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Apollo: Democratizing genome annotation

Nathan A. Dunn, Deepak R. Unni, Colin Diesh, Monica Munoz-Torres, Nomi L. Harris, Eric Yao, Helena Rasche, Ian H. Holmes, Christine G. Elsik, Suzanna E. Lewis, Aaron E. Darling
2019 PLoS Computational Biology  
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]

Nathan Dunn, Deepak Unni, Colin Diesh, Monica Munoz-Torres, Nomi Harris, Eric Yao, Helena Rasche, Ian Holmes, Christine Elsik, Suzanna Lewis
2019 bioRxiv   pre-print
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

Eduardo Lee, Gregg A Helt, Justin T Reese, Monica C Munoz-Torres, Chris P Childers, Robert M Buels, Lincoln Stein, Ian H Holmes, Christine G Elsik, Suzanna E Lewis
2013 Genome Biology  
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

Izumi V. Hinkson, Tanja M. Davidsen, Juli D. Klemm, Ishwar Chandramouliswaran, Anthony R. Kerlavage, Warren A. Kibbe
2017 Frontiers in Cell and Developmental Biology  
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

M. S. Campbell, M. Law, C. Holt, J. C. Stein, G. D. Moghe, D. E. Hufnagel, J. Lei, R. Achawanantakun, D. Jiao, C. J. Lawrence, D. Ware, S.-H. Shiu (+4 others)
2013 Plant Physiology  
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

Daoud Meerzaman, Barbara K Dunn
2019 Cancer Research  
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

Sandra Van Puyvelde, Derek Pickard, Koen Vandelannoote, Eva Heinz, Barbara Barbé, Tessa De Block, Simon Clare, Eve L Coomber, Katherine Harcourt, Sushmita Sridhar, Emily A Lees, Nicole E Wheeler (+12 others)
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

Michael Worobey, Thomas D Watts, Richard McKay, Marc A Suchard, Timothy Granade, Dirk E Teuwen, Beryl A Koblin, Walid Heneine, Philippe Lemey, Harold W Jaffe, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository
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

Sethlina Naa Dodua Aryee, Dennis Owusu-Adjei, Richard Osei-Amponsah, Benjamin Skinner, Emmanuel Sowatey, Carole Anne Sargent, Apollo-University Of Cambridge Repository
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


Fatima Magdi Hamza Baldo, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository, Andreas Bender
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

Heike Sichtig, Timothy Minogue, Yi Yan, Christopher Stefan, Adrienne Hall, Luke Tallon, Lisa Sadzewicz, Suvarna Nadendla, William Klimke, Eneida Hatcher, Martin Shumway, Dayanara Lebron Aldea (+6 others)
2019 Nature Communications  
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

Shahar Avin, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository
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

Samuel Kariuki, Cecilia Mbae, Sandra Van Puyvelde, Robert Onsare, Susan Kavai, Celestine Wairimu, Ronald Ngetich, John Clemens, Gordon Dougan, Apollo-University Of Cambridge Repository, Abiola Editor: Senok
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

Jiaru Bai, Liwei Cao, Sebastian Mosbach, Jethro Akroyd, Alexei Lapkin, Markus Kraft, Apollo-University Of Cambridge Repository
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

David L Stern, Clair Han
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
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