text:
Jia and Su, Hao and Krause, Jonathan and Satheesh, Sanjeev and Ma, Sean and Huang, Zhiheng and Karpathy, Andrej and Khosla, Aditya and Bernstein, Michael and Berg, Alexander C. and Fei-Fei, Li},
eprint = {arXiv:1409.0575v1},
file = {:home/fin/Documents/papers/mendeley/Russakovsky et al.\_2014\_Imagenet large scale visual recognition challenge 2010\_arXiv1409.0575.pdf:pdf},
journal = {arXiv:1409.0575},
keywords = {benchmark,dataset,large-scale,object detection,object recognition},
title = {{Imagenet large scale visual recognition challenge 2010}},
url = {http://scholar.google.com/scholar?hl=en\&btnG=Search\&q=intitle:Large+Scale+Visual+Recognition+Challenge+2010\#2},
year = {2014}
}
@article{Nishimoto2008,
author = {Nishimoto, Yuriko and Arisue, Nobuko and Kawai, Satoru and Escalante, Ananias a. and Horii, Toshihiro and Tanabe, Kazuyuki and Hashimoto, Tetsuo},
doi = {10.1016/j.ympev.2008.01.031},
file = {:home/fin/Documents/papers/mendeley/Nishimoto et al.\_2008\_Evolution and phylogeny of the heterogeneous cytosolic SSU rRNA genes in the genus Plasmodium\_Molecular Phylogenet.pdf:pdf},
issn = {10557903},
journal = {Mol. Phylogenet. Evol.},
keywords = {molecular phylogeny,multi-copy genes,plasmodium,simian malaria parasites,ssu rrna},
pages = {45--53},
title = {{Evolution and phylogeny of the heterogeneous cytosolic SSU rRNA genes in the genus Plasmodium}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790308000559},
volume = {47},
year = {2008}
}
@article{Dorrell2011,
abstract = {The chromalveolate "supergroup" is of key interest in contemporary phycology, as it contains the overwhelming majority of extant algal species, including several phyla of key importance to oceanic net primary productivity such as diatoms, kelps, and dinoflagellates. There is also intense current interest in the exploitation of these algae for industrial purposes, such as biodiesel production. However, the evolution of the constituent species, and in particular the origin and radiation of the chloroplast genomes, remains poorly understood. In this review, we discuss current theories of the origins of the extant red alga-derived chloroplast lineages in the chromalveolates and the potential ramifications of the recent discovery of large numbers of green algal genes in chromalveolate genomes. We consider that the best explanation for this is that chromalveolates historically possessed a cryptic green algal endosymbiont that was subsequently replaced by a red algal chloroplast. We consider how changing selective pressures acting on ancient chromalveolate lineages may have selectively favored the serial endosymbioses of green and red algae and whether a complex endosymbiotic history facilitated the rise of chromalveolates to their current position of ecological prominence.},
author = {Dorrell, Richard G. and Smith, Alison G.},
doi = {10.1128/EC.00326-10},
file = {:home/fin/Documents/papers/mendeley/Dorrell, Smith\_2011\_Do red and green make brown Perspectives on plastid acquisitions within chromalveolates\_Eukaryotic Cell.pdf:pdf},
isbn = {1535-9786 (Electronic)$\backslash$r1535-9786 (Linking)},
issn = {15359778},
journal = {Eukaryot. Cell},
number = {7},
pages = {856--868},
pmid = {21622904},
title = {{Do red and green make brown?: Perspectives on plastid acquisitions within chromalveolates}},
volume = {10},
year = {2011}
}
@article{VanGorkom1974,
abstract = {The complete absorption difference spectrum of the primary electron acceptor of Photosystem II has been measured at room temperature in subchloroplast fragments prepared with deoxycholate. The shape and amplitude of the spectrum indicate that the primary reaction involves the reduction of one bound plastoquinone molecule per reaction center to its semiquinone anion. In addition two small absorbance band shifts occur near 545 (C550) and 685 nm, which may be due to an influence of the semiquinone on the absorption spectrum of a reaction center pigment.},
author = {van Gorkom, Hans J.},
doi = {10.1016/0005-2728(74)90081-4},
file = {:home/fin/Documents/papers/mendeley/van Gorkom\_1974\_Identification of the reduced primary electron acceptor of Photosystem II as a bound semiquinone anion\_Biochimica et Bio.pdf:pdf},
issn = {00052728},
journal = {Biochim. Biophys. Acta - Bioenerg.},
keywords = {1,1-diphenyl-2-picrylhydrazyl,3-(3,4-dichlorophenyl)-1,1-dimethylurea,DCMU,DPPH},
pages = {439--442},
title = {{Identification of the reduced primary electron acceptor of Photosystem II as a bound semiquinone anion}},
url = {http://www.sciencedirect.com/science/article/pii/0005272874900814},
volume = {347},
year = {1974}
}
@article{Shendure2008,
abstract = {DNA sequence represents a single format onto which a broad range of biological phenomena can be projected for high-throughput data collection. Over the past three years, massively parallel DNA sequencing platforms have become widely available, reducing the cost of DNA sequencing by over two orders of magnitude, and democratizing the field by putting the sequencing capacity of a major genome center in the hands of individual investigators. These new technologies are rapidly evolving, and near-term challenges include the development of robust protocols for generating sequencing libraries, building effective new approaches to data-analysis, and often a rethinking of experimental design. Next-generation DNA sequencing has the potential to dramatically accelerate biological and biomedical research, by enabling the comprehensive analysis of genomes, transcriptomes and interactomes to become inexpensive, routine and widespread, rather than requiring significant production-scale efforts.},
archivePrefix = {arXiv},
arxivId = {1111.6189v1},
author = {Shendure, Jay and Ji, Hanlee},
doi = {10.1038/nbt1486},
eprint = {1111.6189v1},
file = {:home/fin/Documents/papers/mendeley/Shendure, Ji\_2008\_Next-generation DNA sequencing.\_Nature biotechnology.pdf:pdf},
isbn = {1087-0156},
issn = {1087-0156},
journal = {Nat. Biotechnol.},
number = {10},
pages = {1135--1145},
pmid = {18846087},
title = {{Next-generation DNA sequencing.}},
volume = {26},
year = {2008}
}
@article{Kopp2015,
author = {Kopp, Christophe and Domart-Coulon, Isabelle and Escrig, Stephane and Humbel, Bruno M. and Hignette, Michel and Meibom, Anders},
doi = {10.1128/mBio.02299-14.Editor},
file = {:home/fin/Documents/papers/mendeley/Kopp et al.\_2015\_Subcellular investigation of photosynthesis-driven carbon and nitrogen assimilation and utilization in the symbiotic re.pdf:pdf},
issn = {21507511},
journal = {Submitted},
number = {1},
pages = {1--9},
title = {{Subcellular investigation of photosynthesis-driven carbon and nitrogen assimilation and utilization in the symbiotic reef coral Pocillopora damicornis}},
volume = {6},
year = {2015}
}
@article{Flemr2013,
abstract = {Summary In mammals, a single Dicer participates in biogenesis of small RNAs in microRNA (miRNA) and RNAi pathways. In mice, endogenous RNAi is highly active in oocytes, but not in somatic cells, which we ascribe here to an oocyte-specific Dicer isoform (DicerO). DicerO lacks the N-terminal DExD helicase domain and has higher cleavage activity than the full-length Dicer in somatic cells (DicerS). Unlike Dicer S, DicerO efficiently produces small RNAs from long double-stranded (dsRNA) substrates. Expression of the DicerO isoform is driven by an intronic MT-C retrotransposon promoter, deletion of which causes loss of DicerO and female sterility. Oocytes from females lacking the MT-C element show meiotic spindle defects and increased levels of endogenous small interfering RNA (endo-siRNA) targets, phenocopying the maternal Dicer null phenotype. The alternative Dicer isoform, whose phylogenetic origin demonstrates evolutionary plasticity of RNA-silencing pathways, is the main determinant of endogenous RNAi activity in the mouse female germline. ?? 2013 Elsevier Inc.},
author = {Flemr, Matyas and Malik, Radek and Franke, Vedran and Nejepinska, Jana and Sedlacek, Radislav and Vlahovicek, Kristian and Svoboda, Petr},
doi = {10.1016/j.cell.2013.10.001},
file = {:home/fin/Documents/papers/mendeley/Flemr et al.\_2013\_A retrotransposon-driven dicer isoform directs endogenous small interfering rna production in mouse oocytes\_Cell.pdf:pdf},
isbn = {0092-8674},
issn = {00928674},
journal = {Cell},
number = {4},
pages = {807--816},
pmid = {24209619},
publisher = {Elsevier Inc.},
title = {{A retrotransposon-driven dicer isoform directs endogenous small interfering rna production in mouse oocytes}},
url = {http://dx.doi.org/10.1016/j.cell.2013.10.001},
volume = {155},
year = {2013}
}
@article{Criscuolo2011,
author = {Criscuolo, Alexis},
doi = {10.1016/j.ympev.2011.08.029},
file = {:home/fin/Documents/papers/mendeley/Criscuolo\_2011\_Molecular Phylogenetics and Evolution morePhyML Improving the phylogenetic tree space exploration with PhyML 3\_Molecular.pdf:pdf},
issn = {1055-7903},
journal = {Mol. Phylogenet. Evol.},
number = {3},
pages = {944--948},
publisher = {Elsevier Inc.},
title = {{Molecular Phylogenetics and Evolution morePhyML : Improving the phylogenetic tree space exploration with PhyML 3}},
url = {http://dx.doi.org/10.1016/j.ympev.2011.08.029},
volume = {61},
year = {2011}
}
@article{Saitou1987,
author = {Saitou, Naruya and Nei, Masatoshi},
file = {:home/fin/Documents/papers/mendeley/Saitou, Nei\_1987\_The Neighbor-joining Method A New Method for Reconstructing Phylogenetic Trees’\_Mol Biol Evol.pdf:pdf},
journal = {Mol Biol Evol},
number = {4},
pages = {406--425},
title = {{The Neighbor-joining Method: A New Method for Reconstructing Phylogenetic Trees’}},
volume = {4},
year = {1987}
}
@article{Galvani2001,
author = {Galvani, Ang\'{e}lique and Sperling, Linda},
file = {:home/fin/Documents/papers/mendeley/Galvani, Sperling\_2001\_Transgene-mediated post-transcriptional gene silencing is inhibited by 3′ non-coding sequences in Paramecium\_Nu.pdf:pdf},
journal = {Nucleic Acids Res.},
number = {21},
pages = {4387--4394},
title = {{Transgene-mediated post-transcriptional gene silencing is inhibited by 3′ non-coding sequences in Paramecium}},
volume = {29},
year = {2001}
}
@article{Pendleton2015,
author = {Pendleton, Matthew and Sebra, Robert and Pang, Andy Wing Chun and Ummat, Ajay and Franzen, Oscar and Rausch, Tobias and St\"{u}tz, Adrian M and Stedman, William and Anantharaman, Thomas and Hastie, Alex and Dai, Heng and Fritz, Markus Hsi-Yang and Cao, Han and Cohain, Ariella and Deikus, Gintaras and Durrett, Russell E and Blanchard, Scott C and Altman, Roger and Chin, Chen-Shan and Guo, Yan and Paxinos, Ellen E and Korbel, Jan O and Darnell, Robert B and McCombie, W Richard and Kwok, Pui-Yan and Mason, Christopher E and Schadt, Eric E and Bashir, Ali},
doi = {10.1038/nmeth.3454},
file = {:home/fin/Documents/papers/mendeley/Pendleton et al.\_2015\_Assembly and diploid architecture of an individual human genome via single-molecule technologies\_Nature Methods.pdf:pdf},
issn = {1548-7091},
journal = {Nat. Methods},
number = {8},
pages = {780--786},
title = {{Assembly and diploid architecture of an individual human genome via single-molecule technologies}},
url = {http://www.nature.com/doifinder/10.1038/nmeth.3454},
volume = {12},
year = {2015}
}
@article{Chain2009,
author = {Chain, P. S. G and Grafham, D. V. and Fulton, R. S. and FitzGerald, M. G. and Hostetler, J. and {D. Muzny} and Ali, J. and Birren, B. and Bruce, D. C. and Buhay, C. and Cole, J. R. and Ding, Y. and Dugan, S. and Field, D. and Garrity, G. M. and Gibbs, R. and Graves, T. and Han, C. S. and Harrison, S. H. and Highlander, S. and Hugenholtz, P. and Khouri, H. M. and Kodira, C. D. and Kolker, E. and Kyrpides, N. C. and Lang, D. and Lapidus, A. and Malfatti, S. A. and Markowitz, V. and Metha, T. and Nelson, K. E. and Parkhill, J. and Pitluck, S. and Qin, X. and Read, T. D. and Schmutz, J. and Sozhamannan, S. and Sterk, P. and Strausberg, R. L. and Sutton, G. and Thomson, N. R. and Tiedje, J. M. and Weinstock, G. and Wollam, A. and Consortium, Genomic Standards Consortium Human Microbiome Project Jumpstart and Detter, J C},
file = {:home/fin/Documents/papers/mendeley/Chain et al.\_2009\_Genome Project Standards in a new era of sequencing\_Science.pdf:pdf},
journal = {Science (80-. ).},
number = {October},
pages = {4--5},
title = {{Genome Project Standards in a new era of sequencing}},
volume = {326},
year = {2009}
}
@article{Johnson2011,
abstract = {Many ciliates acquire the capacity for photosynthesis through stealing plastids or harboring intact endosymbiotic algae. Both phenomena are a form of mixotrophy and are widespread among ciliates. Mixotrophic ciliates may be abundant in freshwater and marine ecosystems, sometimes making substantial contributions toward community primary productivity. While mixotrophic ciliates utilize phagotrophy to capture algal cells, their endomembrane system has evolved to partially bypass typical heterotrophic digestion pathways, enabling metabolic interaction with foreign cells or organelles. Unique adaptations may also be found in certain algal endosymbionts, facilitating establishment of symbiosis and nutritional interactions, while reducing their fitness for survival as free-living cells. Plastid retaining oligotrich ciliates possess little selectivity from which algae they sequester plastids, resulting in unstable kleptoplastids that require frequent ingestion of algal cells to replace them. Mesodinium rubrum (=Myrionecta rubra) possesses cryptophyte organelles that resemble a reduced endosymbont, and is the only ciliate capable of functional phototrophy and plastid division. Certain strains of M. rubrum may have a stable association with their cryptophyte organelles, while others need to acquire a cryptophyte nucleus through feeding. This process of stealing a nucleus, termed karyoklepty, was first described in M. rubrum and may be an evolutionary precursor to a stable, reduced endosymbiont, and perhaps eventually a tertiary plastid. The newly described Mesodinium"chamaeleon," however, is less selective of which cryptophyte species it will retain organelles, and appears less capable of sustained phototrophy. Ciliates likely stem from a phototrophic ancestry, which may explain their propensity to practice acquired phototrophy.},
author = {Johnson, Matthew D},
doi = {10.1111/j.1550-7408.2011.00545.x},
file = {:home/fin/Documents/papers/mendeley/Johnson\_2011\_Acquired phototrophy in ciliates a review of cellular interactions and structural adaptations.\_Journal of Eukaryotic Microb.pdf:pdf},
issn = {1550-7408},
journal = {J. Eukaryot. Microbiol.},
keywords = {Ciliophora,Ciliophora: metabolism,Ciliophora: physiology,Microbial Interactions,Phagocytosis,Phototrophic Processes,Plastids,Plastids: metabolism,Symbiosis},
number = {3},
pages = {185--95},
pmid = {21518077},
title = {{Acquired phototrophy in ciliates: a review of cellular interactions and structural adaptations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21518077},
volume = {58},
year = {2011}
}
@article{Hinton2006,
author = {Hinton, G.E. and Salakhutdinov, R.R.},
file = {:home/fin/Documents/papers/mendeley/Hinton, Salakhutdinov\_2006\_Reducing the Dimensionality of Data with Neural Networks\_Science.pdf:pdf},
journal = {Science (80-. ).},
number = {July},
pages = {504--507},
title = {{Reducing the Dimensionality of Data with Neural Networks}},
volume = {313},
year = {2006}
}
@article{Kim2013,
abstract = {TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat. TopHat2 can align reads of various lengths produced by the latest sequencing technologies, while allowing for variable-length indels with respect to the reference genome. In addition to de novo spliced alignment, TopHat2 can align reads across fusion breaks, which can occur after genomic translocations. TopHat2 combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes. TopHat2 is available at http://ccb.jhu.edu/software/tophat.},
author = {Kim, Daehwan and Pertea, Geo and Trapnell, Cole and Pimentel, Harold and Kelley, Ryan and Salzberg, Steven L},
doi = {10.1186/gb-2013-14-4-r36},
file = {:home/fin/Documents/papers/mendeley/Kim et al.\_2013\_TopHat2 accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.\_Genome biology.pdf:pdf},
isbn = {1465-6914 (Electronic)$\backslash$r1465-6906 (Linking)},
issn = {1465-6914},
journal = {Genome Biol.},
number = {4},
pages = {R36},
pmid = {23618408},
publisher = {BioMed Central Ltd},
title = {{TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.}},
url = {http://genomebiology.com/2013/14/4/R36},
volume = {14},
year = {2013}
}
@article{Xie2012,
abstract = {The symbiotic protists in the hindgut of lower termites are critical for lignocellulose decomposition. Due to the unculturability of these protists, information on lignocellulases and their abundance within the gut is unavailable. The advent of high-throughput sequencing technologies enables an investigation of the gene expression profile in this community without culturing these organisms. Here, we carried out 454 pyrosequencing to profile the metatranscriptome of the protistan community in Coptotermes formosanus. In total, 223,477 reads were obtained by sequencing the enriched protistan mRNA. Phagocytosis and cytoskeletal homeostasis pathways were highly represented in the metatranscriptome. Among the metabolic pathways, starch and sucrose metabolism were dominant. A detailed analysis combining Pfam and KEGG annotation identified 118 glycosyl hydrolases belonging to 18 different glycosyl hydrolase families (GHFs). Subsequently, a novel GHF10 endo-1,4-beta-xylanase was functionally characterized to complement our understanding of the protistan hemicellulases. © 2012 Elsevier Inc.},
author = {Xie, Lei and Zhang, Lei and Zhong, Yi and Liu, Ning and Long, Yanhua and Wang, Shengyue and Zhou, Xuguo and Zhou, Zhihua and Huang, Yongping and Wang, Qian},
doi = {10.1016/j.ygeno.2012.01.009},
file = {:home/fin/Documents/papers/mendeley/Xie et al.\_2012\_Profiling the metatranscriptome of the protistan community in Coptotermes formosanus with emphasis on the lignocelluloly.pdf:pdf},
isbn = {1089-8646 (Electronic)$\backslash$r0888-7543 (Linking)},
issn = {08887543},
journal = {Genomics},
keywords = {Coptotermes formosanu,Lignocellulase,Metatranscriptome,Protist},
number = {4},
pages = {246--255},
pmid = {22326742},
publisher = {Elsevier Inc.},
title = {{Profiling the metatranscriptome of the protistan community in Coptotermes formosanus with emphasis on the lignocellulolytic system}},
url = {http://dx.doi.org/10.1016/j.ygeno.2012.01.009},
volume = {99},
year = {2012}
}
@article{Mardis2008,
abstract = {Recent scientific discoveries that resulted from the application of next-generation DNA sequencing technologies highlight the striking impact of these massively parallel platforms on genetics. These new methods have expanded previously focused readouts from a variety of DNA preparation protocols to a genome-wide scale and have fine-tuned their resolution to single base precision. The sequencing of RNA also has transitioned and now includes full-length cDNA analyses, serial analysis of gene expression (SAGE)-based methods, and noncoding RNA discovery. Next-generation sequencing has also enabled novel applications such as the sequencing of ancient DNA samples, and has substantially widened the scope of metagenomic analysis of environmentally derived samples. Taken together, an astounding potential exists for these technologies to bring enormous change in genetic and biological research and to enhance our fundamental biological knowledge.},
author = {Mardis, Elaine R},
doi = {10.1146/annurev.genom.9.081307.164359},
file = {:home/fin/Documents/papers/mendeley/Mardis\_2008\_Next-generation DNA sequencing methods.\_Annual review of genomics and human genetics.pdf:pdf},
isbn = {1527-8204 (Print)$\backslash$r1527-8204 (Linking)},
issn = {1527-8204},
journal = {Annu. Rev. Genomics Hum. Genet.},
keywords = {massively parallel sequencing,resequencing,sequencing-by-synthesis},
pages = {387--402},
pmid = {18576944},
title = {{Next-generation DNA sequencing methods.}},
volume = {9},
year = {2008}
}
@article{Nowara2010,
author = {Nowara, D. and Gay, a. and Lacomme, C. and Shaw, J. and Ridout, C. and Douchkov, D. and Hensel, G. and Kumlehn, J. and Schweizer, P.},
doi = {10.1105/tpc.110.077040},
file = {:home/fin/Documents/papers/mendeley/Nowara et al.\_2010\_HIGS Host-Induced Gene Silencing in the Obligate Biotrophic Fungal Pathogen Blumeria graminis\_The Plant Cell.pdf:pdf},
issn = {1040-4651},
journal = {Plant Cell},
number = {September},
pages = {3130--3141},
title = {{HIGS: Host-Induced Gene Silencing in the Obligate Biotrophic Fungal Pathogen Blumeria graminis}},
url = {http://www.plantcell.org/cgi/doi/10.1105/tpc.110.077040},
volume = {22},
year = {2010}
}
@article{Pombert2014,
abstract = {The evolution of an obligate parasitic lifestyle is often associated with genomic reduction, in particular with the loss of functions associated with increasing host-dependence. This is evident in many parasites, but perhaps the most extreme transitions are from free-living autotrophic algae to obligate parasites. The best-known examples of this are the apicomplexans such as Plasmodium, which evolved from algae with red secondary plastids. However, an analogous transition also took place independently in the Helicosporidia, where an obligate parasite of animals with an intracellular infection mechanism evolved from algae with green primary plastids. We characterised the nuclear genome of Helicosporidium to compare its transition to parasitism with that of apicomplexans. The Helicosporidium genome is small and compact, even by comparison with the relatively small genomes of the closely related green algae Chlorella and Coccomyxa, but at the functional level we find almost no evidence for reduction. Nearly all ancestral metabolic functions are retained, with the single major exception of photosynthesis, and even here reduction is not complete. The great majority of genes for light-harvesting complexes, photosystems, and pigment biosynthesis have been lost, but those for other photosynthesis-related functions, such as Calvin cycle, are retained. Rather than loss of whole function categories, the predominant reductive force in the Helicosporidium genome is a contraction of gene family complexity, but even here most losses affect families associated with genome maintenance and expression, not functions associated with host-dependence. Other gene families appear to have expanded in response to parasitism, in particular chitinases, including those predicted to digest the chitinous barriers of the insect host or remodel the cell wall of Helicosporidium. Overall, the Helicosporidium genome presents a fascinating picture of the early stages of a transition from free-living autotroph to parasitic heterotroph where host-independence has been unexpectedly preserved.},
author = {Pombert, Jean-Fran\c{c}ois and Blouin, Nicolas Achille and Lane, Chris and Boucias, Drion and Keeling, Patrick J},
doi = {10.1371/journal.pgen.1004355},
file = {:home/fin/Documents/papers/mendeley/Pombert et al.\_2014\_A lack of parasitic reduction in the obligate parasitic green alga Helicosporidium.\_PLoS genetics.pdf:pdf},
issn = {1553-7404},
journal = {PLoS Genet.},
month = may,
number = {5},
pages = {e1004355},
pmid = {24809511},
title = {{A lack of parasitic reduction in the obligate parasitic green alga Helicosporidium.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4014436\&tool=pmcentrez\&rendertype=abstract},
volume = {10},
year = {2014}
}
@inproceedings{benson1948path,
author = {Benson, A A and Calvin, M},
booktitle = {Cold Spring Harb. Symp. Quant. Biol.},
organization = {Cold Spring Harbor Laboratory Press},
pages = {6--10},
title = {{The path of carbon in photosynthesis. III}},
volume = {13},
year = {1948}
}
@article{DeQueiroz2007a,
abstract = {Recent reviews of the construction of large phylogenies have focused on supertree methods that involve separate analyses of data sets and subsequent integration of the resulting trees. Here, we consider the alternative method of analyzing all character data simultaneously. Such 'supermatrix' analyses use information from each character directly and enable straightforward incorporation of diverse kinds of data, including characters from fossils. The approach has been extended by the development of new methods, including model-based techniques for analyzing heterogeneous data and hierarchical methods for constructing extremely large trees. Recent work also suggests that the problem of missing data in supermatrix analyses has been overstated. Although the supermatrix approach is not suited for all cases, we suggest that its inherent strengths will ensure that it will continue to have a central role in inferring large phylogenetic trees from diverse data. ?? 2006 Elsevier Ltd. All rights reserved.},
author = {de Queiroz, Alan and Gatesy, John},
doi = {10.1016/j.tree.2006.10.002},
file = {:home/fin/Documents/papers/mendeley/de Queiroz, Gatesy\_2007\_The supermatrix approach to systematics\_Trends in Ecology and Evolution.pdf:pdf},
isbn = {0169-5347 (Print)$\backslash$r0169-5347 (Linking)},
issn = {01695347},
journal = {Trends Ecol. Evol.},
number = {1},
pages = {34--41},
pmid = {17046100},
title = {{The supermatrix approach to systematics}},
volume = {22},
year = {2007}
}
@article{Tonooka2002a,
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(2).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{Cullis1972,
author = {Cullis, C. A.},
doi = {10.1007/BF00321458},
file = {:home/fin/Documents/papers/mendeley/Cullis\_1972\_DNA amounts in the nuclei of Paramecium bursaria\_Chromosoma.pdf:pdf},
issn = {00095915},
journal = {Chromosoma},
pages = {127--133},
pmid = {4682088},
title = {{DNA amounts in the nuclei of Paramecium bursaria}},
volume = {40},
year = {1972}
}
@article{Price2012,
author = {Price, Dana C and Chan, Cheong Xin and Yoon, Hwan Su and Yang, Eun Chan and Qiu, Huan and Weber, Andreas P M and Schwacke, Rainer and Gross, Jeferson and Blouin, Nicolas a and Lane, Chris},
file = {:home/fin/Documents/papers/mendeley/Price et al.\_2012\_Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants\_Science.pdf:pdf},
issn = {0036-8075},
journal = {Science (80-. ).},
number = {March},
pages = {843--847},
title = {{Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants}},
volume = {335},
year = {2012}
}
@article{Bianchi2010,
author = {Bianchi, Laura and D\'{\i}ez-Sampedro, Ana},
doi = {10.1371/journal.pone.0010241},
file = {:home/fin/Documents/papers/mendeley/Bianchi, D\'{\i}ez-Sampedro\_2010\_A Single Amino Acid Change Converts the Sugar Sensor SGLT3 into a Sugar Transporter\_PLoS ONE.pdf:pdf},
issn = {1932-6203},
journal = {PLoS One},
number = {4},
pages = {e10241},
title = {{A Single Amino Acid Change Converts the Sugar Sensor SGLT3 into a Sugar Transporter}},
url = {http://dx.plos.org/10.1371/journal.pone.0010241},
volume = {5},
year = {2010}
}
@article{Salerno1989,
abstract = {Chlorella vulgaris cultures have been submitted to a chilling shock, bringing down the growing temperature from to 24 degrees C to 4 degrees C. Growth was stopped immediately, and concomitantly there was an accumulation of sucrose and a decrease in the starch content. The enzymes involved in sucrose metabolism were differentially affected by the chilling shock. Sucrose phosphate synthase activity increased while sucrose synthase was not affected. Simultaneously with the chilling shock, raffinose began to accumulate. When algal cultures were returned at 24 degrees C, raffinose disappeared. The presence of raffinose in algal cells has not been reported before.},
author = {Salerno, G L and Pontis, H G},
file = {:home/fin/Documents/papers/mendeley/Salerno, Pontis\_1989\_Raffinose Synthesis in Chlorella vulgaris Cultures after a Cold Shock.\_Plant physiology.pdf:pdf},
issn = {0032-0889},
journal = {Plant Physiol.},
pages = {648--51},
pmid = {16666596},
title = {{Raffinose Synthesis in Chlorella vulgaris Cultures after a Cold Shock.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1055895\&tool=pmcentrez\&rendertype=abstract},
volume = {89},
year = {1989}
}
@article{Matthew2004,
abstract = {A major challenge in the post-genome era of plant biology is to determine the functions of all the genes in the plant genome. A straightforward approach to this problem is to reduce or knock out expression of a gene with the hope of seeing a phenotype that is suggestive of its function. Insertional mutagenesis is a useful tool for this type of study, but it is limited by gene redundancy, lethal knock-outs, nontagged mutants and the inability to target the inserted element to a specific gene. RNA interference (RNAi) of plant genes, using constructs encoding self-complementary 'hairpin' RNA, largely overcomes these problems. RNAi has been used very effectively in Caenorhabditis elegans functional genomics, and resources are currently being developed for the application of RNAi to high-throughput plant functional genomics.},
author = {Matthew, Louisa},
doi = {10.1002/cfg.396},
file = {:home/fin/Documents/papers/mendeley/Matthew\_2004\_RNAi for plant functional genomics.\_Comparative and functional genomics.pdf:pdf},
issn = {1531-6912},
journal = {Comp. Funct. Genomics},
keywords = {high-throughput,post-transcriptional gene silencing,rna interference},
pages = {240--4},
pmid = {18629158},
title = {{RNAi for plant functional genomics.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2447448\&tool=pmcentrez\&rendertype=abstract},
volume = {5},
year = {2004}
}
@book{Crick1966,
author = {Crick, F.},
publisher = {University of Washington},
title = {{Of molecules and man}},
year = {1966}
}
@article{Yang1996,
author = {Yang, Ziheng},
file = {:home/fin/Documents/papers/mendeley/Yang\_1996\_Among-site rate variation and its impact on phylogenetic analyses\_TREE.pdf:pdf},
journal = {TREE},
number = {9},
pages = {367--372},
title = {{Among-site rate variation and its impact on phylogenetic analyses}},
volume = {11},
year = {1996}
}
@article{Kelley2010,
abstract = {We introduce Quake, a program to detect and correct errors in DNA sequencing reads. Using a maximum likelihood approach incorporating quality values and nucleotide specific miscall rates, Quake achieves the highest accuracy on realistically simulated reads. We further demonstrate substantial improvements in de novo assembly and SNP detection after using Quake. Quake can be used for any size project, including more than one billion human reads, and is freely available as open source software from http://www.cbcb.umd.edu/software/quake.},
author = {Kelley, David R and Schatz, Michael C and Salzberg, Steven L},
doi = {10.1186/gb-2010-11-11-r116},
file = {:home/fin/Documents/papers/mendeley/Kelley, Schatz, Salzberg\_2010\_Quake quality-aware detection and correction of sequencing errors.\_Genome biology.pdf:pdf},
isbn = {1465-6906},
issn = {1465-6906},
journal = {Genome Biol.},
number = {11},
pages = {R116},
pmid = {21114842},
publisher = {BioMed Central Ltd},
title = {{Quake: quality-aware detection and correction of sequencing errors.}},
url = {http://genomebiology.com/2010/11/11/R116},
volume = {11},
year = {2010}
}
@article{Yang2013,
author = {Yang, X. and Chockalingam, S. P. and Aluru, S.},
doi = {10.1093/bib/bbs015},
file = {:home/fin/Documents/papers/mendeley/Yang, Chockalingam, Aluru\_2013\_A survey of error-correction methods for next-generation sequencing\_Briefings in Bioinformatics.pdf:pdf},
issn = {1467-5463},
journal = {Brief. Bioinform.},
keywords = {error correction,next-generation sequencing,sequence analysis},
number = {1},
pages = {56--66},
title = {{A survey of error-correction methods for next-generation sequencing}},
url = {http://bib.oxfordjournals.org/cgi/doi/10.1093/bib/bbs015},
volume = {14},
year = {2013}
}
@article{Gortz1982,
author = {Gortz, Hans-dieter},
file = {:home/fin/Documents/papers/mendeley/Gortz\_1982\_Infections of Paramecium Bursaria with Bacteria and Yeasts\_Journal of Cell Science.pdf:pdf},
journal = {J. Cell Sci.},
pages = {445--453},
title = {{Infections of Paramecium Bursaria with Bacteria and Yeasts}},
volume = {58},
year = {1982}
}
@article{Nakai1999,
author = {Nakai, Kenta and Horton, Paul},
doi = {10.1016/S0968-0004(98)01336-X},
file = {:home/fin/Documents/papers/mendeley/Nakai, Horton\_1999\_PSORT a program for detecting sorting signals in proteins and predicting their subcellular localization\_Trends in Bio.pdf:pdf},
isbn = {0968-0004 (Print)$\backslash$n0968-0004 (Linking)},
issn = {09680004},
journal = {Trends Biochem. Sci.},
keywords = {Biochemistry,Bioinformatics,Cell biology,bioinformatics,genome projects,prediction,proteome,sorting signal,subcellular localization},
number = {98},
pages = {34--35},
pmid = {10087920},
title = {{PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization}},
url = {http://www.sciencedirect.com/science/article/pii/S096800049801336X},
volume = {24},
year = {1999}
}
@article{Siegel1963,
author = {Siegel, R W},
file = {:home/fin/Documents/papers/mendeley/Siegel\_1963\_New result on genetics of mating types in Paramecium bursaria\_Genet. Res.pdf:pdf},
journal = {Genet. Res.},
pages = {132--142},
title = {{New result on genetics of mating types in Paramecium bursaria}},
volume = {4},
year = {1963}
}
@article{gordon2010fastx,
author = {Gordon, A and Hannon, G J},
journal = {FASTQ/A Short-reads Pre-processing Tools (Unpublished) http://hannonlab. cshl. edu/fastx\_toolkit},
title = {{Fastx-toolkit}},
year = {2010}
}
@article{Lee2009a,
abstract = {BACKGROUND: Identifying disease causing genes and understanding their molecular mechanisms are essential to developing effective therapeutics. Thus, several computational methods have been proposed to prioritize candidate disease genes by integrating different data types, including sequence information, biomedical literature, and pathway information. Recently, molecular interaction networks have been incorporated to predict disease genes, but most of those methods do not utilize invaluable disease-specific information available in mRNA expression profiles of patient samples.$\backslash$n$\backslash$nRESULTS: Through the integration of protein-protein interaction networks and gene expression profiles of acute myeloid leukemia (AML) patients, we identified subnetworks of interacting proteins dysregulated in AML and characterized known mutation genes causally implicated to AML embedded in the subnetworks. The analysis shows that the set of extracted subnetworks is a reservoir rich in AML genes reflecting key leukemogenic processes such as myeloid differentiation.$\backslash$n$\backslash$nCONCLUSION: We showed that the integrative approach both utilizing gene expression profiles and molecular networks could identify AML causing genes most of which were not detectable with gene expression analysis alone due to the minor changes in mRNA level.},
author = {Lee, Eunjung and Jung, Hyunchul and Radivojac, Predrag and Kim, Jong-Won and Lee, Doheon},
doi = {10.1186/1471-2105-10-S9-S2},
file = {:home/fin/Documents/papers/mendeley/Lee et al.\_2009\_Analysis of AML genes in dysregulated molecular networks.\_BMC bioinformatics.pdf:pdf},
isbn = {1471210510},
issn = {1471-2105},
journal = {BMC Bioinformatics},
keywords = {Computational Biology,Computational Biology: methods,Gene Expression Profiling,Gene Expression Profiling: methods,Gene Regulatory Networks,Humans,Leukemia, Myeloid, Acute,Leukemia, Myeloid, Acute: genetics,RNA, Messenger,RNA, Messenger: metabolism},
pages = {S2},
pmid = {19761572},
title = {{Analysis of AML genes in dysregulated molecular networks.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2745689\&tool=pmcentrez\&rendertype=abstract},
volume = {10 Suppl 9},
year = {2009}
}
@article{C.Mereschkowsky1905,
author = {Mereschkowsky, C.},
file = {:home/fin/Documents/papers/mendeley/Mereschkowsky\_1905\_\"{U}ber Natur und Ursprung der Chromatophoren im Pflanzenreiche\_Biologisches Centralblatt.pdf:pdf},
issn = {0006-3304},
journal = {Biol. Cent.},
number = {July},
pages = {593--604},
title = {{\"{U}ber Natur und Ursprung der Chromatophoren im Pflanzenreiche}},
volume = {25},
year = {1905}
}
@article{Bengio2013,
abstract = {The success of machine learning algorithms generally depends on data representation, and we hypothesize that this is because different representations can entangle and hide more or less the different explanatory factors of variation behind the data. Although specific domain knowledge can be used to help design representations, learning with generic priors can also be used, and the quest for AI is motivating the design of more powerful representation-learning algorithms implementing such priors. This paper reviews recent work in the area of unsupervised feature learning and deep learning, covering advances in probabilistic models, auto-encoders, manifold learning, and deep networks. This motivates longer-term unanswered questions about the appropriate objectives for learning good representations, for computing representations (i.e., inference), and the geometrical connections between representation learning, density estimation and manifold learning.},
archivePrefix = {arXiv},
arxivId = {1206.5538},
author = {Bengio, Yoshua and Courville, Aaron and Vincent, Pascal},
doi = {10.1109/TPAMI.2013.50},
eprint = {1206.5538},
file = {:home/fin/Documents/papers/mendeley/Bengio, Courville, Vincent\_2013\_Representation learning A review and new perspectives\_Pattern Analysis and \ldots.pdf:pdf},
isbn = {0162-8828 VO - 35},
issn = {01628828},
journal = {Pattern Anal. \ldots},
number = {1993},
pages = {1--30},
pmid = {23459267},
title = {{Representation learning: A review and new perspectives}},
url = {http://arxiv.org/abs/1206.5538$\backslash$nhttp://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=6472238},
year = {2013}
}
@article{OMalley2015,
author = {O’Malley, Maureen a.},
doi = {10.1007/s10539-015-9482-2},
file = {:home/fin/Documents/papers/mendeley/O’Malley\_2015\_Molecular organisms\_Biology \& Philosophy.pdf:pdf},
issn = {0169-3867},
journal = {Biol. Philos.},
keywords = {endosymbiosis \'{a} eukaryote evolution,\'{a} molecular evolution \'{a}},
title = {{Molecular organisms}},
url = {http://link.springer.com/10.1007/s10539-015-9482-2},
year = {2015}
}
@inproceedings{Karp1972,
abstract = {A large class of computational problems involve the determination of properties of graphs, digraphs, integers, arrays of integers, finite families of finite sets, boolean formulas and elements of other countable domains. Through simple encodings from such domains into the set of words over a finite alphabet these problems can be converted into language recognition problems, and we can inquire into their computational complexity. It is reasonable to consider such a problem satisfactorily solved when an algorithm for its solution is found which terminates within a number of steps bounded by a polynomial in the length of the input. We show that a large number of classic unsolved problems of covering, matching, packing, routing, assignment and sequencing are equivalent, in the sense that either each of them possesses a polynomial-bounded algorithm or none of them does.},
author = {Karp, Richard M.},
booktitle = {Complex. Comput. Comput. Proc. a Symp. Complex. Comput. Comput.},
doi = {10.1007/978-3-540-68279-0\_8},
file = {:home/fin/Documents/papers/mendeley/Karp\_1972\_Reducibility among combinatorial problems\_Complexity of Computer Computations Proceedings of a symposium on the Complexity of.pdf:pdf},
isbn = {9783540682745},
issn = {00224812},
pages = {85--103},
pmid = {15890271},
title = {{Reducibility among combinatorial problems}},
year = {1972}
}
@article{Mereschkowsky1920,
author = {Mereschkowsky, C.},
journal = {Bull. la Soci\'{e}t\'{e} des Sci. Nat. l’Ouest la Fr.},
pages = {17--98},
title = {{La plante consid\'{e}r\'{e}e comme un complexe symbiotique}},
volume = {6},
year = {1920}
}
@article{Ku2015,
author = {Ku, Chuan and Nelson-Sathi, Shijulal and Roettger, Mayo and Garg, Sriram and Hazkani-Covo, Einat and Martin, William F.},
doi = {10.1073/pnas.1421385112},
file = {:home/fin/Documents/papers/mendeley/Ku et al.\_2015\_Endosymbiotic gene transfer from prokaryotic pangenomes Inherited chimerism in eukaryotes\_Proceedings of the National Aca.pdf:pdf},
isbn = {1421385112},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
pages = {201421385},
title = {{Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes}},
url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1421385112},
year = {2015}
}
@article{Morf2013,
abstract = {RNA interference uses small RNAs (sRNA), which target genes for sequence-specific silencing. The parasite Entamoeba histolytica contains an abundant repertoire of 27 nt antisense (AS) sRNA with 5'-polyphosphate termini, but their roles in regulating gene expression have not been well established. We demonstrate that a gene-coding region to which large numbers of AS sRNAs map can serve as a 'trigger' and silence the gene fused to it. Silencing is mediated by generation of AS sRNAs with 5'-polyphosphate termini that have sequence specificity to the fused gene. The mechanism of silencing is independent of the placement of the trigger relative to the silenced gene but is dependent on the sRNA concentration to the trigger. Silencing requires transcription of the trigger-gene fusion and is maintained despite loss of the trigger plasmid. We used this approach to silence multiple amebic genes, including an E. histolytica Myb gene, which is upregulated during oxidative stress response. Silencing of the EhMyb gene decreased parasite viability under oxidative stress conditions. Thus, we have developed a new tool for genetic manipulation in E. histolytica with many advantages over currently available technologies. Additionally, these data shed mechanistic insights into a eukaryotic RNA interference pathway with many novel aspects.},
author = {Morf, Laura and Pearson, Richard J and Wang, Angelia S and Singh, Upinder},
doi = {10.1093/nar/gkt717},
file = {:home/fin/Documents/papers/mendeley/Morf et al.\_2013\_Robust gene silencing mediated by antisense small RNAs in the pathogenic protist Entamoeba histolytica.\_Nucleic acids r.pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$r0305-1048 (Linking)},
issn = {1362-4962},
journal = {Nucleic Acids Res.},
keywords = {Cell Line,Entamoeba histolytica,Entamoeba histolytica: genetics,Gene Knockdown Techniques,Genes, Reporter,Hydrogen Peroxide,Hydrogen Peroxide: toxicity,Oxidative Stress,RNA Interference,RNA, Antisense,RNA, Antisense: metabolism,RNA, Small Untranslated,RNA, Small Untranslated: metabolism,Transcription Factors,Transcription Factors: genetics},
number = {20},
pages = {9424--37},
pmid = {23935116},
title = {{Robust gene silencing mediated by antisense small RNAs in the pathogenic protist Entamoeba histolytica.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3814356\&tool=pmcentrez\&rendertype=abstract},
volume = {41},
year = {2013}
}
@article{Edgar2004,
author = {Edgar, Robert C},
doi = {10.1186/1471-2105-5-113},
file = {:home/fin/Documents/papers/mendeley/Edgar\_2004\_MUSCLE a multiple sequence alignment method with reduced time and space complexity\_BMC Bioinformatics.pdf:pdf},
journal = {BMC Bioinformatics},
number = {113},
pages = {1--19},
title = {{MUSCLE : a multiple sequence alignment method with reduced time and space complexity}},
volume = {5},
year = {2004}
}
@article{Derelle2015,
author = {Derelle, Romain and Torruella, Guifr\'{e} and Klime, Vladim\'{\i}r},
doi = {10.1073/pnas.1420657112},
file = {:home/fin/Documents/papers/mendeley/Derelle, Torruella, Klime\_2015\_Bacterial proteins pinpoint a single eukaryotic root\_Unknown.pdf:pdf},
pages = {1--7},
title = {{Bacterial proteins pinpoint a single eukaryotic root}},
year = {2015}
}
@article{Bolger2014a,
abstract = {MOTIVATION: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. RESULTS: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. AVAILABILITY AND IMPLEMENTATION: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic CONTACT: usadel@bio1.rwth-aachen.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
author = {Bolger, Anthony M. and Lohse, Marc and Usadel, Bjoern},
doi = {10.1093/bioinformatics/btu170},
file = {:home/fin/Documents/papers/mendeley/Bolger, Lohse, Usadel\_2014\_Trimmomatic A Flexible Trimmer for Illumina Sequence Data\_Bioinformatics.pdf:pdf},
isbn = {1367-4803},
issn = {14602059},
journal = {Bioinformatics},
number = {15},
pages = {2114--2120},
pmid = {24695404},
title = {{Trimmomatic: A Flexible Trimmer for Illumina Sequence Data}},
volume = {30},
year = {2014}
}
@article{Kuhl2012,
abstract = {Liquid chromatography coupled to mass spectrometry is routinely used for metabolomics experiments. In contrast to the fairly routine and automated data acquisition steps, subsequent compound annotation and identification require extensive manual analysis and thus form a major bottleneck in data interpretation. Here we present CAMERA, a Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data. To evaluate the algorithms, we compared the annotation of CAMERA against a manually defined annotation for a mixture of known compounds spiked into a complex matrix at different concentrations. CAMERA successfully extracted accurate masses for 89.7\% and 90.3\% of the annotatable compounds in positive and negative ion modes, respectively. Furthermore, we present a novel annotation approach that combines spectral information of data acquired in opposite ion modes to further improve the annotation rate. We demonstrate the utility of CAMERA in two different, easily adoptable plant metabolomics experiments, where the application of CAMERA drastically reduced the amount of manual analysis.},
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Kuhl, Carsten and Tautenhahn, Ralf and B\"{o}ttcher, Christoph and Larson, Tony R. and Neumann, Steffen},
doi = {10.1021/ac202450g},
eprint = {NIHMS150003},
file = {:home/fin/Documents/papers/mendeley/Kuhl et al.\_2012\_CAMERA An integrated strategy for compound spectra extraction and annotation of liquid chromatographymass spectrometry.pdf:pdf},
isbn = {0003-2700},
issn = {00032700},
journal = {Anal. Chem.},
pages = {283--289},
pmid = {22111785},
title = {{CAMERA: An integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets}},
url = {http://dx.doi.org/10.1021/ac202450g},
volume = {84},
year = {2012}
}
@article{Hackstein1994,
abstract = {We have screened more than 110 representatives of the different taxa of terrestrial arthropods for methane production in order to obtain additional information about the origins of biogenic methane. Methanogenic bacteria occur in the hindguts of nearly all tropical representatives of millipedes (Diplopoda), cockroaches (Blattaria), termites (Isoptera), and scarab beetles (Scarabaeidae), while such methanogens are absent from 66 other arthropod species investigated. Three types of symbiosis were found: in the first type, the arthropod's hindgut is colonized by free methanogenic bacteria; in the second type, methanogens are closely associated with chitinous structures formed by the host's hindgut; the third type is mediated by intestinal anaerobic protists with intracellular methanogens. Such symbiotic associations are likely to be a characteristic property of the particular taxon. Since these taxa represent many families with thousands of species, the world populations of methane-producing arthropods constitute an enormous biomass. We show that arthropod symbionts can contribute substantially to atmospheric methane.},
author = {Hackstein, J H and Stumm, C K},
doi = {10.1073/pnas.91.12.5441},
file = {:home/fin/Documents/papers/mendeley/Hackstein, Stumm\_1994\_Methane production in terrestrial arthropods.\_Proceedings of the National Academy of Sciences of the United States.pdf:pdf},
isbn = {0027-8424},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
number = {June},
pages = {5441--5445},
pmid = {8202505},
title = {{Methane production in terrestrial arthropods.}},
volume = {91},
year = {1994}
}
@article{Wolpert1996,
abstract = {This is the first of two papers that use off-training set (OTS) error to investigate the assumption-free relationship between learning algorithms. This first paper discusses the senses in which there are no a priori distinctions between learning algorithms. (The second paper discusses the senses in which there are such distinctions.) In this first paper it is shown, loosely speaking, that for any two algorithms A and B, there are “as many” targets (or priors over targets) for which A has lower expected OTS error than B as vice versa, for loss functions like zero-one loss. In particular, this is true if A is cross-validation and B is “anti-cross-validation” (choose the learning algorithm with largest cross-validation error). This paper ends with a discussion of the implications of these results for computational learning theory. It is shown that one cannot say: if empirical misclassification rate is low, the Vapnik-Chervonenkis dimension of your generalizer is small, and the training set is large, then with high probability your OTS error is small. Other implications for “membership queries” algorithms and “punting” algorithms are also discussed.},
author = {Wolpert, David H.},
doi = {10.1162/neco.1996.8.7.1391},
file = {:home/fin/Documents/papers/mendeley/Wolpert\_1996\_The Existence of A Priori Distinctions Between Learning Algorithms\_Neural Computation.pdf:pdf},
issn = {0899-7667},
journal = {Neural Comput.},
number = {7},
pages = {1391--1420},
title = {{The Existence of A Priori Distinctions Between Learning Algorithms}},
volume = {8},
year = {1996}
}
@article{Dougherty2008,
abstract = {There is an epistemological crisis in genomics. At issue is what constitutes scientific knowledge in genomic science, or systems biology in general. Does this crisis require a new perspective on knowledge heretofore absent from science or is it merely a matter of interpreting new scientific developments in an existing epistemological framework? This paper discusses the manner in which the experimental method, as developed and understood over recent centuries, leads naturally to a scientific epistemology grounded in an experimental-mathematical duality. It places genomics into this epistemological framework and examines the current situation in genomics. Meaning and the constitution of scientific knowledge are key concerns for genomics, and the nature of the epistemological crisis in genomics depends on how these are understood.},
author = {Dougherty, Edward R},
doi = {10.2174/138920208784139546},
file = {:home/fin/Documents/papers/mendeley/Dougherty\_2008\_On the epistemological crisis in genomics.\_Current genomics.pdf:pdf},
issn = {13892029},
journal = {Curr. Genomics},
pages = {69--79},
pmid = {19440447},
title = {{On the epistemological crisis in genomics.}},
volume = {9},
year = {2008}
}
@article{Felsenstein1978,
author = {Felsenstein, Joseph},
doi = {10.1080/10635150290155881},
file = {:home/fin/Documents/papers/mendeley/Felsenstein\_1978\_Society of Systematic Biologists\_Society of Systematic Biologists.pdf:pdf},
isbn = {1063515060098},
journal = {Soc. Syst. Biol.},
number = {4},
pages = {401--410},
title = {{Society of Systematic Biologists}},
volume = {27},
year = {1978}
}
@incollection{Peng2010,
author = {Peng, Yu and Leung, HenryC.M. and Yiu, S M and Chin, FrancisY.L.},
booktitle = {Res. Comput. Mol. Biol. SE  - 28},
doi = {10.1007/978-3-642-12683-3\_28},
editor = {Berger, Bonnie},
isbn = {978-3-642-12682-6},
keywords = {De novo assembly,de Bruijn graph,high throughput short reads,mate-pair,string graph},
language = {English},
pages = {426--440},
publisher = {Springer Berlin Heidelberg},
series = {Lecture Notes in Computer Science},
title = {{IDBA – A Practical Iterative de Bruijn Graph De Novo Assembler}},
url = {http://dx.doi.org/10.1007/978-3-642-12683-3\_28},
volume = {6044},
year = {2010}
}
@article{Pettersson2009,
abstract = {Advancements in the field of DNA sequencing are changing the scientific horizon and promising an era of personalized medicine for elevated human health. Although platforms are improving at the rate of Moore's Law, thereby reducing the sequencing costs by a factor of two or three each year, we find ourselves at a point in history where individual genomes are starting to appear but where the cost is still too high for routine sequencing of whole genomes. These needs will be met by miniaturized and parallelized platforms that allow a lower sample and template consumption thereby increasing speed and reducing costs. Current massively parallel, state-of-the-art systems are providing significantly improved throughput over Sanger systems and future single-molecule approaches will continue the exponential improvements in the field. ?? 2008 Elsevier Inc. All rights reserved.},
author = {Pettersson, Erik and Lundeberg, Joakim and Ahmadian, Afshin},
doi = {10.1016/j.ygeno.2008.10.003},
file = {:home/fin/Documents/papers/mendeley/Pettersson, Lundeberg, Ahmadian\_2009\_Generations of sequencing technologies\_Genomics.pdf:pdf},
isbn = {08887543},
issn = {08887543},
journal = {Genomics},
keywords = {DNA sequencing,Next generation},
number = {2},
pages = {105--111},
pmid = {18992322},
publisher = {Elsevier Inc.},
title = {{Generations of sequencing technologies}},
url = {http://dx.doi.org/10.1016/j.ygeno.2008.10.003},
volume = {93},
year = {2009}
}
@article{Antonov2008,
author = {Antonov, Alexey V and Dietmann, Sabine and Mewes, Hans W},
doi = {10.1186/gb-2008-9-12-r179},
file = {:home/fin/Documents/papers/mendeley/Antonov, Dietmann, Mewes\_2008\_KEGG spider interpretation of genomics data in the context of the global gene metabolic network\_Genome Bio.pdf:pdf},
issn = {1465-6906},
journal = {Genome Biol.},
number = {12},
pages = {R179},
title = {{KEGG spider: interpretation of genomics data in the context of the global gene metabolic network}},
url = {http://genomebiology.com/2008/9/12/R179},
volume = {9},
year = {2008}
}
@article{Braslavsky2003,
abstract = {The completion of the human genome draft has taken several years and is only the beginning of a period in which large amounts of DNA and RNA sequence information will be required from many individuals and species. Conventional sequencing technology has limitations in cost, speed, and sensitivity, with the result that the demand for sequence information far outstrips current capacity. There have been several proposals to address these issues by developing the ability to sequence single DNA molecules, but none have been experimentally demonstrated. Here we report the use of DNA polymerase to obtain sequence information from single DNA molecules by using fluorescence microscopy. We monitored repeated incorporation of fluorescently labeled nucleotides into individual DNA strands with single base resolution, allowing the determination of sequence fingerprints up to 5 bp in length. These experiments show that one can study the activity of DNA polymerase at the single molecule level with single base resolution and a high degree of parallelization, thus providing the foundation for a practical single molecule sequencing technology.},
author = {Braslavsky, Ido and Braslavsky, Ido and Hebert, Benedict and Hebert, Benedict and Kartalov, Emil and Kartalov, Emil and Quake, Stephen R and Quake, Stephen R},
doi = {10.1073/pnas.0230489100},
file = {:home/fin/Documents/papers/mendeley/Braslavsky et al.\_2003\_Sequence information can be obtained from single DNA molecules.\_Proceedings of the National Academy of Sciences o.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
keywords = {Base Sequence,DNA,DNA Primers,DNA: chemistry,RNA,RNA: chemistry,Templates, Genetic},
pages = {3960--4},
pmid = {12651960},
title = {{Sequence information can be obtained from single DNA molecules.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12651960},
volume = {100},
year = {2003}
}
@article{Alibu2005,
author = {Alibu, Vincent P. and Storm, Lilian and Haile, Simon and Clayton, Christine and Horn, David},
doi = {10.1016/j.molbiopara.2004.10.002},
file = {:home/fin/Documents/papers/mendeley/Alibu et al.\_2005\_A doubly inducible system for RNA interference and rapid RNAi plasmid construction in Trypanosoma brucei\_Molecular and.pdf:pdf},
issn = {01666851},
journal = {Mol. Biochem. Parasitol.},
keywords = {rna interference vector,t7 polymerase,tet repressor,trypanosoma brucei},
pages = {75--82},
title = {{A doubly inducible system for RNA interference and rapid RNAi plasmid construction in Trypanosoma brucei}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0166685104002750},
volume = {139},
year = {2005}
}
@article{Gouy2010,
abstract = {We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and phylogenetic tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous versions) and Phylo\_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating phylogenetic trees. In relation to the wide present offer of tools and algorithms for phylogenetic analyses, SeaView is especially useful for teaching and for occasional users of such software. SeaView is freely available at http://pbil.univ-lyon1.fr/software/seaview.},
author = {Gouy, Manolo and Guindon, St\'{e}phane and Gascuel, Olivier},
doi = {10.1093/molbev/msp259},
file = {:home/fin/Documents/papers/mendeley/Gouy, Guindon, Gascuel\_2010\_SeaView version 4 A multiplatform graphical user interface for sequence alignment and phylogenetic tree buil.pdf:pdf},
issn = {1537-1719},
journal = {Mol. Biol. Evol.},
keywords = {Computer Graphics,Phylogeny,Sequence Alignment,Sequence Alignment: methods,Software,User-Computer Interface},
month = feb,
number = {2},
pages = {221--4},
pmid = {19854763},
title = {{SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19854763},
volume = {27},
year = {2010}
}
@incollection{Miwa2009,
author = {Miwa, Isoji},
booktitle = {Endosymbionts in Paramecium},
chapter = {4},
doi = {10.1007/978-3-540-92677-1},
editor = {Fujishima, Masahiro},
file = {:home/fin/Documents/papers/mendeley/Miwa\_2009\_Regulation of Circadian Rhythms of Paramecium bursaria by Symbiotic Chlorella Species\_Endosymbionts in Paramecium.pdf:pdf},
isbn = {9783540926771},
pages = {83--110},
publisher = {Springer},
series = {Microbiology Monographs},
title = {{Regulation of Circadian Rhythms of Paramecium bursaria by Symbiotic Chlorella Species}},
volume = {12},
year = {2009}
}
@article{Pruitt2007,
abstract = {NCBI's reference sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. The database includes 3774 organisms spanning prokaryotes, eukaryotes and viruses, and has records for 2,879,860 proteins (RefSeq release 19). RefSeq records integrate information from multiple sources, when additional data are available from those sources and therefore represent a current description of the sequence and its features. Annotations include coding regions, conserved domains, tRNAs, sequence tagged sites (STS), variation, references, gene and protein product names, and database cross-references. Sequence is reviewed and features are added using a combined approach of collaboration and other input from the scientific community, prediction, propagation from GenBank and curation by NCBI staff. The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence.},
author = {Pruitt, Kim D. and Tatusova, Tatiana and Maglott, Donna R.},
doi = {10.1093/nar/gkl842},
file = {:home/fin/Documents/papers/mendeley/Pruitt, Tatusova, Maglott\_2007\_NCBI reference sequences (RefSeq) A curated non-redundant sequence database of genomes, transcripts and p.pdf:pdf},
isbn = {1362-4962; 0305-1048},
issn = {03051048},
journal = {Nucleic Acids Res.},
pages = {501--504},
pmid = {17130148},
title = {{NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins}},
volume = {35},
year = {2007}
}
@article{Chen2015,
abstract = {Soluble sugars serve five main purposes in multicellular organisms: as sources of carbon skeletons, osmolytes, signals, and transient energy storage and as transport molecules. Most sugars are derived from photosynthetic organisms, particularly plants. In multicellular organisms, some cells specialize in providing sugars to other cells (e.g., intestinal and liver cells in animals, photosynthetic cells in plants), whereas others depend completely on an external supply (e.g., brain cells, roots and seeds). This cellular exchange of sugars requires transport proteins to mediate uptake or release from cells or subcellular compartments. Thus, not surprisingly, sugar transport is critical for plants, animals, and humans. At present, three classes of eukaryotic sugar transporters have been characterized, namely the glucose transporters (GLUTs), sodium-glucose symporters (SGLTs), and SWEETs. This review presents the history and state of the art of sugar transporter research, covering genetics, biochemistry, and physiology-from their identification and characterization to their structure, function, and physiology. In humans, understanding sugar transport has therapeutic importance (e.g., addressing diabetes or limiting access of cancer cells to sugars), and in plants, these transporters are critical for crop yield and pathogen susceptibility. Expected final online publication date for the Annual Review of Biochemistry Volume 84 is June 02, 2015. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.},
author = {Chen, Li-Qing and Cheung, Lily S and Feng, Liang and Tanner, Widmar and Frommer, Wolf B},
doi = {10.1146/annurev-biochem-060614-033904},
file = {:home/fin/Documents/papers/mendeley/Chen et al.\_2015\_Transport of Sugars.\_Annual review of biochemistry.pdf:pdf},
issn = {1545-4509},
journal = {Annu. Rev. Biochem.},
keywords = {carrier,glucose,glut,sglt,sucrose,sweet},
pages = {1--30},
pmid = {25747398},
title = {{Transport of Sugars.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25747398},
year = {2015}
}
@article{Venter2001,
abstract = {A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies—a whole-genome assembly and a regional chromosome assembly—were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90\% of the genome is in scaffold assemblies of 100,000 bp or more, and 25\% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional ∼12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1\% of the genome is spanned by exons, whereas 24\% is in introns, with 75\% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1\% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.},
author = {Venter, J Craig and Adams, Mark D and Myers, Eugene W and Li, Peter W and Mural, Richard J and Sutton, Granger G and Smith, Hamilton O and Yandell, Mark and Evans, Cheryl a and Holt, Robert a and Gocayne, Jeannine D and Amanatides, Peter and Ballew, Richard M and Huson, Daniel H and Wortman, Jennifer Russo and Zhang, Qing and Kodira, Chinnappa D and Zheng, Xiangqun H and Chen, Lin and Skupski, Marian and Subramanian, Gangadharan and Thomas, Paul D and Zhang, Jinghui and {Gabor Miklos}, George L and Nelson, Catherine and Broder, Samuel and Clark, Andrew G and Nadeau, Joe and McKusick, Victor a and Zinder, Norton and Levine, Arnold J and Roberts, Richard J and Simon, Mel and Slayman, Carolyn and Hunkapiller, Michael and Bolanos, Randall and Delcher, Arthur and Dew, Ian and Fasulo, Daniel and Flanigan, Michael and Florea, Liliana and Halpern, Aaron and Hannenhalli, Sridhar and Kravitz, Saul and Levy, Samuel and Mobarry, Clark and Reinert, Knut and Remington, Karin and Abu-Threideh, Jane and Beasley, Ellen and Biddick, Kendra and Bonazzi, Vivien and Brandon, Rhonda and Cargill, Michele and Chandramouliswaran, Ishwar and Charlab, Rosane and Chaturvedi, Kabir and Deng, Zuoming and Francesco, Valentina Di and Dunn, Patrick and Eilbeck, Karen and Evangelista, Carlos and Gabrielian, Andrei E and Gan, Weiniu and Ge, Wangmao and Gong, Fangcheng and Gu, Zhiping and Guan, Ping and Heiman, Thomas J and Higgins, Maureen E and Ji, Rui-Ru and Ke, Zhaoxi and Ketchum, Karen a and Lai, Zhongwu and Lei, Yiding and Li, Zhenya and Li, Jiayin and Liang, Yong and Lin, Xiaoying and Lu, Fu and Merkulov, Gennady V and Milshina, Natalia and Moore, Helen M and Naik, Ashwinikumar K and Narayan, Vaibhav a and Neelam, Beena and Nusskern, Deborah and Rusch, Douglas B and Salzberg, Steven and Shao, Wei and Shue, Bixiong and Sun, Jingtao and Wang, Zhen Yuan and Wang, Aihui and Wang, Xin and Wang, Jian and Wei, Ming-Hui and Wides, Ron and Xiao, Chunlin and Yan, Chunhua and Yao, Alison and Ye, Jane and Zhan, Ming and Zhang, Weiqing and Zhang, Hongyu and Zhao, Qi and Zheng, Liansheng and Zhong, Fei and Zhong, Wenyan and Zhu, Shiaoping C and Zhao, Shaying and Gilbert, Dennis and Baumhueter, Suzanna and Spier, Gene and Carter, Christine and Cravchik, Anibal and Woodage, Trevor and Ali, Feroze and An, Huijin and Awe, Aderonke and Baldwin, Danita and Baden, Holly and Barnstead, Mary and Barrow, Ian and Beeson, Karen and Busam, Dana and Carver, Amy and Center, Angela and Cheng, Ming Lai and Curry, Liz and Danaher, Steve and Davenport, Lionel and Desilets, Raymond and Dietz, Susanne and Dodson, Kristina and Doup, Lisa and Ferriera, Steven and Garg, Neha and Gluecksmann, Andres and Hart, Brit and Haynes, Jason and Haynes, Charles and Heiner, Cheryl and Hladun, Suzanne and Hostin, Damon and Houck, Jarrett and Howland, Timothy and Ibegwam, Chinyere and Johnson, Jeffery and Kalush, Francis and Kline, Lesley and Koduru, Shashi and Love, Amy and Mann, Felecia and May, David and McCawley, Steven and McIntosh, Tina and McMullen, Ivy and Moy, Mee and Moy, Linda and Murphy, Brian and Nelson, Keith and Pfannkoch, Cynthia and Pratts, Eric and Puri, Vinita and Qureshi, Hina and Reardon, Matthew and Rodriguez, Robert and Rogers, Yu-Hui and Romblad, Deanna and Ruhfel, Bob and Scott, Richard and Sitter, Cynthia and Smallwood, Michelle and Stewart, Erin and Strong, Renee and Suh, Ellen and Thomas, Reginald and Tint, Ni Ni and Tse, Sukyee and Vech, Claire and Wang, Gary and Wetter, Jeremy and Williams, Sherita and Williams, Monica and Windsor, Sandra and Winn-Deen, Emily and Wolfe, Keriellen and Zaveri, Jayshree and Zaveri, Karena and Abril, Josep F and Guig\'{o}, Roderic and Campbell, Michael J and Sjolander, Kimmen V and Karlak, Brian and Kejariwal, Anish and Mi, Huaiyu and Lazareva, Betty and Hatton, Thomas and Narechania, Apurva and Diemer, Karen and Muruganujan, Anushya and Guo, Nan and Sato, Shinji and Bafna, Vineet and Istrail, Sorin and Lippert, Ross and Schwartz, Russell and Walenz, Brian and Yooseph, Shibu and Allen, David and Basu, Anand and Baxendale, James and Blick, Louis and Caminha, Marcelo and Carnes-Stine, John and Caulk, Parris and Chiang, Yen-Hui and Coyne, My and Dahlke, Carl and Mays, Anne Deslattes and Dombroski, Maria and Donnelly, Michael and Ely, Dale and Esparham, Shiva and Fosler, Carl and Gire, Harold and Glanowski, Stephen and Glasser, Kenneth and Glodek, Anna and Gorokhov, Mark and Graham, Ken and Gropman, Barry and Harris, Michael and Heil, Jeremy and Henderson, Scott and Hoover, Jeffrey and Jennings, Donald and Jordan, Catherine and Jordan, James and Kasha, John and Kagan, Leonid and Kraft, Cheryl and Levitsky, Alexander and Lewis, Mark and Liu, Xiangjun and Lopez, John and Ma, Daniel and Majoros, William and McDaniel, Joe and Murphy, Sean and Newman, Matthew and Nguyen, Trung and Nguyen, Ngoc and Nodell, Marc and Pan, Sue and Peck, Jim and Peterson, Marshall and Rowe, William and Sanders, Robert and Scott, John and Simpson, Michael and Smith, Thomas and Sprague, Arlan and Stockwell, Timothy and Turner, Russell and Venter, Eli and Wang, Mei and Wen, Meiyuan and Wu, David and Wu, Mitchell and Xia, Ashley and Zandieh, Ali and Zhu, Xiaohong},
doi = {10.1126/science.1058040},
file = {:home/fin/Documents/papers/mendeley/Venter et al.\_2001\_The Sequence of the Human Genome\_Science.pdf:pdf},
isbn = {0036-8075},
issn = {0036-8075},
journal = {Science (80-. ).},
number = {February},
pages = {1304--1351},
pmid = {11181995},
title = {{The Sequence of the Human Genome}},
url = {http://www.sciencemag.org/content/291/5507/1304.abstract},
volume = {291},
year = {2001}
}
@article{Macmanes2013,
abstract = {The study of functional genomics, particularly in non-model organisms, has been dramatically improved over the last few years by the use of transcriptomes and RNAseq. While these studies are potentially extremely powerful, a computationally intensive procedure, the de novo construction of a reference transcriptome must be completed as a prerequisite to further analyses. The accurate reference is critically important as all downstream steps, including estimating transcript abundance are critically dependent on the construction of an accurate reference. Though a substantial amount of research has been done on assembly, only recently have the pre-assembly procedures been studied in detail. Specifically, several stand-alone error correction modules have been reported on and, while they have shown to be effective in reducing errors at the level of sequencing reads, how error correction impacts assembly accuracy is largely unknown. Here, we show via use of a simulated and empiric dataset, that applying error correction to sequencing reads has significant positive effects on assembly accuracy, and should be applied to all datasets. A complete collection of commands which will allow for the production of Reptile corrected reads is available at https://github.com/macmanes/error\_correction/tree/master/scripts and as File S1.},
archivePrefix = {arXiv},
arxivId = {1304.0817},
author = {Macmanes, Matthew D and Eisen, Michael B},
doi = {10.7717/peerj.113},
eprint = {1304.0817},
file = {:home/fin/Documents/papers/mendeley/Macmanes, Eisen\_2013\_Improving transcriptome assembly through error correction of high-throughput sequence reads.\_PeerJ.pdf:pdf},
isbn = {2167-8359 (Electronic)},
issn = {2167-8359},
journal = {PeerJ},
pages = {e113},
pmid = {23904992},
title = {{Improving transcriptome assembly through error correction of high-throughput sequence reads.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3728768\&tool=pmcentrez\&rendertype=abstract},
volume = {1},
year = {2013}
}
@article{Lange2005,
abstract = {The presence of Archaea is currently being explored in various environments, including extreme geographic positions and eukaryotic habitats. Methanogens are the dominating archaeal organisms found in most animals, from unicellular protozoa to humans. Many methanogens can contribute to the removal of hydrogen, thereby improving the efficiency of fermentation or the reductive capacity of energy-yielding reactions. They may also be involved in tissue damage in periodontal patients. Recent molecular studies demonstrated the presence of Archaea other than methanogens in some animals-but so far, not in humans. The roles of these microorganisms have not yet been established. In the present review, we present the state of the art regarding the archaeal microflora in animals.},
author = {Lange, Marianne and Westermann, Peter and Ahring, Birgitte Ki\ae r},
doi = {10.1007/s00253-004-1790-4},
file = {:home/fin/Documents/papers/mendeley/Lange, Westermann, Ahring\_2005\_Archaea in protozoa and metazoa\_Applied Microbiology and Biotechnology.pdf:pdf},
isbn = {0175-7598 (Print)},
issn = {01757598},
journal = {Appl. Microbiol. Biotechnol.},
pages = {465--474},
pmid = {15630514},
title = {{Archaea in protozoa and metazoa}},
volume = {66},
year = {2005}
}
@article{Dillies2013,
author = {Dillies, M.-a. and Rau, a. and Aubert, J. and Hennequet-Antier, C. and Jeanmougin, M. and Servant, N. and Keime, C. and Marot, G. and Castel, D. and Estelle, J. and Guernec, G. and Jagla, B. and Jouneau, L. and Laloe, D. and {Le Gall}, C. and Schaeffer, B. and {Le Crom}, S. and Guedj, M. and Jaffrezic, F.},
doi = {10.1093/bib/bbs046},
file = {:home/fin/Documents/papers/mendeley/Dillies et al.\_2013\_A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis\_Briefi.pdf:pdf},
issn = {1467-5463},
journal = {Brief. Bioinform.},
keywords = {differential analysis,high-throughput sequencing,normalization,rna-seq},
number = {6},
pages = {671--683},
title = {{A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis}},
url = {http://bib.oxfordjournals.org/cgi/doi/10.1093/bib/bbs046},
volume = {14},
year = {2013}
}
@article{Timmons2001,
abstract = {Genetic interference mediated by double-stranded RNA (RNAi) has been a valuable tool in the analysis of gene function in Caenorhabditis elegans. Here we report an efficient induction of RNAi using bacteria to deliver double-stranded RNA. This method makes use of bacteria that are deficient in RNaseIII, an enzyme that normally degrades a majority of dsRNAs in the bacterial cell. Bacteria deficient for RNaseIII were engineered to produce high quantities of specific dsRNA segments. When fed to C. elegans, such engineered bacteria were found to produce populations of RNAi-affected animals with phenotypes that were comparable in expressivity to the corresponding loss-of-function mutants. We found the method to be most effective in inducing RNAi for non-neuronal tissue of late larval and adult hermaphrodites, with decreased effectiveness in the nervous system, in early larval stages, and in males. Bacteria-induced RNAi phenotypes could be maintained over the course of several generations with continuous feeding, allowing for convenient assessments of the biological consequences of specific genetic interference and of continuous exposure to dsRNAs. ?? 2001 Elsevier Science B.V.},
author = {Timmons, Lisa and Court, Donald L. and Fire, Andrew},
doi = {10.1016/S0378-1119(00)00579-5},
file = {:home/fin/Documents/papers/mendeley/Timmons, Court, Fire\_2001\_Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabdit.pdf:pdf},
isbn = {0378-1119 (Print)$\backslash$n0378-1119 (Linking)},
issn = {03781119},
journal = {Gene},
keywords = {HT115(DE3),RNAi,T7 polymerase,dsRNA},
pages = {103--112},
pmid = {11223248},
title = {{Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans}},
volume = {263},
year = {2001}
}
@article{Li2010a,
abstract = {Most proteins in chloroplasts are encoded by the nuclear genome and synthesized as precursors with N-terminal targeting signals called transit peptides. Novel machinery has evolved to specifically import these proteins from the cytosol into chloroplasts. This machinery consists of more than a dozen components located in and around the chloroplast envelope, including a pair of GTPase receptors, a beta-barrel-type channel across the outer membrane, and an AAA(+)-type motor in the stroma. How individual components assemble into functional subcomplexes and the sequential steps of the translocation process are being mapped out. An increasing number of noncanonical import pathways, including a pathway with initial transport through the endomembrane system, is being revealed. Multiple levels of control on protein transport into chloroplasts have evolved, including the development of two receptor subfamilies, one for photosynthetic proteins and one for housekeeping proteins. The functions or expression levels of some translocon components are further adjusted according to plastid type, developmental stage, and metabolic conditions.},
author = {Li, Hsou-min and Chiu, Chi-Chou},
doi = {10.1146/annurev-arplant-042809-112222},
file = {:home/fin/Documents/papers/mendeley/Li, Chiu\_2010\_Protein transport into chloroplasts.\_Annual review of plant biology.pdf:pdf},
isbn = {1543-5008},
issn = {1543-5008},
journal = {Annu. Rev. Plant Biol.},
keywords = {chloroplast protein import,protein translocation across membranes,regulated transport,translocon},
pages = {157--180},
pmid = {20192748},
title = {{Protein transport into chloroplasts.}},
volume = {61},
year = {2010}
}
@incollection{Fokin2009,
author = {Fokin, Sergei I and G\"{o}rtz, Hans-dieter},
booktitle = {Endosymbionts in Paramecium},
chapter = {7},
doi = {10.1007/978-3-540-92677-1},
editor = {Fujishima, Masahiro},
file = {:home/fin/Documents/papers/mendeley/Fokin, G\"{o}rtz\_2009\_Diversity of Holospora Bacteria in Paramecium and Their Characterization\_Endosymbionts in Paramecium.pdf:pdf},
isbn = {9783540926771},
pages = {161--199},
publisher = {Springer},
series = {Microbiology Monographs},
title = {{Diversity of Holospora Bacteria in Paramecium and Their Characterization}},
volume = {12},
year = {2009}
}
@article{Lowe2014,
author = {Lowe, E.K. and Swalla, B.J. and Brown, C Titus},
doi = {10.7287/peerj.preprints.505v1},
file = {:home/fin/Documents/papers/mendeley/Lowe, Swalla, Brown\_2014\_Evaluating a lightweight transcriptome assembly pipeline on two closely related ascidian species\_PeerJ PrePrint.pdf:pdf},
journal = {PeerJ Prepr.},
keywords = {ascidians,assembly,cloud computing,next-generation sequencing},
pages = {0--10},
title = {{Evaluating a lightweight transcriptome assembly pipeline on two closely related ascidian species}},
volume = {September},
year = {2014}
}
@article{Spits2006,
abstract = {Multiple displacement amplification (MDA) is a recently described method of whole-genome amplification (WGA) that has proven efficient in the amplification of small amounts of DNA, including DNA from single cells. Compared with PCR-based WGA methods, MDA generates DNA with a higher molecular weight and shows better genome coverage. This protocol was developed for preimplantation genetic diagnosis, and details a method for performing single-cell MDA using the phi29 DNA polymerase. It can also be useful for the amplification of other minute quantities of DNA, such as from forensic material or microdissected tissue. The protocol includes the collection and lysis of single cells, and all materials and steps involved in the MDA reaction. The whole procedure takes 3 h and generates 1-2 microg of DNA from a single cell, which is suitable for multiple downstream applications, such as sequencing, short tandem repeat analysis or array comparative genomic hybridization.},
author = {Spits, Claudia and {Le Caignec}, C\'{e}dric and {De Rycke}, Martine and {Van Haute}, Lindsey and {Van Steirteghem}, Andr\'{e} and Liebaers, Inge and Sermon, Karen},
doi = {10.1038/nprot.2006.326},
file = {:home/fin/Documents/papers/mendeley/Spits et al.\_2006\_Whole-genome multiple displacement amplification from single cells.\_Nature protocols.pdf:pdf},
isbn = {1745-2473},
issn = {1754-2189},
journal = {Nat. Protoc.},
number = {4},
pages = {1965--1970},
pmid = {17487184},
title = {{Whole-genome multiple displacement amplification from single cells.}},
volume = {1},
year = {2006}
}
@book{Fujishima,
address = {M\"{u}nster, Germany},
author = {Fujishima, Masahiro},
edition = {Microbiolo},
editor = {Fujishima, Masahiro and Steinb\"{u}chel, Alexander},
file = {:home/fin/Documents/papers/mendeley/Fujishima\_2009\_book about Endosymbionts in Paramecium split into sections cite them\_Unknown.pdf:pdf},
isbn = {9783540926764},
publisher = {Springer},
title = {{book about Endosymbionts in Paramecium split into sections cite them}},
volume = {12},
year = {2009}
}
@article{Bergsten2005,
author = {Bergsten, Johannes},
file = {:home/fin/Documents/papers/mendeley/Bergsten\_2005\_A review of long-branch attraction\_Unknown.pdf:pdf},
pages = {163--193},
title = {{A review of long-branch attraction}},
volume = {21},
year = {2005}
}
@article{Suzuki2014,
abstract = {DNA sequences are translated into protein coding sequences and then further assigned to protein families in metagenomic analyses, because of the need for sensitivity. However, huge amounts of sequence data create the problem that even general homology search analyses using BLASTX become difficult in terms of computational cost. We designed a new homology search algorithm that finds seed sequences based on the suffix arrays of a query and a database, and have implemented it as GHOSTX. GHOSTX achieved approximately 131-165 times acceleration over a BLASTX search at similar levels of sensitivity. GHOSTX is distributed under the BSD 2-clause license and is available for download at http://www.bi.cs.titech.ac.jp/ghostx/. Currently, sequencing technology continues to improve, and sequencers are increasingly producing larger and larger quantities of data. This explosion of sequence data makes computational analysis with contemporary tools more difficult. We offer this tool as a potential solution to this problem.},
author = {Suzuki, Shuji and Kakuta, Masanori and Ishida, Takashi and Akiyama, Yutaka},
doi = {10.1371/journal.pone.0103833},
file = {:home/fin/Documents/papers/mendeley/Suzuki et al.\_2014\_GHOSTX an improved sequence homology search algorithm using a query suffix array and a database suffix array.\_PloS on.pdf:pdf},
issn = {1932-6203},
journal = {PLoS One},
number = {8},
pages = {e103833},
pmid = {25099887},
title = {{GHOSTX: an improved sequence homology search algorithm using a query suffix array and a database suffix array.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4123905\&tool=pmcentrez\&rendertype=abstract},
volume = {9},
year = {2014}
}
@misc{Sequencher,
address = {Ann Arbor, MI USA},
author = {{Gene Codes}},
title = {{Sequencher® version 4.10.1 sequence analysis software}},
url = {http://www.genecodes.com},
year = {2015}
}
@article{Schuster2008,
abstract = {A new generation of non-Sanger-based sequencing technologies has delivered on its promise of sequencing DNA at unprecedented speed, thereby enabling impressive scientific achievements and novel biological applications. However, before stepping into the limelight, next-generation sequencing had to overcome the inertia of a field that relied on Sanger-sequencing for 30 years.},
author = {Schuster, Stephan C},
doi = {10.1038/nmeth1156},
file = {:home/fin/Documents/papers/mendeley/Schuster\_2008\_Next-generation sequencing transforms today's biology.\_Nature methods.pdf:pdf},
isbn = {1548-7105 (Electronic)$\backslash$r1548-7091 (Linking)},
issn = {1548-7091},
journal = {Nat. Methods},
number = {1},
pages = {16--18},
pmid = {18165802},
title = {{Next-generation sequencing transforms today's biology.}},
volume = {5},
year = {2008}
}
@article{Blanc2010a,
abstract = {Chlorella variabilis NC64A, a unicellular photosynthetic green alga (Trebouxiophyceae), is an intracellular photobiont of Paramecium bursaria and a model system for studying virus/algal interactions. We sequenced its 46-Mb nuclear genome, revealing an expansion of protein families that could have participated in adaptation to symbiosis. NC64A exhibits variations in GC content across its genome that correlate with global expression level, average intron size, and codon usage bias. Although Chlorella species have been assumed to be asexual and nonmotile, the NC64A genome encodes all the known meiosis-specific proteins and a subset of proteins found in flagella. We hypothesize that Chlorella might have retained a flagella-derived structure that could be involved in sexual reproduction. Furthermore, a survey of phytohormone pathways in chlorophyte algae identified algal orthologs of Arabidopsis thaliana genes involved in hormone biosynthesis and signaling, suggesting that these functions were established prior to the evolution of land plants. We show that the ability of Chlorella to produce chitinous cell walls likely resulted from the capture of metabolic genes by horizontal gene transfer from algal viruses, prokaryotes, or fungi. Analysis of the NC64A genome substantially advances our understanding of the green lineage evolution, including the genomic interplay with viruses and symbiosis between eukaryotes.},
author = {Blanc, Guillaume and Duncan, Garry and Agarkova, Irina and Borodovsky, Mark and Gurnon, James and Kuo, Alan and Lindquist, Erika and Lucas, Susan and Pangilinan, Jasmyn and Polle, Juergen and Salamov, Asaf and Terry, Astrid and Yamada, Takashi and Dunigan, David D and Grigoriev, Igor V and Claverie, Jean-Michel and {Van Etten}, James L},
doi = {10.1105/tpc.110.076406},
file = {:home/fin/Documents/papers/mendeley/Blanc et al.\_2010\_The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic s(2).pdf:pdf},
issn = {1532-298X},
journal = {Plant Cell},
keywords = {Base Composition,Cell Wall,Cell Wall: metabolism,Chlorella,Chlorella: genetics,Chlorella: virology,DNA, Plant,DNA, Plant: genetics,Evolution, Molecular,Expressed Sequence Tags,Flagella,Flagella: genetics,Genome, Plant,Molecular Sequence Data,Multigene Family,Plant Growth Regulators,Plant Growth Regulators: genetics,Repetitive Sequences, Nucleic Acid,Reproduction,Sequence Analysis, DNA,Symbiosis},
month = sep,
number = {9},
pages = {2943--55},
pmid = {20852019},
title = {{The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2965543\&tool=pmcentrez\&rendertype=abstract},
volume = {22},
year = {2010}
}
@article{Carradec2015,
author = {Carradec, Q. and Gotz, U. and Arnaiz, O. and Pouch, J. and Simon, M. and Meyer, E. and Marker, S.},
doi = {10.1093/nar/gku1331},
file = {:home/fin/Documents/papers/mendeley/Carradec et al.\_2015\_Primary and secondary siRNA synthesis triggered by RNAs from food bacteria in the ciliate Paramecium tetraurelia\_Nu.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {3},
pages = {1818--1833},
title = {{Primary and secondary siRNA synthesis triggered by RNAs from food bacteria in the ciliate Paramecium tetraurelia}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gku1331},
volume = {43},
year = {2015}
}
@article{Jaszczyszyn2014,
author = {Jaszczyszyn, Yan and Thermes, Claude and Dijk, Erwin L Van},
file = {:home/fin/Documents/papers/mendeley/Jaszczyszyn, Thermes, Dijk\_2014\_Ten years of next-generation sequencing technology\_Trends in Genetics.pdf:pdf},
journal = {Trends Genet.},
keywords = {chip-seq,dna-seq,genomics,library preparation,next-generation sequencing,ngs,rna-seq},
number = {9},
title = {{Ten years of next-generation sequencing technology}},
volume = {30},
year = {2014}
}
@article{Ellegaard2013a,
abstract = {The multiple displacement amplification method has revolutionized genomic studies of uncultured bacteria, where the extraction of pure DNA in sufficient quantity for next-generation sequencing is challenging. However, the method is problematic in that it amplifies the target DNA unevenly, induces the formation of chimeric reads and also amplifies contaminating DNA. Here, we have tested the reproducibility of the multiple displacement amplification method using serial dilutions of extracted genomic DNA and intact cells from the cultured endosymbiont Bartonella australis. The amplified DNA was sequenced with the Illumina sequencing technology, and the results were compared to sequence data obtained from unamplified DNA in this study as well as from a previously published genome project. We show that artifacts such as the extent of the amplification bias, the percentage of chimeric reads and the relative fraction of contaminating DNA increase dramatically for the smallest amounts of template DNA. The pattern of read coverage was reproducibly obtained for samples with higher amounts of template DNA, suggesting that the bias is non-random and genome-specific. A re-analysis of previously published sequence data obtained after amplification from clonal endosymbiont populations confirmed these predictions. We conclude that many of the artifacts associated with the use of the multiple displacement amplification method can be alleviated or much reduced by using multiple cells as the template for the amplification. These findings should be particularly useful for researchers studying the genomes of endosymbionts and other uncultured bacteria, for which a small clonal population of cells can be isolated.},
author = {Ellegaard, Kirsten Maren and Klasson, Lisa and Andersson, Siv G E},
doi = {10.1371/journal.pone.0082319},
file = {:home/fin/Documents/papers/mendeley/Ellegaard, Klasson, Andersson\_2013\_Testing the reproducibility of multiple displacement amplification on genomes of clonal endosymbiont.pdf:pdf},
isbn = {10.1371/journal.pone.0082319},
issn = {19326203},
journal = {PLoS One},
number = {11},
pages = {21--25},
pmid = {24312412},
title = {{Testing the reproducibility of multiple displacement amplification on genomes of clonal endosymbiont populations}},
volume = {8},
year = {2013}
}
@article{Smith2005a,
abstract = {Endogenous metabolites have gained increasing interest over the past 5 years largely for their implications in diagnostic and pharmaceutical biomarker discovery. METLIN ( http://metlin.scripps.edu), a freely accessible web-based data repository, has been developed to assist in a broad array of metabolite research and to facilitate metabolite identification through mass analysis. METLIN includes an annotated list of known metabolite structural information that is easily cross-correlated with its catalogue of high-resolution Fourier transform mass spectrometry (FTMS) spectra, tandem mass spectrometry (MS/MS) spectra, and LC/MS data.
(C) 2005 Lippincott Williams \& Wilkins, Inc.},
author = {Smith, Colin A and Maille, Grace O' and Want, Elizabeth J and Qin, Chuan and Trauger, Sunia A and Brandon, Theodore R and Custodio, Darlene E and Abagyan, Ruben and Siuzdak, Gary},
issn = {0163-4356},
journal = {Ther. Drug Monit.},
keywords = {FTMS,LC/MS,METLIN,MS/MS,database,metabolites},
number = {6},
title = {{METLIN: A Metabolite Mass Spectral Database}},
url = {http://journals.lww.com/drug-monitoring/Fulltext/2005/12000/METLIN\_\_A\_Metabolite\_Mass\_Spectral\_Database.16.aspx},
volume = {27},
year = {2005}
}
@article{Huang2007,
abstract = {Ancient endosymbioses are responsible for the origins of mitochondria and plastids, and they contribute to the divergence of several major eukaryotic groups. Although chlamydiae, a group of obligate intracellular bacteria, are not found in plants, an unexpected number of chlamydial genes are most similar to plant homologs, which, interestingly, often contain a plastid-targeting signal. This observation has prompted several hypotheses, including gene transfer between chlamydiae and plant-related groups and an ancestral relationship between chlamydiae and cyanobacteria.},
author = {Huang, Jinling and Gogarten, Johann Peter},
doi = {10.1186/gb-2007-8-6-r99},
file = {:home/fin/Documents/papers/mendeley/Huang, Gogarten\_2007\_Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids\_Genome biology.pdf:pdf},
issn = {1465-6914},
journal = {Genome Biol.},
keywords = {Biological Evolution,Chlamydia,Chlamydia: genetics,Chlamydia: physiology,Cyanobacteria,Cyanobacteria: genetics,Gene Transfer, Horizontal,Genes, Bacterial,Phylogeny,Plastids,Plastids: genetics,Rhodophyta,Rhodophyta: genetics,Rhodophyta: physiology,Symbiosis},
month = jan,
number = {6},
pages = {R99},
pmid = {17547748},
title = {{Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2394758\&tool=pmcentrez\&rendertype=abstract},
volume = {8},
year = {2007}
}
@article{Moissl-Eichinger2011,
abstract = {Several species of Archaea are involved in symbiotic or parasitic associations with representatives of Eukarya, Bacteria and other Archaea. Eukaryal interactions include different members of methanogens, found in the gut of arthropods, in the rumen of cattle, and in the human intestine, while Cenarchaeum symbiosum is a partner of a marine sponge. Examples for bacterial-archaeal associations are the anaerobic methane oxidation consortia and the SM1 Euryarchaeon with its highly unusual 'hami' as extracellular appendages. The so far only known and cultivated association between two Archaea is composed of Nanoarchaeum equitans and its obligate host Ignicoccus hospitalis. All these consortia can often not be assigned to the 'classical' concepts of mutalism, commensialism or parasitism and represent highly specialized interspecies associations. ?? 2011 Elsevier Ltd.},
author = {Moissl-Eichinger, Christine and Huber, Harald},
doi = {10.1016/j.mib.2011.04.016},
file = {:home/fin/Documents/papers/mendeley/Moissl-Eichinger, Huber\_2011\_Archaeal symbionts and parasites\_Current Opinion in Microbiology.pdf:pdf},
isbn = {1369-5274},
issn = {13695274},
journal = {Curr. Opin. Microbiol.},
pages = {364--370},
pmid = {21571580},
title = {{Archaeal symbionts and parasites}},
volume = {14},
year = {2011}
}
@article{Gelman2009,
author = {Gelman, a and Hill, J and Yajima, M},
file = {:home/fin/Documents/papers/mendeley/Gelman, Hill, Yajima\_2009\_Why we (usually) don’t have to worry about multiple comparisons∗\_arXiv0907.2478 stat.AP.pdf:pdf},
journal = {arXiv:0907.2478 [stat.AP]},
keywords = {bayesian inference,error,hierarchical modeling,multiple comparisons,statistical significance,type s},
pages = {1--25},
title = {{Why we (usually) don’t have to worry about multiple comparisons∗}},
year = {2009}
}
@article{Wass2012,
abstract = {Only a small fraction of known proteins have been functionally characterized, making protein function prediction essential to propose annotations for uncharacterized proteins. In recent years many function prediction methods have been developed using various sources of biological data from protein sequence and structure to gene expression data. Here we present the CombFunc web server, which makes Gene Ontology (GO)-based protein function predictions. CombFunc incorporates ConFunc, our existing function prediction method, with other approaches for function prediction that use protein sequence, gene expression and protein-protein interaction data. In benchmarking on a set of 1686 proteins CombFunc obtains precision and recall of 0.71 and 0.64 respectively for gene ontology molecular function terms. For biological process GO terms precision of 0.74 and recall of 0.41 is obtained. CombFunc is available at http://www.sbg.bio.ic.ac.uk/combfunc.},
author = {Wass, Mark N and Barton, Geraint and Sternberg, Michael J E},
doi = {10.1093/nar/gks489},
file = {:home/fin/Documents/papers/mendeley/Wass, Barton, Sternberg\_2012\_CombFunc predicting protein function using heterogeneous data sources.\_Nucleic acids research.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic Acids Res.},
keywords = {Algorithms,Gene Expression,Internet,Protein Interaction Maps,Proteins,Proteins: chemistry,Proteins: genetics,Proteins: physiology,Sequence Analysis, Protein,Software},
number = {May},
pages = {W466--70},
pmid = {22641853},
title = {{CombFunc: predicting protein function using heterogeneous data sources.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3394346\&tool=pmcentrez\&rendertype=abstract},
volume = {40},
year = {2012}
}
@article{Zwickl2002,
abstract = {Several authors have argued recently that extensive taxon sampling has a positive and important effect on the accuracy of phylogenetic estimates. However, other authors have argued that there is little benefit of extensive taxon sampling, and so phylogenetic problems can or should be reduced to a few exemplar taxa as a means of reducing the computational complexity of the phylogenetic analysis. In this paper we examined five aspects of study design that may have led to these different perspectives. First, we considered the measurement of phylogenetic error across a wide range of taxon sample sizes, and conclude that the expected error based on randomly selecting trees (which varies by taxon sample size) must be considered in evaluating error in studies of the effects of taxon sampling. Second, we addressed the scope of the phylogenetic problems defined by different samples of taxa, and argue that phylogenetic scope needs to be considered in evaluating the importance of taxon-sampling strategies. Third, we examined the claim that fast and simple tree searches are as effective as more thorough searches at finding near-optimal trees that minimize error. We show that a more complete search of tree space reduces phylogenetic error, especially as the taxon sample size increases. Fourth, we examined the effects of simple versus complex simulation models on taxonomic sampling studies. Although benefits of taxon sampling are apparent for all models, data generated under more complex models of evolution produce higher overall levels of error and show greater positive effects of increased taxon sampling. Fifth, we asked if different phylogenetic optimality criteria show different effects of taxon sampling. Although we found strong differences in effectiveness of different optimality criteria as a function of taxon sample size, increased taxon sampling improved the results from all the common optimality criteria. Nonetheless, the method that showed the lowest overall performance (minimum evolution) also showed the least improvement from increased taxon sampling. Taking each of these results into account re-enforces the conclusion that increased sampling of taxa is one of the most important ways to increase overall phylogenetic accuracy.},
author = {Zwickl, Derrick J and Hillis, David M},
doi = {10.1080/10635150290102339},
file = {:home/fin/Documents/papers/mendeley/Zwickl, Hillis\_2002\_Increased taxon sampling greatly reduces phylogenetic error.\_Systematic biology.pdf:pdf},
isbn = {1063-5157},
issn = {1063-5157},
journal = {Syst. Biol.},
number = {4},
pages = {588--598},
pmid = {12228001},
title = {{Increased taxon sampling greatly reduces phylogenetic error.}},
volume = {51},
year = {2002}
}
@article{VanBuren2015,
author = {VanBuren, Robert and Bryant, Doug and Edger, Patrick P. and Tang, Haibao and Burgess, Diane and Challabathula, Dinakar and Spittle, Kristi and Hall, Richard and Gu, Jenny and Lyons, Eric and Freeling, Michael and Bartels, Dorothea and {Ten Hallers}, Boudewijn and Hastie, Alex and Michael, Todd P. and Mockler, Todd C.},
doi = {10.1038/nature15714},
file = {:home/fin/Documents/papers/mendeley/VanBuren et al.\_2015\_Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum.\_Nature.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
pmid = {26560029},
publisher = {Nature Publishing Group},
title = {{Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum.}},
url = {http://www.nature.com/doifinder/10.1038/nature15714},
year = {2015}
}
@book{Murphy2012,
author = {Murphy, Kevin P.},
publisher = {MIT Press},
title = {{Machine learning: a probabilistic perspective}},
year = {2012}
}
@article{Welch1947,
author = {Welch, B.L.},
file = {:home/fin/Documents/papers/mendeley/Welch\_1947\_The Generalisation of the 'Student's' Problem when Several Different Population Variances are Involved\_Biometrika.pdf:pdf},
journal = {Biometrika},
number = {1/2},
pages = {28--35},
title = {{The Generalisation of the 'Student's' Problem when Several Different Population Variances are Involved}},
volume = {34},
year = {1947}
}
@article{Sonnhammer1998,
abstract = {A novel method to model and predict the location and orientation of alpha helices in membrane-spanning proteins is presented. It is based on a hidden Markov model (HMM) with an architecture that corresponds closely to the biological system. The model is cyclic with 7 types of states for helix core, helix caps on either side, loop on the cytoplasmic side, two loops for the non-cytoplasmic side, and a globular domain state in the middle of each loop. The two loop paths on the non-cytoplasmic side are used to model short and long loops separately, which corresponds biologically to the two known different membrane insertions mechanisms. The close mapping between the biological and computational states allows us to infer which parts of the model architecture are important to capture the information that encodes the membrane topology, and to gain a better understanding of the mechanisms and constraints involved. Models were estimated both by maximum likelihood and a discriminative method, and a method for reassignment of the membrane helix boundaries were developed. In a cross validated test on single sequences, our transmembrane HMM, TMHMM, correctly predicts the entire topology for 77\% of the sequences in a standard dataset of 83 proteins with known topology. The same accuracy was achieved on a larger dataset of 160 proteins. These results compare favourably with existing methods.},
author = {Sonnhammer, E L and von Heijne, G and Krogh, A},
file = {:home/fin/Documents/papers/mendeley/Sonnhammer, von Heijne, Krogh\_1998\_A hidden Markov model for predicting transmembrane helices in protein sequences.\_Proceedings Sixth In.pdf:pdf},
issn = {1553-0833},
journal = {Proc. Sixth Int. Conf. Intell. Syst. Mol. Biol.},
keywords = {Amino Acid Sequence,Artificial Intelligence,Databases,Factual,Markov Chains,Membrane Proteins,Membrane Proteins: chemistry,Membrane Proteins: genetics,Models,Molecular,Molecular Sequence Data,Protein Structure,Secondary},
month = jan,
pages = {175--82},
pmid = {9783223},
title = {{A hidden Markov model for predicting transmembrane helices in protein sequences.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9783223},
volume = {6},
year = {1998}
}
@article{Reisser1988,
abstract = {Five plaque-forming viruses (Pbi viruses) of the unicellular, eukaryotic, exsymbiotic Chlorella-like green alga strain Pbi were isolated from fresh water collected in Germany. The viruses were compared to two previously characterized plaque-forming viruses (NC64A viruses) of Chlorella strain NC64A. The Pbi viruses do not infect Chlorella NC64A and vice versa. Like the NC64A viruses the Pbi viruses are large polyhedron with a diameter of 140 to 150 nm, are chloroform sensitive, have many structural proteins, and have large dsDNA genomes of at least 300 kb. However, the Pbi viruses are serologically distinct from the NC64A viruses. The five Pbi virus genomes contain 5-methylcytosine, which varied from 14.2 to 43.1\% of the cytosine, and two of them also contained N6-methyladenine. DNAs from the Pbi viruses hybridized poorly with the two NC64A virus DNAs and they have a higher guanine plus cytosine content (ca. 46\%) than the NC64A virus DNAs (ca. 40\%).},
author = {Reisser, W and Burbank, D E and Meints, S M and Meints, R H and Becker, B and {Van Etten}, J L},
issn = {0042-6822 (Print)},
journal = {Virology},
keywords = {Base Composition,Base Sequence,Centrifugation, Density Gradient,Chlorella,DNA Restriction Enzymes,DNA, Viral,Electrophoresis, Agar Gel,Electrophoresis, Polyacrylamide Gel,Nucleic Acid Hybridization,Viral Plaque Assay,Viral Proteins,Virus Physiological Phenomena,Viruses,Water Microbiology,analysis,genetics,growth \& development,physiology},
language = {eng},
month = nov,
number = {1},
pages = {143--149},
pmid = {2847410},
title = {{A comparison of viruses infecting two different Chlorella-like green algae.}},
volume = {167},
year = {1988}
}
@article{Archibald2015,
author = {Archibald, John M.},
doi = {10.1016/j.cub.2015.07.055},
file = {:home/fin/Documents/papers/mendeley/Archibald\_2015\_Endosymbiosis and Eukaryotic Cell Evolution\_Current Biology.pdf:pdf},
issn = {09609822},
journal = {Curr. Biol.},
number = {19},
pages = {R911--R921},
publisher = {Elsevier Ltd},
title = {{Endosymbiosis and Eukaryotic Cell Evolution}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0960982215008891},
volume = {25},
year = {2015}
}
@article{Watnick2000,
abstract = {Mol. . 30:295-304[CrossRef][Medline]. 32. ' , GA, and R. Kolter. 1998. 40. Shimkets, LJ 1999. Intercellular signaling during fruiting-body development of Myxococcus xanthus. . . . 53:525-549[CrossRef][Medline]. 41.},
author = {Watnick, Paula and Kolter, Roberto},
doi = {10.1128/JB.182.10.2675-2679.2000},
file = {:home/fin/Documents/papers/mendeley/Watnick, Kolter\_2000\_Biofilm, city of microbes\_Journal of Bacteriology.pdf:pdf},
isbn = {0021-9193 (Print)$\backslash$r0021-9193 (Linking)},
issn = {00219193},
journal = {J. Bacteriol.},
number = {10},
pages = {2675--2679},
pmid = {10781532},
title = {{Biofilm, city of microbes}},
volume = {182},
year = {2000}
}
@article{Ondov2011,
author = {Ondov, Brian D and Bergman, Nicholas H and Phillippy, Adam M},
doi = {10.1186/1471-2105-12-385},
file = {:home/fin/Documents/papers/mendeley/Ondov, Bergman, Phillippy\_2011\_Interactive metagenomic visualization in a Web browser\_BMC Bioinformatics.pdf:pdf},
issn = {1471-2105},
journal = {BMC Bioinformatics},
number = {1},
pages = {385},
publisher = {BioMed Central Ltd},
title = {{Interactive metagenomic visualization in a Web browser}},
url = {http://www.biomedcentral.com/1471-2105/12/385},
volume = {12},
year = {2011}
}
@article{Hansen2010a,
abstract = {Generation of cDNA using random hexamer priming induces biases in the nucleotide composition at the beginning of transcriptome sequencing