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@article{Gianoulis:2009aa,
	Abstract = {Recently, approaches have been developed to sample the genetic content of heterogeneous environments (metagenomics). However, by what means these sequences link distinct environmental conditions with specific biological processes is not well understood. Thus, a major challenge is how the usage of particular pathways and subnetworks reflects the adaptation of microbial communities across environments and habitats-i.e., how network dynamics relates to environmental features. Previous research has treated environments as discrete, somewhat simplified classes (e.g., terrestrial vs. marine), and searched for obvious metabolic differences among them (i.e., treating the analysis as a typical classification problem). However, environmental differences result from combinations of many factors, which often vary only slightly. Therefore, we introduce an approach that employs correlation and regression to relate multiple, continuously varying factors defining an environment to the extent of particular microbial pathways present in a geographic site. Moreover, rather than looking only at individual correlations (one-to-one), we adapted canonical correlation analysis and related techniques to define an ensemble of weighted pathways that maximally covaries with a combination of environmental variables (many-to-many), which we term a metabolic footprint. Applied to available aquatic datasets, we identified footprints predictive of their environment that can potentially be used as biosensors. For example, we show a strong multivariate correlation between the energy-conversion strategies of a community and multiple environmental gradients (e.g., temperature). Moreover, we identified covariation in amino acid transport and cofactor synthesis, suggesting that limiting amounts of cofactor can (partially) explain increased import of amino acids in nutrient-limited conditions.},
	Author = {Gianoulis, Tara A and Raes, Jeroen and Patel, Prianka V and Bjornson, Robert and Korbel, Jan O and Letunic, Ivica and Yamada, Takuji and Paccanaro, Alberto and Jensen, Lars J and Snyder, Michael and Bork, Peer and Gerstein, Mark B},
	Date-Added = {2019-01-30 08:38:27 -0500},
	Date-Modified = {2019-01-30 08:38:27 -0500},
	Doi = {10.1073/pnas.0808022106},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Mesh = {Amino Acids; Biosensing Techniques; Genomics; Lipid Metabolism; Microbiology; Polysaccharides},
	Month = {Feb},
	Number = {5},
	Pages = {1374-9},
	Pmc = {PMC2629784},
	Pmid = {19164758},
	Pst = {ppublish},
	Title = {Quantifying environmental adaptation of metabolic pathways in metagenomics},
	Volume = {106},
	Year = {2009},
	Bdsk-Url-1 = {https://doi.org/10.1073/pnas.0808022106}}

@article{Rusch:2007aa,
	Abstract = {The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed "fragment recruitment," addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed "extreme assembly," made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS.},
	Author = {Rusch, Douglas B and Halpern, Aaron L and Sutton, Granger and Heidelberg, Karla B and Williamson, Shannon and Yooseph, Shibu and Wu, Dongying and Eisen, Jonathan A and Hoffman, Jeff M and Remington, Karin and Beeson, Karen and Tran, Bao and Smith, Hamilton and Baden-Tillson, Holly and Stewart, Clare and Thorpe, Joyce and Freeman, Jason and Andrews-Pfannkoch, Cynthia and Venter, Joseph E and Li, Kelvin and Kravitz, Saul and Heidelberg, John F and Utterback, Terry and Rogers, Yu-Hui and Falc{\'o}n, Luisa I and Souza, Valeria and Bonilla-Rosso, Germ{\'a}n and Eguiarte, Luis E and Karl, David M and Sathyendranath, Shubha and Platt, Trevor and Bermingham, Eldredge and Gallardo, Victor and Tamayo-Castillo, Giselle and Ferrari, Michael R and Strausberg, Robert L and Nealson, Kenneth and Friedman, Robert and Frazier, Marvin and Venter, J Craig},
	Date-Added = {2019-01-30 08:29:39 -0500},
	Date-Modified = {2019-01-30 08:29:39 -0500},
	Doi = {10.1371/journal.pbio.0050077},
	Journal = {PLoS Biol},
	Journal-Full = {PLoS biology},
	Mesh = {Computational Biology; Food Chain; Oceans and Seas; Plankton; Species Specificity; Water Microbiology},
	Month = {Mar},
	Number = {3},
	Pages = {e77},
	Pmc = {PMC1821060},
	Pmid = {17355176},
	Pst = {ppublish},
	Title = {The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific},
	Volume = {5},
	Year = {2007},
	Bdsk-Url-1 = {https://doi.org/10.1371/journal.pbio.0050077}}

@article{Pasolli:2019aa,
	Abstract = {The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body sites, ages, countries, and lifestyles. We recapitulated 4,930 species-level genome bins (SGBs), 77% without genomes in public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% of well-assembled samples), expand underrepresented phyla, and are enriched in non-Westernized populations (40% of the total SGBs). We annotated 2.85 M genes in SGBs, many associated with conditions including infant development (94,000) or Westernization (106,000). SGBs and uSGBs permit deeper microbiome analyses and increase the average mappability of metagenomic reads from 67.76% to 87.51% in the gut (median 94.26%) and 65.14% to 82.34% in the mouth. We thus identify thousands of microbial genomes from yet-to-be-named species, expand the pangenomes of human-associated microbes, and allow better exploitation of metagenomic technologies.},
	Author = {Pasolli, Edoardo and Asnicar, Francesco and Manara, Serena and Zolfo, Moreno and Karcher, Nicolai and Armanini, Federica and Beghini, Francesco and Manghi, Paolo and Tett, Adrian and Ghensi, Paolo and Collado, Maria Carmen and Rice, Benjamin L and DuLong, Casey and Morgan, Xochitl C and Golden, Christopher D and Quince, Christopher and Huttenhower, Curtis and Segata, Nicola},
	Date-Added = {2019-01-29 19:45:04 -0500},
	Date-Modified = {2019-01-29 19:45:04 -0500},
	Doi = {10.1016/j.cell.2019.01.001},
	Journal = {Cell},
	Journal-Full = {Cell},
	Keywords = {human microbiome; metagenomic assembly; metagenomic mappability; metagenomic meta-analysis; metagenomics; non-Westernized microbiomes; unexplored microbial diversity},
	Month = {Jan},
	Number = {3},
	Pages = {649-662.e20},
	Pmid = {30661755},
	Pst = {ppublish},
	Title = {Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle},
	Volume = {176},
	Year = {2019},
	Bdsk-Url-1 = {https://doi.org/10.1016/j.cell.2019.01.001}}

@article{Schiffer:2019aa,
	Abstract = {Phase 1 of the Human Microbiome Project (HMP) investigated 18 body subsites of 239 healthy American adults, to produce the first comprehensive reference for the composition and variation of the "healthy" human microbiome. Publicly-available data sets from amplicon sequencing of two 16S ribosomal RNA variable regions, with extensive controlled-access participant data, provide a reference for ongoing microbiome studies. However, utilization of these data sets can be hindered by the complex bioinformatic steps required to access, import, decrypt, and merge the various components in formats suitable for ecological and statistical analysis. The HMP16SData package provides count data for both 16S ribosomal RNA variable regions, integrated with phylogeny, taxonomy, public participant data, and controlled participant data for authorized researchers, using standard integrative Bioconductor data objects. By removing bioinformatic hurdles of data access and management, HMP16SData enables epidemiologists with only basic R skills to quickly analyze HMP data.},
	Author = {Schiffer, Lucas and Azhar, Rimsha and Shepherd, Lori and Ramos, Marcel and Geistlinger, Ludwig and Huttenhower, Curtis and Dowd, Jennifer B and Segata, Nicola and Waldron, Levi},
	Date-Added = {2019-01-26 21:29:49 -0500},
	Date-Modified = {2019-01-26 21:29:49 -0500},
	Doi = {10.1093/aje/kwz006},
	Journal = {Am J Epidemiol},
	Journal-Full = {American journal of epidemiology},
	Month = {Jan},
	Pmid = {30649166},
	Pst = {aheadofprint},
	Title = {HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor},
	Year = {2019},
	Bdsk-Url-1 = {https://doi.org/10.1093/aje/kwz006}}

@article{Pasolli:2017aa,
	Author = {Pasolli, Edoardo and Schiffer, Lucas and Manghi, Paolo and Renson, Audrey and Obenchain, Valerie and Truong, Duy Tin and Beghini, Francesco and Malik, Faizan and Ramos, Marcel and Dowd, Jennifer B and Huttenhower, Curtis and Morgan, Martin and Segata, Nicola and Waldron, Levi},
	Date-Added = {2019-01-26 21:19:00 -0500},
	Date-Modified = {2019-01-26 21:19:00 -0500},
	Doi = {10.1038/nmeth.4468},
	Journal = {Nat Methods},
	Journal-Full = {Nature methods},
	Month = {Oct},
	Number = {11},
	Pages = {1023-1024},
	Pmc = {PMC5862039},
	Pmid = {29088129},
	Pst = {ppublish},
	Title = {Accessible, curated metagenomic data through ExperimentHub},
	Volume = {14},
	Year = {2017},
	Bdsk-Url-1 = {https://doi.org/10.1038/nmeth.4468}}

@article{Integrative-HMP-iHMP-Research-Network-Consortium:2014aa,
	Abstract = {Much has been learned about the diversity and distribution of human-associated microbial communities, but we still know little about the biology of the microbiome, how it interacts with the host, and how the host responds to its resident microbiota. The Integrative Human Microbiome Project (iHMP, http://hmp2.org), the second phase of the NIH Human Microbiome Project, will study these interactions by analyzing microbiome and host activities in longitudinal studies of disease-specific cohorts and by creating integrated data sets of microbiome and host functional properties. These data sets will serve as experimental test beds to evaluate new models, methods, and analyses on the interactions of host and microbiome. Here we describe the three models of microbiome-associated human conditions, on the dynamics of preterm birth, inflammatory bowel disease, and type 2 diabetes, and their underlying hypotheses, as well as the multi-omic data types to be collected, integrated, and distributed through public repositories as a community resource. },
	Author = {{Integrative HMP (iHMP) Research Network Consortium}},
	Date-Added = {2019-01-26 20:42:42 -0500},
	Date-Modified = {2019-01-26 20:42:42 -0500},
	Doi = {10.1016/j.chom.2014.08.014},
	Journal = {Cell Host Microbe},
	Journal-Full = {Cell host \& microbe},
	Mesh = {Bacteria; Bacterial Physiological Phenomena; Diabetes Mellitus, Type 2; Health; Humans; Inflammatory Bowel Diseases; Microbiota; Premature Birth},
	Month = {Sep},
	Number = {3},
	Pages = {276-89},
	Pmc = {PMC5109542},
	Pmid = {25211071},
	Pst = {ppublish},
	Title = {The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease},
	Volume = {16},
	Year = {2014},
	Bdsk-Url-1 = {https://doi.org/10.1016/j.chom.2014.08.014}}

@article{McMurdie:2013aa,
	Abstract = {BACKGROUND: the analysis of microbial communities through dna sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data.
RESULTS: Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research.
CONCLUSIONS: The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.},
	Author = {McMurdie, Paul J and Holmes, Susan},
	Date-Added = {2019-01-26 09:23:40 -0500},
	Date-Modified = {2019-01-26 09:23:40 -0500},
	Doi = {10.1371/journal.pone.0061217},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Mesh = {Data Interpretation, Statistical; Humans; Metagenome; Multivariate Analysis; Phylogeny; Principal Component Analysis; Sequence Analysis, DNA; Software},
	Number = {4},
	Pages = {e61217},
	Pmc = {PMC3632530},
	Pmid = {23630581},
	Pst = {epublish},
	Title = {phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data},
	Volume = {8},
	Year = {2013},
	Bdsk-Url-1 = {https://doi.org/10.1371/journal.pone.0061217}}

@article{Callahan:2016ab,
	Abstract = {High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or OTU composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, whether parametric or nonparametric. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests and nonparametric testing using community networks and the ggnetwork package.},
	Author = {Callahan, Ben J and Sankaran, Kris and Fukuyama, Julia A and McMurdie, Paul J and Holmes, Susan P},
	Date-Added = {2019-01-26 09:19:51 -0500},
	Date-Modified = {2019-01-26 09:19:51 -0500},
	Doi = {10.12688/f1000research.8986.2},
	Journal = {F1000Res},
	Journal-Full = {F1000Research},
	Keywords = {community analysis; microbiome; taxonomy},
	Pages = {1492},
	Pmc = {PMC4955027},
	Pmid = {27508062},
	Pst = {epublish},
	Title = {Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses},
	Volume = {5},
	Year = {2016},
	Bdsk-Url-1 = {https://doi.org/10.12688/f1000research.8986.2}}

@article{Callahan:2016aa,
	Abstract = {We present the open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors (https://github.com/benjjneb/dada2). DADA2 infers sample sequences exactly and resolves differences of as little as 1 nucleotide. In several mock communities, DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.},
	Author = {Callahan, Benjamin J and McMurdie, Paul J and Rosen, Michael J and Han, Andrew W and Johnson, Amy Jo A and Holmes, Susan P},
	Date-Added = {2019-01-25 20:33:23 -0500},
	Date-Modified = {2019-01-25 20:33:23 -0500},
	Doi = {10.1038/nmeth.3869},
	Journal = {Nat Methods},
	Journal-Full = {Nature methods},
	Mesh = {Animals; Cohort Studies; Computational Biology; DNA, Bacterial; False Positive Reactions; Feces; Female; High-Throughput Nucleotide Sequencing; Humans; Lactobacillus; Mice; Microbiota; Pregnancy; RNA, Ribosomal, 16S; Reproducibility of Results; Sequence Analysis, DNA; Software; Vagina},
	Month = {07},
	Number = {7},
	Pages = {581-3},
	Pmc = {PMC4927377},
	Pmid = {27214047},
	Pst = {ppublish},
	Title = {DADA2: High-resolution sample inference from Illumina amplicon data},
	Volume = {13},
	Year = {2016},
	Bdsk-Url-1 = {https://doi.org/10.1038/nmeth.3869}}

@article{Buttigieg:2016aa,
	Abstract = {BACKGROUND: The Environment Ontology (ENVO; http://www.environmentontology.org/ ), first described in 2013, is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. However, the need for environmental semantics is common to a multitude of fields, and ENVO's use has steadily grown since its initial description. We have thus expanded, enhanced, and generalised the ontology to support its increasingly diverse applications.
METHODS: We have updated our development suite to promote expressivity, consistency, and speed: we now develop ENVO in the Web Ontology Language (OWL) and employ templating methods to accelerate class creation. We have also taken steps to better align ENVO with the Open Biological and Biomedical Ontologies (OBO) Foundry principles and interoperate with existing OBO ontologies. Further, we applied text-mining approaches to extract habitat information from the Encyclopedia of Life and automatically create experimental habitat classes within ENVO.
RESULTS: Relative to its state in 2013, ENVO's content, scope, and implementation have been enhanced and much of its existing content revised for improved semantic representation. ENVO now offers representations of habitats, environmental processes, anthropogenic environments, and entities relevant to environmental health initiatives and the global Sustainable Development Agenda for 2030. Several branches of ENVO have been used to incubate and seed new ontologies in previously unrepresented domains such as food and agronomy. The current release version of the ontology, in OWL format, is available at http://purl.obolibrary.org/obo/envo.owl .
CONCLUSIONS: ENVO has been shaped into an ontology which bridges multiple domains including biomedicine, natural and anthropogenic ecology, 'omics, and socioeconomic development. Through continued interactions with our users and partners, particularly those performing data archiving and sythesis, we anticipate that ENVO's growth will accelerate in 2017. As always, we invite further contributions and collaboration to advance the semantic representation of the environment, ranging from geographic features and environmental materials, across habitats and ecosystems, to everyday objects in household settings.},
	Author = {Buttigieg, Pier Luigi and Pafilis, Evangelos and Lewis, Suzanna E and Schildhauer, Mark P and Walls, Ramona L and Mungall, Christopher J},
	Date-Added = {2019-01-25 08:00:40 -0500},
	Date-Modified = {2019-01-25 08:00:40 -0500},
	Doi = {10.1186/s13326-016-0097-6},
	Journal = {J Biomed Semantics},
	Journal-Full = {Journal of biomedical semantics},
	Keywords = {Anthropogenic environment; Ecosystem; Environmental semantics; Habitat; Indoor environment; Ontology; Sustainable development},
	Month = {Sep},
	Number = {1},
	Pages = {57},
	Pmc = {PMC5035502},
	Pmid = {27664130},
	Pst = {epublish},
	Title = {The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation},
	Volume = {7},
	Year = {2016},
	Bdsk-Url-1 = {https://doi.org/10.1186/s13326-016-0097-6}}

@article{Quast:2013aa,
	Abstract = {SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.},
	Author = {Quast, Christian and Pruesse, Elmar and Yilmaz, Pelin and Gerken, Jan and Schweer, Timmy and Yarza, Pablo and Peplies, J{\"o}rg and Gl{\"o}ckner, Frank Oliver},
	Date-Added = {2019-01-25 07:12:01 -0500},
	Date-Modified = {2019-01-25 07:12:01 -0500},
	Doi = {10.1093/nar/gks1219},
	Journal = {Nucleic Acids Res},
	Journal-Full = {Nucleic acids research},
	Mesh = {Archaea; Bacteria; Databases, Nucleic Acid; Eukaryota; Genes, rRNA; High-Throughput Nucleotide Sequencing; Internet; Software},
	Month = {Jan},
	Number = {Database issue},
	Pages = {D590-6},
	Pmc = {PMC3531112},
	Pmid = {23193283},
	Pst = {ppublish},
	Title = {The SILVA ribosomal RNA gene database project: improved data processing and web-based tools},
	Volume = {41},
	Year = {2013},
	Bdsk-Url-1 = {https://doi.org/10.1093/nar/gks1219}}

@article{McDonald:2012aa,
	Abstract = {Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a 'taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408,315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.},
	Author = {McDonald, Daniel and Price, Morgan N and Goodrich, Julia and Nawrocki, Eric P and DeSantis, Todd Z and Probst, Alexander and Andersen, Gary L and Knight, Rob and Hugenholtz, Philip},
	Date-Added = {2019-01-25 06:52:04 -0500},
	Date-Modified = {2019-01-25 06:52:04 -0500},
	Doi = {10.1038/ismej.2011.139},
	Journal = {ISME J},
	Journal-Full = {The ISME journal},
	Mesh = {Archaea; Bacteria; Classification; Databases, Genetic; Metagenomics; Phylogeny; RNA, Ribosomal, 16S; Software},
	Month = {Mar},
	Number = {3},
	Pages = {610-8},
	Pmc = {PMC3280142},
	Pmid = {22134646},
	Pst = {ppublish},
	Title = {An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea},
	Volume = {6},
	Year = {2012},
	Bdsk-Url-1 = {https://doi.org/10.1038/ismej.2011.139}}

@article{Amir2017,
	Author = {Amnon Amir and Daniel McDonald and Jose A. Navas-Molina and Evguenia Kopylova and James T. Morton and Zhenjiang Zech Xu and Eric P. Kightley and Luke R. Thompson and Embriette R. Hyde and Antonio Gonzalez and Rob Knight},
	Date-Added = {2019-01-25 06:41:27 -0500},
	Date-Modified = {2019-01-25 06:41:27 -0500},
	Doi = {10.1128/msystems.00191-16},
	Editor = {Jack A. Gilbert},
	Journal = {{mSystems}},
	Month = {mar},
	Number = {2},
	Publisher = {American Society for Microbiology},
	Title = {Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns},
	Url = {https://doi.org/10.1128/msystems.00191-16},
	Volume = {2},
	Year = {2017},
	Bdsk-Url-1 = {https://doi.org/10.1128/msystems.00191-16}}

@article{Caporaso:2011aa,
	Abstract = {The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known "mock communities" at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.},
	Author = {Caporaso, J Gregory and Lauber, Christian L and Walters, William A and Berg-Lyons, Donna and Lozupone, Catherine A and Turnbaugh, Peter J and Fierer, Noah and Knight, Rob},
	Date-Added = {2019-01-25 06:29:36 -0500},
	Date-Modified = {2019-01-25 06:29:36 -0500},
	Doi = {10.1073/pnas.1000080107},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Mesh = {Bacteria; Cluster Analysis; DNA Barcoding, Taxonomic; Environment; Genetic Variation; High-Throughput Nucleotide Sequencing; RNA, Ribosomal, 16S; Reproducibility of Results; Sequence Analysis, DNA; Software; Species Specificity},
	Month = {Mar},
	Pages = {4516-22},
	Pmc = {PMC3063599},
	Pmid = {20534432},
	Pst = {ppublish},
	Title = {Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample},
	Volume = {108 Suppl 1},
	Year = {2011},
	Bdsk-Url-1 = {https://doi.org/10.1073/pnas.1000080107}}

@article{Olsen:1986aa,
	Author = {Olsen, G J and Lane, D J and Giovannoni, S J and Pace, N R and Stahl, D A},
	Date-Added = {2019-01-25 06:23:55 -0500},
	Date-Modified = {2019-01-25 06:23:55 -0500},
	Doi = {10.1146/annurev.mi.40.100186.002005},
	Journal = {Annu Rev Microbiol},
	Journal-Full = {Annual review of microbiology},
	Mesh = {Bacteria; Base Sequence; Chromosome Mapping; DNA, Recombinant; Nucleic Acid Hybridization; Phylogeny; RNA, Bacterial; RNA, Ribosomal},
	Pages = {337-65},
	Pmid = {2430518},
	Pst = {ppublish},
	Title = {Microbial ecology and evolution: a ribosomal RNA approach},
	Volume = {40},
	Year = {1986},
	Bdsk-Url-1 = {https://doi.org/10.1146/annurev.mi.40.100186.002005}}

@article{Thompson:2017aa,
	Abstract = {Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.},
	Author = {Thompson, Luke R and Sanders, Jon G and McDonald, Daniel and Amir, Amnon and Ladau, Joshua and Locey, Kenneth J and Prill, Robert J and Tripathi, Anupriya and Gibbons, Sean M and Ackermann, Gail and Navas-Molina, Jose A and Janssen, Stefan and Kopylova, Evguenia and V{\'a}zquez-Baeza, Yoshiki and Gonz{\'a}lez, Antonio and Morton, James T and Mirarab, Siavash and Zech Xu, Zhenjiang and Jiang, Lingjing and Haroon, Mohamed F and Kanbar, Jad and Zhu, Qiyun and Jin Song, Se and Kosciolek, Tomasz and Bokulich, Nicholas A and Lefler, Joshua and Brislawn, Colin J and Humphrey, Gregory and Owens, Sarah M and Hampton-Marcell, Jarrad and Berg-Lyons, Donna and McKenzie, Valerie and Fierer, Noah and Fuhrman, Jed A and Clauset, Aaron and Stevens, Rick L and Shade, Ashley and Pollard, Katherine S and Goodwin, Kelly D and Jansson, Janet K and Gilbert, Jack A and Knight, Rob and {Earth Microbiome Project Consortium}},
	Date-Added = {2019-01-25 06:23:19 -0500},
	Date-Modified = {2019-01-25 06:23:19 -0500},
	Doi = {10.1038/nature24621},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Animals; Archaea; Bacteria; Biodiversity; Earth (Planet); Ecology; Gene Dosage; Geographic Mapping; Humans; Microbiota; Plants; RNA, Ribosomal, 16S},
	Month = {11},
	Number = {7681},
	Pages = {457-463},
	Pmc = {PMC6192678},
	Pmid = {29088705},
	Pst = {ppublish},
	Title = {A communal catalogue reveals Earth's multiscale microbial diversity},
	Volume = {551},
	Year = {2017},
	Bdsk-Url-1 = {https://doi.org/10.1038/nature24621}}

@article{Gentleman:2004aa,
	Abstract = {The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.},
	Author = {Gentleman, Robert C and Carey, Vincent J and Bates, Douglas M and Bolstad, Ben and Dettling, Marcel and Dudoit, Sandrine and Ellis, Byron and Gautier, Laurent and Ge, Yongchao and Gentry, Jeff and Hornik, Kurt and Hothorn, Torsten and Huber, Wolfgang and Iacus, Stefano and Irizarry, Rafael and Leisch, Friedrich and Li, Cheng and Maechler, Martin and Rossini, Anthony J and Sawitzki, Gunther and Smith, Colin and Smyth, Gordon and Tierney, Luke and Yang, Jean Y H and Zhang, Jianhua},
	Date-Added = {2019-01-24 08:22:03 -0500},
	Date-Modified = {2019-01-24 08:22:03 -0500},
	Doi = {10.1186/gb-2004-5-10-r80},
	Journal = {Genome Biol},
	Journal-Full = {Genome biology},
	Mesh = {Computational Biology; Internet; Reproducibility of Results; Software},
	Number = {10},
	Pages = {R80},
	Pmc = {PMC545600},
	Pmid = {15461798},
	Pst = {ppublish},
	Title = {Bioconductor: open software development for computational biology and bioinformatics},
	Volume = {5},
	Year = {2004},
	Bdsk-Url-1 = {https://doi.org/10.1186/gb-2004-5-10-r80}}

@article{Gonzalez:2018aa,
	Abstract = {Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be fully understood, data must be aggregated into meta-analyses. This makes it possible to generate new hypotheses by finding features that are reproducible across biospecimens and data layers. Qiita dramatically accelerates such integration tasks in a web-based microbiome-comparison platform, which we demonstrate with Human Microbiome Project and Integrative Human Microbiome Project (iHMP) data.},
	Author = {Gonzalez, Antonio and Navas-Molina, Jose A and Kosciolek, Tomasz and McDonald, Daniel and V{\'a}zquez-Baeza, Yoshiki and Ackermann, Gail and DeReus, Jeff and Janssen, Stefan and Swafford, Austin D and Orchanian, Stephanie B and Sanders, Jon G and Shorenstein, Joshua and Holste, Hannes and Petrus, Semar and Robbins-Pianka, Adam and Brislawn, Colin J and Wang, Mingxun and Rideout, Jai Ram and Bolyen, Evan and Dillon, Matthew and Caporaso, J Gregory and Dorrestein, Pieter C and Knight, Rob},
	Date-Added = {2019-01-24 07:08:15 -0500},
	Date-Modified = {2019-01-24 07:08:15 -0500},
	Doi = {10.1038/s41592-018-0141-9},
	Journal = {Nat Methods},
	Journal-Full = {Nature methods},
	Month = {Oct},
	Number = {10},
	Pages = {796-798},
	Pmc = {PMC6235622},
	Pmid = {30275573},
	Pst = {ppublish},
	Title = {Qiita: rapid, web-enabled microbiome meta-analysis},
	Volume = {15},
	Year = {2018},
	Bdsk-Url-1 = {https://doi.org/10.1038/s41592-018-0141-9}}

@article{Duvallet:2017aa,
	Abstract = {Hundreds of clinical studies have demonstrated associations between the human microbiome and disease, yet fundamental questions remain on how we can generalize this knowledge. Results from individual studies can be inconsistent, and comparing published data is further complicated by a lack of standard processing and analysis methods. Here we introduce the MicrobiomeHD database, which includes 28 published case-control gut microbiome studies spanning ten diseases. We perform a cross-disease meta-analysis of these studies using standardized methods. We find consistent patterns characterizing disease-associated microbiome changes. Some diseases are associated with over 50 genera, while most show only 10-15 genus-level changes. Some diseases are marked by the presence of potentially pathogenic microbes, whereas others are characterized by a depletion of health-associated bacteria. Furthermore, we show that about half of genera associated with individual studies are bacteria that respond to more than one disease. Thus, many associations found in case-control studies are likely not disease-specific but rather part of a non-specific, shared response to health and disease.},
	Author = {Duvallet, Claire and Gibbons, Sean M and Gurry, Thomas and Irizarry, Rafael A and Alm, Eric J},
	Date-Added = {2019-01-24 07:04:07 -0500},
	Date-Modified = {2019-01-24 07:04:07 -0500},
	Doi = {10.1038/s41467-017-01973-8},
	Journal = {Nat Commun},
	Journal-Full = {Nature communications},
	Mesh = {Bacteria; Case-Control Studies; Feces; Gastrointestinal Diseases; Gastrointestinal Microbiome; Gastrointestinal Tract; Humans; Population Density; Population Dynamics},
	Month = {12},
	Number = {1},
	Pages = {1784},
	Pmc = {PMC5716994},
	Pmid = {29209090},
	Pst = {epublish},
	Title = {Meta-analysis of gut microbiome studies identifies disease-specific and shared responses},
	Volume = {8},
	Year = {2017},
	Bdsk-Url-1 = {https://doi.org/10.1038/s41467-017-01973-8}}

@article{McDonald:2018aa,
	Abstract = {Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes compared to environmental samples; demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations; uncover new molecules and kinds of molecular communities in the human stool metabolome; and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education. IMPORTANCE We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on hundreds of samples.},
	Author = {McDonald, Daniel and Hyde, Embriette and Debelius, Justine W and Morton, James T and Gonzalez, Antonio and Ackermann, Gail and Aksenov, Alexander A and Behsaz, Bahar and Brennan, Caitriona and Chen, Yingfeng and DeRight Goldasich, Lindsay and Dorrestein, Pieter C and Dunn, Robert R and Fahimipour, Ashkaan K and Gaffney, James and Gilbert, Jack A and Gogul, Grant and Green, Jessica L and Hugenholtz, Philip and Humphrey, Greg and Huttenhower, Curtis and Jackson, Matthew A and Janssen, Stefan and Jeste, Dilip V and Jiang, Lingjing and Kelley, Scott T and Knights, Dan and Kosciolek, Tomasz and Ladau, Joshua and Leach, Jeff and Marotz, Clarisse and Meleshko, Dmitry and Melnik, Alexey V and Metcalf, Jessica L and Mohimani, Hosein and Montassier, Emmanuel and Navas-Molina, Jose and Nguyen, Tanya T and Peddada, Shyamal and Pevzner, Pavel and Pollard, Katherine S and Rahnavard, Gholamali and Robbins-Pianka, Adam and Sangwan, Naseer and Shorenstein, Joshua and Smarr, Larry and Song, Se Jin and Spector, Timothy and Swafford, Austin D and Thackray, Varykina G and Thompson, Luke R and Tripathi, Anupriya and V{\'a}zquez-Baeza, Yoshiki and Vrbanac, Alison and Wischmeyer, Paul and Wolfe, Elaine and Zhu, Qiyun and {American Gut Consortium } and Knight, Rob},
	Date = {2018 May-Jun},
	Date-Added = {2019-01-24 07:00:59 -0500},
	Date-Modified = {2019-01-24 07:00:59 -0500},
	Doi = {10.1128/mSystems.00031-18},
	Journal = {mSystems},
	Journal-Full = {mSystems},
	Number = {3},
	Pmc = {PMC5954204},
	Pmid = {29795809},
	Pst = {epublish},
	Title = {American Gut: an Open Platform for Citizen Science Microbiome Research},
	Volume = {3},
	Year = {2018},
	Bdsk-Url-1 = {https://doi.org/10.1128/mSystems.00031-18}}


text:
@InProceedings{conf/robocup/BaiWC12,
  title =	"Concurrent Hierarchical Reinforcement Learning for {RoboCup Keepaway}",
  author =	"Aijun Bai and Stuart Russell and Xiaoping Chen",
  publisher =	"Springer",
  year = 	"2017",
  booktitle =	"RoboCup-2017: Robot World Cup XX",
  series =	"Lecture Notes in Computer Science",
}

license_type: permissive

branch_name: refs/heads/master

extension: bib


text:
@Article{ekho,
	author = {Hester, Josiah and Sitanayah, Lanny and Scott, Timothy and Sorber, Jacob},
	title = {Realistic and Repeatable Emulation of Energy Harvesting Environments},
	journal = {ACM Trans. Sen. Netw.},
	year = {2017},
	volume = {13},
	number = {2},
	pages = {16:1--16:33},
	month = apr
}

@INPROCEEDINGS{FIT-IoT,
	author={C. Adjih and E. Baccelli and E. Fleury and G. Harter and N. Mitton and T. Noel and R. Pissard-Gibollet and F. Saint-Marcel and G. Schreiner and J. Vandaele and T. Watteyne},
	title={FIT IoT-LAB: A large scale open experimental IoT testbed},
	booktitle={2015 IEEE 2nd World Forum on Internet of Things (WF-IoT)},
	year={2015},
	volume={},
	number={},
	pages={459-464},
	month={Dec}
}

@INPROCEEDINGS{flocklab,
	author={R. Lim and F. Ferrari and M. Zimmerling and C. Walser and P. Sommer and J. Beutel},
	booktitle={2013 ACM/IEEE International Conference on Information Processing in Sensor Networks (IPSN)},
	title={FlockLab: A testbed for distributed, synchronized tracing and profiling of wireless embedded systems},
	year={2013},
	volume={},
	number={},
	pages={153-165},
	month={April}
}

@InProceedings{indriya2,
	author={Appavoo, Paramasiven
	and William, Ebram Kamal
	and Chan, Mun Choon
	and Mohammad, Mobashir},
	editor={Gao, Honghao
	and Yin, Yuyu
	and Yang, Xiaoxian
	and Miao, Huaikou},
	title={Indriya2: A Heterogeneous Wireless Sensor Network (WSN) Testbed"},
	booktitle={Testbeds and Research Infrastructures for the Development of Networks and Communications"},
	year={2019},
	publisher={Springer International Publishing},
	address={Cham},
	pages={3--19}
}

@inproceedings{flicker,
	author = {Hester, Josiah and Sorber, Jacob},
	title = {Flicker: Rapid Prototyping for the Batteryless Internet-of-Things},
	booktitle = {Proceedings of the 15th ACM Conference on Embedded Network Sensor Systems},
	series = {SenSys '17},
	year = {2017},
	isbn = {978-1-4503-5459-2},
	location = {Delft, Netherlands},
	pages = {19:1--19:13},
	articleno = {19},
	numpages = {13},
	url = {http://doi.acm.org/10.1145/3131672.3131674},
	doi = {10.1145/3131672.3131674},
	acmid = {3131674},
	publisher = {ACM},
	address = {New York, NY, USA},
	keywords = {Batteryless, Energy Harvesting, Flicker, Intermittent, Wearable},
}

@article{request,
	author    = {Henko Aantjes and
	Amjad Yousef Majid and
	Przemyslaw Pawelczak},
	title     = {A Testbed for Transiently Powered Computers},
	journal   = {CoRR},
	volume    = {abs/1606.07623},
	year      = {2016},
	url       = {http://arxiv.org/abs/1606.07623},
	archivePrefix = {arXiv},
	eprint    = {1606.07623},
	timestamp = {Mon, 13 Aug 2018 16:48:24 +0200},
	biburl    = {https://dblp.org/rec/bib/journals/corr/AantjesMP16},
	bibsource = {dblp computer science bibliography, https://dblp.org}
}

@ARTICLE{edb,
	author={A. Colin and G. Harvey and A. P. Sample and B. Lucia},
	journal={IEEE Micro},
	title={An Energy-Aware Debugger for Intermittently Powered Systems},
	year={2017},
	volume={37},
	number={3},
	pages={116-125},
	keywords={computer debugging;energy harvesting;power aware computing;energy-aware debugger;intermittently powered systems;energy-harvesting technology;energy-interference-free debugger;EDB;intermittence bugs;debugging tasks;RF-powered energy-harvesting device;Debugging;Monitoring;Software engineering;Energy states;Computer bugs;Energy harvesting;Capacitors;energy harvesting;intermittent computing;memory consistency;embedded systems;testing;debugging},
	doi={10.1109/MM.2017.48},
	ISSN={0272-1732},
	month={},}

@article{wisp,
	title={Design of an RFID-based battery-free programmable sensing platform},
	author={Sample, Alanson P and Yeager, Daniel J and Powledge, Pauline S and Mamishev, Alexander V and Smith, Joshua R and others},
	journal={IEEE transactions on instrumentation and measurement},
	volume={57},
	number={11},
	pages={2608},
	year={2008}
}

@article{moo,
	title={Moo: A batteryless computational RFID and sensing platform},
	author={Zhang, Hong and Gummeson, Jeremy and Ransford, Benjamin and Fu, Kevin},
	journal={University of Massachusetts Computer Science Technical Report UM-CS-2011-020},
	year={2011}
}

@inproceedings{capybara,
	title={A Reconfigurable Energy Storage Architecture for Energy-harvesting Devices},
	author={Colin, Alexei and Ruppel, Emily and Lucia, Brandon},
	booktitle={Proceedings of the Twenty-Third International Conference on Architectural Support for Programming Languages and Operating Systems},
	pages={767--781},
	year={2018},
	organization={ACM}
}

@inproceedings{pible,
	title={Pible: battery-free mote for perpetual indoor BLE applications},
	author={Fraternali, Francesco and Balaji, Bharathan and Agarwal, Yuvraj and Benini, Luca and Gupta, Rajesh},
	booktitle={Proceedings of the 5th Conference on Systems for Built Environments},
	pages={168--171},
	year={2018},
	organization={ACM}
}

@inproceedings{customsoc,
	title={A battery-less 507nw soc with integrated platform power manager and sip interfaces},
	author={Yahya, Farah and Lukas, Christopher J and Breiholz, Jacob and Roy, Abhishek and Patel, Harsh N and Liu, NingXi and Chen, Xing and Kosari, Avish and Li, Shuo and Akella, Divya and others},
	booktitle={VLSI Circuits, 2017 Symposium on},
	pages={C338--C339},
	year={2017},
	organization={IEEE}
}

@inproceedings{monjolo,
	title={Monjolo: An energy-harvesting energy meter architecture},
	author={DeBruin, Samuel and Campbell, Bradford and Dutta, Prabal},
	booktitle={Proceedings of the 11th ACM Conference on Embedded Networked Sensor Systems},
	pages={18},
	year={2013},
	organization={ACM}
}

@article{energywsn,
	title={Energy harvesting in wireless sensor networks: A comprehensive review},
	author={Shaikh, Faisal Karim and Zeadally, Sherali},
	journal={Renewable and Sustainable Energy Reviews},
	volume={55},
	pages={1041--1054},
	year={2016},
	publisher={Elsevier}
}

@article{aerol,
	title={Self-powered wireless sensor node enabled by an aerosol-deposited PZT flexible energy harvester},
	author={Hwang, Geon-Tae and Annapureddy, Venkateswarlu and Han, Jae Hyun and Joe, Daniel J and Baek, Changyeon and Park, Dae Yong and Kim, Dong Hyun and Park, Jung Hwan and Jeong, Chang Kyu and Park, Kwi-Il and others},
	journal={Advanced Energy Materials},
	volume={6},
	number={13},
	pages={1600237},
	year={2016},
	publisher={Wiley Online Library}
}

@article{spwts,
	title={A novel self-powered wireless temperature sensor based on thermoelectric generators},
	author={Shi, Yongming and Wang, Yao and Deng, Yuan and Gao, Hongli and Lin, Zhen and Zhu, Wei and Ye, Huihong},
	journal={Energy Conversion and Management},
	volume={80},
	pages={110--116},
	year={2014},
	publisher={Elsevier}
}

@article{tpcthesis,
	title={System support for transiently-powered embedded sensing systems},
	author={Bhatti, Naveed Anwar},
	year={2018},
	publisher={Italy},
	type={PhD thesis},
	school={Politecnico di Milano}
}

@article{sudevalayam2011energy,
	title={Energy harvesting sensor nodes: Survey and implications},
	author={Sudevalayam, Sujesha and Kulkarni, Purushottam},
	journal={IEEE Communications Surveys \& Tutorials},
	volume={13},
	number={3},
	pages={443--461},
	year={2011},
	publisher={IEEE}
}

@article{kim2014ambient,
	title={Ambient RF energy-harvesting technologies for self-sustainable standalone wireless sensor platforms},
	author={Kim, Sangkil and Vyas, Rushi and Bito, Jo and Niotaki, Kyriaki and Collado, Ana and Georgiadis, Apostolos and Tentzeris, Manos M},
	journal={Proceedings of the IEEE},
	volume={102},
	number={11},
	pages={1649--1666},
	year={2014},
	publisher={IEEE}
}

@inproceedings{talla2015powering,
	title={Powering the next billion devices with Wi-Fi},
	author={Talla, Vamsi and Kellogg, Bryce and Ransford, Benjamin and Naderiparizi, Saman and Gollakota, Shyamnath and Smith, Joshua R},
	booktitle={Proceedings of the 11th ACM Conference on Emerging Networking Experiments and Technologies},
	pages={4},
	year={2015},
	organization={ACM}
}

@article{akhtar2015energy,
	title={Energy replenishment using renewable and traditional energy resources for sustainable wireless sensor networks: A review},
	author={Akhtar, Fayaz and Rehmani, Mubashir Husain},
	journal={Renewable and Sustainable Energy Reviews},
	volume={45},
	pages={769--784},
	year={2015},
	publisher={Elsevier}
}

@article{bhatti2016energy,
	title={Energy harvesting and wireless transfer in sensor network applications: Concepts and experiences},
	author={Bhatti, Naveed Anwar and Alizai, Muhammad Hamad and Syed, Affan A and Mottola, Luca},
	journal={ACM Transactions on Sensor Networks (TOSN)},
	volume={12},
	number={3},
	pages={24},
	year={2016},
	publisher={ACM}
}

@inproceedings{ransford2011mementos,
	title={Mementos: System support for long-running computation on RFID-scale devices},
	author={Ransford, Benjamin and Sorber, Jacob and Fu, Kevin},
	booktitle={ACM SIGARCH Computer Architecture News},
	volume={39},
	number={1},
	pages={159--170},
	year={2011},
	organization={ACM}
}

@article{lucia2015simpler,
	title={A simpler, safer programming and execution model for intermittent systems},
	author={Lucia, Brandon and Ransford, Benjamin},
	journal={ACM SIGPLAN Notices},
	volume={50},
	number={6},
	pages={575--585},
	year={2015},
	publisher={ACM}
}

license: MIT


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  background-color: #fff;
  background-image: -webkit-linear-gradient(bottom left, #efefef 25%, transparent 25%, transparent 75%, #efefef 75%, #efefef),-webkit-linear-gradient(bottom left, #efefef 25%, transparent 25%, transparent 75%, #efefef 75%, #efefef);
  background-image: -moz-linear-gradient(bottom left, #efefef 25%, transparent 25%, transparent 75%, #efefef 75%, #efefef),-moz-linear-gradient(bottom left, #efefef 25%, transparent 25%, transparent 75%, #efefef 75%, #efefef);
  background-image: -o-linear-gradient(bottom left, #efefef 25%, transparent 25%, transparent 75%, #efefef 75%, #efefef),-o-linear-gradient(bottom left, #efefef 25%, transparent 25%, transparent 75%, #efefef 75%, #efefef);
  background-image: linear-gradient(to top right, #efefef 25%, transparent 25%, transparent 75%, #efefef 75%, #efefef),linear-gradient(to top right, #efefef 25%, transparent 25%, transparent 75%, #efefef 75%, #efefef);
  background-position: 0 0,10px 10px;
  -webkit-background-size: 21px 21px;
  background-size: 21px 21px;
}
.image-aside{
  overflow: hidden;
  position: absolute;
  right: 30px;
  left:30px;
  top:70px;
  bottom:40px;
  text-align: center;
}
.image-aside .image-wrap{
  position: absolute;
  left: 0;
  top: 0;
  -webkit-touch-callout: none;
  -webkit-user-select: none;
  -khtml-user-select: none;
  -moz-user-select: none;
  -ms-user-select: none;
  user-select: none;
  box-shadow: 0 3px 5px -2px rgba(0,0,0,.25);
  background-size: cover;
}
.image-mask{
  position: absolute;
  left: 0;
  top: 0;
  width:100%;
  height: 100%;
}
.image-mask .mask {
  position: absolute;
  background-color: rgba(255,255,255,.6);
}
.crop-box{
  z-index: 2000;
  box-sizing: border-box;
  position: absolute;
  background: none;
  cursor: move;
  width:100px;
  height: 100px;
  border:1px solid rgba(255,255,255, .95);
}
.crop-box:after,
.crop-box:before{
  content: '';
  display: block;
  opacity: 0;
  position: absolute;
  left: 33.3333%;
  top: 0;
  width: 33.334%;
  height: 100%;
  background-color: transparent;
  border-color: rgba(255,255,255,.7);
  border-style: solid;
  border-width: 0;
}
.crop-box:active::before,
.crop-box:active::after{
  opacity: 1;
}
.crop-box:before{
  border-left-width: 1px;
  border-right-width: 1px;
}
.crop-box:after{
  top: 33.3333%;
  left: 0;
  height: 33.3334%;
  width: 100%;
  border-top-width: 1px;
  border-bottom-width: 1px;
}
.crop-box .g-resize{
  display: inline-block;
  z-index: 1910;
  position: absolute;
  bottom: -8px;
  right: -8px;
  width: 16px;
  height: 16px;
  cursor: se-resize;
  border-radius: 10px;
  background-color: #fff;
  box-shadow: 0 2px 4px -2px rgba(0,0,0,.25);
}

.g-resize-bar{
   position: absolute;
   bottom: 0px;
   margin: 17px auto;
   height: 6px;
   border-radius: 3px;
   width:200px;
   margin-left: -100px;
   left: 50%;
   background-color: #9cd6fd;
   box-shadow: 0 2px 3px -1px rgba(0,0,0,.3);
 }
 .g-resize-bar .g-resize-highlight{
   position: absolute;
   left: 0;
   top:0;
   height: 6px;
   background-color: #3498db;
   border-radius: 3px;
 }
 .g-resize-bar .circle-btn{
   display: block;
   position: absolute;
   left:0;
   top: -5px;
   width: 14px;
   height: 14px;
   margin-left: -7px;
   background-color: #fff;
   border-radius: 7px;
   box-shadow: 0 2px 3px -2px rgba(0,0,0,.6), 0 -2px 3px -2px rgba(0,0,0,.55);
   border-width: 0;
 }

repository: Vanthink-UED/react-core-image-upload

repo_name: Vanthink-UED/react-core-image-upload

gha_license_id: MIT

gha_language: JavaScript

extension: css


text:
include(RunCMake)

run_cmake(COMPILE_DEFINITIONS)
run_cmake(COMPILE_FEATURES)
run_cmake(COMPILE_OPTIONS)
run_cmake(INCLUDE_DIRECTORIES)
run_cmake(LINK_LIBRARIES)
run_cmake(SOURCES)
run_cmake(USER_PROP)

extension: cmake


text:
DESCRIPTION = "Music Player Daemon"
LICENSE = "GPLv2"
LIC_FILES_CHKSUM = "file://COPYING;md5=751419260aa954499f7abaabaa882bbe"
HOMEPAGE ="http://sourceforge.net/projects/musicpd"

DEPENDS = "alsa-lib libsamplerate0 libsndfile1 libvorbis libogg faad2 ffmpeg curl sqlite bzip2 pulseaudio"

PR = "r4"

SRC_URI = " \
    ${SOURCEFORGE_MIRROR}/musicpd/${PN}/${PV}/${PN}-${PV}.tar.bz2 \
    file://mpd.conf.in \
"

SRC_URI[md5sum] = "da3f3d6617a877192db4c6f53504cd38"
SRC_URI[sha256sum] = "b18cdb1b779ca2ab323e212a0af4a567b7da4881a4e96868a8979bdfdbe7c2e8"

inherit autotools useradd systemd

EXTRA_OECONF = "enable_bzip2=yes"
EXTRA_OECONF += "${@base_contains('DISTRO_FEATURES', 'systemd', '--with-systemdsystemunitdir=${systemd_unitdir}/system/', '--without-systemdsystemunitdir', d)}"

PACKAGECONFIG[mad] = "--enable-mad,--disable-mad,libmad"
PACKAGECONFIG[id3tag] = "--enable-id3,--disable-id3,libid3tag"
PACKAGECONFIG[lame] = "--enable-lame-encoder,--disable-lame-encoder,lame"

do_install_append() {
    install -d ${D}/${localstatedir}/lib/mpd/music
    chmod 775 ${D}/${localstatedir}/lib/mpd/music
    install -d ${D}/${localstatedir}/lib/mpd/playlists
    chown -R mpd ${D}/${localstatedir}/lib/mpd
    chown mpd:mpd ${D}/${localstatedir}/lib/mpd/music

    install -d ${D}/${sysconfdir}
    install -m 644 ${WORKDIR}/mpd.conf.in ${D}/${sysconfdir}/mpd.conf
    sed -i \
        -e 's|%music_directory%|${localstatedir}/lib/mpd/music|' \
        -e 's|%playlist_directory%|${localstatedir}/lib/mpd/playlists|' \
        -e 's|%db_file%|${localstatedir}/lib/mpd/mpd.db|' \
        -e 's|%log_file%|${localstatedir}/log/mpd.log|' \
        -e 's|%state_file%|${localstatedir}/lib/mpd/state|' \
        ${D}/${sysconfdir}/mpd.conf

    if [ -e ${D}/${systemd_unitdir}/system/mpd.service ] ; then
        sed -i \
            's|^ExecStart=.*|ExecStart=${bindir}/mpd --no-daemon|' \
            ${D}/${systemd_unitdir}/system/mpd.service
    fi
}

RPROVIDES_${PN} += "${PN}-systemd"
RREPLACES_${PN} += "${PN}-systemd"
RCONFLICTS_${PN} += "${PN}-systemd"
SYSTEMD_SERVICE_${PN} = "mpd.service"

USERADD_PACKAGES = "${PN}"
USERADD_PARAM_${PN} = " \
    --system --no-create-home \
    --home ${localstatedir}/lib/mpd \
    --groups audio \
    --user-group mpd"

repository: ExorEmbedded/exor-workspace

repo_name: ExorEmbedded/exor-workspace

gha_language: Python

extension: bb


text:
@Conference{2014RojasEdge,
  author = {Carlos Rojas, Alex Tsui, Stewart He, Lance Simons, Shengren Li},
  title = {Edge Length Interpolation},
  year = {2014},
  address = {Hong Kong},
  month = {October~26-28,2014},
  url = {http://solidmodeling.org/2014/program.html}
}

branch_name: refs/heads/main


text:
@InProceedings{juhwang13,
  pdf = {http://jmlr.org/proceedings/papers/v28/juhwang13.pdf},
  number = {3},
  section = {cycle-3},
  title = {Analogy-preserving Semantic Embedding for Visual Object Categorization},
  author = {Ju Hwang, Sung and Grauman, Kristen and Sha, Fei},
  pages = {639-647},
  abstract = {In multi-class categorization tasks, knowledge about the classes' semantic relationships can provide valuable information beyond the class labels themselves.  However, existing techniques focus on preserving the semantic distances between classes (e.g., according to a given object taxonomy for visual recognition), limiting the influence to pairwise structures.  We propose to model \emph{analogies} that reflect the relationships between multiple pairs of classes simultaneously, in the form ``$p$ is to $q$, as $r$ is to $s$"".  We translate semantic analogies into higher-order geometric constraints called \emph{analogical parallelograms}, and use them in a novel convex regularizer for a discriminatively learned label embedding.   Furthermore, we show how to discover analogies from attribute-based class descriptions, and how to prioritize those likely to reduce inter-class confusion.  Evaluating our Analogy-preserving Semantic Embedding (ASE) on two visual recognition datasets, we demonstrate clear improvements over existing approaches, both in terms of recognition accuracy and analogy completion.  },
}

repository: mreid/papersite

repo_name: mreid/papersite

gha_language: TeX


text:
DESCRIPTION = "A friendly program that prints Hello World!"
PRIORITY = "optional"
SECTION = "examples"

LICENSE = "GPLv2"
LIC_FILES_CHKSUM = "file://${COMMON_LICENSE_DIR}/GPL-2.0;md5=801f80980d171dd6425610833a22dbe6"

SRC_URI = "file://helloworld.c"

S = "${WORKDIR}"

do_compile() {
	${CC} ${CFLAGS} ${LDFLAGS} helloworld.c -o helloworld
}

do_install() {
	install -d ${D}${bindir}
	install -m 0755 helloworld ${D}${bindir}
}

gha_language: C


text:
SUMMARY = "A high-level Python Web framework"
DESCRIPTION = "A high-level Python Web framework that encourages rapid \
development and clean, pragmatic design."
HOMEPAGE = "http://www.djangoproject.com/"
SECTION = "devel/python"

LICENSE = "BSD-3-Clause"
LIC_FILES_CHKSUM = "file://LICENSE;md5=f09eb47206614a4954c51db8a94840fa"

SRC_URI[md5sum] = "858e5417a10ce565a15d6e4a2ea0ee37"
SRC_URI[sha256sum] = "861db7f82436ab43e1411832ed8dca81fc5fc0f7c2039c7e07a080a63092fb44"

PYPI_PACKAGE = "Django"

UPSTREAM_CHECK_REGEX = "(?P<pver>1(\.\d+)+)"

FILES:${PN} += "${datadir}/django"

inherit pypi setuptools

RDEPENDS:${PN} += "\
    ${PYTHON_PN}-argparse \
    ${PYTHON_PN}-compression \
    ${PYTHON_PN}-ctypes \
    ${PYTHON_PN}-datetime \
    ${PYTHON_PN}-email \
    ${PYTHON_PN}-html \
    ${PYTHON_PN}-json \
    ${PYTHON_PN}-logging \
    ${PYTHON_PN}-multiprocessing \
    ${PYTHON_PN}-netserver \
    ${PYTHON_PN}-numbers \
    ${PYTHON_PN}-pkgutil \
    ${PYTHON_PN}-pytz \
    ${PYTHON_PN}-subprocess \
    ${PYTHON_PN}-threading \
    ${PYTHON_PN}-unixadmin \
    ${PYTHON_PN}-xml \
    ${PYTHON_PN}-zlib \
"

BBCLASSEXTEND = "native nativesdk"

SKIP_RECIPE[python-django] ?= "${@bb.utils.contains('I_SWEAR_TO_MIGRATE_TO_PYTHON3', 'yes', '', 'python2 is out of support for long time, read https://www.python.org/doc/sunset-python-2/ https://python3statement.org/ and if you really have to temporarily use this, then set I_SWEAR_TO_MIGRATE_TO_PYTHON3 to "yes"', d)}"

branch_name: refs/heads/jansa/master

gha_language: BitBake


text:
@inproceedings{Lee:2014:ETP:2559206.2581370,
 author = {Lee, Myungho and Kim, Kangsoo and Rho, Hyunghwan and Kim, Si Jung},
 title = {Empa Talk: A Physiological Data Incorporated Human-computer Interactions},
 booktitle = {CHI '14 Extended Abstracts on Human Factors in Computing Systems},
 series = {CHI EA '14},
 year = {2014},
 isbn = {978-1-4503-2474-8},
 location = {Toronto, Ontario, Canada},
 pages = {1897--1902},
 numpages = {6},
 url = {http://doi.acm.org/10.1145/2559206.2581370},
 doi = {10.1145/2559206.2581370},
 acmid = {2581370},
 publisher = {ACM},
 address = {New York, NY, USA},
 keywords = {bio feedback, hci, human emotion, human senses, physiology, video chat},
}


text:
@inproceedings{DBLP:conf/pakdd/TomobeON17,
 author = {Katsufumi Tomobe and
Masafumi Oyamada and
Shinji Nakadai},
 bibsource = {dblp computer science bibliography, https://dblp.org},
 biburl = {https://dblp.org/rec/bib/conf/pakdd/TomobeON17},
 booktitle = {Advances in Knowledge Discovery and Data Mining - 21st Pacific-Asia
Conference, PAKDD 2017, Jeju, South Korea, May 23-26, 2017, Proceedings,
Part I},
 crossref = {DBLP:conf/pakdd/2017-1},
 doi = {10.1007/978-3-319-57454-7_12},
 pages = {147--159},
 timestamp = {Sat, 19 Oct 2019 20:33:16 +0200},
 title = {Link Prediction for Isolated Nodes in Heterogeneous Network by Topic-Based
Co-clustering},
 url = {https://doi.org/10.1007/978-3-319-57454-7_12},
 year = {2017}
}

repository: mooz/academic-kickstart

repo_name: mooz/academic-kickstart


text:
@article{Chen-2018-Perfluorobutanesulfonate,
    title = "Perfluorobutanesulfonate Exposure Causes Durable and Transgenerational Dysbiosis of Gut Microbiota in Marine Medaka",
    author = "Chen, Lianguo  and
      Lam, James C. W.  and
      Hu, Chenyan  and
      Tsui, Mirabelle M. P.  and
      Wang, Qi  and
      Giesy, John P.  and
      Lam, Paul K. S.",
    journal = "Environmental Science {\&} Technology Letters, Volume 5, Issue 12",
    volume = "5",
    number = "12",
    year = "2018",
    publisher = "American Chemical Society (ACS)",
    url = "https://aclanthology.org/G18-29001",
    doi = "10.1021/acs.estlett.8b00597",
    pages = "731--738",
}

repository: gwf-uwaterloo/gwf-publications

repo_name: gwf-uwaterloo/gwf-publications


text:
@incollection{Fechner2018,
 address = {Singapore},
 author = {Fechner, Uwe and Schmehl, Roland},
 booktitle = {Airborne Wind Energy -- Advances in Technology Development and Research},
 chapter = {15},
 date = {2018-04-01},
 doi = {10.1007/978-981-10-1947-0_15},
 editor = {Schmehl, Roland},
 pages = {361--390},
 publisher = {Springer},
 series = {Green Energy and Technology},
 title = {Flight Path Planning in a Turbulent Wind Environment},
 year = {2018}
}


text:
@article{Rodrigues_2020,
 author = {Rodrigues, Daniela T. and Peterson, Lenen and de Oliveira, Lucas Boeni and Sosa-G{\'{o}}mez, Daniel R. and Ribeiro, Bergmann Morais and Ardisson-Ara{\'{u}}jo, Daniel M. P.},
 title = {Characterization of a novel alphabaculovirus isolated from the Southern armyworm, Spodoptera eridania (Cramer, 1782) (Lepidoptera: Noctuidae) and the evolution of odv-e66, a bacterium-acquired baculoviral chondroitinase gene},
 journal = {Genomics},
 publisher = {Elsevier {BV}},
 year = {2020},
 month = {nov},
 number = {6},
 volume = {112},
 pages = {3903--3914},
 url = {https://doi.org/10.1016%2Fj.ygeno.2020.06.047},
 doi = {10.1016/j.ygeno.2020.06.047}
}


text:
@inproceedings{ChattopadhyayDK17,
  author    = {Arkadev Chattopadhyay and
               Pavel Dvor{\'{a}}k and
               Michal Kouck{\'{y}} and
               Bruno Loff and
               Sagnik Mukhopadhyay},
  title     = {Lower Bounds for Elimination via Weak Regularity},
  booktitle = {{STACS}},
  series    = {LIPIcs},
  volume    = {66},
  pages     = {21:1--21:14},
  publisher = {Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik},
  year      = {2017}
}

repository: sagnikm/academic-kickstart

repo_name: sagnikm/academic-kickstart


text:
@article{Salari2018a,
 article-number = {3134},
 author = {Ebrahimi Salari, Mahdi and Coleman, Joseph and Toal, Daniel},
 date = {2018-11-13},
 doi = {10.3390/en11113134},
 journal = {Energies},
 number = {11},
 title = {Power Control of Direct Interconnection Technique for Airborne Wind Energy Systems},
 volume = {11},
 year = {2018}
}