text:
issn = {1548-7091},
journal = {Nat. Methods},
number = {11},
pages = {1144--1146},
pmid = {25218180},
title = {{Binning metagenomic contigs by coverage and composition}},
volume = {11},
year = {2014}
}
@article{Kim2011a,
author = {Kim, Eunsoo and Harrison, James W and Sudek, Sebastian and Jones, Meredith D M and Wilcox, Heather M and Richards, Thomas A and Worden, Alexandra Z and Archibald, John M},
doi = {10.1073/pnas.1013337108/-/DCSupplemental.www.pnas.org/cgi/doi/10.1073/pnas.1013337108},
file = {:home/fin/Documents/papers/mendeley/Kim et al.\_2011\_Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life\_Proceedings of the National Academy o.pdf:pdf},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
number = {4},
pages = {1496--1500},
title = {{Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life}},
volume = {108},
year = {2011}
}
@article{Ris1962,
author = {Ris, Hans and Plaut, Walter},
file = {:home/fin/Documents/papers/mendeley/Ris, Plaut\_1962\_Ultrastructure of DNA-containing areas in the chloroplast of Chlamydomonas\_Journal of Cell Biology.pdf:pdf},
journal = {J. Cell Biol.},
pages = {383--391},
title = {{Ultrastructure of DNA-containing areas in the chloroplast of Chlamydomonas}},
volume = {13},
year = {1962}
}
@article{Oren2014,
abstract = {Understanding the mechanisms that generate variation is a common pursuit unifying the life sciences. Bacteria represent an especially striking puzzle, because closely related strains possess radically different metabolic and ecological capabilities. Differences in protein repertoire arising from gene transfer are currently considered the primary mechanism underlying phenotypic plasticity in bacteria. Although bacterial coding plasticity has been extensively studied in previous decades, little is known about the role that regulatory plasticity plays in bacterial evolution. Here, we show that bacterial genes can rapidly shift between multiple regulatory modes by acquiring functionally divergent nonhomologous promoter regions. Through analysis of 270,000 regulatory regions across 247 genomes, we demonstrate that regulatory "switching" to nonhomologous alternatives is ubiquitous, occurring across the bacterial domain. Using comparative transcriptomics, we show that at least 16\% of the expression divergence between Escherichia coli strains can be explained by this regulatory switching. Further, using an oligonucleotide regulatory library, we establish that switching affects bacterial promoter architecture. We provide evidence that regulatory switching can occur through horizontal regulatory transfer, which allows regulatory regions to move across strains, and even genera, independently from the genes they regulate. Finally, by experimentally characterizing the fitness effect of a regulatory transfer on a pathogenic E. coli strain, we demonstrate that regulatory switching elicits important phenotypic consequences. Taken together, our findings expose previously unappreciated regulatory plasticity in bacteria and provide a gateway for understanding bacterial phenotypic variation and adaptation.},
author = {Oren, Yaara and Smith, Mark B and Johns, Nathan I and {Kaplan Zeevi}, Millie and Biran, Dvora and Ron, Eliora Z and Corander, Jukka and Wang, Harris H and Alm, Eric J and Pupko, Tal},
doi = {10.1073/pnas.1413272111},
file = {:home/fin/Documents/papers/mendeley/Oren et al.\_2014\_Transfer of noncoding DNA drives regulatory rewiring in bacteria.\_Proceedings of the National Academy of Sciences of th.pdf:pdf},
issn = {1091-6490},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
month = oct,
number = {45},
pmid = {25313052},
title = {{Transfer of noncoding DNA drives regulatory rewiring in bacteria.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25313052},
volume = {111},
year = {2014}
}
@article{Betermier2004,
abstract = {In Paramecium, during the development of the somatic macronucleus, precise excision of thousands of single-copy non-coding sequences is initiated by specific DNA double-strand breaks, while imprecise elimination of germ-line-limited repeated sequences leads to internal deletions or chromosome fragmentation. Recent data point to a role of non-coding RNAs in the epigenetic programming of these rearrangements. © 2004 Elsevier SAS. All rights reserved.},
author = {B\'{e}termier, Mireille},
doi = {10.1016/j.resmic.2004.01.017},
file = {:home/fin/Documents/papers/mendeley/B\'{e}termier\_2004\_Large-scale genome remodelling by the developmentally programmed elimination of germ line sequences in the ciliate Param.pdf:pdf},
issn = {09232508},
journal = {Res. Microbiol.},
keywords = {DNA excision,Double-strand break,Epigenetic control,IES},
pages = {399--408},
pmid = {15207872},
title = {{Large-scale genome remodelling by the developmentally programmed elimination of germ line sequences in the ciliate Paramecium}},
volume = {155},
year = {2004}
}
@article{Droge2012,
abstract = {Metagenome research uses random shotgun sequencing of microbial community DNA to study the genetic sequences of its members without cultivation. This development has been strongly supported by improvements in sequencing technologies, which have rendered sequencing cheaper than before. As a consequence, downstream computational analysis of metagenome sequence samples is now faced with large amounts of complex data. One of the essential steps in metagenome analysis is reconstruction of draft genomes for populations of a community or of draft 'pan-genomes' for higher level clades. 'Taxonomic binning' corresponds to the process of assigning a taxonomic identifier to sequence fragments, based on information such as sequence similarity, sequence composition or read coverage. This is used for draft genome reconstruction, if sequencing coverage is insufficient for reconstruction based on assembly information alone. Subsequent functional and metabolic annotation of draft genomes allows a genome-level analysis of novel uncultured microbial species and even inference of their cultivation requirements.},
author = {Dr\"{o}ge, Johannes and Mchardy, Alice C.},
doi = {10.1093/bib/bbs031},
file = {:home/fin/Documents/papers/mendeley/Dr\"{o}ge, Mchardy\_2012\_Taxonomic binning of metagenome samples generated by next-generation sequencing technologies\_Briefings in Bioinformati.:},
isbn = {1477-4054 (Electronic)$\backslash$r1467-5463 (Linking)},
issn = {14675463},
journal = {Brief. Bioinform.},
keywords = {Metagenomics,Next-generation sequencing,Taxonomic binning},
number = {6},
pages = {646--655},
pmid = {22851513},
title = {{Taxonomic binning of metagenome samples generated by next-generation sequencing technologies}},
volume = {13},
year = {2012}
}
@article{Yang1994a,
abstract = {Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called the "discrete gamma model," uses several categories of rates to approximate the gamma distribution, with equal probability for each category. The mean of each category is used to represent all the rates falling in the category. The performance of this method is found to be quite good, and four such categories appear to be sufficient to produce both an optimum, or near-optimum fit by the model to the data, and also an acceptable approximation to the continuous distribution. The second method, called "fixed-rates model", classifies sites into several classes according to their rates predicted assuming the star tree. Sites in different classes are then assumed to be evolving at these fixed rates when other tree topologies are evaluated. Analyses of the data sets suggest that this method can produce reasonable results, but it seems to share some properties of a least-squares pairwise comparison; for example, interior branch lengths in nonbest trees are often found to be zero. The computational requirements of the two methods are comparable to that of Felsenstein's (1981, J Mol Evol 17:368-376) model, which assumes a single rate for all the sites.},
author = {Yang, Z},
doi = {10.1007/BF00160154},
file = {:home/fin/Documents/papers/mendeley/Yang\_1994\_Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites approximate methods.\_Journal of m.pdf:pdf},
isbn = {0022-2844 (Print)$\backslash$n0022-2844 (Linking)},
issn = {0022-2844},
journal = {J. Mol. Evol.},
keywords = {-,- the gamma distribution,likelihood - -,phylogeny - - maximum,rate variation over sites},
pages = {306--314},
pmid = {7932792},
title = {{Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods.}},
volume = {39},
year = {1994}
}
@article{Horton2007,
abstract = {WoLF PSORT is an extension of the PSORT II program for protein subcellular location prediction. WoLF PSORT converts protein amino acid sequences into numerical localization features; based on sorting signals, amino acid composition and functional motifs such as DNA-binding motifs. After conversion, a simple k-nearest neighbor classifier is used for prediction. Using html, the evidence for each prediction is shown in two ways: (i) a list of proteins of known localization with the most similar localization features to the query, and (ii) tables with detailed information about individual localization features. For convenience, sequence alignments of the query to similar proteins and links to UniProt and Gene Ontology are provided. Taken together, this information allows a user to understand the evidence (or lack thereof) behind the predictions made for particular proteins. WoLF PSORT is available at wolfpsort.org.},
author = {Horton, Paul and Park, Keun-Joon and Obayashi, Takeshi and Fujita, Naoya and Harada, Hajime and Adams-Collier, C J and Nakai, Kenta},
doi = {10.1093/nar/gkm259},
file = {:home/fin/Documents/papers/mendeley/Horton et al.\_2007\_WoLF PSORT protein localization predictor.\_Nucleic Acids Research.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic Acids Res.},
keywords = {Arabidopsis,Computational Biology,Computational Biology: methods,Databases,Humans,Internet,Membrane Proteins,Membrane Proteins: analysis,Membrane Proteins: chemistry,Models,Programming Languages,Protein,Protein Sorting Signals,Protein Structure,Protein: methods,Proteins,Proteins: analysis,Proteins: chemistry,Reproducibility of Results,Secondary,Sequence Analysis,Software,Statistical},
month = jul,
number = {Web Server issue},
pages = {W585--7},
pmid = {17517783},
title = {{WoLF PSORT: protein localization predictor.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1933216\&tool=pmcentrez\&rendertype=abstract},
volume = {35},
year = {2007}
}
@article{Li2015b,
author = {Li, Bin and Kim, Sok Ho and Zhang, Yang and Hanfrey, Colin C. and Elliott, Katherine a. and Ealick, Steven E. and Michael, Anthony J.},
doi = {10.1111/mmi.13066},
file = {:home/fin/Documents/papers/mendeley/Li et al.\_2015\_Different polyamine pathways from bacteria have replaced eukaryotic spermidine biosynthesis in ciliates Tetrahymena therm.pdf:pdf},
issn = {0950382X},
journal = {Mol. Microbiol.},
number = {June},
pages = {n/a--n/a},
title = {{Different polyamine pathways from bacteria have replaced eukaryotic spermidine biosynthesis in ciliates Tetrahymena thermophila and Paramecium tetaurelia}},
url = {http://doi.wiley.com/10.1111/mmi.13066},
volume = {97},
year = {2015}
}
@article{Bradnam2013,
abstract = {BACKGROUND: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly.$\backslash$n$\backslash$nRESULTS: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies.$\backslash$n$\backslash$nCONCLUSIONS: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.},
archivePrefix = {arXiv},
arxivId = {1301.5406},
author = {Bradnam, Keith R and Fass, Joseph N and Alexandrov, Anton and Baranay, Paul and Bechner, Michael and Birol, Inan\c{c} and Boisvert, S\'{e}bastien and Chapman, Jarrod a and Chapuis, Guillaume and Chikhi, Rayan and Chitsaz, Hamidreza and Chou, Wen-Chi and Corbeil, Jacques and {Del Fabbro}, Cristian and Docking, T Roderick and Durbin, Richard and Earl, Dent and Emrich, Scott and Fedotov, Pavel and Fonseca, Nuno a and Ganapathy, Ganeshkumar and Gibbs, Richard a and Gnerre, Sante and Godzaridis, El\'{e}nie and Goldstein, Steve and Haimel, Matthias and Hall, Giles and Haussler, David and Hiatt, Joseph B and Ho, Isaac Y and Howard, Jason and Hunt, Martin and Jackman, Shaun D and Jaffe, David B and Jarvis, Erich D and Jiang, Huaiyang and Kazakov, Sergey and Kersey, Paul J and Kitzman, Jacob O and Knight, James R and Koren, Sergey and Lam, Tak-Wah and Lavenier, Dominique and Laviolette, Fran\c{c}ois and Li, Yingrui and Li, Zhenyu and Liu, Binghang and Liu, Yue and Luo, Ruibang and Maccallum, Iain and Macmanes, Matthew D and Maillet, Nicolas and Melnikov, Sergey and Naquin, Delphine and Ning, Zemin and Otto, Thomas D and Paten, Benedict and Paulo, Oct\'{a}vio S and Phillippy, Adam M and Pina-Martins, Francisco and Place, Michael and Przybylski, Dariusz and Qin, Xiang and Qu, Carson and Ribeiro, Filipe J and Richards, Stephen and Rokhsar, Daniel S and Ruby, J Graham and Scalabrin, Simone and Schatz, Michael C and Schwartz, David C and Sergushichev, Alexey and Sharpe, Ted and Shaw, Timothy I and Shendure, Jay and Shi, Yujian and Simpson, Jared T and Song, Henry and Tsarev, Fedor and Vezzi, Francesco and Vicedomini, Riccardo and Vieira, Bruno M and Wang, Jun and Worley, Kim C and Yin, Shuangye and Yiu, Siu-Ming and Yuan, Jianying and Zhang, Guojie and Zhang, Hao and Zhou, Shiguo and Korf, Ian F},
doi = {10.1186/2047-217X-2-10},
eprint = {1301.5406},
file = {:home/fin/Documents/papers/mendeley/Bradnam et al.\_2013\_Assemblathon 2 evaluating de novo methods of genome assembly in three vertebrate species.\_GigaScience.pdf:pdf},
isbn = {2047-217X},
issn = {2047-217X},
journal = {Gigascience},
keywords = {assessment,compass,genome assembly,heterozygosity,n50,scaffolds},
pages = {10},
pmid = {23870653},
title = {{Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3844414\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2013}
}
@article{Cho1981,
abstract = {In autotrophically grown Chlorella cells, glucose induces a hexose transport system but, at the same time, the synthesis of two amino acid transport systems is also induced. Thus, the rates of uptake of glycine, L-alanine, L-proline, and L-serine, all of which compete with each other for entry into the cells, increase more than 100-fold when the algae are pretreated with glucose. The rates of L-arginine and L-lysine uptake increase by a factor of 25 to 50. The accumulation of proline and arginine within the cells amounts to 200- and 600-fold, respectively. Glucose does not cause the positive effect on amino acid uptake by serving as metabolic substrate because the nonmetabolizable 6-deoxyglucose also acts as inducer. Cycloheximide prevents the induction. The induced transport system for the four neutral amino acids has a turnover with a half-life of 7 hr, which corresponds closely to the half-life of the hexose transport system. The transport system for the basic amino acids, on the other hand, disappears with a half-life of 25 hr.},
author = {Cho, B H and Sauer, N and Komor, E and Tanner, W},
doi = {10.1073/pnas.78.6.3591},
file = {:home/fin/Documents/papers/mendeley/Cho et al.\_1981\_Glucose induces two amino acid transport systems in Chlorella.\_Proceedings of the National Academy of Sciences of the Un.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
keywords = {Active,Active: drug effects,Alanine,Alanine: metabolism,Amino Acids,Amino Acids: metabolism,Arginine,Arginine: metabolism,Biological Transport,Carrier Proteins,Carrier Proteins: metabolism,Chlorophyta,Chlorophyta: metabolism,Glucose,Glucose: pharmacology,Proline,Proline: metabolism},
number = {6},
pages = {3591--4},
pmid = {6943560},
title = {{Glucose induces two amino acid transport systems in Chlorella.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/6732237},
volume = {78},
year = {1981}
}
@article{Nakajima1989,
author = {Nakajima, B Y Kaname and Nakaoka, Yasuo},
file = {:home/fin/Documents/papers/mendeley/Nakajima, Nakaoka\_1989\_Circadian Change of Photosensiuvity in Paramecium Bursaria\_Journal of Experimental Biology.pdf:pdf},
journal = {J. Exp. Biol.},
pages = {43--51},
title = {{Circadian Change of Photosensiuvity in Paramecium Bursaria}},
volume = {144},
year = {1989}
}
@article{Ku2014,
author = {Ku, Chuan and Roettger, Mayo and Zimorski, Verena and Nelson-Sathi, Shijulal and Sousa, Filipa L. and Martin, William F.},
doi = {10.5586/asbp.2014.045},
file = {:home/fin/Documents/papers/mendeley/Ku et al.\_2014\_Plastid origin who, when and why\_Acta Societatis Botanicorum Poloniae.pdf:pdf},
issn = {2083-9480},
journal = {Acta Soc. Bot. Pol.},
keywords = {1,110 years since mereschkowsky,and a variety of,compartments re-,cyanobacteria,endosymbiosis,evolution,gene transfer,genomics,metabolic,organelle,photosynthesis,phylogeny,plastid origin,plastids are eukaryotic metabolic,sponsible for photosynthesis},
month = dec,
number = {4},
pages = {281--289},
title = {{Plastid origin: who, when and why?}},
url = {https://pbsociety.org.pl/journals/index.php/asbp/article/view/asbp.2014.045},
volume = {83},
year = {2014}
}
@article{Ziesenisz1981,
author = {Ziesenisz, Egmont and Reisser, Werner and Wiessner, Wolfgang},
file = {:home/fin/Documents/papers/mendeley/Ziesenisz, Reisser, Wiessner\_1981\_Evidence of de novo synthesis of maltose excreted by the endosymbiotic Chlorella from Paramecium bursa.pdf:pdf},
journal = {Planta},
keywords = {apoplast - assimilate transport,cellus- oryza - pigment,n d - symplast-,nu-,s t r a,transport},
pages = {481--485},
title = {{Evidence of de novo synthesis of maltose excreted by the endosymbiotic Chlorella from Paramecium bursaria}},
volume = {153},
year = {1981}
}
@article{Albers1982,
author = {Albers, D and Reisser, W and Wiessner, W},
doi = {10.1016/0304-4211(82)90210-3},
file = {:home/fin/Documents/papers/mendeley/Albers, Reisser, Wiessner\_1982\_Studies on the nitrogen supply of endosymbiotic chlorellae in greem paramecium bursaria\_Plant Science Let.pdf:pdf},
issn = {03044211},
journal = {Plant Sci. Lett.},
pages = {85--90},
title = {{Studies on the nitrogen supply of endosymbiotic chlorellae in greem paramecium bursaria}},
url = {http://www.sciencedirect.com/science/article/pii/0304421182902103},
volume = {25},
year = {1982}
}
@article{Bengio2007,
author = {Bengio, Yoshua and Lamblin, Pascal and Popovici, Dan and Larochelle, Hugo},
file = {:home/fin/Documents/papers/mendeley/Bengio et al.\_2007\_Greedy Layer-Wise Training of Deep Networks\_Advances in neural information processing systems.pdf:pdf},
journal = {Adv. Neural Inf. Process. Syst.},
number = {1},
pages = {153},
title = {{Greedy Layer-Wise Training of Deep Networks}},
volume = {19},
year = {2007}
}
@article{Rinke2013,
abstract = {Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called 'microbial dark matter'. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20\% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.},
author = {Rinke, Christian and Schwientek, Patrick and Sczyrba, Alexander and Ivanova, Natalia N and Anderson, Iain J and Cheng, Jan-Fang and Darling, Aaron E and Malfatti, Stephanie and Swan, Brandon K and Gies, Esther a and Dodsworth, Jeremy a and Hedlund, Brian P and Tsiamis, George and Sievert, Stefan M and Liu, Wen-Tso and Eisen, Jonathan a and Hallam, Steven J and Kyrpides, Nikos C and Stepanauskas, Ramunas and Rubin, Edward M and Hugenholtz, Philip and Woyke, Tanja},
doi = {10.1038/nature12352},
file = {:home/fin/Documents/papers/mendeley/Rinke et al.\_2013\_Insights into the phylogeny and coding potential of microbial dark matter.\_Nature.pdf:pdf},
isbn = {1476-4687 (Electronic)$\backslash$r0028-0836 (Linking)},
issn = {1476-4687},
journal = {Nature},
number = {7459},
pages = {431--437},
pmid = {23851394},
publisher = {Nature Publishing Group},
title = {{Insights into the phylogeny and coding potential of microbial dark matter.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23851394},
volume = {499},
year = {2013}
}
@article{Funfak2015,
author = {Funfak, Anette and Fisch, Cathy and {Abdel Motaal}, Hatem T. and Diener, Julien and Combettes, Laurent and Baroud, Charles N. and Dupuis-Williams, Pascale},
doi = {10.1039/C4IB00181H},
file = {:home/fin/Documents/papers/mendeley/Funfak et al.\_2015\_Paramecium swimming and ciliary beating patterns a study on four RNA interference mutations\_Integr. Biol.pdf:pdf},
issn = {1757-9694},
journal = {Integr. Biol.},
pages = {90--100},
publisher = {Royal Society of Chemistry},
title = {{Paramecium swimming and ciliary beating patterns: a study on four RNA interference mutations}},
url = {http://xlink.rsc.org/?DOI=C4IB00181H},
volume = {7},
year = {2015}
}
@article{Hori1985,
abstract = {We have constructed a phylogenic tree for green plants by comparing 5S rRNA sequences. The tree suggests that the emergence of most of the uni- and multicellular green algae such as Chlamydomonas, Spirogyra, Ulva, and Chlorella occurred in the early stage of green plant evolution. The branching point of Nitella is a little earlier than that of land plants and much later than that of the above green algae, supporting the view that Nitella-like green algae may be the direct precursor to land plants. The Bryophyta and the Pteridophyta separated from each other after emergence of the Spermatophyta. The result is consistent with the view that the Bryophyta evolved from ferns by degeneration. In the Pteridophyta, Psilotum (whisk fern) separated first, and a little later Lycopodium (club moss) separated from the ancestor common to Equisetum (horsetail) and Dryopteris (fern). This order is in accordance with the classical view. During the Spermatophyta evolution, the gymnosperms (Cycas, Ginkgo, and Metasequoia have been studied here) and the angiosperms (flowering plants) separated, and this was followed by the separation of Metasequoia and Cycas (cycad)/Ginkgo (maidenhair tree) on one branch and various flowering plants on the other.},
author = {Hori, H and Lim, B L and Osawa, S},
doi = {10.1073/pnas.82.3.820},
file = {:home/fin/Documents/papers/mendeley/Hori, Lim, Osawa\_1985\_Evolution of green plants as deduced from 5S rRNA sequences.\_Proceedings of the National Academy of Sciences of th.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
number = {February},
pages = {820--823},
pmid = {16593540},
title = {{Evolution of green plants as deduced from 5S rRNA sequences.}},
volume = {82},
year = {1985}
}
@misc{michael_waskom_2015_19108,
author = {Waskom, Michael and Botvinnik, Olga and Hobson, Paul and Warmenhoven, Jordi and Cole, John B and Halchenko, Yaroslav and Vanderplas, Jake and Hoyer, Stephan and Villalba, Santi and Quintero, Eric and Miles, Alistair and Augspurger, Tom and Yarkoni, Tal and Evans, Constantine and Wehner, Daniel and Rocher, Luc and Megies, Tobias and Coelho, Luis Pedro and Ziegler, Erik and Hoppe, Travis and Seabold, Skipper and Pascual, Sergio and Cloud, Phillip and Koskinen, Miikka and Hausler, Chris and Kjemmett and Milajevs, Dmitrijs and Qalieh, Adel and Allan, Dan and Meyer, Kyle},
doi = {10.5281/zenodo.19108},
month = jun,
title = {{seaborn: v0.6.0 (June 2015)}},
url = {http://dx.doi.org/10.5281/zenodo.19108},
year = {2015}
}
@article{Perez1997,
author = {P\'{e}rez, M T and Dolan, J R and Fukai, E},
file = {:home/fin/Documents/papers/mendeley/P\'{e}rez, Dolan, Fukai\_1997\_Planktonic oligotrich ciliates in the NW Mediterranean growth rates and consumption by copepods\_Marine Ecology.pdf:pdf},
journal = {Mar. Ecol. Prog. Ser.},
pages = {89--101},
title = {{Planktonic oligotrich ciliates in the NW Mediterranean: growth rates and consumption by copepods}},
volume = {155},
year = {1997}
}
@article{Tierney2012,
abstract = {The ability to adapt to diverse micro-environmental challenges encountered within a host is of pivotal importance to the opportunistic fungal pathogen Candida albicans. We have quantified C. albicans and M. musculus gene expression dynamics during phagocytosis by dendritic cells in a genome-wide, time-resolved analysis using simultaneous RNA-seq. A robust network inference map was generated from this dataset using NetGenerator, predicting novel interactions between the host and the pathogen. We experimentally verified predicted interdependent sub-networks comprising Hap3 in C. albicans, and Ptx3 and Mta2 in M. musculus. Remarkably, binding of recombinant Ptx3 to the C. albicans cell wall was found to regulate the expression of fungal Hap3 target genes as predicted by the network inference model. Pre-incubation of C. albicans with recombinant Ptx3 significantly altered the expression of Mta2 target cytokines such as IL-2 and IL-4 in a Hap3-dependent manner, further suggesting a role for Mta2 in host-pathogen interplay as predicted in the network inference model. We propose an integrated model for the functionality of these sub-networks during fungal invasion of immune cells, according to which binding of Ptx3 to the C. albicans cell wall induces remodeling via fungal Hap3 target genes, thereby altering the immune response to the pathogen. We show the applicability of network inference to predict interactions between host-pathogen pairs, demonstrating the usefulness of this systems biology approach to decipher mechanisms of microbial pathogenesis.},
author = {Tierney, Lanay and Linde, J\"{o}rg and M\"{u}ller, Sebastian and Brunke, Sascha and Molina, Juan Camilo and Hube, Bernhard and Sch\"{o}ck, Ulrike and Guthke, Reinhard and Kuchler, Karl},
doi = {10.3389/fmicb.2012.00085},
file = {:home/fin/Documents/papers/mendeley/Tierney et al.\_2012\_An interspecies regulatory network inferred from simultaneous RNA-seq of Candida albicans invading innate immune cel.pdf:pdf},
isbn = {1664-302X (Electronic)$\backslash$r1664-302X (Linking)},
issn = {1664302X},
journal = {Front. Microbiol.},
keywords = {Candida,Dendritic cells,Host-pathogen,Modeling,Network inference,RNA-seq,Reverse engineering},
number = {March},
pages = {1--14},
pmid = {22416242},
title = {{An interspecies regulatory network inferred from simultaneous RNA-seq of Candida albicans invading innate immune cells}},
volume = {3},
year = {2012}
}
@article{Petersen2011,
author = {Petersen, Thomas Nordahl and Brunak, S\o ren and von Heijne, Gunnar and Nielsen, Henrik},
doi = {10.1038/nmeth.1701},
file = {:home/fin/Documents/papers/mendeley/Petersen et al.\_2011\_SignalP 4.0 discriminating signal peptides from transmembrane regions.\_Nature Methods.pdf:pdf},
issn = {1548-7105},
journal = {Nat. Methods},
keywords = {Algorithms,Cell Membrane,Cell Membrane: metabolism,Computational Biology,Protein Sorting Signals,Software},
month = jan,
number = {10},
pages = {785--6},
pmid = {21959131},
publisher = {Nature Publishing Group},
title = {{SignalP 4.0: discriminating signal peptides from transmembrane regions.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21959131},
volume = {8},
year = {2011}
}
@manual{RCoreTeam2015,
address = {Vienna, Austria},
author = {{R Core Team}},
organization = {R Foundation for Statistical Computing},
title = {{R: A Language and Environment for Statistical Computing}},
url = {http://www.r-project.org/},
year = {2015}
}
@article{Schmieder2011,
abstract = {SUMMARY: Here, we present PRINSEQ for easy and rapid quality control and data preprocessing of genomic and metagenomic datasets. Summary statistics of FASTA (and QUAL) or FASTQ files are generated in tabular and graphical form and sequences can be filtered, reformatted and trimmed by a variety of options to improve downstream analysis. Availability and Implementation: This open-source application was implemented in Perl and can be used as a stand alone version or accessed online through a user-friendly web interface. The source code, user help and additional information are available at http://prinseq.sourceforge.net/.},
author = {Schmieder, Robert and Edwards, Robert},
doi = {10.1093/bioinformatics/btr026},
file = {:home/fin/Documents/papers/mendeley/Schmieder, Edwards\_2011\_Quality Control and Preprocessing of Metagenomic Datasets\_Bioinformatics.pdf:pdf},
isbn = {1367-4811 (Electronic)$\backslash$r1367-4803 (Linking)},
issn = {13674803},
journal = {Bioinformatics},
number = {6},
pages = {863--864},
pmid = {21278185},
title = {{Quality Control and Preprocessing of Metagenomic Datasets}},
volume = {27},
year = {2011}
}
@article{Thompson2011,
author = {Thompson, Julie D. and Linard, Benjamin and Lecompte, Odile and Poch, Olivier},
doi = {10.1371/journal.pone.0018093},
file = {:home/fin/Documents/papers/mendeley/Thompson et al.\_2011\_A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods Current Challenges and Future Perspectives\_P.pdf:pdf},
issn = {1932-6203},
journal = {PLoS One},
number = {3},
pages = {e18093},
title = {{A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives}},
url = {http://dx.plos.org/10.1371/journal.pone.0018093},
volume = {6},
year = {2011}
}
@misc{ClavijoKAT,
author = {Clavijo, B and {Mapleson. D} and Ayling, S and Caccamo, M},
title = {{KAT—Kmer Analysis Tool. Available online at: http://www.tgac.ac.uk/kat}},
year = {2015}
}
@article{Kajitani2014a,
author = {Kajitani, Rei and Toshimoto, Kouta and Noguchi, Hideki and Toyoda, Atsushi and Ogura, Yoshitoshi and Okuno, Miki and Yabana, Mitsuru and Harada, Masayuki and Nagayasu, Eiji and Maruyama, Haruhiko and Kohara, Yuji and Fujiyama, Asao and Hayashi, Tetsuya and Itoh, Takehiko},
doi = {10.1101/gr.170720.113.Freely},
file = {:home/fin/Documents/papers/mendeley/Kajitani et al.\_2014\_Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads\_Genome Research(2).pdf:pdf},
journal = {Genome Res.},
pages = {1384--1395},
title = {{Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads}},
volume = {24},
year = {2014}
}
@article{Federhen2012,
abstract = {The NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy) is the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases. It includes organism names and taxonomic lineages for each of the sequences represented in the INSDC's nucleotide and protein sequence databases. The taxonomy database is manually curated by a small group of scientists at the NCBI who use the current taxonomic literature to maintain a phylogenetic taxonomy for the source organisms represented in the sequence databases. The taxonomy database is a central organizing hub for many of the resources at the NCBI, and provides a means for clustering elements within other domains of NCBI web site, for internal linking between domains of the Entrez system and for linking out to taxon-specific external resources on the web. Our primary purpose is to index the domain of sequences as conveniently as possible for our user community.},
author = {Federhen, Scott},
doi = {10.1093/nar/gkr1178},
file = {:home/fin/Documents/papers/mendeley/Federhen\_2012\_The NCBI Taxonomy database\_Nucleic Acids Research.pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$r0305-1048 (Linking)},
issn = {03051048},
journal = {Nucleic Acids Res.},
number = {December 2011},
pages = {136--143},
pmid = {22139910},
title = {{The NCBI Taxonomy database}},
volume = {40},
year = {2012}
}
@article{Weis1976,
author = {Weis, Dale S and Ayala, Alfred},
file = {:home/fin/Documents/papers/mendeley/Weis, Ayala\_1976\_Effect of Exposure Period and Algal Concentration on the Frequency of Infection of Aposymbiotic Ciliates by Symbiotic A.pdf:pdf},
journal = {J. Protozool.},
number = {2},
pages = {245--248},
title = {{Effect of Exposure Period and Algal Concentration on the Frequency of Infection of Aposymbiotic Ciliates by Symbiotic Algae from Paramecium bursaria}},
volume = {26},
year = {1976}
}
@article{Conesa2005,
abstract = {SUMMARY: We present here Blast2GO (B2G), a research tool designed with the main purpose of enabling Gene Ontology (GO) based data mining on sequence data for which no GO annotation is yet available. B2G joints in one application GO annotation based on similarity searches with statistical analysis and highlighted visualization on directed acyclic graphs. This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process. AVAILABILITY: Blast2GO is freely available via Java Web Start at http://www.blast2go.de. SUPPLEMENTARY MATERIAL: http://www.blast2go.de -> Evaluation.},
author = {Conesa, Ana and G\"{o}tz, Stefan and Garc\'{\i}a-G\'{o}mez, Juan Miguel and Terol, Javier and Tal\'{o}n, Manuel and Robles, Montserrat},
doi = {10.1093/bioinformatics/bti610},
file = {:home/fin/Documents/papers/mendeley/Conesa et al.\_2005\_Blast2GO a universal tool for annotation, visualization and analysis in functional genomics research.\_Bioinformatics.pdf:pdf},
issn = {1367-4803},
journal = {Bioinformatics},
keywords = {Algorithms,Computational Biology,Computational Biology: methods,Computer Graphics,Database Management Systems,Databases,Gene Expression Profiling,Gene Expression Profiling: methods,Genome,Genomics,Information Storage and Retrieval,Information Storage and Retrieval: methods,Internet,Oligonucleotide Array Sequence Analysis,Protein,Sequence Alignment,Sequence Analysis,Software,User-Computer Interface},
month = sep,
number = {18},
pages = {3674--6},
pmid = {16081474},
title = {{Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16081474},
volume = {21},
year = {2005}
}
@article{Rahman2013,
abstract = {Assembly algorithms have been extensively benchmarked using simulated data so that results can be compared to ground truth. However, in de novo assembly, only crude metrics such as contig number and size are typically used to evaluate assembly quality. We present CGAL, a novel likelihood-based approach to assembly assessment in the absence of a ground truth. We show that likelihood is more accurate than other metrics currently used for evaluating assemblies, and describe its application to the optimization and comparison of assembly algorithms. Our methods are implemented in software that is freely available at http://bio.math.berkeley.edu/cgal/.},
author = {Rahman, Atif and Pachter, Lior},
doi = {10.1186/gb-2013-14-1-r8},
file = {:home/fin/Documents/papers/mendeley/Rahman, Pachter\_2013\_CGAL computing genome assembly likelihoods.\_Genome Biol.pdf:pdf},
isbn = {1465-6914 (Electronic)$\backslash$r1465-6906 (Linking)},
issn = {1465-6914},
journal = {Genome Biol},
keywords = {evaluation,genome assembly,likelihood,sequencing},
pages = {R8},
pmid = {23360652},
title = {{CGAL: computing genome assembly likelihoods.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3663106\&tool=pmcentrez\&rendertype=abstract},
volume = {14},
year = {2013}
}
@article{Dohm2008,
abstract = {Novel sequencing technologies permit the rapid production of large sequence data sets. These technologies are likely to revolutionize genetics and biomedical research, but a thorough characterization of the ultra-short read output is necessary. We generated and analyzed two Illumina 1G ultra-short read data sets, i.e. 2.8 million 27mer reads from a Beta vulgaris genomic clone and 12.3 million 36mers from the Helicobacter acinonychis genome. We found that error rates range from 0.3\% at the beginning of reads to 3.8\% at the end of reads. Wrong base calls are frequently preceded by base G. Base substitution error frequencies vary by 10- to 11-fold, with A > C transversion being among the most frequent and C > G transversions among the least frequent substitution errors. Insertions and deletions of single bases occur at very low rates. When simulating re-sequencing we found a 20-fold sequencing coverage to be sufficient to compensate errors by correct reads. The read coverage of the sequenced regions is biased; the highest read density was found in intervals with elevated GC content. High Solexa quality scores are over-optimistic and low scores underestimate the data quality. Our results show different types of biases and ways to detect them. Such biases have implications on the use and interpretation of Solexa data, for de novo sequencing, re-sequencing, the identification of single nucleotide polymorphisms and DNA methylation sites, as well as for transcriptome analysis.},
author = {Dohm, Juliane C. and Lottaz, Claudio and Borodina, Tatiana and Himmelbauer, Heinz},
doi = {10.1093/nar/gkn425},
file = {:home/fin/Documents/papers/mendeley/Dohm et al.\_2008\_Substantial biases in ultra-short read data sets from high-throughput DNA sequencing\_Nucleic Acids Research.pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$r0305-1048 (Linking)},
issn = {03051048},
journal = {Nucleic Acids Res.},
number = {16},
pmid = {18660515},
title = {{Substantial biases in ultra-short read data sets from high-throughput DNA sequencing}},
volume = {36},
year = {2008}
}
@article{Sung2012,
abstract = {Mutation plays a central role in all evolutionary processes and is also the basis of genetic disorders. Established base-substitution mutation rates in eukaryotes range between ∼5 × 10(-10) and 5 × 10(-8) per site per generation, but here we report a genome-wide estimate for Paramecium tetraurelia that is more than an order of magnitude lower than any previous eukaryotic estimate. Nevertheless, when the mutation rate per cell division is extrapolated to the length of the sexual cycle for this protist, the measure obtained is comparable to that for multicellular species with similar genome sizes. Because Paramecium has a transcriptionally silent germ-line nucleus, these results are consistent with the hypothesis that natural selection operates on the cumulative germ-line replication fidelity per episode of somatic gene expression, with the germ-line mutation rate per cell division evolving downward to the lower barrier imposed by random genetic drift. We observe ciliate-specific modifications of widely conserved amino acid sites in DNA polymerases as one potential explanation for unusually high levels of replication fidelity.},
author = {Sung, Way and Tucker, Abraham E and Doak, Thomas G and Choi, Eunjin and Thomas, W Kelley and Lynch, Michael},
doi = {10.1073/pnas.1210663109},
file = {:home/fin/Documents/papers/mendeley/Sung et al.\_2012\_Extraordinary genome stability in the ciliate Paramecium tetraurelia.\_Proceedings of the National Academy of Sciences o.pdf:pdf},
issn = {1091-6490},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
keywords = {Amino Acid Substitution,Amino Acid Substitution: genetics,DNA-Directed DNA Polymerase,DNA-Directed DNA Polymerase: metabolism,Genome, Protozoan,Genome, Protozoan: genetics,Genomic Instability,Genomic Instability: genetics,Mitochondria,Mitochondria: genetics,Mutation Rate,Paramecium tetraurelia,Paramecium tetraurelia: enzymology,Paramecium tetraurelia: genetics,Reproduction,Reproduction: genetics},
number = {47},
pages = {19339--44},
pmid = {23129619},
title = {{Extraordinary genome stability in the ciliate Paramecium tetraurelia.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3511141\&tool=pmcentrez\&rendertype=abstract},
volume = {109},
year = {2012}
}
@article{Vapnik1963,
abstract = {This is the first paper on Support Vector type algorithms.},
author = {Vapnik, V and Lerner, a},
doi = {citeulike-article-id:619639},
file = {:home/fin/Documents/papers/mendeley/Vapnik, Lerner\_1963\_Pattern recognition using generalized portrait method\_Automation and remote control.pdf:pdf},
issn = {0005-1179},
journal = {Autom. Remote Control},
pages = {774--780},
title = {{Pattern recognition using generalized portrait method}},
url = {http://scholar.google.com/scholar?hl=en\&btnG=Search\&q=intitle:No+Title\#0$\backslash$nhttp://ci.nii.ac.jp/naid/10020952249/},
volume = {24},
year = {1963}
}
@article{Rowe2014,
abstract = {The PBCV-1/Chlorella variabilis NC64A system is a model for studies on interactions between viruses and algae. Here we present the first global analyses of algal host transcripts during the early stages of infection, prior to virus replication. During the course of the experiment stretching over 1 hour, about a third of the host genes displayed significant changes in normalized mRNA abundance that either increased or decreased compared to uninfected levels. The population of genes with significant transcriptional changes gradually increased until stabilizing at 40 minutes post infection. Functional categories including cytoplasmic ribosomal proteins, jasmonic acid biosynthesis and anaphase promoting complex/cyclosomes had a significant excess in upregulated genes, whereas spliceosomal snRNP complexes and the shikimate pathway had significantly more down-regulated genes, suggesting that these pathways were activated or shut-down in response to the virus infection. Lastly, we examined the expression of C. varibilis RNA polymerase subunits, as PBCV-1 transcription depends on host RNA polymerases. Two subunits were up-regulated, RPB10 and RPC34, suggesting that they may function to support virus transcription. These results highlight genes and pathways, as well as overall trends, for further refinement of our understanding of the changes that take place during the early stages of viral infection.},
author = {Rowe, Janet M. and Jeanniard, Adrien and Gurnon, James R. and Xia, Yuannan and Dunigan, David D. and {Van Etten}, James L. and Blanc, Guillaume},
doi = {10.1371/journal.pone.0090988},
file = {:home/fin/Documents/papers/mendeley/Rowe et al.\_2014\_Global analysis of Chlorella variabilis NC64A mRNA profiles during the early phase of Paramecium bursaria chlorella vir.pdf:pdf},
issn = {19326203},
journal = {PLoS One},
number = {3},
pmid = {24608695},
title = {{Global analysis of Chlorella variabilis NC64A mRNA profiles during the early phase of Paramecium bursaria chlorella virus-1 infection}},
volume = {9},
year = {2014}
}
@article{Hoshina2010,
author = {Hoshina, Ryo and Iwataki, Mitsunori and Imamura, Nobutaka},
doi = {10.1111/j.1440-1835.2010.00579.x},
file = {:home/fin/Documents/papers/mendeley/Hoshina, Iwataki, Imamura\_2010\_Chlorella variabilis and Micractinium reisseri sp. nov. (Chlorellaceae, Trebouxiophyceae) Redescription o.pdf:pdf},
issn = {13220829},
journal = {Phycol. Res.},
keywords = {chlorella variabilis,its2,micractinium reis-,paramecium bursaria,seri,species concept},
month = jun,
number = {3},
pages = {188--201},
title = {{Chlorella variabilis and Micractinium reisseri sp. nov. (Chlorellaceae, Trebouxiophyceae): Redescription of the endosymbiotic green algae of Paramecium bursaria (Peniculia, Oligohymenophorea) in the 120th year}},
url = {http://doi.wiley.com/10.1111/j.1440-1835.2010.00579.x},
volume = {58},
year = {2010}
}
@article{Nabhan2012,
abstract = {Over the past two decades, there has been a long-standing debate about the impact of taxon sampling on phylogenetic inference. Studies have been based on both real and simulated data sets, within actual and theoretical contexts, and using different inference methods, to study the impact of taxon sampling. In some cases, conflicting conclusions have been drawn for the same data set. The main questions explored in studies to date have been about the effects of using sparse data, adding new taxa, including more characters from genome sequences and using different (or concatenated) locus regions. These questions can be reduced to more fundamental ones about the assessment of data quality and the design guidelines of taxon sampling in phylogenetic inference experiments. This review summarizes progress to date in understanding the impact of taxon sampling on the accuracy of phylogenetic analysis.},
author = {Nabhan, Ahmed Ragab and Sarkar, Indra Neil},
doi = {10.1093/bib/bbr014},
file = {:home/fin/Documents/papers/mendeley/Nabhan, Sarkar\_2012\_The impact of taxon sampling on phylogenetic inference A review of two decades of controversy\_Briefings in Bioinform.pdf:pdf},
isbn = {1477-4054 (Electronic)$\backslash$n1467-5463 (Linking)},
issn = {14675463},
journal = {Brief. Bioinform.},
keywords = {Bioinformatics,Phylogenetics,Taxonomic sampling},
number = {1},
pages = {122--134},
pmid = {21436145},
title = {{The impact of taxon sampling on phylogenetic inference: A review of two decades of controversy}},
volume = {13},
year = {2012}
}
@article{Weis1977,
author = {Weis, Dale S},
file = {:home/fin/Documents/papers/mendeley/Weis\_1977\_Synchronous Development of Symbiotic Chlorellae within Paramecium bursaria\_Transactions of the American Microscopical Society.pdf:pdf},
journal = {Trans. Am. Microsc. Soc.},
number = {1},
pages = {82--86},
title = {{Synchronous Development of Symbiotic Chlorellae within Paramecium bursaria}},
volume = {96},
year = {1977}
}
@article{Hoshina2008,
author = {Hoshina, Ryo and Imamura, Nobutaka},
doi = {10.1016/j.protis.2007.08.002},
file = {:home/fin/Documents/papers/mendeley/Hoshina, Imamura\_2008\_Multiple Origins of the Symbioses in Paramecium bursaria\_Protist.pdf:pdf},
journal = {Protist},
keywords = {bursaria,cbc,chlorella vulgaris,coccomyxa,compensatory base change,its2 phylogeny,paramecium,symbiotic algae},
number = {January},
title = {{Multiple Origins of the Symbioses in Paramecium bursaria}},
volume = {159},
year = {2008}
}
@article{Liu2013,
author = {Liu, Yongchu and Guo, Jiangtao and Hu, Gangqing and Zhu, Huaiqiu},
doi = {10.1186/1471-2105-14-S5-S12},
file = {:home/fin/Documents/papers/mendeley/Liu et al.\_2013\_Gene prediction in metagenomic fragments based on the SVM algorithm\_BMC Bioinformatics.pdf:pdf},
issn = {1471-2105},
journal = {BMC Bioinformatics},
number = {Suppl 5},
pages = {S12},
publisher = {BioMed Central Ltd},
title = {{Gene prediction in metagenomic fragments based on the SVM algorithm}},
url = {http://www.biomedcentral.com/1471-2105/14/S5/S12},
volume = {14},
year = {2013}
}
@article{Timmis2004,
abstract = {Genome sequences reveal that a deluge of DNA from organelles has constantly been bombarding the nucleus since the origin of organelles. Recent experiments have shown that DNA is transferred from organelles to the nucleus at frequencies that were previously unimaginable. Endosymbiotic gene transfer is a ubiquitous, continuing and natural process that pervades nuclear DNA dynamics. This relentless influx of organelle DNA has abolished organelle autonomy and increased nuclear complexity.},
author = {Timmis, Jeremy N and Ayliffe, Michael a and Huang, Chun Y and Martin, William},
doi = {10.1038/nrg1271},
file = {:home/fin/Documents/papers/mendeley/Timmis et al.\_2004\_Endosymbiotic gene transfer organelle genomes forge eukaryotic chromosomes.\_Nature reviews. Genetics.pdf:pdf},
isbn = {1471-0056},
issn = {1471-0056},
journal = {Nat. Rev. Genet.},
number = {February},
pages = {123--135},
pmid = {14735123},
title = {{Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes.}},
volume = {5},
year = {2004}
}
@article{Quinlan2010,
abstract = {MOTIVATION: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner.$\backslash$n$\backslash$nRESULTS: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets.$\backslash$n$\backslash$nAVAILABILITY AND IMPLEMENTATION: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools$\backslash$n$\backslash$nCONTACT: aaronquinlan@gmail.com; imh4y@virginia.edu$\backslash$n$\backslash$nSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
author = {Quinlan, Aaron R and Hall, Ira M},
doi = {10.1093/bioinformatics/btq033},
file = {:home/fin/Documents/papers/mendeley/Quinlan, Hall\_2010\_BEDTools a flexible suite of utilities for comparing genomic features.\_Bioinformatics (Oxford, England).pdf:pdf},
isbn = {1367-4811 (Electronic)$\backslash$n1367-4803 (Linking)},
issn = {1367-4811},
journal = {Bioinformatics},
keywords = {Genome,Genomics,Genomics: methods,Internet,Software},
number = {6},
pages = {841--842},
pmid = {20110278},
title = {{BEDTools: a flexible suite of utilities for comparing genomic features.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2832824\&tool=pmcentrez\&rendertype=abstract$\backslash$nhttp://bioinformatics.oxfordjournals.org/content/26/6/841.short},
volume = {26},
year = {2010}
}
@article{Whitehead2003,
abstract = {Dinoflagellate algae of the genus Symbiodinium in symbiosis with marine animals release much of their photosynthetic carbon to the animal host. The compounds translocated to the host ('mobile compounds') were investigated by metabolite comparison as follows: a substrate was identified as a candidate mobile compound when comparable profiles of metabolites were generated from host metabolism of this substrate (supplied exogenously) and the endogenous mobile compounds. When the sea anemone Anemonia viridis was incubated with NaH14CO2 under photosynthesizing conditions, most of the radioactivity in the animal tissue was recovered from the low-molecular-mass fraction and distributed in the ratio 1:2:1 between the neutral, acidic and basic sub-fractions. Prominent 14C-labelled compounds included glucose, malate and glucose-6-phosphate. When the symbiosis was incubated with 14C-labelled glucose plus succinate or fumarate (but none of eight other substrate combinations tested), the 14C-labelled metabolites closely matched those obtained with NaH14CO2. These data suggest that glucose and succinate/fumarate (or metabolically allied compounds) may be important photosynthetic compounds transferred from the Symbiodinium cells to the tissues of A. viridis. Metabolite comparisons can be applied to study nutritional interactions in symbioses involving photosynthetic algae and, with appropriate modification, other associations between microorganisms and plants or animals.},
author = {Whitehead, L F and Douglas, Angela E},
doi = {10.1242/jeb.00539},
file = {:home/fin/Documents/papers/mendeley/Whitehead, Douglas\_2003\_Metabolite comparisons and the identity of nutrients translocated from symbiotic algae to an animal host.\_The Jo.pdf:pdf},
isbn = {0022-0949},
issn = {0022-0949},
journal = {J. Exp. Biol.},
pages = {3149--3157},
pmid = {12909696},
title = {{Metabolite comparisons and the identity of nutrients translocated from symbiotic algae to an animal host.}},
volume = {206},
year = {2003}
}
@article{Peng2013,
author = {Peng, Y. and Leung, H. C. M. and Yiu, S.-M. and Lv, M.-J. and Zhu, X.-G. and Chin, F. Y. L.},
doi = {10.1093/bioinformatics/btt219},
file = {:home/fin/Documents/papers/mendeley/Peng et al.\_2013\_IDBA-tran a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels\_Bioinformati.pdf:pdf},
issn = {1367-4803},
journal = {Bioinformatics},
pages = {i326--i334},
title = {{IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels}},
url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btt219},
volume = {29},
year = {2013}
}
@article{Lassmann2005,
author = {Lassmann, Timo and Sonnhammer, Erik L L},
doi = {10.1186/1471-2105-6-298},
file = {:home/fin/Documents/papers/mendeley/Lassmann, Sonnhammer\_2005\_Kalign - an accurate and fast multiple sequence alignment algorithm\_BMC bioinformatics.pdf:pdf},
journal = {BMC Bioinformatics},
number = {298},
pages = {1--9},
title = {{Kalign - an accurate and fast multiple sequence alignment algorithm}},
volume = {6},
year = {2005}
}
@article{Feldmesser2014,
abstract = {BACKGROUND: The advent of Next Generation Sequencing technologies and corresponding bioinformatics tools allows the definition of transcriptomes in non-model organisms. Non-model organisms are of great ecological and biotechnological significance, and consequently the understanding of their unique metabolic pathways is essential. Several methods that integrate de novo assembly with genome-based assembly have been proposed. Yet, there are many open challenges in defining genes, particularly where genomes are not available or incomplete. Despite the large numbers of transcriptome assemblies that have been performed, quality control of the transcript building process, particularly on the protein level, is rarely performed if ever. To test and improve the quality of the automated transcriptome reconstruction, we used manually defined and curated genes, several of them experimentally validated.$\backslash$n$\backslash$nRESULTS: Several approaches to transcript construction were utilized, based on the available data: a draft genome, high quality RNAseq reads, and ESTs. In order to maximize the contribution of the various data, we integrated methods including de novo and genome based assembly, as well as EST clustering. After each step a set of manually curated genes was used for quality assessment of the transcripts. The interplay between the automated pipeline and the quality control indicated which additional processes were required to improve the transcriptome reconstruction. We discovered that E. huxleyi has a very high percentage of non-canonical splice junctions, and relatively high rates of intron retention, which caused unique issues with the currently available tools. While individual tools missed genes and artificially joined overlapping transcripts, combining the results of several tools improved the completeness and quality considerably. The final collection, created from the integration of several quality control and improvement rounds, was compared to the manually defined set both on the DNA and protein levels, and resulted in an improvement of 20\% versus any of the read-based approaches alone.$\backslash$n$\backslash$nCONCLUSIONS: To the best of our knowledge, this is the first time that an automated transcript definition is subjected to quality control using manually defined and curated genes and thereafter the process is improved. We recommend using a set of manually curated genes to troubleshoot transcriptome reconstruction.},
author = {Feldmesser, Ester and Rosenwasser, Shilo and Vardi, Assaf and Ben-Dor, Shifra},
doi = {10.1186/1471-2164-15-148},
file = {:home/fin/Documents/papers/mendeley/Feldmesser et al.\_2014\_Improving transcriptome construction in non-model organisms integrating manual and automated gene definition in E.pdf:pdf},
issn = {1471-2164},
journal = {BMC Genomics},
keywords = {Emilania huxleyi,Manual curation,Non-model organism,RNAseq,Transcriptome assembly,ac,ben-dor,correspondence,emilania huxleyi,ester,feldmesser,il,manual curation,non-model organism,rnaseq,shifra,transcriptome assembly,weizmann},
number = {1},
pages = {148},
pmid = {24559402},
publisher = {BMC Genomics},
title = {{Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi.}},
url = {http://www.biomedcentral.com/1471-2164/15/148},
volume = {15},
year = {2014}
}
@article{Winnepenninckx1993,
author = {Winnepenninckx, B. and Backeljau, T. and {De Wachter}, R.},
file = {:home/fin/Documents/papers/mendeley/Winnepenninckx, Backeljau, De Wachter\_1993\_Extraction of high molecular weight DNA from molluscs\_Trends in Genetics.pdf:pdf},
journal = {Trends Genet.},
number = {127},
pages = {407},
title = {{Extraction of high molecular weight DNA from molluscs}},
volume = {9},
year = {1993}
}
@article{Kolisko2014,
author = {Kolisko, Martin and Boscaro, Vittorio and Burki, Fabien and Lynn, Denis H and Keeling, Patrick J},
doi = {10.1016/j.cub.2014.10.026},
file = {:home/fin/Documents/papers/mendeley/Kolisko et al.\_2014\_Transcriptomics for Microbial Eukaryotes\_Current Biology.pdf:pdf},
issn = {0960-9822},
journal = {Curr. Biol.},
number = {22},
pages = {R1081--R1082},
publisher = {Elsevier},
title = {{Transcriptomics for Microbial Eukaryotes}},
url = {http://dx.doi.org/10.1016/j.cub.2014.10.026},
volume = {24},
year = {2014}
}
@article{Dohra1998,
abstract = {The reproductive form of a macronucleus-specific symbiont Holospora obtusa, when harbored by the macronucleus of the ciliate Paramecium caudatum, selectively synthesized a 63-kDa protein which is immunologically related to GroEL, or HSP60, of Escherichia coil. Heat shock treatment of isolated cells of the reproductive and infectious form of the bacterium also induced the synthesis of the GroEL homolog. Immunoblotting showed that the amount of this protein per cell, whether the reproductive or infectious form, is roughly constant. Cloning and sequencing of a gene coding for the GroEL homolog suggested that the protein is 55.2\% identical to GroEL of E. coli at the amino acid sequence level, and that the gene is preceded by an open reading frame which encodes a protein 39.6\% identical to GroES of E. coli. Northern blot hybridization showed that the groEL homologous gene is highly expressed in the reproductive form, but only in a trace amount in the intermediate and infectious form. Immunoelectron microscopy revealed that the GroEL homolog is localized in the cytoplasm of the reproductive and infectious form.},
author = {Dohra, H and Fujishima, M and Ishikawa, H},
doi = {Doi 10.1111/J.1550-7408.1998.Tb05072.X},
file = {:home/fin/Documents/papers/mendeley/Dohra, Fujishima, Ishikawa\_1998\_Structure and expression of a GroE-homologous operon of a macronucleus-specific symbiont Holospora obtus.pdf:pdf},
isbn = {1066-5234},
issn = {1066-5234},
journal = {J. Eukaryot. Microbiol.},
keywords = {aphid endosymbiont,bacterial symbionts,chlamydia,endonucleobiont,escherichia-coli,groel,heat shock protein,infection,polypeptide differences,protein synthesis,protozoa,reproductive forms,sequence,stress proteins,symbiosis,translation},
pages = {71--79},
pmid = {9495035},
title = {{Structure and expression of a GroE-homologous operon of a macronucleus-specific symbiont Holospora obtusa of the ciliate Paramecium caudatum}},
url = {<Go to ISI>://000072155900010},
volume = {45},
year = {1998}
}
@book{PearceWilliams1965,
address = {London},
author = {{Pearce Williams}, L.},
pages = {196},
publisher = {Chapman \& Hall},
title = {{Michael Faraday: A Biography}},
year = {1965}
}
@article{Binga2008,
author = {Binga, Erik K and Lasken, Roger S and Neufeld, Josh D},
doi = {10.1038/ismej.2008.10},
file = {:home/fin/Documents/papers/mendeley/Binga, Lasken, Neufeld\_2008\_Something from (almost) nothing the impact of multiple displacement amplification on microbial ecology\_The I.pdf:pdf},
issn = {1751-7362},
journal = {ISME J.},
keywords = {metagenomics,microbial ecology,multiple displacement amplification,phi29 dna,polymerase,single-cell microbiology,whole genome amplification},
pages = {233--241},
title = {{Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology}},
url = {http://www.nature.com/doifinder/10.1038/ismej.2008.10},
volume = {2},
year = {2008}
}
@article{Kafsack2010,
author = {Kafsack, Bj\"{o}rn F.C. and Llin\'{a}s, Manuel},
doi = {10.1016/j.chom.2010.01.008},
file = {:home/fin/Documents/papers/mendeley/Kafsack, Llin\'{a}s\_2010\_Eating at the Table of Another Metabolomics of Host-Parasite Interactions\_Cell Host \& Microbe.pdf:pdf},
issn = {19313128},
journal = {Cell Host Microbe},
pages = {90--99},
title = {{Eating at the Table of Another: Metabolomics of Host-Parasite Interactions}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S193131281000034X},
volume = {7},
year = {2010}
}
@article{Grun2014,
abstract = {Single-cell transcriptomics has recently emerged as a powerful technology to explore gene expression heterogeneity among single cells. Here we identify two major sources of technical variability: sampling noise and global cell-to-cell variation in sequencing efficiency. We propose noise models to correct for this, which we validate using single-molecule FISH. We demonstrate that gene expression variability in mouse embryonic stem cells depends on the culture condition.},
author = {Gr\"{u}n, Dominic and Kester, Lennart and van Oudenaarden, Alexander},
doi = {10.1038/nmeth.2930},
file = {:home/fin/Documents/papers/mendeley/Gr\"{u}n, Kester, van Oudenaarden\_2014\_Validation of noise models for single-cell transcriptomics.\_Nature methods.pdf:pdf},
isbn = {1548-7105 (Electronic)
1548-7091 (Linking)},
issn = {1548-7105},
journal = {Nat. Methods},
number = {6},
pages = {637--40},
pmid = {24747814},
title = {{Validation of noise models for single-cell transcriptomics.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24747814},
volume = {11},
year = {2014}
}
@article{Kawaida2013,
abstract = {Although many physiological studies have been reported on the symbiosis between hydra and green algae, very little information from a molecular phylogenetic aspect of symbiosis is available. In order to understand the origin and evolution of symbiosis between the two organisms, we compared the phylogenetic relationships among symbiotic green algae with the phylogenetic relationships among host hydra strains. To do so, we reconstructed molecular phylogenetic trees of several strains of symbiotic chlorella harbored in the endodermal epithelial cells of viridissima group hydra strains and investigated their congruence with the molecular phylogenetic trees of the host hydra strains. To examine the species specificity between the host and the symbiont with respect to the genetic distance, we also tried to introduce chlorella strains into two aposymbiotic strains of viridissima group hydra in which symbiotic chlorella had been eliminated in advance. We discussed the origin and history of symbiosis between hydra and green algae based on the analysis.},
author = {Kawaida, Hitomi and Ohba, Kohki and Koutake, Yuhki and Shimizu, Hiroshi and Tachida, Hidenori and Kobayakawa, Yoshitaka},
doi = {10.1016/j.ympev.2012.11.018},
file = {:home/fin/Documents/papers/mendeley/Kawaida et al.\_2013\_Symbiosis between hydra and chlorella molecular phylogenetic analysis and experimental study provide insight into it.pdf:pdf},
issn = {1095-9513},
journal = {Mol. Phylogenet. Evol.},
keywords = {Animals,Base Sequence,Biological Evolution,Chlorella,Chlorella: genetics,Cluster Analysis,DNA Primers,DNA Primers: genetics,DNA, Mitochondrial,DNA, Mitochondrial: genetics,Genetic Speciation,Hydra,Hydra: genetics,Likelihood Functions,Models, Genetic,Molecular Sequence Data,Phylogeny,RNA, Ribosomal, 18S,RNA, Ribosomal, 18S: genetics,Sequence Analysis, DNA,Symbiosis,Symbiosis: genetics},
number = {3},
pages = {906--14},
pmid = {23219706},
title = {{Symbiosis between hydra and chlorella: molecular phylogenetic analysis and experimental study provide insight into its origin and evolution.}},
url = {http://www.sciencedirect.com/science/article/pii/S1055790312004691},
volume = {66},
year = {2013}
}
@article{H1986,
author = {H, B},
file = {:home/fin/Documents/papers/mendeley/H\_1986\_An Introduction to Hidden Markov Models\_Unknown.pdf:pdf},
number = {January},
title = {{An Introduction to Hidden Markov Models}},
year = {1986}
}
@article{Collins2003,
abstract = {The Human Genome Project has been the first major foray of the biological and medical research communities into "big science." In this Viewpoint, we present some of our experiences in organizing and managing such a complicated, publicly funded, international effort. We believe that many of the lessons we learned will be applicable to future large-scale projects in biology. "It},
author = {Collins, Francis S and Morgan, Michael and Patrinos, Aristides},
doi = {10.1126/science.1084564},
file = {:home/fin/Documents/papers/mendeley/Collins, Morgan, Patrinos\_2003\_The Human Genome Project lessons from large-scale biology.\_Science (New York, N.Y.).pdf:pdf},
isbn = {1095-9203 (Electronic)$\backslash$r0036-8075 (Linking)},
issn = {00368075},
journal = {Science},
number = {April},
pages = {286--290},
pmid = {12690187},
title = {{The Human Genome Project: lessons from large-scale biology.}},
volume = {300},
year = {2003}
}
@article{Wang2012,
abstract = {BACKGROUND: Short-read data from next-generation sequencing technologies are now being generated across a range of research projects. The fidelity of this data can be affected by several factors and it is important to have simple and reliable approaches for monitoring it at the level of individual experiments.$\backslash$n$\backslash$nRESULTS: We developed a fast, scalable and accurate approach to estimating error rates in short reads, which has the added advantage of not requiring a reference genome. We build on the fundamental observation that there is a linear relationship between the copy number for a given read and the number of erroneous reads that differ from the read of interest by one or two bases. The slope of this relationship can be transformed to give an estimate of the error rate, both by read and by position. We present simulation studies as well as analyses of real data sets illustrating the precision and accuracy of this method, and we show that it is more accurate than alternatives that count the difference between the sample of interest and a reference genome. We show how this methodology led to the detection of mutations in the genome of the PhiX strain used for calibration of Illumina data. The proposed method is implemented in an R package, which can be downloaded from http://bcb.dfci.harvard.edu/∼vwang/shadowRegression.html.$\backslash$n$\backslash$nCONCLUSIONS: The proposed method can be used to monitor the quality of sequencing pipelines at the level of individual experiments without the use of reference genomes. Furthermore, having an estimate of the error rates gives one the opportunity to improve analyses and inferences in many applications of next-generation sequencing data.},
author = {Wang, Xin Victoria and Blades, Natalie and Ding, Jie and Sultana, Razvan and Parmigiani, Giovanni},
doi = {10.1186/1471-2105-13-185},
file = {:home/fin/Documents/papers/mendeley/Wang et al.\_2012\_Estimation of sequencing error rates in short reads\_BMC Bioinformatics.pdf:pdf},
isbn = {1471-2105 (Electronic)$\backslash$r1471-2105 (Linking)},
issn = {1471-2105},
journal = {BMC Bioinformatics},
pages = {185},
pmid = {22846331},
title = {{Estimation of sequencing error rates in short reads}},
volume = {13},
year = {2012}
}
@article{Gribaldo2010,
abstract = {The origin of eukaryotes and their evolutionary relationship with the Archaea is a major biological question and the subject of intense debate. In the context of the classical view of the universal tree of life, the Archaea and the Eukarya have a common ancestor, the nature of which remains undetermined. Alternative views propose instead that the Eukarya evolved directly from a bona fide archaeal lineage. Several recent large-scale phylogenomic studies using an array of approaches are divided in supporting either one or the other scenario, despite analysing largely overlapping data sets of universal genes. We examine the reasons for such a lack of consensus and consider how alternative approaches may enable progress in answering this fascinating and as-yet-unresolved question.},
author = {Gribaldo, Simonetta and Poole, Anthony M and Daubin, Vincent and Forterre, Patrick and Brochier-Armanet, C\'{e}line},
doi = {10.1038/nrmicro2426},
file = {:home/fin/Documents/papers/mendeley/Gribaldo et al.\_2010\_The origin of eukaryotes and their relationship with the Archaea are we at a phylogenomic impasse\_Nature reviews. M.pdf:pdf},
issn = {1740-1534},
journal = {Nat. Rev. Microbiol.},
keywords = {Archaea,Archaea: classification,Archaea: genetics,Bacteria,Bacteria: classification,Bacteria: genetics,Biological Evolution,Classification,Classification: methods,Eukaryota,Eukaryota: classification,Eukaryota: genetics,Genome,Genome: genetics},
month = oct,
number = {10},
pages = {743--52},
pmid = {20844558},
publisher = {Nature Publishing Group},
title = {{The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20844558},
volume = {8},
year = {2010}
}
@article{Westermann2012,
abstract = {A comprehensive understanding of host-pathogen interactions requires a knowledge of the associated gene expression changes in both the pathogen and the host. Traditional, probe-dependent approaches using microarrays or reverse transcription PCR typically require the pathogen and host cells to be physically separated before gene expression analysis. However, the development of the probe-independent RNA sequencing (RNA-seq) approach has begun to revolutionize transcriptomics. Here, we assess the feasibility of taking transcriptomics one step further by performing 'dual RNA-seq', in which gene expression changes in both the pathogen and the host are analysed simultaneously.},
author = {Westermann, Alexander J. and Gorski, Stanislaw a. and Vogel, J\"{o}rg},
doi = {10.1038/nrmicro2852},
file = {:home/fin/Documents/papers/mendeley/Westermann, Gorski, Vogel\_2012\_Dual RNA-seq of pathogen and host\_Nature Reviews Microbiology.pdf:pdf},
isbn = {1740-1534 (Electronic)$\backslash$n1740-1526 (Linking)},
issn = {1740-1526},
journal = {Nat. Rev. Microbiol.},
number = {9},
pages = {618--630},
pmid = {22890146},
publisher = {Nature Publishing Group},
title = {{Dual RNA-seq of pathogen and host}},
url = {http://dx.doi.org/10.1038/nrmicro2852},
volume = {10},
year = {2012}
}
@article{neyman1971molecular,
author = {Neyman, Jerzy},
journal = {Stat. Decis. theory Relat. Top.},
pages = {1--27},
title = {{Molecular studies of evolution: a source of novel statistical problems}},
year = {1971}
}
@article{Glenn2011,
abstract = {The diversity of available 2(nd) and 3(rd) generation DNA sequencing platforms is increasing rapidly. Costs for these systems range from <\$100 000 to more than \$1 000 000, with instrument run times ranging from minutes to weeks. Extensive trade-offs exist among these platforms. I summarize the major characteristics of each commercially available platform to enable direct comparisons. In terms of cost per megabase (Mb) of sequence, the Illumina and SOLiD platforms are clearly superior (≤\$0.10/Mb vs. >\$10/Mb for 454 and some Ion Torrent chips). In terms of cost per nonmultiplexed sample and instrument run time, the Pacific Biosciences and Ion Torrent platforms excel, with the 454 GS Junior and Illumina MiSeq also notable in this regard. All platforms allow multiplexing of samples, but details of library preparation, experimental design and data analysis can constrain the options. The wide range of characteristics among available platforms provides opportunities both to conduct groundbreaking studies and to waste money on scales that were previously infeasible. Thus, careful thought about the desired characteristics of these systems is warranted before purchasing or using any of them. Updated information from this guide will be maintained at: http://dna.uga.edu/ and http://tomato.biol.trinity.edu/blog/.},
author = {Glenn, Travis C.},
doi = {10.1111/j.1755-0998.2011.03024.x},
file = {:home/fin/Documents/papers/mendeley/Glenn\_2011\_Field guide to next-generation DNA sequencers\_Molecular Ecology Resources.pdf:pdf},
isbn = {1755-098X},
issn = {1755098X},
journal = {Mol. Ecol. Resour.},
keywords = {2 $\backslash$n                        nd and 3,454,Helicos,Illumina,Ion Torrent,Life technologies,Massively parallel sequencing,Pacific biosystems,Roche,SOLiD},
pages = {759--769},
pmid = {21592312},
title = {{Field guide to next-generation DNA sequencers}},
volume = {11},
year = {2011}
}
@article{Regalado2014,
author = {Regalado, A.},
journal = {MIT Technol. Rev.},
number = {The Year in Review: Health Care},
title = {{EmTech: Illumina Says 228,000 Human Genomes Will Be Sequenced This Year}},
year = {2014}
}
@article{Compeau2011,
abstract = {A mathematical concept known as a de Bruijn graph turns the formidable challenge of assembling a contiguous genome from billions of short sequencing reads into a tractable computational problem.},
archivePrefix = {arXiv},
arxivId = {doi:10.1038/nbt.2023},
author = {Compeau, Phillip E C and Pevzner, Pavel a and Tesler, Glenn},
doi = {10.1038/nbt.2023},
eprint = {nbt.2023},
file = {:home/fin/Documents/papers/mendeley/Compeau, Pevzner, Tesler\_2011\_How to apply de Bruijn graphs to genome assembly\_Nature Biotechnology.pdf:pdf},
isbn = {0000110010111},
issn = {1087-0156},
journal = {Nat. Biotechnol.},
number = {11},
pages = {987--991},
pmid = {22068540},
primaryClass = {doi:10.1038},
publisher = {Nature Publishing Group},
title = {{How to apply de Bruijn graphs to genome assembly}},
url = {http://dx.doi.org/10.1038/nbt.2023},
volume = {29},
year = {2011}
}
@article{Eddy2004,
author = {Eddy, Sean R},
file = {:home/fin/Documents/papers/mendeley/Eddy\_2004\_What is a hidden Markov model \_Nature biotechnology.pdf:pdf},
journal = {Nat. Biotechnol.},
number = {10},
pages = {1315--1316},
title = {{What is a hidden Markov model ?}},
volume = {22},
year = {2004}
}
@article{Lusk2014,
abstract = {Background Trace quantities of contaminating DNA are widespread in the laboratory environment, but their presence has received little attention in the context of high throughput sequencing. This issue is highlighted by recent works that have rested controversial claims upon sequencing data that appear to support the presence of unexpected exogenous species. Results I used reads that preferentially aligned to alternate genomes to infer the distribution of potential contaminant species in a set of independent sequencing experiments. I confirmed that dilute samples are more exposed to contaminating DNA, and, focusing on four single-cell sequencing experiments, found that these contaminants appear to originate from a wide diversity of clades. Although negative control libraries prepared from "blank" samples recovered the highest-frequency contaminants, low-frequency contaminants, which appeared to make heterogeneous contributions to samples prepared in parallel within a single experiment, were not well controlled for. I used these results to show that, despite heavy replication and plausible controls, contamination can explain all of the observations used to support a recent claim that complete genes pass from food to human blood. Conclusions Contamination must be considered a potential source of signals of exogenous species in sequencing data, even if these signals are replicated in independent experiments, vary across conditions, or indicate a species which seems a priori unlikely to contaminate. Negative control libraries processed in parallel are essential to control for contaminant DNAs, but their limited ability to recover low-frequency contaminants must be recognized.},
archivePrefix = {arXiv},
arxivId = {1401.7975},
author = {Lusk, R. W.},
doi = {10.1101/002279},
eprint = {1401.7975},
file = {:home/fin/Documents/papers/mendeley/Lusk\_2014\_Diverse and widespread contamination evident in the unmapped depths of high throughput sequencing data\_PLoS ONE.pdf:pdf},
isbn = {1932-6203 (Electronic) 1932-6203 (Linking)},
issn = {19326203},
journal = {PLoS One},
number = {10},
pmid = {25354084},
title = {{Diverse and widespread contamination evident in the unmapped depths of high throughput sequencing data}},
url = {http://biorxiv.org/content/early/2014/01/30/002279.abstract},
volume = {9},
year = {2014}
}
@article{Kodama2007,
abstract = {Paramecium bursaria free of symbiotic Chlorella species can be experimentally reinfected with algae isolated from algae-bearing cells by ingestion into digestive vacuoles. Isolated symbiotic algae were cloned, mixed with the algae-free P. bursaria at 25 +/- 1 degrees C for 1.5 min, washed and chased, with or without fixation 3 h after mixing. Though genetically identical, a few of the algae were not digested but coexisted with the digested ones in the same vacuole after lysosomal fusion. Light microscopy showed that algal fate did not depend on cell cycle stage or location in the vacuole. Electron microscopy showed that the nondigested algae were not protected by a perialgal vacuole membrane in the digestive vacuole. Moreover, this phenomenon was also observed in the presence of cycloheximide and puromycin, which are known to inhibit algal and host protein synthesis, respectively. These observations suggest that a few algae can acquire temporary resistance to host lysosomal enzymes in order to establish endosymbiosis without algal protein synthesis.},
author = {Kodama, Yuuki and Nakahara, Miho and Fujishima, Masahiro},
doi = {10.1007/s00709-006-0193-z},
file = {:home/fin/Documents/papers/mendeley/Kodama, Nakahara, Fujishima\_2007\_Symbiotic alga Chlorella vulgaris of the ciliate Paramecium bursaria shows temporary resistance to host.pdf:pdf},
issn = {0033-183X},
journal = {Protoplasma},
keywords = {Animals,Biological,Cell Division,Cell Division: drug effects,Cell Survival,Cell Survival: drug effects,Chlorella vulgaris,Chlorella vulgaris: cytology,Chlorella vulgaris: physiology,Chlorella vulgaris: ultrastructure,Cycloheximide,Cycloheximide: pharmacology,Electron,Lysosomes,Lysosomes: enzymology,Microscopy,Models,Paramecium,Paramecium: enzymology,Paramecium: physiology,Polarization,Puromycin,Puromycin: pharmacology,Symbiosis,Transmission},
month = jan,
number = {1-2},
pages = {61--7},
pmid = {17111098},
title = {{Symbiotic alga Chlorella vulgaris of the ciliate Paramecium bursaria shows temporary resistance to host lysosomal enzymes during the early infection process.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17111098},
volume = {230},
year = {2007}
}
@article{Huerta-Cepas2010,
abstract = {BACKGROUND: Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale.$\backslash$n$\backslash$nRESULTS: Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations.$\backslash$n$\backslash$nCONCLUSIONS: ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org.},
author = {Huerta-Cepas, Jaime and Dopazo, Joaqu\'{\i}n and Gabald\'{o}n, Toni},
doi = {10.1186/1471-2105-11-24},
file = {:home/fin/Documents/papers/mendeley/Huerta-Cepas, Dopazo, Gabald\'{o}n\_2010\_ETE a python Environment for Tree Exploration.\_BMC bioinformatics.pdf:pdf},
isbn = {1471-2105},
issn = {1471-2105},
journal = {BMC Bioinformatics},
keywords = {Computational Biology,Computational Biology: methods,Databases, Genetic,Phylogeny,Software},
pages = {24},
pmid = {20070885},
title = {{ETE: a python Environment for Tree Exploration.}},
url = {http://www.biomedcentral.com/1471-2105/11/24},
volume = {11},
year = {2010}
}
@article{Torgerson1952,
author = {Torgerson, W.S.},
file = {:home/fin/Documents/papers/mendeley/Torgerson\_1952\_Multidimensional Scaling I Theory and Method\_Psychometrika.pdf:pdf},
journal = {Psychometrika},
number = {4},
pages = {401--419},
title = {{Multidimensional Scaling: I Theory and Method}},
volume = {17},
year = {1952}
}
@article{Quinlan1986,
address = {Hingham, MA, USA},
author = {Quinlan, J R},
doi = {10.1023/A:1022643204877},
issn = {0885-6125},
journal = {Mach. Learn.},
keywords = {classification,decision trees,expert systems,induction,information theory,knowledge acquisition},
month = mar,
number = {1},
pages = {81--106},
publisher = {Kluwer Academic Publishers},
title = {{Induction of Decision Trees}},
url = {http://dx.doi.org/10.1023/A:1022643204877},
volume = {1},
year = {1986}
}
@article{Collins2006,
abstract = {Endogenous small RNAs function in RNA interference (RNAi) pathways to guide RNA cleavage, translational repression, or methylation of DNA or chromatin. In Tetrahymena thermophila, developmentally regulated DNA elimination is governed by an RNAi mechanism involving approximately 27-30-nucleotide (nt) RNAs. Here we characterize the sequence features of the approximately 27-30-nt RNAs and a approximately 23-24-nt RNA class representing a second RNAi pathway. The approximately 23-24-nt RNAs accumulate strain-specifically manner and map to the genome in clusters that are antisense to predicted genes. These findings reveal the existence of distinct endogenous RNAi pathways in the unicellular T. thermophila, a complexity previously demonstrated only in multicellular organisms.},
author = {Collins, Kathleen and Lee, Suzanne R},
doi = {10.1101/gad.1377006},
file = {:home/fin/Documents/papers/mendeley/Collins, Lee\_2006\_Two classes of endogenous small RNAs in Tetrahymena thermophila.\_Genes and Development.pdf:pdf},
isbn = {0890-9369 (Print)$\backslash$r0890-9369 (Linking)},
issn = {0890-9369},
journal = {Genes Dev.},
keywords = {Animals,Genome,Protozoan,Protozoan: classification,Protozoan: genetics,Protozoan: physiology,RNA,Ribonuclease III,Ribonuclease III: genetics,Small Interfering,Small Interfering: classification,Small Interfering: genetics,Small Interfering: physiology,Tetrahymena thermophila,Tetrahymena thermophila: genetics,Tetrahymena thermophila: physiology},
pages = {28--33},
pmid = {16357212},
title = {{Two classes of endogenous small RNAs in Tetrahymena thermophila.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16357212},
volume = {20},
year = {2006}
}
@article{Tang2009,
abstract = {Next-generation sequencing technology is a powerful tool for transcriptome analysis. However, under certain conditions, only a small amount of material is available, which requires more sensitive techniques that can preferably be used at the single-cell level. Here we describe a single-cell digital gene expression profiling assay. Using our mRNA-Seq assay with only a single mouse blastomere, we detected the expression of 75\% (5,270) more genes than microarray techniques and identified 1,753 previously unknown splice junctions called by at least 5 reads. Moreover, 8-19\% of the genes with multiple known transcript isoforms expressed at least two isoforms in the same blastomere or oocyte, which unambiguously demonstrated the complexity of the transcript variants at whole-genome scale in individual cells. Finally, for Dicer1(-/-) and Ago2(-/-) (Eif2c2(-/-)) oocytes, we found that 1,696 and 1,553 genes, respectively, were abnormally upregulated compared to wild-type controls, with 619 genes in common.},
author = {Tang, Fuchou and Barbacioru, Catalin and Wang, Yangzhou and Nordman, Ellen and Lee, Clarence and Xu, Nanlan and Wang, Xiaohui and Bodeau, John and Tuch, Brian B and Siddiqui, Asim and Lao, Kaiqin and Surani, M Azim},
doi = {10.1038/nmeth.1315},
file = {:home/fin/Documents/papers/mendeley/Tang et al.\_2009\_mRNA-Seq whole-transcriptome analysis of a single cell.\_Nature methods.pdf:pdf},
isbn = {1548-7105 (Electronic)$\backslash$n1548-7091 (Linking)},
issn = {1548-7091},
journal = {Nat. Methods},
number = {5},
pages = {377--382},
pmid = {19349980},
title = {{mRNA-Seq whole-transcriptome analysis of a single cell.}},
volume = {6},
year = {2009}
}
@article{Altun2003,
author = {Altun, Yasemin and Tsochantaridis, Ioannis and Hofmann, Thomas},
file = {:home/fin/Documents/papers/mendeley/Altun, Tsochantaridis, Hofmann\_2003\_Hidden Markov Support Vector Machines\_Proceedings of the Twentieth International Conference on Machi.pdf:pdf},
journal = {Proc. Twent. Int. Conf. Mach. Learn.},
title = {{Hidden Markov Support Vector Machines}},
year = {2003}
}
@article{Thompson1994,
abstract = {The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.},
author = {Thompson, J D and Higgins, D G and Gibson, T J},
doi = {10.1093/nar/22.22.4673},
file = {:home/fin/Documents/papers/mendeley/Thompson, Higgins, Gibson\_1994\_CLUSTAL W improving the sensitivity of progressive multiple sequence alignment through sequence weighting.pdf:pdf},
isbn = {0305-1048 (Print)$\backslash$n0305-1048 (Linking)},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {22},
pages = {4673--4680},
pmid = {7984417},
title = {{CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.}},
volume = {22},
year = {1994}
}
@article{Knip2014,
abstract = {This review focuses on the mobility of small RNA (sRNA) molecules from the perspective of trans-kingdom gene silencing. Mobility of sRNA molecules within organisms is a well-known phenomenon, facilitating gene silencing between cells and tissues. sRNA signals are also transmitted between organisms of the same species and of different species. Remarkably, in recent years many examples of RNA-signal exchange have been described to occur between organisms of different kingdoms. These examples are predominantly found in interactions between hosts and their pathogens, parasites, and symbionts. However, they may only represent the tip of the iceberg, since the emerging picture suggests that organisms in biological niches commonly exchange RNA-silencing signals. In this case, we need to take this into account fully to understand how a given biological equilibrium is obtained. Despite many observations of trans-kingdom RNA signal transfer, several mechanistic aspects of these signals remain unknown. Such RNA signal transfer is already being exploited for practical purposes, though. Pathogen genes can be silenced by plant-produced sRNAs designed to affect these genes. This is also known as Host-Induced Genes Silencing (HIGS), and it has the potential to become an important disease-control method in the future.},
author = {Knip, Marijn and Constantin, Maria E and Thordal-Christensen, Hans},
doi = {10.1371/journal.pgen.1004602},
file = {:home/fin/Documents/papers/mendeley/Knip, Constantin, Thordal-Christensen\_2014\_Trans-kingdom cross-talk small RNAs on the move.\_PLoS genetics.pdf:pdf},
isbn = {1553-7404 (Electronic)$\backslash$r1553-7390 (Linking)},
issn = {1553-7404},
journal = {PLoS Genet.},
number = {9},
pages = {e1004602},
pmid = {25188222},
title = {{Trans-kingdom cross-talk: small RNAs on the move.}},
url = {http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004602},
volume = {10},
year = {2014}
}
@article{Sasagawa2013,
abstract = {A highly reproducible and sensitive single-cell RNA-Seq method will facilitate the understanding of the biological roles and underlying mechanisms of the non-genetic cellular heterogeneity. In this study, we report a novel single-cell RNA-Seq method called Quartz-Seq that has a simpler protocol and higher reproducibility and sensitivity compared to previously developed methods. We demonstrate that single-cell Quartz-Seq quantitatively detects various kind of non-genetic cellular heterogeneity. The method detects different cell types and different cell-cycle phases of a single-cell type. Moreover, this method can comprehensively reveal gene expression heterogeneity between single-cells of the same cell type at the same cell-cycle phase.},
author = {Sasagawa, Yohei and Nikaido, Itoshi and Hayashi, Tetsutaro and Danno, Hiroki and Uno, Kenichiro D. and Imai, Takeshi and Ueda, Hiroki R.},
doi = {10.1186/gb-2013-14-4-r31},
file = {:home/fin/Documents/papers/mendeley/Sasagawa et al.\_2013\_Quartz-Seq a highly reproducible and sensitive single-cell RNA-Seq reveals non-genetic gene expression heterogeneit.pdf:pdf},
isbn = {1465-6914 (Electronic)$\backslash$n1465-6906 (Linking)},
issn = {1465-6906},
journal = {Genome Biol.},
keywords = {bioinformatics,cell biology,cellular heterogeneity,rna-seq,sequencing,single cell,transcriptome},
number = {4},
pages = {R31},
pmid = {23594475},
publisher = {BioMed Central Ltd},
title = {{Quartz-Seq: a highly reproducible and sensitive single-cell RNA-Seq reveals non-genetic gene expression heterogeneity}},
url = {http://genomebiology.com/2013/14/4/R31/abstract$\backslash$nhttp://genomebiology.com/content/pdf/gb-2013-14-4-r31.pdf},
volume = {14},
year = {2013}
}
@article{Stover2010,
author = {St\"{o}ver, Ben C and M\"{u}ller, Kai F},
doi = {10.1186/1471-2105-11-7},
file = {:home/fin/Documents/papers/mendeley/St\"{o}ver, M\"{u}ller\_2010\_TreeGraph 2 Combining and visualizing evidence from different phylogenetic analyses\_BMC Bioinformatics.pdf:pdf},
issn = {1471-2105},
journal = {BMC Bioinformatics},
pages = {7},
title = {{TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses}},
url = {http://www.biomedcentral.com/1471-2105/11/7},
volume = {11},
year = {2010}
}
@article{Le2013,
abstract = {Sequencing of RNAs (RNA-Seq) has revolutionized the field of transcriptomics, but the reads obtained often contain errors. Read error correction can have a large impact on our ability to accurately assemble transcripts. This is especially true for de novo transcriptome analysis, where a reference genome is not available. Current read error correction methods, developed for DNA sequence data, cannot handle the overlapping effects of non-uniform abundance, polymorphisms and alternative splicing. Here we present SEquencing Error CorrEction in Rna-seq data (SEECER), a hidden Markov Model (HMM)-based method, which is the first to successfully address these problems. SEECER efficiently learns hundreds of thousands of HMMs and uses these to correct sequencing errors. Using human RNA-Seq data, we show that SEECER greatly improves on previous methods in terms of quality of read alignment to the genome and assembly accuracy. To illustrate the usefulness of SEECER for de novo transcriptome studies, we generated new RNA-Seq data to study the development of the sea cucumber Parastichopus parvimensis. Our corrected assembled transcripts shed new light on two important stages in sea cucumber development. Comparison of the assembled transcripts to known transcripts in other species has also revealed novel transcripts that are unique to sea cucumber, some of which we have experimentally validated. Supporting website: http://sb.cs.cmu.edu/seecer/.},
author = {Le, Hai Son and Schulz, Marcel H. and Mccauley, Brenna M. and Hinman, Veronica F. and Bar-Joseph, Ziv},
doi = {10.1093/nar/gkt215},
file = {:home/fin/Documents/papers/mendeley/Le et al.\_2013\_Probabilistic error correction for RNA sequencing\_Nucleic Acids Research.pdf:pdf},
isbn = {0305-1048},
issn = {03051048},
journal = {Nucleic Acids Res.},
pages = {1--11},
pmid = {23558750},
title = {{Probabilistic error correction for RNA sequencing}},
volume = {41},
year = {2013}
}
@article{Xiang2015,
author = {Xiang, Tingting and Nelson, William and Rodriguez, Jesse and Tolleter, Dimitri and Grossman, Arthur R.},
doi = {10.1111/tpj.12789},
file = {:home/fin/Documents/papers/mendeley/Xiang et al.\_2015\_Symbiodinium transcriptome and global responses of cells to immediate changes in light intensity when grown under auto.pdf:pdf},
issn = {09607412},
journal = {Plant J.},
keywords = {acclimation,cell adhesion,chromatin condensation,cnidarian symbiosis,dinoflagellate,light,rna-seq,spliced leader,symbiodinium transcriptome},
pages = {67--80},
title = {{Symbiodinium transcriptome and global responses of cells to immediate changes in light intensity when grown under autotrophic or mixotrophic conditions}},
url = {http://doi.wiley.com/10.1111/tpj.12789},
volume = {82},
year = {2015}
}
@article{Brown2012,
abstract = {Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and high sequencing error rates of modern sequencers present many new computational challenges in data interpretation. These challenges have led to the development of new classes of mapping tools and \{$\backslash$em de novo\} assemblers. These algorithms are challenged by the continued improvement in sequencing throughput. We here describe digital normalization, a single-pass computational algorithm that systematizes coverage in shotgun sequencing data sets, thereby decreasing sampling variation, discarding redundant data, and removing the majority of errors. Digital normalization substantially reduces the size of shotgun data sets and decreases the memory and time requirements for \{$\backslash$em de novo\} sequence assembly, all without significantly impacting content of the generated contigs. We apply digital normalization to the assembly of microbial genomic data, amplified single-cell genomic data, and transcriptomic data. Our implementation is freely available for use and modification.},
archivePrefix = {arXiv},
arxivId = {1203.4802},
author = {Brown, C. Titus and Howe, Adina and Zhang, Qingpeng and Pyrkosz, Alexis B. and Brom, Timothy H.},
doi = {10.1128/genomeA.00802-14.Copyright},
eprint = {1203.4802},
file = {:home/fin/Documents/papers/mendeley/Brown et al.\_2012\_A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data\_arXiv.pdf:pdf},
issn = {<null>},
journal = {arXiv},
pages = {1--18},
title = {{A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data}},
url = {http://arxiv.org/abs/1203.4802},
volume = {1203.4802},
year = {2012}
}
@article{Reed2006,
abstract = {Our information about the gene content of organisms continues to grow as more genomes are sequenced and gene products are characterized. Sequence-based annotation efforts have led to a list of cellular components, which can be thought of as a one-dimensional annotation. With growing information about component interactions, facilitated by the advancement of various high-throughput technologies, systemic, or two-dimensional, annotations can be generated. Knowledge about the physical arrangement of chromosomes will lead to a three-dimensional spatial annotation of the genome and a fourth dimension of annotation will arise from the study of changes in genome sequences that occur during adaptive evolution. Here we discuss all four levels of genome annotation, with specific emphasis on two-dimensional annotation methods.},
author = {Reed, Jennifer L and Famili, Iman and Thiele, Ines and Palsson, Bernhard O},
doi = {10.1038/nrg1769},
file = {:home/fin/Documents/papers/mendeley/Reed et al.\_2006\_Towards multidimensional genome annotation.\_Nature reviews. Genetics.pdf:pdf},
isbn = {1471-0056},
issn = {1471-0056},
journal = {Nat. Rev. Genet.},
number = {February},
pages = {130--141},
pmid = {16418748},
title = {{Towards multidimensional genome annotation.}},
volume = {7},
year = {2006}
}
@inproceedings{Gilbert2013,
address = {Notre Dame},
author = {Gilbert, Donald G},
booktitle = {7th Annu. Arthropod Genomics Symp.},
file = {:home/fin/Documents/papers/mendeley/Gilbert\_2013\_Gene-omes built from mRNA-seq not genome DNA\_7th Annual Arthropod Genomics Symposium.pdf:pdf},
title = {{Gene-omes built from mRNA-seq not genome DNA}},
url = {http://arthropods.eugenes.org/EvidentialGene/about/EvigeneRNA2013poster.pdf},
year = {2013}
}
@article{jukes1969evolution,
author = {Jukes, Thomas H and Cantor, Charles R},
journal = {Mamm. protein Metab.},
pages = {21--132},
publisher = {New York},
title = {{Evolution of protein molecules}},
volume = {3},
year = {1969}
}
@article{Smith2006,
author = {Smith, Ca and Elizabeth, J and O'Maille, G and Abagyan, Ruben and Siuzdak, Gray},
doi = {10.1021/ac051437y},
file = {:home/fin/Documents/papers/mendeley/Smith et al.\_2006\_XCMS processing mass spectrometry data for metabolite profiling using Nonlinear Peak Alignment,Matching,and Identifica.pdf:pdf},
isbn = {0003-2700 (Print)$\backslash$n0003-2700 (Linking)},
issn = {00032700},
journal = {ACS Publ.},
number = {3},
pages = {779--787},
pmid = {16448051},
title = {{XCMS: processing mass spectrometry data for metabolite profiling using Nonlinear Peak Alignment,Matching,and Identification}},
volume = {78},
year = {2006}
}
@article{Needleman1970,
abstract = {A computer adaptable method for finding similarities in the amino acid sequences of two proteins has been developed. From these findings it is possible to determine whether significant homology exists between the proteins. This information is used to trace their possible evolutionary development. The maximum match is a number dependent upon the similarity of the sequences. One of its definitions is the largest number of amino acids of one protein that can be matched with those of a second protein allowing for all possible interruptions in either of the sequences. While the interruptions give rise to a very large number of comparisons, the method efficiently excludes from consideration those comparisons that cannot contribute to the maximum match. Comparisons are made from the smallest unit of significance, a pair of amino acids, one from each protein. All possible pairs are represented by a two-dimensional array, and all possible comparisons are represented by pathways through the array. For this maximum match only certain of the possible pathways must be evaluated. A numerical value, one in this case, is assigned to every cell in the array representing like amino acids. The maximum match is the largest number that would result from summing the cell values of every pathway.},
author = {Needleman, S B and Wunsch, C D},
doi = {10.1016/0022-2836(70)90057-4},
file = {:home/fin/Documents/papers/mendeley/Needleman, Wunsch\_1970\_A general method applicable to the search for similarities in the amino acid sequence of two proteins.\_Journal of.pdf:pdf},
isbn = {0022-2836},
issn = {00222836},
journal = {J. Mol. Biol.},
pages = {443--453},
pmid = {5420325},
title = {{A general method applicable to the search for similarities in the amino acid sequence of two proteins.}},
volume = {48},
year = {1970}
}
@article{Schimper1883,
author = {Schimper, A F W},
file = {:home/fin/Documents/papers/mendeley/Schimper\_1883\_Ueber die Entwickelung der Chlorophyllk\"{o}rner und Farbk\"{o}rper\_Botanische Zeitung.pdf:pdf},
journal = {Bot. Zeitung},
pages = {106--162},
title = {{Ueber die Entwickelung der Chlorophyllk\"{o}rner und Farbk\"{o}rper}},
volume = {February},
year = {1883}
}
@article{Bray2015,
abstract = {We present a novel approach to RNA-Seq quantification that is near optimal in speed and accuracy. Software implementing the approach, called kallisto, can be used to analyze 30 million unaligned RNA-Seq reads in less than 5 minutes on a standard laptop computer while providing results as accurate as those of the best existing tools. This removes a major computational bottleneck in RNA-Seq analysis.},
archivePrefix = {arXiv},
arxivId = {1505.02710},
author = {Bray, Nicolas L and Pimentel, Harold and Melsted, P\'{a}ll and Pachter, Lior},
eprint = {1505.02710},
file = {:home/fin/Documents/papers/mendeley/Bray et al.\_2015\_Near-optimal RNA-Seq quantification\_aRxiv.pdf:pdf},
journal = {aRxiv},
keywords = {1,2,3 and lior pachter,4,bray 1,department of computer science,harold pimentel,innovative genomics initiative,nicolas l,p\'{a}ll melsted,r-optimal rna-seq quantification,uc berkeley},
title = {{Near-optimal RNA-Seq quantification}},
year = {2015}
}
@article{Achilles-Day2013a,
author = {Achilles-Day, Undine E.M. and Day, John G.},
doi = {10.1016/j.mimet.2013.01.007},
file = {:home/fin/Documents/papers/mendeley/Achilles-Day, Day\_2013\_Isolation of clonal cultures of endosymbiotic green algae from their ciliate hosts\_Journal of Microbiological Met.pdf:pdf},
issn = {01677012},
journal = {J. Microbiol. Methods},
keywords = {Algal endosymbiosis,Euplotes daidaleos,Loxodes rostrum,Micromanipulation,Paramecium bursaria},
number = {3},
pages = {355--357},
publisher = {Elsevier B.V.},
title = {{Isolation of clonal cultures of endosymbiotic green algae from their ciliate hosts}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0167701213000110},
volume = {92},
year = {2013}
}
@article{Karp2010,
author = {Karp, P. D. and Paley, S. M. and Krummenacker, M. and Latendresse, M. and Dale, J. M. and Lee, T. J. and Kaipa, P. and Gilham, F. and Spaulding, a. and Popescu, L. and Altman, T. and Paulsen, I. and Keseler, I. M. and Caspi, R.},
doi = {10.1093/bib/bbp043},
file = {:home/fin/Documents/papers/mendeley/Karp et al.\_2010\_Pathway Tools version 13.0 integrated software for pathwaygenome informatics and systems biology\_Briefings in Bioinform.pdf:pdf},
issn = {1467-5463},
journal = {Brief. Bioinform.},
keywords = {biological networks,genome databases,genome informatics,metabolic pathways,model organism databases,pathway bioinformatics,regulatory networks},
number = {1},
pages = {40--79},
title = {{Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology}},
url = {http://bib.oxfordjournals.org/cgi/doi/10.1093/bib/bbp043},
volume = {11},
year = {2010}
}
@article{Sanger1977,
abstract = {A DNA sequence for the genome of bacteriophage phi X174 of approximately 5,375 nucleotides has been determined using the rapid and simple 'plus and minus' method. The sequence identifies many of the features responsible for the production of the proteins of the nine known genes of the organism, including initiation and termination sites for the proteins and RNAs. Two pairs of genes are coded by the same region of DNA using different reading frames.},
author = {Sanger, F and Air, G M and Barrell, B G and Brown, N L and Coulson, a R and Fiddes, C a and Hutchison, C a and Slocombe, P M and Smith, M},
doi = {5,386 base pairs...},
file = {:home/fin/Documents/papers/mendeley/Sanger et al.\_1977\_Nucleotide sequence of bacteriophage phi X174 DNA.\_Nature.pdf:pdf},
isbn = {0028-0836 (Print)$\backslash$r0028-0836 (Linking)},
issn = {0028-0836},
journal = {Nature},
pages = {687--695},
pmid = {870828},
title = {{Nucleotide sequence of bacteriophage phi X174 DNA.}},
volume = {265},
year = {1977}
}
@article{Nakai1992,
abstract = {To automate examination of massive amounts of sequence data for biological function, it is important to computerize interpretation based on empirical knowledge of sequence-function relationships. For this purpose, we have been constructing a knowledge base by organizing various experimental and computational observations as a collection of if-then rules. Here we report an expert system, which utilizes this knowledge base, for predicting localization sites of proteins only from the information on the amino acid sequence and the source origin. We collected data for 401 eukaryotic proteins with known localization sites (subcellular and extracellular) and divided them into training data and testing data. Fourteen localization sites were distinguished for animal cells and 17 for plant cells. When sorting signals were not well characterized experimentally, various sequence features were computationally derived from the training data. It was found that 66\% of the training data and 59\% of the testing data were correctly predicted by our expert system. This artificial intelligence approach is powerful and flexible enough to be used in genome analyses.},
author = {Nakai, K and Kanehisa, M},
doi = {10.1016/S0888-7543(05)80111-9},
file = {:home/fin/Documents/papers/mendeley/Nakai, Kanehisa\_1992\_A knowledge base for predicting protein localization sites in eukaryotic cells.\_Genomics.pdf:pdf},
isbn = {0888-7543 (Print)},
issn = {0888-7543},
journal = {Genomics},
pages = {897--911},
pmid = {1478671},
title = {{A knowledge base for predicting protein localization sites in eukaryotic cells.}},
volume = {14},
year = {1992}
}
@article{Klukas2007,
author = {Klukas, C. and Schreiber, F.},
doi = {10.1093/bioinformatics/btl611},
file = {:home/fin/Documents/papers/mendeley/Klukas, Schreiber\_2007\_Dynamic exploration and editing of KEGG pathway diagrams\_Bioinformatics.pdf:pdf},
issn = {1367-4803},
journal = {Bioinformatics},
number = {3},
pages = {344--350},
title = {{Dynamic exploration and editing of KEGG pathway diagrams}},
url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btl611},
volume = {23},
year = {2007}
}
@article{Katoh2005,
abstract = {The accuracy of multiple sequence alignment program MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed higher accuracy than currently available methods including TCoffee version 2 and CLUSTAL W in benchmark tests consisting of alignments of >50 sequences. Like the previously available options, the new options of MAFFT can handle hundreds of sequences on a standard desktop computer. We also examined the effect of the number of homologues included in an alignment. For a multiple alignment consisting of approximately 8 sequences with low similarity, the accuracy was improved (2-10 percentage points) when the sequences were aligned together with dozens of their close homologues (E-value < 10(-5)-10(-20)) collected from a database. Such improvement was generally observed for most methods, but remarkably large for the new options of MAFFT proposed here. Thus, we made a Ruby script, mafftE.rb, which aligns the input sequences together with their close homologues collected from SwissProt using NCBI-BLAST.},
author = {Katoh, Kazutaka and Kuma, Kei-ichi and Toh, Hiroyuki and Miyata, Takashi},
doi = {10.1093/nar/gki198},
file = {:home/fin/Documents/papers/mendeley/Katoh et al.\_2005\_MAFFT version 5 improvement in accuracy of multiple sequence alignment.\_Nucleic acids research.pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$n0305-1048 (Linking)},
issn = {1362-4962},
journal = {Nucleic Acids Res.},
number = {2},
pages = {511--518},
pmid = {15661851},
title = {{MAFFT version 5: improvement in accuracy of multiple sequence alignment.}},
volume = {33},
year = {2005}
}
@article{Koch2013,
author = {Koch, a. and Kumar, N. and Weber, L. and Keller, H. and Imani, J. and Kogel, K.-H.},
doi = {10.1073/pnas.1306373110},
file = {:home/fin/Documents/papers/mendeley/Koch et al.\_2013\_Host-induced gene silencing of cytochrome P450 lanosterol C14 -demethylase-encoding genes confers strong resistance to.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
number = {48},
pages = {19324--19329},
title = {{Host-induced gene silencing of cytochrome P450 lanosterol C14 -demethylase-encoding genes confers strong resistance to Fusarium species}},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1306373110},
volume = {110},
year = {2013}
}
@article{Berg2014,
archivePrefix = {arXiv},
arxivId = {arXiv:1409.0575v1},
author = {Russakovsky, Olga and Deng,

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib