Results 41 to 50 of about 152,624 (261)
Extreme-Scale De Novo Genome Assembly [PDF]
, 2017 De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code ...
Evangelos Georganas +6 more
openaire +2 more sources
Genome assembly using quantum and quantum-inspired annealing
Scientific Reports, 2021 Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine.
A. S. Boev +7 more
doaj +1 more source
Hyperosmotic stress induces PARP1‐mediated HPF1‐dependent mono(ADP‐ribosyl)ation
FEBS Letters, EarlyView.Sorbitol‐induced hyperosmotic stress rapidly induces reversible mono(ADP‐ribosyl)ation (MARylation) on PARP1 without the signs of genotoxic signaling. We show that PARP1 autoMARylation is HPF1 dependent and forms hydroxylamine‐resistant O‐glycosidic linkages.
Anna Georgina Kopasz +11 more
wiley +1 more source
FEBS Letters, EarlyView.Septin 9 polybasic domains couple phosphoinositide‐rich membrane binding to centrosome positioning, Golgi organization, and microtubule acetylation to control epithelial polarity. Their loss disrupts this axis, causing centrosome mispositioning, Golgi fragmentation, reduced microtubule acetylation, and polarity inversion via upregulation of the ...
Ting ting Cai +4 more
wiley +1 more source
Kermit: linkage map guided long read assembly
Algorithms for Molecular Biology, 2019 Background With long reads getting even longer and cheaper, large scale sequencing projects can be accomplished without short reads at an affordable cost.
Riku Walve, Pasi Rastas, Leena Salmela
doaj +1 more source
Clover: a clustering-oriented de novo assembler for Illumina sequences
BMC Bioinformatics, 2020 Background Next-generation sequencing technologies revolutionized genomics by producing high-throughput reads at low cost, and this progress has prompted the recent development of de novo assemblers.
Ming-Feng Hsieh +2 more
doaj +1 more source
Reconstructing enzyme evolution by protein engineering
FEBS Letters, EarlyView.Natural enzyme evolution can be retraced by protein engineering methods such as directed evolution, rational design, and ancestral sequence reconstruction. These approaches reveal how enzymes emerged from ligand‐binding scaffolds, developed varying substrate preferences, formed oligomeric complexes, adapted to environmental changes, and evolved novel ...
Lukas Drexler +2 more
wiley +1 more source
Comparison of De Novo Transcriptome Assemblers and k-mer Strategies Using the Killifish, Fundulus heteroclitus. [PDF]
PLoS ONE, 2016 BACKGROUND:De novo assembly of non-model organism's transcriptomes has recently been on the rise in concert with the number of de novo transcriptome assembly software programs.
Satshil B Rana +4 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
Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)
BMC Bioinformatics, 2019 Background De novo assembling of large genomes, such as in conifers (~ 12–30 Gbp), which also consist of ~ 80% of repetitive DNA, is a very complex and computationally intense endeavor.
Dmitry A. Kuzmin +7 more
doaj +1 more source