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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
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Genomic surveillance of Neisseria gonorrhoeae in the Philippines, 2013–2014

Western Pacific Surveillance and Response, 2021
Antimicrobial-resistant Neisseria gonorrhoeae is a major threat to public health and is of particular concern in the Western Pacific Region, where the incidence of gonorrhoea is high.
Manuel C. Jamoralin, Jr, Silvia Argimon, Marietta L. Lagrada, Alfred S. Villamin, Melissa L. Masim, June M. Gayeta, Karis D. Boehme, Agnettah M. Olorosa, Sonia B. Sia, Charmian M. Hufano, Victoria Cohen, Lara T. Hernandez, Benjamin Jeffrey, Khalil Abudahab, John Stelling, Matthew T.G. Holden, David M. Aanensen, Celia C. Carlos   +17 more
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Inflammatory Nasal Swelling due to Leishmania tropica

Case Reports in Dermatological Medicine, 2021
Since its discovery in the 19th century, cutaneous leishmaniasis has been a major public health problem, especially with the appearance of more and more unusual cases of cutaneous lesions due to this parasite. Indeed, the present study joins the previous
Hajiba Fellah, Maryam Hakkour, Bouchra Delouane, Asmae Hmamouch, Abdelhakim Bouyahya, Faiza Sebti, Abderrahim Sadak   +6 more
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SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels

BMC Genomics, 2021
Background Faced with the ongoing global pandemic of coronavirus disease, the ‘National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis’ (GENPAT) formally established at the ‘Istituto ...
Adriano Di Pasquale, Nicolas Radomski, Iolanda Mangone, Paolo Calistri, Alessio Lorusso, Cesare Cammà   +5 more
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Genetic Basis of Dorper Sheep (Ovis aries) Revealed by Long-Read De Novo Genome Assembly

Frontiers in Genetics, 2022
Dorper sheep (Ovis aries) (DPS), developed in the 1930s by crossing Dorset Horn and Blackhead Persian sheep in South Africa, is a world-famous composite breed for mutton production. The genetic basis underlying this breed is yet to be elucidated.
Guoyan Qiao, Guoyan Qiao, Pan Xu, Tingting Guo, Tingting Guo, Yi Wu, Yi Wu, Xiaofang Lu, Xiaofang Lu, Qingfeng Zhang, Qingfeng Zhang, Xue He, Shaohua Zhu, Shaohua Zhu, Hongchang Zhao, Hongchang Zhao, Zhihui Lei, Zhihui Lei, Weibo Sun, Weibo Sun, Bohui Yang, Bohui Yang, Yaojing Yue, Yaojing Yue   +23 more
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Harmonization of supervised machine learning practices for efficient source attribution of Listeria monocytogenes based on genomic data

BMC Genomics, 2023
Background Genomic data-based machine learning tools are promising for real-time surveillance activities performing source attribution of foodborne bacteria such as Listeria monocytogenes.
Pierluigi Castelli, Andrea De Ruvo, Andrea Bucciacchio, Nicola D’Alterio, Cesare Cammà, Adriano Di Pasquale, Nicolas Radomski   +6 more
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Genomic Resources to Guide Improvement of the Shea Tree

Frontiers in Plant Science, 2021
A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree (Vitellaria paradoxa) is central to sustaining local livelihoods and the farming environments of rural communities. Despite its economic and cultural value,
Iago Hale, Xiao Ma, Xiao Ma, Arthur T. O. Melo, Francis Kwame Padi, Prasad S. Hendre, Sarah B. Kingan, Shawn T. Sullivan, Shiyu Chen, Jean-Marc Boffa, Alice Muchugi, Alice Muchugi, Agyemang Danquah, Michael Teye Barnor, Ramni Jamnadass, Yves Van de Peer, Yves Van de Peer, Yves Van de Peer, Yves Van de Peer, Allen Van Deynze, Allen Van Deynze   +20 more
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Genomic surveillance of Acinetobacter baumannii in the Philippines, 2013–2014

Western Pacific Surveillance and Response, 2021
Objective: Acinetobacter baumannii is an opportunistic nosocomial pathogen that has increasingly become resistant to carbapenems worldwide. In the Philippines, rates of carbapenem resistance and multidrug resistance are above 50%.
Jeremiah Chilam, Silvia Argimon, Marilyn T Limas, Melissa L Masim, June M Gayeta, Marietta L Lagrada, Agnettah M Olorosa, Victoria Cohen, Lara T Hernandez, Benjamin Jeffrey, Khalil Abudahab, Charmian M Hufano, Sonia B Sia, Matthew TG Holden, John Stelling, David M Aanensen, Celia C Carlos   +16 more
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The new bovine reference genome assembly provides new insight into genomic organization of the bovine major histocompatibility complex [PDF]

Journal of Central European Agriculture, 2019
The reference genome sequence represents a key resource for genetic studies of the target species. In 2009, two reference assemblies of the cattle (Bos taurus) genome, were published (Btau 4.0 and UMD 2.0).
Minja Zorc, Jernej Ogorevc, Peter Dovc
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Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines

Nature Communications, 2020
Whole-genome sequencing (WGS) can support drug resistance surveillance, but is rare in low- and middle-income countries. Here, the authors integrate WGS within the national antimicrobial resistance surveillance program in the Philippines and conduct a ...
Silvia Argimón, Melissa A. L. Masim, June M. Gayeta, Marietta L. Lagrada, Polle K. V. Macaranas, Victoria Cohen, Marilyn T. Limas, Holly O. Espiritu, Janziel C. Palarca, Jeremiah Chilam, Manuel C. Jamoralin, Alfred S. Villamin, Janice B. Borlasa, Agnettah M. Olorosa, Lara F. T. Hernandez, Karis D. Boehme, Benjamin Jeffrey, Khalil Abudahab, Charmian M. Hufano, Sonia B. Sia, John Stelling, Matthew T. G. Holden, David M. Aanensen, Celia C. Carlos   +23 more
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