Results 111 to 120 of about 9,695,054 (384)
Galba: genome annotation with miniprot and AUGUSTUS
BMC Bioinformatics, 2023 Background The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation of protein-coding genes.
Tomáš Brůna +9 more
doaj +1 more source
Inferring spatial and signaling relationships between cells from single cell transcriptomic data. [PDF]
, 2020 Single-cell RNA sequencing (scRNA-seq) provides details for individual cells; however, crucial spatial information is often lost. We present SpaOTsc, a method relying on structured optimal transport to recover spatial properties of scRNA-seq data by ...
Cang, Zixuan, Nie, Qing
core
BMC Genomics, 2015 The impact of gene annotation quality on functional and comparative genomics makes gene prediction an important process, particularly in non-model species, including many fungi. Sets of homologous protein sequences are rarely complete with respect to the
Alison C. Testa +3 more
semanticscholar +1 more source
FEBS Letters, EarlyView.UDP‐glucuronic acid 4‐epimerase (UGAepi) catalyzes NAD+‐dependent interconversion of UDP‐glucuronic acid (UDP‐GlcA) and UDP‐galacturonic acid (UDP‐GalA) via C4‐oxidation, 4‐keto‐intermediate rotation, and C4‐reduction. Here, Borg et al. examined the role of the substrate's carboxylate group in the enzymic mechanism by analyzing NADH‐dependent reduction
Annika J. E. Borg +2 more
wiley +1 more source
Biological process annotation of proteins across the plant kingdom
Current Plant Biology, 2014 Accurate annotation of protein function is key to understanding life at the molecular level, but automated annotation of functions is challenging.
Joachim W. Bargsten +4 more
doaj +1 more source
Engineering genes for predictable protein expression
Protein Expression and Purification, 2012 The DNA sequence used to encode a polypeptide can have dramatic effects on its expression. Lack of readily available tools has until recently inhibited meaningful experimental investigation of this phenomenon. Advances in synthetic biology and the application of modern engineering approaches now provide the tools for systematic analysis of the sequence
Sridhar Govindarajan +5 more
openaire +3 more sources
Predictability of human differential gene expression [PDF]
Proceedings of the National Academy of Sciences, 2019 Differential expression (DE) is commonly used to explore molecular mechanisms of biological conditions. While many studies report significant results between their groups of interest, the degree to which results are specific to the question at hand is not generally assessed, potentially leading to inaccurate interpretation.
Crow, M +4 more
openaire +3 more sources
FEBS Letters, EarlyView.B cells sense external mechanical forces and convert them into biochemical signals through mechanotransduction. Understanding how malignant B cells respond to physical stimuli represents a groundbreaking area of research. This review examines the key mechano‐related molecules and pathways in B lymphocytes, highlights the most relevant techniques to ...
Marta Sampietro +2 more
wiley +1 more source
The effect of sequencing errors on metagenomic gene prediction
BMC Genomics, 2009 Background Gene prediction is an essential step in the annotation of metagenomic sequencing reads. Since most metagenomic reads cannot be assembled into long contigs, specialized statistical gene prediction tools have been developed for short and ...
Hoff Katharina J
doaj +1 more source
Exploiting single-molecule transcript sequencing for eukaryotic gene prediction
Genome Biology, 2015 We develop a method to predict and validate gene models using PacBio single-molecule, real-time (SMRT) cDNA reads. Ninety-eight percent of full-insert SMRT reads span complete open reading frames.
A. Minoche +8 more
semanticscholar +1 more source