Results 71 to 80 of about 399,495 (297)

Whole Genome Sequencing of Hepatitis A Virus Using a PCR-Free Single-Molecule Nanopore Sequencing Approach

Frontiers in Microbiology, 2020
Hepatitis A virus (HAV) is one of the most common causes of acute viral hepatitis in humans. Although HAV has a relatively small genome, there are several factors limiting whole genome sequencing such as PCR amplification artefacts and ambiguities in de ...
Frederico M. Batista, Tina Stapleton, James A. Lowther, Vera G. Fonseca, Rebecca Shaw, Christopher Pond, David I. Walker, Ronny van Aerle, Jaime Martinez-Urtaza, Jaime Martinez-Urtaza   +9 more
doaj   +1 more source

Menadione-induced oxidative stress re-shapes the oxylipin profile of Aspergillus flavus and its lifestyle [PDF]

, 2015
Aspergillus flavus is an efficient producer of mycotoxins, particularly aflatoxin B1, probably the most hepatocarcinogenic naturally-occurring compound.
Cigliano, Riccardo Aiese, Fanelli, Corrado, Ippolito, Antonio, Ludovici, Matteo, Reverberi, Massimo, Sanseverino, Walter, Sanzani, Simona Marianna, Scala, Valeria, Scarpari, Marzia, Zaccaria, Marco   +9 more
core   +2 more sources

Investigating the cell of origin and novel molecular targets in Merkel cell carcinoma: a historic misnomer

Molecular Oncology, EarlyView.
This study indicates that Merkel cell carcinoma (MCC) does not originate from Merkel cells, and identifies gene, protein & cellular expression of immune‐linked and neuroendocrine markers in primary and metastatic Merkel cell carcinoma (MCC) tumor samples, linked to Merkel cell polyomavirus (MCPyV) status, with enrichment of B‐cell and other immune cell
Richie Jeremian, Sriraam Sivachandran, Melissa Galati, Brandon Ramchatesingh, Hibo Rijal, Johnny Hanna, Elena Netchiporouk, May Chergui, Margaret Redpath, Samy Abou Setah, Ivan V. Litvinov   +10 more
wiley   +1 more source

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks.

PLoS Computational Biology, 2018
Multiplexing, the simultaneous sequencing of multiple barcoded DNA samples on a single flow cell, has made Oxford Nanopore sequencing cost-effective for small genomes.
Ryan R Wick, Louise M Judd, Kathryn E Holt   +2 more
doaj   +1 more source

FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads [PDF]

Scientific Reports, 2016
Abstract We have developed a computational method that counts the frequencies of unique k -mers in FASTQ-formatted genome data and uses this information to infer the genotypes of known variants.
Pajuste, Fanny-Dhelia, Kaplinski, Lauris, Möls, Märt, Puurand, Tarmo, Lepamets, Maarja, Remm, Maido   +5 more
openaire   +3 more sources

YAP1::TFE3 mediates endothelial‐to‐mesenchymal plasticity in epithelioid hemangioendothelioma

Molecular Oncology, EarlyView.
The YAP1::TFE3 fusion protein drives endothelial‐to‐mesenchymal transition (EndMT) plasticity, resulting in the loss of endothelial characteristics and gain of mesenchymal‐like properties, including resistance to anoikis, increased migratory capacity, and loss of contact growth inhibition in endothelial cells.
Ant Murphy, Samuel Hartzler, Paula A. Vargas Carranza, Shyaman Jayasundara, Madison E. Yates, Nimod D. Janson, Bozhi Liu, Annaleigh Benton, Majid Kazemian, Jason A. Hanna   +9 more
wiley   +1 more source

pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires [PDF]

Bioinformatics, 2014
Abstract Summary: Driven by dramatic technological improvements, large-scale characterization of lymphocyte receptor repertoires via high-throughput sequencing is now feasible. Although promising, the high germline and somatic diversity, especially of B-cell immunoglobulin repertoires, presents challenges for analysis requiring the ...
Jason A, Vander Heiden, Gur, Yaari, Mohamed, Uduman, Joel N H, Stern, Kevin C, O'Connor, David A, Hafler, Francois, Vigneault, Steven H, Kleinstein   +7 more
openaire   +2 more sources

Emerging role of ARHGAP29 in melanoma cell phenotype switching

Molecular Oncology, EarlyView.
This study gives first insights into the role of ARHGAP29 in malignant melanoma. ARHGAP29 was revealed to be connected to tumor cell plasticity, promoting a mesenchymal‐like, invasive phenotype and driving tumor progression. Further, it modulates cell spreading by influencing RhoA/ROCK signaling and affects SMAD2 activity. Rho GTPase‐activating protein
Beatrice Charlotte Tröster, Melanie Kappelmann‐Fenzl, Anja Katrin Bosserhoff, Nicole Rachinger   +3 more
wiley   +1 more source

Survey of endosymbionts in the Diaphorina citri metagenome and assembly of a Wolbachia wDi draft genome. [PDF]

PLoS ONE, 2012
Diaphorina citri (Hemiptera: Psyllidae), the Asian citrus psyllid, is the insect vector of Ca. Liberibacter asiaticus, the causal agent of citrus greening disease. Sequencing of the D.
Surya Saha, Wayne B Hunter, Justin Reese, J Kent Morgan, Mizuri Marutani-Hert, Hong Huang, Magdalen Lindeberg   +6 more
doaj   +1 more source

Modeling hepatic fibrosis in TP53 knockout iPSC‐derived human liver organoids

Molecular Oncology, EarlyView.
This study developed iPSC‐derived human liver organoids with TP53 gene knockout to model human liver fibrosis. These organoids showed elevated myofibroblast activation, early disease markers, and advanced fibrotic hallmarks. The use of profibrotic differentiation medium further amplified the fibrotic signature seen in the organoids.
Mustafa Karabicici, Soheil Akbari, Ceyda Caliskan, Canan Celiker, Ozden Oz, Leman Binokay, Gökhan Karakulah, Serif Senturk, Esra Erdal   +8 more
wiley   +1 more source