = {2122633255},
issn = {15378276},
journal = {Curr. Biol.},
number = {13},
pages = {956--962},
pmid = {1000000221},
title = {{Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic}},
volume = {18},
year = {2008}
}
@article{Jennings1944,
author = {Jennings, H S and Opitz, P},
file = {:home/fin/Documents/papers/mendeley/Jennings, Opitz\_1944\_Genetics of Paramecium Bursaria. IV. a Fourth Variety from Russia. Lethal Crosses with an American Variety.\_Genetic.pdf:pdf},
journal = {Genetics},
number = {November},
pages = {576--583},
pmid = {17247139},
title = {{Genetics of Paramecium Bursaria. IV. a Fourth Variety from Russia. Lethal Crosses with an American Variety.}},
volume = {29},
year = {1944}
}
@article{Green2011,
abstract = {The chromalveolate hypothesis proposed by Cavalier-Smith (J Euk Microbiol 46:347-366, 1999) suggested that all the algae with chlorophyll c (heterokonts, haptophytes, cryptophytes, and dinoflagellates), as well as the ciliates, apicomplexans, oomycetes, and other non-photosynthetic relatives, shared a common ancestor that acquired a chloroplast by secondary endosymbiosis of a red alga. Much of the evidence from plastid and nuclear genomes supports a red algal origin for plastids of the photosynthetic lineages, but the number of secondary endosymbioses and the number of plastid losses have not been resolved. The issue is complicated by the fact that nuclear genomes are mosaics of genes acquired over a very long time period, not only by vertical descent but also by endosymbiotic and horizontal gene transfer. Phylogenomic analysis of the available whole-genome data has suggested major alterations to our view of eukaryotic evolution, and given rise to alternative models. The next few years may see even more changes once a more representative collection of sequenced genomes becomes available.},
author = {Green, Beverley R.},
doi = {10.1007/s11120-010-9584-2},
file = {:home/fin/Documents/papers/mendeley/Green\_2011\_After the primary endosymbiosis An update on the chromalveolate hypothesis and the origins of algae with Chl c\_Photosynthesis.pdf:pdf},
isbn = {1573-5079 (Electronic)$\backslash$r0166-8595 (Linking)},
issn = {01668595},
journal = {Photosynth. Res.},
keywords = {Algae,Chlorophyll c,Chloroplasts,Chromalveolate hypothesis,Molecular evolution,Phylogeny,Plastids,Secondary endosymbiosis},
pages = {103--115},
pmid = {20676772},
title = {{After the primary endosymbiosis: An update on the chromalveolate hypothesis and the origins of algae with Chl c}},
volume = {107},
year = {2011}
}
@article{Muller2007,
abstract = {Given two organisms, how can one distinguish whether they belong to the same species or not? This might be straightforward for two divergent organisms, but can be extremely difficult and laborious for closely related ones. A molecular marker giving a clear distinction would therefore be of immense benefit. The internal transcribed spacer 2 (ITS2) has been widely used for low-level phylogenetic analyses. Case studies revealed that a compensatory base change (CBC) in the helix II or helix III ITS2 secondary structure between two organisms correlated with sexual incompatibility. We analyzed more than 1300 closely related species to test whether this correlation is generally applicable. In 93\%, where a CBC was found between organisms classified within the same genus, they belong to different species. Thus, a CBC in an ITS2 sequence-structure alignment is a sufficient condition to distinguish even closely related species.},
author = {M\"{u}ller, Tobias and Philippi, Nicole and Dandekar, Thomas and Schultz, J\"{o}rg and Wolf, Matthias},
doi = {10.1261/rna.617107},
file = {:home/fin/Documents/papers/mendeley/M\"{u}ller et al.\_2007\_Distinguishing species.\_RNA (New York, N.Y.).pdf:pdf},
isbn = {10.1261/rna.617107},
issn = {1355-8382},
journal = {RNA},
keywords = {cbc,compensatory base change,internal transcribed spacer 2,its2,phylogeny,species concept},
pages = {1469--1472},
pmid = {17652131},
title = {{Distinguishing species.}},
volume = {13},
year = {2007}
}
@article{Barker1998,
abstract = {From its origin the Protein Information Resource (http://www-nbrf.georgetown.edu/pir/) has supported research on evolution and computational biology by designing and compiling a comprehensive, quality controlled, and well-organized protein sequence database, The database has been produced and updated on a regular schedule since 1984, Since 1988 it has been maintained collaboratively by the PIR-International, an association of data collection centers engaged in international cooperation for the development of this research resource during a period of explosive acquisition of new data. As of June 1997, essentially all sequence entries have been classified into families, allowing the efficient application of methods to propagate and standardize annotation among related sequences, The databases are available through the Internet by the World-Wide Web and FTP, or on CD-ROM and magnetic media.},
author = {Barker, W. C. and Garavelli, J. S. and Haft, D. H. and Hunt, L. T. and Marzec, C. R. and Orcutt, B. C. and Srinivasarao, G. Y. and Yeh, L. S. L. and Ledley, R. S. and Mewes, H. W. and Pfeiffer, F. and Tsugita, a.},
file = {:home/fin/Documents/papers/mendeley/Barker et al.\_1998\_The PIR-international Protein Sequence Database\_Nucleic Acids Research.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {1},
pages = {27--32},
title = {{The PIR-international Protein Sequence Database}},
url = {//000071778900005},
volume = {26},
year = {1998}
}
@article{Blainey2011,
abstract = {Multiple displacement amplification (MDA) is an isothermal, sequence-independent method for the amplification of high molecular weight DNA that is driven by $\phi$29 DNA polymerase (DNAP). Here we report digital MDA (dMDA), an ultrasensitive method for quantifying nucleic acid fragments of unknown sequence. We use the new assay to show that our custom $\phi$29 DNAP preparation is free of contamination at the limit of detection of the dMDA assay (1 contaminating molecule per assay microliter). Contamination in commercially available preparations is also investigated. The results of the dMDA assay provide strong evidence that the so-called 'template-independent' MDA background can be attributed to high-molecular weight contaminants and is not primer-derived in the commercial kits tested. dMDA is orders of magnitude more sensitive than PCR-based techniques for detection of microbial genomic DNA fragments and opens up new possibilities for the ultrasensitive quantification of DNA fragments in a wide variety of application areas using MDA chemistry and off-the-shelf hardware developed for digital PCR.},
author = {Blainey, Paul C. and Quake, Stephen R.},
doi = {10.1093/nar/gkq1074},
file = {:home/fin/Documents/papers/mendeley/Blainey, Quake\_2011\_Digital MDA for enumeration of total nucleic acid contamination\_Nucleic Acids Research.pdf:pdf},
isbn = {1362-4962 (Electronic) 0305-1048 (Linking)},
issn = {03051048},
journal = {Nucleic Acids Res.},
number = {4},
pages = {1--9},
pmid = {21071419},
title = {{Digital MDA for enumeration of total nucleic acid contamination}},
volume = {39},
year = {2011}
}
@inproceedings{Ester1996,
abstract = {Clustering techniques are often used for data exploration. In the literature, there are many examples of applications of different clustering methods. The density-based approaches form a separate group within the clustering techniques since they take into account the density of the data. Using the density of data as a similarity measure is practical in many real situations, because clusters of arbitrary shapes can be handled, what is not possible with convectional clustering methods.?? 2009 Elsevier B.V. All rights reserved.},
archivePrefix = {arXiv},
arxivId = {10.1.1.71.1980},
author = {Ester, M. and Kriegel, H. P. and Sander, J. and Xu, X.},
booktitle = {Proc. 2nd Int. Conf. Knowl. Discov. Data Min.},
doi = {10.1.1.71.1980},
eprint = {10.1.1.71.1980},
file = {:home/fin/Documents/papers/mendeley/Ester et al.\_1996\_A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise\_Proceedings of the 2nd Intern.pdf:pdf},
isbn = {1577350049},
issn = {09758887},
keywords = {Color maps,Core plot,Density-based techniques,Inliers,Natural clusters,Outliers,Reachability plot},
pages = {226--231},
title = {{A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise}},
year = {1996}
}
@article{Wolpert1995,
abstract = {We show that all algorithms that search for an extremum of a cost function perform exactly the same, when averaged over all possible cost functions. In particular, if algorithm A outperforms algorithm B on some cost functions, then loosely speaking there must exist exactly as many other functions where B outperforms A. Starting from this we analyze a number of the other a priori characteristics of the search problem, like its geometry and its information-theoretic aspects. This analysis allows us to derive mathematical benchmarks for assessing a particular search algorithm 's performance. We also investigate minimax aspects of the search problem, the validity of using characteristics of a partial search over a cost function to predict future behavior of the search algorithm on that cost function, and time-varying cost functions. We conclude with some discussion of the justifiability of biologically-inspired search methods.},
author = {Wolpert, D.H. and Macready, William G.},
doi = {10.1145/1389095.1389254},
file = {:home/fin/Documents/papers/mendeley/Wolpert, Macready\_1995\_No free lunch theorems for search\_Technical Report SFI-TR-95-02-010.pdf:pdf},
isbn = {9781605581309},
issn = {1089778X},
journal = {Tech. Rep. SFI-TR-95-02-010},
pages = {1--38},
title = {{No free lunch theorems for search}},
url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.47.7505\&rep=rep1\&type=pdf},
year = {1995}
}
@article{Pillmann1997,
abstract = {Caulerpa (Chlorophyta, Ulvophyceae) is a common marine tropical-subtropical genus of about 70 species, inhabiting the eulittoral zone on rocks and corals as well as mangroves. The genus is particularly diverse and abundant along southern Australian coasts, where it is thought to have originated. Here, we compare sequences from the nuclear ribosomal cistron among five species of Caulerpa, including nine populations of Caulerpa filiformis from two biogeographic regions : five from Australia and four from South Africa. Species relationships were well resolved by internal transcribed spacer (ITS) sequences and supported by high bootstrap values as follows: (C. geminata (C. simpliciuscula (C. trifaria (C. scalpelliformis (C. filiformis ? Australia, C. filiformis ? South Africa ))))). Nucleotide divergence within C. filiformis was low with four and five nucleotide differences present in ITS1 and ITS2 respectively. Unexpectedly, the 5.8S rRNA gene showed eight nucleotide differences between the Australian and South African populations and may indicate cryptic species. The Australian C. filiformis is probably not a South African introduction. These sequences provide an independent means for assessment of species relationships and appear, in so far as limited taxon sampling permits, to follow chloroplast ultrastructural groupings proposed 20 years ago. Caulerpa (Chlorophyta, Ulvophyceae) is a common marine tropical-subtropical genus of about 70 species, inhabiting the eulittoral zone on rocks and corals as well as mangroves. The genus is particularly diverse and abundant along southern Australian coasts, where it is thought to have originated. Here, we compare sequences from the nuclear ribosomal cistron among five species of Caulerpa, including nine populations of Caulerpa filiformis from two biogeographic regions : five from Australia and four from South Africa. Species relationships were well resolved by internal transcribed spacer (ITS) sequences and supported by high bootstrap values as follows: (C. geminata (C. simpliciuscula (C. trifaria (C. scalpelliformis (C. filiformis ? Australia, C. filiformis ? South Africa ))))). Nucleotide divergence within C. filiformis was low with four and five nucleotide differences present in ITS1 and ITS2 respectively. Unexpectedly, the 5.8S rRNA gene showed eight nucleotide differences between the Australian and South African populations and may indicate cryptic species. The Australian C. filiformis is probably not a South African introduction. These sequences provide an independent means for assessment of species relationships and appear, in so far as limited taxon sampling permits, to follow chloroplast ultrastructural groupings proposed 20 years ago.},
author = {Pillmann, a. and Woolcott, G. W. and Olsen, J. L. and Stam, W. T. and King, R. J.},
doi = {10.1080/09670269710001737319},
file = {:home/fin/Documents/papers/mendeley/Pillmann et al.\_1997\_Inter- and intraspecific genetic variation in Caulerpa (Chlorophyta) based on nuclear rDNA ITS sequences\_European J.pdf:pdf},
isbn = {0967-0262},
issn = {0967-0262},
journal = {Eur. J. Phycol.},
keywords = {biogeography,caulerpa,internal transcribed spacer,its,phylogeny,rdna},
number = {December},
pages = {379--386},
title = {{Inter- and intraspecific genetic variation in Caulerpa (Chlorophyta) based on nuclear rDNA ITS sequences}},
url = {http://www.tandfonline.com/doi/abs/10.1080/09670269710001737319},
volume = {32},
year = {1997}
}
@article{Chen2010,
abstract = {BACKGROUND: The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL+matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72\%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over.

METHODOLOGY/PRINCIPAL FINDINGS: Here, we compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species. Our ranking criteria included PCR amplification efficiency, differential intra- and inter-specific divergences, and the DNA barcoding gap. Our data suggest that the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications. Furthermore, we tested the discrimination ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the ITS2 was 92.7\% at the species level.

CONCLUSIONS: The ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species. We also propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa.},
author = {Chen, Shilin and Yao, Hui and Han, Jianping and Liu, Chang and Song, Jingyuan and Shi, Linchun and Zhu, Yingjie and Ma, Xinye and Gao, Ting and Pang, Xiaohui and Luo, Kun and Li, Ying and Li, Xiwen and Jia, Xiaocheng and Lin, Yulin and Leon, Christine},
doi = {10.1371/journal.pone.0008613},
file = {:home/fin/Documents/papers/mendeley/Chen et al.\_2010\_Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species.\_PloS one.pdf:pdf},
issn = {1932-6203},
journal = {PLoS One},
keywords = {Automatic Data Processing,DNA, Plant,DNA, Plant: genetics,Plants, Medicinal,Plants, Medicinal: genetics,Polymerase Chain Reaction},
month = jan,
number = {1},
pages = {e8613},
pmid = {20062805},
title = {{Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2799520\&tool=pmcentrez\&rendertype=abstract},
volume = {5},
year = {2010}
}
@article{Kodama2012a,
abstract = {The association of ciliate Paramecium bursaria with symbiotic Chlorella sp. is a mutualistic symbiosis. However, both the alga-free paramecia and symbiotic algae can still grow independently and can be reinfected experimentally by mixing them. Effects of the host's nutritional conditions against the symbiotic algal cell division and density were examined during early reinfection. Transmission electron microscopy revealed that algal cell division starts 24 h after mixing with alga-free P. bursaria, and that the algal mother cell wall is discarded from the perialgal vacuole membrane, which encloses symbiotic alga. Labelling of the mother cell wall with Calcofluor White Stain, a cell-wall-specific fluorochrome, was used to show whether alga had divided or not. Pulse labelling of alga-free P. bursaria cells with Calcofluor White Stain-stained algae with or without food bacteria for P. bursaria revealed that the fluorescence of Calcofluor White Stain in P. bursaria with bacteria disappeared within 3 days after mixing, significantly faster than without bacteria. Similar results were obtained both under constant light and dark conditions. This report is the first describing that the cell division and density of symbiotic algae of P. bursaria are controlled by the host's nutritional conditions during early infection.},
author = {Kodama, Yuuki and Fujishima, Masahiro},
doi = {10.1111/j.1462-2920.2012.02793.x},
file = {:home/fin/Documents/papers/mendeley/Kodama, Fujishima\_2012\_Cell division and density of symbiotic Chlorella variabilis of the ciliate Paramecium bursaria is controlled by t.pdf:pdf},
isbn = {1462-2912},
issn = {14622912},
journal = {Environ. Microbiol.},
pages = {2800--2811},
pmid = {22672708},
title = {{Cell division and density of symbiotic Chlorella variabilis of the ciliate Paramecium bursaria is controlled by the host's nutritional conditions during early infection process}},
volume = {14},
year = {2012}
}
@article{Blainey2013,
abstract = {Interest in the expanding catalog of uncultivated microorganisms, increasing recognition of heterogeneity among seemingly similar cells, and technological advances in whole-genome amplification and single-cell manipulation are driving considerable progress in single-cell genomics. Here, the spectrum of applications for single-cell genomics, key advances in the development of the field, and emerging methodology for single-cell genome sequencing are reviewed by example with attention to the diversity of approaches and their unique characteristics. Experimental strategies transcending specific methodologies are identified and organized as a road map for future studies in single-cell genomics of environmental microorganisms. Over the next decade, increasingly powerful tools for single-cell genome sequencing and analysis will play key roles in accessing the genomes of uncultivated organisms, determining the basis of microbial community functions, and fundamental aspects of microbial population biology.},
archivePrefix = {arXiv},
arxivId = {3878092},
author = {Blainey, Paul C.},
doi = {10.1111/1574-6976.12015},
eprint = {3878092},
file = {:home/fin/Documents/papers/mendeley/Blainey\_2013\_The future is now Single-cell genomics of bacteria and archaea\_FEMS Microbiology Reviews.pdf:pdf},
isbn = {1574-6976 (Electronic)$\backslash$n0168-6445 (Linking)},
issn = {01686445},
journal = {FEMS Microbiol. Rev.},
keywords = {Microencapsulation,Microfluidics,Micromanipulation,Multiple displacement amplification,Single-cell analysis,Whole-genome amplification},
pages = {407--427},
pmid = {23298390},
title = {{The future is now: Single-cell genomics of bacteria and archaea}},
volume = {37},
year = {2013}
}
@article{sugiura1978further,
author = {Sugiura, Nariaki},
journal = {Commun. Stat. Methods},
number = {1},
pages = {13--26},
publisher = {Taylor \& Francis},
title = {{Further analysts of the data by akaike's information criterion and the finite corrections: Further analysts of the data by akaike's}},
volume = {7},
year = {1978}
}
@article{Kall2007,
abstract = {When using conventional transmembrane topology and signal peptide predictors, such as TMHMM and SignalP, there is a substantial overlap between these two types of predictions. Applying these methods to five complete proteomes, we found that 30-65\% of all predicted signal peptides and 25-35\% of all predicted transmembrane topologies overlap. This impairs predictions of 5-10\% of the proteome, hence this is an important issue in protein annotation. To address this problem, we previously designed a hidden Markov model, Phobius, that combines transmembrane topology and signal peptide predictions. The method makes an optimal choice between transmembrane segments and signal peptides, and also allows constrained and homology-enriched predictions. We here present a web interface (http://phobius.cgb.ki.se and http://phobius.binf.ku.dk) to access Phobius.},
author = {K\"{a}ll, Lukas and Krogh, Anders and Sonnhammer, Erik L L},
doi = {10.1093/nar/gkm256},
file = {:home/fin/Documents/papers/mendeley/K\"{a}ll, Krogh, Sonnhammer\_2007\_Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server\_Nuc. Acids-: Acids-},
isbn = {13624962 (ISSN)},
issn = {03051048},
journal = {Nucleic Acids Res.},
pages = {429--432},
pmid = {17483518},
title = {{Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server}},
volume = {35},
year = {2007}
}
@article{Reisser1980,
author = {Reisser, Werner},
file = {:home/fin/Documents/papers/mendeley/Reisser\_1980\_The Metabolic Interactions Between Paramecium bursaria Ehrbg. and Chlorella spec. in the Paramecium bursaria-Symbiosis\_Arch.pdf:pdf},
journal = {Arch. Microbiol.},
keywords = {-,paramecium bursaria - chlorella,spec},
pages = {291--293},
title = {{The Metabolic Interactions Between Paramecium bursaria Ehrbg. and Chlorella spec. in the Paramecium bursaria-Symbiosis}},
volume = {125},
year = {1980}
}
@article{Servant2002,
abstract = {The ProDom database is a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases. An associated database, ProDom-CG, has been derived as a restriction of ProDom to completely sequenced genomes. The ProDom construction method is based on iterative PSI-BLAST searches and multiple alignments are generated for each domain family. The ProDom web server provides the user with a set of tools to visualise multiple alignments, phylogenetic trees and domain architectures of proteins, as well as a BLAST-based server to analyse new sequences for homologous domains. The comprehensive nature of ProDom makes it particularly useful to help sustain the growth of InterPro.},
author = {Servant, Florence and Bru, Catherine and Carr\`{e}re, S\'{e}bastien and Courcelle, Emmanuel and Gouzy, J\'{e}rĵme and Peyruc, David and Kahn, Daniel},
doi = {10.1093/bib/3.3.246},
file = {:home/fin/Documents/papers/mendeley/Servant et al.\_2002\_ProDom automated clustering of homologous domains.\_Briefings in bioinformatics.pdf:pdf},
isbn = {1467-5463 (Print)},
issn = {1467-5463},
journal = {Brief. Bioinform.},
keywords = {clustering,database,domain family,protein,sequence alignment},
number = {3},
pages = {246--251},
pmid = {12230033},
title = {{ProDom: automated clustering of homologous domains.}},
volume = {3},
year = {2002}
}
@article{Fitch1967,
author = {Fitch, Walter M. and Magoliash, Emanuel},
file = {:home/fin/Documents/papers/mendeley/Fitch, Magoliash\_1967\_Construction of Phylogenetic Tress\_Science.pdf:pdf},
journal = {Science (80-. ).},
number = {279},
title = {{Construction of Phylogenetic Tress}},
volume = {155},
year = {1967}
}
@article{Salim2008,
abstract = {We used the recently sequenced genomes of the ciliates Tetrahymena thermophila and Paramecium tetraurelia to analyze the codon usage patterns in both organisms; we have analyzed codon usage bias, Gln codon usage, GC content and the nucleotide contexts of initiation and termination codons in Tetrahymena and Paramecium. We also studied how these trends change along the length of the genes and in a subset of highly expressed genes. Our results corroborate some of the trends previously described in Tetrahymena, but also negate some specific observations. In both genomes we found a strong bias toward codons with low GC content; however, in highly expressed genes this bias is smaller and codons ending in GC tend to be more frequent. We also found that codon bias increases along gene segments and in highly expressed genes and that the context surrounding initiation and termination codons are always AT rich. Our results also suggest differences in the efficiency of translation of the reassigned stop codons between the two species and between the reassigned codons. Finally, we discuss some of the possible causes for such translational efficiency differences. ?? 2007 Elsevier GmbH. All rights reserved.},
author = {Salim, H. M W and Ring, Karen L. and Cavalcanti, a. R O},
doi = {10.1016/j.protis.2007.11.003},
file = {:home/fin/Documents/papers/mendeley/Salim, Ring, Cavalcanti\_2008\_Patterns of Codon Usage in two Ciliates that Reassign the Genetic Code Tetrahymena thermophila and Parameci.pdf:pdf},
issn = {14344610},
journal = {Protist},
keywords = {codon bias,codon reassignment,codon usage,genetic code},
number = {April},
pages = {283--298},
pmid = {18207458},
title = {{Patterns of Codon Usage in two Ciliates that Reassign the Genetic Code: Tetrahymena thermophila and Paramecium tetraurelia}},
volume = {159},
year = {2008}
}
@article{Kaminuma2011,
abstract = {The DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) provides a nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotation analysis. The DDBJ collected and released 3,637,446 entries/2,272,231,889 bases between July 2009 and June 2010. A highlight of the released data was archive datasets from next-generation sequencing reads of Japanese rice cultivar, Koshihikari submitted by the National Institute of Agrobiological Sciences. In this period, we started a new archive for quantitative genomics data, the DDBJ Omics aRchive (DOR). The DOR stores quantitative data both from the microarray and high-throughput new sequencing platforms. Moreover, we improved the content of the DDBJ patent sequence, released a new submission tool of the DDBJ Sequence Read Archive (DRA) which archives massive raw sequencing reads, and enhanced a cloud computing-based analytical system from sequencing reads, the DDBJ Read Annotation Pipeline. In this article, we describe these new functions of the DDBJ databases and support tools.},
author = {Kaminuma, Eli and Kosuge, Takehide and Kodama, Yuichi and Aono, Hideo and Mashima, Jun and Gojobori, Takashi and Sugawara, Hideaki and Ogasawara, Osamu and Takagi, Toshihisa and Okubo, Kousaku and Nakamura, Yasukazu},
doi = {10.1093/nar/gkq1041},
file = {:home/fin/Documents/papers/mendeley/Kaminuma et al.\_2011\_DDBJ progress report.\_Nucleic acids research.pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$r0305-1048 (Linking)},
issn = {1362-4962},
journal = {Nucleic Acids Res.},
keywords = {Amino Acid Sequence,Databases, Nucleic Acid,Databases, Protein,Genomics,Molecular Sequence Annotation,Patents as Topic,Software},
number = {September 2010},
pages = {D22--7},
pmid = {21062814},
title = {{DDBJ progress report.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3013661\&tool=pmcentrez\&rendertype=abstract},
volume = {39},
year = {2011}
}
@article{Koga2003,
abstract = {Almost all aphids harbour an endosymbiotic bacterium, Buchnera aphidicola, in bacteriocytes. Buchnera synthesizes essential nutrients and supports growth and reproduction of the host. Over the long history of endosymbiosis, many essential genes have been lost from the Buchnera genome, resulting in drastic genome reduction and the inability to live outside the host cells. In turn, when deprived of Buchnera, the host aphid suffers retarded growth and sterility. Buchnera and the host aphid are often referred to as highly integrated almost inseparable mutualistic partners. However, we discovered that, even after complete elimination of Buchnera, infection with a facultative endosymbiotic gamma-proteobacterium called pea aphid secondary symbiont (PASS) enabled survival and reproduction of the pea aphid. In the Buchnera-free aphid, PASS infected the cytoplasms of bacteriocytes that normally harbour Buchnera, establishing a novel endosymbiotic system. These results indicate that PASS can compensate for the essential role of Buchnera by physiologically and cytologically taking over the symbiotic niche. By contrast, PASS negatively affected the growth and reproduction of normal host aphids by suppressing the essential symbiont Buchnera. These findings illuminate complex symbiont-symbiont and host-symbiont interactions in an endosymbiotic system, and suggest a possible evolutionary route to novel obligate endosymbiosis by way of facultative endosymbiotic associations.},
author = {Koga, Ryuichi and Tsuchida, Tsutomu and Fukatsu, Takema},
doi = {10.1098/rspb.2003.2537},
file = {:home/fin/Documents/papers/mendeley/Koga, Tsuchida, Fukatsu\_2003\_Changing partners in an obligate symbiosis a facultative endosymbiont can compensate for loss of the essent.pdf:pdf},
isbn = {0962-8452 (Print)},
issn = {0962-8452},
journal = {Proc. Biol. Sci.},
keywords = {buchnera,endosymbiotic evolution,host,pea aphid,pea aphid secondary symbiont,symbiont,symbiont interactions},
number = {April},
pages = {2543--2550},
pmid = {14728775},
title = {{Changing partners in an obligate symbiosis: a facultative endosymbiont can compensate for loss of the essential endosymbiont Buchnera in an aphid.}},
volume = {270},
year = {2003}
}
@article{Milinkovitch1998,
abstract = {Considerable confusion remains among theoreticians and practicioners of phylogenetic science on the use of outgroup taxa. Here, we show that, despite claims to the contrary, details of the optimal ingroup topology can be changed by switching outgroup taxa. This has serious implications for phylogenetic accuracy. We delineate between the process of outgroup selection and the various possible processes involved in using an outgroup taxon after one has been selected. Criteria are needed for the determination that particular outgroup taxa do not reduce the accuracy of evolutionary tree topologies and inferred character state transformations. We compare previous results from a sensitivity bootstrap analysis of the mitochondrial cytochrome b phylogenetic