text:
3,
author = {Looso, Mario and Preussner, Jens and Sousounis, Konstantinos and Bruckskotten, Marc and Michel, Christian S and Lignelli, Ettore and Reinhardt, Richard and H\"{o}ffner, Sabrina and Kr\"{u}ger, Marcus and Tsonis, Panagiotis a and Borchardt, Thilo and Braun, Thomas},
doi = {10.1186/gb-2013-14-2-r16},
file = {:home/fin/Documents/papers/mendeley/Looso et al.\_2013\_A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expres.pdf:pdf},
issn = {1465-6906},
journal = {Genome Biol.},
number = {2},
pages = {R16},
publisher = {BioMed Central Ltd},
title = {{A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration}},
url = {http://genomebiology.com/content/14/2/R16},
volume = {14},
year = {2013}
}
@article{Thorne1991,
abstract = {Most algorithms for the alignment of biological sequences are not derived from an evolutionary model. Consequently, these alignment algorithms lack a strong statistical basis. A maximum likelihood method for the alignment of two DNA sequences is presented. This method is based upon a statistical model of DNA sequence evolution for which we have obtained explicit transition probabilities. The evolutionary model can also be used as the basis of procedures that estimate the evolutionary parameters relevant to a pair of unaligned DNA sequences. A parameter-estimation approach which takes into account all possible alignments between two sequences is introduced; the danger of estimating evolutionary parameters from a single alignment is discussed.},
author = {Thorne, Jeffrey L. and Kishino, Hirohisa and Felsenstein, Joseph},
doi = {10.1007/BF02193625},
file = {:home/fin/Documents/papers/mendeley/Thorne, Kishino, Felsenstein\_1991\_An evolutionary model for maximum likelihood alignment of DNA sequences\_Journal of Molecular Evolution.pdf:pdf},
isbn = {0022-2844 (Print)$\backslash$n0022-2844 (Linking)},
issn = {00222844},
journal = {J. Mol. Evol.},
keywords = {DNA sequence alignment,Dynamic programming,Evolutionary model,Insertion-deletion model,Maximum likelihood procedure},
pages = {114--124},
pmid = {1920447},
title = {{An evolutionary model for maximum likelihood alignment of DNA sequences}},
volume = {33},
year = {1991}
}
@article{Tateno2002,
abstract = {The DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) has made an effort to collect as much data as possible mainly from Japanese researchers. The increase rates of the data we collected, annotated and released to the public in the past year are 43\% for the number of entries and 52\% for the number of bases. The increase rates are accelerated even after the human genome was sequenced, because sequencing technology has been remarkably advanced and simplified, and research in life science has been shifted from the gene scale to the genome scale. In addition, we have developed the Genome Information Broker (GIB, http://gib.genes.nig.ac.jp) that now includes more than 50 complete microbial genome and Arabidopsis genome data. We have also developed a database of the human genome, the Human Genomics Studio (HGS, http://studio.nig.ac.jp). HGS provides one with a set of sequences being as continuous as possible in any one of the 24 chromosomes. Both GIB and HGS have been updated incorporating newly available data and retrieval tools.},
author = {Tateno, Y and Imanishi, T and Miyazaki, S and Fukami-Kobayashi, K and Saitou, N and Sugawara, H and Gojobori, T},
doi = {10.1093/nar/30.1.27},
file = {:home/fin/Documents/papers/mendeley/Tateno et al.\_2002\_DNA Data Bank of Japan (DDBJ) for genome scale research in life science.\_Nucleic acids research.pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$r0305-1048 (Linking)},
issn = {1362-4962},
journal = {Nucleic Acids Res.},
number = {1},
pages = {27--30},
pmid = {11752245},
title = {{DNA Data Bank of Japan (DDBJ) for genome scale research in life science.}},
volume = {30},
year = {2002}
}
@article{Gabrielsen2011,
abstract = {The dinoflagellates have repeatedly replaced their ancestral peridinin-plastid by plastids derived from a variety of algal lineages ranging from green algae to diatoms. Here, we have characterized the genome of a dinoflagellate plastid of tertiary origin in order to understand the evolutionary processes that have shaped the organelle since it was acquired as a symbiont cell. To address this, the genome of the haptophyte-derived plastid in Karlodinium veneficum was analyzed by Sanger sequencing of library clones and 454 pyrosequencing of plastid enriched DNA fractions. The sequences were assembled into a single contig of 143 kb, encoding 70 proteins, 3 rRNAs and a nearly full set of tRNAs. Comparative genomics revealed massive rearrangements and gene losses compared to the haptophyte plastid; only a small fraction of the gene clusters usually found in haptophytes as well as other types of plastids are present in K. veneficum. Despite the reduced number of genes, the K. veneficum plastid genome has retained a large size due to expanded intergenic regions. Some of the plastid genes are highly diverged and may be pseudogenes or subject to RNA editing. Gene losses and rearrangements are also features of the genomes of the peridinin-containing plastids, apicomplexa and Chromera, suggesting that the evolutionary processes that once shaped these plastids have occurred at multiple independent occasions over the history of the Alveolata.},
author = {Gabrielsen, Tove M. and Minge, Marianne a. and Espelund, Mari and Tooming-Klunderud, Ave and Patil, Vishwanath and Nederbragt, Alexander J. and Otis, Christian and Turmel, Monique and Shalchian-Tabrizi, Kamran and Lemieux, Claude and Jakobsen, Kjetill S.},
doi = {10.1371/journal.pone.0019132},
file = {:home/fin/Documents/papers/mendeley/Gabrielsen et al.\_2011\_Genome evolution of a tertiary dinoflagellate plastid\_PLoS ONE.pdf:pdf},
isbn = {1932-6203 (Electronic)$\backslash$r1932-6203 (Linking)},
issn = {19326203},
journal = {PLoS One},
number = {4},
pmid = {21541332},
title = {{Genome evolution of a tertiary dinoflagellate plastid}},
volume = {6},
year = {2011}
}
@book{shihira1965chlorella,
author = {Shihira, Ikuko and Krauss, Robert Wallfar},
publisher = {University of Maryland},
title = {{Chlorella: physiology and taxonomy of forty-one isolates}},
year = {1965}
}
@incollection{Schrallhammer2009,
author = {Schrallhammer, Martina and Schweikert, Michael},
booktitle = {Endosymbionts in Paramecium},
chapter = {9},
doi = {10.1007/978-3-540-92677-1},
editor = {Fujishima, Masahiro},
file = {:home/fin/Documents/papers/mendeley/Schrallhammer, Schweikert\_2009\_The Killer Effect of Paramecium and Its Causative Agents\_Endosymbionts in Paramecium.pdf:pdf},
isbn = {978-3-540-92676-4},
pages = {227--246},
publisher = {Springer},
series = {Microbiology Monographs},
title = {{The Killer Effect of Paramecium and Its Causative Agents}},
url = {http://link.springer.com/10.1007/978-3-540-92677-1},
volume = {12},
year = {2009}
}
@article{Archibald2012,
author = {Archibald, John M.},
doi = {10.1016/j.cub.2011.12.003},
file = {:home/fin/Documents/papers/mendeley/Archibald\_2012\_Lynn Margulis (1938–2011)\_Current Biology.pdf:pdf},
issn = {09609822},
journal = {Curr. Biol.},
month = jan,
number = {1},
pages = {R4--R6},
publisher = {Elsevier},
title = {{Lynn Margulis (1938–2011)}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0960982211013753},
volume = {22},
year = {2012}
}
@article{weis1984effect,
author = {Weis, D S},
institution = {SOC PROTOZOOLOGISTS 810 E 10TH ST, LAWRENCE, KS 66044},
journal = {J. Protozool.},
number = {4},
pages = {A13----A14},
title = {{The Effect of Accumulated Time of Separate Cultivation on the Frequency of Infection of Aposymbiotic Ciliates by Symbiotic Algae in Paramebium bursaria}},
volume = {31},
year = {1984}
}
@incollection{Fujishima2009,
author = {Fujishima, Masahiro},
booktitle = {Endosymbionts in Paramecium},
chapter = {8},
doi = {10.1007/978-3-540-92677-1},
editor = {Fujishima, Masahiro},
file = {:home/fin/Documents/papers/mendeley/Fujishima\_2009\_Infection and Maintenance of Holospora Species in Paramecium caudatum\_Endosymbionts in Paramecium.pdf:pdf},
isbn = {978-3-540-92676-4},
pages = {201--225},
publisher = {Springer},
series = {Microbiology Monographs},
title = {{Infection and Maintenance of Holospora Species in Paramecium caudatum}},
url = {http://link.springer.com/10.1007/978-3-540-92677-1},
volume = {12},
year = {2009}
}
@article{Kuper2010,
abstract = {ATP synthase catalyzes ATP synthesis at the expense of an electrochemical ion gradient across a membrane that can be generated by different exergonic reactions. Sulfur reduction is the main energy-yielding reaction in the hyperthermophilic strictly anaerobic Crenarchaeon Ignicoccus hospitalis. This organism is unusual in having an inner and an outer membrane that are separated by a huge intermembrane compartment. Here we show, on the basis of immuno-EM analyses of ultrathin sections and immunofluorescence experiments with whole I. hospitalis cells, that the ATP synthase and H(2):sulfur oxidoreductase complexes of this organism are located in the outer membrane. These two enzyme complexes are mandatory for the generation of an electrochemical gradient and for ATP synthesis. Thus, among all prokaryotes possessing two membranes in their cell envelope (including Planctomycetes, gram-negative bacteria), I. hospitalis is a unique organism, with an energized outer membrane and ATP synthesis within the periplasmic space. In addition, DAPI staining and EM analyses showed that DNA and ribosomes are localized in the cytoplasm, leading to the conclusion that in I. hospitalis energy conservation is separated from information processing and protein biosynthesis. This raises questions regarding the function of the two membranes, the interaction between these compartments, and the general definition of a cytoplasmic membrane.},
author = {K\"{u}per, Ulf and Meyer, Carolin and M\"{u}ller, Volker and Rachel, Reinhard and Huber, Harald},
doi = {10.1073/pnas.0911711107},
file = {:home/fin/Documents/papers/mendeley/K\"{u}per et al.\_2010\_Energized outer membrane and spatial separation of metabolic processes in the hyperthermophilic Archaeon Ignicoccus h.pdf:pdf},
isbn = {0027-8424},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
pages = {3152--3156},
pmid = {20133662},
title = {{Energized outer membrane and spatial separation of metabolic processes in the hyperthermophilic Archaeon Ignicoccus hospitalis.}},
volume = {107},
year = {2010}
}
@article{Sanger1977a,
abstract = {A new method for determining nucleotide sequences in DNA is described. It is similar to the "plus and minus" method [Sanger, F. \& Coulson, A. R. (1975) J. Mol. Biol. 94, 441-448] but makes use of the 2',3'-dideoxy and arabinonucleoside analogues of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase. The technique has been applied to the DNA of bacteriophage varphiX174 and is more rapid and more accurate than either the plus or the minus method.},
author = {Sanger, F and Nicklen, S and Coulson, a R},
doi = {10.1073/pnas.74.12.5463},
file = {:home/fin/Documents/papers/mendeley/Sanger, Nicklen, Coulson\_1977\_DNA sequencing with chain-terminating inhibitors.\_Proceedings of the National Academy of Sciences of the U.pdf:pdf},
isbn = {0027-8424 (Print)$\backslash$r0027-8424 (Linking)},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
number = {12},
pages = {5463--5467},
pmid = {271968},
title = {{DNA sequencing with chain-terminating inhibitors.}},
volume = {74},
year = {1977}
}
@article{Parker1926,
author = {Parker, Raymond C.},
doi = {10.1002/jez.1400460102},
file = {:home/fin/Documents/papers/mendeley/Parker\_1926\_Symbiosis in Paramecium bursaria\_Journal of Experimental Zoology.pdf:pdf},
issn = {0022-104X},
journal = {J. Exp. Zool.},
month = aug,
number = {1},
pages = {1--12},
title = {{Symbiosis in Paramecium bursaria}},
url = {http://doi.wiley.com/10.1002/jez.1400460102},
volume = {46},
year = {1926}
}
@article{Hirsch1992,
abstract = {Many legumes respond to Rhizobium inoculation by developing unique structures known as nodules on their roots. The development of a legume nodule in which rhizobia convert atmospheric N.j into ammonia is a finely tuned process. Gene expression from both partners of the symbiosis must be temporally and spatially coordinated. Exactly how this coordination takes place is an area of intense study. Nodule morphogenesis appears to be elicited by at least two distinct signals: one from Rhizobium, a product of the nod genes (Nod factor), and a second signal, which is generated within plant tissues after treatment with Nod factor. The identity of the second signal is unknown but changes in the balance of endogenous plant hormones or the sensitivity of plant tissues to these hormones are likely to be involved. These hormonal changes may be triggered by endogenous flavonoids produced by the root in response to inoculation with Rhizobium. There is some controversy as to whether the legume nodule is an organ sui generis or a highly derived lateral root. A resolution of this question may become more critical as attempts to induce nodules on non-legume hosts, such as rice or maize, increase in number and scope.},
author = {Hirsch, Annm Am},
doi = {10.1111/j.1469-8137.1992.tb04227.x},
file = {:home/fin/Documents/papers/mendeley/Hirsch\_1992\_Developmental biology of legume nodulation\_New phytologist.pdf:pdf},
isbn = {0028-646X},
issn = {0028-646X},
journal = {New Phytol.},
keywords = {development,flavonoids,lectin,legume nodulation,rhizobium},
number = {40},
pages = {211--237},
title = {{Developmental biology of legume nodulation}},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.1992.tb04227.x/pdf$\backslash$nhttp://www.jstor.org/stable/10.2307/2557483},
year = {1992}
}
@book{Wickham2009,
author = {Wickham, Hadley},
isbn = {978-0-387-98140-6},
publisher = {Springer New York},
title = {ggplot2: elegant graphics for data analysis},
url = {http://had.co.nz/ggplot2/book},
year = {2009}
}
@article{Zhou2010,
abstract = {Heterotachy, the variation of substitution rate at a site across time, is a prevalent phenomenon in nucleotide and amino acid alignments, which may mislead probabilistic-based phylogenetic inferences. The covarion model is a special case of heterotachy, in which sites change between the "ON" state (allowing substitutions according to any particular model of sequence evolution) and the "OFF" state (prohibiting substitutions). In current implementations, the switch rates between ON and OFF states are homogeneous across sites, a hypothesis that has never been tested. In this study, we developed an infinite mixture model, called the covarion mixture (CM) model, which allows the covarion parameters to vary across sites, controlled by a Dirichlet process prior. Moreover, we combine the CM model with other approaches. We use a second independent Dirichlet process that models the heterogeneities of amino acid equilibrium frequencies across sites, known as the CAT model, and general rate-across-site heterogeneity is modeled by a gamma distribution. The application of the CM model to several large alignments demonstrates that the covarion parameters are significantly heterogeneous across sites. We describe posterior predictive discrepancy tests and use these to demonstrate the importance of these different elements of the models.},
author = {Zhou, Yan and Brinkmann, Henner and Rodrigue, Nicolas and Lartillot, Nicolas and Philippe, Herv\'{e}},
doi = {10.1093/molbev/msp248},
file = {:home/fin/Documents/papers/mendeley/Zhou et al.\_2010\_A dirichlet process covarion mixture model and its assessments using posterior predictive discrepancy tests\_Molecular B.pdf:pdf},
isbn = {1537-1719 (Electronic)$\backslash$n0737-4038 (Linking)},
issn = {07374038},
journal = {Mol. Biol. Evol.},
keywords = {Covarion,Heterotachy,Model violations,Phylogenetics,Posterior predictive discrepancy},
number = {2},
pages = {371--384},
pmid = {19822637},
title = {{A dirichlet process covarion mixture model and its assessments using posterior predictive discrepancy tests}},
volume = {27},
year = {2010}
}
@article{Garcia-Cuetos2012,
abstract = {We provide a detailed study of four marine Mesodinium species and compare the data to the companion article on Mesodinium chamaeleon and other available studies on Mesodinium, to shed some light on the taxonomy of the genus. Micrographs of two red phototrophic Mesodinium species, Mesodinium rubrum and Mesodinium major n. sp., as well as the first published micrographs of two heterotrophic species, M. pulex and M. pupula are presented in combination with molecular analyses based on the ribosomal genes. The main conclusion of this study is the invalidity of the genus Myrionecta based on the arrangements of the basal bodies forming the cirri and the separation of species formerly known as M. rubrum resulting in an emended description of M. rubrum and the description of a related new species M. major n. sp.},
author = {Garcia-Cuetos, Lydia and Moestrup, Ojvind and Hansen, Per J.},
doi = {10.1111/j.1550-7408.2012.00630.x},
file = {:home/fin/Documents/papers/mendeley/Garcia-Cuetos, Moestrup, Hansen\_2012\_Studies on the genus mesodinium II. Ultrastructural and molecular investigations of five marine spe.pdf:pdf},
isbn = {1066-5234},
issn = {10665234},
journal = {J. Eukaryot. Microbiol.},
keywords = {Ciliate,Mesodinium,Myrionecta,Phylogeny,Ultrastructure},
number = {4},
pages = {374--400},
pmid = {22708786},
title = {{Studies on the genus mesodinium II. Ultrastructural and molecular investigations of five marine species help clarifying the taxonomy}},
volume = {59},
year = {2012}
}
@article{Pop2009,
abstract = {Research into genome assembly algorithms has experienced a resurgence due to new challenges created by the development of next generation sequencing technologies. Several genome assemblers have been published in recent years specifically targeted at the new sequence data; however, the ever-changing technological landscape leads to the need for continued research. In addition, the low cost of next generation sequencing data has led to an increased use of sequencing in new settings. For example, the new field of metagenomics relies on large-scale sequencing of entire microbial communities instead of isolate genomes, leading to new computational challenges. In this article, we outline the major algorithmic approaches for genome assembly and describe recent developments in this domain.},
author = {Pop, Mihai},
doi = {10.1093/bib/bbp026},
file = {:home/fin/Documents/papers/mendeley/Pop\_2009\_Genome assembly reborn Recent computational challenges\_Briefings in Bioinformatics.pdf:pdf},
isbn = {1477-4054 (Electronic)$\backslash$n1467-5463 (Linking)},
issn = {14675463},
journal = {Brief. Bioinform.},
keywords = {Genome assembly,Genome sequencing,Next generation sequencing technologies},
number = {4},
pages = {354--366},
pmid = {19482960},
title = {{Genome assembly reborn: Recent computational challenges}},
volume = {10},
year = {2009}
}
@article{Brown1974,
author = {Brown, Jack a and Nielsen, P. James},
file = {:home/fin/Documents/papers/mendeley/Brown, Nielsen\_1974\_Transfer of photosynthetically produced carbohydrate from endosymbiotic chlorellae to Paramecium bursaria\_Journal of.pdf:pdf},
journal = {J. Protozool.},
pages = {569--570},
title = {{Transfer of photosynthetically produced carbohydrate from endosymbiotic chlorellae to Paramecium bursaria}},
volume = {21},
year = {1974}
}
@article{Elbashir2001,
abstract = {Duplexes of 21-23 nucleotide (nt) RNAs are the sequence-specific mediators of RNA interference (RNAi) and post-transcriptional gene silencing (PTGS). Synthetic, short interfering RNAs (siRNAs) were examined in Drosophila melanogaster embryo lysate for their requirements regarding length, structure, chemical composition and sequence in order to mediate efficient RNAi. Duplexes of 21 nt siRNAs with 2 nt 3' overhangs were the most efficient triggers of sequence-specific mRNA degradation. Substitution of one or both siRNA strands by 2'-deoxy or 2'-O-methyl oligonucleotides abolished RNAi, although multiple 2'-deoxynucleotide substitutions at the 3' end of siRNAs were tolerated. The target recognition process is highly sequence specific, but not all positions of a siRNA contribute equally to target recognition; mismatches in the centre of the siRNA duplex prevent target RNA cleavage. The position of the cleavage site in the target RNA is defined by the 5' end of the guide siRNA rather than its 3' end. These results provide a rational basis for the design of siRNAs in future gene targeting experiments.},
author = {Elbashir, S. M. and Martinez, J. and Patkaniowska, a. and Lendeckel, W. and Tuschl, T.},
doi = {10.1093/emboj/20.23.6877},
file = {:home/fin/Documents/papers/mendeley/Elbashir et al.\_2001\_Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate\_EMBO Journal.pdf:pdf},
isbn = {doi:10.1093/emboj/20.23.6877},
issn = {02614189},
journal = {EMBO J.},
keywords = {PTGS,RNA interference,Small interfering RNA},
number = {23},
pages = {6877--6888},
pmid = {11726523},
title = {{Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate}},
volume = {20},
year = {2001}
}
@article{Maguire2014a,
abstract = {Shared derived genomic characters can be useful for polarizing phylogenetic relationships, for example, gene fusions have been used to identify deep-branching relationships in the eukaryotes. Here, we report the evolutionary analysis of a three-gene fusion of folB, folK, and folP, which encode enzymes that catalyze consecutive steps in de novo folate biosynthesis. The folK-folP fusion was found across the eukaryotes and a sparse collection of prokaryotes. This suggests an ancient derivation with a number of gene losses in the eukaryotes potentially as a consequence of adaptation to heterotrophic lifestyles. In contrast, the folB-folK-folP gene is specific to a mosaic collection of Amorphea taxa (a group encompassing: Amoebozoa, Apusomonadida, Breviatea, and Opisthokonta). Next, we investigated the stability of this character. We identified numerous gene losses and a total of nine gene fission events, either by break up of an open reading frame (four events identified) or loss of a component domain (five events identified). This indicates that this three gene fusion is highly labile. These data are consistent with a growing body of data indicating gene fission events occur at high relative rates. Accounting for these sources of homoplasy, our data suggest that the folB-folK-folP gene fusion was present in the last common ancestor of Amoebozoa and Opisthokonta but absent in the Metazoa including the human genome. Comparative genomic data of these genes provides an important resource for designing therapeutic strategies targeting the de novo folate biosynthesis pathway of a variety of eukaryotic pathogens such as Acanthamoeba castellanii.},
author = {Maguire, Finlay and Henriquez, Fiona L and Leonard, Guy and Dacks, Joel B and Brown, Matthew W and Richards, Thomas a},
doi = {10.1093/gbe/evu213},
file = {:home/fin/Documents/papers/mendeley/Maguire et al.\_2014\_Complex patterns of gene fission in the eukaryotic folate biosynthesis pathway.\_Genome biology and evolution.pdf:pdf},
isbn = {1759-6653},
issn = {1759-6653},
journal = {Genome Biol. Evol.},
keywords = {comparative genomics,diaphoretickes,phylogenetics,pterin biosynthesis},
number = {10},
pages = {2709--20},
pmid = {25252772},
title = {{Complex patterns of gene fission in the eukaryotic folate biosynthesis pathway.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25252772},
volume = {6},
year = {2014}
}
@article{Hadfield2014,
abstract = {The availability of massive amounts of DNA sequence data, from 1000s of genomes even in a single project has had a huge impact on our understanding of biology, but also creates several problems for biologists carrying out those experiments. Bioinformatic analysis of sequence data is perhaps the most obvious challenge but upstream of this even basic quality control of sequence run performance is challenging for many users given the volume of data. Users need to be able to assess run quality efficiently so that only high-quality data are passed through to computationally-, financially-, and time-intensive processes. There is a clear need to make human review of sequence data as efficient as possible. The multi-genome alignment tool presented here presents next-generation sequencing run data in visual and tabular formats simplifying assessment of run yield and quality, as well as presenting some sample-based quality metrics and screening for contamination from adapter sequences and species other than the one being sequenced.},
author = {Hadfield, James and Eldridge, Matthew D.},
doi = {10.3389/fgene.2014.00031},
file = {:home/fin/Documents/papers/mendeley/Hadfield, Eldridge\_2014\_Multi-genome alignment for quality control and contamination screening of next-generation sequencing data\_Fronti.pdf:pdf},
isbn = {1664-8021 (Electronic)
1664-8021 (Linking)},
issn = {16648021},
journal = {Front. Genet.},
keywords = {Contamination screen,Next-generation sequencing,Quality control},
number = {February},
pages = {5--8},
pmid = {24600470},
title = {{Multi-genome alignment for quality control and contamination screening of next-generation sequencing data}},
volume = {5},
year = {2014}
}
@book{cooper2013the,
address = {Sunderland, MA},
author = {Cooper, Geoffrey},
isbn = {978-0-87893-964-0},
publisher = {Sinauer Associates},
title = {{The cell : a molecular approach}},
year = {2013}
}
@book{Wilson1928,
address = {New York},
author = {Wilson, E.B.},
edition = {3rd Revise},
publisher = {Garland Publishing},
title = {{The Cell in Development and Heredity}},
year = {1928}
}
@article{Wernegreen2012,
abstract = {The phenomenon of endosymbiosis, or one organism living within another, has deeply impacted the evolution of life and continues to shape the ecology of countless species. Traditionally, biologists have viewed evolution as a largely bifurcating pattern, reflecting mutations and other changes in existing genetic information and the occasional speciation and divergence of lineages. While lineage bifurcation has clearly been important in evolution, the merging of two lineages through endosymbiosis has also made profound contributions to evolutionary novelty. Mitochondria and chloroplasts are relicts of ancient bacterial endosymbionts that ultimately extended the range of acceptable habitats for life by allowing hosts to thrive in the presence of oxygen and to convert light into energy. Today, the sheer abundance of endosymbiotic relationships across diverse host lineages and habitats testifies to their continued significance. © 2012 Elsevier Ltd.},
author = {Wernegreen, Jennifer J.},
doi = {10.1016/j.cub.2012.06.010},
file = {:home/fin/Documents/papers/mendeley/Wernegreen\_2012\_Endosymbiosis\_Current Biology.pdf:pdf},
issn = {09609822},
journal = {Curr. Biol.},
pages = {555--561},
pmid = {22835786},
title = {{Endosymbiosis}},
volume = {22},
year = {2012}
}
@article{Soneson2013a,
abstract = {BACKGROUND: Finding genes that are differentially expressed between conditions is an integral part of understanding the molecular basis of phenotypic variation. In the past decades, DNA microarrays have been used extensively to quantify the abundance of mRNA corresponding to different genes, and more recently high-throughput sequencing of cDNA (RNA-seq) has emerged as a powerful competitor. As the cost of sequencing decreases, it is conceivable that the use of RNA-seq for differential expression analysis will increase rapidly. To exploit the possibilities and address the challenges posed by this relatively new type of data, a number of software packages have been developed especially for differential expression analysis of RNA-seq data.

RESULTS: We conducted an extensive comparison of eleven methods for differential expression analysis of RNA-seq data. All methods are freely available within the R framework and take as input a matrix of counts, i.e. the number of reads mapping to each genomic feature of interest in each of a number of samples. We evaluate the methods based on both simulated data and real RNA-seq data.

CONCLUSIONS: Very small sample sizes, which are still common in RNA-seq experiments, impose problems for all evaluated methods and any results obtained under such conditions should be interpreted with caution. For larger sample sizes, the methods combining a variance-stabilizing transformation with the 'limma' method for differential expression analysis perform well under many different conditions, as does the nonparametric SAMseq method.},
author = {Soneson, Charlotte and Delorenzi, Mauro},
doi = {10.1186/1471-2105-14-91},
file = {:home/fin/Documents/papers/mendeley/Soneson, Delorenzi\_2013\_A comparison of methods for differential expression analysis of RNA-seq data.\_BMC bioinformatics.pdf:pdf},
issn = {1471-2105},
journal = {BMC Bioinformatics},
keywords = {Animals,DNA, Complementary,DNA, Complementary: genetics,Gene Expression Profiling,Gene Expression Profiling: methods,Genome,Genomics,Genomics: methods,Mice,Mice, Inbred C57BL,Mice, Inbred DBA,RNA, Messenger,RNA, Messenger: metabolism,Sequence Analysis, RNA,Software},
month = jan,
number = {1},
pages = {91},
pmid = {23497356},
publisher = {BMC Bioinformatics},
title = {{A comparison of methods for differential expression analysis of RNA-seq data.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3608160\&tool=pmcentrez\&rendertype=abstract},
volume = {14},
year = {2013}
}
@article{Zdobnov2001,
abstract = {InterProScan is a tool that scans given protein sequences against the protein signatures of the InterPro member databases, currently--PROSITE, PRINTS, Pfam, ProDom and SMART. The number of signature databases and their associated scanning tools as well as the further refinement procedures make the problem complex. InterProScan is designed to be a scalable and extensible system with a robust internal architecture. AVAILABILITY: The Perl-based InterProScan implementation is available from the EBI ftp server (ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/) and the SRS-basedInterProScan is available upon request. We provide the public web interface (http://www.ebi.ac.uk/interpro/scan.html) as well as email submission server (interproscan@ebi.ac.uk).},
author = {Zdobnov, E M and Apweiler, R},
doi = {10.1093/bioinformatics/17.9.847},
file = {:home/fin/Documents/papers/mendeley/Zdobnov, Apweiler\_2001\_InterProScan--an integration platform for the signature-recognition methods in InterPro.\_Bioinformatics (Oxford,.pdf:pdf},
isbn = {1367-4803 (Print)$\backslash$n1367-4803 (Linking)},
issn = {1367-4803},
journal = {Bioinformatics},
number = {9},
pages = {847--848},
pmid = {11590104},
title = {{InterProScan--an integration platform for the signature-recognition methods in InterPro.}},
url = {http://bioinformatics.oxfordjournals.org/content/17/9/847.short},
volume = {17},
year = {2001}
}
@article{Hoffmeister2003,
abstract = {Microbial symbioses are interesting in their own right and also serve as exemplary models to help biologists to understand two important symbioses in the evolutionary past of eukaryotic cells: the origins of chloroplasts and mitochondria. Most, if not all, microbial symbioses have a chemical basis: compounds produced by one partner are useful for the other. But symbioses can also entail the transfer of genes from one partner to the other, which in some cases cements two cells into a bipartite, co-evolving unit. Here, we discuss some microbial symbioses in which progress is being made in uncovering the nature of symbiotic interactions: anaerobic methane-oxidizing consortia, marine worms that possess endosymbionts instead of a digestive tract, amino acid-producing endosymbionts of aphids, prokaryotic endosymbionts living within a prokaryotic host within mealybugs, endosymbionts of an insect vector of human disease and a photosynthetic sea slug that steals chloroplasts from algae. In the case of chloroplasts and mitochondria, examples of recent and ancient gene transfer to the chromosomes of their host cell illustrate the process of genetic merger in the wake of organelle origins.},
author = {Hoffmeister, Meike and Martin, William},
doi = {10.1046/j.1462-2920.2003.00454.x},
file = {:home/fin/Documents/papers/mendeley/Hoffmeister, Martin\_2003\_Interspecific evolution microbial symbiosis, endosymbiosis and gene transfer.\_Environmental microbiology.pdf:pdf},
isbn = {1462-2912},
issn = {1462-2912},
journal = {Environ. Microbiol.},
keywords = {Animals,Archaea,Archaea: physiology,Bacterial,Bacterial Physiological Phenomena,Biological Evolution,Chlorophyta,Chlorophyta: genetics,Chlorophyta: physiology,Chlorophyta: ultrastructure,Chloroplasts,Chloroplasts: physiology,Gene Transfer,Genes,Horizontal,Invertebrates,Invertebrates: genetics,Invertebrates: microbiology,Invertebrates: physiology,Mitochondria,Mitochondria: physiology,Symbiosis},
pages = {641--9},
pmid = {12871231},
title = {{Interspecific evolution: microbial symbiosis, endosymbiosis and gene transfer.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12871231},
volume = {5},
year = {2003}
}
@article{Peralta2011,
author = {Peralta, Humberto and Guerrero, Gabriela and Aguilar, Alejandro and Mora, Jaime},
doi = {10.1186/1745-6150-6-48},
file = {:home/fin/Documents/papers/mendeley/Peralta et al.\_2011\_Sequence variability of Rhizobiales orthologs and relationship with physico-chemical characteristics of proteins\_Bio.pdf:pdf},
issn = {1745-6150},
journal = {Biol. Direct},
keywords = {adaptation,comparative genomics,evolutionary rates,nonsynonymous substitution,rhizobia},
number = {1},
pages = {48},
publisher = {BioMed Central Ltd},
title = {{Sequence variability of Rhizobiales orthologs and relationship with physico-chemical characteristics of proteins}},
url = {http://www.biology-direct.com/content/6/1/48},
volume = {6},
year = {2011}
}
@article{Moriya2007a,
author = {Moriya, Y. and Itoh, M. and Okuda, S. and Yoshizawa, a. C. and Kanehisa, M.},
doi = {10.1093/nar/gkm321},
file = {:home/fin/Documents/papers/mendeley/Moriya et al.\_2007\_KAAS an automatic genome annotation and pathway reconstruction server\_Nucleic Acids Research.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
pages = {W182--W185},
title = {{KAAS: an automatic genome annotation and pathway reconstruction server}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkm321},
volume = {35},
year = {2007}
}
@article{Raikov1995,
author = {Raikov, I.B.},
file = {:home/fin/Documents/papers/mendeley/Raikov\_1995\_Structure and Genetic Organization of the Polyploid Macronucleus of Ciliates a Comparative Review\_Acta Protozoologica.pdf:pdf},
journal = {Acta Protozool.},
pages = {151--171},
title = {{Structure and Genetic Organization of the Polyploid Macronucleus of Ciliates: a Comparative Review}},
volume = {34},
year = {1995}
}
@article{vonDohlen2001,
author = {von Dohlen, Carol D and Kohler, Shawn and Alsop, Skylar T and McManus, William R},
file = {:home/fin/Documents/papers/mendeley/von Dohlen et al.\_2001\_Mealybug $\beta$-proteobacterial endosymbionts contain $\gamma$-proteobacterial symbionts\_Nature.pdf:pdf},
journal = {Nature},
number = {July},
pages = {433--436},
title = {{Mealybug $\beta$-proteobacterial endosymbionts contain $\gamma$-proteobacterial symbionts}},
volume = {412},
year = {2001}
}
@article{Gerhard2004,
abstract = {The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5'-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline.},
author = {Gerhard, Daniela S. and Wagner, Lukas and Feingold, Elise a. and Shenmen, Carolyn M. and Grouse, Lynette H. and Schuler, Greg and Klein, Steven L. and Old, Susan and Rasooly, Rebekah and Good, Peter and Guyer, Mark and Peck, Allison M. and Derge, Jeffery G. and Lipman, David and Collins, Francis S. and Jang, Wonhee and Sherry, Steven and Feolo, Mike and Misquitta, Leonie and Lee, Eduardo and Rotmistrovsky, Kirill and Greenhut, Susan F. and Schaefer, Carl F. and Buetow, Kenneth H. and Bonner, Tom I. and Haussler, David and Kent, Jim and Diekhans, Mark and Furey, Terry and Brent, Michael and Prange, Christa and Schreiber, Kirsten and Shapiro, Nicole and Bhat, Narayan K. and Hopkins, Ralph F. and Hsie, Florence and Driscoll, Tom and Soares, M. Bento and Bonaldo, Maria F. and Casavant, Tom L. and Scheetz, Todd E. and Brownstein, Michael J. and Usdin, Ted B. and Toshiyuki, Shiraki and Carninci, Piero and Piao, Yulan and Dudekula, Dawood B. and Ko, Minoru S H and Kawakami, Koichi and Suzuki, Yutaka and Sugano, Sumio and Gruber, C. E. and Smith, M. R. and Simmons, Blake and Moore, Troy and Waterman, Richard and Johnson, Stephen L. and Ruan, Yijun and {Lin Wei}, Chia and Mathavan, S. and Gunaratne, Preethi H. and Wu, Jiaqian and Garcia, Angela M. and Hulyk, Stephen W. and Fuh, Edwin and Yuan, Ye and Sneed, Anna and Kowis, Carla and Hodgson, Anne and Muzny, Donna M. and McPherson, John and Gibbs, Richard a. and Fahey, Jessica and Helton, Erin and Ketteman, Mark and Madan, Anuradha and Rodrigues, Stephanie and Sanchez, Amy and Whiting, Michelle and Madan, Anup and Young, Alice C. and Wetherby, Keith D. and Granite, Steven J. and Kwong, Peggy N. and Brinkley, Charles P. and Pearson, Russell L. and Bouffard, Gerard G. and Blakesly, Robert W. and Green, Eric D. and Dickson, Mark C. and Rodriguez, Alex C. and Grimwood, Jane and Schmutz, Jeremy and Myers, Richard M. and Butterfield, Yaron S N and Griffith, Malachi and Griffith, Obi L. and Krzywinski, Martin I. and Liao, Nancy and Morrin, Ryan and Palmquist, Diana and Petrescu, Anca S. and Skalska, Ursula and Smailus, Duane E. and Stott, Jeff M. and Schnerch, Angelique and Schein, Jacqueline E. and Jones, Steven J M and Holt, Robert a. and Baross, Agnes and Marra, Marco a. and Clifton, Sandra and Makowski, Kathryn a. and Bosak, Stephanie and Malek, Joel},
doi = {10.1101/gr.2596504},
file = {:home/fin/Documents/papers/mendeley/Gerhard et al.\_2004\_The status, quality, and expansion of the NIH full-length cDNA project The Mammalian Gene Collection (MGC)\_Genome Re.pdf:pdf},
isbn = {1088-9051 (Print) 1088-9051 (Linking)},
issn = {10889051},
journal = {Genome Res.},
pages = {2121--2127},
pmid = {15489334},
title = {{The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC)}},
volume = {14},
year = {2004}
}
@article{Tonooka2002,
abstract = {Paramecium bursaria contains hundreds of algae in its cytoplasm as symbionts and retains them over many generations. Recently, aposymbiotic cells of P. bursaria were collected from a pond. To know whether the natural aposymbiotic strain (Ysa2) lost ability to associate with algae, infection experiments were performed using symbiotic algae isolated from green paramecia. Results showed that Ysa2 establish symbiotic association in the same way as artificially obtained aposymbiotic cells (control). However, clustered algae appeared in some Ysa2 cells after infection. Algal clusters differ in number and size from cell to cell. Isolation line culture was performed to pursue the fate of cells having algal clusters. Within several cell divisions, some descendants retained large clusters and such cells were sometimes misshapen, ceasing proliferation and eventually dying. At cell division of cluster-bearing cells, unequal distribution of clustered algae occurred because many algal clusters tend to locate in the posterior of the host cell. Most extremely, all algae were distributed to the posterior daughter cell, whereas the anterior daughter cell contained no algae. This is one possible mechanism of production of Ysa2 in nature. From these results, we conclude that Ysa2 can make symbiotic association with potentially symbiotic algae, but they have some incompatibilities with the algae.},
author = {Tonooka, Yuki and Watanabe, Tsuyoshi},
doi = {10.1078/0932-4739-00846},
file = {:home/fin/Documents/papers/mendeley/Tonooka, Watanabe\_2002\_A natural strain of Paramecium bursaria lacking symbiotic algae\_European Journal of Protistology.pdf:pdf},
isbn = {09324739},
issn = {09324739},
journal = {Eur. J. Protistol.},
keywords = {algae,infection,paramecium bursaria,symbiosis},
pages = {55--58},
title = {{A natural strain of Paramecium bursaria lacking symbiotic algae}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0932473904700486},
volume = {38},
year = {2002}
}
@article{Achilles-Day2013,
abstract = {Using Paramecium bursaria as a model organism improved protocols have been developed to isolate clonal endosymbiotic algae. This involved micromanipulation of individual protists, rupturing to release endosymbionts followed by enrichment on complex media and a series of plating steps, under low light (PAR \~{}10$\mu$mol photons m(-2)s(-1)).},
author = {Achilles-Day, Undine E M and Day, John G},
doi = {10.1016/j.mimet.2013.01.007},
file = {:home/fin/Documents/papers/mendeley/Achilles-Day, Day\_2013\_Isolation of clonal cultures of endosymbiotic green algae from their ciliate hosts.\_Journal of Microbiological Me.pdf:pdf},
issn = {1872-8359},
journal = {J. Microbiol. Methods},
keywords = {Chlorophyta,Chlorophyta: physiology,Microbiological Techniques,Microbiological Techniques: methods,Paramecium,Paramecium: microbiology,Symbiosis},
month = mar,
number = {3},
pages = {355--7},
pmid = {23337811},
publisher = {Elsevier B.V.},
title = {{Isolation of clonal cultures of endosymbiotic green algae from their ciliate hosts.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23337811},
volume = {92},
year = {2013}
}
@article{Imanian2007,
abstract = {Mitochondria and plastids originated through endosymbiosis, and subsequently became reduced and integrated with the host in similar ways. Plastids spread between lineages through further secondary or even tertiary endosymbioses, but mitochondria appear to have originated once and have not spread between lineages. Mitochondria are also generally lost in secondary and tertiary endosymbionts, with the single exception of the diatom tertiary endosymbiont of dinoflagellates like Kryptoperidinium foliaceum, where both host and endosymbiont are reported to contain mitochondria. Here we describe the first mitochondrial genes from this system: cytochrome c oxidase 1 (cox1), cytochrome oxidase 3 (cox3), and cytochrome b (cob). Phylogenetic analyses demonstrated that all characterized genes were derived from the pennate diatom endosymbiont, and not the host. We also demonstrated that all three genes are expressed, that cox1 contains spliced group II introns, and that cob and cox3 form an operon, all like their diatom relatives. The endosymbiont mitochondria not only retain a genome, but also express their genes, and are therefore likely involved in electron transport. Ultrastructural examination confirmed the endosymbiont mitochondria retain normal tubular cristae. Overall, these data suggest the endosymbiont mitochondria have not reduced at the genomic or functional level.},
author = {Imanian, Behzad and Carpenter, Kevin J. and Keeling, Patrick J.},
doi = {10.1111/j.1550-7408.2007.00245.x},
file = {:home/fin/Documents/papers/mendeley/Imanian, Carpenter, Keeling\_2007\_Mitochondrial genome of a tertiary endosymbiont retains genes for electron transport proteins\_Journal o.pdf:pdf},
isbn = {1066-5234},
issn = {10665234},
journal = {J. Eukaryot. Microbiol.},
keywords = {Cytochrome b,Cytochrome c oxidase 1,Cytochrome oxidase 3,Endosymbiosis,Kryptoperidinium foliaceum,Reductive evolution,Type II introns,Ultrastructure},
number = {2},
pages = {146--153},
pmid = {17403155},
title = {{Mitochondrial genome of a tertiary endosymbiont retains genes for electron transport proteins}},
volume = {54},
year = {2007}
}
@article{Summerer2007,
abstract = {The ciliate Paramecium bursaria living in mutualistic relationship with the unicellular green alga Chlorella is known to be easily infected by various potential symbionts/parasites such as bacteria, yeasts and other algae. Permanent symbiosis, however, seems to be restricted to Chlorella taxa. To test the specificity of this association, we designed infection experiments with two aposymbiotic P. bursaria strains and Chlorella symbionts isolated from four Paramecium strains, seven other ciliate hosts and two Hydra strains, as well as three free-living Chlorella species. Paramecium bursaria established stable symbioses with all tested Chlorella symbionts of ciliates, but never with symbiotic Chlorella of Hydra viridissima or with free-living Chlorella. Furthermore, we tested the infection specificity of P. bursaria with a 1:1:1 mixture of three compatible Chlorella strains, including the native symbiont, and then identified the strain of the newly established symbiosis by sequencing the internal transcribed spacer region 1 of the 18S rRNA gene. The results indicated that P. bursaria established symbiosis with its native symbiont. We conclude that despite clear preferences for their native Chlorella, the host-symbiont relationship in P. bursaria is flexible.},
author = {Summerer, Monika and Sonntag, Bettina and Sommaruga, Ruben},
doi = {10.1111/j.1462-2920.2007.01322.x},
file = {:home/fin/Documents/papers/mendeley/Summerer, Sonntag, Sommaruga\_2007\_An experimental test of the symbiosis specificity between the ciliate Paramecium bursaria and strains.pdf:pdf},
issn = {1462-2912},
journal = {Environ. Microbiol.},
keywords = {Animals,Chlorella,Chlorella: genetics,Chlorella: physiology,DNA, Algal,DNA, Algal: genetics,DNA, Ribosomal Spacer,DNA, Ribosomal Spacer: genetics,Paramecium,Paramecium: genetics,Paramecium: microbiology,Paramecium: physiology,RNA, Ribosomal, 18S,RNA, Ribosomal, 18S: genetics,Symbiosis},
month = aug,
number = {8},
pages = {2117--22},
pmid = {17635555},
title = {{An experimental test of the symbiosis specificity between the ciliate Paramecium bursaria and strains of the unicellular green alga Chlorella.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17635555},
volume = {9},
year = {2007}
}
@article{Kamako2005,
abstract = {Cells of the green paramecium, Paramecium bursaria, contain several hundred endosymbiont cells. The properties of the symbionts are considered to vary depending on the collection site of the host. Difficulties in achieving axenic cells and maintenance of axenic strains for long periods have been reported for symbiotic algae from P. bursaria isolated in Japan. To establish axenic algal strains from such Japanese P. bursaria, symbionts were isolated carefully, and isolated axenic strains were grown on an agar medium containing organic nitrogen compounds. Symbiotic algal strains were obtained from three Japanese P. bursaria strains and their axenicity was confirmed by DAPI staining, cultural tests of bacterial contamination, and DGGE-PCR. These axenic strains have been maintained for over 2 years. Utilization of carbohydrates and nitrogen compounds by symbionts was examined. Monosaccharides (glucose and fructose) increased the growth of the symbiont but disaccharides (maltose and sucrose) did not. Japanese axenic symbionts were able to use ammonia and amino acids, but not nitrate or nitrite. While potent nitrite reductase activity was stimulated by nitrate induction, nitrate reductase activity was not. Nitrate utilization of Japanese symbionts differed from that reported for European and American symbionts.},
author = {Kamako, Shin-ichiro and Hoshina, Ryo and Ueno, Seiko and Imamura, Nobutaka},
doi = {10.1016/j.ejop.2005.04.001},
file = {:home/fin/Documents/papers/mendeley/Kamako et al.\_2005\_Establishment of axenic endosymbiotic strains of Japanese Paramecium bursaria and the utilization of carbohydrate and.pdf:pdf},
isbn = {09324739},
issn = {09324739},
journal = {Eur. J. Protistol.},
keywords = {Axenic culture,DGGE,Endosymbiont,Nitrate utilization,Paramecium bursaria},
pages = {193--202},
title = {{Establishment of axenic endosymbiotic strains of Japanese Paramecium bursaria and the utilization of carbohydrate and nitrogen compounds by the isolated algae}},
url = {http://www.sciencedirect.com/science/article/pii/S0932473905000283},
volume = {41},
year = {2005}
}
@article{Li2009,
abstract = {SUMMARY: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. AVAILABILITY: http://samtools.sourceforge.net.},
author = {Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard and Subgroup, 1000 Genome Project Data Processing},
doi = {10.1093/bioinformatics/btp352},
file = {:home/fin/Documents/papers/mendeley/Li et al.\_2009\_The Sequence AlignmentMap format and SAMtools\_Bioinformatics.pdf:pdf},
isbn = {1367-4803$\backslash$r1460-2059},
issn = {1367-4811},
journal = {Bioinformatics},
number = {16},
pages = {2078--2079},
pmid = {19505943},
title = {{The Sequence Alignment/Map format and SAMtools}},
url = {http://bioinformatics.oxfordjournals.org/cgi/content/full/25/16/2078},
volume = {25},
year = {2009}
}
@article{Johnson2010,
abstract = {BACKGROUND: Profile hidden Markov models (profile-HMMs) are sensitive tools for remote protein homology detection, but the main scoring algorithms, Viterbi or Forward, require considerable time to search large sequence databases.$\backslash$n$\backslash$nRESULTS: We have designed a series of database filtering steps, HMMERHEAD, that are applied prior to the scoring algorithms, as implemented in the HMMER package, in an effort to reduce search time. Using this heuristic, we obtain a 20-fold decrease in Forward and a 6-fold decrease in Viterbi search time with a minimal loss in sensitivity relative to the unfiltered approaches. We then implemented an iterative profile-HMM search method, JackHMMER, which employs the HMMERHEAD heuristic. Due to our search heuristic, we eliminated the subdatabase creation that is common in current iterative profile-HMM approaches. On our benchmark, JackHMMER detects 14\% more remote protein homologs than SAM's iterative method T2K.$\backslash$n$\backslash$nCONCLUSIONS: Our search heuristic, HMMERHEAD, significantly reduces the time needed to score a profile-HMM against large sequence databases. This search heuristic allowed us to implement an iterative profile-HMM search method, JackHMMER, which detects significantly more remote protein homologs than SAM's T2K and NCBI's PSI-BLAST.},
author = {Johnson, L Steven and Eddy, Sean R and Portugaly, Elon},
doi = {10.1186/1471-2105-11-431},
file = {:home/fin/Documents/papers/mendeley/Johnson, Eddy, Portugaly\_2010\_Hidden Markov model speed heuristic and iterative HMM search procedure.\_BMC bioinformatics.pdf:pdf},
isbn = {1471-2105 (Electronic)$\backslash$r1471-2105 (Linking)},
issn = {1471-2105},
journal = {BMC Bioinformatics},
keywords = {Algorithms,Artificial Intelligence,Base Sequence,Databases, Protein,Markov Chains,Proteins,Proteins: chemistry,Sequence Alignment,Sequence Alignment: methods,Software},
pages = {431},
pmid = {20718988},
title = {{Hidden Markov model speed heuristic and iterative HMM search procedure.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2931519\&tool=pmcentrez\&rendertype=abstract},
volume = {11},
year = {2010}
}
@article{Redelings2005,
abstract = {We describe a novel model and algorithm for simultaneously estimating multiple molecular sequence alignments and the phylogenetic trees that relate the sequences. Unlike current techniques that base phylogeny estimates on a single estimate of the alignment, we take alignment uncertainty into account by considering all possible alignments. Furthermore, because the alignment and phylogeny are constructed simultaneously, a guide tree is not needed. This sidesteps the problem in which alignments created by progressive alignment are biased toward the guide tree used to generate them. Joint estimation also allows us to model rate variation between sites when estimating the alignment and to use the evidence in shared insertion/deletions (indels) to group sister taxa in the phylogeny. Our indel model makes use of affine gap penalties and considers indels of multiple letters. We make the simplifying assumption that the indel process is identical on all branches. As a result, the probability of a gap is independent of branch length. We use a Markov chain Monte Carlo (MCMC) method to sample from the posterior of the joint model, estimating the most probable alignment and tree and their support simultaneously. We describe a new MCMC transition kernel that improves our algorithm's mixing efficiency, allowing the MCMC chains to converge even when started from arbitrary alignments. Our software implementation can estimate alignment uncertainty and we describe a method for summarizing this uncertainty in a single plot.},
author = {Redelings, Benjamin D and Suchard, Marc a},
doi = {10.1080/10635150590947041},
file = {:home/fin/Documents/papers/mendeley/Redelings, Suchard\_2005\_Joint Bayesian estimation of alignment and phylogeny.\_Systematic biology.pdf:pdf},
isbn = {1063-5157},
issn = {1063-5157},
journal = {Syst. Biol.},
number = {3},
pages = {401--418},
pmid = {16012107},
title = {{Joint Bayesian estimation of alignment and phylogeny.}},
volume = {54},
year = {2005}
}
@article{Gascuel1997,
abstract = {We propose an improved version of the neighbor-joining (NJ) algorithm of Saitou and Nei. This new algorithm, BIONJ, follows the same agglomerative scheme as NJ, which consists of iteratively picking a pair of taxa, creating a new mode which represents the cluster of these taxa, and reducing the distance matrix by replacing both taxa by this node. Moreover, BIONJ uses a simple first-order model of the variances and covariances of evolutionary distance estimates. This model is well adapted when these estimates are obtained from aligned sequences. At each step it permits the selection, from the class of admissible reductions, of the reduction which minimizes the variance of the new distance matrix. In this way, we obtain better estimates to choose the pair of taxa to be agglomerated during the next steps. Moreover, in comparison with NJ's estimates, these estimates become better and better as the algorithm proceeds. BIONJ retains the good properties of NJ--especially its low run time. Computer simulations have been performed with 12-taxon model trees to determine BIONJ's efficiency. When the substitution rates are low (maximum pairwise divergence approximately 0.1 substitutions per site) or when they are constant among lineages, BIONJ is only slightly better than NJ. When the substitution rates are higher and vary among lineages,BIONJ clearly has better topological accuracy. In the latter case, for the model trees and the conditions of evolution tested, the topological error reduction is on the average around 20\%. With highly-varying-rate trees and with high substitution rates (maximum pairwise divergence approximately 1.0 substitutions per site), the error reduction may even rise above 50\%, while the probability of finding the correct tree may be augmented by as much as 15\%.},
author = {Gascuel, O},
doi = {10.1093/oxfordjournals.molbev.a025808},
file = {:home/fin/Documents/papers/mendeley/Gascuel\_1997\_BIONJ an improved version of the NJ algorithm based on a simple model of sequence data.\_Molecular biology and evolution.pdf:pdf},
isbn = {0737-4038 (Print)},
issn = {0737-4038},
journal = {Mol. Biol. Evol.},
keywords = {address for correspondence,distance estimates,distance method,model,neighbor-joining,of data,phylogeny,variances and covariances of},
pages = {685--695},
pmid = {9254330},
title = {{BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.}},
volume = {14},
year = {1997}
}
@article{Anisimova2006,
abstract = {We revisit statistical tests for branches of evolutionary trees reconstructed upon molecular data. A new, fast, approximate likelihood-ratio test (aLRT) for branches is presented here as a competitive alternative to nonparametric bootstrap and Bayesian estimation of branch support. The aLRT is based on the idea of the conventional LRT, with the null hypothesis corresponding to the assumption that the inferred branch has length 0. We show that the LRT statistic is asymptotically distributed as a maximum of three random variables drawn from the chi(0)2 + chi(1)2 distribution. The new aLRT of interior branch uses this distribution for significance testing, but the test statistic is approximated in a slightly conservative but practical way as 2(l1- l2), i.e., double the difference between the maximum log-likelihood values corresponding to the best tree and the second best topological arrangement around the branch of interest. Such a test is fast because the log-likelihood value l2 is computed by optimizing only over the branch of interest and the four adjacent branches, whereas other parameters are fixed at their optimal values corresponding to the best ML tree. The performance of the new test was studied on simulated 4-, 12-, and 100-taxon data sets with sequences of different lengths. The aLRT is shown to be accurate, powerful, and robust to certain violations of model assumptions. The aLRT is implemented within the algorithm used by the recent fast maximum likelihood tree estimation program PHYML (Guindon and Gascuel, 2003).},
author = {Anisimova, Maria and Gascuel, Olivier},
doi = {10.1080/10635150600755453},
file = {:home/fin/Documents/papers/mendeley/Anisimova, Gascuel\_2006\_Approximate likelihood-ratio test for branches A fast, accurate, and powerful alternative.\_Systematic biology.pdf:pdf},
issn = {1063-5157},
journal = {Syst. Biol.},
keywords = {Classification,Classification: methods,Computer Simulation,Likelihood Functions,Models, Statistical,Phylogeny},
month = aug,
number = {4},
pages = {539--52},
pmid = {16785212},
title = {{Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16785212},
volume = {55},
year = {2006}
}
@article{Perez-Cobas2013,
author = {Perez-Cobas, a. E. and Gosalbes, M. J. and Friedrichs, a. and Knecht, H. and Artacho, a. and Eismann, K. and Otto, W. and Rojo, D. and Bargiela, R. and von Bergen, M. and Neulinger, S. C. and Daumer, C. and Heinsen, F.-a. and Latorre, a. and Barbas, C. and Seifert, J. and dos Santos, V. M. and Ott, S. J. and Ferrer, M. and Moya, a.},
doi = {10.1136/gutjnl-2012-303184},
file = {:home/fin/Documents/papers/mendeley/Perez-Cobas et al.\_2013\_Gut microbiota disturbance during antibiotic therapy a multi-omic approach\_Gut.pdf:pdf},
issn = {0017-5749},
journal = {Gut},
pages = {1591--1601},
title = {{Gut microbiota disturbance during antibiotic therapy: a multi-omic approach}},
url = {http://gut.bmj.com/cgi/doi/10.1136/gutjnl-2012-303184},
volume = {62},
year = {2013}
}
@article{Ronaghi1996,
abstract = {An approach for real-time DNA sequencing without the need for electrophoresis has been developed. The approach relies on the detection of DNA polymerase activity by an enzymatic luminometric inorganic pyrophosphate (PPi) detection assay (ELIDA) (Nyr\'{e}n, P. (1987) Anal. Biochem. 167, 235-238). The PPi formed in the DNA polymerase reaction is converted to ATP by ATP sulfurylase and the ATP production is continuously monitored by the firefly luciferase. In the sequencing procedure, immobilized single-stranded template was used in a repeated cycle of deoxynucleotide extension. Real-time signals in the ELIDA, proportional to the amount of incorporated nucleotide, were observed when complementary bases were incorporated. An increased signal-to-noise ratio was obtained by substitution of deoxyadenosine alpha-thiotriphosphate (dATP alpha S) for the natural deoxyadenosine triphosphate, dATP alpha S is efficiently used by the DNA polymerase, but is not recognized by the luciferase. As a model, 15 bases of a single-stranded PCR product were sequenced. The possibility for parallel processing of many samples in an automated manner is discussed.},
author = {Ronaghi, M and Karamohamed, S and Pettersson, B and Uhl\'{e}n, M and Nyr\'{e}n, P},
doi = {10.1006/abio.1996.0432},
file = {:home/fin/Documents/papers/mendeley/Ronaghi et al.\_1996\_Real-time DNA sequencing using detection of pyrophosphate release.\_Analytical biochemistry.pdf:pdf},
isbn = {0003-2697 (Print)$\backslash$r0003-2697 (Linking)},
issn = {0003-2697},
journal = {Anal. Biochem.},
pages = {84--89},
pmid = {8923969},
title = {{Real-time DNA sequencing using detection of pyrophosphate release.}},
volume = {242},
year = {1996}
}
@article{He2015,
abstract = {Rectified activation units (rectifiers) are essential for state-of-the-art neural networks. In this work, we study rectifier neural networks for image classification from two aspects. First, we propose a Parametric Rectified Linear Unit (PReLU) that generalizes the traditional rectified unit. PReLU improves model fitting with nearly zero extra com-putational cost and little overfitting risk. Second, we de-rive a robust initialization method that particularly consid-ers the rectifier nonlinearities. This method enables us to train extremely deep rectified models directly from scratch and to investigate deeper or wider network architectures. Based on our PReLU networks (PReLU-nets), we achieve 4.94\% top-5 test error on the ImageNet 2012 classifica-tion dataset. This is a 26\% relative improvement over the ILSVRC 2014 winner (GoogLeNet, 6.66\% [29]). To our knowledge, our result is the first to surpass human-level per-formance (5.1\%, [22]) on this visual recognition challenge.},
archivePrefix = {arXiv},
arxivId = {1502.01852},
author = {He, Kaiming and Zhang, Xiangyu and Ren, Shaoqing and Sun, Jian},
eprint = {1502.01852},
file = {:home/fin/Documents/papers/mendeley/He et al.\_2015\_Delving Deep into Rectifiers Surpassing Human-Level Performance on ImageNet Classification\_arXiv1502.01852.pdf:pdf},
journal = {arXiv:1502.01852},
title = {{Delving Deep into Rectifiers: Surpassing Human-Level Performance on ImageNet Classification}},
year = {2015}
}
@article{Feng1987,
abstract = {A progressive alignment method is described that utilizes the Needleman and Wunsch pairwise alignment algorithm iteratively to achieve the multiple alignment of a set of protein sequences and to construct an evolutionary tree depicting their relationship. The sequences are assumed a priori to share a common ancestor, and the trees are constructed from difference matrices derived directly from the multiple alignment. The thrust of the method involves putting more trust in the comparison of recently diverged sequences than in those evolved in the distant past. In particular, this rule is followed: "once a gap, always a gap." The method has been applied to three sets of protein sequences: 7 superoxide dismutases, 11 globins, and 9 tyrosine kinase-like sequences. Multiple alignments and phylogenetic trees for these sets of sequences were determined and compared with trees derived by conventional pairwise treatments. In several instances, the progressive method led to trees that appeared to be more in line with biological expectations than were trees obtained by more commonly used methods.},
author = {Feng, D F and Doolittle, R F},
doi = {061/6},
file = {:home/fin/Documents/papers/mendeley/Feng, Doolittle\_1987\_Progressive sequence alignment as a prerequisite to correct phylogenetic trees.\_Journal of molecular evolution.pdf:pdf},
isbn = {0022-2844 (Print)$\backslash$r0022-2844 (Linking)},
issn = {0022-2844},
journal = {J. Mol. Evol.},
pages = {351--360},
pmid = {3118049},
title = {{Progressive sequence alignment as a prerequisite to correct phylogenetic trees.}},
volume = {25},
year = {1987}
}
@article{Goodacre2007,
abstract = {The goal of this group is to define the reporting requirements associated with the statistical analysis (including univariate, multivariate, informatics, machine learning etc.) of metabolite data with respect to other measured/collected experimental data (often called metadata). These definitions will embrace as many aspects of a complete metabolomics study as possible at this time. In chronological order this will include: Experimental Design, both in terms of sample collection/matching, and data acquisition scheduling of samples through whichever spectroscopic technology used; Deconvolution (if required); Pre-processing, for example, data cleaning, outlier detection, row/column scaling, or other transformations; Definition and parameterization of subsequent visualizations and Statistical/Machine learning Methods applied to the dataset; If required, a clear definition of the Model Validation Scheme used (including how data are split into training/validation/test sets); Formal indication on whether the data analysis has been Independently Tested (either by experimental reproduction, or blind hold out test set). Finally, data interpretation and the visual representations and hypotheses obtained from the data analyses.},
author = {Goodacre, Royston and Broadhurst, David and Smilde, Age K. and Kristal, Bruce S. and Baker, J. David and Beger, Richard and Bessant, Conrad and Connor, Susan and Capuani, Giorgio and Craig, Andrew and Ebbels, Tim and Kell, Douglas B. and Manetti, Cesare and Newton, Jack and Paternostro, Giovanni and Somorjai, Ray and Sj\"{o}str\"{o}m, Michael and Trygg, Johan and Wulfert, Florian},
doi = {10.1007/s11306-007-0081-3},
file = {:home/fin/Documents/papers/mendeley/Goodacre et al.\_2007\_Proposed minimum reporting standards for data analysis in metabolomics\_Metabolomics.pdf:pdf},
isbn = {1573-3882$\backslash$r1573-3890},
issn = {15733882},
journal = {Metabolomics},
keywords = {Bioinformatics,Biostatistics,Chemometrics,Informatics,Machine learning,Megavariate,Multivariate,Statistical learning,Statistics,Supervised learning,Unsupervised learning},
pages = {231--241},
pmid = {24039616},
title = {{Proposed minimum reporting standards for data analysis in metabolomics}},
volume = {3},
year = {2007}
}
@article{Penny2001,
abstract = {There is an apparent paradox in our understanding of molecular evolution. Current biochemically based models predict that evolutionary trees should not be recoverable for divergences beyond a few hundred million years. In practice, however, trees often appear to be recovered from much older times. Mathematical models, such as those assuming that sites evolve at different rates [including a $\Gamma$ distribution of rates across sites (RAS)] may in theory allow the recovery of some ancient divergences. However, such models require that each site maintain its characteristic rate over the whole evolutionary period. This assumption, however, contradicts the knowledge that tertiary structures diverge with time, invalidating the rate-constancy assumption of purely mathematical models. We report here that a hidden Markov version of the covarion model can meet both biochemical and statistical requirements for the analysis of sequence data. The model was proposed on biochemical grounds and can be implemented with only two additional parameters. The two hidden parts of this model are the proportion of sites free to vary (covarions) and the rate of interchange between fixed sites and these variable sites. Simulation results are consistent with this approach, providing a better framework for understanding anciently diverged sequences than the standard RAS models. However, a F distribution of rates may approximate a covarion model and may possibly be justified on these grounds. The accurate reconstruction of older divergences from sequence data is still a major problem, and molecular evolution still requires mathematical models that also have a sound biochemical basis.},
author = {Penny, David and McComish, Bennet J. and Charleston, Michael a. and Hendy, Michael D.},
doi = {10.1007/s002390010258},
file = {:home/fin/Documents/papers/mendeley/Penny et al.\_2001\_Mathematical elegance with biochemical realism The covarion model of molecular evolution\_Journal of Molecular Evolutio.pdf:pdf},
isbn = {0022-2844},
issn = {00222844},
journal = {J. Mol. Evol.},
keywords = {Covarion model,Hidden Markov model,Rates across sites,Role of models in science},
pages = {711--723},
pmid = {11677631},
title = {{Mathematical elegance with biochemical realism: The covarion model of molecular evolution}},
volume = {53},
year = {2001}
}
@article{Henneberger2006,
abstract = {In the surface waters of sulfidic springs near Regensburg, Bavaria, Germany, the SM1 euryarchaeon, together with filamentous bacteria, forms the recently described unique string-of-pearls community. In addition to naturally occurring string-of-pearls communities, the growth of these communities was also observed on polyethylene nets provided as an artificial attachment material in the streamlets of springs. In order to learn more about the distribution and origin of the SM1 euryarchaeon and its possible occurrence in the subsurface, polyethylene nets were incubated as deeply as possible in different spring holes. After a short residence time, slime-like, milky drops, almost completely composed of SM1 euryarchaeon, were attached to the nets, indicating that this organism grows independent of a partner in deeper earth layers. A newly designed in situ biofilm trapping system allowed the quantitative harvesting of organisms exhibiting this newly discovered lifestyle of the SM1 euryarchaeon for detailed biological studies. The discovery of naturally occurring archaeal biofilms extends our knowledge of the biology and ecological significance of archaea in their environments.},
author = {Henneberger, Ruth and Moissl, Christine and Amann, Thomas and Rudolph, Christian and Huber, Robert},
doi = {10.1128/AEM.72.1.192-199.2006},
file = {:home/fin/Documents/papers/mendeley/Henneberger et al.\_2006\_New insights into the lifestyle of the cold-loving SM1 euryarchaeon Natural growth as a monospecies biofilm in t.pdf:pdf},
isbn = {0099-2240},
issn = {00992240},
journal = {Appl. Environ. Microbiol.},
number = {1},
pages = {192--199},
pmid = {16391042},
title = {{New insights into the lifestyle of the cold-loving SM1 euryarchaeon: Natural growth as a monospecies biofilm in the subsurface}},
volume = {72},
year = {2006}
}
@article{Leinonen2011,
author = {Leinonen, R. and Sugawara, H. and Shumway, M.},
doi = {10.1093/nar/gkq1019},
file = {:home/fin/Documents/papers/mendeley/Leinonen, Sugawara, Shumway\_2011\_The Sequence Read Archive\_Nucleic Acids Research.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {November 2010},
pages = {D19--D21},
title = {{The Sequence Read Archive}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkq1019},
volume = {39},
year = {2011}
}
@article{Harrison1945,
author = {Harrison, J.A. and Fowler, E.H.},
file = {:home/fin/Documents/papers/mendeley/Harrison, Fowler\_1945\_Serologic evidence of cytoplasmic interchange during conjugation in Paramecium bursaria\_Science.pdf:pdf},
journal = {Science (80-. ).},
number = {2650},
pages = {377--378},
title = {{Serologic evidence of cytoplasmic interchange during conjugation in Paramecium bursaria}},
volume = {102},
year = {1945}
}
@misc{rambaut2007tracer,
author = {Rambaut, Andrew and Drummond, Alexei J},
title = {{Tracer v1. 4}},
year = {2007}
}
@article{Ronquist2012,
author = {Ronquist, F. and Teslenko, M. and van der Mark, P. and Ayres, D. L. and Darling, a. and Hohna, S. and Larget, B. and Liu, L. and Suchard, M. a. and Huelsenbeck, J. P.},
doi = {10.1093/sysbio/sys029},
file = {:home/fin/Documents/papers/mendeley/Ronquist et al.\_2012\_MrBayes 3.2 Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space\_Systematic Biolog.pdf:pdf},
issn = {1063-5157},
journal = {Syst. Biol.},
number = {3},
pages = {539--542},
title = {{MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space}},
url = {http://sysbio.oxfordjournals.org/cgi/doi/10.1093/sysbio/sys029},
volume = {61},
year = {2012}
}
@incollection{Gortz2009,
author = {G\"{o}rtz, Hans-dieter and Fokin, Sergei I},
booktitle = {Endosymbionts in Paramecium},
chapter = {6},
doi = {10.1007/978-3-540-92677-1},
editor = {Fujishima, Masahiro},
file = {:home/fin/Documents/papers/mendeley/G\"{o}rtz, Fokin\_2009\_Diversity of Endosymbiotic Bacteria in Paramecium\_Endosymbionts in Paramecium.pdf:pdf},
isbn = {9783540926771},
pages = {131--160},
publisher = {Springer},
series = {Microbiology Monographs},
title = {{Diversity of Endosymbiotic Bacteria in Paramecium}},
volume = {12},
year = {2009}
}
@article{Komer2014,
author = {Komer, Brent and Bergstra, James and Eliasmith, Chris},
file = {:home/fin/Documents/papers/mendeley/Komer, Bergstra, Eliasmith\_2014\_Hyperopt-Sklearn Automatic Hyperparameter Configuration for Scikit-Learn\_Proc. of the 13th Python in Sci.pdf:pdf},
journal = {Proc. 13th Python Sci. Conf.},
number = {Scipy},
pages = {33--39},
title = {{Hyperopt-Sklearn: Automatic Hyperparameter Configuration for Scikit-Learn}},
year = {2014}
}
@article{Setter1979,
author = {Setter, T L and Greenway, H},
file = {:home/fin/Documents/papers/mendeley/Setter, Greenway\_1979\_Growth and osmoregulation of Chlorella emersonii in NaCl and neutral osmotica\_Plant Physiol.pdf:pdf},
journal = {Plant Physiol.},
pages = {47--60},
title = {{Growth and osmoregulation of Chlorella emersonii in NaCl and neutral osmotica}},
volume = {6},
year = {1979}
}
@article{Wrede2012,
abstract = {During the last few years, the analysis of microbial diversity in various habitats greatly increased our knowledge on the kingdom Archaea. At the same time, we became aware of the multiple ways in which Archaea may interact with each other and with organisms of other kingdoms. The large group of euryarchaeal methanogens and their methane oxidizing relatives, in particular, take part in essential steps of the global methane cycle. Both of these processes, which are in reverse to each other, are partially conducted in a symbiotic interaction with different partners, either ciliates and xylophagous animals or sulfate reducing bacteria. Other symbiotic interactions are mostly of unknown ecological significance but depend on highly specific mechanisms. This paper will give an overview on interactions between Archaea and other organisms and will point out the ecological relevance of these symbiotic processes, as long as these have been already recognized.},
author = {Wrede, Christoph and Dreier, Anne and Kokoschka, Sebastian and Hoppert, Michael},
doi = {10.1155/2012/596846},
file = {:home/fin/Documents/papers/mendeley/Wrede et al.\_2012\_Archaea in symbioses\_Archaea.pdf:pdf},
issn = {1472-3654},
journal = {Archaea},
keywords = {Animals,Archaea,Archaea: physiology,Bacterial Physiological Phenomena,Ecosystem,Eukaryota,Eukaryota: physiology,Humans,Metagenome,Methane,Methane: biosynthesis,Symbiosis,Symbiosis: physiology},
month = jan,
pages = {596846},
pmid = {23326206},
title = {{Archaea in symbioses}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3544247\&tool=pmcentrez\&rendertype=abstract},
volume = {2012},
year = {2012}
}
@article{Phillips1980,
abstract = {Leguminous crops have played a crucial role in agricultural production throughout history. Their success in N-deficient soils results from root nodules containing symbiotic Rhizobium bacteria that reduce N2 to NH3. Chemical synthesis of alternative N fertilizers requires fossil fuel, but$\backslash$nRhizobium uses solar energy collected by plant photosynthesis. Increased awareness of the importance of Rhizobiurn-legume symbioses in many agricultural and marginal land environments has prompted scientists from diverse disciplines to consider enhancing the efficiency of symbiotic N2 fixation in legumes.$\backslash$nEfficiency in biological systems is the effectiveness with which energy is used for a particular process. Energy efficiency is calculated by relating energy use to minimum energy cost under defined conditions. Information summarized previously on the energy costs of symbiotic N2 fixation at the cellular (9, 22, 31, 96) and whole-plant (7, 93) levels is used herein as a basis$\backslash$nfor discussing enhancement of the efficiency of symbiotic N2 fixation in agronomic communities of legumes.},
author = {Phillips, D a},
doi = {10.1146/annurev.pp.31.060180.000333},
file = {:home/fin/Documents/papers/mendeley/Phillips\_1980\_Efficiency of Symbiotic Nitrogen Fixation in Legumes\_Annual Review of Plant Physiology.pdf:pdf},
isbn = {0066-4294 (Print)},
issn = {0066-4294},
journal = {Annu. Rev. Plant Physiol.},
pages = {29--49},
title = {{Efficiency of Symbiotic Nitrogen Fixation in Legumes}},
volume = {31},
year = {1980}
}
@article{Berk1991,
abstract = {Bacteriovorous protozoa harboring symbiotic algae are abundant in aquatic ecosystems, yet despite a recent interest in protozoan bacterivory, the influence of light on their ingestion rates has not been investigated. In this study, Paramecium bursaria containing endosymbiotic Chlorella was tested for the effect of light on its ingestion rate. P. bursaria was grown for 4 to 6 days under five different light fluxes ranging from 1 to 90 microeinsteins s m. Ingestion rates were determined by using 0.77-mum-diameter fluorescent microspheres. 4',6-Diamidino-2-phenylindole dihydrochloride-labeled Enterobacter cloacae was used in one experiment to confirm differences in uptake rates of bacteria by P. bursaria. Unlike phagotrophic phytoflagellates, the ciliates demonstrated different ingestion rates in response to different light intensities. Although symbionts contribute carbon to their host via photosynthesis, the paramecia of the present study fed faster after exposure to higher light intensities, whereas their aposymbiotic counterparts (lacking endosymbionts) were unaffected. Light-induced changes in ingestion rates were not immediate, but corresponded to the period of time required for endosymbiont populations to change significantly. This strongly suggests that the symbionts, stimulated by higher light levels, may dictate the feeding rates of their hosts. Thus, light, apart from temperature, may influence the impact of certain protists on natural bacteria and may affect laboratory-based determinations of protistan feeding rates.},
author = {Berk, S. G. and Parks, L. H. and Ting, R. S.},
file = {:home/fin/Documents/papers/mendeley/Berk, Parks, Ting\_1991\_Photoadaptation alters the ingestion rate of Paramecium bursaria, a mixotrophic ciliate\_Applied and Environmental.pdf:pdf},
isbn = {0099-2240 (Print)},
issn = {00992240},
journal = {Appl. Environ. Microbiol.},
pages = {2312--2316},
pmid = {16348540},
title = {{Photoadaptation alters the ingestion rate of Paramecium bursaria, a mixotrophic ciliate}},
volume = {57},
year = {1991}
}
@article{Oldroyd2009,
abstract = {The establishment of arbuscular mycorrhizal (AM) symbioses, formed by most flowering plants in association with glomeromycotan fungi, and the root-nodule (RN) symbiosis, formed by legume plants and rhizobial bacteria, requires an ongoing molecular dialogue that underpins the reprogramming of root cells for compatibility. In both endosymbioses, there are distinct phases to the interaction, including a presymbiotic anticipation phase and, subsequently, an intraradical accommodation of the microsymbiont. Maintenance of the endosymbiosis then depends on reciprocal nutrient exchange with the microsymbiont-obtaining plant photosynthates in exchange for mineral nutrients: enhanced phosphate and nitrogen uptake from AM fungi and fixed nitrogen from rhizobia. Despite the taxonomically distinct groups of symbionts, commonalities are observed in the signaling components and the modulation of host cell responses in both AM and RN symbioses, reflecting common mechanisms for plant cell reprogramming during endosymbiosis.},
author = {Oldroyd, Giles E D and Harrison, Maria J and Paszkowski, Uta},
doi = {10.1126/science.1171644},
file = {:home/fin/Documents/papers/mendeley/Oldroyd, Harrison, Paszkowski\_2009\_Reprogramming plant cells for endosymbiosis.\_Science (New York, N.Y.).pdf:pdf},
isbn = {0036-8075},
issn = {0036-8075},
journal = {Science},
pages = {753--754},
pmid = {19423817},
title = {{Reprogramming plant cells for endosymbiosis.}},
volume = {324},
year = {2009}
}
@misc{NCLCCAP,
author = {CCAP},
title = {{NCL Media Recipe}},
urldate = {2012-01-01},
year = {2012}
}
@article{Jahn2002,
abstract = {The germline genomes of ciliated protozoa are dynamic structures, undergoing massive DNA rearrangement during the formation of a functional macronucleus. Macronuclear development involves chromosome fragmentation coupled with de novo telomere synthesis, numerous DNA splicing events that remove internal segments of DNA, and, in some ciliates, the reordering of scrambled gene segments. Despite the fact that all ciliates share similar forms of DNA rearrangement, there appears to be great diversity in both the nature of the rearranged DNA and the molecular mechanisms involved. Epigenetic effects on rearrangement have also been observed, and recent work suggests that chromatin differentiation plays a role in specifying DNA segments either for rearrangement or for elimination.},
author = {Jahn, Carolyn L and Klobutcher, Lawrence a},
doi = {10.1146/annurev.micro.56.012302.160916},
file = {:home/fin/Documents/papers/mendeley/Jahn, Klobutcher\_2002\_Genome remodeling in ciliated protozoa.\_Annual review of microbiology.pdf:pdf},
issn = {0066-4227},
journal = {Annu. Rev. Microbiol.},
keywords = {chromosome fragmentation,dna rearrangement,dna splicing,gene},
pages = {489--520},
pmid = {12142486},
title = {{Genome remodeling in ciliated protozoa.}},
volume = {56},
year = {2002}
}
@article{Parzen1962,
abstract = {Stanford University 0. Introduction. Given a sequence of independent identically distributed random variables Xi, X2, ... , Xn, ... with common func- tion f(x), how can one estimate f(x) The problem of of a f(x) is interesting for many},
author = {Parzen, Emanuel},
doi = {10.1214/aoms/1177704472},
file = {:home/fin/Documents/papers/mendeley/Parzen\_1962\_On Estimation of a Probability Density Function and Mode\_The Annals of Mathematical Statistics.pdf:pdf},
isbn = {0003-4851},
issn = {0003-4851},
journal = {Ann. Math. Stat.},
pages = {1065--1076},
title = {{On Estimation of a Probability Density Function and Mode}},
volume = {33},
year = {1962}
}
@article{Krogh2001,
abstract = {We describe and validate a new membrane protein topology prediction method, TMHMM, based on a hidden Markov model. We present a detailed analysis of TMHMM's performance, and show that it correctly predicts 97-98 \% of the transmembrane helices. Additionally, TMHMM can discriminate between soluble and membrane proteins with both specificity and sensitivity better than 99 \%, although the accuracy drops when signal peptides are present. This high degree of accuracy allowed us to predict reliably integral membrane proteins in a large collection of genomes. Based on these predictions, we estimate that 20-30 \% of all genes in most genomes encode membrane proteins, which is in agreement with previous estimates. We further discovered that proteins with N(in)-C(in) topologies are strongly preferred in all examined organisms, except Caenorhabditis elegans, where the large number of 7TM receptors increases the counts for N(out)-C(in) topologies. We discuss the possible relevance of this finding for our understanding of membrane protein assembly mechanisms. A TMHMM prediction service is available at http://www.cbs.dtu.dk/services/TMHMM/.},
author = {Krogh, a and Larsson, B and von Heijne, G and Sonnhammer, E L},
doi = {10.1006/jmbi.2000.4315},
file = {:home/fin/Documents/papers/mendeley/Krogh et al.\_2001\_Predicting transmembrane protein topology with a hidden Markov model application to complete genomes.\_Journal of Molec.pdf:pdf},
issn = {0022-2836},
journal = {J. Mol. Biol.},
keywords = {Animals,Bacterial Proteins,Bacterial Proteins: chemistry,Computational Biology,Computational Biology: methods,Databases as Topic,Fungal Proteins,Fungal Proteins: chemistry,Genome,Internet,Markov Chains,Membrane Proteins,Membrane Proteins: chemistry,Plant Proteins,Plant Proteins: chemistry,Porins,Porins: chemistry,Protein Sorting Signals,Protein Structure,Reproducibility of Results,Research Design,Secondary,Sensitivity and Specificity,Software,Solubility},
month = jan,
number = {3},
pages = {567--80},
pmid = {11152613},
title = {{Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11152613},
volume = {305},
year = {2001}
}
@article{Adl2013,
author = {Adl, S.M. and Simpson, A.G. and Lane, C.E. and Luke\v{s}, J. and Bass, D. and Bowser, S.S. and Brown, M. and Burki, F. and Dunthorn, M. and Hampl, V. and Heiss, A. and Hoppenrath, M. and Lara, E. and LeGall, L. and Lynn, D.H. and McManus, H. and Mitchell, E.A.D. and Mozley-Stanridge, S.E. and Parfrey, L.W. and Pawlowski, J. and Rueckert, S. and Shadwick, L. and Schoch, C. and Smirnov, A. and Spiegel, F.W.},
doi = {10.1111/j.1550-7408.2012.00644.x.The},
file = {:home/fin/Documents/papers/mendeley/Adl et al.\_2013\_The Revised Classification of Eukaryotes\_Journal of Eukaryotic Microbiology.pdf:pdf},
journal = {J. Eukaryot. Microbiol.},
number = {5},
pages = {1--45},
title = {{The Revised Classification of Eukaryotes}},
volume = {59},
year = {2013}
}
@article{Wu2014a,
abstract = {Interest in single-cell whole-transcriptome analysis is growing rapidly, especially for profiling rare or heterogeneous populations of cells. We compared commercially available single-cell RNA amplification methods with both microliter and nanoliter volumes, using sequence from bulk total RNA and multiplexed quantitative PCR as benchmarks to systematically evaluate the sensitivity and accuracy of various single-cell RNA-seq approaches. We show that single-cell RNA-seq can be used to perform accurate quantitative transcriptome measurement in individual cells with a relatively small number of sequencing reads and that sequencing large numbers of single cells can recapitulate bulk transcriptome complexity.},
author = {Wu, Angela R and Neff, Norma F and Kalisky, Tomer and Dalerba, Piero and Treutlein, Barbara and Rothenberg, Michael E and Mburu, Francis M and Mantalas, Gary L and Sim, Sopheak and Clarke, Michael F and Quake, Stephen R},
doi = {10.1038/nmeth.2694},
file = {:home/fin/Documents/papers/mendeley/Wu et al.\_2014\_Quantitative assessment of single-cell RNA-sequencing methods.\_Nature methods.pdf:pdf},
isbn = {1548-7105 (Electronic)$\backslash$n1548-7091 (Linking)},
issn = {1548-7105},
journal = {Nat. Methods},
keywords = {Automatic Data Processing,Data Interpretation, Statistical,Gene Expression Profiling,Gene Expression Regulation,HCT116 Cells,Humans,Microfluidics,Nucleic Acid Amplification Techniques,Polymerase Chain Reaction,Polymerase Chain Reaction: methods,Reproducibility of Results,Sequence Analysis, DNA,Sequence Analysis, RNA,Sequence Analysis, RNA: methods,Single-Cell Analysis,Single-Cell Analysis: methods,Transcriptome},
number = {1},
pages = {41--6},
pmid = {24141493},
title = {{Quantitative assessment of single-cell RNA-sequencing methods.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4022966\&tool=pmcentrez\&rendertype=abstract},
volume = {11},
year = {2014}
}
@article{VonHeijne2006,
author = {von Heijne, Gunnar},
doi = {10.1038/nrm2063},
file = {:home/fin/Documents/papers/mendeley/von Heijne\_2006\_Membrane-protein topology\_Nature Reviews Molecular Cell Biology.pdf:pdf},
issn = {1471-0072},
journal = {Nat. Rev. Mol. Cell Biol.},
number = {December},
pages = {909--918},
title = {{Membrane-protein topology}},
url = {http://www.nature.com/doifinder/10.1038/nrm2063},
volume = {7},
year = {2006}
}
@article{Torres-Machorro2010,
author = {Torres-Machorro, Ana Lilia and Hern\'{a}ndez, Roberto and Cevallos, Ana Mar\'{\i}a and L\'{o}pez-Villase\~{n}or, Imelda},
doi = {10.1111/j.1574-6976.2009.00196.x},
file = {:home/fin/Documents/papers/mendeley/Torres-Machorro et al.\_2010\_Ribosomal RNA genes in eukaryotic microorganisms witnesses of phylogeny\_FEMS Microbiology Reviews.pdf:pdf},
issn = {1574-6976},
journal = {FEMS Microbiol. Rev.},
keywords = {5s rrna,extrachromosomal gene,repeated sequence,ribosomal cistron organization,rrna,unicellular eukaryote},
pages = {59--86},
title = {{Ribosomal RNA genes in eukaryotic microorganisms: witnesses of phylogeny?}},
url = {http://femsre.oxfordjournals.org/lookup/doi/10.1111/j.1574-6976.2009.00196.x},
volume = {34},
year = {2010}
}
@article{Iwasaki2015,
author = {Iwasaki, Yuka W. and Siomi, Mikiko C. and Siomi, Haruhiko},
doi = {10.1146/annurev-biochem-060614-034258},
file = {:home/fin/Documents/papers/mendeley/Iwasaki, Siomi, Siomi\_2015\_PIWI-Interacting RNA Its Biogenesis and Functions\_Annual Review of Biochemistry.pdf:pdf},
issn = {0066-4154},
journal = {Annu. Rev. Biochem.},
keywords = {gene regulation,pirna,piwi proteins,rna silencing,rnai,transposon},
pages = {405--433},
title = {{PIWI-Interacting RNA: Its Biogenesis and Functions}},
url = {http://www.annualreviews.org/doi/abs/10.1146/annurev-biochem-060614-034258},
volume = {84},
year = {2015}
}
@article{Eisen2006,
abstract = {The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance.},
author = {Eisen, Jonathan a. and Coyne, Robert S. and Wu, Martin and Wu, Dongying and Thiagarajan, Mathangi and Wortman, Jennifer R. and Badger, Jonathan H. and Ren, Qinghu and Amedeo, Paolo and Jones, Kristie M. and Tallon, Luke J. and Delcher, Arthur L. and Salzberg, Steven L. and Silva, Joana C. and Haas, Brian J. and Majoros, William H. and Farzad, Maryam and Carlton, Jane M. and Smith, Roger K. and Garg, Jyoti and Pearlman, Ronald E. and Karrer, Kathleen M. and Sun, Lei and Manning, Gerard and Elde, Nels C. and Turkewitz, Aaron P. and Asai, David J. and Wilkes, David E. and Wang, Yufeng and Cai, Hong and Collins, Kathleen and Stewart, B. Andrew and Lee, Suzanne R. and Wilamowska, Katarzyna and Weinberg, Zasha and Ruzzo, Walter L. and Wloga, Dorota and Gaertig, Jacek and Frankel, Joseph and Tsao, Che Chia and Gorovsky, Martin a. and Keeling, Patrick J. and Waller, Ross F. and Patron, Nicola J. and Cherry, J. Michael and Stover, Nicholas a. and Krieger, Cynthia J. and {Del Toro}, Christina and Ryder, Hilary F. and Williamson, Sondra C. and Barbeau, Rebecca a. and Hamilton, Eileen P. and Orias, Eduardo},
doi = {10.1371/journal.pbio.0040286},
file = {:home/fin/Documents/papers/mendeley/Eisen et al.\_2006\_Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote\_PLoS Biology.pdf:pdf},
isbn = {1545-7885 (Electronic)$\backslash$r1544-9173 (Linking)},
issn = {15457885},
journal = {PLoS Biol.},
number = {9},
pages = {1620--1642},
pmid = {16933976},
title = {{Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote}},
volume = {4},
year = {2006}
}
@article{Yellowlees2008,
author = {Yellowlees, David and Rees, T. Alwyn V. and Leggat, William},
doi = {10.1111/j.1365-3040.2008.01802.x},
file = {:home/fin/Documents/papers/mendeley/Yellowlees, Rees, Leggat\_2008\_Metabolic interactions between algal symbionts and invertebrate hosts\_Plant, Cell \& Environment.pdf:pdf},
issn = {0140-7791},
journal = {Plant. Cell Environ.},
pages = {679--694},
title = {{Metabolic interactions between algal symbionts and invertebrate hosts}},
url = {http://doi.wiley.com/10.1111/j.1365-3040.2008.01802.x},
volume = {31},
year = {2008}
}
@article{Eddy2011,
abstract = {Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the "multiple segment Viterbi" (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call "sparse rescaling". These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches.},
author = {Eddy, S and R, Ean},
doi = {10.1371/journal.pcbi.1002195},
file = {:home/fin/Documents/papers/mendeley/Eddy, R\_2011\_Accelerated Profile HMM Searches.\_PLoS Computational Biology.pdf:pdf},
issn = {1553-7358},
journal = {PLoS Comput. Biol.},
keywords = {Algorithms,Computational Biology,Computational Biology: methods,Databases,Information Storage and Retrieval,Information Storage and Retrieval: methods,Markov Chains,Protein,Sequence Alignment,Sequence Alignment: methods,Software},
month = oct,
number = {10},
pages = {e1002195},
pmid = {22039361},
title = {{Accelerated Profile HMM Searches.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3197634\&tool=pmcentrez\&rendertype=abstract},
volume = {7},
year = {2011}
}
@article{Okuda2008,
author = {Okuda, S. and Yamada, T. and Hamajima, M. and Itoh, M. and Katayama, T. and Bork, P. and Goto, S. and Kanehisa, M.},
doi = {10.1093/nar/gkn282},
file = {:home/fin/Documents/papers/mendeley/Okuda et al.\_2008\_KEGG Atlas mapping for global analysis of metabolic pathways\_Nucleic Acids Research.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {May},
pages = {W423--W426},
title = {{KEGG Atlas mapping for global analysis of metabolic pathways}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkn282},
volume = {36},
year = {2008}
}
@article{MendesMaia2014,
author = {{Mendes Maia}, T. and Gogendeau, D. and Pennetier, C. and Janke, C. and Basto, R.},
doi = {10.1242/bio.20146577},
file = {:home/fin/Documents/papers/mendeley/Mendes Maia et al.\_2014\_Bug22 influences cilium morphology and the post-translational modification of ciliary microtubules\_Biology Open.pdf:pdf},
issn = {2046-6390},
journal = {Biol. Open},
keywords = {basal bodies,cilia,sperm individualization,spermatogenesis,tubulin post translation modifications},
pages = {138--151},
title = {{Bug22 influences cilium morphology and the post-translational modification of ciliary microtubules}},
url = {http://bio.biologists.org/cgi/doi/10.1242/bio.20146577},
volume = {3},
year = {2014}
}
@article{Chang2012,
abstract = {RNA interference (RNAi) is a conserved eukaryotic gene regulatory mechanism that uses small noncoding RNAs to mediate posttranscriptional/transcriptional gene silencing. The fission yeast Schizosaccharomyces pombe and the filamentous fungus Neurospora crassa have served as important model systems for RNAi research. Studies on these two organisms and other fungi have contributed significantly to our understanding of the mechanisms and functions of RNAi in eukaryotes. In addition, surprisingly diverse RNAi-mediated processes and small RNA biogenesis pathways have been discovered in fungi. In this review, we give an overview of different fungal RNAi pathways with a focus on their mechanisms and functions.},
author = {Chang, Shwu-Shin and Zhang, Zhenyu and Liu, Yi},
doi = {10.1146/annurev-micro-092611-150138},
file = {:home/fin/Documents/papers/mendeley/Chang, Zhang, Liu\_2012\_RNA Interference Pathways in Fungi Mechanisms and Functions\_Annual Review of Microbiology.pdf:pdf},
isbn = {1545-3251 (Electronic)$\backslash$n0066-4227 (Linking)},
issn = {0066-4227},
journal = {Annu. Rev. Microbiol.},
keywords = {neurospora,schizosaccharomyces pombe,small noncoding rna},
pages = {305--323},
pmid = {22746336},
title = {{RNA Interference Pathways in Fungi: Mechanisms and Functions}},
volume = {66},
year = {2012}
}
@article{Felsenstein1981,
abstract = {The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of ;the estimate of the tree.},
author = {Felsenstein, J},
doi = {10.1007/BF01734359},
file = {:home/fin/Documents/papers/mendeley/Felsenstein\_1981\_Evolutionary trees from DNA sequences a maximum likelihood approach.\_Journal of molecular evolution.pdf:pdf},
isbn = {0022-2844 (Print)$\backslash$r0022-2844 (Linking)},
issn = {0022-2844},
journal = {J. Mol. Evol.},
keywords = {estimation - dna sequences,evolution - phylogeny -,hood - parsimony -,maximum likeli-},
pages = {368--376},
pmid = {7288891},
title = {{Evolutionary trees from DNA sequences: a maximum likelihood approach.}},
volume = {17},
year = {1981}
}
@article{Kato2008a,
abstract = {Symbiotic Chlorella F36-ZK isolated from Paramecium bursaria F36 has constitutive amino acid transport systems, whereas free-living Chlorella does not. We found that in symbiotic algae, the rate of serine (Ser) uptake increased in the presence of glucose (Glc) and non-metabolisable analogues, whilst incorporation of Ser into protein was not affected. The activation did not involve new protein synthesis and was enhanced under alkaline conditions. An increase in the rate of Ser transport resulted from Glc treatment even when pulsed for only 1 min at low concentrations (EC(50)=3 microM). No uptake of Glc itself was observed in F36-ZK. Thus, the transport signal appears to be transmitted via a glucose sensing and signalling pathway. Many Glc-related compounds also increased the rate of Ser uptake without an additive effect, suggesting recognition of these sugars by the same receptor and providing some insight into features of the structure-activity relationship. Ser uptake by F36-ZK is inhibited by Ca(2+), which is typically considered to be a positive modulator of amino acid uptake. Given that Glc restored Ser uptake from inhibition by Ca(2+), we propose that this compound is possibly involved in regulation of amino acid transport in this symbiotic relationship.},
author = {Kato, Yutaka and Imamura, Nobutaka},
doi = {10.1016/j.plaphy.2008.05.010},
file = {:home/fin/Documents/papers/mendeley/Kato, Imamura\_2008\_Effect of sugars on amino acid transport by symbiotic Chlorella.\_Plant physiology and biochemistry PPB Soci\'{e}t\'{e}.pdf:pdf},
issn = {0981-9428},
journal = {Plant Physiol. Biochem.},
keywords = {Amino Acids,Amino Acids: metabolism,Biological Transport,Carbohydrate Metabolism,Chlorella,Chlorella: metabolism,Structure-Activity Relationship,Symbiosis},
month = oct,
number = {10},
pages = {911--7},
pmid = {18617416},
title = {{Effect of sugars on amino acid transport by symbiotic Chlorella.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18617416},
volume = {46},
year = {2008}
}
@misc{Hoffman1997,
author = {Hoffman, P and Grinstein, G and Marx, K and Grosse, I and Stanley, E},
booktitle = {Vis. '97., Proc.},
doi = {10.1109/VISUAL.1997.663916},
isbn = {VO  -},
keywords = {AMI,Biological cells,DNA,DNA sequence classification,Data analysis,Data mining,Data visualization,Frequency,Neural networks,Organisms,Proteins,Sequences,accuracy,analytic data mining,average mutual information,biology computing,coding DNA sequences,data exploration techniques,data visualisation,data visualization,deductive databases,exons,fundamental position-dependent DNA nucleotide freq,introns,knowledge acquisition,neural nets,neural network classifiers,noncoding DNA sequences,nonlinear combination,pattern classification,rule-based classifiers,sequences,visual data mining},
pages = {437--441},
title = {{DNA visual and analytic data mining}},
year = {1997}
}
@article{Meng2014,
author = {Meng, D. and Cao, M. and Oda, T. and Pan, J.},
doi = {10.1242/jcs.140723},
file = {:home/fin/Documents/papers/mendeley/Meng et al.\_2014\_The conserved ciliary protein Bug22 controls planar beating of Chlamydomonas flagella\_Journal of Cell Science.pdf:pdf},
issn = {0021-9533},
journal = {J. Cell Sci.},
keywords = {1967,bug22,chlamydomonas,cilia,cilia motility,flagella,on inherent,planar beating,ringo,strokes,structural studies have revealed,structures of the axoneme,the,the waveform switch depends},
pages = {281--287},
title = {{The conserved ciliary protein Bug22 controls planar beating of Chlamydomonas flagella}},
url = {http://jcs.biologists.org/cgi/doi/10.1242/jcs.140723},
volume = {127},
year = {2014}
}
@book{Archibald2014,
author = {Archibald, John M.},
publisher = {Oxford University Press},
title = {{One plus one equals one: Symbiosis and the evolution of complex life}},
year = {2014}
}
@article{Akaike1974,
abstract = {H. Akaike, 'A new look at the statistical model identification', IEEE Transactions$\backslash$non Automatic Control, Vol. 19, No. 6, pp. 716-723, 1974},
author = {Akaike, H},
doi = {10.1109/TAC.1974.1100705},
file = {:home/fin/Documents/papers/mendeley/Akaike\_1974\_A new look at the statistical model identification\_IEEE Transactionson Automatic Control.pdf:pdf},
isbn = {0018-9286 VO - 19},
issn = {0018-9286},
journal = {IEEE Trans. Autom. Control},
keywords = {MODEL},
pages = {716--723},
pmid = {1100705},
title = {{A new look at the statistical model identification}},
volume = {19},
year = {1974}
}
@misc{Gribskov1988,
abstract = {Profile analysis measures the similarity between a target sequence and a group of aligned sequences (the probe). The probe sequences are used to produce a position-specific scoring table (the profile) that can be aligned with any sequence (the target) using standard dynamic programming methods. We are developing a library of profiles, each describing a different structural motif. This allows any target sequence to be rapidly scanned for the presence of structural motifs. Levels of significance for the comparison of target sequences with the profile are determined in advance, permitting an objective decision to be made as to whether a protein is likely to possess a structural motif.},
author = {Gribskov, M and Homyak, M and Edenfield, J and Eisenberg, D},
booktitle = {Comput. Appl. Biosci.},
doi = {061/13},
file = {:home/fin/Documents/papers/mendeley/Gribskov et al.\_1988\_Profile scanning for three-dimensional structural patterns in protein sequences\_Computer applications in the biosc.html:html},
isbn = {0266-7061 (Print)$\backslash$n0266-7061 (Linking)},
issn = {02667061},
pages = {61--66},
pmid = {3383004},
title = {{Profile scanning for three-dimensional structural patterns in protein sequences}},
volume = {4},
year = {1988}
}
@inproceedings{OCallaghan2002,
author = {O'Callaghan, Liadan and Mishra, Nina and Meyerson, Adam and Guha, Sudipto and Motwani, Rajeev},
booktitle = {Proc. 18th Int. Conf. Data Eng.},
file = {:home/fin/Documents/papers/mendeley/O'Callaghan et al.\_2002\_Streaming-Data Algorithms for High-Quality Clustering\_Proceedings 18th International Conference on Data Engineer.pdf:pdf},
pages = {0685},
publisher = {IEEE},
title = {{Streaming-Data Algorithms for High-Quality Clustering}},
year = {2002}
}
@book{vapnik1982estimation,
author = {Vapnik, Vladimir Naumovich and Kotz, Samuel},
publisher = {Springer-Verlag New York},
title = {{Estimation of dependences based on empirical data}},
volume = {41},
year = {1982}
}
@article{Huelsenbeck2001,
abstract = {SUMMARY: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. AVAILABILITY: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.},
author = {Huelsenbeck, J P and Ronquist, F},
file = {:home/fin/Documents/papers/mendeley/Huelsenbeck, Ronquist\_2001\_MRBAYES Bayesian inference of phylogenetic trees.\_Bioinformatics (Oxford, England).pdf:pdf},
issn = {1367-4803},
journal = {Bioinformatics},
keywords = {Algorithms,Bayes Theorem,Computational Biology,Markov Chains,Phylogeny,Software},
month = aug,
number = {8},
pages = {754--5},
pmid = {11524383},
title = {{MRBAYES: Bayesian inference of phylogenetic trees.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11524383},
volume = {17},
year = {2001}
}
@article{Hershkovitz1996,
author = {Hershkovitz, M.A. and Lewis, Louise A},
file = {:home/fin/Documents/papers/mendeley/Hershkovitz, Lewis\_1996\_Deep-Level Diagnostic Value of the rDNA-ITS Region\_Mol Biol Evol.pdf:pdf},
journal = {Mol Biol Evol},
keywords = {5,8s,among-site rate variation,its,likelihood,rdna evolution},
number = {9},
pages = {1276--1295},
title = {{Deep-Level Diagnostic Value of the rDNA-ITS Region}},
volume = {13},
year = {1996}
}
@article{Wu2008,
abstract = {The downregulation of gene expression by miRNAs and siRNAs is a complex process involving both translational repression and accelerated mRNA turnover, each of which appears to occur by multiple mechanisms. Moreover, under certain conditions, miRNAs are also capable of activating translation. A variety of cellular proteins have been implicated in these regulatory mechanisms, yet their exact roles remain largely unresolved. ?? 2008 Elsevier Inc. All rights reserved.},
author = {Wu, Ligang and Belasco, Joel G.},
doi = {10.1016/j.molcel.2007.12.010},
file = {:home/fin/Documents/papers/mendeley/Wu, Belasco\_2008\_Let Me Count the Ways Mechanisms of Gene Regulation by miRNAs and siRNAs\_Molecular Cell.pdf:pdf},
isbn = {1097-2765 (Print)$\backslash$n1097-2765 (Linking)},
issn = {10972765},
journal = {Mol. Cell},
pages = {1--7},
pmid = {18206964},
title = {{Let Me Count the Ways: Mechanisms of Gene Regulation by miRNAs and siRNAs}},
volume = {29},
year = {2008}
}
@article{Tsochantaridis2005,
author = {Tsochantaridis, Ioannis and Joachims, Thorsten and Hofmann, Thomas and Altun, Yasemin},
file = {:home/fin/Documents/papers/mendeley/Tsochantaridis et al.\_2005\_Large Margin Methods for Structured and Interdependent Output Variables\_Journal of Machine Learning Research.pdf:pdf},
journal = {J. Mach. Learn. Res.},
pages = {1453--1484},
title = {{Large Margin Methods for Structured and Interdependent Output Variables}},
volume = {6},
year = {2005}
}
@article{white1990amplification,
author = {White, Thomas J and Bruns, T and Lee, SJWT and Taylor, J W and Others},
journal = {PCR Protoc. a Guid. to methods Appl.},
pages = {315--322},
title = {{Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics}},
volume = {18},
year = {1990}
}
@article{Reyes-Prieto2007,
abstract = {The establishment of the photosynthetic organelle (plastid) in eukaryotes and the diversification of algae and plants were landmark evolutionary events because these taxa form the base of the food chain for many ecosystems on our planet. The plastid originated via a putative single, ancient primary endosymbiosis in which

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