Results 101 to 110 of about 495,544 (318)
Molecular Oncology, EarlyView.The COMBAT classification system, developed through multi‐omics integration, stratifies adult patients with B‐cell acute lymphoblastic leukemia(B‐ALL) into three molecular subtypes with distinct surface antigen patterns, immune landscape, methylation patterns, biological pathways and prognosis.
Yang Song +11 more
wiley +1 more source
Ten steps to get started in Genome Assembly and Annotation [version 1; referees: 2 approved]
F1000Research, 2018 As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation.
Victoria Dominguez Del Angel +15 more
doaj +1 more source
Annotating the genome by DNA methylation
The International Journal of Developmental Biology, 2017 DNA methylation plays a prominent role in setting up and stabilizing the molecular design of gene regulation and by understanding this process one gains profound insight into the underlying biology of mammals. In this article, we trace the discoveries that provided the foundations of this field, starting with the mapping of methyl groups in the genome ...
Howard Cedar, Aharon Razin
openaire +4 more sources
Whole-Genome Annotation with BRAKER [PDF]
, 2019 BRAKER is a pipeline for highly accurate and fully automated gene prediction in novel eukaryotic genomes. It combines two major tools: GeneMark-ES/ET and AUGUSTUS. GeneMark-ES/ET learns its parameters from a novel genomic sequence in a fully automated fashion; if available, it uses extrinsic evidence for model refinement.
Katharina J. Hoff +4 more
openaire +2 more sources
Genomics‐led approach to drug testing in models of undifferentiated pleomorphic sarcoma
Molecular Oncology, EarlyView.GA text Genomic data from undifferentiated pleomorphic sarcoma patients and preclinical models were used to inform a targeted drug screen. Selected compounds were tested in 2D and 3D cultures of UPS cell lines. A combination of trametinib and infigratinib was synergistic in the majority of UPS cell lines tested, which was further confirmed in an ex ...
Piotr J. Manasterski +19 more
wiley +1 more source
BMC Bioinformatics, 2019 Background With sequencing technologies becoming cheaper and easier to use, more groups are able to obtain whole genome sequences of viruses of public health and scientific importance.
Ryan C. Shean +4 more
doaj +1 more source
Unraveling LINE‐1 retrotransposition in head and neck squamous cell carcinoma
Molecular Oncology, EarlyView.The novel RetroTest method allows the detection of L1 activation in clinical samples with low DNA input, providing global L1 activity and the identification of the L1 source element. We applied RetroTest to a real‐world cohort of HNSCC patients where we reported an early L1 activation, with more than 60% of T1 patients showing L1 activity.
Jenifer Brea‐Iglesias +12 more
wiley +1 more source
Predicting variant deleteriousness in non-human species: applying the CADD approach in mouse
BMC Bioinformatics, 2018 Background Predicting the deleteriousness of observed genomic variants has taken a step forward with the introduction of the Combined Annotation Dependent Depletion (CADD) approach, which trains a classifier on the wealth of available human genomic ...
Christian Groß +2 more
doaj +1 more source
Molecular Oncology, EarlyView.Overexpression of CHRDL2 in colon cancer cells makes them more stem‐like and resistant to chemo‐ and radiotherapy. CHRDL2‐high cells have upregulation of the WNT pathway, genes involved in the DNA damage response (DDR) pathway and epithelial‐to‐mesenchymal transition (EMT). This leads to quicker repair of damaged DNA and more cell migration.
Eloise Clarkson, Annabelle Lewis
wiley +1 more source
Annotation of 2,507 Saccharomyces cerevisiae genomes
Microbiology SpectrumSaccharomyces cerevisiae (baker’s yeast, budding yeast) is one of the most important model organisms for biological research and is a crucial microorganism in industry.
Meng Wang +8 more
doaj +1 more source