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The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. [PDF]

PLoS Computational Biology, 2009
The Gene Ontology (GO) is a collaborative effort that provides structured vocabularies for annotating the molecular function, biological role, and cellular location of gene products in a highly systematic way and in a species-neutral manner with the aim ...
Reference Genome Group of the Gene Ontology Consortium
doaj   +1 more source

Genome Sequences of Four Isolates of Xanthomonas campestris pv. campestris, the Causal Agent of Black Rot

PhytoFrontiers, 2023
Black rot caused by Xanthomonas campestris pv. campestris (Xcc) poses a threat to cruciferous crops worldwide. Here, we report the genome sequences of four Xcc isolates, which were assembled using a combination of Nanopore long-read and MGISEQ-2000 short-
Fangwei Yu, Wei Zhang, Shenyun Wang, Li Yu, Zhangjun Fei, Jianbin Li   +5 more
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Visual Genome: Connecting Language and Vision Using Crowdsourced Dense Image Annotations [PDF]

International Journal of Computer Vision, 2016
Despite progress in perceptual tasks such as image classification, computers still perform poorly on cognitive tasks such as image description and question answering.
Ranjay Krishna, Yuke Zhu, O. Groth, Justin Johnson, K. Hata, Joshua Kravitz, Stephanie Chen, Yannis Kalantidis, Li-Jia Li, David A. Shamma, Michael S. Bernstein, Li Fei-Fei   +11 more
semanticscholar   +1 more source

First Report and Draft Genome Resource of a Unique Opportunistic Fusarium solani Pathogen Associated with Unknown Dark Galls in Sugarbeet

PhytoFrontiers, 2023
Fusarium disease of sugarbeet is a threat to sugarbeet production and can cause significant losses. During routine evaluation, a unique Fusarium species was solely isolated from unknown dark galls in sugarbeets from Wilkin County, MN, U.S.A.
Abbeah Navasca, Jatinder Singh, Viviana Rivera-Varas, Barney Geddes, Gary Secor, Upinder Gill, Thomas Baldwin   +6 more
doaj   +1 more source

Genome Resource Announcement of 3 Phylotype I and 14 Phylotype II Ralstonia solanacearum Species Complex Isolates from South America

PhytoFrontiers, 2023
The Ralstonia solanacearum species complex is a group of gram-negative bacteria that cause lethal wilting on a broad range of plant species. Ralstonia pathogens were responsible for the Moko disease epidemic in plantains, bananas, and Heliconia sp.
Nathalie Aoun, Jason K. Avalos, Matthew L. Cope-Arguello, Claudia Enriquez, Trung-Hieu Nguyen, Alexandra Olyushinets, Gabriel A. Subuyuj, Cloe Tom, Tiffany M. Lowe-Power   +8 more
doaj   +1 more source

High-Quality Genome Resource of the Pathogen of Botryosphaeria dothidea Causing Kiwifruit Soft Rot

PhytoFrontiers, 2021
Kiwifruit soft rot caused by the fungal pathogen Botryosphaeria dothidea is a serious disease in kiwifruit-growing regions worldwide. In this study, we reported the high-quality genome sequence of the highly virulent B.
Kuan Liang, Jianbin Lan, Baoquan Wang, Yuanyuan Liu, Qi Lu, Pu Liu   +5 more
doaj   +1 more source

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

Bioinform., 2019
Summary The Genome Taxonomy Database Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the GTDB. GTDB-Tk is computationally efficient and able to classify thousands of draft genomes in parallel.
Pierre-Alain Chaumeil, A. Mussig, P. Hugenholtz, Donovan H. Parks   +3 more
semanticscholar   +1 more source

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

bioRxiv, 2016
The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platforms generate long reads that can ...
R. Wick, L. Judd, C. Gorrie, K. Holt
semanticscholar   +1 more source

CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline

BMC Genomics, 2017
Background The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled ...
Sonia Agrawal, Cesar Arze, Ricky S. Adkins, Jonathan Crabtree, David Riley, Mahesh Vangala, Kevin Galens, Claire M. Fraser, Hervé Tettelin, Owen White, Samuel V. Angiuoli, Anup Mahurkar, W. Florian Fricke   +12 more
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NCBI prokaryotic genome annotation pipeline

Nucleic Acids Research, 2016
Recent technological advances have opened unprecedented opportunities for large-scale sequencing and analysis of populations of pathogenic species in disease outbreaks, as well as for large-scale diversity studies aimed at expanding our knowledge across ...
T. Tatusova, Michael DiCuccio, Azat Badretdin, V. Chetvernin, Eric P. Nawrocki, L. Zaslavsky, A. Lomsadze, K. Pruitt, M. Borodovsky, J. Ostell   +9 more
semanticscholar   +1 more source