text:
evolutionary rate.}},
volume = {1},
year = {2009}
}
@article{Bergstra2012,
abstract = {Grid search and manual search are the most widely used strategies for hyper-parameter optimiza- tion. This paper shows empirically and theoretically that randomly chosen trials are more efficient for hyper-parameter optimization than trials on a grid. Empirical evidence comes from a compar- ison with a large previous study that used grid search and manual search to configure neural net- works and deep belief networks. Compared with neural networks configured by a pure grid search, we find that random search over the same domain is able to find models that are as good or better within a small fraction of the computation time. Granting random search the same computational budget, random search finds better models by effectively searching a larger, less promising con- figuration space. Compared with deep belief networks configured by a thoughtful combination of manual search and grid search, purely random search over the same 32-dimensional configuration space found statistically equal performance on four of seven data sets, and superior performance on one of seven. A Gaussian process analysis of the function from hyper-parameters to validation set performance reveals that for most data sets only a few of the hyper-parameters really matter, but that different hyper-parameters are important on different data sets. This phenomenon makes grid search a poor choice for configuring algorithms for new data sets. Our analysis casts some light on why recent “High Throughput”methods achieve surprising success—they appear to search through a large number of hyper-parameters because most hyper-parameters do not matter much. We anticipate that growing interest in large hierarchical models will place an increasing burden on techniques for hyper-parameter optimization; this work shows that randomsearch is a natural base- line against which to judge progress in the development of adaptive (sequential) hyper-parameter optimization algorithms.},
author = {Bergstra, James and Bengio, Yoshua},
file = {:home/fin/Documents/papers/mendeley/Bergstra, Bengio\_2012\_Random Search for Hyper-Parameter Optimization\_Journal ofMachine Learning Research.pdf:pdf},
isbn = {1532-4435},
issn = {1532-4435},
journal = {J. ofMachine Learn. Res.},
keywords = {deep learning,global optimization,model selection,neural networks,response surface},
pages = {281--305},
title = {{Random Search for Hyper-Parameter Optimization}},
volume = {13},
year = {2012}
}
@misc{ISOInternationalStandard2011,
author = {{ISO International Standard}},
title = {{ISO/IEC 14882:2011(E) – Programming Language C++}},
url = {https://isocpp.org/std/the-standard},
year = {2011}
}
@article{Maaten2008,
abstract = {We present a new technique called “t-SNE” that visualizes high-dimensional data by giving each datapoint a location in a two or three-dimensional map. The technique is a variation of Stochastic Neighbor Embedding (Hinton and Roweis, 2002) that is much easier to optimize, and produces significantly better visualizations by reducing the tendency to crowd points together in the center of the map. t-SNE is better than existing techniques at creating a single map that reveals structure at many different scales. This is particularly important for high-dimensional data that lie on several different, but related, low-dimensional manifolds, such as images of objects from multiple classes seen from multiple viewpoints. For visualizing the structure of very large data sets, we show how t-SNE can use random walks on neighborhood graphs to allow the implicit structure of all of the data to influence theway in which a subset of the data is displayed. We illustrate the performance of t-SNE on a wide variety of data sets and compare it with many other non-parametric visualization techniques, including Sammon mapping, Isomap, and Locally Linear Embedding. The visualiza- tions produced by t-SNE are significantly better than those produced by the other techniques on almost all of the data sets.},
author = {Maaten, Laurens Van Der and Hinton, Geoffrey},
doi = {10.1007/s10479-011-0841-3},
file = {:home/fin/Documents/papers/mendeley/Maaten, Hinton\_2008\_Visualizing Data using t-SNE\_Journal of Machine Learning Research.pdf:pdf},
isbn = {1532-4435},
issn = {02545330},
journal = {J. Mach. Learn. Res.},
keywords = {dimensionality reduction,embedding algorithms,manifold learning,multidimensional scaling,visualization},
pages = {2579--2605},
title = {{Visualizing Data using t-SNE}},
volume = {9},
year = {2008}
}
@article{Sassera2006,
abstract = {An intracellular bacterium with the unique ability to enter mitochondria exists in the European vector of Lyme disease, the hard tick Ixodes ricinus. Previous phylogenetic analyses based on 16S rRNA gene sequences suggested that the bacterium formed a divergent lineage within the Rickettsiales (Alphaproteobacteria). Here, we present additional phylogenetic evidence, based on the gyrB gene sequence, that confirms the phylogenetic position of the bacterium. Based on these data, as well as electron microscopy (EM), in situ hybridization and other observations, we propose the name 'Candidatus Midichloria mitochondrii' for this bacterium. The symbiont appears to be ubiquitous in females of I. ricinus across the tick's distribution, while lower prevalence is observed in males (44\%). Based on EM and in situ hybridization studies, the presence of 'Candidatus M. mitochondrii' in females appears to be restricted to ovarian cells. The bacterium was found to be localized both in the cytoplasm and in the intermembrane space of the mitochondria of ovarian cells. 'Candidatus M. mitochondrii' is the first bacterium to be identified that resides within animal mitochondria.},
author = {Sassera, Davide and Beninati, Tiziana and Bandi, Claudio and Bouman, Edwin a P and Sacchi, Luciano and Fabbi, Massimo and Lo, Nathan},
doi = {10.1099/ijs.0.64386-0},
file = {:home/fin/Documents/papers/mendeley/Sassera et al.\_2006\_Candidatus Midichloria mitochondrii', an endosymbiont of the Ixodes ricinus with a unique intramitochondrial lifesty.pdf:pdf},
isbn = {1466-5026},
issn = {14665026},
journal = {Int. J. Syst. Evol. Microbiol.},
pages = {2535--2540},
pmid = {17082386},
title = {{Candidatus Midichloria mitochondrii', an endosymbiont of the Ixodes ricinus with a unique intramitochondrial lifestyle}},
volume = {56},
year = {2006}
}
@article{Buck2014,
author = {Buck, Amy H. and Coakley, Gillian and Simbari, Fabio and McSorley, Henry J. and Quintana, Juan F. and {Le Bihan}, Thierry and Kumar, Sujai and Abreu-Goodger, Cei and Lear, Marissa and Harcus, Yvonne and Ceroni, Alessandro and Babayan, Simon a. and Blaxter, Mark and Ivens, Alasdair and Maizels, Rick M.},
doi = {10.1038/ncomms6488},
file = {:home/fin/Documents/papers/mendeley/Buck et al.\_2014\_Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity\_Nature Comm.pdf:pdf},
issn = {2041-1723},
journal = {Nat. Commun.},
pages = {5488},
publisher = {Nature Publishing Group},
title = {{Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity}},
url = {http://www.nature.com/doifinder/10.1038/ncomms6488},
volume = {5},
year = {2014}
}
@article{DeQueiroz2007,
abstract = {The issue of species delimitation has long been confused with that of species conceptualization, leading to a half century of controversy concerning both the definition of the species category and methods for inferring the boundaries and numbers of species. Alternative species concepts agree in treating existence as a separately evolving metapopulation lineage as the primary defining property of the species category, but they disagree in adopting different properties acquired by lineages during the course of divergence (e.g., intrinsic reproductive isolation, diagnosability, monophyly) as secondary defining properties (secondary species criteria). A unified species concept can be achieved by treating existence as a separately evolving metapopulation lineage as the only necessary property of species and the former secondary species criteria as different lines of evidence (operational criteria) relevant to assessing lineage separation. This unified concept of species has several consequences for species delimitation, including the following: First, the issues of species conceptualization and species delimitation are clearly separated; the former secondary species criteria are no longer considered relevant to species conceptualization but only to species delimitation. Second, all of the properties formerly treated as secondary species criteria are relevant to species delimitation to the extent that they provide evidence of lineage separation. Third, the presence of any one of the properties (if appropriately interpreted) is evidence for the existence of a species, though more properties and thus more lines of evidence are associated with a higher degree of corroboration. Fourth, and perhaps most significantly, a unified species concept shifts emphasis away from the traditional species criteria, encouraging biologists to develop new methods of species delimitation that are not tied to those properties.},
author = {{De Queiroz}, Kevin},
doi = {10.1080/10635150701701083},
file = {:home/fin/Documents/papers/mendeley/De Queiroz\_2007\_Species concepts and species delimitation.\_Systematic biology.pdf:pdf},
isbn = {1063-5157},
issn = {1063-5157},
journal = {Syst. Biol.},
number = {6},
pages = {879--886},
pmid = {18027281},
title = {{Species concepts and species delimitation.}},
volume = {56},
year = {2007}
}
@article{Bannai2002,
abstract = {MOTIVATION: The prediction of localization sites of various proteins is an important and challenging problem in the field of molecular biology. TargetP, by Emanuelsson et al. (J. Mol. Biol., 300, 1005-1016, 2000) is a neural network based system which is currently the best predictor in the literature for N-terminal sorting signals. One drawback of neural networks, however, is that it is generally difficult to understand and interpret how and why they make such predictions. In this paper, we aim to generate simple and interpretable rules as predictors, and still achieve a practical prediction accuracy. We adopt an approach which consists of an extensive search for simple rules and various attributes which is partially guided by human intuition.

RESULTS: We have succeeded in finding rules whose prediction accuracies come close to that of TargetP, while still retaining a very simple and interpretable form. We also discuss and interpret the discovered rules.},
author = {Bannai, H. and Tamada, Y. and Maruyama, O. and Nakai, K. and Miyano, S.},
doi = {10.1093/bioinformatics/18.2.298},
file = {:home/fin/Documents/papers/mendeley/Bannai et al.\_2002\_Extensive feature detection of N-terminal protein sorting signals\_Bioinformatics.pdf:pdf},
issn = {1367-4803},
journal = {Bioinformatics},
keywords = {Amino Acid Sequence,Computational Biology,Neural Networks (Computer),Protein Sorting Signals,Protein Sorting Signals: genetics,Proteins,Proteins: genetics,Proteins: metabolism,Software,Subcellular Fractions,Subcellular Fractions: metabolism},
number = {2},
pages = {298--305},
pmid = {11847077},
title = {{Extensive feature detection of N-terminal protein sorting signals}},
volume = {18},
year = {2002}
}
@article{Wilhelm2009,
author = {Wilhelm, Brian T. and Landry, Josette-Ren\'{e}e},
doi = {10.1016/j.ymeth.2009.03.016},
file = {:home/fin/Documents/papers/mendeley/Wilhelm, Landry\_2009\_RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing\_Methods.pdf:pdf},
issn = {10462023},
journal = {Methods},
keywords = {massively parallel sequencing},
number = {3},
pages = {249--257},
publisher = {Elsevier Inc.},
title = {{RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1046202309000632},
volume = {48},
year = {2009}
}
@book{Picardi,
author = {Picardi, Ernesto},
edition = {Methods in},
editor = {Picardi, Ernesto},
file = {:home/fin/Documents/papers/mendeley/Picardi\_1111\_RNA Bioinformatics NOT PROPER CITATION\_Unknown.pdf:pdf},
isbn = {9781493922901},
publisher = {Spring Protocols},
title = {{RNA Bioinformatics NOT PROPER CITATION}},
year = {1111}
}
@article{Muscatine1967,
author = {Muscatine, L},
file = {:home/fin/Documents/papers/mendeley/Muscatine\_1967\_Glycerol Excretion by Symbiotic Algae from Corals and Tridacna and Its Control by the Host\_Science.pdf:pdf},
journal = {Science (80-. ).},
number = {April},
pages = {516--519},
title = {{Glycerol Excretion by Symbiotic Algae from Corals and Tridacna and Its Control by the Host}},
volume = {156},
year = {1967}
}
@article{Sonneborn1950,
author = {Sonneborn, T.M.},
file = {:home/fin/Documents/papers/mendeley/Sonneborn\_1950\_Methods in the general biology and genetics of Paramecium aurelia\_Journal of Experimental Zoology.pdf:pdf},
journal = {J. Exp. Zool.},
number = {1},
pages = {87--147},
title = {{Methods in the general biology and genetics of Paramecium aurelia}},
volume = {113},
year = {1950}
}
@article{Guindon2003,
author = {Guindon, St\&\#x000E9;phane and Gascuel, Olivier},
doi = {10.1080/10635150390235520},
file = {:home/fin/Documents/papers/mendeley/Guindon, Gascuel\_2003\_A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood\_Systematic Biology.pdf:pdf},
issn = {1063-5157},
journal = {Syst. Biol.},
number = {5},
pages = {696--704},
title = {{A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood}},
url = {http://sysbio.oxfordjournals.org/cgi/doi/10.1080/10635150390235520},
volume = {52},
year = {2003}
}
@article{Shalek2013,
abstract = {Recent molecular studies have shown that, even when derived from a seemingly homogenous population, individual cells can exhibit substantial differences in gene expression, protein levels and phenotypic output, with important functional consequences. Existing studies of cellular heterogeneity, however, have typically measured only a few pre-selected RNAs or proteins simultaneously, because genomic profiling methods could not be applied to single cells until very recently. Here we use single-cell RNA sequencing to investigate heterogeneity in the response of mouse bone-marrow-derived dendritic cells (BMDCs) to lipopolysaccharide. We find extensive, and previously unobserved, bimodal variation in messenger RNA abundance and splicing patterns, which we validate by RNA-fluorescence in situ hybridization for select transcripts. In particular, hundreds of key immune genes are bimodally expressed across cells, surprisingly even for genes that are very highly expressed at the population average. Moreover, splicing patterns demonstrate previously unobserved levels of heterogeneity between cells. Some of the observed bimodality can be attributed to closely related, yet distinct, known maturity states of BMDCs; other portions reflect differences in the usage of key regulatory circuits. For example, we identify a module of 137 highly variable, yet co-regulated, antiviral response genes. Using cells from knockout mice, we show that variability in this module may be propagated through an interferon feedback circuit, involving the transcriptional regulators Stat2 and Irf7. Our study demonstrates the power and promise of single-cell genomics in uncovering functional diversity between cells and in deciphering cell states and circuits.},
author = {Shalek, Alex K and Satija, Rahul and Adiconis, Xian and Gertner, Rona S and Gaublomme, Jellert T and Raychowdhury, Raktima and Schwartz, Schraga and Yosef, Nir and Malboeuf, Christine and Lu, Diana and Trombetta, John J and Gennert, Dave and Gnirke, Andreas and Goren, Alon and Hacohen, Nir and Levin, Joshua Z and Park, Hongkun and Regev, Aviv},
doi = {10.1038/nature12172},
file = {:home/fin/Documents/papers/mendeley/Shalek et al.\_2013\_Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.\_Nature.pdf:pdf},
isbn = {1476-4687 (Electronic)$\backslash$n0028-0836 (Linking)},
issn = {1476-4687},
journal = {Nature},
keywords = {Animals,Bone Marrow Cells,Bone Marrow Cells: cytology,Bone Marrow Cells: immunology,Dendritic Cells,Dendritic Cells: cytology,Dendritic Cells: immunology,Dendritic Cells: metabolism,Gene Expression Profiling,Gene Expression Regulation,Gene Expression Regulation: immunology,In Situ Hybridization, Fluorescence,Interferon Regulatory Factor-7,Interferons,Interferons: immunology,Lipopolysaccharides,Lipopolysaccharides: immunology,Mice,Mice, Knockout,Protein Isoforms,Protein Isoforms: genetics,RNA Splicing,RNA Splicing: immunology,RNA, Messenger,RNA, Messenger: analysis,RNA, Messenger: genetics,Reproducibility of Results,STAT2 Transcription Factor,Sequence Analysis, RNA,Single-Cell Analysis,Transcriptome,Transcriptome: genetics,Viruses,Viruses: immunology},
number = {7453},
pages = {236--40},
pmid = {23685454},
publisher = {Nature Publishing Group},
title = {{Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3683364\&tool=pmcentrez\&rendertype=abstract},
volume = {498},
year = {2013}
}
@article{Burki2014,
author = {Burki, Fabien},
doi = {10.1101/cshperspect.a016147},
file = {:home/fin/Documents/papers/mendeley/Burki\_2014\_The Eukaryotic Tree of Life from a Global Phylogenomic Perspective\_Cold Spring Harbor Perspectives in Biology.pdf:pdf},
journal = {Cold Spring Harb. Perspect. Biol.},
number = {5},
pages = {1--18},
title = {{The Eukaryotic Tree of Life from a Global Phylogenomic Perspective}},
volume = {6},
year = {2014}
}
@article{Abascal2005,
abstract = {SUMMARY: Using an appropriate model of amino acid replacement is very important for the study of protein evolution and phylogenetic inference. We have built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment. AVAILABILITY: ProtTest is available under the GNU license from http://darwin.uvigo.es},
author = {Abascal, Federico and Zardoya, Rafael and Posada, David},
doi = {10.1093/bioinformatics/bti263},
file = {:home/fin/Documents/papers/mendeley/Abascal, Zardoya, Posada\_2005\_ProtTest Selection of best-fit models of protein evolution\_Bioinformatics.pdf:pdf},
isbn = {1367-4803 (Print)$\backslash$n1367-4803 (Linking)},
issn = {13674803},
journal = {Bioinformatics},
number = {9},
pages = {2104--2105},
pmid = {15647292},
title = {{ProtTest: Selection of best-fit models of protein evolution}},
volume = {21},
year = {2005}
}
@article{Hayden2014,
author = {Hayden, Katherine J. and Garbelotto, Matteo and Knaus, Brian J. and Cronn, Richard C. and Rai, Hardeep and Wright, Jessica W.},
doi = {10.1007/s11295-014-0698-0},
file = {:home/fin/Documents/papers/mendeley/Hayden et al.\_2014\_Dual RNA-seq of the plant pathogen Phytophthora ramorum and its tanoak host\_Tree Genetics and Genomes.pdf:pdf},
issn = {16142950},
journal = {Tree Genet. Genomes},
keywords = {Hemibiotroph,Host-pathogen interactions,Oomycete,Pathogenesis,Sudden oak death},
pages = {489--502},
title = {{Dual RNA-seq of the plant pathogen Phytophthora ramorum and its tanoak host}},
volume = {10},
year = {2014}
}
@article{Lima2009,
abstract = {The growth in the number of completely sequenced microbial genomes (bacterial and archaeal) has generated a need for a procedure that provides UniProtKB/Swiss-Prot-quality annotation to as many protein sequences as possible. We have devised a semi-automated system, HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes), that uses manually built annotation templates for protein families to propagate annotation to all members of manually defined protein families, using very strict criteria. The HAMAP system is composed of two databases, the proteome database and the family database, and of an automatic annotation pipeline. The proteome database comprises biological and sequence information for each completely sequenced microbial proteome, and it offers several tools for CDS searches, BLAST options and retrieval of specific sets of proteins. The family database currently comprises more than 1500 manually curated protein families and their annotation templates that are used to annotate proteins that belong to one of the HAMAP families. On the HAMAP website, individual sequences as well as whole genomes can be scanned against all HAMAP families. The system provides warnings for the absence of conserved amino acid residues, unusual sequence length, etc. Thanks to the implementation of HAMAP, more than 200,000 microbial proteins have been fully annotated in UniProtKB/Swiss-Prot (HAMAP website: http://www.expasy.org/sprot/hamap).},
author = {Lima, Tania and Auchincloss, Andrea H and Coudert, Elisabeth and Keller, Guillaume and Michoud, Karine and Rivoire, Catherine and Bulliard, Virginie and de Castro, Edouard and Lachaize, Corinne and Baratin, Delphine and Phan, Isabelle and Bougueleret, Lydie and Bairoch, Amos},
doi = {10.1093/nar/gkn661},
file = {:home/fin/Documents/papers/mendeley/Lima et al.\_2009\_HAMAP a database of completely sequenced microbial proteome sets and manually curated microbial protein families in Uni.pdf:pdf},
isbn = {9781857883862},
issn = {1362-4962},
journal = {Nucleic Acids Res.},
keywords = {Archaeal Proteins,Archaeal Proteins: chemistry,Archaeal Proteins: classification,Archaeal Proteins: genetics,Bacterial Proteins,Bacterial Proteins: chemistry,Bacterial Proteins: classification,Bacterial Proteins: genetics,Databases, Protein,Genomics,Proteome,Proteome: chemistry,Proteomics,Sequence Alignment,Sequence Analysis, Protein,Software},
number = {October 2008},
pages = {D471--8},
pmid = {18849571},
title = {{HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18849571},
volume = {37},
year = {2009}
}
@article{Wootton2007,
abstract = {Planktonic flagellates and ciliates are the major consumers of phytoplankton and bacterioplankton in aquatic environments, playing a pivotal role in carbon cycling and nutrient regeneration. Despite certain unicellular predators using chemosensory responses to locate and select their prey, the biochemical mechanisms behind prey reception and selection have not been elucidated. Here we identify a Ca(2+)-dependent, mannose-binding lectin on the marine dinoflagellate Oxyrrhis marina, which is used as a feeding receptor for recognizing prey. Blocking the receptor using 20 microM mannose-BSA inhibited ingestion of phytoplankton prey, Isochrysis galbana, by 60\%. In prey selection studies, O. marina ingested twice as many 6 mum diameter beads coated with mannose-BSA as those coated with galNac-BSA. When pre-incubated with mannose-BSA, O. marina was no longer able to discriminate between different sugar-coated beads. Thus, these findings reveal molecular mechanisms of protozoan prey recognition. Our results also indicate the functional similarity between cellular recognition used by planktonic protozoa to discriminate between different prey items, and those used by metazoan phagocytic blood cells to recognize invading microorganisms.},
author = {Wootton, Emma C and Zubkov, Mikhail V and Jones, D Hugh and Jones, Ruth H and Martel, Claire M and Thornton, Catherine a and Roberts, Emily C},
doi = {10.1111/j.1462-2920.2006.01130.x},
file = {:home/fin/Documents/papers/mendeley/Wootton et al.\_2007\_Biochemical prey recognition by planktonic protozoa.\_Environmental microbiology.pdf:pdf},
issn = {1462-2912},
journal = {Environ. Microbiol.},
keywords = {Animals,Calcium,Calcium: metabolism,Dinoflagellida,Dinoflagellida: chemistry,Dinoflagellida: cytology,Dinoflagellida: metabolism,Mannose-Binding Lectins,Mannose-Binding Lectins: metabolism,Phagocytosis,Phytoplankton,Phytoplankton: metabolism,Zooplankton,Zooplankton: chemistry,Zooplankton: cytology,Zooplankton: metabolism},
month = jan,
number = {1},
pages = {216--22},
pmid = {17227426},
title = {{Biochemical prey recognition by planktonic protozoa.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17227426},
volume = {9},
year = {2007}
}
@misc{JoshiGitHub,
author = {Joshi, N.A. and Fass, J.N.},
title = {{Sickle: A Sliding-Window, Adaptive, Quality-based Trimming Tool for FastQ Files (Version 1.33)}},
url = {https://github.com/najoshi/sickle.git},
urldate = {2015-02-15},
year = {2015}
}
@article{Tanaka2002,
abstract = {The green paramecium, Paramecium bursaria, has several hundred green algae in the cytoplasm. Symbiotic algae can be removed from their host cells by treatment with a herbicide, paraquat. The presence of symbiotic algae in P. bursaria can be microscopically examined by detecting the red fluorescence of the algal chlorophyll. However, etiolated algae could not be detected by fluorescent microscopic analyses. Therefore, the absence of symbiotic algae should be confirmed by examining the presence or absence of algal DNA in P. bursaria. In this study, we tried to detect the DNA of symbiotic algae by polymerase chain reaction (PCR) using plant genome-specific primers designed to amplify the DNA sequence in the ribulose-1,5-bisphosphate carboxylase small subunit (rbcS) encoding gene. Using this technique, it was confirmed that the DNA of endosymbiotic algae was absent in paraquat-treated paramecia.},
author = {Tanaka, Miho and Murata-Hori, Maki and Kadono, Takashi and Yamada, Takashi and Kawano, Tomonori and Kosaka, Toshikazu and Hosoya, Hiroshi},
file = {:home/fin/Documents/papers/mendeley/Tanaka et al.\_2002\_Complete elimination of endosymbiotic algae from Paramecium bursaria and its confirmation by diagnostic PCR\_Acta Prot.pdf:pdf},
isbn = {0065-1583},
issn = {00651583},
journal = {Acta Protozool.},
keywords = {Algae-free paramecia,Constant darkness,Endosymbiosis,Paraquat,Ribulose-1,5-bisphosphate carboxylase small subuni,Small subunit rDNA},
pages = {255--261},
title = {{Complete elimination of endosymbiotic algae from Paramecium bursaria and its confirmation by diagnostic PCR}},
volume = {41},
year = {2002}
}
@article{Vert2002,
abstract = {MOTIVATION: The phylogenetic profile of a protein is a string that encodes the presence or absence of the protein in every fully sequenced genome. Because proteins that participate in a common structural complex or metabolic pathway are likely to evolve in a correlated fashion, the phylogenetic profiles of such proteins are often 'similar' or at least 'related' to each other. The question we address in this paper is the following: how to measure the 'similarity' between two profiles, in an evolutionarily relevant way, in order to develop efficient function prediction methods? RESULTS: We show how the profiles can be mapped to a high-dimensional vector space which incorporates evolutionarily relevant information, and we provide an algorithm to compute efficiently the inner product in that space, which we call the tree kernel. The tree kernel can be used by any kernel-based analysis method for classification or data mining of phylogenetic profiles. As an application a Support Vector Machine (SVM) trained to predict the functional class of a gene from its phylogenetic profile is shown to perform better with the tree kernel than with a naive kernel that does not include any information about the phylogenetic relationships among species. Moreover a kernel principal component analysis (KPCA) of the phylogenetic profiles illustrates the sensitivity of the tree kernel to evolutionarily relevant variations.},
author = {Vert, Jean-Philippe},
doi = {10.1093/bioinformatics/18.suppl\_1.S276},
file = {:home/fin/Documents/papers/mendeley/Vert\_2002\_A tree kernel to analyse phylogenetic profiles.\_Bioinformatics (Oxford, England).pdf:pdf},
isbn = {1367-4803 (Print)$\backslash$r1367-4803 (Linking)},
issn = {1367-4803},
journal = {Bioinformatics},
keywords = {gene function prediction,kernel,phylogenetic profile,support,tree,vector machine},
pages = {S276--S284},
pmid = {12169557},
title = {{A tree kernel to analyse phylogenetic profiles.}},
volume = {18 Suppl 1},
year = {2002}
}
@article{Lalonde1999,
abstract = {Introduction: Sucrose and its derivatives represent the major transport forms of photosynthetically assimilated carbon in plants. Sucrose synthesized in green leaves is exported via the phloem, the long-distance distribution network for assimilates, to supply nonphotosynthetic organs with energy and carbon resources. Sucrose not only functions as a transport metabolite but also contributes to the osmotic driving force for phloem translocation (mass flow) and serves as a signal to activate or repress specific genes in a variety of different tissues. The long-distance transport of sucrose depends on a family of proteins that act as sucrose carriers. The analysis of transgenic plants impaired in sucrose transporter expression has demonstrated that sucrose transporter1 (SUT1) is essential for sucrose translocation in potato and tobacco. These results, together with the localization of SUT1 to sieve elements (SEs), indicate that phloem loading occurs in SEs by transmembrane uptake of sucrose directly from the apoplasm. The sucrose transporters identified so far arise from a single gene family. Some of the newly identified members of the family are involved in specific functions, such as nutrition of developing seeds or pollen. Physiological and molecular studies show that sucrose transport is highly regulated at multiple levels of biological organization and in response to changing sucrose concentrations. Thus, one of the most exciting topics in the regulation of sucrose transport is signal perception. By analogy to yeast, in which members of the sugar transport family serve as sugar sensors, we propose that members of the plant sugar transporter family play a direct role in the signal transduction responsible for regulation of sugar transport and, thus, metabolism in general.},
author = {Lalonde, S and Boles, E and Hellmann, H and Barker, L and Patrick, Jw and Frommer, Wb and Ward, Jm},
doi = {10.1105/tpc.11.4.707},
file = {:home/fin/Documents/papers/mendeley/Lalonde et al.\_1999\_The dual function of sugar carriers. Transport and sugar sensing\_The Plant cell.pdf:pdf},
isbn = {1040-4651},
issn = {1532-298X},
journal = {Plant Cell},
number = {April},
pages = {707--726},
pmid = {10213788},
title = {{The dual function of sugar carriers. Transport and sugar sensing}},
volume = {11},
year = {1999}
}
@article{Edwards2005,
abstract = {Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been explored widely for DNA sequencing. Compared to gel electrophoresis based sequencing systems, mass spectrometry produces very high resolution of sequencing fragments, rapid separation on microsecond time scales, and completely eliminates compressions associated with gel-based systems. While most of the research efforts have focused on using mass spectrometers to analyze the DNA products from Sanger sequencing or enzymatic digestion reactions, the read lengths attainable are currently insufficient for large-scale de novo sequencing. The advantage of mass-spectrometry sequencing is that one can unambiguously identify frameshift mutations and heterozygous mutations making it an ideal choice for resequencing projects. In these applications, DNA sequencing fragments that are the same length but with different base compositions are generated, which are challenging to consistently distinguish in gel-based sequencing systems. In contrast, MALDI-TOF MS produces mass spectra of these DNA sequencing fragments with nearly digital resolution, allowing accurate determination of the mixed bases. For these reasons mass spectrometry based sequencing has mainly been focused on the detection of frameshift mutations and single nucleotide polymorphisms (SNPs). More recently, assays have been developed to indirectly sequence DNA by first converting it into RNA. These assays take advantage of the increased resolution and detection ability of MALDI-TOF MS for RNA. © 2005 Elsevier B.V. All rights reserved.},
author = {Edwards, John R. and Ruparel, Hameer and Ju, Jingyue},
doi = {10.1016/j.mrfmmm.2004.07.021},
file = {:home/fin/Documents/papers/mendeley/Edwards, Ruparel, Ju\_2005\_Mass-spectrometry DNA sequencing\_Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis.pdf:pdf},
isbn = {0027-5107},
issn = {00275107},
journal = {Mutat. Res. - Fundam. Mol. Mech. Mutagen.},
keywords = {DNA sequencing,MALDI-TOF mass spectrometry,Single nucleotide polymorphism},
pages = {3--12},
pmid = {15829234},
title = {{Mass-spectrometry DNA sequencing}},
volume = {573},
year = {2005}
}
@article{Jiang2011,
author = {Jiang, Lichun and Schlesinger, Felix and Davis, Carrie a and Zhang, Yu and Li, Renhua and Salit, Marc and Gingeras, Thomas R and Oliver, Brian},
doi = {10.1101/gr.121095.111.Freely},
file = {:home/fin/Documents/papers/mendeley/Jiang et al.\_2011\_Synthetic spike-in standards for RNA-seq experiments\_Genome Research.pdf:pdf},
journal = {Genome Res.},
number = {9},
pages = {1543--1551},
title = {{Synthetic spike-in standards for RNA-seq experiments}},
volume = {21},
year = {2011}
}
@article{Greff2015,
abstract = {Several variants of the Long Short-Term Memory (LSTM) architecture for recurrent neural networks have been proposed since its inception in 1995. In recent years, these networks have become the state-of-the-art models for a variety of machine learning problems. This has led to a renewed interest in understanding the role and utility of various computational components of typical LSTM variants. In this paper, we present the first large-scale analysis of eight LSTM variants on three representative tasks: speech recognition, handwriting recognition, and polyphonic music modeling. The hyperparameters of all LSTM variants for each task were optimized separately using random search and their importance was assessed using the powerful fANOVA framework. In total, we summarize the results of 5400 experimental runs (about 15 years of CPU time), which makes our study the largest of its kind on LSTM networks. Our results show that none of the variants can improve upon the standard LSTM architecture significantly, and demonstrate the forget gate and the output activation function to be its most critical components. We further observe that the studied hyperparameters are virtually independent and derive guidelines for their efficient adjustment.},
archivePrefix = {arXiv},
arxivId = {1503.04069},
author = {Greff, Klaus and Srivastava, Rupesh Kumar and Koutn\'{\i}k, Jan and Steunebrink, Bas R and Schmidhuber, J\"{u}rgen},
eprint = {1503.04069},
file = {:home/fin/Documents/papers/mendeley/Greff et al.\_2015\_LSTM A Search Space Odyssey\_arXiv.pdf:pdf},
journal = {arXiv},
pages = {10},
title = {{LSTM: A Search Space Odyssey}},
url = {http://arxiv.org/abs/1503.04069},
year = {2015}
}
@article{McCutcheon2014,
abstract = {New work in aphids shows that a nuclear-encoded protein resulting from a horizontal gene transfer is targeted to a bacterial symbiont, further blurring the distinction between organelle and symbiont.},
author = {McCutcheon, John P and Keeling, Patrick J},
doi = {10.1016/j.cub.2014.05.073},
file = {:home/fin/Documents/papers/mendeley/McCutcheon, Keeling\_2014\_Endosymbiosis protein targeting further erodes the organellesymbiont distinction.\_Current biology.pdf:pdf},
issn = {1879-0445},
journal = {Curr. Biol.},
month = jul,
number = {14},
pages = {R654--5},
pmid = {25050964},
publisher = {Elsevier Ltd},
title = {{Endosymbiosis: protein targeting further erodes the organelle/symbiont distinction.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25050964},
volume = {24},
year = {2014}
}
@article{Merkel2014,
author = {Merkel, Dirk},
journal = {Linux J.},
number = {March},
title = {{Docker: Lightweight Linux Containers for Consistent Development and Deployment}},
volume = {239},
year = {2014}
}
@article{Hoshina2012,
author = {Hoshina, Ryo},
doi = {10.4236/aim.2012.23027},
file = {:home/fin/Documents/papers/mendeley/Hoshina\_2012\_Photobiont Flexibility in Paramecium bursaria Double and Triple Photobiont Co-Habitation\_Advances in Microbiology.pdf:pdf},
issn = {2165-3402},
journal = {Adv. Microbiol.},
keywords = {paramecium bursaria,photobiont,symbiosis},
number = {September},
pages = {227--233},
title = {{Photobiont Flexibility in Paramecium bursaria: Double and Triple Photobiont Co-Habitation}},
volume = {02},
year = {2012}
}
@article{Galvani2002a,
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},
doi = {10.1016/S0168-9525(01)02548-3},
file = {:home/fin/Documents/papers/mendeley/Galvani, Sperling\_2002\_RNA interference by feeding in iParameciumi\_Trends in Genetics.pdf:pdf},
isbn = {01689525},
issn = {01689525},
journal = {Trends Genet.},
number = {1},
pages = {11--12},
pmid = {11750689},
title = {{RNA interference by feeding in <i>Paramecium</i>}},
volume = {18},
year = {2002}
}
@article{Raven1997,
author = {Raven, JA},
file = {:home/fin/Documents/papers/mendeley/Raven\_1997\_Phagotrophy in phototrophs\_Limnol. Oceanogr.pdf:pdf},
journal = {Limnol. Ocean.},
number = {1},
pages = {198--205},
title = {{Phagotrophy in phototrophs}},
volume = {42},
year = {1997}
}
@article{Hosono2003,
abstract = {Preparation of genomic DNA from clinical samples is a bottleneck in genotyping and DNA sequencing analysis and is frequently limited by the amount of specimen available. We use Multiple Displacement Amplification (MDA) to amplify the whole genome 10,000-fold directly from small amounts of whole blood, dried blood, buccal cells, cultured cells, and buffy coats specimens, generating large amounts of DNA for genetic testing. Genomic DNA was evenly amplified with complete coverage and consistent representation of all genes. All 47 loci analyzed from 44 individuals were represented in the amplified DNA at between 0.5- and 3.0-fold of the copy number in the starting genomic DNA template. A high-fidelity DNA polymerase ensures accurate representation of the DNA sequence. The amplified DNA was indistinguishable from the original genomic DNA template in 5 SNP and 10 microsatellite DNA assays on three different clinical sample types for 20 individuals. Amplification of genomic DNA directly from cells is highly reproducible, eliminates the need for DNA template purification, and allows genetic testing from small clinical samples. The low amplification bias of MDA represents a dramatic technical improvement in the ability to amplify a whole genome compared with older, PCR-based methods.},
author = {Hosono, Seiyu and Faruqi, a. Faward and Dean, Frank B. and Du, Yuefen and Sun, Zhenyu and Wu, Xiaohong and Du, Jing and Kingsmore, Stephen F. and Egholm, Michael and Lasken, Roger S.},
doi = {10.1101/gr.816903},
file = {:home/fin/Documents/papers/mendeley/Hosono et al.\_2003\_Unbiased whole-genome amplification directly from clinical samples\_Genome Research.pdf:pdf},
isbn = {1088-9051 (Print)},
issn = {10889051},
journal = {Genome Res.},
pages = {954--964},
pmid = {12695328},
title = {{Unbiased whole-genome amplification directly from clinical samples}},
volume = {13},
year = {2003}
}
@article{Yang1994,
abstract = {Knowledge of the pattern of nucleotide substitution is important both to our understanding of molecular sequence evolution and to reliable estimation of phylogenetic relationships. The method of parsimony analysis, which has been used to estimate substitution patterns in real sequences, has serious drawbacks and leads to results difficult to interpret. In this paper a model-based maximum likelihood approach is proposed for estimating substitution patterns in real sequences. Nucleotide substitution is assumed to follow a homogeneous Markov process, and the general reversible process model (REV) and the unrestricted model without the reversibility assumption are used. These models are also applied to examine the adequacy of the model of Hasegawa et al. (J. Mol. Evol. 1985;22:160-174) (HKY85). Two data sets are analyzed. For the psi eta-globin pseudogenes of six primate species, the REV models fits the data much better than HKY85, while, for a segment of mtDNA sequences from nine primates, REV cannot provide a significantly better fit than HKY85 when rate variation over sites is taken into account in the models. It is concluded that the use of the REV model in phylogenetic analysis can be recommended, especially for large data sets or for sequences with extreme substitution patterns, while HKY85 may be expected to provide a good approximation. The use of the unrestricted model does not appear to be worthwhile.},
author = {Yang, Z},
doi = {10.1007/BF00178256},
file = {:home/fin/Documents/papers/mendeley/Yang\_1994\_Estimating the pattern of nucleotide substitution.\_Journal of molecular evolution.pdf:pdf},
isbn = {0022-2844 (Print)$\backslash$r0022-2844 (Linking)},
issn = {0022-2844},
journal = {J. Mol. Evol.},
keywords = {likelihood - - dna,markov process - -,models - -,reversible process - -,sequence di-,sequences,substitution patterns - -,vergence - - maximum},
pages = {105--111},
pmid = {8064867},
title = {{Estimating the pattern of nucleotide substitution.}},
volume = {39},
year = {1994}
}
@article{Saji1974,
author = {Saji, M. and Oosawa, F.},
doi = {10.1007/BF02823050},
file = {:home/fin/Documents/papers/mendeley/Saji, Oosawa\_1974\_Mechanism of Photoaccumulation in Paramecium bursaria\_Journal of Protozoology.pdf:pdf},
issn = {0369-3546},
journal = {J. Protozool.},
number = {4},
pages = {57--65},
title = {{Mechanism of Photoaccumulation in Paramecium bursaria}},
volume = {22},
year = {1974}
}
@article{Yang1993,
abstract = {Felsenstein's maximum-likelihood approach for inferring phylogeny from DNA sequences assumes that the rate of nucleotide substitution is constant over different nucleotide sites. This assumption is sometimes unrealistic, as has been revealed by analysis of real sequence data. In the present paper Felsenstein's method is extended to the case where substitution rates over sites are described by the gamma distribution. A numerical example is presented to show that the method fits the data better than do previous models.},
author = {Yang, Z},
file = {:home/fin/Documents/papers/mendeley/Yang\_1993\_Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites.\_Molecular biology and.pdf:pdf},
isbn = {0737-4038},
issn = {0737-4038},
journal = {Mol. Biol. Evol.},
number = {6},
pages = {1396--1401},
pmid = {8277861},
title = {{Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites.}},
volume = {10},
year = {1993}
}
@article{Simao2015,
abstract = {ABSTRACT Motivation: Genomics has revolutionised biological research, but quality assessment of the resulting assembled sequences is compli- cated and remains mostly limited to technical measures like N50. Results: We propose a measure for quantitative assessment of genome assembly and annotation completeness based on evolu- tionarily informed expectations of gene content. We implemented the assessment procedure in open-source software, with sets of Benchmarking Universal Single-Copy Orthologs, named BUSCO. Availability and Implementation: Software implemented in Python and datasets available for download from http://busco.ezlab.org. Contact: Evgeny.Zdobnov@unige.ch Genomics},
author = {Sim\~{a}o, Felipe a and Waterhouse, Robert M and Ioannidis, Panagiotis and Kriventseva, Evgenia V},
doi = {10.1093/bioinformatics/btv351},
file = {:home/fin/Documents/papers/mendeley/Sim\~{a}o et al.\_2015\_BUSCO assessing genome assembly and annotation completeness with single-copy orthologs\_Genome analysis.pdf:pdf},
issn = {1367-4803},
journal = {Genome Anal.},
number = {June},
pages = {9--10},
pmid = {26059717},
title = {{BUSCO : assessing genome assembly and annotation completeness with single-copy orthologs}},
volume = {31},
year = {2015}
}
@book{DeBary1869,
address = {Strassburg},
author = {de Bary, Anton},
publisher = {Verlag von Karl J. Tr\"{u}bner},
title = {{Dir Erscheinung der Symbiose}},
year = {1869}
}
@article{Schultz1998,
abstract = {Accurate multiple alignments of 86 domains that occur in signaling proteins have been constructed and used to provide a Web-based tool (SMART: simple modular architecture research tool) that allows rapid identification and annotation of signaling domain sequences. The majority of signaling proteins are multidomain in character with a considerable variety of domain combinations known. Comparison with established databases showed that 25\% of our domain set could not be deduced from SwissProt and 41\% could not be annotated by Pfam. SMART is able to determine the modular architectures of single sequences or genomes; application to the entire yeast genome revealed that at least 6.7\% of its genes contain one or more signaling domains, approximately 350 greater than previously annotated. The process of constructing SMART predicted (i) novel domain homologues in unexpected locations such as band 4.1-homologous domains in focal adhesion kinases; (ii) previously unknown domain families, including a citron-homology domain; (iii) putative functions of domain families after identification of additional family members, for example, a ubiquitin-binding role for ubiquitin-associated domains (UBA); (iv) cellular roles for proteins, such predicted DEATH domains in netrin receptors further implicating these molecules in axonal guidance; (v) signaling domains in known disease genes such as SPRY domains in both marenostrin/pyrin and Midline 1; (vi) domains in unexpected phylogenetic contexts such as diacylglycerol kinase homologues in yeast and bacteria; and (vii) likely protein misclassifications exemplified by a predicted pleckstrin homology domain in a Candida albicans protein, previously described as an integrin.},
author = {Schultz, J and Milpetz, F and Bork, P and Ponting, C P},
doi = {10.1073/pnas.95.11.5857},
file = {:home/fin/Documents/papers/mendeley/Schultz et al.\_1998\_SMART, a simple modular architecture research tool identification of signaling domains.\_Proceedings of the National.pdf:pdf},
isbn = {0027-8424},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
number = {May},
pages = {5857--5864},
pmid = {9600884},
title = {{SMART, a simple modular architecture research tool: identification of signaling domains.}},
volume = {95},
year = {1998}
}
@article{Jeon1972,
abstract = {Nuclei and cytoplasm were transferred between a normal strain anda variant strain of Amoeba discoides heavily infected with bacteria. After 5 years of infection, the infective bacteria that were initially harmful to the host cells became harmless, and the nucleus of the host cell became dependent on the infective organisms for its normal functions.},
author = {Jeon, K W},
doi = {10.1126/science.176.4039.1122},
file = {:home/fin/Documents/papers/mendeley/Jeon\_1972\_Development of cellular dependence on infective organisms micrurgical studies in amoebas.\_Science (New York, N.Y.).pdf:pdf},
issn = {0036-8075},
journal = {Science},
number = {3},
pages = {1122--1123},
pmid = {5035468},
title = {{Development of cellular dependence on infective organisms: micrurgical studies in amoebas.}},
volume = {176},
year = {1972}
}
@article{Laligne2010,
author = {Laligne, C. and Klotz, C. and {Garreau de Loubresse}, N. and Lemullois, M. and Hori, M. and Laurent, F. X. and Papon, J. F. and Louis, B. and Cohen, J. and Koll, F.},
doi = {10.1128/EC.00368-09},
file = {:home/fin/Documents/papers/mendeley/Laligne et al.\_2010\_Bug22p, a Conserved CentrosomalCiliary Protein Also Present in Higher Plants, Is Required for an Effective Ciliary S.pdf:pdf},
issn = {1535-9778},
journal = {Eukaryot. Cell},
number = {4},
pages = {645--655},
title = {{Bug22p, a Conserved Centrosomal/Ciliary Protein Also Present in Higher Plants, Is Required for an Effective Ciliary Stroke in Paramecium}},
url = {http://ec.asm.org/cgi/doi/10.1128/EC.00368-09},
volume = {9},
year = {2010}
}
@article{Beisson1965,
author = {Beisson, Janine and Sonneborn, T.M.},
file = {:home/fin/Documents/papers/mendeley/Beisson, Sonneborn\_1965\_Cytoplasmic inheritance of the organization of the cell cortex in Paramecium aurelia\_Proceedings of the National.pdf:pdf},
journal = {Proc. Natl. Acad. Sci. USA},
number = {2},
pages = {275--282},
title = {{Cytoplasmic inheritance of the organization of the cell cortex in Paramecium aurelia}},
volume = {53},
year = {1965}
}
@article{Lassmann2009a,
abstract = {In the growing field of genomics, multiple alignment programs are confronted with ever increasing amounts of data. To address this growing issue we have dramatically improved the running time and memory requirement of Kalign, while maintaining its high alignment accuracy. Kalign version 2 also supports nucleotide alignment, and a newly introduced extension allows for external sequence annotation to be included into the alignment procedure. We demonstrate that Kalign2 is exceptionally fast and memory-efficient, permitting accurate alignment of very large numbers of sequences. The accuracy of Kalign2 compares well to the best methods in the case of protein alignments while its accuracy on nucleotide alignments is generally superior. In addition, we demonstrate the potential of using known or predicted sequence annotation to improve the alignment accuracy. Kalign2 is freely available for download from the Kalign web site (http://msa.sbc.su.se/).},
author = {Lassmann, Timo and Frings, Oliver and Sonnhammer, E. L L},
doi = {10.1093/nar/gkn1006},
file = {:home/fin/Documents/papers/mendeley/Lassmann, Frings, Sonnhammer\_2009\_Kalign2 High-performance multiple alignment of protein and nucleotide sequences allowing external feat.pdf:pdf},
isbn = {0305-1048},
issn = {03051048},
journal = {Nucleic Acids Res.},
number = {3},
pages = {858--865},
pmid = {19103665},
title = {{Kalign2: High-performance multiple alignment of protein and nucleotide sequences allowing external features}},
volume = {37},
year = {2009}
}
@article{Conesa2005a,
author = {Conesa, a. and Gotz, S. and Garcia-Gomez, J. M. and Terol, J. and Talon, M. and Robles, M.},
doi = {10.1093/bioinformatics/bti610},
file = {:home/fin/Documents/papers/mendeley/Conesa et al.\_2005\_Blast2GO a universal tool for annotation, visualization and analysis in functional genomics research\_Bioinformatics.pdf:pdf},
issn = {1367-4803},
journal = {Bioinformatics},
number = {18},
pages = {3674--3676},
title = {{Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research}},
url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/bti610},
volume = {21},
year = {2005}
}
@article{Lao2009,
abstract = {We have developed a sequencing-based gene expression profiling assay at single-cell resolution by combining a modified single-cell whole transcriptome amplification method with the next generation sequencing technique, the SOLiD system. Using this assay, we have shown that blastomeres in a four-cell stage embryo have similar gene expression, which is compatible with the fact that they have similar developmental potential. We proved that compared with cDNA microarray technique, our single-cell cDNA SOLiD sequencing assay can detect expression of thousands of more genes. Moreover, for the genes detected by microarray and SOLiD sequencing, our assay detected new transcript variants for a large proportion of them, which confirms unambiguously at single-cell resolution that the transcriptome complexity is higher than expected traditionally. Finally, by using our assay to Dicer knockout (KO) and Ago2 KO oocytes, we showed that a significant amount of transposons were up-regulated abnormally in Dicer/Ago2 KO mature oocytes compared with wild-type controls.},
author = {Lao, Kai Q and Tang, Fuchou and Barbacioru, Catalin and Wang, Yangzhou and Nordman, Ellen and Lee, Clarence and Xu, Nanlan and Wang, Xiaohui and Tuch, Brain and Bodeau, John and Siddiqui, Asim and Surani, M Azim},
file = {:home/fin/Documents/papers/mendeley/Lao et al.\_2009\_mRNA-sequencing whole transcriptome analysis of a single cell on the SOLiD system.\_Journal of biomolecular techniques J.pdf:pdf},
isbn = {1943-4731 (Electronic)
1524-0215 (Linking)},
issn = {1943-4731},
journal = {J. Biomol. Tech.},
pages = {266--271},
pmid = {19949700},
title = {{mRNA-sequencing whole transcriptome analysis of a single cell on the SOLiD system.}},
volume = {20},
year = {2009}
}
@article{Corduneanu2001,
abstract = {Variational methods, which have become popular in the neural computing/machine learning literature, are applied to the Bayesian analysis of mixtures of Gaussian distributions. It is also shown how the deviance information criterion, (DIC), can be extended to these types of model by exploiting the use of variational approximations. The use of variational methods for model selection and the calculation of a DIC are illustrated with real and simulated data. The variational approach allows the simultaneous estimation of the component parameters and the model complexity. It is found that initial selection of a large number of components results in superfluous components being eliminated as the method converges to a solution. This corresponds to an automatic choice of model complexity. The appropriateness of this is reflected in the DIC values.},
author = {Corduneanu, Adrian and Bishop, Christopher M},
doi = {10.1016/j.csda.2006.07.020},
file = {:home/fin/Documents/papers/mendeley/Corduneanu, Bishop\_2001\_Variational Bayesian Model Selection for Mixture Distributions\_Artificial Intelligence.pdf:pdf},
issn = {01679473},
journal = {Artif. Intell.},
pages = {27--34},
title = {{Variational Bayesian Model Selection for Mixture Distributions}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0167947306002362},
volume = {51},
year = {2001}
}
@article{Raj2008,
abstract = {Gene expression is a fundamentally stochastic process, with randomness in transcription and translation leading to cell-to-cell variations in mRNA and protein levels. This variation appears in organisms ranging from microbes to metazoans, and its characteristics depend both on the biophysical parameters governing gene expression and on gene network structure. Stochastic gene expression has important consequences for cellular function, being beneficial in some contexts and harmful in others. These situations include the stress response, metabolism, development, the cell cycle, circadian rhythms, and aging. ?? 2008 Elsevier Inc. All rights reserved.},
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Raj, Arjun and van Oudenaarden, Alexander},
doi = {10.1016/j.cell.2008.09.050},
eprint = {NIHMS150003},
file = {:home/fin/Documents/papers/mendeley/Raj, van Oudenaarden\_2008\_Nature, Nurture, or Chance Stochastic Gene Expression and Its Consequences\_Cell.pdf:pdf},
isbn = {1097-4172 (Electronic)$\backslash$r0092-8674 (Linking)},
issn = {00928674},
journal = {Cell},
number = {2},
pages = {216--226},
pmid = {18957198},
title = {{Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences}},
volume = {135},
year = {2008}
}
@article{Chambouvet2015,
author = {Chambouvet, Aur\'{e}lie and Gower, David J and Jirk, Miloslav and Yabsley, Michael J and Davis, Andrew K and Leonard, Guy and Maguire, Finlay and Doherty-bone, Thomas M and Bittencourt-silva, Gabriela Bueno and Wilkinson, Mark},
doi = {10.1073/pnas.1500163112},
file = {:home/fin/Documents/papers/mendeley/Chambouvet et al.\_2015\_Cryptic infection of a broad taxonomic and geographic diversity of tadpoles by Perkinsea protists\_Unknown.pdf:pdf},
isbn = {1500163112},
pages = {1--9},
title = {{Cryptic infection of a broad taxonomic and geographic diversity of tadpoles by Perkinsea protists}},
year = {2015}
}
@article{Pell2012,
author = {Pell, J. and Hintze, a. and Canino-Koning, R. and Howe, a. and Tiedje, J. M. and Brown, C. T.},
doi = {10.1073/pnas.1121464109},
file = {:home/fin/Documents/papers/mendeley/Pell et al.\_2012\_Scaling metagenome sequence assembly with probabilistic de Bruijn graphs\_Proceedings of the National Academy of Science.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
number = {33},
pages = {13272--13277},
title = {{Scaling metagenome sequence assembly with probabilistic de Bruijn graphs}},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1121464109},
volume = {109},
year = {2012}
}
@article{Horton1997,
abstract = {We have compared four classifiers on the problem of predicting the cellular localization sites of proteins in yeast and E. coli. A set of sequence derived features, such as regions of high hydrophobicity, were used for each classifier. The methods compared were a structured probabilistic model specifically designed for the localization problem, the k nearest neighbors classifier, the binary decision tree classifier, and the na\"{\i}ve Bayes classifier. The result of tests using stratified cross validation shows the k nearest neighbors classifier to perform better than the other methods. In the case of yeast this difference was statistically significant using a cross-validated paired t test. The result is an accuracy of approximately 60\% for 10 yeast classes and 86\% for 8 E. coli classes. The best previously reported accuracies for these datasets were 55\% and 81\% respectively.},
author = {Horton, P and Nakai, K},
file = {:home/fin/Documents/papers/mendeley/Horton, Nakai\_1997\_Better prediction of protein cellular localization sites with the k nearest neighbors classifier.\_Proceedings ... In.pdf:pdf},
isbn = {1553-0833 (Print)},
issn = {1553-0833},
journal = {Proc. Int. Conf. Intell. Syst. Mol. Biol.},
keywords = {classification,classifier,colz,e,k nearest neighbor,protein localization,yeast},
pages = {147--152},
pmid = {9322029},
title = {{Better prediction of protein cellular localization sites with the k nearest neighbors classifier.}},
volume = {5},
year = {1997}
}
@article{Yanagi2004,
abstract = {When isolated single cells of Paramecium bursaria were treated with 1.25\% methyl cellulose, most of the single cells showed nuclear changes which were substantially similar to those seen in conjugation, suggesting that the cells undergo autogamy. Additional cytological observations indicated that the cells underwent normal nuclear processes during autogamy. The ability to induce autogamy will facilitate genetic studies in P. bursaria. ?? 2004 Elsevier GmbH. All rights reserved.},
author = {Yanagi, Akira},
doi = {10.1016/j.ejop.2004.05.007},
file = {:home/fin/Documents/papers/mendeley/Yanagi\_2004\_Autogamy is induced in Paramecium bursaria by methyl cellulose\_European Journal of Protistology.pdf:pdf},
issn = {09324739},
journal = {Eur. J. Protistol.},
keywords = {Autogamy,Chemical induction of autogamy,Methyl cellulose,Paramecium bursaria},
pages = {313--315},
title = {{Autogamy is induced in Paramecium bursaria by methyl cellulose}},
volume = {40},
year = {2004}
}
@article{Hamel2011,
abstract = {Paramecium and other protists are able to swim at velocities reaching several times their body size per second by beating their cilia in an organized fashion. The cilia beat in an asymmetric stroke, which breaks the time reversal symmetry of small scale flows. Here we show that Paramecium uses three different swimming gaits to escape from an aggression, applied in the form of a focused laser heating. For a weak aggression, normal swimming is sufficient and produces a steady swimming velocity. As the heating amplitude is increased, a higher acceleration and faster swimming are achieved through synchronized beating of the cilia, which begin by producing oscillating swimming velocities and later give way to the usual gait. Finally, escape from a life-threatening aggression is achieved by a "jumping" gait, which does not rely on the cilia but is achieved through the explosive release of a group of trichocysts in the direction of the hot spot. Measurements through high-speed video explain the role of trichocysts in defending against aggressions while showing unexpected transitions in the swimming of microorganisms. These measurements also demonstrate that Paramecium optimizes its escape pattern by taking advantage of its inertia.},
author = {Hamel, Amandine and Fisch, Cathy and Combettes, Laurent and Dupuis-Williams, Pascale and Baroud, Charles N},
doi = {10.1073/pnas.1016687108},
file = {:home/fin/Documents/papers/mendeley/Hamel et al.\_2011\_Transitions between three swimming gaits in Paramecium escape.\_Proceedings of the National Academy of Sciences of the.pdf:pdf},
isbn = {1091-6490 (Electronic)$\backslash$r0027-8424 (Linking)},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
pages = {7290--7295},
pmid = {21464291},
title = {{Transitions between three swimming gaits in Paramecium escape.}},
volume = {108},
year = {2011}
}
@article{Fokin2004,
abstract = {Paramecium schewiakoffi sp. nov. is described from a pond in Shanghai, China. It is a freshwater species belonging to the "aurelia" subgroup of the genus. It is of similar size and shape to P. jenningsi, but has a single large micronucleus of the "chromosomal" morphological type, while P. jenningsi has two smaller micronuclei. The general morphology, morphometric characteristics and nuclear reorganization pattern, a random amplified polymorphic DNA (RAPD) fingerprint pattern, and the small subunit rRNA gene sequence are presented for the species. Comparison of P. schewiakoffi with the other species of Paramecium indicates that it is a valid new species of the genus. Geographical locations reported for many Paramecium species do not support the theory that all ciliates have a cosmopolitan distribution. It is proposed that, in an extension of Jankowski's earlier suggestion, the genus Paramecium should be subdivided into four subgenera: Chloroparamecium, Helianter, Cypriostomum and Paramecium, on the basis of morphometric, biological and molecular differences. © 2004 Elsevier GmbH. All rights reserved.},
author = {Fokin, Sergei I. and Przybo\'{s}, Ewa and Chivilev, Sergei M. and Beier, Cora L. and Horn, Matthias and Skotarczak, Bogumila and Wodecka, Beata and Fujishima, Masahiro},
doi = {10.1016/j.ejop.2004.02.001},
file = {:home/fin/Documents/papers/mendeley/Fokin et al.\_2004\_Morphological and molecular investigations of Paramecium schewiakoffi sp. nov. (Ciliophora, Oligohymenophorea) and cur.pdf:pdf},
issn = {09324739},
journal = {Eur. J. Protistol.},
keywords = {Biology,New species,Paramecium schewiakoffi,Paramecium subgenera,Species distribution,Taxonomy},
pages = {225--243},
title = {{Morphological and molecular investigations of Paramecium schewiakoffi sp. nov. (Ciliophora, Oligohymenophorea) and current status of distribution and taxonomy of Paramecium spp.}},
volume = {40},
year = {2004}
}
@article{Loefer1936,
author = {Loefer, John B},
file = {:home/fin/Documents/papers/mendeley/Loefer\_1936\_Bacteria-free culture of Paramecium bursaria and concentration of the medium as a factor in growth\_Journal of Experimental Z.pdf:pdf},
journal = {J. Exp. Zool.},
number = {3},
pages = {387--407},
title = {{Bacteria-free culture of Paramecium bursaria and concentration of the medium as a factor in growth}},
volume = {72},
year = {1936}
}
@article{Kim2015,
author = {Kim, Jong Kyoung and Kolodziejczyk, Aleksandra a. and Illicic, Tomislav and Teichmann, Sarah a. and Marioni, John C.},
doi = {10.1038/ncomms9687},
file = {:home/fin/Documents/papers/mendeley/Kim et al.\_2015\_Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.pdf:pdf},
issn = {2041-1723},
journal = {Nat. Commun.},
number = {May},
pages = {8687},
pmid = {26489834},
title = {{Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression}},
url = {http://www.nature.com/doifinder/10.1038/ncomms9687},
volume = {6},
year = {2015}
}
@article{Preer1997,
author = {{Preer Jr}, John R.},
file = {:home/fin/Documents/papers/mendeley/Preer Jr\_1997\_What Happened to Paramecium Genetics\_Genetics.pdf:pdf},
journal = {Genetics},
number = {2},
pages = {217--225},
title = {{What Happened to Paramecium Genetics}},
volume = {145},
year = {1997}
}
@article{Notredame2000,
abstract = {We describe a new method (T-Coffee) for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most commonly used alternatives. The method is broadly based on the popular progressive approach to multiple alignment but avoids the most serious pitfalls caused by the greedy nature of this algorithm. With T-Coffee we pre-process a data set of all pair-wise alignments between the sequences. This provides us with a library of alignment information that can be used to guide the progressive alignment. Intermediate alignments are then based not only on the sequences to be aligned next but also on how all of the sequences align with each other. This alignment information can be derived from heterogeneous sources such as a mixture of alignment programs and/or structure superposition. Here, we illustrate the power of the approach by using a combination of local and global pair-wise alignments to generate the library. The resulting alignments are significantly more reliable, as determined by comparison with a set of 141 test cases, than any of the popular alternatives that we tried. The improvement, especially clear with the more difficult test cases, is always visible, regardless of the phylogenetic spread of the sequences in the tests.},
author = {Notredame, C and Higgins, D G and Heringa, J},
doi = {10.1006/jmbi.2000.4042},
file = {:home/fin/Documents/papers/mendeley/Notredame, Higgins, Heringa\_2000\_T-Coffee A novel method for fast and accurate multiple sequence alignment.\_Journal of molecular biology.pdf:pdf},
isbn = {0022-2836 (Print)},
issn = {0022-2836},
journal = {J. Mol. Biol.},
keywords = {global alignment,local alignment,multiple sequence alignment,pair-wise alignment,progressive alignment},
pages = {205--217},
pmid = {10964570},
title = {{T-Coffee: A novel method for fast and accurate multiple sequence alignment.}},
volume = {302},
year = {2000}
}
@book{Aho1987,
address = {Boston, MA, USA},
author = {Aho, Alfred V and Kernighan, Brian W and Weinberger, Peter J},
isbn = {0-201-07981-X},
publisher = {Addison-Wesley Longman Publishing Co., Inc.},
title = {{The AWK Programming Language}},
year = {1987}
}
@article{Nei1987,
author = {Nei, Masatoshi},
file = {:home/fin/Documents/papers/mendeley/Nei\_1987\_The Neighbor-joining Method A New Method for Reconstructing Phylogenetic Trees’\_Mol Biol Evol.pdf:pdf},
journal = {Mol Biol Evol},
number = {4},
pages = {406--425},
title = {{The Neighbor-joining Method: A New Method for Reconstructing Phylogenetic Trees’}},
volume = {4},
year = {1987}
}
@article{Monteith2011,
abstract = {Bayesian methods are theoretically optimal in many situations. Bayesian model averaging is generally considered the standard model for creating ensembles of learners using Bayesian methods, but this technique is often out-performed by more ad hoc methods in empirical studies. The reason for this failure has important theoretical implications for our understanding of why ensembles work. It has been proposed that Bayesian model averaging struggles in practice because it accounts for uncertainty about which model is correct but still operates under the assumption that only one of them is. In order to more effectively access the benefits inherent in ensembles, Bayesian strategies should therefore be directed more towards model combination rather than the model selection implicit in Bayesian model averaging. This work provides empirical verification for this hypothesis using several different Bayesian model combination approaches tested on a wide variety of classification problems. We show that even the most simplistic of Bayesian model combination strategies outperforms the traditional ad hoc techniques of bagging and boosting, as well as outperforming BMA over a wide variety of cases. This suggests that the power of ensembles does not come from their ability to account for model uncertainty, but instead comes from the changes in representational and preferential bias inherent in the process of combining several different models.},
author = {Monteith, Kristine and Carroll, James L. and Seppi, Kevin and Martinez, Tony},
doi = {10.1109/IJCNN.2011.6033566},
file = {:home/fin/Documents/papers/mendeley/Monteith et al.\_2011\_Turning Bayesian model averaging into Bayesian model combination\_The 2011 International Joint Conference on Neural.pdf:pdf},
isbn = {978-1-4244-9636-5},
issn = {2161-4393},
journal = {2011 Int. Jt. Conf. Neural Networks},
pages = {2657--2663},
title = {{Turning Bayesian model averaging into Bayesian model combination}},
year = {2011}
}
@misc{DeLano2002,
author = {Delano, W L},
keywords = {model\_building,xtal\_software},
title = {{The PyMOL Molecular Graphics System}},
url = {http://www.pymol.org},
year = {2002}
}
@article{Aronesty2013,
abstract = {High throughput sequencing (HTS) has resulted in extreme growth rates of sequencing data. At our lab, we generate terabytes of data every day. It is usually seen as required for data output to be “cleaned” and processed in various ways prior to use for common tasks such as variant calling, expression quantification and assembly. Two common tasks associated with HTS are adapter trimming and paired-end joining. I have developed two tools at Expression Analysis, Inc. to address these common tasks. The names of these programs are fastq-mcf and fastq-join. I compared the performance of these tools to similar open-source utilities, both in terms of resource efficiency, and effectiveness.},
author = {Aronesty, Erik},
doi = {10.2174/1875036201307010001},
file = {:home/fin/Documents/papers/mendeley/Aronesty\_2013\_Comparison of Sequencing Utility Programs\_The Open Bioinformatics Journal.pdf:pdf},
isbn = {1875-0362},
issn = {18750362},
journal = {Open Bioinforma. J.},
keywords = {clipping,illumina,ngs and next-generation,sequencing,utilities},
pages = {1--8},
title = {{Comparison of Sequencing Utility Programs}},
url = {http://benthamopen.com/openaccess.php?tobioij/articles/V007/1TOBIOIJ.htm$\backslash$nhttps://code.google.com/p/ea-utils/},
volume = {7},
year = {2013}
}
@article{Posada2008,
abstract = {jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" (Guindon and Gascuel 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.). It implements 5 different selection strategies, including "hierarchical and dynamical likelihood ratio tests," the "Akaike information criterion," the "Bayesian information criterion," and a "decision-theoretic performance-based" approach. This program also calculates the relative importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny. jModelTest is written in Java and runs under Mac OSX, Windows, and Unix systems with a Java Runtime Environment installed. The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo.es.},
author = {Posada, David},
doi = {10.1093/molbev/msn083},
file = {:home/fin/Documents/papers/mendeley/Posada\_2008\_jModelTest Phylogenetic Model Averaging\_Molecular Biology and Evolution.pdf:pdf},
isbn = {1537-1719 (Electronic)$\backslash$n0737-4038 (Linking)},
issn = {07374038},
journal = {Mol. Biol. Evol.},
keywords = {1253,1256,2008,25,7,aic,bic,biol,dposada,e-mail,es,evol,likelihood ratio tests,model selection,mol,performance-based selection,statistical phylogenetics,uvigo},
pages = {1253--1256},
pmid = {18397919},
title = {{jModelTest: Phylogenetic Model Averaging}},
url = {http://mbe.oxfordjournals.org/cgi/content/abstract/25/7/1253},
volume = {25},
year = {2008}
}
@article{Lee2002,
abstract = {Previous work has shown that transcription of a number of chloroplast-encoded genes, including those for photosynthesis, are under circadian clock control in Chlamydomonas reinhardtii. However, some of these genes encode long-lived mRNAs that are also subject to translational control. Rates of synthesis of the major chloroplast translation products vary dramatically (10-20-fold) during light-dark (LD) cycles, peaking in the light period. To determine whether this pattern reflects circadian clock control, LD-grown cells were shifted to continuous light (LL) and chloroplast protein synthesis monitored by periodic pulse-labeling in the presence of cycloheximide; chloroplast protein synthesis in LD was also examined for comparison. The LD patterns of synthesis of the major polypeptides (including D1, D2, and the large subunit of ribulose-1,5-bisphosphate carboxylase (LS)) were similar to those obtained previously in the absence of cycloheximide. In the LL condition, rates of synthesis of the major chloroplast translation products were high throughout the period examined ( approximately 36 h), fluctuating > 3-fold, although they were generally higher in the subjective light period. LD-grown cells were also shifted to continuous dark (DD) and chloroplast protein synthesis analyzed for approximately 24 h starting from the mid-dark period. There was a gradual decline in synthesis of the major proteins during the first subjective light period, which was followed by a very small peak in synthesis around the second subjective dark --> light transition. RNA blot analysis showed that the mRNAs for D1, D2 and LS were present at high levels during the period of declining translation. These results indicate that with photoautotrophic growth in LD cycles, the illumination conditions per se are more important than the clock in determining chloroplast translation, but the clock may contribute to this regulation. The advantages of controlling translation by a direct light response and transcription primarily by the circadian clock are discussed. Finally, evidence of translational control of elongation factor Tu synthesis was obtained.},
author = {Lee, Jaesung and Herrin, David L.},
doi = {10.1023/A:1019881306640},
file = {:home/fin/Documents/papers/mendeley/Lee, Herrin\_2002\_Assessing the relative importance of light and the circadian clock in controlling chloroplast translation in Chlamydomo.pdf:pdf},
isbn = {1573-5079 (Electronic)$\backslash$n0166-8595 (Linking)},
issn = {01668595},
journal = {Photosynth. Res.},
keywords = {Chlamydomonas,Chloroplast genes,Circadian clock,Gene regulation,Photosynthesis,Translational control},
number = {Ld},
pages = {295--306},
pmid = {16228528},
title = {{Assessing the relative importance of light and the circadian clock in controlling chloroplast translation in Chlamydomonas reinhardtii}},
volume = {72},
year = {2002}
}
@article{NovakovaLenkaandStepankova2006,
abstract = {The paper reviews those properties of RadViz visualization method [2] mapping data from n dimen- sional space into the planewhich are important for identification of clusters in themultidimensional original data. It uses 2 characteristic examples of datasets which clearly point to a certain drawback of the original RadViz mapping. The identified problemcan be resolved using 2minormodifications of the RadViz algorithmwhich are suggested in the last section of this contribution.},
author = {{Novakova, Lenka and Stepankova}, Olga},
file = {:home/fin/Documents/papers/mendeley/Novakova, Lenka and Stepankova\_2006\_Multidimensional clusters in RadViz\_Proceedings of the 6th WSEAS International Conference on Simulat.pdf:pdf},
journal = {Proc. 6th WSEAS Int. Conf. Simulation, Model. Optim.},
keywords = {Clustering,Data Visualization,Data mining,RadViz},
pages = {470--475},
title = {{Multidimensional clusters in RadViz}},
url = {http://www.wseas.us/e-library/conferences/2006lisbon/papers/517-566.pdf},
year = {2006}
}
@article{Zhou2014,
abstract = {A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/\~{}zhouchan/AST.php.},
author = {Zhou, Chan and Mao, Fenglou and Yin, Yanbin and Huang, Jinling and Gogarten, Johann Peter and Xu, Ying},
doi = {10.1371/journal.pone.0098844},
file = {:home/fin/Documents/papers/mendeley/Zhou et al.\_2014\_AST An automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees\_PLoS ONE.pdf:pdf},
issn = {19326203},
journal = {PLoS One},
number = {6},
pages = {2--10},
pmid = {24892935},
title = {{AST: An automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees}},
volume = {9},
year = {2014}
}
@book{Margulis1998,
address = {New York},
author = {Margulis, Lynn},
edition = {1st},
isbn = {0-465-07271-2},
publisher = {Basic Books},
title = {{The Symbiotic Planet: A New Look At Evolution}},
year = {1998}
}
@article{Picelli2014,
abstract = {Emerging methods for the accurate quantification of gene expression in individual cells hold promise for revealing the extent, function and origins of cell-to-cell variability. Different high-throughput methods for single-cell RNA-seq have been introduced that vary in coverage, sensitivity and multiplexing ability. We recently introduced Smart-seq for transcriptome analysis from single cells, and we subsequently optimized the method for improved sensitivity, accuracy and full-length coverage across transcripts. Here we present a detailed protocol for Smart-seq2 that allows the generation of full-length cDNA and sequencing libraries by using standard reagents. The entire protocol takes ∼2 d from cell picking to having a final library ready for sequencing; sequencing will require an additional 1-3 d depending on the strategy and sequencer. The current limitations are the lack of strand specificity and the inability to detect nonpolyadenylated (polyA(-)) RNA.},
author = {Picelli, Simone and Faridani, Omid R and Bj\"{o}rklund, Asa K and Winberg, G\"{o}sta and Sagasser, Sven and Sandberg, Rickard},
doi = {10.1038/nprot.2014.006},
file = {:home/fin/Documents/papers/mendeley/Picelli et al.\_2014\_Full-length RNA-seq from single cells using Smart-seq2.\_Nature protocols.pdf:pdf},
isbn = {doi:10.1038/nprot.2014.006},
issn = {1750-2799},
journal = {Nat. Protoc.},
number = {1},
pages = {171--81},
pmid = {24385147},
title = {{Full-length RNA-seq from single cells using Smart-seq2.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24385147},
volume = {9},
year = {2014}
}
@article{Horton2006,
abstract = {We present a new program for predicting protein subcellular localization from amino acid sequence. WoLF PSORT is a major update to the PSORTII program, based on new sequence data and incorporating new features with a feature selection procedure. Following SWISS-PROT, we divided eukaryotes into three groups: fungi, plant, and animal. For the 2113 fungi proteins divided into 14 categories; we found that, combined with BLAST,WoLF PSORT yields a cross-validated accuracy of 83\%, eliminating about 1/3 of the errors made when using BLAST alone. For 12771 animal proteins a combined accuracy of 95.6\% is obtained, eliminating 1/4 of BLAST alone errors, and for 2333 plant proteins the accuracy can be improved to 86\% from 84\%. 1.},
author = {Horton, P and Park, Kj and Obayashi, T and Nakai, K},
doi = {10.1142/9781860947292\_0007},
file = {:home/fin/Documents/papers/mendeley/Horton et al.\_2006\_Protein Subcellular Localisation Prediction with WoLF PSORT.\_Ser Adv Bioinform.pdf:pdf},
isbn = {9781860946233},
journal = {Ser Adv Bioinform},
pages = {39--48},
title = {{Protein Subcellular Localisation Prediction with WoLF PSORT.}},
url = {http://scholar.google.com/scholar?hl=en\&btnG=Search\&q=intitle:Protein+subcellular+localization+prediction+with+wolf+psort\#0},
volume = {3},
year = {2006}
}
@article{Zhang2015,
author = {Zhang, Qingpeng and Awad, Sherine and Brown, Charles},
doi = {10.7287/peerj.preprints.890v1},
file = {:home/fin/Documents/papers/mendeley/Zhang, Awad, Brown\_2015\_Crossing the streams a framework for streaming analysis of short DNA sequencing reads PrePrints analysis of sho.pdf:pdf},
issn = {2167-9843},
pages = {0--27},
title = {{Crossing the streams : a framework for streaming analysis of short DNA sequencing reads PrePrints analysis of short DNA sequencing reads PrePrints}},
year = {2015}
}
@article{Kreutz2012,
author = {Kreutz, M. and Stoeck, T. and Foissner, W.},
doi = {10.1111/j.1550-7408.2012.00638.x.Morphological},
file = {:home/fin/Documents/papers/mendeley/Kreutz, Stoeck, Foissner\_2012\_Morphological and Molecular Characterization of Paramecium (Viridoparamecium nov. subgen.) chlorelligerum.pdf:pdf},
journal = {J. Eukaryot. Microbiol.},
keywords = {biodiversity,chloroparamecium,germany,meyerella,oligohymenophora,simmelried},
number = {6},
title = {{Morphological and Molecular Characterization of Paramecium (Viridoparamecium nov. subgen.) chlorelligerum Kahl, 1935 (Ciliophora)}},
volume = {59},
year = {2012}
}
@article{Beisson2010,
author = {Beisson, Janine and B\'{e}termier, Mireille and Br\'{e}, Marie-H\'{e}l\`{e}ne and Cohen, Jean and Duharcourt, Sandra and Duret, Laurent and Kung, Ching and Malinsky, Sophie and Meyer, Eric and Preer, John R and Sperling, Linda},
doi = {10.1101/pdb.prot5363},
file = {:home/fin/Documents/papers/mendeley/Beisson et al.\_2010\_Silencing specific Paramecium tetraurelia genes by feeding double-stranded RNA.\_CSH protocols.pdf:pdf},
issn = {1559-6095},
journal = {CSH Protoc.},
number = {1},
pages = {pdb.prot5363},
pmid = {20150122},
title = {{Silencing specific Paramecium tetraurelia genes by feeding double-stranded RNA.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20150122},
volume = {2010},
year = {2010}
}
@article{Macmanes2015,
author = {Macmanes, Matthew D},
doi = {10.1101/020123},
file = {:home/fin/Documents/papers/mendeley/Macmanes\_2015\_Optimizing error correction of RNAseq reads\_bioRxiv preprint.pdf:pdf},
journal = {bioRxiv Prepr.},
pages = {1--4},
title = {{Optimizing error correction of RNAseq reads}},
year = {2015}
}
@article{Ronquist2003a,
author = {Ronquist, F. and Huelsenbeck, J. P.},
doi = {10.1093/bioinformatics/btg180},
file = {:home/fin/Documents/papers/mendeley/Ronquist, Huelsenbeck\_2003\_MrBayes 3 Bayesian phylogenetic inference under mixed models\_Bioinformatics(2).pdf:pdf},
issn = {1367-4803},
journal = {Bioinformatics},
number = {12},
pages = {1572--1574},
title = {{MrBayes 3: Bayesian phylogenetic inference under mixed models}},
url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btg180},
volume = {19},
year = {2003}
}
@book{NationalCenterforBiotechnologyInformation2011,
author = {{National Center for Biotechnology Information}},
title = {{SRA Knowledge Base}},
url = {http://www.ncbi.nlm.nih.gov/books/NBK158900/},
year = {2011}
}
@incollection{Hoshina2009,
author = {Hoshina, Ryo and Imamura, Nobutaka},
booktitle = {Endosymbionts in Paramecium},
chapter = {1},
doi = {10.1007/978-3-540-92677-1},
editor = {Fujishima, Masahiro},
file = {:home/fin/Documents/papers/mendeley/Hoshina, Imamura\_2009\_Origins of Algal Symbionts of Paramecium bursaria\_Endosymbionts in Paramecium.pdf:pdf},
isbn = {978-3-540-92676-4},
pages = {2--29},
publisher = {Springer},
series = {Microbiology Monographs 12},
title = {{Origins of Algal Symbionts of Paramecium bursaria}},
url = {http://link.springer.com/10.1007/978-3-540-92677-1},
volume = {12},
year = {2009}
}
@article{Freund1997,
abstract = {In the first part of the paper we consider the problem of dynamically apportioning resources among a set of options in a worst-case on-line framework. The model we study can be interpreted as a broad, abstract extension of the well-studied on-line prediction model to a general decision-theoretic setting. We show that the multiplicative weight-update Littlestone–Warmuth rule can be adapted to this model, yielding bounds that are slightly weaker in some cases, but applicable to a considerably more general class of learning problems. We show how the resulting learning algorithm can be applied to a variety of problems, including gambling, multiple-outcome prediction, repeated games, and prediction of points in Rn. In the second part of the paper we apply the multiplicative weight-update technique to derive a new boosting algorithm. This boosting algorithm does not require any prior knowledge about the performance of the weak learning algorithm. We also study generalizations of the new boosting algorithm to the problem of learning functions whose range, rather than being binary, is an arbitrary finite set or a bounded segment of the real line.},
author = {Freund, Yoav and Schapire, Robert E},
doi = {10.1006/jcss.1997.1504},
file = {:home/fin/Documents/papers/mendeley/Freund, Schapire\_1997\_A Decision-Theoretic Generalization of On-Line Learning and an Application to Boosting\_Journal of Computer and Sys.pdf:pdf},
isbn = {3540591192},
issn = {00220000},
journal = {J. Comput. Syst. Sci.},
pages = {119--139},
pmid = {10394},
title = {{A Decision-Theoretic Generalization of On-Line Learning and an Application to Boosting}},
url = {http://www.sciencedirect.com/science/article/pii/S002200009791504X},
volume = {55},
year = {1997}
}
@article{Stocking1959,
author = {Stocking, C.R. and {Gifford Jr.}, E.M.},
file = {:home/fin/Documents/papers/mendeley/Stocking, Gifford Jr.\_1959\_Incorporation of thymidine into chloroplats of Spirogyra\_Biochemical and Biophysical Research Communications.pdf:pdf},
journal = {Biochem. Biophys. Res. Commun.},
number = {3},
pages = {159--164},
title = {{Incorporation of thymidine into chloroplats of Spirogyra}},
volume = {1},
year = {1959}
}
@article{Carthew2009,
abstract = {Over the last decade, ∼20−30 nucleotide RNA molecules have emerged as critical regulators in the expression and function of eukaryotic genomes. Two primary categories of these small RNAs— short interfering RNAs (siRNAs) and microRNAs (miRNAs)—act in both somatic and germline line-ages in a broad range of eukaryotic species to regulate endogenous genes and to defend the genome from invasive nucleic acids. Recent advances have revealed unexpected diversity in their biogenesis pathways and the regulatory mechanisms that they access. Our understanding of siRNA- and miRNA-based regulation has direct implications for fundamental biology as well as disease etiology and treatment.},
author = {Carthew, Richard W. and Sontheimer, Erik J},
doi = {10.1016/j.cell.2009.01.035.Origins},
file = {:home/fin/Documents/papers/mendeley/Carthew, Sontheimer\_2009\_Origins and Mechanisms of miRNAs and siRNAs\_Cell.pdf:pdf},
isbn = {1097-4172 (Electronic)$\backslash$r0092-8674 (Linking)},
issn = {00928674},
journal = {Cell},
number = {4},
pages = {642--655},
pmid = {19239886},
publisher = {Elsevier Inc.},
title = {{Origins and Mechanisms of miRNAs and siRNAs}},
url = {http://dx.doi.org/10.1016/j.cell.2009.01.035},
volume = {136},
year = {2009}
}
@article{Price2010,
abstract = {BACKGROUND: We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacrificing scalability. METHODOLOGY/PRINCIPAL FINDINGS: Where FastTree 1 used nearest-neighbor interchanges (NNIs) and the minimum-evolution criterion to improve the tree, FastTree 2 adds minimum-evolution subtree-pruning-regrafting (SPRs) and maximum-likelihood NNIs. FastTree 2 uses heuristics to restrict the search for better trees and estimates a rate of evolution for each site (the "CAT" approximation). Nevertheless, for both simulated and genuine alignments, FastTree 2 is slightly more accurate than a standard implementation of maximum-likelihood NNIs (PhyML 3 with default settings). Although FastTree 2 is not quite as accurate as methods that use maximum-likelihood SPRs, most of the splits that disagree are poorly supported, and for large alignments, FastTree 2 is 100-1,000 times faster. FastTree 2 inferred a topology and likelihood-based local support values for 237,882 distinct 16S ribosomal RNAs on a desktop computer in 22 hours and 5.8 gigabytes of memory. CONCLUSIONS/SIGNIFICANCE: FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments. FastTree 2 is freely available at http://www.microbesonline.org/fasttree.},
author = {Price, Morgan N and Dehal, Paramvir S and Arkin, Adam P},
doi = {10.1371/journal.pone.0009490},
file = {:home/fin/Documents/papers/mendeley/Price, Dehal, Arkin\_2010\_FastTree 2 -- approximately maximum-likelihood trees for large alignments.\_PLoS One.pdf:pdf},
issn = {1932-6203},
journal = {PLoS One},
keywords = {16S,16S: genetics,Algorithms,Animals,Computers,Data Interpretation,Databases,Genetic,Genetic Techniques,Humans,Likelihood Functions,Models,Phylogeny,Protein,RNA,Ribosomal,Sequence Alignment,Sequence Alignment: methods,Software,Statistical},
month = jan,
number = {3},
pages = {e9490},
pmid = {20224823},
title = {{FastTree 2 -- approximately maximum-likelihood trees for large alignments.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2835736\&tool=pmcentrez\&rendertype=abstract},
volume = {5},
year = {2010}
}
@article{Kodama2011a,
abstract = {Treatment of symbiotic alga-bearing Paramecium bursaria cells with a protein synthesis inhibitor, cycloheximide, induces synchronous swelling of all perialgal vacuoles at about 24h after treatment under a constant light condition. Subsequently, the vacuoles detach from the host cell cortex. The algae in the vacuoles are digested by the host's lysosomal fusion to the vacuoles. To elucidate the timing of algal degeneration, P. bursaria cells were treated with cycloheximide under a constant light condition. Then the cells were observed using transmission electron microscopy. Results show that algal chloroplasts and nuclei degenerated within 9h after treatment, but before the synchronous swelling of the perialgal vacuole and appearance of acid phosphatase activity in the perialgal vacuole by lysosomal fusion. Treatment with cycloheximide under a constant dark condition and treatment with chloramphenicol under a constant light condition induced neither synchronous swelling of the vacuoles nor digestion of the algae inside the vacuoles. These results demonstrate that algal proteins synthesized during photosynthesis are necessary to maintain chloroplastic and nuclear structures, and that inhibition of protein synthesis induces rapid lysis of these organelles, after which synchronous swelling of the perialgal vacuole and fusion occur with the host lysosomes.},
author = {Kodama, Yuuki and Inouye, Isao and Fujishima, Masahiro},
doi = {10.1016/j.protis.2010.06.005},
file = {:home/fin/Documents/papers/mendeley/Kodama, Inouye, Fujishima\_2011\_Symbiotic Chlorella vulgaris of the ciliate Paramecium bursaria plays an important role in maintaining pe.pdf:pdf},
issn = {1618-0941},
journal = {Protist},
keywords = {Cell Nucleus,Cell Nucleus: drug effects,Cell Nucleus: metabolism,Chlorella vulgaris,Chlorella vulgaris: drug effects,Chlorella vulgaris: physiology,Chloroplasts,Chloroplasts: drug effects,Chloroplasts: metabolism,Cycloheximide,Cycloheximide: pharmacology,Lysosomes,Lysosomes: drug effects,Lysosomes: metabolism,Paramecium,Paramecium: drug effects,Paramecium: physiology,Photosynthesis,Photosynthesis: drug effects,Protein Biosynthesis,Protein Biosynthesis: drug effects,Symbiosis,Vacuoles,Vacuoles: drug effects,Vacuoles: metabolism},
month = apr,
number = {2},
pages = {288--303},
pmid = {20884291},
publisher = {Elsevier GmbH.},
title = {{Symbiotic Chlorella vulgaris of the ciliate Paramecium bursaria plays an important role in maintaining perialgal vacuole membrane functions.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20884291},
volume = {162},
year = {2011}
}
@article{Yang2012,
abstract = {Phylogenies are important for addressing various biological questions such as relationships among species or genes, the origin and spread of viral infection and the demographic changes and migration patterns of species. The advancement of sequencing technologies has taken phylogenetic analysis to a new height. Phylogenies have permeated nearly every branch of biology, and the plethora of phylogenetic methods and software packages that are now available may seem daunting to an experimental biologist. Here, we review the major methods of phylogenetic analysis, including parsimony, distance, likelihood and Bayesian methods. We discuss their strengths and weaknesses and provide guidance for their use.},
author = {Yang, Ziheng and Rannala, Bruce},
doi = {10.1038/nrg3186},
file = {:home/fin/Documents/papers/mendeley/Yang, Rannala\_2012\_Molecular phylogenetics principles and practice\_Nature Reviews Genetics.pdf:pdf},
isbn = {1471-0064 (Electronic)$\backslash$r1471-0056 (Linking)},
issn = {1471-0056},
journal = {Nat. Rev. Genet.},
number = {May},
pages = {303--314},
pmid = {22456349},
publisher = {Nature Publishing Group},
title = {{Molecular phylogenetics: principles and practice}},
url = {http://dx.doi.org/10.1038/nrg3186},
volume = {13},
year = {2012}
}
@article{Keeling2008,
author = {Keeling, Patrick J. and Archibald, John M.},
doi = {10.1016/j.cub.2008.02.059},
file = {:home/fin/Documents/papers/mendeley/Keeling, Archibald\_2008\_Organelle Evolution What's in a Name\_Current Biology.pdf:pdf},
issn = {09609822},
journal = {Curr. Biol.},
pages = {1896--1899},
pmid = {18430635},
title = {{Organelle Evolution: What's in a Name?}},
volume = {18},
year = {2008}
}
@article{Pfanner2001,
annote = {10.1038/35073006},
author = {Pfanner, Nikolaus and Geissler, Andreas},
issn = {1471-0072},
journal = {Nat Rev Mol Cell Biol},
month = may,
number = {5},
pages = {339--349},
publisher = {Nature Publishing Group},
title = {{Versatility of the mitochondrial protein import machinery}},
url = {http://dx.doi.org/10.1038/35073006},
volume = {2},
year = {2001}
}
@article{Sauer1986,
author = {Sauer, N},
file = {:home/fin/Documents/papers/mendeley/Sauer\_1986\_Hexose-transport-deficient mutants of Chlorella vulgaris\_Planta.pdf:pdf},
journal = {Planta},
keywords = {- transport,a -,a n s p,amino acid t r,c h l o,chlorella,hexose transport - mutant,o r t -,r e l l},
pages = {139--144},
title = {{Hexose-transport-deficient mutants of Chlorella vulgaris}},
volume = {168},
year = {1986}
}
@article{Duret2008,
author = {Duret, Laurent and Cohen, Jean and Jubin, Claire and Dessen, Philippe and Go\^{u}t, Jean-fran\c{c}ois and Mousset, Sylvain and Jaillon, Olivier and No\"{e}l, Benjamin and Arnaiz, Olivier and B\'{e}termier, Mireille and Wincker, Patrick and Meyer, Eric and Aury, Jean-marc},
doi = {10.1101/gr.074534.107},
file = {:home/fin/Documents/papers/mendeley/Duret et al.\_2008\_Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia A somatic view of the germline\_Gen.pdf:pdf},
isbn = {1088-9051 (Print)},
journal = {Genome Res.},
pages = {585--596},
title = {{Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia : A somatic view of the germline}},
volume = {18},
year = {2008}
}
@article{Rees1995,
abstract = {A malachite green colorimetric assay for glutamine synthetase is described. Glutamine synthetase activity was determined in situ in the marine diatom Phaeodactylum tricornutum Bohlin using cells permeabilized by freeze/thawing. Higher activities were obtained with cells permeabilized in N-2-hydroxyethylpiperazine-N[prime]-2-ethanesulfonic acid compared with N-tris(hydroxymethyl)methyl-3-aminopropanesulfonic acid, tris(hydroxymethyl)aminomethane, or imidazole, and the optimum pH was 7.9. Activities were higher in cells permeabilized in the presence of reductant, particularly dithiothreitol. Glutamine synthetase activities were markedly decreased in the presence of methionine sulfoximine. In the presence of saturating concentrations of glutamate and ATP, the apparent Km for ammonia was 320 [mu]M, but this value decreased to 110 [mu]M with subsaturating concentrations of glutamate and ATP. The apparent Km values for glutamate and ATP, in the presence of saturating concentrations of ammonia, were 9.7 and 2.9 mM, respectively. Ammonia-grown cells had lower glutamine synthetase activities than did nitrate-grown cells. During nitrogen starvation of both ammonia- and nitrate-grown cells, glutamine synthetase activities increased rapidly during the first 8 h, reaching maximum values after 24 to 48 h. Moreover, the time course for the increases in glutamine synthetase activities and rate of methylamine uptake following the transfer of nitrate-grown cells to nitrogen-deficient medium were very similar. In nitrate-grown cells and cells deprived of combined nitrogen, glutamine synthetase activities and maximum rates of ammonia uptake gave comparable values when measured at the same temperature (20[deg]C).},
author = {Rees, Tav. and Larson, T. R. and Heldens, Jwg. and Huning, Fgj.},
doi = {109/4/1405 [pii]},
file = {:home/fin/Documents/papers/mendeley/Rees et al.\_1995\_In Situ Glutamine Synthetase Activity in a Marine Unicellular Alga (Development of a Sensitive Colorimetric Assay and t.pdf:pdf},
isbn = {1532-2548 (Electronic)$\backslash$r0032-0889 (Linking)},
issn = {1532-2548},
journal = {Plant Physiol.},
number = {1 995},
pages = {1405--1410},
pmid = {12228676},
title = {{In Situ Glutamine Synthetase Activity in a Marine Unicellular Alga (Development of a Sensitive Colorimetric Assay and the Effects of Nitrogen Status on Enzyme Activity).}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=157675\&tool=pmcentrez\&rendertype=abstract},
volume = {109},
year = {1995}
}
@article{Xiong2012,
abstract = {BACKGROUND: The ciliated protozoan Tetrahymena thermophila is a well-studied single-celled eukaryote model organism for cellular and molecular biology. However, the lack of extensive T. thermophila cDNA libraries or a large expressed sequence tag (EST) database limited the quality of the original genome annotation.$\backslash$n$\backslash$nMETHODOLOGY/PRINCIPAL FINDINGS: This RNA-seq study describes the first deep sequencing analysis of the T. thermophila transcriptome during the three major stages of the life cycle: growth, starvation and conjugation. Uniquely mapped reads covered more than 96\% of the 24,725 predicted gene models in the somatic genome. More than 1,000 new transcribed regions were identified. The great dynamic range of RNA-seq allowed detection of a nearly six order-of-magnitude range of measurable gene expression orchestrated by this cell. RNA-seq also allowed the first prediction of transcript untranslated regions (UTRs) and an updated (larger) size estimate of the T. thermophila transcriptome: 57 Mb, or about 55\% of the somatic genome. Our study identified nearly 1,500 alternative splicing (AS) events distributed over 5.2\% of T. thermophila genes. This percentage represents a two order-of-magnitude increase over previous EST-based estimates in Tetrahymena. Evidence of stage-specific regulation of alternative splicing was also obtained. Finally, our study allowed us to completely confirm about 26.8\% of the genes originally predicted by the gene finder, to correct coding sequence boundaries and intron-exon junctions for about a third, and to reassign microarray probes and correct earlier microarray data.$\backslash$n$\backslash$nCONCLUSIONS/SIGNIFICANCE: RNA-seq data significantly improve the genome annotation and provide a fully comprehensive view of the global transcriptome of T. thermophila. To our knowledge, 5.2\% of T. thermophila genes with AS is the highest percentage of genes showing AS reported in a unicellular eukaryote. Tetrahymena thus becomes an excellent unicellular model eukaryote in which to investigate mechanisms of alternative splicing.},
author = {Xiong, Jie and Lu, Xingyi and Zhou, Zhemin and Chang, Yue and Yuan, Dongxia and Tian, Miao and Zhou, Zhigang and Wang, Lei and Fu, Chengjie and Orias, Eduardo and Miao, Wei},
doi = {10.1371/journal.pone.0030630},
file = {:home/fin/Documents/papers/mendeley/Xiong et al.\_2012\_Transcriptome analysis of the model protozoan, tetrahymena thermophila, using deep RNA sequencing\_PLoS ONE.pdf:pdf},
issn = {19326203},
journal = {PLoS One},
number = {2},
pages = {1--13},
pmid = {22347391},
title = {{Transcriptome analysis of the model protozoan, tetrahymena thermophila, using deep RNA sequencing}},
volume = {7},
year = {2012}
}
@article{Kato2008,
author = {Kato, Yutaka and Imamura, Nobutaka},
doi = {10.1016/j.plantsci.2007.10.001},
file = {:home/fin/Documents/papers/mendeley/Kato, Imamura\_2008\_Effect of calcium ion on uptake of amino acids by symbiotic Chlorella F36-ZK isolated from Japanese Paramecium bursar.pdf:pdf},
issn = {01689452},
journal = {Plant Sci.},
keywords = {amino acid transport,calcium,chlorella,divalent cation,paramecium bursaria,symbiosis},
month = jan,
number = {1},
pages = {88--96},
title = {{Effect of calcium ion on uptake of amino acids by symbiotic Chlorella F36-ZK isolated from Japanese Paramecium bursaria}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0168945207002713},
volume = {174},
year = {2008}
}
@article{Domman2015,
author = {Domman, Daryl and Horn, Matthias and Embley, T Martin and Williams, Tom a},
doi = {10.1038/ncomms7421},
file = {:home/fin/Documents/papers/mendeley/Domman et al.\_2015\_Plastid establishment did not require a chlamydial partner\_Nature Communications.pdf:pdf},
journal = {Nat. Commun.},
pages = {1--8},
publisher = {Nature Publishing Group},
title = {{Plastid establishment did not require a chlamydial partner}},
url = {http://dx.doi.org/10.1038/ncomms7421},
volume = {6},
year = {2015}
}
@article{Wald1949,
author = {Wald, Abraham},
file = {:home/fin/Documents/papers/mendeley/Wald\_1949\_Note on the consistency of the maximum likelihood estimate\_Annals of Mathematical Statistics.pdf:pdf},
journal = {Ann. Math. Stat.},
pages = {595--601},
title = {{Note on the consistency of the maximum likelihood estimate}},
volume = {20},
year = {1949}
}
@article{Li2015a,
abstract = {Summary: MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252 Gbps in 44.1 and 99.6 h on a single computing node with and without a graphics processing unit, respectively. MEGAHIT assembles the data as a whole, i.e. no pre-processing like partitioning and normalization was needed. When compared with previous methods on assembling the soil data, MEGAHIT generated a three-time larger assembly, with longer contig N50 and average contig length; furthermore, 55.8\% of the reads were aligned to the assembly, giving a fourfold improvement. Availability and implementation: The source code of MEGAHIT is freely available at https://github.com/voutcn/megahit under GPLv3 license. Contact: rb@l3-bioinfo.com or twlam@cs.hku.hk Supplementary information: Supplementary data are available at Bioinformatics online.},
archivePrefix = {arXiv},
arxivId = {1401.7457},
author = {Li, D. and Liu, C.-M. and Luo, R. and Sadakane, K. and Lam, T.-W.},
doi = {10.1093/bioinformatics/btv033},
eprint = {1401.7457},
file = {:home/fin/Documents/papers/mendeley/Li et al.\_2015\_MEGAHIT An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph\_Bioin.pdf:pdf},
isbn = {1367-4803},
issn = {1367-4803},
journal = {Bioinformatics},
number = {January},
pages = {btv033--},
pmid = {25609793},
title = {{MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph}},
url = {http://bioinformatics.oxfordjournals.org/content/early/2015/02/18/bioinformatics.btv033.abstract?papetoc},
volume = {31},
year = {2015}
}
@incollection{Sommaruga2009,
author = {Sommaruga, Ruben and Sonntag, Bettina},
booktitle = {Endosymbionts in Paramecium},
chapter = {5},
doi = {10.1007/978-3-540-92677-1},
editor = {Fujishima, Masahiro},
file = {:home/fin/Documents/papers/mendeley/Sommaruga, Sonntag\_2009\_Photobiological Aspects of the Mutualistic Association Between Paramecium bursaria and Chlorella\_Endosymbionts i.pdf:pdf},
isbn = {978-3-540-92676-4},
pages = {111--130},
publisher = {Springer},
series = {Microbiology Monographs},
title = {{Photobiological Aspects of the Mutualistic Association Between Paramecium bursaria and Chlorella}},
url = {http://link.springer.com/10.1007/978-3-540-92677-1},
volume = {12},
year = {2009}
}
@article{Fang2011,
abstract = {A reductionistic approach to science, epitomized by molecular biology, is often contrasted with the holistic approach of systems biology. However, molecular biology and systems biology are actually interdependent and complementary ways in which to study and make sense of complex phenomena.},
author = {Fang, Ferric C. and Casadevall, Arturo},
doi = {10.1128/IAI.01343-10},
file = {:home/fin/Documents/papers/mendeley/Fang, Casadevall\_2011\_Reductionistic and holistic science\_Infection and Immunity.pdf:pdf},
issn = {00199567},
journal = {Infect. Immun.},
number = {4},
pages = {1401--1404},
pmid = {21321076},
title = {{Reductionistic and holistic science}},
volume = {79},
year = {2011}
}
@article{Zhang1996,
abstract = {Finding useful patterns in large datasets has attracted considerable interest recently, and one of the most widely studied problems in this area is the identification of clusters, or densely populated regions, in a multi-dimensional dataset. Prior work does not adequately address the problem of large datasets and minimization of I/O costs.This paper presents a data clustering method named BIRCH (Balanced Iterative Reducing and Clustering using Hierarchies), and demonstrates that it is especially suitable for very large databases. BIRCH incrementally and dynamically clusters incoming multi-dimensional metric data points to try to produce the best quality clustering with the available resources (i.e., available memory and time constraints). BIRCH can typically find a good clustering with a single scan of the data, and improve the quality further with a few additional scans. BIRCH is also the first clustering algorithm proposed in the database area to handle "noise" (data points that are not part of the underlying pattern) effectively.We evaluate BIRCH's time/space efficiency, data input order sensitivity, and clustering quality through several experiments. We also present a performance comparisons of BIRCH versus CLARANS, a clustering method proposed recently for large datasets, and show that BIRCH is consistently superior.},
author = {Zhang, Tian and Ramakrishnan, Raghu and Livny, Miron},
doi = {10.1145/233269.233324},
file = {:home/fin/Documents/papers/mendeley/Zhang, Ramakrishnan, Livny\_1996\_BIRCH An Efficient Data Clustering Databases Method for Very Large\_ACM SIGMOD International Conference o.pdf:pdf},
isbn = {0897917944},
issn = {01635808},
journal = {ACM SIGMOD Int. Conf. Manag. Data},
keywords = {BIRCH,Hierarchical clustering,large databases},
pages = {103--114},
title = {{BIRCH: An Efficient Data Clustering Databases Method for Very Large}},
volume = {1},
year = {1996}
}
@electronic{fastqc2015,
author = {Andrews, S},
booktitle = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/},
keywords = {bioinformatics,ngs,qc},
title = {{FastQC: A Quality Control tool for High Throughput Sequence Data}},
url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/},
year = {2015}
}
@article{Wang2009,
abstract = {RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes. RNA-Seq also provides a far more precise measurement of levels of transcripts and their isoforms than other methods. This article describes the RNA-Seq approach, the challenges associated with its application, and the advances made so far in characterizing several eukaryote transcriptomes.},
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Wang, Zhong and Gerstein, Mark and Snyder, Michael},
doi = {10.1038/nrg2484},
eprint = {NIHMS150003},
file = {:home/fin/Documents/papers/mendeley/Wang, Gerstein, Snyder\_2009\_RNA-Seq a revolutionary tool for transcriptomics.\_Nature reviews. Genetics.pdf:pdf},
isbn = {1471-0064 (Electronic)$\backslash$r1471-0056 (Linking)},
issn = {1471-0056},
journal = {Nat. Rev. Genet.},
pages = {57--63},
pmid = {19015660},
title = {{RNA-Seq: a revolutionary tool for transcriptomics.}},
volume = {10},
year = {2009}
}
@article{Lei2014,
author = {Lei, Rex and Ye, Kaixiong and Gu, Zhenglong and Sun, Xuepeng},
doi = {10.1016/j.gene.2014.12.013},
file = {:home/fin/Documents/papers/mendeley/Lei et al.\_2014\_Diminishing returns in next-generation sequencing (NGS) transcriptome data\_Gene.pdf:pdf},
issn = {03781119},
journal = {Gene},
keywords = {RNA-seq efficiency,rna-seq ef fi ciency},
month = dec,
number = {1},
pages = {82--87},
publisher = {Elsevier B.V.},
title = {{Diminishing returns in next-generation sequencing (NGS) transcriptome data}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0378111914013869},
volume = {557},
year = {2014}
}
@book{Huygens,
address = {The Hague},
author = {Huygens, Christiaan},
editor = {Nijhoff, Martinus},
pages = {1, 90--93},
publisher = {Dutch Society of Sciences},
title = {{\OE uvres compl\`{e}tes de Christiaan Huygens, Correspondances Volume VII: 1676-1684}},
year = {1899}
}
@article{Tindall1988,
author = {Tindall, K.R. and Kunkel, T.A.},
file = {:home/fin/Documents/papers/mendeley/Tindall, Kunkel\_1988\_Fidelity of DNA Synthesis by the Thermus aquaticus DNA Polymerase\_Biochemistry.pdf:pdf},
journal = {Biochemistry},
pages = {6008--6013},
title = {{Fidelity of DNA Synthesis by the Thermus aquaticus DNA Polymerase}},
volume = {27},
year = {1988}
}
@article{Alneberg2014,
abstract = {Shotgun sequencing enables the reconstruction of genomes from complex microbial communities, but because assembly does not reconstruct entire genomes, it is necessary to bin genome fragments. Here we present CONCOCT, a new algorithm that combines sequence composition and coverage across multiple samples, to automatically cluster contigs into genomes. We demonstrate high recall and precision on artificial as well as real human gut metagenome data sets.},
author = {Alneberg, Johannes and Bjarnason, Brynjar Sm\'{a}ri and de Bruijn, Ino and Schirmer, Melanie and Quick, Joshua and Ijaz, Umer Z and Lahti, Leo and Loman, Nicholas J and Andersson, Anders F and Quince, Christopher},
doi = {10.1038/nmeth.3103},
file = {:home/fin/Documents/papers/mendeley/Alneberg et al.\_2014\_Binning metagenomic contigs by coverage and composition\_Nature Methods.pdf:pdf},
isbn = {1548-7105 (Electronic)
1548-7091 (Linking)},