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Microbial source tracking by molecular fingerprinting

Jan Lorenz Soliman, Alex Dekhtyar, Jennifer Vanderkellen, Aldrin Montana, Michael Black, Emily Neal, Kevin Webb, Chris Kitts, Anya Goodman
2012 Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '12  
To date, microbial source tracking (MST), i.e. determining the source of microbial contamination based on the specific strains observed in environment, is done using methods that are time-consuming, expensive  ...  The actual source tracking is achieved by comparing a newly obtained pyroprint to the pyroprints of known provenance from a database.  ...  Microbial Source Tracking (MST), a relatively new field of study related to epidemiology, is focused on identifying and tracking pathogen contamination in foods and resource waters.  ... 
doi:10.1145/2382936.2383042 dblp:conf/bcb/SolimanDVMBNWKG12 fatcat:tftg4dva6venvkdtheyj3wv5w4

An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays

Hong Fang, Joshua Xu, Don Ding, Scott A Jackson, Isha R Patel, Jonathan G Frye, Wen Zou, Rajesh Nayak, Steven Foley, James Chen, Zhenqiang Su, Yanbin Ye (+5 others)
2010 BMC Bioinformatics  
ArrayTrack TM 's data processing and visualization tools were enhanced with analysis capabilities designed specifically for microbial genomics including flag-based hierarchical clustering analysis (HCA  ...  It was populated with bioinformatics data from public databases such as NCBI, Swiss-Prot, KEGG Pathway, and Gene Ontology to facilitate pathogen detection and characterization.  ...  For USDA CRIS funding project number 6612-32000-002-00, the authors thank Rebecca L, Lindsey, Jennifer Bauer-Turpin, and Jonathan Cudnik (USDA) for their technical assistance.  ... 
doi:10.1186/1471-2105-11-s6-s4 pmid:20946615 pmcid:PMC3026378 fatcat:yic2fhgfjnam5m5mz7zufhab5m

Chromes from Chromatin: Sonification of the Epigenome [article]

Davide Cittaro, Dejan Lazarevic, Paolo Provero
2016 bioRxiv   pre-print
Hierarchical clustering of 14 the distance matrix identifies eight major clusters (Figure 3, left) .  ...  Colors are given by the corresponding Area Under the Curve (AUC) Hierarchical clustering of genomic regions identifies 8 main clusters (left).  ... 
doi:10.1101/037523 fatcat:c5odlchyt5fxpmjit7txtxziwm

Addressing the biomedical informatics needs of a microarray laboratory in a clinical microbiology context

Guillermo Lopez-Campos, Victoria Lopez Alonso, Fernando Martin-Sanchez
2008 Studies in Health Technology and Informatics  
For an effective integration of microarray-based technologies in clinical settings a number of contributions from biomedical informatics technologies and techniques are needed to facilitate the improvement  ...  to laboratories conducting microarray experiments and how our unit is coping with these requirements imposed by the routine clinical work of the National Centre of Microbiology, a reference laboratory for  ...  There are now several technologies that are useful for the design of microarrays for a selected set of model organisms based on Gene Ontology (GO) classification or using UniGene clusters [11] .  ... 
pmid:18487706 fatcat:yn7i6yqyqnawvk3cspqghkyn3e

Chromas from chromatin: sonification of the epigenome

Davide Cittaro, Dejan Lazarevic, Paolo Provero
2016 F1000Research  
.: Accessing Music Collections Via Representative Cluster Prototypes in a Hierarchical Organization Scheme. ISMIR. 2008. Reference Source 14.  ...  Logan B: Mel Frequency Cepstral Coefficients for Music Modeling. ISMIR. 2000. Reference Source 13.  ...  Acknowledgements Authors would like to acknowledge Piotr Traczyk (Soltan Institute for Nuclear Studies, Warsaw, Poland) who inspired our research with his sonification of the Higgs Boson.  ... 
doi:10.12688/f1000research.8001.1 pmid:27019695 pmcid:PMC4805159 fatcat:txti52kl7zhdlbdqxdh4iqdega

Towards bioinformatics assisted infectious disease control

Vitali Sintchenko, Blanca Gallego, Grace Chung, Enrico Coiera
2009 BMC Bioinformatics  
This paper proposes a novel framework for bioinformatics assisted biosurveillance and early warning to address the inefficiencies in traditional surveillance as well as the need for more timely and comprehensive  ...  A pilot study of Salmonella typhimurium genotype clustering and temporospatial outbreak analysis demonstrated better discrimination power than traditional phage typing.  ...  Acknowledgements The authors thank Drs Q Wang, JR Iredell, L Hiley and GL Gilbert for their expert advice and providing genotyping data.  ... 
doi:10.1186/1471-2105-10-s2-s10 pmid:19208185 pmcid:PMC2646247 fatcat:x4jds5naerdhdenvsnltgi3chi

OMeta: an ontology-based, data-driven metadata tracking system

Indresh Singh, Mehmet Kuscuoglu, Derek M. Harkins, Granger Sutton, Derrick E. Fouts, Karen E. Nelson
2019 BMC Bioinformatics  
Some tools exist for tracking metadata, but they do not provide event based capabilities to configure, collect, validate, and distribute metadata.  ...  OMeta enables configuration in various presentation types: checkbox, file, drop-box, ontology, and fields can be configured to use the National Center for Biomedical Ontology (NCBO), a biomedical ontology  ...  Acknowledgements We thank Hyunsoo Kim, Les Foster and Jason Inman for their contributions to the OMeta application.  ... 
doi:10.1186/s12859-018-2580-9 fatcat:vj4zhyyd6reihi5crop3k2ac4i

ToolsAU

Maria Victoria Schneider, MADISON FLANNERY
2017 Figshare  
Our software takes a set of reads that have been multi-mapped to the transcriptome (where multiple alignments per read were reported) and hierarchically clusters the transcripts based on the proportion  ...  QIIME Description: QIIME, Quantitative Insights Into Microbial Ecology., is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.  ... 
doi:10.6084/m9.figshare.5011793.v1 fatcat:vsflwotpr5hypa564avdbywn5y

Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance

Emma Griffiths, Damion Dooley, Morag Graham, Gary Van Domselaar, Fiona S. L. Brinkman, William W. L. Hsiao
2017 Frontiers in Microbiology  
Fit-for-purpose ontologies provide contextual information with the auditability required for food safety laboratory accreditation.  ...  Our research efforts include the development of a Genomic Epidemiology Ontology (GenEpiO), and Food Ontology (FoodOn) that harmonize important laboratory, clinical and epidemiological data fields, as well  ...  Consortium, and Jane Ireland and Anders Møller of The Danish Food Informatics (DFI) group, for their ongoing development efforts.  ... 
doi:10.3389/fmicb.2017.01068 pmid:28694792 pmcid:PMC5483436 fatcat:wpqdgygedzgxnk3jk2pq2wog34

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

Konstantinos Liolios, I-Min A. Chen, Konstantinos Mavromatis, Nektarios Tavernarakis, Philip Hugenholtz, Victor M. Markowitz, Nikos C. Kyrpides
2009 Nucleic Acids Research  
The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide.  ...  As of September 2009, GOLD contains information for more than 5800 sequencing projects, of which 1100 have been completed and their sequence data deposited in a public repository.  ...  ACKNOWLEDGEMENTS We would like to thank Merry Youle for her excellent editorial assistance. GOLD has been maintained and developed mostly based on the volunteer work of its small team.  ... 
doi:10.1093/nar/gkp848 pmid:19914934 pmcid:PMC2808860 fatcat:xbdodff77bajdf7oripak5xjku

The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata

K. Liolios, K. Mavromatis, N. Tavernarakis, N. C. Kyrpides
2007 Nucleic Acids Research  
The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide.  ...  As of September 2009, GOLD contains information for more than 5800 sequencing projects, of which 1100 have been completed and their sequence data deposited in a public repository.  ...  ACKNOWLEDGEMENTS We would like to thank Merry Youle for her excellent editorial assistance. GOLD has been maintained and developed mostly based on the volunteer work of its small team.  ... 
doi:10.1093/nar/gkm884 pmid:17981842 pmcid:PMC2238992 fatcat:lkpxhueuvfbxdha6ydwp3gx5ay

Interactive exploration of integrated biological datasets using context-sensitive workflows

Fabian Horn, Martin Rittweger, Jan Taubert, Artem Lysenko, Christopher Rawlings, Reinhard Guthke
2014 Frontiers in Genetics  
We demonstrate the advantages of our approach by proposing new hypotheses for the functional annotation of specific genes of differentially expressed fungal gene clusters.  ...  We provide new functionalities for on-the-fly data integration using InterProScan, PubMed Central literature search, and sequence-based homology search.  ...  An arrow between two gene ontologies reflects the hierarchical structure of the directed acyclic graph of the gene ontologies.  ... 
doi:10.3389/fgene.2014.00021 pmid:24600467 pmcid:PMC3929842 fatcat:pzzmhnzljvhwtg6qwfgblojb7m

Metagenomic Analysis of the Structure and Function of the Human Gut Microbiota in Crohn's Disease

Claire Fraser-Liggett, Claire Fraser-Liggett
2010 Nature Precedings  
We will perform hierarchical clustering to explore protein abundance patterns in the different samples.  ...  In collaboration with HMP Program Officers, we will develop a plan for release of whole microbial community shotgun sequencing data generated under this project.  ... 
doi:10.1038/npre.2010.4958.1 fatcat:yxoshow5ffchtndygbyoxig2km

Metagenomic Analysis of the Structure and Function of the Human Gut Microbiota in Crohn's Disease

Claire Fraser-Liggett, Claire Fraser-Liggett
2010 Nature Precedings  
We will perform hierarchical clustering to explore protein abundance patterns in the different samples.  ...  In collaboration with HMP Program Officers, we will develop a plan for release of whole microbial community shotgun sequencing data generated under this project.  ... 
doi:10.1038/npre.2010.4958 fatcat:t3gwkgcfjneu7ft5kv75b4fuei

Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access

Eduardo N. Taboada, Morag R. Graham, João A. Carriço, Gary Van Domselaar
2017 Frontiers in Microbiology  
Celine Nadon for her helpful review of the manuscript.  ...  The need to annotate existing sequence-based microbial typing data also prompted the development of TypON, the microbial typing ontology (Vaz et al., 2014) .  ...  For example, genomics and bioinformatics have been crucial in developing the standard molecular typing technologies currently in routine use for laboratory-based identification and tracking of foodborne  ... 
doi:10.3389/fmicb.2017.00909 pmid:28588568 pmcid:PMC5440521 fatcat:fnittouu6ncwzeywcrvsp6uyoi
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