Mingke Wei,Jo-Wei Allison Hsieh,Jr-Fong Dang et al.
Mingke Wei et al.
Background: Xylem development is a dynamic, continuous process fundamental to secondary growth in woody plants and to biomass accumulation on earth. While single-cell RNA sequencing (scRNA-seq) enables reconstruction of e...
krepp: a k-mer-based maximum pseudo-likelihood method for estimating read distances and genome-wide phylogenetic placement [0.03%]
Ali Osman Berk Şapcı,Siavash Mirarab
Ali Osman Berk Şapcı
Comparing each sequencing read in a sample to a reference database is a fundamental step in wide-ranging applications. Results of these comparisons can enable phylogenetic characterization. However, phylogenetic placement is currently only ...
Mahdi Assari,Brandon J Chew,Mohammad Amin Bayat Tork et al.
Mahdi Assari et al.
Background: Transfer RNA (tRNA) modifications play important roles in regulating gene expression and protein synthesis, yet their dynamic interplay remains elusive. The human tRNAome contains approximately 40 modification...
Genomic and epidemiological identification of Pseudomonas aeruginosa transmission chains and in hospital ICUs [0.03%]
Lucia Graña-Miraglia,Xiaoyi Hu,Cheryl Volling et al.
Lucia Graña-Miraglia et al.
Background: Pseudomonas aeruginosa (PA) is an opportunistic pathogen that poses a significant threat to hospitalized patients, particularly in intensive care units (ICUs) due to its ability to contaminate the environment ...
Network-based framework for studying etiology and phenotypic diversity in primary ciliopathies [0.03%]
Ellen M Aarts,Diederik S Laman Trip,Ruxandra Neatu et al.
Ellen M Aarts et al.
Feng Yan,Pedro L Baldoni,James Lancaster et al.
Feng Yan et al.
Introduction: Recently, de novo transcriptome assembly methods have been developed to utilise long-read data in cases where a reference genome is unavailable, such as in non-model organisms. Despite the potential of these...
saseR: juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval [0.03%]
Alexandre Segers,Jeroen Gilis,Mattias Van Heetvelde et al.
Alexandre Segers et al.
RNA-seq data analysis relies on many different tools, each tailored to specific applications and coming with unique assumptions and limitations. Indeed, tools for differential transcript usage or rare disease diagnosis through splicing and ...
Anja Hess,Alexander Kovacsovics,Fabian Bachinger et al.
Anja Hess et al.
Individual CpG methylation signatures characterize each mammalian cell type, thereby offering a powerful readout for clinical and diagnostic applications. Here, we apply this principle to in vitro cellular systems, using cell-free DNA relea...
Joshua D Kapp,Ciara Wanket,Remy Nguyen et al.
Joshua D Kapp et al.
The small amount of fragmented DNA present in rootless hair shafts is unsuitable for many assays, including most PCR-based assays. Thus, rootless hair DNA is often overlooked in biomedical and forensic analysis. Here we apply methods for ef...
Sequence bias in chromatin fragmentation leads to misinterpretation of protein-DNA interactions in vivo [0.03%]
染色质断裂的序列偏向会导致对体内蛋白质- DNA 相互作用的误读
Laura Durán,Laura Rodríguez,Alicia García et al.
Laura Durán et al.
Genome regulation depends on the binding of regulatory proteins to chromatin. V-plots are widely used to assess the binding of transcription factors and other protein complexes to DNA in vivo. However, we show here that V-plots result from ...