A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Filters
Apollo: Democratizing genome annotation
2019
PLoS Computational Biology
Preserved Fulltext
Genome annotation is the process of identifying the location and function of a genome's encoded features. ...
Finally, we consider the implications that Apollo and related applications may have on how the results of genome research are published and made accessible. ...
Acknowledgments Thanks to the Apollo and JBrowse communities for bringing issues to our attention, requesting new features, contributing code, integrating and using our product. ...
doi:10.1371/journal.pcbi.1006790
pmid:30726205
pmcid:PMC6380598
fatcat:vkcph2mvofavlhadbdxrhqzbrq
Apollo: Democratizing genome annotation
[article]
2019
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Genome annotation is the process of identifying the location and function of a genome's encoded features. ...
Finally, we consider the implications that Apollo and related applications may have on how the results of genome research are published and made accessible. ...
Acknowledgements Thanks to the Apollo and JBrowse communities for bringing issues to our attention, requesting new features, contributing code, integrating and using our product. ...
doi:10.1101/512376
fatcat:vnyf6dwbrfecrj5s6vh7psxfli
Web Apollo: a web-based genomic annotation editing platform
2013
Genome Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
We thank the Honey Bee and Bumble Bee Genome Sequencing Consortiums for genome assemblies and accompanying computed gene prediction evidence for honey bee (Amel_4.5) and Bombus impatiens (Bimp_1.0), which ...
We would especially like to thank Mitch Skinner for the development of JBrowse, Nomi Harris for preliminary work on the Web Apollo client, Thomas Down for permitting the reuse of his binary parsing libraries ...
Technical advances have made sequencing faster and cheaper, thereby democratizing genome-scale sequencing and allowing a rapidly growing number of researchers to launch sequencing projects ranging from ...
doi:10.1186/gb-2013-14-8-r93
pmid:24000942
pmcid:PMC4053811
fatcat:zlsy4ygui5colc4oi3ml5n3e5u
A Comprehensive Infrastructure for Big Data in Cancer Research: Accelerating Cancer Research and Precision Medicine
2017
Frontiers in Cell and Developmental Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
During its pilot phase, the Cloud Resources tested multiple cloud-based approaches for enhancing data access, collaboration, computational scalability, resource democratization, and reproducibility. ...
The GDC ensures data and metadata quality, ingests and harmonizes genomic data, and securely redistributes the data. ...
ACKNOWLEDGMENTS We thank NCI Center for Biomedical Informatics and Information Technology (CBIIT), Center for Cancer Genomics, Office of Clinical Cancer Proteomics Research, GDC, and the CGC Pilot teams ...
doi:10.3389/fcell.2017.00083
pmid:28983483
pmcid:PMC5613113
fatcat:jzwud34zvbgcbk5myj2kaffjnq
MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations
2013
Plant Physiology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
We have optimized and extended the widely used annotation engine MAKER in order to better support plant genome annotation efforts. ...
Our results demonstrate that MAKER-P can be used to manage and improve the annotations of even Arabidopsis, perhaps the best-annotated plant genome. ...
MAKER-P thus provides the plant genome research community with a basic resource that democratizes genome annotation. ...
doi:10.1104/pp.113.230144
pmid:24306534
pmcid:PMC3912085
fatcat:66akszwoobf33mnj2nfa4p2jpu
Value of collaboration among multidomain experts in analysis of high-throughput genomics data
2019
Cancer Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
projects such as The Cancer Genome Atlas. ...
of discomfort in applying such genomic knowledge to patient care. ...
These include the International Cancer Genome Consortium (ICGC) (8) and the The Applied Proteogenomics OrganizationaL Learning and Outcomes (APOLLO) (9) . ...
doi:10.1158/0008-5472.can-19-0769
pmid:31337654
pmcid:PMC6801074
fatcat:2zjqgw5t4ba7jaqamidn5k6sca
An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation
2019
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
The annotated Pacbio'd reference genome of Salmonella Typhimurium strain 10433_3 is uploaded to GenBank with accession ID ERS1310131. ...
The genomes of S. ...
doi:10.17863/cam.45176
fatcat:5gtzs3pyijenxcrv5cv44jmihy
1970s and 'Patient 0' HIV-1 genomes illuminate early HIV/AIDS history in North America
2016
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Here, we report eight coding-complete genomes from US serum samples from 1978–1979—eight of the nine oldest HIV-1 group M genomes to date. ...
Comparisons with more recent data reveal many of these insights to be unattainable without archival, full-genome sequences. ...
A fully annotated tree for this data set ('full genome 38', which 350 includes only sequences sampled early in the US epidemic) is shown in ED Fig. 2b; 'full genome 351 46' which includes all available ...
doi:10.17863/cam.6154
fatcat:ucnnw5trzbgb3pyg7uit3nstzm
Sustainable genomic research for food security in sub-Saharan Africa
2021
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
The objective of this review is to highlight the rich agricultural biodiversity of sub-Saharan Africa, the potential of genomics in their sustainable use for food security, the challenges of genomic research ...
and the strategies that can be adopted to overcome them in the implementation of agricultural genomic research in Africa. ...
We have outlined how genomics may be an important tool for democratic consolidation and political stability. ...
doi:10.17863/cam.64269
fatcat:gklrszzu2jhitbxvek3hqjcyve
INTEGRATING CHEMICAL, BIOLOGICAL AND PHYLOGENETIC SPACES OF AFRICAN NATURAL PRODUCTS TO UNDERSTAND THEIR THERAPEUTIC ACTIVITY
2019
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
The WikiPathways annotations in PIDGIN2 were used for pathway annotation due to their interpretability 141, 142 . ...
ConMedNP was published in 2014 and contains compounds from plants mainly from countries in the Congo Basin (Burundi, Central African Republic, Chad, Congo, Equatorial Guinea, Gabon, the Democratic Republic ...
doi:10.17863/cam.36962
fatcat:njz2kwvv5jdirj3hahmhctniqu
FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science
2019
Nature Communications
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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. ...
FDA-ARGOS genome annotations. Genomes were annotated with NCBI's annotation tools to streamline the process [38] [39] [40] [41] [42] . ...
doi:10.1038/s41467-019-11306-6
pmid:31346170
pmcid:PMC6658474
fatcat:ek46vv5u6rghbbt6rpfhr2vuei
Breaking the grant cycle: on the rational allocation of public resources to scientific research projects
2015
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
the number of nearest-neighbours of each genome. ...
For example, if arranged by genotype, genome G will be adjacent to all genomes that are one-allele change from being identical to G. ...
doi:10.17863/cam.16172
fatcat:xiu6uusrvjgutpt4gfogvbfrwm
High relatedness of invasive multi-drug resistant non-typhoidal Salmonella genotypes among patients and asymptomatic carriers in endemic informal settlements in Kenya
2020
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Presence of multidrug resistance markers (MDR; bla, dfrA, sul, cat) and SNPs in gyr are annotated. ...
genome used for read mapping. ...
doi:10.17863/cam.56249
fatcat:ginrc7kwozcejmm62lvqyf2nja
From Platform to Knowledge Graph: Evolution of Laboratory Automation
2022
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
Most of the schemas classify items using annotations based on ontological taxonomies. ...
Therefore, interoperability is key toward the democratization of chemical automation. By design, the knowledge graph approach is able to connect to any laboratory. ...
doi:10.17863/cam.83288
fatcat:igsnqxp52fhlxowgcbck7ub2xu
Gene structure-based homology search identifies highly divergent putative effector gene family
2022
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
To test the potential roles of bicycle genes in other aphids, we sequenced the genome of a second gall-forming aphid, Tetraneura nigriabdominalis, and found that many bicycle genes are strongly expressed ...
Apollo: Democratizing genome annotation. PLoS Comput Biol 15:e1006790. doi:10.1371/journal.pcbi.1006790 Eddy SR. 2011. Accelerated profile HMM searches. ...
doi:10.1093/gbe/evac069
pmid:35533072
pmcid:PMC9168663
fatcat:wvqdlp2j4ja37hzbjuv7lm5iji
« Previous
Showing results 1 — 15 out of 63 results