Bovo, Samuele Schiavo, Giuseppina Ribani, Anisa Utzeri, Valerio J. Taurisano, Valeria Ballan, Mohamad Muñoz, Maria Alves, Estefania Araujo, Jose P. Bozzi, Riccardo
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Published in
Scientific Reports
Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a “One Health” perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the varia...
Stodolna, Agata He, Miao Vasipalli, Mahesh Kingsbury, Zoya Becq, Jennifer Stockton, Joanne D. Dilworth, Mark P. James, Jonathan Sillo, Toju Blakeway, Daniel
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Published in
Genome Medicine
Background Clinical-grade whole-genome sequencing (cWGS) has the potential to become the standard of care within the clinic because of its breadth of coverage and lack of bias towards certain regions of the genome. Colorectal cancer presents a difficult treatment paradigm, with over 40% of patients presenting at diagnosis with metastatic disease. W...
de Oliveira Ribeiro, Geovani da Costa, Antonio Charlys Gill, Danielle Elise Ribeiro, Edcelha Soares D’Athaide Rego, Marlisson Octavio da S. Monteiro, Fred Julio Costa Villanova, Fabiola Nogueira, Juliana Silva Maeda, Adriana Yurika de Souza, Renato Pereira
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Published in
Scientific Reports
Classical insect-flaviviruses (cISFVs) and dual host-related insect-specific flavivirus (dISFV) are within the major group of insect-specific flavivirus. Remarkably dISFV are evolutionarily related to some of the pathogenic flavivirus, such as Zika and dengue viruses. The Evolutionary relatedness of dISFV to flavivirus allowed us to investigate the...
Marchesi, Jorge Augusto Petroli Ono, Rafael Keith Cantão, Maurício Egídio Ibelli, Adriana Mércia Guaratini Peixoto, Jane de Oliveira Moreira, Gabriel Costa Monteiro Godoy, Thaís Fernanda Coutinho, Luiz Lehmann Munari, Danísio Prado Ledur, Mônica Corrêa
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Published in
Scientific Reports
Chicken feed efficiency (FE) traits are the most important economic traits in broiler production. Several studies evaluating genetic factors affecting food consumption in chickens are available. However, most of these studies identified genomic regions containing putative quantitative trait loci for each trait separately. It is still a challenge to...
Glessner, Joseph T. Chang, Xiao Liu, Yichuan Li, Jin Khan, Munir Wei, Zhi Sleiman, Patrick M. A. Hakonarson, Hakon
Published in
BMC Genomics
Background Not all cells in a given individual are identical in their genomic makeup. Mosaicism describes such a phenomenon where a mixture of genotypic states in certain genomic segments exists within the same individual. Mosaicism is a prevalent and impactful class of non-integer state copy number variation (CNV). Mosaicism implies that certain c...
Ryzhkova, Anastasia Taskina, Alena Khabarova, Anna Fishman, Veniamin Battulin, Nariman
Published in
Scientific Reports
Generation of mature red blood cells, consisting mainly of hemoglobin, is a remarkable example of coordinated action of various signaling networks. Chromatin condensation is an essential step for terminal erythroid differentiation and subsequent nuclear expulsion in mammals. Here, we profiled 3D genome organization in the blood cells from ten speci...
Zhu, Haishan Deng, Mignhua Yang, Zhengan Mao, Lianzhen Jiang, Shurui Yue, Yanling Zhao, Kai
Published in
Phytopathology
Late blight (caused by Phytophthora infestans) poses a serious threat to tomato production, but the number of late blight resistance genes isolated from tomato is limited, making resistance gene mining a high research priority. In this study, highly resistant CLN2037E and susceptible No.5 tomato inbred lines were used to identify late blight resist...
Wardell, Christopher Paul Ashby, Cody Bauer, Michael Anton
Published in
BMC Bioinformatics
Background Somatic variant callers are used to find mutations in sequencing data from cancer samples. They are very sensitive and have high recall, but also may produce low precision data with a large proportion of false positives. Further ad hoc filtering is commonly performed after variant calling and before further analysis. Improving the filter...
Morales, Leah Simpson, Danny Ferguson, Robert Cadley, John Esteva, Eduardo Monson, Kelsey Chat, Vylyny Martinez, Carlos Weber, Jeffrey Osman, Iman
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Published in
Journal of Translational Medicine
Background Tumor mutation burden (TMB) has been associated with melanoma immunotherapy (IT) outcomes, including survival. We explored whether combining TMB with immunogenomic signatures recently identified by The Cancer Genome Atlas (TCGA) can refine melanoma prognostic models of overall survival (OS) in patients not treated by IT. Methods Cox prop...
Tarbell, Evan Jiang, Kaiyu Hennon, Teresa R. Holmes, Lucy Williams, Sonja Fu, Yao Gaffney, Patrick M. Liu, Tao Jarvis, James N.
Published in
Scientific Reports
Juvenile idiopathic arthritis (JIA) is one of the most common chronic diseases in children. While clinical outcomes for patients with juvenile JIA have improved, the underlying biology of the disease and mechanisms underlying therapeutic response/non-response are poorly understood. We have shown that active JIA is associated with distinct transcrip...
