Results 81 to 90 of about 273,042 (329)

Virus Detection by High-Throughput Sequencing of Small RNAs: Large-Scale Performance Testing of Sequence Analysis Strategies.

Phytopathology, 2019
Recent developments in high-throughput sequencing (HTS), also called next-generation sequencing (NGS), technologies and bioinformatics have drastically changed research on viral pathogens and spurred growing interest in the field of virus diagnostics ...
S. Massart, M. Chiumenti, K. De Jonghe, R. Glover, A. Haegeman, I. Koloniuk, P. Komínek, J. Kreuze, D. Kutnjak, L. Lotos, François Maclot, V. Maliogka, H. J. Maree, T. Olivier, A. Olmos, M. Pooggin, J. Reynard, A. Ruiz-García, D. Šafářová, P. H. Schneeberger, N. Sela, S. Turco, E. Vainio, É. Várallyay, E. Verdin, M. Westenberg, Y. Brostaux, T. Candresse   +27 more
semanticscholar   +1 more source

Transcriptional network analysis of PTEN‐protein‐deficient prostate tumors reveals robust stromal reprogramming and signs of senescent paracrine communication

Molecular Oncology, EarlyView.
Combining PTEN protein assessment and transcriptomic profiling of prostate tumors, we uncovered a network enriched in senescence and extracellular matrix (ECM) programs associated with PTEN loss and conserved in a mouse model. We show that PTEN‐deficient cells trigger paracrine remodeling of the surrounding stroma and this information could help ...
Ivana Rondon‐Lorefice, Jose I. Lopez, Aitziber Ugalde‐Olano, Maite Zufiaurre, Ianire Astobiza, Natalia Martin‐Martin, Laura Bozal‐Basterra, Saioa Garcia‐Longarte, Amaia Zabala‐Letona, Sofia Rey, Aida Santos‐Martin, Miguel Unda, Ana Loizaga‐Iriarte, Mariona Graupera, Paolo Nuciforo, Arkaitz Carracedo, Isabel Mendizabal   +16 more
wiley   +1 more source

Interplay between RNA‐protein interactions and RNA structures in gene regulation

FEBS Open Bio, EarlyView.
Methodological advances in mapping transcriptome‐wide RNA‐protein interactions and RNA structures have started to uncover the potential of RNP conformations in gene regulation. Competing RNA–RNA, RNA‐protein and protein–protein interactions shape the compaction and function of RNPs throughout their lifetime and may provide novel therapeutic targets in ...
Jenni Rapakko, Mauro Scaravilli, Minna‐Liisa Änkö   +2 more
wiley   +1 more source

Evolutionary dynamics of the chloroplast genome in Daphne (Thymelaeaceae): comparative analysis with related genera and insights into phylogenetics

FEBS Open Bio, EarlyView.
Comparative analysis of chloroplast genomes from 14 genera of Thymelaeaceae revealed variation in gene content, ranging from 128 to 142 genes, primarily influenced by IR expansion/contraction events and pseudogenization of ndhF, ndhI, and ndhG. Two large inversions were detected within the large single‐copy region, including a synapomorphic inversion ...
Abdullah, Hui Li, Rushan Yan, Chengyu Chen, Madiha Islam, Abdul Majid, Ibrar Ahmed, Parviz Heidari, Xiaoxuan Tian   +8 more
wiley   +1 more source

Application of high-throughput sequencing to whole rabies viral genome characterisation and its use for phylogenetic re-evaluation of a raccoon strain incursion into the province of Ontario [PDF]

, 2017
Raccoon rabies remains a serious public health problem throughout much of the eastern seaboard of North America due to the urban nature of the reservoir host and the many challenges inherent in multi-jurisdictional efforts to administer co-ordinated and ...
Biek, Roman, Colville, Adam, Nadin-Davis, Susan A., Real, Leslie, Trewby, Hannah   +4 more
core   +1 more source

Additional file 2 of Correcting nucleotide-specific biases in high-throughput sequencing data

, 2017
Table S1. Area under curve (AUC) values for the ROC curves representing sensitivity and specificity of footprint detection for several transcription factors. AUC values at increasing false positive rates (FPR) are computed independently for each motif before and after correction.
Wang, Jeremy, Quach, Bryan, Furey, Terrence   +2 more
openaire   +1 more source

Genome Detective: an automated system for virus identification from high-throughput sequencing data

Bioinform., 2018
Summary Genome Detective is an easy to use web-based software application that assembles the genomes of viruses quickly and accurately. The application uses a novel alignment method that constructs genomes by reference-based linking of de novo contigs by
Michael Vilsker, Y. Moosa, S. Nooij, V. Fonseca, Yoika Ghysens, K. Dumon, Raf Pauwels, L. Alcântara, E. V. Eynden, A. Vandamme, K. Deforche, T. Oliveira   +11 more
semanticscholar   +1 more source

dUTPase is essential in zebrafish development and possesses several single‐nucleotide variants with pronounced structural and functional consequences

FEBS Open Bio, EarlyView.
dUTPases are involved in balancing the appropriate nucleotide pools. We showed that dUTPase is essential for normal development in zebrafish. The different zebrafish genomes contain several single‐nucleotide variations (SNPs) of the dut gene. One of the dUTPase variants displayed drastically lower protein stability and catalytic efficiency as compared ...
Viktória Perey‐Simon, Angéla Békesi, Latifa Kazzazy, Jázmin Mihály, Máté Varga, Beáta G. Vértessy, Kinga Nyíri   +6 more
wiley   +1 more source

Experience of copy number variation sequencing applied in spontaneous abortion

BMC Medical Genomics
Purpose We evaluated the value of copy number variation sequencing (CNV-seq) and quantitative fluorescence (QF)-PCR for analyzing chromosomal abnormalities (CA) in spontaneous abortion specimens.
Yi-Fang Dai, Xiao-Qing Wu, Hai-Long Huang, Shu-Qiong He, Dan-Hua Guo, Ying Li, Na Lin, Liang-Pu Xu   +7 more
doaj   +1 more source

Effects of Somatic Mutations Are Associated with SNP in the Progression of Individual Acute Myeloid Leukemia Patient: The Two-Hit Theory Explains Inherited Predisposition to Pathogenesis [PDF]

Genomics & Informatics, 2013
This study evaluated the effects of somatic mutations and single nucleotide polymorphisms (SNPs) on disease progression and tried to verify the two-hit theory in cancer pathogenesis.
Soyoung Park, Youngil Koh, Sung-Soo Yoon
doaj   +1 more source