text:
otic Zoochlorellae\_Journal of General Mi.pdf:pdf},
journal = {J. Gen. Microbiol.},
pages = {397--404},
title = {{Feeding Behaviour of Didinium nasutum on Paramecium bursaria with Normal or Apochlorotic Zoochlorellae}},
volume = {118},
year = {1980}
}
@article{Laskowski2005,
abstract = {ProFunc (http://www.ebi.ac.uk/thornton-srv/databases/ProFunc) is a web server for predicting the likely function of proteins whose 3D structure is known but whose function is not. Users submit the coordinates of their structure to the server in PDB format. ProFunc makes use of both existing and novel methods to analyse the protein's sequence and structure identifying functional motifs or close relationships to functionally characterized proteins. A summary of the analyses provides an at-a-glance view of what each of the different methods has found. More detailed results are available on separate pages. Often where one method has failed to find anything useful another may be more forthcoming. The server is likely to be of most use in structural genomics where a large proportion of the proteins whose structures are solved are of hypothetical proteins of unknown function. However, it may also find use in a comparative analysis of members of large protein families. It provides a convenient compendium of sequence and structural information that often hold vital functional clues to be followed up experimentally.},
author = {Laskowski, Roman a. and Watson, James D. and Thornton, Janet M.},
doi = {10.1093/nar/gki414},
file = {:home/fin/Documents/papers/mendeley/Laskowski, Watson, Thornton\_2005\_ProFunc A server for predicting protein function from 3D structure\_Nucleic Acids Research.pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$n0305-1048 (Linking)},
issn = {03051048},
journal = {Nucleic Acids Res.},
pages = {89--93},
pmid = {15980588},
title = {{ProFunc: A server for predicting protein function from 3D structure}},
volume = {33},
year = {2005}
}
@article{Simmons2003,
author = {Simmons, M. P.},
doi = {10.1093/molbev/msh014},
file = {:home/fin/Documents/papers/mendeley/Simmons\_2003\_How Meaningful Are Bayesian Support Values\_Molecular Biology and Evolution.pdf:pdf},
issn = {0737-4038},
journal = {Mol. Biol. Evol.},
keywords = {alternatively,and holmes 1996,ayesian phylogenetic inference,berry,bootstrap support,branch support,efron,halloran,jackknife support,parsimony,posterior probabilities,reflect type 1 error,rodrigo 1993,zharkikh and li 1995},
number = {1},
pages = {188--199},
title = {{How Meaningful Are Bayesian Support Values?}},
url = {http://mbe.oupjournals.org/cgi/doi/10.1093/molbev/msh014},
volume = {21},
year = {2003}
}
@article{Simpson1951,
author = {Simpson, E.H.},
file = {:home/fin/Documents/papers/mendeley/Simpson\_1951\_The Interpretation of Interaction in Contingency Tables\_Journal of the Royal Statistical Society Series B.pdf:pdf},
journal = {J. R. Stat. Soc. Ser. B},
number = {2},
pages = {238--241},
title = {{The Interpretation of Interaction in Contingency Tables}},
volume = {13},
year = {1951}
}
@article{Liang2014,
author = {Liang, Jialong and Cai, Wanshi and Sun, Zhongsheng},
doi = {10.1016/j.jgg.2014.09.005},
file = {:home/fin/Documents/papers/mendeley/Liang, Cai, Sun\_2014\_Single-Cell Sequencing Technologies Current and Future\_Journal of Genetics and Genomics.pdf:pdf},
issn = {16738527},
journal = {J. Genet. Genomics},
keywords = {epigenome,genome,sequencing,single-cell,transcriptome},
month = oct,
number = {10},
pages = {513--528},
publisher = {Elsevier Limited and Science Press},
title = {{Single-Cell Sequencing Technologies: Current and Future}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1673852714001684},
volume = {41},
year = {2014}
}
@article{Aoki2007,
author = {Aoki, Kazuma and Moriguchi, Hiromi and Yoshioka, Tomoko and Okawa, Katsuya and Tabara, Hiroaki},
doi = {10.1038/sj.emboj.7601910},
file = {:home/fin/Documents/papers/mendeley/Aoki et al.\_2007\_In vitro analyses of the production and activity of secondary small interfering RNAs in C. elegans\_The EMBO Journal.pdf:pdf},
issn = {0261-4189},
journal = {EMBO J.},
keywords = {argonaute,rdrp,rnai,sirna},
number = {24},
pages = {5007--5019},
title = {{In vitro analyses of the production and activity of secondary small interfering RNAs in C. elegans}},
url = {http://emboj.embopress.org/cgi/doi/10.1038/sj.emboj.7601910},
volume = {26},
year = {2007}
}
@article{Kruschke2013,
author = {Kruschke, John K.},
doi = {10.1037/a0029146},
file = {:home/fin/Documents/papers/mendeley/Kruschke\_2013\_Bayesian estimation supersedes the t test.\_Journal of Experimental Psychology General.pdf:pdf},
issn = {1939-2222},
journal = {J. Exp. Psychol. Gen.},
keywords = {bayes factor,bayesian statistics,confidence interval,effect size,robust estimation},
number = {2},
pages = {573--603},
title = {{Bayesian estimation supersedes the t test.}},
url = {http://doi.apa.org/getdoi.cfm?doi=10.1037/a0029146},
volume = {142},
year = {2013}
}
@article{Kuppers1993,
abstract = {Germinal centres are areas of intense B lymphocyte proliferation inside primary B cell follicles in spleen and lymph nodes. Rearranged V genes from single human B cells, isolated from histological sections of two such structures by micromanipulation, were amplified and sequenced. Cells from the follicular mantle were clonally diverse and largely expressed germline V genes. Germinal centres were dominated by a few large B cell clones dispersed throughout these structures and exhibiting intraclonal diversity by ongoing somatic hypermutation. Pronounced counterselection of replacement mutations seen in one of the germinal centres may indicate a late phase of the germinal centre reaction. A polyclonal population of activated B cells expressing unmutated antibodies in the dark zone of the other germinal centre may represent the initial founder cells.},
author = {K\"{u}ppers, R and Zhao, M and Hansmann, M L and Rajewsky, K},
file = {:home/fin/Documents/papers/mendeley/K\"{u}ppers et al.\_1993\_Tracing B cell development in human germinal centres by molecular analysis of single cells picked from histological.pdf:pdf},
isbn = {0261-4189 (Print)$\backslash$r0261-4189 (Linking)},
issn = {0261-4189},
journal = {EMBO J.},
keywords = {b cell development,germinal centre,hypermutation,single cell pcr,somatic,v gene rearrangement},
number = {13},
pages = {4955--4967},
pmid = {8262038},
title = {{Tracing B cell development in human germinal centres by molecular analysis of single cells picked from histological sections.}},
volume = {12},
year = {1993}
}
@article{Takeda1998,
author = {Takeda, Hiroshi and Sekiguchi, Tamami and Nunokawa, Sumi and Usuki, Itaru},
doi = {10.1016/S0932-4739(98)80023-0},
file = {:home/fin/Documents/papers/mendeley/Takeda et al.\_1998\_Species-specificity of Chlorella for establishment of symbiotic association with Paramecium bursaria — Does infecti.pdf:pdf},
issn = {09324739},
journal = {Eur. J. Protistol.},
keywords = {chlorella sp,endosymbiosis,glucosamine,infection,paramecium bursaria,rigid wall,species specifici-},
month = jun,
number = {2},
pages = {133--137},
publisher = {Gustav Fischer Verlag},
title = {{Species-specificity of Chlorella for establishment of symbiotic association with Paramecium bursaria — Does infectivity depend upon sugar components of the cell wall?}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0932473998800230},
volume = {34},
year = {1998}
}
@article{Hu2008,
abstract = {Chlorella was known to show enhanced antifreeze capability after cold hardening. We isolated Chlorella strains NJ-7 and NJ-18, which display alternative cold response modes from rock surfaces in Antarctica. On the basis of 18S ribosomal (rRNA) sequences, NJ-7 is an Antarctic type of Chlorella vulgaris; NJ-18 is also a 'true' Chlorella species but differs from any previously reported species in structure. NJ-7 partially retained the enhancing effects of low temperature cultivation on freeze tolerance, which correlates with an increase of C18:3-fatty acid content and up-regulation of two antifreeze protein genes. NJ-18, however, showed stable freeze tolerance regardless of the precultivation temperature. We propose that cold response modes vary widely in Chlorella and that the adaptation of C. vulgaris to Antarctica may serve as a model system for the evolution of antifreeze mechanisms in a single species of photosynthetic microorganism.},
author = {Hu, Hanhua and Li, Huiying and Xu, Xudong},
doi = {10.2216/07-28.1},
file = {:home/fin/Documents/papers/mendeley/Hu, Li, Xu\_2008\_Alternative Cold Response Modes in Chlorella (Chlorophyta, Trebouxiophyceae) from Antarctica\_Phycologia.pdf:pdf},
isbn = {0031-8884},
issn = {0031-8884},
journal = {Phycologia},
number = {January},
pages = {28--34},
title = {{Alternative Cold Response Modes in Chlorella (Chlorophyta, Trebouxiophyceae) from Antarctica}},
volume = {47},
year = {2008}
}
@article{Siegel1960,
author = {Siegel, R W and Larison, L L},
doi = {10.1073/pnas.46.3.344},
file = {:home/fin/Documents/papers/mendeley/Siegel, Larison\_1960\_The Genic Control of Mating Types in Paramecium Bursaria.\_Proceedings of the National Academy of Sciences of the Un.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
number = {variety 8},
pages = {344--349},
pmid = {16578490},
title = {{The Genic Control of Mating Types in Paramecium Bursaria.}},
volume = {46},
year = {1960}
}
@article{Knittel2009,
abstract = {Methane is the most abundant hydrocarbon in the atmosphere, and it is an important greenhouse gas, which has so far contributed an estimated 20\% of postindustrial global warming. A great deal of biogeochemical research has focused on the causes and effects of the variation in global fluxes of methane throughout earth's history, but the underlying microbial processes and their key agents remain poorly understood. This is a disturbing knowledge gap because 85\% of the annual global methane production and about 60\% of its consumption are based on microbial processes. Only three key functional groups of microorganisms of limited diversity regulate the fluxes of methane on earth, namely the aerobic methanotrophic bacteria, the methanogenic archaea, and their close relatives, the anaerobic methanotrophic archaea (ANME). The ANME represent special lines of descent within the Euryarchaeota and appear to gain energy exclusively from the anaerobic oxidation of methane (AOM), with sulfate as the final electron acceptor according to the net reaction: CH(4) + SO(42-) ---> HCO(3-) + HS(-) + H(2)O. This review summarizes what is known and unknown about AOM on earth and its key catalysts, the ANME clades and their bacterial partners.},
author = {Knittel, Katrin and Boetius, Antje},
doi = {10.1146/annurev.micro.61.080706.093130},
file = {:home/fin/Documents/papers/mendeley/Knittel, Boetius\_2009\_Anaerobic oxidation of methane progress with an unknown process.\_Annual review of microbiology.pdf:pdf},
isbn = {1545-3251 (Electronic)},
issn = {0066-4227},
journal = {Annu. Rev. Microbiol.},
keywords = {anme,archaea,mcr a,microbial consortia,sulfate-reducing bacteria},
pages = {311--334},
pmid = {19575572},
title = {{Anaerobic oxidation of methane: progress with an unknown process.}},
volume = {63},
year = {2009}
}
@article{Saier2014,
abstract = {The Transporter Classification Database (TCDB), freely accessible at http://www.tcdb.org, is a relational database containing sequence, structural, functional and evolutionary information about transport systems from a variety of living organisms, based on the International Union of Biochemistry and Molecular Biology-approved transporter classification (TC) system. It is a curated repository for factual information compiled largely from published references. It uses a functional/phylogenetic system of classification, and currently encompasses about 5000 representative transporters and putative transporters in more than 500 families. We here describe novel software designed to support and extend the usefulness of TCDB. Our recent efforts render it more user friendly, incorporate machine learning to input novel data in a semiautomatic fashion, and allow analyses that are more accurate and less time consuming. The availability of these tools has resulted in recognition of distant phylogenetic relationships and tremendous expansion of the information available to TCDB users.},
author = {Saier, Milton H. and Reddy, Vamsee S. and Tamang, Dorjee G. and V\"{a}stermark, \AA ke},
doi = {10.1093/nar/gkt1097},
file = {:home/fin/Documents/papers/mendeley/Saier et al.\_2014\_The transporter classification database\_Nucleic Acids Research.pdf:pdf},
isbn = {1362-4962 (Electronic)},
issn = {03051048},
journal = {Nucleic Acids Res.},
number = {November 2013},
pages = {251--258},
pmid = {19022853},
title = {{The transporter classification database}},
volume = {42},
year = {2014}
}
@article{Cortes1995,
abstract = {The support-vector network is a new leaming machine for two-group classification problems. The machine conceptually implements the following idea: input vectors are non-linearly mapped to a very high- dimension feature space. In this feature space a linear decision surface is constructed. Special properties of the decision surface ensures high generalization ability of the learning machine. The idea behind the support-vector network was previously implemented for the restricted case where the training data can be separated without errors. We here extend this result to non-separable training data. High generalization ability of support-vector networks utilizing polynomial input transformations is demon- strated. We also compare the performance of the support-vector network to various classical learning algorithms that all took part in a benchmark study of Optical Character Recognition.},
author = {Cortes, Corinna and Vapnik, Vladimir},
doi = {10.1007/BF00994018},
file = {:home/fin/Documents/papers/mendeley/Cortes, Vapnik\_1995\_Support-vector networks\_Machine Learning.pdf:pdf},
isbn = {0885-6125},
issn = {08856125},
journal = {Mach. Learn.},
keywords = {efficient learning algorithms,neural networks,pattern recognition,polynomial classifiers,radial basis function classifiers},
pages = {273--297},
pmid = {9052598814225336358},
title = {{Support-vector networks}},
volume = {20},
year = {1995}
}
@article{Bernstein2001,
abstract = {RNA interference (RNAi) is the mechanism through which double-stranded RNAs silence cognate genes. In plants, this can occur at both the transcriptional and the post-transcriptional levels; however, in animals, only post-transcriptional RNAi has been reported to date. In both plants and animals, RNAi is characterized by the presence of RNAs of about 22 nucleotides in length that are homologous to the gene that is being suppressed. These 22-nucleotide sequences serve as guide sequences that instruct a multicomponent nuclease, RISC, to destroy specific messenger RNAs. Here we identify an enzyme, Dicer, which can produce putative guide RNAs. Dicer is a member of the RNase III family of nucleases that specifically cleave double-stranded RNAs, and is evolutionarily conserved in worms, flies, plants, fungi and mammals. The enzyme has a distinctive structure, which includes a helicase domain and dual RNase III motifs. Dicer also contains a region of homology to the RDE1/QDE2/ARGONAUTE family that has been genetically linked to RNAi.},
author = {Bernstein, E and Caudy, a a and Hammond, S M and Hannon, G J},
doi = {10.1038/35053110},
file = {:home/fin/Documents/papers/mendeley/Bernstein et al.\_2001\_Role for a bidentate ribonuclease in the initiation step of RNA interference.\_Nature.pdf:pdf},
isbn = {0028-0836 (Print)$\backslash$r0028-0836 (Linking)},
issn = {0028-0836},
journal = {Nature},
number = {1997},
pages = {363--366},
pmid = {11201747},
title = {{Role for a bidentate ribonuclease in the initiation step of RNA interference.}},
volume = {409},
year = {2001}
}
@article{Peters2007,
author = {Peters, Lasse and Meister, Gunter},
doi = {10.1016/j.molcel.2007.05.001},
file = {:home/fin/Documents/papers/mendeley/Peters, Meister\_2007\_Argonaute Proteins Mediators of RNA Silencing\_Molecular Cell.pdf:pdf},
issn = {10972765},
journal = {Mol. Cell},
pages = {611--623},
title = {{Argonaute Proteins: Mediators of RNA Silencing}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276507002572},
volume = {26},
year = {2007}
}
@article{Yuan1994,
abstract = {The SecA protein is an essential, azide-sensitive component of the bacterial protein translocation machinery. A SecA protein homolog (CPSecA) now identified in pea chloroplasts was purified to homogeneity. CPSecA supported protein transport into thylakoids, the chloroplast internal membrane network, in an azide-sensitive fashion. Only one of three pathways for protein transport into thylakoids uses the CPSecA mechanism. The use of a bacteria-homologous mechanism in intrachloroplast protein transport provides evidence for conservative sorting of proteins within chloroplasts.},
author = {Yuan, J G and Henry, R and Mccaffery, M and Cline, K},
doi = {Doi 10.1126/Science.7973633},
file = {:home/fin/Documents/papers/mendeley/Yuan et al.\_1994\_Seca Homolog in Protein-Transport within Chloroplasts - Evidence for Endosymbiont-Derived Sorting\_Science.pdf:pdf},
isbn = {0036-8075},
journal = {Science (80-. ).},
keywords = {chromophytic alga,escherichia-coli,genome,import,integration,machinery,membrane,red alga,thylakoid precursor protein,translocation},
number = {18},
pages = {796--798},
title = {{Seca Homolog in Protein-Transport within Chloroplasts - Evidence for Endosymbiont-Derived Sorting}},
url = {<Go to ISI>://A1994PP75300037},
volume = {266},
year = {1994}
}
@article{Mochizuki2004,
abstract = {We proposed a scan-RNA model for genome rearrangement based on finding small RNAs that hybridized preferentially to micronuclear-specific sequences and on the properties of Twi1p, a PPD protein required for both sequence elimination and small RNA accumulation in Tetrahymena. Here we show that Twi1p interacts with the small RNAs in both the old and the developing macronucleus, and is required for their stability. We show that the specificity of the small RNAs for micronuclear-limited sequences increases during conjugation. These results indicate that the small RNAs observed in conjugating cells have the properties predicted for scan RNAs.},
author = {Mochizuki, Kazufumi and Gorovsky, Martin a.},
doi = {10.1101/gad.1219904},
file = {:home/fin/Documents/papers/mendeley/Mochizuki, Gorovsky\_2004\_Conjugation-specific small RNAs in Tetrahymena have predicted properties of scan (scn) RNAs involved in genome.pdf:pdf},
isbn = {0890-9369 (Print)$\backslash$r0890-9369 (Linking)},
issn = {08909369},
journal = {Genes Dev.},
keywords = {Genome rearrangement,PPD protein,RNAi,Small RNA,Tetrahymena},
number = {Nanney 1974},
pages = {2068--2073},
pmid = {15314029},
title = {{Conjugation-specific small RNAs in Tetrahymena have predicted properties of scan (scn) RNAs involved in genome rearrangement}},
volume = {18},
year = {2004}
}
@article{Putt1990,
author = {Putt, Mary},
file = {:home/fin/Documents/papers/mendeley/Putt\_1990\_Abundance, chlorophyll content and photosynthetic rates of ciliates in the Nordic Seas during summer\_Deep-Sea Research.pdf:pdf},
journal = {Deep. Res.},
number = {11},
pages = {1713--1731},
title = {{Abundance, chlorophyll content and photosynthetic rates of ciliates in the Nordic Seas during summer}},
volume = {37},
year = {1990}
}
@article{Attwood1994,
abstract = {PRINTS is a compendium of protein motif 'fingerprints'. A fingerprint is defined as a group of motifs excised from conserved regions of a sequence alignment, whose diagnostic power or potency is refined by iterative databasescanning (in this case the OWL composite sequence database). Generally, the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. The use of groups of independent, linearly- or spatially-distinct motifs allows protein folds and functionalities to be characterised more flexibly and powerfully than conventional single-component patterns or regular expressions. The current version of the database contains 200 entries (encoding 950 motifs), covering a wide range of globular and membrane proteins, modular polypeptides, and so on. The growth of the databaseis influenced by a number of factors; e.g. the use of multiple motifs; the maximisation of sequence information through iterative database scanning; and the fact that the database searched is a large composite. The information contained within PRINTS is distinct from, but complementary to the consensus expressions stored in the widely-used PROSITE dictionary of patterns.},
author = {Attwood, T K and Beck, M E and Bleasby, a J and Parry-Smith, D J},
doi = {10.1093/protein/7.7.841},
file = {:home/fin/Documents/papers/mendeley/Attwood et al.\_1994\_PRINTS--a database of protein motif fingerprints.\_Nucleic acids research.pdf:pdf},
isbn = {0305-1048 (Print)},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {17},
pages = {3590--3596},
pmid = {7937065},
title = {{PRINTS--a database of protein motif fingerprints.}},
volume = {22},
year = {1994}
}
@article{Swart2013,
abstract = {The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (∼5\%) of its precursor "silent" germline micronuclear genome by a process of "unscrambling" and fragmentation. The tiny macronuclear "nanochromosomes" typically encode single, protein-coding genes (a small portion, 10\%, encode 2-8 genes), have minimal noncoding regions, and are differentially amplified to an average of ∼2,000 copies. We report the high-quality genome assembly of ∼16,000 complete nanochromosomes (∼50 Mb haploid genome size) that vary from 469 bp to 66 kb long (mean ∼3.2 kb) and encode ∼18,500 genes. Alternative DNA fragmentation processes ∼10\% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is ∼4.0\%), suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb) suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing studies of rearrangements arising during evolution and disease.},
author = {Swart, Estienne C. and Bracht, John R. and Magrini, Vincent and Minx, Patrick and Chen, Xiao and Zhou, Yi and Khurana, Jaspreet S. and Goldman, Aaron D. and Nowacki, Mariusz and Schotanus, Klaas and Jung, Seolkyoung and Fulton, Robert S. and Ly, Amy and McGrath, Sean and Haub, Kevin and Wiggins, Jessica L. and Storton, Donna and Matese, John C. and Parsons, Lance and Chang, Wei Jen and Bowen, Michael S. and Stover, Nicholas a. and Jones, Thomas a. and Eddy, Sean R. and Herrick, Glenn a. and Doak, Thomas G. and Wilson, Richard K. and Mardis, Elaine R. and Landweber, Laura F.},
doi = {10.1371/journal.pbio.1001473},
file = {:home/fin/Documents/papers/mendeley/Swart et al.\_2013\_The Oxytricha trifallax Macronuclear Genome A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes\_PLoS Biology.pdf:pdf},
isbn = {1545-7885 (Electronic)$\backslash$r1544-9173 (Linking)},
issn = {15449173},
journal = {PLoS Biol.},
number = {1},
pmid = {23382650},
title = {{The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes}},
volume = {11},
year = {2013}
}
@article{Casadevall2008,
author = {Casadevall, Arturo and Fang, Ferric C.},
doi = {10.1128/IAI.00743-08},
file = {:home/fin/Documents/papers/mendeley/Casadevall, Fang\_2008\_Descriptive Science\_Infection and Immunity.pdf:pdf},
issn = {00199567},
journal = {Infect. Immun.},
number = {9},
pages = {3835--3836},
pmid = {18625736},
title = {{Descriptive Science}},
volume = {76},
year = {2008}
}
@article{Smith2005,
abstract = {To improve the utility of increasingly large numbers of available unannotated and initially poorly annotated genomic sequences for proteome analysis, we demonstrate that effective protein identification can be made on a large and unannotated genome. The strategy developed is to translate the unannotated genome sequence into amino acid sequence encoding putative proteins in all six reading frames, to identify peptides by tandem mass spectrometry (MS/MS), to localize them on the genome sequence, and to preliminarily annotate the protein via a similarity search by BLAST. These tasks have been optimized and automated. Optimization to obtain multiple peptide matches in effect extends the searchable region and results in more robust protein identification. The viability of this strategy is demonstrated with the identification of 223 cilia proteins in the unicellular eukaryotic model organism Tetrahymena thermophila, whose initial genomic sequence draft was released in November 2003. To the best of our knowledge, this is the first demonstration of large-scale protein identification based on such a large, unannotated genome. Of the 223 cilia proteins, 84 have no similarity to proteins in NCBI's nonredundant (nr) database. This methodology allows identifying the locations of the genes encoding these novel proteins, which is a necessary first step to downstream functional genomic experimentation.},
author = {Smith, Jeffrey C. and Northey, Julian G B and Garg, Jyoti and Pearlman, Ronald E. and Siu, K. W Michael},
doi = {10.1021/pr050013h},
file = {:home/fin/Documents/papers/mendeley/Smith et al.\_2005\_Robust method for proteome analysis by MSMS using an entire translated genome Demonstration on the ciliome of Tetrahym.pdf:pdf},
issn = {15353893},
journal = {J. Proteome Res.},
keywords = {223 cilia proteins,BLAST analysis,Entire unannotated genome-sequence translation,Multiple-peptide matches,Shotgun proteomic analysis,Tetrahymena thermophila cilia},
pages = {909--919},
pmid = {15952738},
title = {{Robust method for proteome analysis by MS/MS using an entire translated genome: Demonstration on the ciliome of Tetrahymena thermophila}},
volume = {4},
year = {2005}
}
@incollection{ONeil2013,
author = {O'Neil, Dominic and Glowatz, Heike and Schlumpberger, Martin},
booktitle = {Curr. Protoc. Mol. Biol.},
chapter = {4},
doi = {10.1002/0471142727.mb0419s103},
isbn = {9780471142720},
keywords = {RNA-seq,next generation sequencing,rRNA depletion,sample preparation,transcriptome},
publisher = {John Wiley \& Sons, Inc.},
title = {{Ribosomal RNA Depletion for Efficient Use of RNA-Seq Capacity}},
url = {http://dx.doi.org/10.1002/0471142727.mb0419s103},
volume = {Unit 4.19},
year = {2013}
}
@article{Hofmann2004,
author = {Hofmann, Thomas and Joachims, Thorsten},
file = {:home/fin/Documents/papers/mendeley/Hofmann, Joachims\_2004\_Support Vector Machine Learning for Interdependent and Structured Output Spaces\_Unknown.pdf:pdf},
title = {{Support Vector Machine Learning for Interdependent and Structured Output Spaces}},
year = {2004}
}
@incollection{Lane2007a,
author = {Lane, Nick},
booktitle = {Orig. Mitochondria Hydrog. SE  - 2},
doi = {10.1007/978-3-540-38502-8\_2},
editor = {Martin, WilliamF. and M\"{u}ller, Mikl\'{o}s},
isbn = {978-3-540-38501-1},
language = {English},
pages = {13--38},
publisher = {Springer Berlin Heidelberg},
title = {{Mitochondria: Key to Complexity}},
url = {http://dx.doi.org/10.1007/978-3-540-38502-8\_2},
year = {2007}
}
@misc{Gnuplot44,
author = {Williams, Thomas and Kelley, Colin and Many others},
howpublished = {http://gnuplot.sourceforge.net/},
month = mar,
title = {{Gnuplot 4.4: an interactive plotting program}},
year = {2010}
}
@article{Leung2013,
annote = {doi: 10.1089/cmb.2013.0042},
author = {Leung, Henry C M and Yiu, Siu-Ming and Parkinson, John and Chin, Francis Y L},
doi = {10.1089/cmb.2013.0042},
issn = {1066-5277},
journal = {J. Comput. Biol.},
month = jul,
number = {7},
pages = {540--550},
publisher = {Mary Ann Liebert, Inc., publishers},
title = {{IDBA-MT: De Novo Assembler for Metatranscriptomic Data Generated from Next-Generation Sequencing Technology}},
url = {http://dx.doi.org/10.1089/cmb.2013.0042},
volume = {20},
year = {2013}
}
@article{Boetius2000,
abstract = {A large fraction of globally produced methane is converted to CO2 by anaerobic oxidation in marine sediments. Strong geochemical evidence for net methane consumption in anoxic sediments is based on methane profiles, radiotracer experiments and stable carbon isotope data. But the elusive microorganisms mediating this reaction have not yet been isolated, and the pathway of anaerobic oxidation of methane is insufficiently understood. Recent data suggest that certain archaea reverse the process of methanogenesis by interaction with sulphate-reducing bacteria. Here we provide microscopic evidence for a structured consortium of archaea and sulphate-reducing bacteria, which we identified by fluorescence in situ hybridization using specific 16S rRNA-targeted oligonucleotide probes. In this example of a structured archaeal-bacterial symbiosis, the archaea grow in dense aggregates of about 100 cells and are surrounded by sulphate-reducing bacteria. These aggregates were abundant in gas-hydrate-rich sediments with extremely high rates of methane-based sulphate reduction, and apparently mediate anaerobic oxidation of methane.},
author = {Boetius, a and Ravenschlag, K and Schubert, C J and Rickert, D and Widdel, F and Gieseke, a and Amann, R and J\o rgensen, B B and Witte, U and Pfannkuche, O},
doi = {10.1038/35036572},
file = {:home/fin/Documents/papers/mendeley/Boetius et al.\_2000\_A marine microbial consortium apparently mediating anaerobic oxidation of methane.\_Nature.pdf:pdf},
isbn = {0028-0836 (Print)$\backslash$r0028-0836 (Linking)},
issn = {0028-0836},
journal = {Nature},
number = {October},
pages = {623--626},
pmid = {11034209},
title = {{A marine microbial consortium apparently mediating anaerobic oxidation of methane.}},
volume = {407},
year = {2000}
}
@article{Yolken2014,
author = {Yolken, Robert H. and Jones-Brando, Lorraine and Dunigan, David D. and Kannan, Geetha and Dickerson, Faith and Severance, Emily and Sabunciyan, Sarven and Talbot, C. Conover and Prandovszky, Emese and Gurnon, James R. and Agarkova, Irina V. and Leister, Flora and Gressitt, Kristin L. and Chen, Ou and Deuber, Bryan and Ma, Fangrui and Pletnikov, Mikhail V. and {Van Etten}, James L.},
doi = {10.1073/pnas.1418895111},
file = {:home/fin/Documents/papers/mendeley/Yolken et al.\_2014\_Chlorovirus ATCV-1 is part of the human oropharyngeal virome and is associated with changes in cognitive functions in.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
number = {45},
pages = {16106--16111},
title = {{Chlorovirus ATCV-1 is part of the human oropharyngeal virome and is associated with changes in cognitive functions in humans and mice}},
url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1418895111},
volume = {111},
year = {2014}
}
@article{Tuffley1997,
abstract = {Stochastic models of nucleotide substitution are playing an increasingly important role in phylogenetic reconstruction through such methods as maximum likelihood. Here, we examine the behaviour of a simple substitution model, and establish some links between the methods of maximum parsimony and maximum likelihood under this model.},
author = {Tuffley, C and Steel, M},
doi = {10.1007/BF02459467},
file = {:home/fin/Documents/papers/mendeley/Tuffley, Steel\_1997\_Links between maximum likelihood and maximum parsimony under a simple model of site substitution.\_Bulletin of mathem.pdf:pdf},
isbn = {0092-8240},
issn = {0092-8240},
journal = {Bull. Math. Biol.},
keywords = {Base Sequence,DNA,DNA: chemistry,DNA: genetics,Genetic,Models,Mutation,Phylogeny,Probability,Theoretical},
number = {3},
pages = {581--607},
pmid = {9172826},
title = {{Links between maximum likelihood and maximum parsimony under a simple model of site substitution.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9172826},
volume = {59},
year = {1997}
}
@article{LaMonte2012,
author = {LaMonte, Gregory and Philip, Nisha and Reardon, Joseph and Lacsina, Joshua R. and Majoros, William and Chapman, Lesley and Thornburg, Courtney D. and Telen, Marilyn J. and Ohler, Uwe and Nicchitta, Christopher V. and Haystead, Timothy and Chi, Jen-Tsan},
doi = {10.1016/j.chom.2012.06.007},
file = {:home/fin/Documents/papers/mendeley/LaMonte et al.\_2012\_Translocation of Sickle Cell Erythrocyte MicroRNAs into Plasmodium falciparum Inhibits Parasite Translation and Cont.pdf:pdf},
issn = {19313128},
journal = {Cell Host Microbe},
pages = {187--199},
title = {{Translocation of Sickle Cell Erythrocyte MicroRNAs into Plasmodium falciparum Inhibits Parasite Translation and Contributes to Malaria Resistance}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S193131281200234X},
volume = {12},
year = {2012}
}
@article{Rosenblatt1956,
author = {Rosenblatt, M.},
file = {:home/fin/Documents/papers/mendeley/Rosenblatt\_1956\_Remarks on Some Non-parametric Estimates of a Density Function\_Annals of Mathematical Statistics.pdf:pdf},
journal = {Ann. Math. Stat.},
number = {3},
pages = {832--837},
title = {{Remarks on Some Non-parametric Estimates of a Density Function}},
volume = {27},
year = {1956}
}
@article{Jiang2014,
abstract = {BACKGROUND: Adapter trimming is a prerequisite step for analyzing next-generation sequencing (NGS) data when the reads are longer than the target DNA/RNA fragments. Although typically used in small RNA sequencing, adapter trimming is also used widely in other applications, such as genome DNA sequencing and transcriptome RNA/cDNA sequencing, where fragments shorter than a read are sometimes obtained because of the limitations of NGS protocols. For the newly emerged Nextera long mate-pair (LMP) protocol, junction adapters are located in the middle of all properly constructed fragments; hence, adapter trimming is essential to gain the correct paired reads. However, our investigations have shown that few adapter trimming tools meet both efficiency and accuracy requirements simultaneously. The performances of these tools can be even worse for paired-end and/or mate-pair sequencing.$\backslash$n$\backslash$nRESULTS: To improve the efficiency of adapter trimming, we devised a novel algorithm, the bit-masked k-difference matching algorithm, which has O(kn) expected time with O(m) space, where k is the maximum number of differences allowed, n is the read length, and m is the adapter length. This algorithm makes it possible to fully enumerate all candidates that meet a specified threshold, e.g. error ratio, within a short period of time. To improve the accuracy of this algorithm, we designed a simple and easy-to-explain statistical scoring scheme to evaluate candidates in the pattern matching step. We also devised scoring schemes to fully exploit the paired-end/mate-pair information when it is applicable. All these features have been implemented in an industry-standard tool named Skewer (https://sourceforge.net/projects/skewer). Experiments on simulated data, real data of small RNA sequencing, paired-end RNA sequencing, and Nextera LMP sequencing showed that Skewer outperforms all other similar tools that have the same utility. Further, Skewer is considerably faster than other tools that have comparative accuracies; namely, one times faster for single-end sequencing, more than 12 times faster for paired-end sequencing, and 49\% faster for LMP sequencing.$\backslash$n$\backslash$nCONCLUSIONS: Skewer achieved as yet unmatched accuracies for adapter trimming with low time bound.},
author = {Jiang, Hongshan and Lei, Rong and Ding, Shou-Wei and Zhu, Shuifang},
doi = {10.1186/1471-2105-15-182},
file = {:home/fin/Documents/papers/mendeley/Jiang et al.\_2014\_Skewer a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.\_BMC bioinformatics.pdf:pdf},
issn = {1471-2105},
journal = {BMC Bioinformatics},
keywords = {adapter trimming,alignment,approximate string matching,barcode demultiplexing,local sequence,next generation sequencing},
pages = {182},
pmid = {24925680},
title = {{Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.}},
url = {http://www.biomedcentral.com/1471-2105/15/182},
volume = {15},
year = {2014}
}
@article{Clark2013,
author = {Clark, S.C. and Egan, Rob and Frazier, Peter I. and Wang, Z.},
file = {:home/fin/Documents/papers/mendeley/Clark et al.\_2013\_ALE a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies\_.pdf:pdf},
journal = {Bioinformatics},
number = {4},
pages = {435--443},
title = {{ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies}},
volume = {29},
year = {2013}
}
@article{Richards2013,
author = {Richards, Thomas a. and Talbot, Nicholas J.},
doi = {10.1038/nrmicro3108},
file = {:home/fin/Documents/papers/mendeley/Richards, Talbot\_2013\_Horizontal gene transfer in osmotrophs playing with public goods\_Nature Reviews Microbiology.pdf:pdf},
issn = {1740-1526},
journal = {Nat. Rev. Microbiol.},
number = {10},
pages = {720--727},
publisher = {Nature Publishing Group},
title = {{Horizontal gene transfer in osmotrophs: playing with public goods}},
url = {http://www.nature.com/doifinder/10.1038/nrmicro3108},
volume = {11},
year = {2013}
}
@article{Kallberg2012,
author = {K\"{a}llberg, Morten and Wang, Haipeng and Wang, Sheng and Peng, Jian and Wang, Zhiyong and Lu, Hui and Xu, Jinbo},
doi = {10.1038/nprot.2012.085},
file = {:home/fin/Documents/papers/mendeley/K\"{a}llberg et al.\_2012\_Template-based protein structure modeling using the RaptorX web server\_Nature Protocols.pdf:pdf},
issn = {1754-2189},
journal = {Nat. Protoc.},
number = {8},
pages = {1511--1522},
title = {{Template-based protein structure modeling using the RaptorX web server}},
url = {http://www.nature.com/doifinder/10.1038/nprot.2012.085},
volume = {7},
year = {2012}
}
@article{McGrath2014,
abstract = {Paramecium has long been a model eukaryote. The sequence of the Paramecium tetraurelia genome reveals a history of three successive whole-genome duplications (WGDs), and the sequences of P. biaurelia and P. sexaurelia suggest that these WGDs are shared by all members of the aurelia species complex. Here, we present the genome sequence of P. caudatum, a species closely related to the P. aurelia species group. P. caudatum shares only the most ancient of the three WGDs with the aurelia complex. We found that P. caudatum maintains twice as many paralogs from this early event as the P. aurelia species, suggesting that post-WGD gene retention is influenced by subsequent WGDs and supporting the importance of selection for dosage in gene retention. The availability of P. caudatum as an outgroup allows an expanded analysis of the aurelia intermediate and recent WGD events. Both the Guanine+Cytosine (GC) content and the expression level of preduplication genes are significant predictors of duplicate retention. We find widespread asymmetrical evolution among aurelia paralogs, which is likely caused by gradual pseudogenization rather than by neofunctionalization. Finally, cases of divergent resolution of intermediate WGD duplicates between aurelia species implicate this process acts as an ongoing reinforcement mechanism of reproductive isolation long after a WGD event.},
author = {McGrath, Casey L and Gout, Jean-Francois and Doak, Thomas G and Yanagi, Akira and Lynch, Michael},
doi = {10.1534/genetics.114.163287},
file = {:home/fin/Documents/papers/mendeley/McGrath et al.\_2014\_Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence.\_Genetics.pdf:pdf},
issn = {1943-2631},
journal = {Genetics},
month = aug,
number = {4},
pages = {1417--28},
pmid = {24840360},
title = {{Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24840360},
volume = {197},
year = {2014}
}
@article{Dolan1992,
author = {Dolan, John.},
file = {:home/fin/Documents/papers/mendeley/Dolan\_1992\_Mixotrophy in Ciliates A Review of Chlorella Symbiosis and Chloroplast Retention\_Marine Microbial Food Webs.pdf:pdf},
journal = {Mar. Microb. Food Webs},
number = {2},
pages = {115--132},
title = {{Mixotrophy in Ciliates: A Review of Chlorella Symbiosis and Chloroplast Retention}},
volume = {6},
year = {1992}
}
@article{Raj2009,
abstract = {Both the transcription of mRNAs from genes and their subsequent translation into proteins are inherently stochastic biochemical events, and this randomness can lead to substantial cell-to-cell variability in mRNA and protein numbers in otherwise identical cells. Recently, a number of studies have greatly enhanced our understanding of stochastic processes in gene expression by utilizing new methods capable of counting individual mRNAs and proteins in cells. In this review, we examine the insights that these studies have yielded in the field of stochastic gene expression. In particular, we discuss how these studies have played in understanding the properties of bursts in gene expression. We also compare the array of different methods that have arisen for single mRNA and protein detection, highlighting their relative strengths and weaknesses. In conclusion, we point out further areas where single-molecule techniques applied to gene expression may lead to new discoveries.},
author = {Raj, Arjun and van Oudenaarden, Alexander},
doi = {10.1146/annurev.biophys.37.032807.125928},
file = {:home/fin/Documents/papers/mendeley/Raj, van Oudenaarden\_2009\_Single-molecule approaches to stochastic gene expression.\_Annual review of biophysics.pdf:pdf},
isbn = {1936-122X (Print)},
issn = {1936-122X},
journal = {Annu. Rev. Biophys.},
keywords = {gene expression noise,single-molecule mrna protein},
pages = {255--270},
pmid = {19416069},
title = {{Single-molecule approaches to stochastic gene expression.}},
volume = {38},
year = {2009}
}
@article{Dressman2003,
abstract = {Many areas of biomedical research depend on the analysis of uncommon variations in individual genes or transcripts. Here we describe a method that can quantify such variation at a scale and ease heretofore unattainable. Each DNA molecule in a collection of such molecules is converted into a single magnetic particle to which thousands of copies of DNA identical in sequence to the original are bound. This population of beads then corresponds to a one-to-one representation of the starting DNA molecules. Variation within the original population of DNA molecules can then be simply assessed by counting fluorescently labeled particles via flow cytometry. This approach is called BEAMing on the basis of four of its principal components (beads, emulsion, amplification, and magnetics). Millions of individual DNA molecules can be assessed in this fashion with standard laboratory equipment. Moreover, specific variants can be isolated by flow sorting and used for further experimentation. BEAMing can be used for the identification and quantification of rare mutations as well as to study variations in gene sequences or transcripts in specific populations or tissues.},
author = {Dressman, Devin and Yan, Hai and Traverso, Giovanni and Kinzler, Kenneth W and Vogelstein, Bert},
doi = {10.1073/pnas.1133470100},
file = {:home/fin/Documents/papers/mendeley/Dressman et al.\_2003\_Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic vari.pdf:pdf},
isbn = {0027-8424 (Print)},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
number = {M},
pages = {8817--8822},
pmid = {12857956},
title = {{Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations.}},
volume = {100},
year = {2003}
}
@article{Aury2006,
abstract = {The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly understood. Here we show that in the unicellular eukaryote Paramecium tetraurelia, a ciliate, most of the nearly 40,000 genes arose through at least three successive whole-genome duplications. Phylogenetic analysis indicates that the most recent duplication coincides with an explosion of speciation events that gave rise to the P. aurelia complex of 15 sibling species. We observed that gene loss occurs over a long timescale, not as an initial massive event. Genes from the same metabolic pathway or protein complex have common patterns of gene loss, and highly expressed genes are over-retained after all duplications. The conclusion of this analysis is that many genes are maintained after whole-genome duplication not because of functional innovation but because of gene dosage constraints.},
author = {Aury, Jean-Marc and Jaillon, Olivier and Duret, Laurent and Noel, Benjamin and Jubin, Claire and Porcel, Betina M and S\'{e}gurens, B\'{e}atrice and Daubin, Vincent and Anthouard, V\'{e}ronique and Aiach, Nathalie and Arnaiz, Olivier and Billaut, Alain and Beisson, Janine and Blanc, Isabelle and Bouhouche, Khaled and C\^{a}mara, Francisco and Duharcourt, Sandra and Guigo, Roderic and Gogendeau, Delphine and Katinka, Michael and Keller, Anne-Marie and Kissmehl, Roland and Klotz, Catherine and Koll, France and {Le Mou\"{e}l}, Anne and Lep\`{e}re, Gersende and Malinsky, Sophie and Nowacki, Mariusz and Nowak, Jacek K and Plattner, Helmut and Poulain, Julie and Ruiz, Fran\c{c}oise and Serrano, Vincent and Zagulski, Marek and Dessen, Philippe and B\'{e}termier, Mireille and Weissenbach, Jean and Scarpelli, Claude and Sch\"{a}chter, Vincent and Sperling, Linda and Meyer, Eric and Cohen, Jean and Wincker, Patrick},
doi = {10.1038/nature05230},
file = {:home/fin/Documents/papers/mendeley/Aury et al.\_2006\_Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.\_Nature.pdf:pdf},
issn = {1476-4687},
journal = {Nature},
keywords = {Animals,Duplicate,Duplicate: genetics,Eukaryotic Cells,Eukaryotic Cells: metabolism,Evolution,Gene Duplication,Genes,Genome,Genomics,Molecular,Molecular Sequence Data,Paramecium tetraurelia,Paramecium tetraurelia: genetics,Phylogeny,Protozoan,Protozoan: genetics},
month = nov,
number = {7116},
pages = {171--8},
pmid = {17086204},
title = {{Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17086204},
volume = {444},
year = {2006}
}
@article{Fernandez-Delgado2014,
author = {Fern\'{a}ndez-Delgado, Manuel and Cernadas, Eva and Barro, Sen\'{e}n and Amorim, Dinani},
file = {:home/fin/Documents/papers/mendeley/Fern\'{a}ndez-Delgado et al.\_2014\_Do we Need Hundreds of Classifiers to Solve Real World Classification Problems\_Journal of Machine Learnin.pdf:pdf},
journal = {J. Mach. Learn. Res.},
pages = {3133--3181},
title = {{Do we Need Hundreds of Classifiers to Solve Real World Classification Problems?}},
volume = {15},
year = {2014}
}
@article{Sebe-Pedros2013,
abstract = {The evolution of metazoans from their unicellular ancestors was one of the most important events in the history of life. However, the cellular and genetic changes that ultimately led to the evolution of multicellularity are not known. In this study, we describe an aggregative multicellular stage in the protist Capsaspora owczarzaki, a close unicellular relative of metazoans. Remarkably, transition to the aggregative stage is associated with significant upregulation of orthologs of genes known to establish multicellularity and tissue architecture in metazoans. We further observe transitions in regulated alternative splicing during the C. owczarzaki life cycle, including the deployment of an exon network associated with signaling, a feature of splicing regulation so far only observed in metazoans. Our results reveal the existence of a highly regulated aggregative stage in C. owczarzaki and further suggest that features of aggregative behavior in an ancestral protist may had been co-opted to develop some multicellular properties currently seen in metazoans. DOI: http://dx.doi.org/10.7554/eLife.01287.001.},
author = {Seb\'{e}-Pedr\'{o}s, Arnau and Irimia, Manuel and del Campo, Javier and Parra-Acero, Helena and Russ, Carsten and Nusbaum, Chad and Blencowe, Benjamin J. and Ruiz-Trillo, I\~{n}aki},
doi = {10.7554/eLife.01287},
file = {:home/fin/Documents/papers/mendeley/Seb\'{e}-Pedr\'{o}s et al.\_2013\_Regulated aggregative multicellularity in a close unicellular relative of metazoa\_eLife.pdf:pdf},
isbn = {10.7554/eLife.01287},
issn = {2050084X},
journal = {Elife},
pages = {1--20},
pmid = {24368732},
title = {{Regulated aggregative multicellularity in a close unicellular relative of metazoa}},
volume = {2013},
year = {2013}
}
@article{Rich1992,
author = {Rich, Marvin R and de Strulle, Ronald and Ferraro, Greg and Brody, Steven S},
doi = {10.1111/j.1751-1097.1992.tb02180.x},
issn = {1751-1097},
journal = {Photochem. Photobiol.},
number = {3},
pages = {413--416},
publisher = {Blackwell Publishing Ltd},
title = {{DIHYDROXY-CAROTENOID LIPOSOMES INHIBIT PHOTOTOXICITY IN Paramecium caudatum}},
url = {http://dx.doi.org/10.1111/j.1751-1097.1992.tb02180.x},
volume = {56},
year = {1992}
}
@misc{Miller1974,
abstract = {Research on the jackknife technique since its introduction by Quenouille and Tukey is reviewed. Both its role in bias reduction and in robust interval estimation are treated. Some speculations and suggestions about future research are made. The bibliography attempts to include all published work on jackknife methodology.},
author = {Miller, Rupert G.},
booktitle = {Biometrika},
doi = {10.1093/biomet/61.1.1},
file = {:home/fin/Documents/papers/mendeley/Miller\_1974\_The Jackknife - A Review\_Biometrika.pdf:pdf},
isbn = {0006-3444},
issn = {0006-3444},
keywords = {bias reduction,interval estimation,jackknife,pseudo-value,robustness},
pages = {1--15},
title = {{The Jackknife - A Review}},
volume = {61},
year = {1974}
}
@article{Nakao1999,
abstract = {The massively parallel hybridization technologies by DNA chips and microarrays make it possible to monitor expression patterns of the whole set of genes in a genome under various conditions. The vast amount of data generated by such technologies necessitates the development of a new database management system that integrates expression data with other molecular biology databases and various analysis tools. We report here an extension of our KEGG (Kyoto Encyclopedia of Genes and Genomes) and DBGET/LinkDB systems for analyzing gene expression data in conjunction with pathway information and genomic information. It is now possible to make use of expression data for the reconstruction of pathways from the complete genome sequences.},
author = {Nakao, M and Bono, H and Kawashima, S and Kamiya, T and Sato, K and Goto, S and Kanehisa, M},
file = {:home/fin/Documents/papers/mendeley/Nakao et al.\_1999\_Genome-scale Gene Expression Analysis and Pathway Reconstruction in KEGG.\_Genome Informatics. Workshop on Genome Infor.pdf:pdf},
isbn = {0919-9454 (Print)$\backslash$r0919-9454 (Linking)},
issn = {0919-9454},
journal = {Genome Inform. Ser. Workshop Genome Inform.},
pages = {94--103},
pmid = {11072346},
title = {{Genome-scale Gene Expression Analysis and Pathway Reconstruction in KEGG.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11072346},
volume = {10},
year = {1999}
}
@article{Agre1993,
abstract = {Despite longstanding interest by nephrologists and physiologists, the molecular identities of membrane water channels remained elusive until recognition of CHIP, a 28-kDa channel-forming integral membrane protein from human red blood cells originally referred to as "CHIP28." CHIP functions as an osmotically driven, water-selective pore; 1) expression of CHIP conferred Xenopus oocytes with markedly increased osmotic water permeability but did not allow transmembrane passage of ions or other small molecules; 2) reconstitution of highly purified CHIP into proteoliposomes permitted determination of the unit water permeability, i.e., 3.9 x 10(9) water molecules.channel subunit-1 x s-1. Although CHIP exists as a homotetramer in the native red blood cell membrane, site-directed mutagenesis studies suggested that each subunit contains an individually functional pore that may be reversibly occluded by mercurial inhibitors reacting with cysteine-189. CHIP is a major component of both apical and basolateral membranes of water-permeable segments of the nephron, where it facilitates transcellular water flow during reabsorption of glomerular filtrate. CHIP is also abundant in certain other absorptive or secretory epithelia, including choroid plexus, ciliary body of the eye, hepatobiliary ductules, gall bladder, and capillary endothelia. Distinct patterns of CHIP expression occur at these sites during fetal development and maturity. Similar proteins from other mammalian tissues and plants were later shown to transport water, and the group is now referred to as the "aquaporins." Recognition of CHIP has provided molecular insight into the biological phenomenon of osmotic water movement, and it is hoped that pharmacological modulation of CHIP function may provide novel treatments of renal failure and other clinical problems.},
author = {Agre, P and Preston, G M and Smith, B L and Jung, J S and Raina, S and Moon, C and Guggino, W B and Nielsen, S},
doi = {10.1085/jgp.79.5.791},
file = {:home/fin/Documents/papers/mendeley/Agre et al.\_1993\_Aquaporin CHIP the archetypal molecular water channel.\_The American journal of physiology.pdf:pdf},
isbn = {0002-9513 (Print)$\backslash$r0002-9513 (Linking)},
issn = {0002-9513},
journal = {Am. J. Physiol.},
pages = {F463--F476},
pmid = {7694481},
title = {{Aquaporin CHIP: the archetypal molecular water channel.}},
volume = {265},
year = {1993}
}
@article{Wu2014,
archivePrefix = {arXiv},
arxivId = {arXiv:1501.02876v2},
author = {Wu, Ren and Shengen, Yan and Shan, Yi and Dang, Qingqing and Sun, Gang},
eprint = {arXiv:1501.02876v2},
file = {:home/fin/Documents/papers/mendeley/Wu et al.\_2015\_Deep Image Scaling up Image Recognition\_arXiv1501.02876.pdf:pdf},
journal = {arXiv:1501.02876},
title = {{Deep Image: Scaling up Image Recognition}},
year = {2015}
}
@article{Karp2002,
abstract = {MOTIVATION: Bioinformatics requires reusable software tools for creating model-organism databases (MODs). RESULTS: The Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc (see http://ecocyc.org) integrates our evolving understanding of the genes, proteins, metabolic network, and genetic network of an organism. This paper provides an overview of the four main components of the Pathway Tools: The PathoLogic component supports creation of new PGDBs from the annotated genome of an organism. The Pathway/Genome Navigator provides query, visualization, and Web-publishing services for PGDBs. The Pathway/Genome Editors support interactive updating of PGDBs. The Pathway Tools ontology defines the schema of PGDBs. The Pathway Tools makes use of the Ocelot object database system for data management services for PGDBs. The Pathway Tools has been used to build PGDBs for 13 organisms within SRI and by external users.},
author = {Karp, Peter D and Paley, Suzanne and Romero, Pedro},
doi = {10.1093/bioinformatics/18.suppl\_1.S225},
file = {:home/fin/Documents/papers/mendeley/Karp, Paley, Romero\_2002\_The Pathway Tools software\_Bioinformatics.pdf:pdf},
isbn = {1367-4803 (Print)},
issn = {1367-4803},
journal = {Bioinformatics},
keywords = {Abstracting and Indexing as Topic,Abstracting and Indexing as Topic: methods,Animals,Biological,Database Management Systems,Databases,Gene Expression Regulation,Gene Expression Regulation: physiology,Genetic,Humans,Information Storage and Retrieval,Information Storage and Retrieval: methods,Models,Proteome,Proteome: genetics,Proteome: metabolism,Signal Transduction,Signal Transduction: physiology,Software,User-Computer Interface},
pages = {S225--S232},
pmid = {12169551},
title = {{The Pathway Tools software}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12169551},
volume = {18 Suppl 1},
year = {2002}
}
@article{Janssen2005,
abstract = {Summary: The challenge of annotating 200 genomes with 4 million publications},
author = {Janssen, Paul and Goldovsky, Leon and Kunin, Victor and Darzentas, Nikos and Ouzounis, Christos a.},
doi = {10.1038/sj.embor.7400412},
file = {:home/fin/Documents/papers/mendeley/Janssen et al.\_2005\_Genome coverage, literally speaking\_EMBO reports.pdf:pdf},
issn = {1469-221X},
journal = {EMBO Rep.},
number = {5},
pages = {397--399},
pmid = {15864286},
title = {{Genome coverage, literally speaking}},
volume = {6},
year = {2005}
}
@article{Haas2013,
abstract = {De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms. We also present Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes. In the procedure, we provide a workflow for genome-independent transcriptome analysis leveraging the Trinity platform. The software, documentation and demonstrations are freely available from http://trinityrnaseq.sourceforge.net. The run time of this protocol is highly dependent on the size and complexity of data to be analyzed. The example data set analyzed in the procedure detailed herein can be processed in less than 5 h.},
author = {Haas, Brian J and Papanicolaou, Alexie and Yassour, Moran and Grabherr, Manfred and Blood, Philip D and Bowden, Joshua and Couger, Matthew Brian and Eccles, David and Li, Bo and Lieber, Matthias and Macmanes, Matthew D and Ott, Michael and Orvis, Joshua and Pochet, Nathalie and Strozzi, Francesco and Weeks, Nathan and Westerman, Rick and William, Thomas and Dewey, Colin N and Henschel, Robert and Leduc, Richard D and Friedman, Nir and Regev, Aviv},
doi = {10.1038/nprot.2013.084},
file = {:home/fin/Documents/papers/mendeley/Haas et al.\_2013\_De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysi.pdf:pdf},
issn = {1750-2799},
journal = {Nat. Protoc.},
keywords = {Base Sequence,Gene Expression Profiling,Gene Expression Profiling: methods,RNA,RNA: chemistry,RNA: methods,Schizosaccharomyces,Schizosaccharomyces pombe Proteins,Schizosaccharomyces pombe Proteins: chemistry,Schizosaccharomyces pombe Proteins: genetics,Schizosaccharomyces: genetics,Sequence Analysis,Software,Transcriptome},
month = aug,
number = {8},
pages = {1494--512},
pmid = {23845962},
title = {{De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3875132\&tool=pmcentrez\&rendertype=abstract},
volume = {8},
year = {2013}
}
@article{VanEtten1982,
abstract = {We previously reported that isolation of symbiotic Chlorella-like algae from the Florida strain of Hydra viridis induced replication of a virus (designated HVCV-1) in the algae. We now report that isolation of symbiotic Chlorella-like algae from four other sources of green hydra and one source of the protozoan Paramecium bursaria also induced virus synthesis. Algae from one of these hydra contained a virus identical to HVCV-1 (based on its rate of sedimentation, buoyant density, reaction to HVCV-1 antiserum, and DNA restriction fragments) whereas algae from the other three hydra contained another similar, but distinct, virus (designated HVCV-2). The virus from the paramecium algae (designated PBCV-1) was distinct from both HVCV-1 and HVCV-2. The symbiotic algae in the hydra could also be distinguished ultrastructurally. Chloroplasts of both algae that produced HVCV-1 lacked a pyrenoid whereas chloroplasts of the other three symbiotic algae contained pyrenoids. Since all symbiotic eukaryotic algae we have examined have had virus, a potential viral role in symbiosis is suggested.},
author = {{Van Etten}, J L and Meints, R H and Kuczmarski, D and Burbank, D E and Lee, K},
file = {:home/fin/Documents/papers/mendeley/Van Etten et al.\_1982\_Viruses of symbiotic Chlorella-like algae isolated from Paramecium bursaria and Hydra viridis.\_Proceedings of the.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
month = jul,
number = {12},
pages = {3867--71},
pmid = {16593198},
title = {{Viruses of symbiotic Chlorella-like algae isolated from Paramecium bursaria and Hydra viridis.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=346529\&tool=pmcentrez\&rendertype=abstract},
volume = {79},
year = {1982}
}
@article{Breiman2001,
abstract = {Random forests are a combination of tree predictors such that each tree depends on the values of a random vector sampled independently and with the same distribution for all trees in the forest. The generalization error for forests converges a.s. to a limit as the number of trees in the forest becomes large. The generalization error of a forest of tree classifiers depends on the strength of the individual trees in the forest and the corre- lation between them. Using a random selection of features to split each node yields error rates that compare favorably to Adaboost (Y. Freund \& R. Schapire, Machine Learning: Proceedings of the Thirteenth Interna- tional conference, ∗∗∗, 148–156), but are more robust with respect to noise. Internal estimates monitor error, strength, and correlation and these are used to show the response to increasing the number of features used in the splitting. Internal estimates are also used to measure variable importance. These ideas are also applicable to regression. Keywords:},
archivePrefix = {arXiv},
arxivId = {http://dx.doi.org/10.1023\%2FA\%3A1010933404324},
author = {Breiman, L},
doi = {10.1023/A:1010933404324},
eprint = {/dx.doi.org/10.1023\%2FA\%3A1010933404324},
file = {:home/fin/Documents/papers/mendeley/Breiman\_2001\_Random forests\_Machine learning.pdf:pdf},
isbn = {0885-6125},
issn = {0885-6125},
journal = {Mach. Learn.},
keywords = {classification,ensemble,regression},
pages = {5--32},
pmid = {21816105},
primaryClass = {http:},
title = {{Random forests}},
url = {http://link.springer.com/article/10.1023/A:1010933404324},
year = {2001}
}
@article{DelFabbro2013,
abstract = {Next Generation Sequencing is having an extremely strong impact in biological and medical research and diagnostics, with applications ranging from gene expression quantification to genotyping and genome reconstruction. Sequencing data is often provided as raw reads which are processed prior to analysis 1 of the most used preprocessing procedures is read trimming, which aims at removing low quality portions while preserving the longest high quality part of a NGS read. In the current work, we evaluate nine different trimming algorithms in four datasets and three common NGS-based applications (RNA-Seq, SNP calling and genome assembly). Trimming is shown to increase the quality and reliability of the analysis, with concurrent gains in terms of execution time and computational resources needed.},
author = {{Del Fabbro}, Cristian and Scalabrin, Simone and Morgante, Michele and Giorgi, Federico M.},
doi = {10.1371/journal.pone.0085024},
file = {:home/fin/Documents/papers/mendeley/Del Fabbro et al.\_2013\_An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis\_PLoS ONE.pdf:pdf},
issn = {19326203},
journal = {PLoS One},
number = {12},
pages = {1--13},
pmid = {24376861},
title = {{An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis}},
volume = {8},
year = {2013}
}
@article{Li2006,
abstract = {MOTIVATION: In 2001 and 2002, we published two papers (Bioinformatics, 17, 282-283, Bioinformatics, 18, 77-82) describing an ultrafast protein sequence clustering program called cd-hit. This program can efficiently cluster a huge protein database with millions of sequences. However, the applications of the underlying algorithm are not limited to only protein sequences clustering, here we present several new programs using the same algorithm including cd-hit-2d, cd-hit-est and cd-hit-est-2d. Cd-hit-2d compares two protein datasets and reports similar matches between them; cd-hit-est clusters a DNA/RNA sequence database and cd-hit-est-2d compares two nucleotide datasets. All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST.},
author = {Li, Weizhong and Godzik, Adam},
doi = {10.1093/bioinformatics/btl158},
file = {:home/fin/Documents/papers/mendeley/Li, Godzik\_2006\_Cd-hit A fast program for clustering and comparing large sets of protein or nucleotide sequences\_Bioinformatics.pdf:pdf},
isbn = {1367-4803 (Print)$\backslash$n1367-4803 (Linking)},
issn = {13674803},
journal = {Bioinformatics},
number = {13},
pages = {1658--1659},
pmid = {16731699},
title = {{Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences}},
volume = {22},
year = {2006}
}
@article{Lander2001,
abstract = {The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.},
archivePrefix = {arXiv},
arxivId = {11237011},
author = {Lander, E S and Linton, L M and Birren, B and Nusbaum, C and Zody, M C and Baldwin, J and Devon, K and Dewar, K and Doyle, M and FitzHugh, W and Funke, R and Gage, D and Harris, K and Heaford, a and Howland, J and Kann, L and Lehoczky, J and LeVine, R and McEwan, P and McKernan, K and Meldrim, J and Mesirov, J P and Miranda, C and Morris, W and Naylor, J and Raymond, C and Rosetti, M and Santos, R and Sheridan, a and Sougnez, C and Stange-Thomann, N and Stojanovic, N and Subramanian, a and Wyman, D and Rogers, J and Sulston, J and Ainscough, R and Beck, S and Bentley, D and Burton, J and Clee, C and Carter, N and Coulson, a and Deadman, R and Deloukas, P and Dunham, a and Dunham, I and Durbin, R and French, L and Grafham, D and Gregory, S and Hubbard, T and Humphray, S and Hunt, a and Jones, M and Lloyd, C and McMurray, a and Matthews, L and Mercer, S and Milne, S and Mullikin, J C and Mungall, a and Plumb, R and Ross, M and Shownkeen, R and Sims, S and Waterston, R H and Wilson, R K and Hillier, L W and McPherson, J D and Marra, M a and Mardis, E R and Fulton, L a and Chinwalla, a T and Pepin, K H and Gish, W R and Chissoe, S L and Wendl, M C and Delehaunty, K D and Miner, T L and Delehaunty, a and Kramer, J B and Cook, L L and Fulton, R S and Johnson, D L and Minx, P J and Clifton, S W and Hawkins, T and Branscomb, E and Predki, P and Richardson, P and Wenning, S and Slezak, T and Doggett, N and Cheng, J F and Olsen, a and Lucas, S and Elkin, C and Uberbacher, E and Frazier, M and Gibbs, R a and Muzny, D M and Scherer, S E and Bouck, J B and Sodergren, E J and Worley, K C and Rives, C M and Gorrell, J H and Metzker, M L and Naylor, S L and Kucherlapati, R S and Nelson, D L and Weinstock, G M and Sakaki, Y and Fujiyama, a and Hattori, M and Yada, T and Toyoda, a and Itoh, T and Kawagoe, C and Watanabe, H and Totoki, Y and Taylor, T and Weissenbach, J and Heilig, R and Saurin, W and Artiguenave, F and Brottier, P and Bruls, T and Pelletier, E and Robert, C and Wincker, P and Smith, D R and Doucette-Stamm, L and Rubenfield, M and Weinstock, K and Lee, H M and Dubois, J and Rosenthal, a and Platzer, M and Nyakatura, G and Taudien, S and Rump, a and Yang, H and Yu, J and Wang, J and Huang, G and Gu, J and Hood, L and Rowen, L and Madan, a and Qin, S and Davis, R W and Federspiel, N a and Abola, a P and Proctor, M J and Myers, R M and Schmutz, J and Dickson, M and Grimwood, J and Cox, D R and Olson, M V and Kaul, R and Raymond, C and Shimizu, N and Kawasaki, K and Minoshima, S and Evans, G a and Athanasiou, M and Schultz, R and Roe, B a and Chen, F and Pan, H and Ramser, J and Lehrach, H and Reinhardt, R and McCombie, W R and de la Bastide, M and Dedhia, N and Bl\"{o}cker, H and Hornischer, K and Nordsiek, G and Agarwala, R and Aravind, L and Bailey, J a and Bateman, a and Batzoglou, S and Birney, E and Bork, P and Brown, D G and Burge, C B and Cerutti, L and Chen, H C and Church, D and Clamp, M and Copley, R R and Doerks, T and Eddy, S R and Eichler, E E and Furey, T S and Galagan, J and Gilbert, J G and Harmon, C and Hayashizaki, Y and Haussler, D and Hermjakob, H and Hokamp, K and Jang, W and Johnson, L S and Jones, T a and Kasif, S and Kaspryzk, a and Kennedy, S and Kent, W J and Kitts, P and Koonin, E V and Korf, I and Kulp, D and Lancet, D and Lowe, T M and McLysaght, a and Mikkelsen, T and Moran, J V and Mulder, N and Pollara, V J and Ponting, C P and Schuler, G and Schultz, J and Slater, G and Smit, a F and Stupka, E and Szustakowski, J and Thierry-Mieg, D and Thierry-Mieg, J and Wagner, L and Wallis, J and Wheeler, R and Williams, a and Wolf, Y I and Wolfe, K H and Yang, S P and Yeh, R F and Collins, F and Guyer, M S and Peterson, J and Felsenfeld, a and Wetterstrand, K a and Patrinos, a and Morgan, M J and de Jong, P and Catanese, J J and Osoegawa, K and Shizuya, H and Choi, S and Chen, Y J},
doi = {10.1038/35057062},
eprint = {11237011},
file = {:home/fin/Documents/papers/mendeley/Lander et al.\_2001\_Initial sequencing and analysis of the human genome.\_Nature.pdf:pdf},
isbn = {0028-0836 (Print)$\backslash$r0028-0836 (Linking)},
issn = {0028-0836},
journal = {Nature},
number = {February},
pages = {860--921},
pmid = {11237011},
title = {{Initial sequencing and analysis of the human genome.}},
volume = {409},
year = {2001}
}
@article{Fenchel1992,
abstract = {palae- formis and Plagiopyla frontata (cell volumes, numbers and volume of the symbionts, generation times, etc.) derived from and ( c) and},
author = {Fenchel, T and Finlay, B},
file = {:home/fin/Documents/papers/mendeley/Fenchel, Finlay\_1992\_Production of methane and hydrogen by anaerobic ciliates containing symbiotic \ldots\_Microbiology.pdf:pdf},
issn = {0302-8933},
journal = {Microbiology},
keywords = {- endosymbiotic methanogens -,accumulations of decaying detritus,anaerobic,anaerobic ciliates - metopus,e,g,hydrogen transfer,many anaerobic environments,marine and 1ironic,plagiopyla,sediments},
pages = {475--480},
title = {{Production of methane and hydrogen by anaerobic ciliates containing symbiotic \ldots}},
url = {http://www.springerlink.com/index/RQ52W61QTU2W5LVN.pdf$\backslash$npapers3://publication/uuid/90D8BDA5-5E26-4EA7-BBBE-48910CDD31B8},
year = {1992}
}
@article{Chang2015,
abstract = {We present a new de novo transcriptome assembler, Bridger, which takes advantage of techniques employed in Cufflinks to overcome limitations of the existing de novo assemblers. When tested on dog, human, and mouse RNA-seq data, Bridger assembled more full-length reference transcripts while reporting considerably fewer candidate transcripts, hence greatly reducing false positive transcripts in comparison with the state-of-the-art assemblers. It runs substantially faster and requires much less memory space than most assemblers. More interestingly, Bridger reaches a comparable level of sensitivity and accuracy with Cufflinks. Bridger is available at https://sourceforge.net/projects/rnaseqassembly/files/?source=navbar. B},
author = {Chang, Zheng and Li, Guojun and Liu, Juntao and Zhang, Yu and Ashby, Cody and Liu, Deli and Cramer, Carole L and Huang, Xiuzhen},
doi = {10.1186/s13059-015-0596-2},
file = {:home/fin/Documents/papers/mendeley/Chang et al.\_2015\_Bridger a new framework for de novo transcriptome assembly using RNA-seq data\_Genome Biology.pdf:pdf},
issn = {1465-6906},
journal = {Genome Biol.},
pages = {30},
pmid = {25723335},
title = {{Bridger: a new framework for de novo transcriptome assembly using RNA-seq data}},
url = {http://genomebiology.com/2015/16/1/30},
volume = {16},
year = {2015}
}
@article{Gabow1985,
abstract = {This paper presents a linear-time algorithm for the special case of the disjoint set union problem in which the structure of the unions (defined by a “union tree”) is known in advance. The algorithm executes an intermixed sequence of m union and find operations on n elements in O(m+n) time and O(n) space. This is a slight but theoretically significant improvement over the fastest known algorithm for the general problem, which runs in O(m$\alpha$(m+n, n)+n) time and O(n) space, where a is a functional inverse of Ackermann's function. Used as a subroutine, the algorithm gives similar improvements in the efficiency of algorithms for solving several other problems, including two-processor scheduling, matching on convex graphs, finding nearest common ancestors off-line, testing a flow graph for reducibility, and finding two disjoint directed spanning trees. The algorithm obtains its efficiency by combining the fast algorithm for the general problem with table look-up on small sets, and requires a random access machine for its implementation. The algorithm extends to the case in which single-node additions to the union tree are allowed. The extended algorithm is useful in finding maximum cardinality matchings in nonbipartite graphs.},
author = {Gabow, Harold N. and Tarjan, Robert Endre},
doi = {10.1016/0022-0000(85)90014-5},
file = {:home/fin/Documents/papers/mendeley/Gabow, Tarjan\_1985\_A linear-time algorithm for a special case of disjoint set union\_Journal of Computer and System Sciences.pdf:pdf},
isbn = {0897910990},
issn = {00220000},
journal = {J. Comput. Syst. Sci.},
pages = {209--221},
title = {{A linear-time algorithm for a special case of disjoint set union}},
url = {http://www.sciencedirect.com/science/article/pii/0022000085900145},
volume = {30},
year = {1985}
}
@book{Bishop2006,
author = {Bishop, Christopher M.},
publisher = {Springer},
series = {Information Science and Statistics},
title = {{Pattern Recognition and Machine Learning}},
year = {2006}
}
@article{Fedurco2006,
abstract = {The tricarboxylate reagent benzene-1,3,5-triacetic acid (BTA) was used to attach 5'-aminated DNA primers and templates on an aminosilanized glass surface for subsequent generation of DNA colonies by in situ solid-phase amplification. We have characterized the derivatized surfaces for the chemical attachment of oligonucleotides and evaluate the properties relevant for the amplification process: surface density, thermal stability towards thermocycling, functionalization reproducibility and storage stability. The derivatization process, first developed for glass slides, was then adapted to microfabricated glass channels containing integrated fluidic connections. This implementation resulted in an important reduction of reaction times, consumption of reagents and process automation. Innovative analytical methods for the characterization of attached DNA were developed for assessing the surface immobilized DNA content after amplification. The results obtained showed that the BTA chemistry is compatible and suitable for forming highly dense arrays of DNA colonies with optimal surface coverage of about 10 million colonies/cm(2) from the amplification of initial single-template DNA molecules immobilized. We also demonstrate that the dsDNA colonies generated can be quantitatively processed in situ by restriction enzymes digestion. DNA colonies generated using the BTA reagent can be used for further sequence analysis in an unprecedented parallel fashion for low-cost genomic studies.},
author = {Fedurco, Milan and Romieu, Anthony and Williams, Scott and Lawrence, Isabelle and Turcatti, Gerardo},
doi = {10.1093/nar/gnj023},
file = {:home/fin/Documents/papers/mendeley/Fedurco et al.\_2006\_BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies\_Nucl.pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$r0305-1048 (Linking)},
issn = {03051048},
journal = {Nucleic Acids Res.},
number = {3},
pmid = {16473845},
title = {{BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies}},
volume = {34},
year = {2006}
}
@article{Bouchard-Cote2013,
abstract = {We address the problem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences. This problem is generally formulated in terms of string-valued evolutionary processes along the branches of a phylogenetic tree. The classic evolutionary process, the TKF91 model [Thorne JL, Kishino H, Felsenstein J (1991) J Mol Evol 33(2):114-124] is a continuous-time Markov chain model composed of insertion, deletion, and substitution events. Unfortunately, this model gives rise to an intractable computational problem: The computation of the marginal likelihood under the TKF91 model is exponential in the number of taxa. In this work, we present a stochastic process, the Poisson Indel Process (PIP), in which the complexity of this computation is reduced to linear. The Poisson Indel Process is closely related to the TKF91 model, differing only in its treatment of insertions, but it has a global characterization as a Poisson process on the phylogeny. Standard results for Poisson processes allow key computations to be decoupled, which yields the favorable computational profile of inference under the PIP model. We present illustrative experiments in which Bayesian inference under the PIP model is compared with separate inference of phylogenies and alignments.},
archivePrefix = {arXiv},
arxivId = {arXiv:1207.6327v2},
author = {Bouchard-C\^{o}t\'{e}, Alexandre and Jordan, Michael I},
doi = {10.1073/pnas.1220450110},
eprint = {arXiv:1207.6327v2},
file = {:home/fin/Documents/papers/mendeley/Bouchard-C\^{o}t\'{e}, Jordan\_2013\_Evolutionary inference via the Poisson Indel Process.\_Proceedings of the National Academy of Sciences of th.pdf:pdf},
issn = {1091-6490},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
keywords = {Bayes Theorem,Biostatistics,Evolution, Molecular,INDEL Mutation,Likelihood Functions,Markov Chains,Models, Genetic,Models, Statistical,Phylogeny,Poisson Distribution,Sequence Alignment,Sequence Alignment: statistics \& numerical data},
number = {4},
pages = {1160--6},
pmid = {23275296},
title = {{Evolutionary inference via the Poisson Indel Process.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3557041\&tool=pmcentrez\&rendertype=abstract},
volume = {110},
year = {2013}
}
@article{Rusch1995,
annote = {doi: 10.3109/09687689509072431},
author = {Rusch, Sharyn L and Kendall, Debra A},
doi = {10.3109/09687689509072431},
issn = {0968-7688},
journal = {Mol. Membr. Biol.},
month = jan,
number = {4},
pages = {295--307},
publisher = {Taylor \& Francis},
title = {{Protein transport via amino-terminal targeting sequences: common themes in diverse systems (Review)}},
url = {http://www.tandfonline.com/doi/abs/10.3109/09687689509072431},
volume = {12},
year = {1995}
}
@article{Lassmann2009,
abstract = {MOTIVATION: Next-generation parallel sequencing technologies produce large quantities of short sequence reads. Due to experimental procedures various types of artifacts are commonly sequenced alongside the targeted RNA or DNA sequences. Identification of such artifacts is important during the development of novel sequencing assays and for the downstream analysis of the sequenced libraries. RESULTS: Here we present TagDust, a program identifying artifactual sequences in large sequencing runs. Given a user-defined cutoff for the false discovery rate, TagDust identifies all reads explainable by combinations and partial matches to known sequences used during library preparation. We demonstrate the quality of our method on sequencing runs performed on Illumina's Genome Analyzer platform. AVAILABILITY: Executables and documentation are available from http://genome.gsc.riken.jp/osc/english/software/. CONTACT: timolassmann@gmail.com.},
author = {Lassmann, Timo and Hayashizaki, Yoshihide and Daub, Carsten O.},
doi = {10.1093/bioinformatics/btp527},
file = {:home/fin/Documents/papers/mendeley/Lassmann, Hayashizaki, Daub\_2009\_TagDust - A program to eliminate artifacts from next generation sequencing data\_Bioinformatics.pdf:pdf},
isbn = {1367-4811 (Linking)},
issn = {13674803},
journal = {Bioinformatics},
number = {21},
pages = {2839--2840},
pmid = {19737799},
title = {{TagDust - A program to eliminate artifacts from next generation sequencing data}},
volume = {25},
year = {2009}
}
@article{Bruno1996b,
abstract = {A computational method is presented for characterizing residue usage, i.e., site-specific residue frequencies, in aligned protein sequences. The method obtains frequency estimates that maximize the likelihood of the sequences in a simple model for sequence evolution, given a tree or a set of candidate trees computed by other methods. These maximum-likelihood frequencies constitute a profile of the sequences, and thus the method offers a rigorous alternative to sequence weighting for constructing such a profile. The ability of this method to discard misleading phylogenetic effects allows the biochemical propensities of different positions in a sequence to be more clearly observed and interpreted.},
author = {Bruno, W J},
file = {:home/fin/Documents/papers/mendeley/Bruno\_1996\_Modeling residue usage in aligned protein sequences via maximum likelihood.\_Molecular biology and evolution.pdf:pdf},
issn = {0737-4038},
journal = {Mol. Biol. Evol.},
keywords = {address for correspondence,and reprints,bruno,function,motifs,sequence,sequence analysis,sequence weights,site-specific residue,structure,the-,william j},
number = {10},
pages = {1368--1374},
pmid = {8952081},
title = {{Modeling residue usage in aligned protein sequences via maximum likelihood.}},
volume = {13},
year = {1996}
}
@article{Whangbo2008,
abstract = {The discovery of RNA interference (RNAi), the process of sequence-specific gene silencing initiated by double-stranded RNA (dsRNA), has broadened our understanding of gene regulation and has revolutionized methods for genetic analysis. A remarkable property of RNAi in the nematode Caenorhabditis elegans and in some other multicellular organisms is its systemic nature: silencing signals can cross cellular boundaries and spread between cells and tissues. Furthermore, C. elegans and some other organisms can also perform environmental RNAi: sequence-specific gene silencing in response to environmentally encountered dsRNA. This phenomenon has facilitated significant technological advances in diverse fields including functional genomics and agricultural pest control. Here, we describe the characterization and current understanding of environmental RNAi and discuss its potential applications. ?? 2008 Elsevier Ltd. All rights reserved.},
author = {Whangbo, Jennifer S. and Hunter, Craig P.},
doi = {10.1016/j.tig.2008.03.007},
file = {:home/fin/Documents/papers/mendeley/Whangbo, Hunter\_2008\_Environmental RNA interference\_Trends in Genetics.pdf:pdf},
isbn = {0168-9525 (Print)$\backslash$n0168-9525 (Linking)},
issn = {01689525},
journal = {Trends Genet.},
number = {April},
pages = {297--305},
pmid = {18450316},
title = {{Environmental RNA interference}},
volume = {24},
year = {2008}
}
@article{Nuez2012,
abstract = {BACKGROUND: The nematode Caenorhabditis elegans is able to take up external double-stranded RNAs (dsRNAs) and mount an RNA interference response, leading to the inactivation of specific gene expression. The uptake of ingested dsRNAs into intestinal cells has been shown to require the SID-2 transmembrane protein in C. elegans. By contrast, C. briggsae was shown to be naturally insensitive to ingested dsRNAs, yet could be rendered sensitive by transgenesis with the C. elegans sid-2 gene. Here we aimed to elucidate the evolution of the susceptibility to external RNAi in the Caenorhabditis genus.$\backslash$n$\backslash$nPRINCIPAL FINDINGS: We study the sensitivity of many new species of Caenorhabditis to ingested dsRNAs matching a conserved actin gene sequence from the nematode Oscheius tipulae. We find ample variation in the Caenorhabditis genus in the ability to mount an RNAi response. We map this sensitivity onto a phylogenetic tree, and show that sensitivity or insensitivity have evolved convergently several times. We uncover several evolutionary losses in sensitivity, which may have occurred through distinct mechanisms. We could render C. remanei and C. briggsae sensitive to ingested dsRNAs by transgenesis of the Cel-sid-2 gene. We thus provide tools for RNA interference studies in these species. We also show that transgenesis by injection is possible in many Caenorhabditis species.$\backslash$n$\backslash$nCONCLUSIONS: The ability of animals to take up dsRNAs or to respond to them by gene inactivation is under rapid evolution in the Caenorhabditis genus. This study provides a framework and tools to use RNA interference and transgenesis in various Caenorhabditis species for further comparative and evolutionary studies.},
author = {Nuez, Isabelle and F\'{e}lix, Marie Anne},
doi = {10.1371/journal.pone.0029811},
file = {:home/fin/Documents/papers/mendeley/Nuez, F\'{e}lix\_2012\_Evolution of susceptibility to ingested double-stranded rnas in Caenorhabditis nematodes\_PLoS ONE.pdf:pdf},
isbn = {1932-6203 (Electronic)$\backslash$r1932-6203 (Linking)},
issn = {19326203},
journal = {PLoS One},
number = {1},
pages = {1--12},
pmid = {22253787},
title = {{Evolution of susceptibility to ingested double-stranded rnas in Caenorhabditis nematodes}},
volume = {7},
year = {2012}
}
@article{Markell1993,
abstract = {Five species of symbiotic dinoflagellates in culture exude water-soluble glycoconjugates. Recovered glycoconjugates of three of the five species were composed of more carbohydrate than protein. The uronic acid content of three algal species that infect scyphistomae of the jellyfish Cassiopeia were higher than those of the two species that do not infect. Analyses of hydrolysates by high-performance liquid chromatography indicated that the protein components were rich in aspartic acid (asparagine), glutamic acid (glutamine), serine, glycine, leucine, and threonine and contain proline and lysine. Histidine and methionine, when present, were in low concentration. Other sugars detected were glucose and galactose and their respective amines, ribose, mannose, and fucose. Neither sialic acid nor arabinose was detected. The release of glycoconjugates by symbiotic dinoflagellates appears to be a general phenomenon. Some components of these macromolecules could serve as signals that pass between symbionts and hosts, while other components, assuming host digestion, could be a source of previously undetected essential amino acids.},
author = {Markell, D.a. and Trench, R.K.},
doi = {10.1111/j.1529-8817.1993.tb00280.x},
file = {:home/fin/Documents/papers/mendeley/Markell, Trench\_1993\_Macromolecules Exuded By Symbiotic Dinoflagellates in Culture Amino Acid and Sugar Composition1\_Journal of Phycolog.pdf:pdf},
isbn = {1529-8817},
issn = {00223646},
journal = {J. Phycol.},
pages = {64--68},
title = {{Macromolecules Exuded By Symbiotic Dinoflagellates in Culture: Amino Acid and Sugar Composition1}},
url = {http://dx.doi.org/10.1111/j.1529-8817.1993.tb04346.x},
volume = {29},
year = {1993}
}
@article{Kodama2014,
abstract = {BACKGROUND: The ciliate Paramecium bursaria harbors several hundred cells of the green-alga Chlorella sp. in their cytoplasm. Irrespective of the mutual relation between P. bursaria and the symbiotic algae, both cells retain the ability to grow without the partner. They can easily reestablish endosymbiosis when put in contact with each other. Consequently, P. bursaria is an excellent model for studying cell-cell interaction and the evolution of eukaryotic cells through secondary endosymbiosis between different protists. Despite the importance of this organism, no genomic resources have been identified for P. bursaria to date. This investigation compared gene expressions through RNA-Seq analysis and de novo transcriptome assembly of symbiont-free and symbiont-bearing host cells.$\backslash$n$\backslash$nRESULTS: To expedite the process of gene discovery related to the endosymbiosis, we have undertaken Illumina deep sequencing of mRNAs prepared from symbiont-bearing and symbiont-free P. bursaria cells. We assembled the reads de novo to build the transcriptome. Sequencing using Illumina HiSeq2000 platform yielded 232.3 million paired-end sequence reads. Clean reads filtered from the raw reads were assembled into 68,175 contig sequences. Of these, 10,557 representative sequences were retained after removing Chlorella sequences and lowly expressed sequences. Nearly 90\% of these transcript sequences were annotated by similarity search against protein databases. We identified differentially expressed genes in the symbiont-bearing P. bursaria cells relative to the symbiont-free cells, including heat shock 70 kDa protein and glutathione S-transferase.$\backslash$n$\backslash$nCONCLUSIONS: This is the first reported comprehensive sequence resource of Paramecium - Chlorella endosymbiosis. Results provide some keys for the elucidation of secondary endosymbiosis in P. bursaria. We identified P. bursaria genes that are differentially expressed in symbiont-bearing and symbiont-free conditions.},
author = {Kodama, Yuuki and Suzuki, Haruo and Dohra, Hideo and Sugii, Manabu and Kitazume, Tatsuya and Yamaguchi, Katsushi and Shigenobu, Shuji and Fujishima, Masahiro},
doi = {10.1186/1471-2164-15-183},
file = {:home/fin/Documents/papers/mendeley/Kodama et al.\_2014\_Comparison of gene expression of Paramecium bursaria with and without Chlorella variabilis symbionts.\_BMC Genomics.pdf:pdf},
isbn = {1471216415183},
issn = {1471-2164},
journal = {BMC Genomics},
keywords = {chlorella variabilis,paramecium bursaria,secondary symbiosis,transcriptome analysis},
pages = {183},
pmid = {24612690},
title = {{Comparison of gene expression of Paramecium bursaria with and without Chlorella variabilis symbionts.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4029085\&tool=pmcentrez\&rendertype=abstract},
volume = {15},
year = {2014}
}
@article{Felsenstein2001,
abstract = {none},
author = {Felsenstein, J},
doi = {10.1080/10635150119297},
file = {:home/fin/Documents/papers/mendeley/Felsenstein\_2001\_The troubled growth of statistical phylogenetics.\_Systematic biology.pdf:pdf},
isbn = {1063-5157},
issn = {1063-5157},
journal = {Syst. Biol.},
number = {4},
pages = {465--467},
pmid = {12116645},
title = {{The troubled growth of statistical phylogenetics.}},
volume = {50},
year = {2001}
}
@article{Suchard2006,
abstract = {SUMMARY: BAli-Phy is a Bayesian posterior sampler that employs Markov chain Monte Carlo to explore the joint space of alignment and phylogeny given molecular sequence data. Simultaneous estimation eliminates bias toward inaccurate alignment guide-trees, employs more sophisticated substitution models during alignment and automatically utilizes information in shared insertion/deletions to help infer phylogenies.

AVAILABILITY: Software is available for download at http://www.biomath.ucla.edu/msuchard/bali-phy.},
author = {Suchard, Marc a and Redelings, Benjamin D},
doi = {10.1093/bioinformatics/btl175},
file = {:home/fin/Documents/papers/mendeley/Suchard, Redelings\_2006\_BAli-Phy simultaneous Bayesian inference of alignment and phylogeny.\_Bioinformatics (Oxford, England).pdf:pdf},
issn = {1367-4811},
journal = {Bioinformatics},
keywords = {Algorithms,Amino Acid Sequence,Bayes Theorem,Computational Biology,Computational Biology: methods,Internet,Markov Chains,Molecular Sequence Data,Monte Carlo Method,Phylogeny,Programming Languages,Sequence Alignment,Software},
month = aug,
number = {16},
pages = {2047--8},
pmid = {16679334},
title = {{BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16679334},
volume = {22},
year = {2006}
}
@article{Karakashian1963,
author = {Karakashian, S.J.},
file = {:home/fin/Documents/papers/mendeley/Karakashian\_1963\_Growth of Paramecium bursaria as Influenced by the Presence of Algal Symbionts\_Physiological Zoology.pdf:pdf},
journal = {Physiol. Zool.},
number = {1},
pages = {52--68},
title = {{Growth of Paramecium bursaria as Influenced by the Presence of Algal Symbionts}},
volume = {36},
year = {1963}
}
@article{Meier1989,
author = {Meier, Renate and Wiessner, Wolfgang},
file = {:home/fin/Documents/papers/mendeley/Meier, Wiessner\_1989\_Infection of algae-free Pammecium bursaria with symbiotic Chlorella sp. isolated from green paramecia\_Journal of Ce.pdf:pdf},
journal = {J. Cell Sci.},
keywords = {chlorella sp,digestive vacuole,endosymbiosis,infection experiment,paramecium bursaria,perialgal},
pages = {571--579},
title = {{Infection of algae-free Pammecium bursaria with symbiotic Chlorella sp. isolated from green paramecia}},
volume = {93},
year = {1989}
}
@article{Stadler1995,
abstract = {The unicellular green alga Chlorella kessleri can induce monosaccharide-H+ symport catalyzing the energy-dependent transport of D-glucose (D-Glc) and several other pentoses and hexoses across the plasmalemma. The gene coding for the inducible HUP1 monosaccharide-H+ symporter has been cloned and the protein has been characterized previously. The data presented in this paper demonstrate that the presence of the HUP1 gene product alone is not sufficient to cover the broad substrate specificity of monosaccharide transport in induced Chlorella cells. Two other HUP genes are shown to be co-induced in Chlorella in response to D-Glc in the medium. The cloning of HUP2 and HUP3 cDNA and genomic sequences is described, both being very homologous to HUP1. Modification of the 5' untranslated sequences of full-length cDNA clones of HUP2 and HUP3 allowed the functional expression of both transporters in Schizosaccharomyces pombe. HUP2 was shown to be a galactose-H+ symporter, whereas the substrate specificity of the HUP3 gene product is very similar to that of the HUP1 protein. However, HUP3 does not seem to be induced to high levels in Glc-treated Chlorella cells. Results are also presented proving that the product of the HUP1 gene is localized in the plasmalemma of D-Glc-induced Chlorella cells and is absent in plasma membranes of noninduced cells. Incubation of thin sections of Chlorella cells with anti-HUP1 antibodies and a fluorescence-labeled, second antibody yielded a ring of fluorescence on the surface of Glc-induced Chlorella cells.},
author = {Stadler, R and Wolf, K and Hilgarth, C and Tanner, W and Sauer, N},
doi = {107/1/33 [pii]},
file = {:home/fin/Documents/papers/mendeley/Stadler et al.\_1995\_Subcellular localization of the inducible Chlorella HUP1 monosaccharide-H symporter and cloning of a Co-induced gala.pdf:pdf},
isbn = {0032-0889 (Print)$\backslash$r0032-0889 (Linking)},
journal = {Plant Physiol},
keywords = {*Calcium-Binding Proteins,*Periplasmic Binding Proteins,Base Sequence,Biological Transport,Carrier Proteins/genetics/*metabolism,Cell Membrane/metabolism,Chlorella/*metabolism,Cloning, Molecular,DNA, Complementary,Galactose/*metabolism,Hydrogen/metabolism,Immunochemistry,Membrane Proteins/genetics/*metabolism,Molecular Sequence Data,Monosaccharide Transport Proteins/*metabolism,Schizosaccharomyces/genetics,Subcellular Fractions/*metabolism,Symporters},
number = {1 995},
pages = {33--41},
pmid = {7870840},
title = {{Subcellular localization of the inducible Chlorella HUP1 monosaccharide-H+ symporter and cloning of a Co-induced galactose-H+ symporter}},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list\_uids=7870840},
volume = {107},
year = {1995}
}
@article{Gomaa2014,
abstract = {Endosymbiosis is a central and much studied process in the evolution of eukaryotes. While plastid evolution in eukaryotic algae has been extensively studied, much less is known about the evolution of mixotrophy in amoeboid protists, which has been found in three of the five super groups of Eukaryotes. We identified the green endosymbionts in four obligate mixotrophic testate amoeba species belonging to three major eukaryotic clades, Hyalosphenia papilio and Heleopera sphagni (Amoebozoa: Arcellinida), Placocista spinosa (Rhizaria: Euglyphida), and Archerella flavum (Stramenopiles: Labyrinthulomycetes) based on rbcL (ribulose-1,5-diphosphate carboxylase/oxygenase large subunit) gene sequences. We further investigated whether there were different phylotypes of algal endosymbionts within single H. papilio cells and the degree of host-symbiont specificity by amplifying two genes: COI (mitochondrial cytochrome oxydase subunit 1) from the testate amoeba host, and rbcL from the endosymbiont. Results show that all studied endosymbionts belong to genus Chlorella sensu stricto, closely related to Paramecium bursaria Chlorella symbionts, some lichen symbionts and also several free-living algae. Most rbcL gene sequences derived from symbionts from all testate amoeba species were almost identical (at most 3 silent nucleotides difference out of 780. bp) and were assigned to a new Trebouxiophyceae taxon we named TACS (Testate Amoeba Chlorella Symbionts). This "one alga fits all mixotrophic testate amoeba" pattern suggests that photosynthetic symbionts have pre-adaptations to endosymbiosis and colonise diverse hosts from a free-living stage. ?? 2014 Elsevier GmbH.},
author = {Gomaa, Fatma and Kosakyan, Anush and Heger, Thierry J. and Corsaro, Daniele and Mitchell, Edward a D and Lara, Enrique},
doi = {10.1016/j.protis.2014.01.002},
file = {:home/fin/Documents/papers/mendeley/Gomaa et al.\_2014\_One Alga to Rule them All Unrelated Mixotrophic Testate Amoebae (Amoebozoa, Rhizaria and Stramenopiles) Share the Same.pdf:pdf},
issn = {16180941},
journal = {Protist},
keywords = {COI gene,Chlorella,Co-evolution,Hyalosphenia papilio,Peatlands,RbcL gene,Secondary endosymbiosis},
number = {2},
pages = {161--176},
pmid = {24646792},
publisher = {Elsevier GmbH.},
title = {{One Alga to Rule them All: Unrelated Mixotrophic Testate Amoebae (Amoebozoa, Rhizaria and Stramenopiles) Share the Same Symbiont (Trebouxiophyceae)}},
url = {http://dx.doi.org/10.1016/j.protis.2014.01.002},
volume = {165},
year = {2014}
}
@incollection{Kaufman1987,
abstract = {When partitioning a set of objects into k clusters, the main objective is to find clusters the objects of which show a high degree of similarity. There are several possible criteria for quantifying this objective, the best known of which are based on sums of squares. An alternative approach, used in the k-medoid method, is of the L 1 type. It searches for k `representative' objects, called medoids, which minimize the average dissimilarity of all objects of the data set to the nearest medoid. A cluster is then defined as the set of objects which have been assigned to the same medoid. An algorithm for this method has been implemented in the PAM program which is described in the paper. The k-medoid method offers the advantage of not requiring the actual measurement data, as it can also be applied to a collection of dissimilarities. Such dissimilarities are for example subjective assessments of relationships between objects, in which case no measurements exist. An example of the latter type is analyzed. Furthermore, the k-medoid method is less susceptible to outlying values},
author = {Kaufman, L and Rousseeuw, P J},
booktitle = {Stat. Data Anal. Based L 1-Norm Relat. Methods},
editor = {Dodge, Y.},
file = {:home/fin/Documents/papers/mendeley/Kaufman, Rousseeuw\_1987\_Clustering by means of medoids\_Statistical Data Analysis Based on the L 1-Norm and Related Methods.pdf:pdf},
isbn = {0444702733},
pages = {405--416},
title = {{Clustering by means of medoids}},
year = {1987}
}
@article{Forgy1965,
author = {Forgy, E W},
journal = {Biometrics},
pages = {768--769},
title = {{Cluster Analysis of Multivariate Data : Efficiency Versus Interpretability of Classifications}},
url = {http://ci.nii.ac.jp/naid/10009668881/en/},
volume = {21},
year = {1965}
}
@article{Adessi2000,
abstract = {Different chemical methods used to attach oligonucleotides by their 5'-end on a glass surface were tested in the framework of solid phase PCR where surface-bound instead of freely-diffusing primers are used to amplify DNA. Each method was first evaluated for its capacity to provide a high surface coverage of oligonucleotides essentially attached via a 5'-specific linkage that satisfyingly withstands PCR conditions and leaves the 3'-ends available for DNA polymerase activity. The best results were obtained with 5'-thiol-modified oligonucleotides attached to amino-silanised glass slides using a heterobifunctional cross-linker reagent. It was then demonstrated that the primers bound to the glass surface using the optimal chemistry can be involved in attaching and amplifying DNA molecules present in the reaction mix in the absence of freely-diffusing primers. Two distinct amplification processes called interfacial and surface amplification have been observed and characterised. The newly synthesised DNA can be detected and quantified by radioactive and fluorescent hybridisation assays. These new surface amplification processes are seen as an interesting approach for attachment of DNA molecules by their 5'-end on a solid support and can be used as an alternative route for producing DNA chips for genomic studies.},
author = {Adessi, C and Matton, G and Ayala, G and Turcatti, G and Mermod, J J and Mayer, P and Kawashima, E},
doi = {10.1093/nar/28.20.e87},
file = {:home/fin/Documents/papers/mendeley/Adessi et al.\_2000\_Solid phase DNA amplification characterisation of primer attachment and amplification mechanisms.\_Nucleic acids resea.pdf:pdf},
isbn = {1362-4962; 0305-1048},
issn = {1362-4962},
journal = {Nucleic Acids Res.},
number = {20},
pages = {E87},
pmid = {11024189},
title = {{Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms.}},
volume = {28},
year = {2000}
}
@article{Stamatakis2008,
author = {Stamatakis, Alexandros and Hoover, Paul and Rougemont, Jacques},
doi = {10.1080/10635150802429642},
file = {:home/fin/Documents/papers/mendeley/Stamatakis, Hoover, Rougemont\_2008\_A Rapid Bootstrap Algorithm for the RAxML Web Servers\_Systematic Biology.pdf:pdf},
issn = {1063-5157},
journal = {Syst. Biol.},
number = {5},
pages = {758--771},
title = {{A Rapid Bootstrap Algorithm for the RAxML Web Servers}},
url = {http://sysbio.oxfordjournals.org/cgi/doi/10.1080/10635150802429642},
volume = {57},
year = {2008}
}
@article{Harris2008,
abstract = {The full promise of human genomics will be realized only when the genomes of thousands of individuals can be sequenced for comparative analysis. A reference sequence enables the use of short read length. We report an amplification-free method for determining the nucleotide sequence of more than 280,000 individual DNA molecules simultaneously. A DNA polymerase adds labeled nucleotides to surface-immobilized primer-template duplexes in stepwise fashion, and the asynchronous growth of individual DNA molecules was monitored by fluorescence imaging. Read lengths of >25 bases and equivalent phred software program quality scores approaching 30 were achieved. We used this method to sequence the M13 virus to an average depth of >150x and with 100\% coverage; thus, we resequenced the M13 genome with high-sensitivity mutation detection. This demonstrates a strategy for high-throughput low-cost resequencing.},
author = {Harris, Timothy D and Buzby, Phillip R and Babcock, Hazen and Beer, Eric and Bowers, Jayson and Braslavsky, Ido and Causey, Marie and Colonell, Jennifer and Dimeo, James and Efcavitch, J William and Giladi, Eldar and Gill, Jaime and Healy, John and Jarosz, Mirna and Lapen, Dan and Moulton, Keith and Quake, Stephen R and Steinmann, Kathleen and Thayer, Edward and Tyurina, Anastasia and Ward, Rebecca and Weiss, Howard and Xie, Zheng},
doi = {10.1126/science.1150427},
file = {:home/fin/Documents/papers/mendeley/Harris et al.\_2008\_Single-molecule DNA sequencing of a viral genome.\_Science (New York, N.Y.).pdf:pdf},
isbn = {1095-9203 (Electronic)},
issn = {0036-8075},
journal = {Science},
number = {April},
pages = {106--109},
pmid = {18388294},
title = {{Single-molecule DNA sequencing of a viral genome.}},
volume = {320},
year = {2008}
}
@article{Lee2008,
abstract = {MOTIVATION: We present a method for inferring and constructing transport reactions for transporter proteins based primarily on the analysis of the names of individual proteins in the genome annotation of an organism. Transport reactions are declarative descriptions of transporter activities, and thus can be manipulated computationally, unlike free-text protein names. Once transporter activities are encoded as transport reactions, a number of computational analyses are possible including database queries by transporter activity; inclusion of transporters into an automatically generated metabolic-map diagram that can be painted with omics data to aid in their interpretation; detection of anomalies in the metabolic and transport networks, such as substrates that are transported into the cell but are not inputs to any metabolic reaction or pathway; and comparative analyses of the transport capabilities of different organisms. RESULTS: On randomly selected organisms, the method achieves precision and recall rates of 0.93 and 0.90, respectively in identifying transporter proteins by name within the complete genome. The method obtains 67.5\% accuracy in predicting complete transport reactions; if allowance is made for predictions that are overly general yet not incorrect, reaction prediction accuracy is 82.5\%. AVAILABILITY: The method is implemented as part of PathoLogic, the inference component of the Pathway Tools software. Pathway Tools is freely available to researchers at non-commercial institutions, including source code; a fee applies to commercial institutions. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
author = {Lee, Thomas J and Paulsen, Ian and Karp, Peter},
doi = {10.1093/bioinformatics/btn180},
file = {:home/fin/Documents/papers/mendeley/Lee, Paulsen, Karp\_2008\_Annotation-based inference of transporter function.\_Bioinformatics (Oxford, England).pdf:pdf},
isbn = {1460-2059 (Electronic)},
issn = {1367-4811},
journal = {Bioinformatics},
keywords = {Biological,Computer Simulation,Databases,Information Storage and Retrieval,Information Storage and Retrieval: methods,Membrane Transport Proteins,Membrane Transport Proteins: classification,Membrane Transport Proteins: metabolism,Models,Natural Language Processing,Protein,Signal Transduction,Signal Transduction: physiology},
pages = {i259--67},
pmid = {18586723},
title = {{Annotation-based inference of transporter function.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18586723},
volume = {24},
year = {2008}
}
@article{Cerutti2006,
author = {Cerutti, Heriberto and Casas-Mollano, J. Armando},
doi = {10.1007/s00294-006-0078-x},
file = {:home/fin/Documents/papers/mendeley/Cerutti, Casas-Mollano\_2006\_On the origin and functions of RNA-mediated silencing from protists to man\_Current Genetics.pdf:pdf},
isbn = {0029400600},
issn = {0172-8083},
journal = {Curr. Genet.},
keywords = {heterochromatin,rna interference,rnai phylogenetics,transposon silencing},
pages = {81--99},
title = {{On the origin and functions of RNA-mediated silencing: from protists to man}},
url = {http://link.springer.com/10.1007/s00294-006-0078-x},
volume = {50},
year = {2006}
}
@article{Schulz2012a,
abstract = {MOTIVATION: High-throughput sequencing has made the analysis of new model organisms more affordable. Although assembling a new genome can still be costly and difficult, it is possible to use RNA-seq to sequence mRNA. In the absence of a known genome, it is necessary to assemble these sequences de novo, taking into account possible alternative isoforms and the dynamic range of expression values.$\backslash$n$\backslash$nRESULTS: We present a software package named Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms. It achieves this by using an array of hash lengths, a dynamic filtering of noise, a robust resolution of alternative splicing events and the efficient merging of multiple assemblies. It was tested on human and mouse RNA-seq data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome assemblers.$\backslash$n$\backslash$nAVAILABILITY AND IMPLEMENTATION: Oases is freely available under the GPL license at www.ebi.ac.uk/\~{}zerbino/oases/.},
author = {Schulz, Marcel H. and Zerbino, Daniel R. and Vingron, Martin and Birney, Ewan},
doi = {10.1093/bioinformatics/bts094},
file = {:home/fin/Documents/papers/mendeley/Schulz et al.\_2012\_Oases Robust de novo RNA-seq assembly across the dynamic range of expression levels\_Bioinformatics.pdf:pdf},
isbn = {1367-4811 (Electronic)$\backslash$r1367-4803 (Linking)},
issn = {13674803},
journal = {Bioinformatics},
number = {8},
pages = {1086--1092},
pmid = {22368243},
title = {{Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels}},
volume = {28},
year = {2012}
}
@article{Looso201