Results 121 to 130 of about 4,905,249 (270)

Biological Averaging in RNA-Seq [PDF]

arXiv, 2013
RNA-seq has become a de facto standard for measuring gene expression. Traditionally, RNA-seq experiments are mathematically averaged -- they sequence the mRNA of individuals from different treatment groups, hoping to correlate phenotype with differences in arithmetic read count averages at shared loci of interest.
arxiv  

The Role of the Chloroplast in the Replication of Positive-Sense Single-Stranded Plant RNA Viruses

Frontiers in Plant Science, 2018
Positive-sense single-stranded plant RNA viruses are obligate intracellular parasites that infect many agriculturally important crops. Most known plant RNA viruses are characterized by small genomes encoding a limited number of multifunctional viral ...
Marta Budziszewska, Aleksandra Obrępalska-Stęplowska   +1 more
doaj   +1 more source

Obesity alters the fitness of peritumoral adipose tissue, exacerbating tumor invasiveness in renal cancer through the induction of ADAM12 and CYP1B1

Molecular Oncology, EarlyView.
Tumor microenvironment drives cancer formation and progression. We analyzed the role of human cancer‐associated adipocytes from patients with renal cell carcinoma (RCC) stratified as lean, overweight, or obese. RNA‐seq demonstrated that, among the most altered genes involved in the tumor–stroma crosstalk, are ADAM12 and CYP1B1, which were proven to be ...
Sepehr Torabinejad, Caterina Miro, Annarita Nappi, Francesco Del Giudice, Annunziata Gaetana Cicatiello, Serena Sagliocchi, Lucia Acampora, Federica Restolfer, Melania Murolo, Emery Di Cicco, Federico Capone, Ciro Imbimbo, Monica Dentice, Felice Crocetto   +13 more
wiley   +1 more source

Shapes of interacting RNA complexes [PDF]

arXiv, 2014
Shapes of interacting RNA complexes are studied using a filtration via their topological genus. A shape of an RNA complex is obtained by (iteratively) collapsing stacks and eliminating hairpin loops. This shape-projection preserves the topological core of the RNA complex and for fixed topological genus there are only finitely many such shapes.Our main ...
arxiv  

Addressing persistent challenges in digital image analysis of cancer tissue: resources developed from a hackathon

Molecular Oncology, EarlyView.
Large multidimensional digital images of cancer tissue are becoming prolific, but many challenges exist to automatically extract relevant information from them using computational tools. We describe publicly available resources that have been developed jointly by expert and non‐expert computational biologists working together during a virtual hackathon
Sandhya Prabhakaran, Clarence Yapp, Gregory J. Baker, Johanna Beyer, Young Hwan Chang, Allison L. Creason, Robert Krueger, Jeremy Muhlich, Nathan Heath Patterson, Kevin Sidak, Damir Sudar, Adam J. Taylor, Luke Ternes, Jakob Troidl, Xie Yubin, Artem Sokolov, Darren R. Tyson   +16 more
wiley   +1 more source

Editorial: Plant RNA structure

Frontiers in Plant Science, 2023
Huakun Zhang, Betty Y.-W. Chung, Zhiye Wang, Yiliang Ding   +3 more
doaj   +1 more source

Targeted metabolomics reveals novel diagnostic biomarkers for colorectal cancer

Molecular Oncology, EarlyView.
This study employed targeted metabolomic profiling to identify 302 distinct metabolites present in platelet‐rich plasma (PRP), revealing aberrant metabolic profiles amongst individuals diagnosed with colorectal cancer (CRC). Compared to carcinoembryonic antigen (CEA) and cancer antigen 19‐9 (CA199), our metabolite panel showed improved sensitivity ...
Zuojian Hu, Fenglin Shen, Yang Liu, Ziqing Zhong, Yongling Chen, Zhiyuan Xia, Cuiju Mo, Hongxiu Yu   +7 more
wiley   +1 more source

KMT2A degradation is observed in decitabine‐responsive acute lymphoblastic leukemia cells

Molecular Oncology, EarlyView.
We demonstrate that decitabine (DEC) not only degrades the DNA methyltransferase DNMT1 but also the leukemic driver lysine methyltransferase KMT2A likely due to structural similarity of the DNA‐binding CXXC domains. DEC influences KMT2A downstream processes and synergizes with menin inhibitor revumenib (REV) to decrease leukemic cell proliferation, and
Luisa Brock, Lina Benzien, Sandra Lange, Maja Huehns, Alexandra Runge, Catrin Roolf, Anett Sekora, Gudrun Knuebel, Hugo Murua Escobar, Christian Junghanss, Anna Richter   +10 more
wiley   +1 more source

Co-Translational mRNA Decay in Plants: Recent advances and future directions [PDF]

arXiv
Tight regulation of messenger RNA (mRNA) stability is essential to ensure accurate gene expression in response to developmental and environmental cues. mRNA stability is controlled by mRNA decay pathways, which have traditionally been proposed to occur independently of translation. However, the recent discovery of a co-translational mRNA decay pathway (
arxiv  

Polyfunctional CD8+CD226+RUNX2hi effector T cells are diminished in advanced stages of chronic lymphocytic leukemia

Molecular Oncology, EarlyView.
CD226+CD8+ T cells express elevated levels of RUNX2, exhibit higher proliferation capacity, cytokines and cytolytic molecules expression, and migratory capacity. In contrast, CD226−CD8+ T cells display an exhausted phenotype associated with the increased expression of co‐inhibitory receptors and impaired effector functions.
Maryam Rezaeifar, Shima Shahbaz, Anthea C. Peters, Spencer B. Gibson, Shokrollah Elahi   +4 more
wiley   +1 more source