text:
@article{Achtman2012,
abstract = {Salmonella enterica subspecies enterica is traditionally subdivided into serovars by serological and nutritional characteristics. We used Multilocus Sequence Typing (MLST) to assign 4,257 isolates from 554 serovars to 1092 sequence types (STs). The majority of the isolates and many STs were grouped into 138 genetically closely related clusters called eBurstGroups (eBGs). Many eBGs correspond to a serovar, for example most Typhimurium are in eBG1 and most Enteritidis are in eBG4, but many eBGs contained more than one serovar. Furthermore, most serovars were polyphyletic and are distributed across multiple unrelated eBGs. Thus, serovar designations confounded genetically unrelated isolates and failed to recognize natural evolutionary groupings. An inability of serotyping to correctly group isolates was most apparent for Paratyphi B and its variant Java. Most Paratyphi B were included within a sub-cluster of STs belonging to eBG5, which also encompasses a separate sub-cluster of Java STs. However, diphasic Java variants were also found in two other eBGs and monophasic Java variants were in four other eBGs or STs, one of which is in subspecies salamae and a second of which includes isolates assigned to Enteritidis, Dublin and monophasic Paratyphi B. Similarly, Choleraesuis was found in eBG6 and is closely related to Paratyphi C, which is in eBG20. However, Choleraesuis var. Decatur consists of isolates from seven other, unrelated eBGs or STs. The serological assignment of these Decatur isolates to Choleraesuis likely reflects lateral gene transfer of flagellar genes between unrelated bacteria plus purifying selection. By confounding multiple evolutionary groups, serotyping can be misleading about the disease potential of S. enterica. Unlike serotyping, MLST recognizes evolutionary groupings and we recommend that Salmonella classification by serotyping should be replaced by MLST or its equivalents.},
author = {Achtman, Mark and Wain, John and Weill, Fran{\c{c}}ois-Xavier and Nair, Satheesh and Zhou, Zhemin and Sangal, Vartul and Krauland, Mary G. and Hale, James L. and Harbottle, Heather and Uesbeck, Alexandra and Dougan, Gordon and Harrison, Lee H. and Brisse, Sylvain and study Group, the S. enterica MLST},
doi = {10.1371/journal.ppat.1002776},
editor = {Bessen, Debra E.},
file = {:home/nicholas/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Achtman et al. - 2012 - Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica.pdf:pdf},
issn = {1553-7374},
journal = {PLoS Pathogens},
month = {jun},
number = {6},
pages = {e1002776},
publisher = {Public Library of Science},
title = {{Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica}},
url = {http://dx.plos.org/10.1371/journal.ppat.1002776},
volume = {8},
year = {2012}
}
@article{Alikhan2018,
abstract = {For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further subdivided for epidemiological tracing by a variety of diagnostic tests with higher resolution. Recently, it has been proposed that so-called eBurst groups (eBGs) based on the alleles of seven housekeeping genes (legacy multilocus sequence typing [MLST]) corresponded to natural populations and could replace serotyping. However, this approach lacks the resolution needed for epidemiological tracing and the existence of natural populations had not been independently validated by independent criteria. Here, we describe EnteroBase, a web-based platform that assembles draft genomes from Illumina short reads in the public domain or that are uploaded by users. EnteroBase implements legacy MLST as well as ribosomal gene MLST (rMLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST) and currently contains over 100,000 assembled genomes from Salmonella. It also provides graphical tools for visual interrogation of these genotypes and those based on core single nucleotide polymorphisms (SNPs). eBGs based on legacy MLST are largely consistent with eBGs based on rMLST, thus demonstrating that these correspond to natural populations. rMLST also facilitated the selection of representative genotypes for SNP analyses of the entire breadth of diversity within Salmonella. In contrast, cgMLST provides the resolution needed for epidemiological investigations. These observations show that genomic genotyping, with the assistance of EnteroBase, can be applied at all levels of diversity within the Salmonella genus.},
author = {Alikhan, Nabil-Fareed and Zhou, Zhemin and Sergeant, Martin J. and Achtman, Mark},
doi = {10.1371/journal.pgen.1007261},
editor = {Casades{\'{u}}s, Josep},
file = {:home/nicholas/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Alikhan et al. - 2018 - A genomic overview of the population structure of Salmonella.pdf:pdf},
issn = {1553-7404},
journal = {PLOS Genetics},
month = {apr},
number = {4},
pages = {e1007261},
publisher = {Public Library of Science},
title = {{A genomic overview of the population structure of Salmonella}},
url = {http://dx.plos.org/10.1371/journal.pgen.1007261},
volume = {14},
year = {2018}
}
@article{Clermont2000,
abstract = {Phylogenetic analysis has shown that Escherichia coli is composed of four main phylogenetic groups (A, B1, B2, and D) and that virulent extra-intestinal strains mainly belong to groups B2 and D. Actually, phylogenetic groups can be determined by multilocus enzyme electrophoresis or ribotyping, both of which are complex, time-consuming techniques. We describe a simple and rapid phylogenetic grouping technique based on triplex PCR. The method, which uses a combination of two genes (chuA and yjaA) and an anonymous DNA fragment, was tested with 230 strains and showed excellent correlation with reference methods.},
author = {Clermont, Olivier and Bonacorsi, St{\'{e}}phane and Bingen, Edouard},
doi = {10.1128/AEM.66.10.4555-4558.2000},
file = {:home/nicholas/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Clermont, Bonacorsi, Bingen - 2000 - Rapid and Simple Determination of the Escherichia coli Phylogenetic Group.pdf:pdf},
issn = {0099-2240},
journal = {Applied and environmental microbiology},
month = {oct},
number = {10},
pages = {4555--8},
pmid = {11010916},
publisher = {American Society for Microbiology (ASM)},
title = {{Rapid and simple determination of the Escherichia coli phylogenetic group.}},
url = {http://aem.asm.org/cgi/doi/10.1128/AEM.66.10.4555-4558.2000 http://www.ncbi.nlm.nih.gov/pubmed/11010916 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC92342},
volume = {66},
year = {2000}
}
@article{Clermont2013,
author = {Clermont, Olivier and Christenson, Julia K. and Denamur, Erick and Gordon, David M.},
doi = {10.1111/1758-2229.12019},
file = {:home/nicholas/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Clermont et al. - 2013 - The Clermont iEscherichia colii phylo-typing method revisited improvement of specificity and detection of new p.pdf:pdf},
issn = {17582229},
journal = {Environmental Microbiology Reports},
month = {feb},
number = {1},
pages = {58--65},
title = {{The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups}},
url = {http://doi.wiley.com/10.1111/1758-2229.12019},
volume = {5},
year = {2013}
}
@article{Denamur2015,
abstract = {Numerous tools allowing the rapid and universal identification of the clones/clonal complexes/ phylogroups of Escherichia coli have been developed, as it is a commensal of the vertebrate gut, a major pathogen in veterinary and human medicine, and a bacterial indicator of faecal contamination. The ability to identify clones/clonal complexes/phylogroups is crucial, as a strain's ecological niche, lifestyle and propensity to cause disease vary with its phylogenetic origins. There are currently three multi-locus sequence typing (MLST) schemes for E. coli, as well as several PCR-based assays for determining a strain's phylogroup or clonal complex. In this work, we present data that will enable investigators to determine the correspondence between the PCR-based assays and the three MLST schemes, and provide the means for assigning a sequence type (ST) to a phylogroup when no other data on the strain phylogroup membership are available. Such information will help the scientific community to accurately identify the E. coli clones reported in various publications. Although whole-genome sequencing will replace classical MLST and most alternative PCR-based methods, the ST nomenclature of the MLST scheme hosted at the University of Warwick will largely persist.},
author = {Clermont, Olivier and Gordon, David and Denamur, Erick},
doi = {10.1099/mic.0.000063},
file = {:home/nicholas/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Clermont, Gordon, Denamur - Unknown - Guide to the various phylogenetic classification schemes for Escherichia coli and the corresponden.pdf:pdf},
issn = {1350-0872},
journal = {Microbiology},
month = {may},
number = {5},
pages = {980--988},
publisher = {Microbiology Society},
title = {{Guide to the various phylogenetic classification schemes for Escherichia coli and the correspondence among schemes}},
url = {http://www.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.000063},
volume = {161},
year = {2015}
}
@article{DeBeen2015,
abstract = {{\textless}p{\textgreater} {\textless}named-content content-type="genus-species"{\textgreater}Enterococcus faecium{\textless}/named-content{\textgreater} , a common inhabitant of the human gut, has emerged in the last 2 decades as an important multidrug-resistant nosocomial pathogen. Since the start of the 21st century, multilocus sequence typing (MLST) has been used to study the molecular epidemiology of {\textless}named-content content-type="genus-species"{\textgreater}E. faecium{\textless}/named-content{\textgreater} . However, due to the use of a small number of genes, the resolution of MLST is limited. Whole-genome sequencing (WGS) now allows for high-resolution tracing of outbreaks, but current WGS-based approaches lack standardization, rendering them less suitable for interlaboratory prospective surveillance. To overcome this limitation, we developed a core genome MLST (cgMLST) scheme for {\textless}named-content content-type="genus-species"{\textgreater}E. faecium{\textless}/named-content{\textgreater} . cgMLST transfers genome-wide single nucleotide polymorphism (SNP) diversity into a standardized and portable allele numbering system that is far less computationally intensive than SNP-based analysis of WGS data. The {\textless}named-content content-type="genus-species"{\textgreater}E. faecium{\textless}/named-content{\textgreater} cgMLST scheme was built using 40 genome sequences that represented the diversity of the species. The scheme consists of 1,423 cgMLST target genes. To test the performance of the scheme, we performed WGS analysis of 103 outbreak isolates from five different hospitals in the Netherlands, Denmark, and Germany. The cgMLST scheme performed well in distinguishing between epidemiologically related and unrelated isolates, even between those that had the same sequence type (ST), which denotes the higher discriminatory power of this cgMLST scheme over that of conventional MLST. We also show that in terms of resolution, the performance of the {\textless}named-content content-type="genus-species"{\textgreater}E. faecium{\textless}/named-content{\textgreater} cgMLST scheme is equivalent to that of an SNP-based approach. In conclusion, the cgMLST scheme developed in this study facilitates rapid, standardized, and high-resolution tracing of {\textless}named-content content-type="genus-species"{\textgreater}E. faecium{\textless}/named-content{\textgreater} outbreaks. {\textless}/p{\textgreater}},
author = {de Been, Mark and Pinholt, Mette and Top, Janetta and Bletz, Stefan and Mellmann, Alexander and van Schaik, Willem and Brouwer, Ellen and Rogers, Malbert and Kraat, Yvette and Bonten, Marc and Corander, Jukka and Westh, Henrik and Harmsen, Dag and Willems, Rob J. L.},
doi = {10.1128/JCM.01946-15},
editor = {Carroll, K. C.},
issn = {0095-1137},
journal = {Journal of Clinical Microbiology},
month = {dec},
number = {12},
pages = {3788--3797},
pmid = {26400782},
title = {{Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26400782 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4652124 http://jcm.asm.org/lookup/doi/10.1128/JCM.01946-15},
volume = {53},
year = {2015}
}
@article{Gardner2015a,
abstract = {We announce the release of kSNP3.0, a program for SNP identification and phylogenetic analysis without genome alignment or the requirement for reference genomes. kSNP3.0 is a significantly improved version of kSNP v2. AVAILABILITY AND IMPLEMENTATION kSNP3.0 is implemented as a package of stand-alone executables for Linux and Mac OS X under the open-source BSD license. The executable packages, source code and a full User Guide are freely available at https://sourceforge.net/projects/ksnp/files/ CONTACT},
author = {Gardner, Shea N and Slezak, Tom and Hall, Barry G.},
doi = {10.1093/bioinformatics/btv271},
issn = {1367-4803},
journal = {Bioinformatics},
month = {sep},
number = {17},
pages = {2877--2878},
pmid = {25913206},
title = {{kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome: Table 1}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25913206 https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv271},
volume = {31},
year = {2015}
}
@article{Hazen2017,
abstract = {Escherichia coli that are capable of causing human disease are often classified into pathogenic variants (pathovars) based on their virulence gene content. However, disease-associated hybrid E. coli, containing unique combinations of multiple canonical virulence factors have also been described. Such was the case of the E. coli O104:H4 outbreak in 2011, which caused significant morbidity and mortality. Among the pathovars of diarrheagenic E. coli that cause significant human disease are the enteropathogenic E. coli (EPEC) and enterotoxigenic E. coli (ETEC). In the current study we use comparative genomics, transcriptomics, and functional studies to characterize isolates that contain virulence factors of both EPEC and ETEC. Based on phylogenomic analysis, these hybrid isolates are more genomically-related to EPEC, but appear to have acquired ETEC virulence genes. Global transcriptional analysis using RNA sequencing, demonstrated that the EPEC and ETEC virulence genes of these hybrid isolates were differentially-expressed under virulence-inducing laboratory conditions, similar to reference isolates. Immunoblot assays further verified that the virulence gene products were produced and that the T3SS effector EspB of EPEC, and heat-labile toxin of ETEC were secreted. These findings document the existence and virulence potential of an E. coli pathovar hybrid that blurs the distinction between E. coli pathovars.},
author = {Hazen, Tracy H and Michalski, Jane and Luo, Qingwei and Shetty, Amol C and Daugherty, Sean C and Fleckenstein, James M and Rasko, David A},
doi = {10.1038/s41598-017-03489-z},
issn = {2045-2322},
journal = {Scientific reports},
month = {jun},
number = {1},
pages = {3513},
pmid = {28615618},
publisher = {Nature Publishing Group},
title = {{Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic E. coli.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/28615618 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5471185},
volume = {7},
year = {2017}
}
@article{Herzer1990,
abstract = {Multicopy single-stranded DNA (msDNA), a branched DNA-RNA molecule, has been shown in Escherichia coli B and clinical strain Cl-1 to be synthesized by reverse transcriptase. We report that 13{\%} of the strains of the ECOR collection, a sample of 72 E. coli isolates representing the breadth of genetic variation of the species, produce msDNA. Three of the four major subspecific groups include msDNA-producing strains. Screening of 25 isolates that are genetically related to msDNA-producing clinical strains uncovered 22 additional msDNA-producing strains. A phylogenetic tree based on allelic variation detected electrophoretically at 20 enzyme-encoding loci revealed two major clusters and several deep branches composed of strains that synthesize msDNA. Although E. coli K-12 does not harbor msDNA, other closely related strains of the K-12 family do. The results support the hypothesis that msDNA-synthesizing systems, including reverse transcriptase genes, were acquired recently and independently in different lineages of E. coli.},
author = {Herzer, P J and Inouye, S and Inouye, M and Whittam, T S},
issn = {0021-9193},
journal = {Journal of bacteriology},
month = {nov},
number = {11},
pages = {6175--81},
pmid = {1699928},
publisher = {American Society for Microbiology (ASM)},
title = {{Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/1699928 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC526797},
volume = {172},
year = {1990}
}
@article{Jolley2012,
abstract = {No single genealogical reconstruction or typing method currently encompasses all levels of bacterial diversity, from domain to strain. We propose ribosomal multilocus sequence typing (rMLST), an approach which indexes variation of the 53 genes encoding the bacterial ribosome protein subunits (rps genes), as a means of integrating microbial genealogy and typing. As with multilocus sequence typing (MLST), rMLST employs curated reference sequences to identify gene variants efficiently and rapidly. The rps loci are ideal targets for a universal characterization scheme as they are: (i) present in all bacteria; (ii) distributed around the chromosome; and (iii) encode proteins which are under stabilizing selection for functional conservation. Collectively, the rps loci exhibit variation that resolves bacteria into groups at all taxonomic and most typing levels, providing significantly more resolution than 16S small subunit rRNA gene phylogenies. A web-accessible expandable database, comprising whole-genome data from more than 1900 bacterial isolates, including 28 draft genomes assembled de novo from the European Bioinformatics Institute (EBI) sequence read archive, has been assembled. The rps gene variation catalogued in this database permits rapid and computationally non-intensive identification of the phylogenetic position of any bacterial sequence at the domain, phylum, class, order, family, genus, species and strain levels. The groupings generated with rMLST data are consistent with current nomenclature schemes and independent of the clustering algorithm used. This approach is applicable to the other domains of life, potentially providing a rational and universal approach to the classification of life that is based on one of its fundamental features, the translation mechanism.},
author = {Jolley, K. A. and Bliss, C. M. and Bennett, J. S. and Bratcher, H. B. and Brehony, C. and Colles, F. M. and Wimalarathna, H. and Harrison, O. B. and Sheppard, S. K. and Cody, A. J. and Maiden, M. C. J.},
doi = {10.1099/mic.0.055459-0},
issn = {1350-0872},
journal = {Microbiology},
month = {apr},
number = {Pt{\_}4},
pages = {1005--1015},
pmid = {22282518},
title = {{Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22282518 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3492749 http://mic.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.055459-0},
volume = {158},
year = {2012}
}
@article{Lukjancenko2010,
abstract = {Escherichia coli is an important component of the biosphere and is an ideal model for studies of processes involved in bacterial genome evolution. Sixty-one publically available E. coli and Shigella spp. sequenced genomes are compared, using basic methods to produce phylogenetic and proteomics trees, and to identify the pan-and core genomes of this set of sequenced strains. A hierarchical clustering of variable genes allowed clear separation of the strains into clusters, including known pathotypes; clinically relevant serotypes can also be resolved in this way. In contrast, when in silico MLST was performed, many of the various strains appear jumbled and less well resolved. The predicted pan-genome comprises 15,741 gene families, and only 993 (6{\%}) of the families are represented in every genome, comprising the core genome. The variable or 'accessory' genes thus make up more than 90{\%} of the pan-genome and about 80{\%} of a typical genome; some of these variable genes tend to be co-localized on genomic islands. The diversity within the species E. coli, and the overlap in gene content between this and related species, suggests a continuum rather than sharp species borders in this group of Enterobacteriaceae.},
author = {Lukjancenko, Oksana and Wassenaar, Trudy M. and Ussery, David W.},
doi = {10.1007/s00248-010-9717-3},
file = {:home/nicholas/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Lukjancenko, Wassenaar, Ussery - 2010 - Comparison of 61 Sequenced Escherichia coli Genomes.pdf:pdf},
journal = {Microbial Ecology},
title = {{Comparison of 61 Sequenced Escherichia coli Genomes}},
volume = {60},
year = {2010}
}
@article{Qi2004,
abstract = {In order to provide a portable and accurate typing system for the unambiguous characterization of pathogenic Escherichia coli isolates to the scientific community, we have constructed an online database for MultiLocus Sequence Typing of pathogenic E. coli (EcMLST) using current internet and open source technology.},
author = {Qi, Weihong and Lacher, David W and Bumbaugh, Alyssa C and Hyma, Katie E and Ouellette, Lindsey M and Large, Teresa M and Tarr, Cheryl L and Whittam, Thomas S},
file = {:home/nicholas/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Qi et al. - 2004 - EcMLST an Online Database for Multi Locus Sequence Typing of Pathogenic Escherichia coli.pdf:pdf},
journal = {IEEE Computational Systems Bioinformatics Conference},
title = {{EcMLST: an Online Database for Multi Locus Sequence Typing of Pathogenic Escherichia coli}},
url = {http://www.shigatox.net/ecmlst/EcMLST.pdf},
year = {2004}
}
@incollection{Selander1987,
abstract = {This is the long-awaited second edition of an invaluable classic! Escherichia coli occupies a central role in contemporary molecular biology. It is the unicellular organism about which most is known - all molecular and cellular biologists will want a copy of this book. In 154 chapters, 250 expert authors and editors present the state of the art. Completely rewritten and restructured, the second edition offers a whole new approach to the subject.},
address = {Washington, D.C. :},
author = {Selander, R K and Caugant, D A and Whittam, T S},
booktitle = {Escherichia coli and Salmonella : cellular and molecular biology},
editor = {Neidhardt, Frederick C.},
isbn = {0914826891},
pages = {1625--1648},
publisher = {American Society for Microbiology Press},
title = {{Genetic structure and variation in natural populations of Escherichia coli.}},
volume = {2},
year = {1987}
}
@article{Sims2011,
abstract = {A whole-genome phylogeny of the Escherichia coli/Shigella group was constructed by using the feature frequency profile (FFP) method. This alignment-free approach uses the frequencies of l-mer features of whole genomes to infer phylogenic distances. We present two phylogenies that accentuate different aspects of E. coli/Shigella genomic evolution: (i) one based on the compositions of all possible features of length l = 24 (∼8.4 million features), which are likely to reveal the phenetic grouping and relationship among the organisms and (ii) the other based on the compositions of core features with low frequency and low variability (∼0.56 million features), which account for ∼69{\%} of all commonly shared features among 38 taxa examined and are likely to have genome-wide lineal evolutionary signal. Shigella appears as a single clade when all possible features are used without filtering of noncore features. However, results using core features show that Shigella consists of at least two distantly related subclades, implying that the subclades evolved into a single clade because of a high degree of convergence influenced by mobile genetic elements and niche adaptation. In both FFP trees, the basal group of the E. coli/Shigella phylogeny is the B2 phylogroup, which contains primarily uropathogenic strains, suggesting that the E. coli/Shigella ancestor was likely a facultative or opportunistic pathogen. The extant commensal strains diverged relatively late and appear to be the result of reductive evolution of genomes. We also identify clade distinguishing features and their associated genomic regions within each phylogroup. Such features may provide useful information for understanding evolution of the groups and for quick diagnostic identification of each phylogroup.},
author = {Sims, Gregory E and Kim, Sung-Hou},
doi = {10.1073/pnas.1105168108},
file = {:home/nicholas/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Sims, Kim - 2011 - Whole-genome phylogeny of Escherichia coliShigella group by feature frequency profiles (FFPs).pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
month = {may},
number = {20},
pages = {8329--34},
pmid = {21536867},
publisher = {National Academy of Sciences},
title = {{Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs).}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21536867 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3100984},
volume = {108},
year = {2011}
}
@article{Stadhouders2010,
abstract = {Real-time polymerase chain reaction (PCR) is the current method of choice for detection and quantification of nucleic acids, especially for molecular diagnostics. Complementarity between primers and template is often crucial for PCR applications, as mismatches can severely reduce priming efficiency. However, little quantitative data on the effect of these mismatches is available. We quantitatively investigated the effects of primer-template mismatches within the 3'-end primer region on real-time PCR using the 5'-nuclease assay. Our results show that single mismatches instigate a broad variety of effects, ranging from minor ({\textless}1.5 cycle threshold, eg, A-C, C-A, T-G, G-T) to severe impact ({\textgreater}7.0 cycle threshold, eg, A-A, G-A, A-G, C-C) on PCR amplification. A clear relationship between specific mismatch types, position, and impact was found, which remained consistent for DNA versus RNA amplifications and Taq/Moloney murine leukemia virus versus rTth based amplifications. The overall size of the impact among the various master mixes used differed substantially (up to sevenfold), and for certain master mixes a reverse or forward primer-specific impact was observed, emphasizing the importance of the experimental conditions used. Taken together these data suggest that mismatch impact follows a consistent pattern and enabled us to formulate several guidelines for predicting primer-template mismatch behavior when using specific 5-nuclease assay master mixes. Our study provides novel insight into mismatch behavior and should allow for more optimized development of real-time PCR assays involving primer-template mismatches.},
author = {Stadhouders, Ralph and Pas, Suzan D and Anber, Jeer and Voermans, Jolanda and Mes, Ted H M and Schutten, Martin},
doi = {10.2353/jmoldx.2010.090035},
file = {:home/nicholas/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Stadhouders et al. - 2010 - The effect of primer-template mismatches on the detection and quantification of nucleic acids using the 5' n.pdf:pdf},
issn = {1943-7811},
journal = {The Journal of molecular diagnostics : JMD},
month = {jan},
number = {1},
pages = {109--17},
pmid = {19948821},
publisher = {American Society for Investigative Pathology},
title = {{The effect of primer-template mismatches on the detection and quantification of nucleic acids using the 5' nuclease assay.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19948821 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC2797725},
volume = {12},
year = {2010}
}
@article{Vangchhia2016,
abstract = {Unlike Escherichia coli strains belonging to phylogroup B2, the clinical significance of strains belonging to phylogroup F is not well understood. Here we report on a collection of phylogroup F strains recovered in Australia from faeces and extra-intestinal sites from humans, companion animals and native animals, as well as from poultry meat and water samples. The distribution of sequence types was clearly non-random with respect to isolate source. The antimicrobial resistance and virulence trait profiles also varied with the sequence type of the isolate. Phylogroup F strains tended to lack the virulence traits typically associated with phylogroup B2 strains responsible for extra-intestinal infection in humans. Resistance to fluoroquinolones and/or expanded-spectrum cephalosporins was common within ST648, ST354 and ST3711. Although ST354 and ST3711 are part of the same clonal complex, the ST3711 isolates were only recovered from native birds being cared for in a single wildlife rehabilitation centre, whereas the ST354 isolates were from faeces and extra-intestinal sites of dogs and humans, as well as from poultry meat. Although ST354 isolates from chicken meat in Western Australia were distinct from all other ST354 isolates, those from poultry meat samples collected in eastern Australia shared many similarities with other ST354 isolates from humans and companion animals.},
author = {Vangchhia, Belinda and Abraham, Sam and Bell, Jan M. and Collignon, Peter and Gibson, Justine S. and Ingram, Paul R. and Johnson, James R. and Kennedy, Karina and Trott, Darren J. and Turnidge, John D. and Gordon, David M.},
doi = {10.1099/mic.0.000367},
issn = {1350-0872},
journal = {Microbiology},
keywords = {E. coli,antimicrobial resistance,birds,fluoroquinolone resistance,phylogenetic relationships,phylogroups,poultry meat,virulence},
month = {nov},
number = {11},
pages = {1904--1912},
publisher = {Microbiology Society},
title = {{Phylogenetic diversity, antimicrobial susceptibility and virulence characteristics of phylogroup F Escherichia coli in Australia}},
url = {http://www.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.000367},
volume = {162},
year = {2016}
}
@article{Weissman2012,
abstract = {{\textless}p{\textgreater} Multilocus sequence typing (MLST) is usually based on the sequencing of 5 to 8 housekeeping loci in the bacterial chromosome and has provided detailed descriptions of the population structure of bacterial species important to human health. However, even strains with identical MLST profiles (known as sequence types or STs) may possess distinct genotypes, which enable different eco- or pathotypic lifestyles. Here we describe a two-locus, sequence-based typing scheme for {\textless}named-content content-type="genus-species"{\textgreater}Escherichia coli{\textless}/named-content{\textgreater} that utilizes a 489-nucleotide (nt) internal fragment of {\textless}italic{\textgreater}fimH{\textless}/italic{\textgreater} (encoding the type 1 fimbrial adhesin) and the 469-nt internal {\textless}italic{\textgreater}fumC{\textless}/italic{\textgreater} fragment used in standard MLST. Based on sequence typing of 191 model commensal and pathogenic isolates plus 853 freshly isolated clinical {\textless}named-content content-type="genus-species"{\textgreater}E. coli{\textless}/named-content{\textgreater} strains, this 2-locus approach—which we call CH ( {\textless}italic{\textgreater}fum{\textless}/italic{\textgreater} {\textless}underline{\textgreater} {\textless}italic{\textgreater}C{\textless}/italic{\textgreater} {\textless}/underline{\textgreater} / {\textless}italic{\textgreater}fim{\textless}/italic{\textgreater} {\textless}underline{\textgreater} {\textless}italic{\textgreater}H{\textless}/italic{\textgreater} {\textless}/underline{\textgreater} ) typing—consistently yielded more haplotypes than standard 7-locus MLST, splitting large STs into multiple clonal subgroups and often distinguishing different within-ST eco- and pathotypes. Furthermore, specific CH profiles corresponded to specific STs, or ST complexes, with 95{\%} accuracy, allowing excellent prediction of MLST-based profiles. Thus, 2-locus CH typing provides a genotyping tool for molecular epidemiology analysis that is more economical than standard 7-locus MLST but has superior clonal discrimination power and, at the same time, corresponds closely to MLST-based clonal groupings. {\textless}/p{\textgreater}},
author = {Weissman, Scott J. and Johnson, James R. and Tchesnokova, Veronika and Billig, Mariya and Dykhuizen, Daniel and Riddell, Kim and Rogers, Peggy and Qin, Xuan and Butler-Wu, Susan and Cookson, Brad T. and Fang, Ferric C. and Scholes, Delia and Chattopadhyay, Sujay and Sokurenko, Evgeni},
doi = {10.1128/AEM.06663-11},
issn = {0099-2240},
journal = {Applied and Environmental Microbiology},
month = {mar},
number = {5},
pages = {1353--1360},
pmid = {22226951},
title = {{High-Resolution Two-Locus Clonal Typing of Extraintestinal Pathogenic Escherichia coli}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22226951 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3294456 http://aem.asm.org/lookup/doi/10.1128/AEM.06663-11},
volume = {78},
year = {2012}
}
@article{Yu2017a,
author = {Yu, Guangchuang and Smith, David K. and Zhu, Huachen and Guan, Yi and Lam, Tommy Tsan-Yuk},
doi = {10.1111/2041-210X.12628},
editor = {McInerny, Greg},
file = {:home/nicholas/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Yu et al. - 2017 - ggtree an r package for visualization and annotation of phylogenetic trees with their covariates and other associate.pdf:pdf},
issn = {2041210X},
journal = {Methods in Ecology and Evolution},
keywords = {annotation,bioconductor,evolution,phylogeny,r package,visualization},
month = {jan},
number = {1},
pages = {28--36},
publisher = {Wiley/Blackwell (10.1111)},
title = {ggtree : an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data},
url = {http://doi.wiley.com/10.1111/2041-210X.12628},
volume = {8},
year = {2017}
}

@article{zhou_users_2019,
	title = {The user’s guide to comparative genomics with {EnteroBase}, including case studies on transmissions of micro-clades of {Salmonella}, the phylogeny of ancient and modern {Yersinia} pestis genomes, and the core genomic diversity of all {Escherichia}},
	url = {https://www.biorxiv.org/content/early/2019/11/25/613554},
	doi = {10.1101/613554},
	abstract = {EnteroBase is an integrated software environment which supports the identification of global population structures within several bacterial genera that include pathogens. Here we provide an overview on how EnteroBase works, what it can do, and its future prospects. EnteroBase has currently assembled more than 300,000 genomes from Illumina short reads from Salmonella, Escherichia, Yersinia, Clostridiodes, Helicobacter, Vibrio, and Moraxella, and genotyped those assemblies by core genome Multilocus Sequence Typing (cgMLST). Hierarchical clustering of cgMLST sequence types allows mapping, a new bacterial strain to predefined population structures at multiple levels of resolution within a few hours after uploading its short reads. Case study 1 illustrates this process for local transmissions of Salmonella enterica serovar Agama between neighboring social groups of badgers and humans. EnteroBase also supports SNP calls from both genomic assemblies and after extraction from metagenomic sequences, as illustrated by case study 2 which summarizes the microevolution of Yersinia pestis over the last 5,000 years of pandemic plague. EnteroBase can also provide a global overview of the genomic diversity within an entire genus, as illustrated by case study 3 which presents a novel, global overview of the population structure of all of the species, subspecies and clades within Escherichia.wgMLSTwhole genome MultiLocus Sequence Typing (Maiden et al. 2013);cgMLSTcore genome MultiLocus Sequence Typing (Mellmann et al. 2011);rMLSTribosomal MultiLocus Sequence Typing (Jolley et al. 2012).},
	journal = {bioRxiv},
	author = {Zhou, Zhemin and Alikhan, Nabil-Fareed and Mohamed, Khaled and Fan, Yulei and Achtman, Mark},
	year = {2019}
}

@article{beghain_clermontyping:_2018,
	title = {{ClermonTyping}: an easy-to-use and accurate in silico method for {Escherichia} genus strain phylotyping},
	volume = {4},
	url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000192},
	doi = {https://doi.org/10.1099/mgen.0.000192},
	abstract = {The genus {\textless}em class=},
	number = {7},
	journal = {Microbial Genomics},
	author = {Beghain, Johann and Bridier-Nahmias, Antoine and Le Nagard, Hervé and Denamur, Erick and Clermont, Olivier},
	year = {2018},
	keywords = {typing}
}
@article{lindsey_multiplex_2017,
  title = {Multiplex Polymerase Chain Reaction for Identification of {{Escherichia}} Coli, {{Escherichia}} Albertii and {{Escherichia}} Fergusonii},
  author = {Lindsey, Rebecca L. and {Garcia-Toledo}, L. and Fasulo, D. and Gladney, L.M. and Strockbine, N.},
  year = {2017},
  month = sep,
  volume = {140},
  pages = {1--4},
  issn = {0167-7012},
  doi = {10.1016/j.mimet.2017.06.005},
  abstract = {Escherichia coli, Escherichia albertii, and Escherichia fergusonii are closely related bacteria that can cause illness in humans, such as bacteremia, urinary tract infections and diarrhea. Current identification strategies for these three species vary in complexity and typically rely on the use of multiple phenotypic and genetic tests. To facilitate their rapid identification, we developed a multiplex PCR assay targeting conserved, species-specific genes. We used the Daydreamer\texttrademark{} (Pattern Genomics, USA) software platform to concurrently analyze whole genome sequence assemblies (WGS) from 150 Enterobacteriaceae genomes (107 E. coli, 5 Shigella spp., 21 E. albertii, 12 E. fergusonii and 5 other species) and design primers for the following species-specific regions: a 212 bp region of the cyclic di-GMP regulator gene (cdgR, AW869\_22935 from genome K-12 MG1655, CP014225) for E. coli/Shigella; a 393 bp region of the DNA-binding transcriptional activator of cysteine biosynthesis gene (EAKF1\_ch4033 from genome KF1, CP007025) for E. albertii; and a 575 bp region of the palmitoleoyl-acyl carrier protein (ACP)-dependent acyltransferase (EFER\_0790 from genome ATCC 35469, CU928158) for E. fergusonii. We incorporated the species-specific primers into a conventional multiplex PCR assay and assessed its performance with a collection of 97 Enterobacteriaceae strains. The assay was 100\% sensitive and specific for detecting the expected species and offers a quick and accurate strategy for identifying E. coli, E. albertii, and E. fergusonii in either a single reaction or by in silico PCR with sequence assemblies.},
  file = {/Users/nick/Zotero/storage/MRIKZA96/Lindsey et al. - 2017 - Multiplex polymerase chain reaction for identifica.pdf},
  journal = {Journal of microbiological methods},
  pmcid = {PMC5603207},
  pmid = {28599915}
}

@article{sichtig_fdaargos_2019,
  title = {{{FDA}}-{{ARGOS}} Is a Database with Public Quality-Controlled Reference Genomes for Diagnostic Use and Regulatory Science},
  author = {Sichtig, Heike and Minogue, Timothy and Yan, Yi and Stefan, Christopher and Hall, Adrienne and Tallon, Luke and Sadzewicz, Lisa and Nadendla, Suvarna and Klimke, William and Hatcher, Eneida and Shumway, Martin and Aldea, Dayanara Lebron and Allen, Jonathan and Koehler, Jeffrey and Slezak, Tom and Lovell, Stephen and Schoepp, Randal and Scherf, Uwe},
  year = {2019},
  month = jul,
  volume = {10},
  pages = {3313},
  issn = {2041-1723},
  doi = {10.1038/s41467-019-11306-6},
  abstract = {FDA proactively invests in tools to support innovation of emerging technologies, such as infectious disease next generation sequencing (ID-NGS). Here, we introduce FDA-ARGOS quality-controlled reference genomes as a public database for diagnostic purposes and demonstrate its utility on the example of two use cases. We provide quality control metrics for the FDA-ARGOS genomic database resource and outline the need for genome quality gap filling in the public domain. In the first use case, we show more accurate microbial identification of Enterococcus avium from metagenomic samples with FDA-ARGOS reference genomes compared to non-curated GenBank genomes. In the second use case, we demonstrate the utility of FDA-ARGOS reference genomes for Ebola virus target sequence comparison as part of a composite validation strategy for ID-NGS diagnostic tests. The use of FDA-ARGOS as an in silico target sequence comparator tool combined with representative clinical testing could reduce the burden for completing ID-NGS clinical trials.},
  file = {/Users/nick/Zotero/storage/JQMCPQ33/Sichtig et al. - 2019 - FDA-ARGOS is a database with public quality-contro.pdf},
  journal = {Nature Communications},
  keywords = {Access to Information,Communicable Diseases,Databases; Nucleic Acid,Genome,High-Throughput Nucleotide Sequencing,Humans,United States,United States Food and Drug Administration},
  language = {eng},
  number = {1},
  pmcid = {PMC6658474},
  pmid = {31346170}
}

@article{clermont_characterization_2019,
  ids = {clermont\_characterization\_2019a,clermont\_characterization\_2019b,clermont\_characterization\_2019c},
  title = {Characterization and Rapid Identification of Phylogroup {{G}} in {{Escherichia}} Coli, a Lineage with High Virulence and Antibiotic Resistance Potential},
  author = {Clermont, Olivier and Dixit, Ojas V. A. and Vangchhia, Belinda and Condamine, B{\'e}n{\'e}dicte and Dion, Sara and {Bridier-Nahmias}, Antoine and Denamur, Erick and Gordon, David},
  year = {2019},
  month = aug,
  volume = {21},
  pages = {3107--3117},
  publisher = {{John Wiley \& Sons, Ltd}},
  issn = {1462-2920},
  doi = {10.1111/1462-2920.14713},
  abstract = {The phylogeny of the Escherichia coli species, with the identification of seven phylogroups (A, B1, B2, C, D, E and F), is linked to the lifestyle of the strains. With the accumulation of whole genome sequence data, it became clear that some strains belong to a group intermediate between the F and B2 phylogroups, designated as phylogroup G. Here, we studied the complete sequences of 112 strains representative of the G phylogroup diversity and showed that it is composed of one main sequence type complex (STc)117 and four other STcs (STc657, STc454, STc738 and STc174). STc117, which phylogeny is characterized by very short internal branches, exhibits extensive O diversity, but little H-type and fimH allele diversity, whereas the other STcs are characterized by a main O, H and fimH type. STc117 strains possess many traits associated with extra-intestinal virulence, are virulent in a mouse sepsis model and exhibit multi-drug resistance such as CTX-M production. Epidemiologic data on 4,524 Australian and French strains suggest that STc117 is a poultry-associated lineage that can also establish in humans and cause extra-intestinal diseases. We propose an easy identification method that will help to trace this potentially virulent and resistant phylogroup in epidemiologic studies.},
  file = {/Users/nick/Zotero/storage/V4JV2GMC/Clermont et al. - 2019 - Characterization and rapid identification of phylo.pdf;/Users/nick/Zotero/storage/6KJPR8VB/1462-2920.html;/Users/nick/Zotero/storage/8B4QAM9Y/1462-2920.html},
  journal = {Environmental Microbiology},
  language = {eng},
  number = {8},
  pmid = {31188527}
}

@article{cockBiopythonFreelyAvailable2009,
  title = {Biopython: Freely Available {{Python}} Tools for Computational Molecular Biology and Bioinformatics},
  author = {Cock, Peter J. A. and Antao, Tiago and Chang, Jeffrey T. and Chapman, Brad A. and Cox, Cymon J. and Dalke, Andrew and Friedberg, Iddo and Hamelryck, Thomas and Kauff, Frank and Wilczynski, Bartek and De Hoon, Michiel J. L.},
  year = {2009},
  volume = {25},
  pages = {1422--1423},
  doi = {10.1093/bioinformatics/btp163},
  abstract = {The Biopython project is a mature open source inter-national collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro-molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/Mailing\_lists; peter.cock@scri.ac.uk.},
  file = {/Users/nick/Zotero/storage/V5J2W8NW/Cock et al. - 2009 - Biopython freely available Python tools for computational molecular biology and bioinformatics.pdf},
  journal = {Bioinformatics},
  number = {1110}
}


text:
@article{10.1021/ja412563e,
  title={Iridium-catalyzed C--H borylation of heteroarenes: scope, regioselectivity, application to late-stage functionalization, and mechanism},
  author={Larsen, M. A. and Hartwig, J. F.},
  journal={J. Am. Chem. Soc.},
  volume={136},
  number={11},
  pages={4287--4299},
  year={2014},
}

@article{10.1002/ange.202001520,
  title={Iridium Catalysed C-H Borylation of Heteroarenes: Balancing steric and electronic regiocontrol},
  author={Wright, J. S. and Scott, P. J. H. and Steel, P. G.},
  journal={Angew. Chem. Int. Ed.},
  volume={59},
  pages={2--28},
  year={2020},
}

@article{10.1021/acs.orglett.9b02299,
  title={C--H Borylation Catalysts that Distinguish Between Similarly Sized Substituents Like Fluorine and Hydrogen},
  author={Miller, S. L. and Chotana, G. A. and Fritz, J. A. and Chattopadhyay, B. and Maleczka Jr, R. E. and Smith III, M. R.},
  journal={Org. Lett.},
  volume={21},
  number={16},
  pages={6388--6392},
  year={2019},
}

license: MIT

license_type: permissive

branch_name: refs/heads/main

extension: bib


text:
@article{driscollIntendedUnintendedConsequences2014,
 abstract = {What are the political consequences of democratization assistance to regimes transitioning from authoritarian rule? By exploiting the downstream effects of a field experiment designed to encourage citizen monitoring of Georgia’s 2008 parliamentary elections, we evaluate the political consequences of one type of democracy promotion aid. The intervention increased citizen activism, but it also had the unanticipated effect of suppressing overall voter turnout by approximately 5%. We hypothesize that the civic education campaign was interpreted as a sign of increased political attention to a selected voting precinct, which suppressed opposition turnout. Two additional experiments provide additional evidence for the hypothesis.},
 author = {Driscoll, Jesse and Hidalgo, F Daniel},
 doi = {10.1177/2053168014530279},
 file = {SAGE PDF Full Text:/Users/dhidalgo/Zotero/storage/MLBHL5UX/Driscoll and Hidalgo - 2014 - Intended and unintended consequences of democracy .pdf:application/pdf},
 issn = {2053-1680},
 journal = {Research & Politics},
 language = {en},
 month = {May},
 number = {1},
 pages = {2053168014530279},
 title = {Intended and unintended consequences of democracy promotion assistance to Georgia after the Rose Revolution},
 url = {https://doi.org/10.1177/2053168014530279},
 urldate = {2019-07-08},
 volume = {1},
 year = {2014}
}

repository: fdhidalgo/academic-kickstart

repo_name: fdhidalgo/academic-kickstart

branch_name: refs/heads/master

gha_license_id: MIT


text:
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Automatically generated by Mendeley Desktop 1.19.4
Any changes to this file will be lost if it is regenerated by Mendeley.

BibTeX export options can be customized via Preferences -> BibTeX in Mendeley Desktop

@article{Shimkin2009,
abstract = {4th from "Learning in Complex Systems: Lecture Notes, Winter"},
author = {Shimkin, Nahum},
file = {:Users/sepmein/Qsync/Papers/Shimkin{\_}2009{\_}Reinforcement Learning – Basic Algorithms.pdf:pdf},
pages = {1--16},
title = {{Reinforcement Learning – Basic Algorithms}},
year = {2009}
}

license: Unlicense

repository: sepmein/references

repo_name: sepmein/references


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@article{bresson2019two,
 author = {Bresson, Xavier and Laurent, Thomas},
 journal = {arXiv preprint arXiv:1906.03412},
 title = {A Two-Step Graph Convolutional Decoder for Molecule Generation},
 year = {2019}
}

repository: davidlowjw/gdl

repo_name: davidlowjw/gdl


text:
@misc{Whalley_JOSS2018,
  author       = {Lucy D. Whalley},
  title        = {effmass: An effective mass package},
  volume       = {3},
  issue        = {28},
  pages        = {797},
  month        = {Aug},
  year         = {2018},
  doi          = {10.21105/joss.00797},
  url          = {http://joss.theoj.org/papers/10.21105/joss.00797}
}

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repo_name: lucydot/effmass

gha_language: Jupyter Notebook


text:
@article{obolenskaya1999,
  title={Does nitric oxide regulate the tumor necrosis factor signal transduction?},
  author={Obolenskaya, M Yu and Samoilenko, AA},
  journal={Biopolymers and Cell},
  volume={15},
  number={4},
  pages={262--274},
  year={1999},
  publisher={National Academy of Sciences of Ukraine, Institute of Molecular Biology and Genetics of the NAS of Ukraine}
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text:
@proceedings{ws-2016-metaphor,
    title = "Proceedings of the Fourth Workshop on Metaphor in {NLP}",
    editor = "Beigman Klebanov, Beata  and
      Shutova, Ekaterina  and
      Lichtenstein, Patricia",
    month = jun,
    year = "2016",
    address = "San Diego, California",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W16-1100",
    doi = "10.18653/v1/W16-11",
}
@inproceedings{lederer-2016-finding,
    title = "Finding metaphorical triggers through source (not target) domain lexicalization patterns",
    author = "Lederer, Jenny",
    booktitle = "Proceedings of the Fourth Workshop on Metaphor in {NLP}",
    month = jun,
    year = "2016",
    address = "San Diego, California",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W16-1101",
    doi = "10.18653/v1/W16-1101",
    pages = "1--9",
}
@inproceedings{haagsma-bjerva-2016-detecting,
    title = "Detecting novel metaphor using selectional preference information",
    author = "Haagsma, Hessel  and
      Bjerva, Johannes",
    booktitle = "Proceedings of the Fourth Workshop on Metaphor in {NLP}",
    month = jun,
    year = "2016",
    address = "San Diego, California",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W16-1102",
    doi = "10.18653/v1/W16-1102",
    pages = "10--17",
}
@inproceedings{rai-etal-2016-supervised,
    title = "Supervised Metaphor Detection using Conditional Random Fields",
    author = "Rai, Sunny  and
      Chakraverty, Shampa  and
      Tayal, Devendra K.",
    booktitle = "Proceedings of the Fourth Workshop on Metaphor in {NLP}",
    month = jun,
    year = "2016",
    address = "San Diego, California",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W16-1103",
    doi = "10.18653/v1/W16-1103",
    pages = "18--27",
}
@inproceedings{do-dinh-gurevych-2016-token,
    title = "Token-Level Metaphor Detection using Neural Networks",
    author = "Do Dinh, Erik-L{\^a}n  and
      Gurevych, Iryna",
    booktitle = "Proceedings of the Fourth Workshop on Metaphor in {NLP}",
    month = jun,
    year = "2016",
    address = "San Diego, California",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W16-1104",
    doi = "10.18653/v1/W16-1104",
    pages = "28--33",
}
@inproceedings{veale-2016-round,
    title = "Round Up The Usual Suspects: Knowledge-Based Metaphor Generation",
    author = "Veale, Tony",
    booktitle = "Proceedings of the Fourth Workshop on Metaphor in {NLP}",
    month = jun,
    year = "2016",
    address = "San Diego, California",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W16-1105",
    doi = "10.18653/v1/W16-1105",
    pages = "34--41",
}

repository: emorynlp/nlprankings

repo_name: emorynlp/nlprankings

gha_license_id: NOASSERTION

gha_language: TeX


text:
@inproceedings{TrogliaFaIRFederatedIncumbent2019,
 abstract = {The next-generation spectrum access system (SAS) for the Citizens Broadband Radio Service band is equipped with environmental sensors (ESCs) to detect the presence of non-informed incumbent users, which allows the SAS to dynamically reassign spectrum resource for low privilege users to avoid interference. However, the performance of existing single-node detection model is limited by the sensor's geo-locations; whereas a naive distributed sensing network with improved detection accuracy introduces a high bandwidth overhead due to the frequent communication of spectrum data. In addition, many existing coherent spectrum sensing methods are not feasible for CBRS band due to the unknown operational characteristics of incumbent military wireless applications. To address these issues, we propose a machine learning based non-coherent spectrum sensing system: (F)eder(a)ted (I)ncumbent Detection in CB(R)S (FaIR). FaIR leverages a communication-efficient distributed learning framework, federated learning, for ESCs to collaborate and train a data-driven machine learning model for incumbent detection under minimal communication bandwidth. Our preliminary results show that the federated learning method can exploit the spatial diversity of ESCs and obtain an improved detection model comparing to a naive distributed sensing and centralized model framework. We evaluate the FaIR model with a variety of spectrum waveforms at varying SNRs. Our experiments showed that FaIR improves the average detection accuracy compared to the single-node method, using a fraction of the bandwidth compared to the naive multi-node method.},
 author = {Troglia, Matthew and Melcher, Jordan and Zheng, Yao and Anthony, Dylan and Yang, Alvin and Yang, Thomas},
 booktitle = {2019 IEEE International Symposium on Dynamic Spectrum Access Networks (DySPAN) - Workshop on Data-Driven Dynamic Spectrum Sharing},
 doi = {10.1109/DySPAN.2019.8935736},
 keywords = {conference},
 month = {November},
 pages = {1--6},
 title = {FaIR: Federated Incumbent Detection in CBRS Band},
 year = {2019}
}


text:
%
%  An example of a bibliographical database for bibTeX
%
%  Recommended software for maintenance of *.bib files:
%    JabRef, http://jabref.sourceforge.net/
%
%  BEWARE:
%
%    *  If a name contains a capital letter, which must be kept such,
%       use curly brackets ({T}hailand, {HIV}).
%
%  ===========================================================================

@online{fcl,
	author = {Lander, Rich},
	title = {Framework Libraries},
	maintitle = {Microsoft Docs .NET Guide},
	date = {2016-06-20},
	url = {https://docs.microsoft.com/en-us/dotnet/standard/framework-libraries},
	urldate = {2018-04-11}
}

@online{csharp-spec,
	title = {C\# 6.0 draft language specification},
	maintitle = {Microsoft Docs C\# Guide},
	date = {2018-05-22},
	url = {https://docs.microsoft.com/en-us/dotnet/csharp/language-reference/language-specification/},
	urldate = {2018-06-17}
}

@online{roslyn,
	title = {The .NET Compiler Platform},
	maintitle = {GitHub},
	url = {https://github.com/dotnet/roslyn},
	urldate = {2018-06-17}
}

@online{ecma-335,
	author = {Ecma International},
	title = {Standard ECMA-335: Common Language Infrastructure (CLI)},
	date = {2012-06},
	url = {https://www.ecma-international.org/publications/standards/Ecma-335.htm},
	urldate = {2018-06-17}
}

@online{tour,
	author = {Carter, Phillip},
	title = {Tour of .NET},
	maintitle = {Microsoft Docs .NET Guide},
	date = {2017-05-22},
	url = {https://docs.microsoft.com/en-us/dotnet/standard/tour},
	urldate = {2018-06-18}
}

@online{implementations,
	author = {Carter, Phillip},
	title = {.NET architectural components},
	maintitle = {Microsoft Docs .NET Guide},
	date = {2017-08-23},
	url = {https://docs.microsoft.com/en-us/dotnet/standard/components},
	urldate = {2018-06-17}
}

@online{nuget,
	title = {NuGet Gallery},
	url = {https://www.nuget.org/},
	urldate = {2018-07-30}
}

@online{T4,
	author = {Warren, Genevieve},
	title = {Code Generation and T4 Text Templates},
	maintitle = {Microsoft Docs Visual Studio documentation},
	date = {2016-11-04},
	url = {https://docs.microsoft.com/en-us/visualstudio/modeling/code-generation-and-t4-text-templates},
	urldate = {2018-08-09}
}

@online{codedom,
	author = {Petrusha, Ron},
	title = {Dynamic Source Code Generation and Compilation},
	maintitle = {Microsoft Docs .NET Framework Guide},
	date = {2017-03-30},
	url = {https://docs.microsoft.com/en-us/dotnet/framework/reflection-and-codedom/dynamic-source-code-generation-and-compilation},
	urldate = {2018-08-09}
}

@online{refemit,
	author = {Petrusha, Ron},
	title = {Emitting Dynamic Methods and Assemblies},
	maintitle = {Microsoft Docs .NET Framework Guide},
	date = {2017-08-30},
	url = {https://docs.microsoft.com/en-us/dotnet/framework/reflection-and-codedom/emitting-dynamic-methods-and-assemblies},
	urldate = {2018-08-09}
}

@online{cecil,
	title = {Mono.Cecil},
	maintitle = {Mono documentation},
	url = {https://www.mono-project.com/docs/tools+libraries/libraries/Mono.Cecil/},
	urldate = {2018-08-09}
}

@online{expression-trees,
	author = {Wagner, Bill},
	title = {Expression Trees},
	maintitle = {Microsoft Docs C\# Guide},
	date = {2015-07-20},
	url = {https://docs.microsoft.com/en-us/dotnet/csharp/programming-guide/concepts/expression-trees/},
	urldate = {2018-08-10}
}

@online{postsharp,
	title = {PostSharp},
	url = {https://www.postsharp.net/},
	urldate = {2018-08-13}
}

@online{fody,
	title = {Fody},
	maintitle = {GitHub},
	url = {https://github.com/Fody/Fody},
	urldate = {2018-08-14}
}

@online{type-providers,
	author = {Carter, Phillip},
	title = {Type Providers},
	maintitle = {Microsoft Docs F\# Guide},
	date = {2018-04-02},
	url = {https://docs.microsoft.com/en-us/dotnet/fsharp/tutorials/type-providers/},
	urldate = {2018-08-14}
}

@online{fdg-naming,
	author = {Cwalina, Krzysztof  and Abrams, Brad},
	title = {Framework Design Guidelines},
	subtitle = {General Naming Conventions},
	maintitle = {Microsoft Docs .NET Guide},
	date = {2008-10-22},
	url = {https://docs.microsoft.com/en-us/dotnet/standard/design-guidelines/general-naming-conventions},
	urldate = {2018-08-17}
}

@online{ecma-334,
	author = {Ecma International},
	title = {C\# Language Specification},
	date = {2017-12},
	url = {https://www.ecma-international.org/publications/files/ECMA-ST/ECMA-334.pdf},
	urldate = {2018-12-04}
}

@online{finalizer,
	author = {Wagner, Bill},
	title = {Finalizers},
	maintitle = {Microsoft Docs C\# Guide},
	date = {2018-10-08},
	url = {https://docs.microsoft.com/en-us/dotnet/csharp/programming-guide/classes-and-structs/destructors},
	urldate = {2018-12-04}
}

@online{parallel-foreach,
	author = {Petrusha, Ron},
	title = {How to: Write a Simple Parallel.ForEach Loop},
	maintitle = {Microsoft Docs .NET Guide},
	date = {2018-09-12},
	url = {https://docs.microsoft.com/en-us/dotnet/standard/parallel-programming/how-to-write-a-simple-parallel-foreach-loop},
	urldate = {2018-09-20}
}

@online{codegen-differences,
	author = {Sadov, Vladimir},
	title = {Code generation differences compared to previous compilers},
	maintitle = {The .NET Compiler Platform documentation},
	date = {2015-07-14},
	url = {https://github.com/dotnet/roslyn/blob/master/docs/compilers/CSharp/CodeGen%20Differences.md},
	urldate = {2018-10-07}
}

@online{fdg-extension-methods,
	author = {Cwalina, Krzysztof  and Abrams, Brad},
	title = {Framework Design Guidelines},
	subtitle = {Extension Methods},
	maintitle = {Microsoft Docs .NET Guide},
	date = {2008-10-22},
	url = {https://docs.microsoft.com/en-us/dotnet/standard/design-guidelines/extension-methods},
	urldate = {2018-09-26}
}

@online{debugger-break,
	title = {Debugger.Break Method},
	maintitle = {Microsoft Docs .NET API Reference},
	url = {https://docs.microsoft.com/en-us/dotnet/api/system.diagnostics.debugger.break},
	urldate = {2018-12-04}
}

@online{red-green-trees,
	author = {Lippert, Eric},
	title = {Persistence, Facades and Roslyn’s Red-Green Trees},
	maintitle = {Fabulous Adventures In Coding},
	date = {2012-06-08},
	url = {https://blogs.msdn.microsoft.com/ericlippert/2012/06/08/persistence-facades-and-roslyns-red-green-trees/},
	urldate = {2018-12-27}
}

@online{roslyn-annotations,
	author = {Varty, Josh},
	title = {Learn Roslyn Now: Part 13 Keeping track of syntax nodes with Syntax Annotations},
	maintitle = {Shotgun Debugging},
	date = {2015-09-18},
	url = {https://joshvarty.com/2015/09/18/learn-roslyn-now-part-13-keeping-track-of-syntax-nodes-with-syntax-annotations/},
	urldate = {2018-12-27}
}

@online{fdg-events,
	author = {Cwalina, Krzysztof and Abrams, Brad},
	title = {Framework Design Guidelines},
	subtitle = {Event Design},
	maintitle = {Microsoft Docs .NET Guide},
	date = {2008-10-22},
	url = {https://docs.microsoft.com/en-us/dotnet/standard/design-guidelines/event},
	urldate = {2019-01-08}
}

@online{iacta,
	author = {Wojcieszyn, Filip},
	title = {No InternalsVisibleTo, no problem – bypassing C\# visibility rules with Roslyn},
	maintitle = {StrathWeb},
	date = {2018-10-08},
	url = {https://www.strathweb.com/2018/10/no-internalvisibleto-no-problem-bypassing-c-visibility-rules-with-roslyn/},
	urldate = {2019-01-17}
}

@online{iactg,
	author = {Arbel, Eli},
	title = {IgnoresAccessChecksTo Generator},
	maintitle = {GitHub},
	date = {2017-08-14},
	url = {https://github.com/aelij/IgnoresAccessChecksToGenerator},
	urldate = {2019-01-17}
}

@online{iactg-net46,
	author = {Onderka, Petr},
	title = {IgnoresAccessChecksTo Generator: AssemblyResolutionException when publicizing internals on .Net Framework 4.6},
	maintitle = {GitHub},
	date = {2018-10-09},
	url = {https://github.com/aelij/IgnoresAccessChecksToGenerator/issues/4},
	urldate = {2019-05-02}
}

@online{nb-msbe,
	author = {Arnott, Andrew},
	title = {Nerdbank.MSBuildExtension},
	maintitle = {GitHub},
	date = {2018-05-11},
	url = {https://github.com/AArnott/Nerdbank.MSBuildExtension},
	urldate = {2019-02-20}
}

@online{design-time-builds,
	author = {Kean, David},
	title = {C\#, F\# and Visual Basic project system documentation: Design-time builds},
	maintitle = {GitHub},
	date = {2019-02-22},
	url = {https://github.com/dotnet/project-system/blob/master/docs/design-time-builds.md},
	urldate = {2019-03-12}
}

@online{postsharp-diag,
	title = {PostSharp Diagnostics},
	url = {https://www.postsharp.net/logging},
	urldate = {2019-05-02}
}

repository: svick/CSharpE

repo_name: svick/CSharpE


text:
@book{xie_r_2019,
  address = {Boca Raton},
  title = {R {Markdown}: the definitive guide},
  isbn = {978-0-429-78296-1},
  shorttitle = {R {Markdown}},
  publisher = {CRC Press, Taylor and Francis Group},
  author = {Xie, Yihui and Allaire, J. J. and Grolemund, Garrett},
  year = {2019},
  keywords = {Computer programs, Markdown (Document markup language), R (Computer program language), Web site development},
}

@article{hernandez_ExplorationExplorationMeasuring_2021,
	title = {An {Exploration} of {Exploration}: {Measuring} the ability of lexicase selection to find obscure pathways to optimality},
	shorttitle = {An {Exploration} of {Exploration}},
	url = {http://arxiv.org/abs/2107.09760},
	abstract = {Parent selection algorithms (selection schemes) steer populations through a problem's search space, often trading off between exploitation and exploration. Understanding how selection schemes affect exploitation and exploration within a search space is crucial to tackling increasingly challenging problems. Here, we introduce an "exploration diagnostic" that diagnoses a selection scheme's capacity for search space exploration. We use our exploration diagnostic to investigate the exploratory capacity of lexicase selection and several of its variants: epsilon lexicase, down-sampled lexicase, cohort lexicase, and novelty-lexicase. We verify that lexicase selection out-explores tournament selection, and we show that lexicase selection's exploratory capacity can be sensitive to the ratio between population size and the number of test cases used for evaluating candidate solutions. Additionally, we find that relaxing lexicase's elitism with epsilon lexicase can further improve exploration. Both down-sampling and cohort lexicase -- two techniques for applying random subsampling to test cases -- degrade lexicase's exploratory capacity; however, we find that cohort partitioning better preserves lexicase's exploratory capacity than down-sampling. Finally, we find evidence that novelty-lexicase's addition of novelty test cases can degrade lexicase's capacity for exploration. Overall, our findings provide hypotheses for further exploration and actionable insights and recommendations for using lexicase selection. Additionally, this work demonstrates the value of selection scheme diagnostics as a complement to more conventional benchmarking approaches to selection scheme analysis.},
	urldate = {2021-08-23},
	journal = {arXiv:2107.09760 [cs]},
	author = {Hernandez, Jose Guadalupe and Lalejini, Alexander and Ofria, Charles},
	month = jul,
	year = {2021},
	note = {arXiv: 2107.09760},
	keywords = {Computer Science - Neural and Evolutionary Computing, ⛔ No DOI found}
}

@article{allen_RaincloudPlotsMultiplatform_2021a,
	title = {Raincloud plots: a multi-platform tool for robust data visualization},
	volume = {4},
	issn = {2398-502X},
	shorttitle = {Raincloud plots},
	url = {https://wellcomeopenresearch.org/articles/4-63/v2},
	doi = {10/ghvbc6},
	abstract = {Across scientific disciplines, there is a rapidly growing recognition of the need for more statistically robust, transparent approaches to data visualization. Complementary to this, many scientists have called for plotting tools that accurately and transparently convey key aspects of statistical effects and raw data with minimal distortion. Previously common approaches, such as plotting conditional mean or median barplots together with error-bars have been criticized for distorting effect size, hiding underlying patterns in the raw data, and obscuring the assumptions upon which the most commonly used statistical tests are based. Here we describe a data visualization approach which overcomes these issues, providing maximal statistical information while preserving the desired ‘inference at a glance’ nature of barplots and other similar visualization devices. These “raincloud plots” can visualize raw data, probability density, and key summary statistics such as median, mean, and relevant confidence intervals in an appealing and flexible format with minimal redundancy. In this tutorial paper, we provide basic demonstrations of the strength of raincloud plots and similar approaches, outline potential modifications for their optimal use, and provide open-source code for their streamlined implementation in R, Python and Matlab (
              https://github.com/RainCloudPlots/RainCloudPlots
              ). Readers can investigate the R and Python tutorials interactively in the browser using Binder by Project Jupyter.},
	language = {en},
	urldate = {2021-07-15},
	journal = {Wellcome Open Research},
	author = {Allen, Micah and Poggiali, Davide and Whitaker, Kirstie and Marshall, Tom Rhys and van Langen, Jordy and Kievit, Rogier A.},
	month = jan,
	year = {2021},
	pages = {63}
}