Results 81 to 90 of about 141,521 (289)
A survey of sequence-to-graph mapping algorithms in the pangenome era
Genome BiologyA pangenome can reveal the genetic diversity across different individuals simultaneously. It offers a more comprehensive reference for genome analysis compared to a single linear genome that may introduce allele bias.
Yingbo Cui +4 more
doaj +1 more source
Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ
Nature Communications, 2020 Multiple whole-genome alignment is a challenging problem in bioinformatics, especially when computational resources are limited. Here the authors present SibeliaZ, an algorithm and software based on analysis of de Bruijn graphs, which provides improved ...
Ilia Minkin, Paul Medvedev
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Molecular Oncology, EarlyView.Glioma cells mainly express the endothelin receptor EDNRB, while EDNRA is restricted to a perivascular tumor subpopulation. Endothelin signaling reduces glioma cell proliferation while promoting migration and a proneural‐to‐mesenchymal transition associated with poor prognosis. This pathway activates Ca2+, K+, ERK, and STAT3 signalings and is regulated
Donovan Pineau +36 more
wiley +1 more source
GrapHi-C: graph-based visualization of Hi-C datasets
BMC Research Notes, 2018 Objectives Hi-C is a proximity-based ligation reaction used to detect regions of the genome that are close in 3D space (or “interacting”). Typically, results from Hi-C experiments (contact maps) are visualized as heatmaps or Circos plots.
Kimberly MacKay +2 more
doaj +1 more source
Somatic mutational landscape in von Hippel–Lindau familial hemangioblastoma
Molecular Oncology, EarlyView.The causes of central nervous system (CNS) hemangioblastoma in Von Hippel–Lindau (vHL) disease are unclear. We used Whole Exome Sequencing (WES) on familial hemangioblastoma to investigate events that underlie tumor development. Our findings suggest that VHL loss creates a permissive environment for tumor formation, while additional alterations ...
Maja Dembic +5 more
wiley +1 more source
Handbook of Graphs and Networks - From the Genome to the Internet [PDF]
, 2006 Handbook of Graphs and Networks - From the Genome to the ...
Bornholdt, Stefan et. al., ed.
core
The use of weighted graphs for large-scale genome analysis.
PLoS ONE, 2014 There is an acute need for better tools to extract knowledge from the growing flood of sequence data. For example, thousands of complete genomes have been sequenced, and their metabolic networks inferred. Such data should enable a better understanding of
Fang Zhou, Hannu Toivonen, Ross D King
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Hybrid-hybrid correction of errors in long reads with HERO
Genome Biology, 2023 Although generally superior, hybrid approaches for correcting errors in third-generation sequencing (TGS) reads, using next-generation sequencing (NGS) reads, mistake haplotype-specific variants for errors in polyploid and mixed samples. We suggest HERO,
Xiongbin Kang +3 more
doaj +1 more source
Molecular Oncology, EarlyView.In the present work, we have identified a transcriptional signature based on the differential expression of six genes (BCL2&MAST4, HSH2D&LAT2, METRN&PITPNM2) that would facilitate the early detection of T‐cell acute lymphoblastic leukemia (T‐ALL) patients prone to a poor treatment response and could be implemented at diagnosis, along with other risk ...
Antonio Lahera +11 more
wiley +1 more source
CCDC80 suppresses high‐grade serous ovarian cancer migration via negative regulation of B7‐H3
Molecular Oncology, EarlyView.PAX8 is a lineage‐specific master regulator of transcription in high‐grade serous ovarian cancer (HGSC) progression. We show for the first time that PAX8 facilitates proliferation and metastasis by repressing the cell autonomous tumor suppressor CCDC80 and inducing B7‐H3 expression.
Aya Saleh +12 more
wiley +1 more source