Systems & Computational Biology
Gapless provides combined scaffolding, gap filling, and assembly correction with long readsgapless is a new tool for combined execution of correction, scaffolding and gap filling using PacBio or Oxford Nanopore reads.
Proteomic analysis reveals microvesicles containing NAMPT as mediators of radioresistance in gliomaGlioma patients often relapse because of resistance to radiation therapy. The transfer of the metabolic enzyme NAMPT via microvesicles and the accompanying elevated levels of NAD are found to be a mechanism by which glioma cells become resistant to radiation.
Analysis of context-specific KRAS–effector (sub)complexes in Caco-2 cellsWe used affinity purification of KRAS in different genetic and growth contexts to determine KRAS-mediated complexes, their rewiring in specific contexts, and their link to functional outcomes.
RAS and PP2A activities converge on epigenetic gene regulationThis study reveals a hidden regulatory layer in epigenetic gene expression in cancer by co-operative phosphoregulation by RAS and tumor suppressor phosphatase PP2A.
Assessing the impacts of various factors on circular RNA reliabilityThis study systematically assesses the impacts of numerous factors related to circRNA identification, conservation, biogenesis, and function on circRNA reliability, providing a useful guideline and an important resource for selecting high-confidence circRNAs for further investigations.
New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing readsInnovative algorithmic approaches were used to perform assembly of complex genomes across the tree of life, from long DNA sequencing data.
Plasma proteome dynamics of COVID-19 severity learnt by a graph convolutional network of multi-scale topologyWe used a graph convolutional network to model the plasma proteome of 384 COVID-19 patients. The model incorporates clinical data and is able to predict severity. We identified the proteins that shifted most in expression depending on severity.
A practical comparison of the next-generation sequencing platform and assemblers using yeast genomeThis research analyzes the general and optimal de novo yeast assembly pipeline using the repetitive yeast genome assembly by benchmarking four different sequencing platforms and seven assembly programs.
A genome-wide CRISPR functional survey of the human phagocytosis molecular machineryThe validation and interpretation of a genome-wide CRISRPko FACS screen via protein–protein interaction data yield a broad view of the molecular network-regulating phagocytosis in human cells.
De novo discovery of traits co-occurring with chronic obstructive pulmonary diseaseThis paper integrates different levels of biological information to identify shared genetic and biological pathways underlying the diverse clinical presentations of COPD. Thus, it identifies a collection of genetic variants and genes that may aid COPD patient stratification and treatment.