Results 81 to 90 of about 10,955,529 (276)
Disk-based k-mer counting on a PC [PDF]
BMC Bioinformatics, 2013 The k-mer counting problem, which is to build the histogram of occurrences of every k-symbol long substring in a given text, is important for many bioinformatics applications. They include developing de Bruijn graph genome assemblers, fast multiple sequence alignment and repeat detection.We propose a simple, yet efficient, parallel disk-based algorithm
Deorowicz, Sebastian +2 more
openaire +2 more sources
Epstein‐Barr Virus Expressed Long Non‐Coding RNA (lncBARTs) Regulate EBV Latent Genome Replication
Advanced Science, EarlyView.EBV produces abundant level of lncBARTs, which are essential for maintaining viral genome replication in EBV‐associated cancers. LncBARTs interact with a complex comprising BRD4, CTCF and viral protein EBNA1 at EBV oriP region. This interaction tethers oriP to host chromosomes, facilitating EBV episome replication.
Jiayan Liu +12 more
wiley +1 more source
Space-efficient computation of k-mer dictionaries for large values of k
Algorithms for Molecular BiologyComputing k-mer frequencies in a collection of reads is a common procedure in many genomic applications. Several state-of-the-art k-mer counters rely on hash tables to carry out this task but they are often optimised for small k as a hash table keeping ...
Diego Díaz-Domínguez +2 more
doaj +1 more source
Mining Discriminative K-Mers in DNA Sequences Using Sketches and Hardware Acceleration
IEEE Access, 2020 Extracting discriminative k-mers is an important and challenging problem in DNA sequence analysis with applications in metagenomics and motif discovery.
Antonio Saavedra +4 more
semanticscholar +1 more source
Advanced Science, EarlyView.Cryopreserved lung‐humanized mice overcome the dependency to fresh tissues and permit head‐to‐head profiling of all four human common cold coronaviruses versus SARS‐CoV‐2 infection; the model validates Paxlovid efficacy against HKU1 and, when coupled with human immune‐system engraftment, enables interrogation of lung‐resident human immunity and HKU1 ...
Chunyu Cheng +9 more
wiley +1 more source
K-mer Frequency Encoding Model for Cable Defect Identification: A Combination of Non-Destructive Testing Approach with Artificial Intelligence [PDF]
, 2023 Brijesh Patel +4 more
openalex +1 more source
Advanced Science, EarlyView.Current SARS‐CoV‐2 vaccines generate short‐lived, strain‐specific immunity. A polymeric TLR7 agonist nanoparticle (TLR7‐NP) adjuvant enhances lymph node targeting and promotes early and sustained germinal center responses toward conserved S2 epitopes of the spike protein.
Sijin Huang +12 more
wiley +1 more source
F1000ResearchBackground The rise of antibiotic-resistant bacteria presents a pressing need for exploring new natural compounds with innovative mechanisms to replace existing antibiotics.
Jonathan Cruz-Varela +4 more
doaj +1 more source
Gerbil: a fast and memory-efficient k-mer counter with GPU-support
Algorithms for Molecular Biology, 2017 Background A basic task in bioinformatics is the counting of k-mers in genome sequences. Existing k-mer counting tools are most often optimized for small k < 32 and suffer from excessive memory resource consumption or degrading performance for large k ...
Marius Erbert +2 more
doaj +1 more source
Space-efficient representation of genomic k-mer count tables
Algorithms for Molecular Biology, 2022 Abstract Motivation k-mer counting is a common task in bioinformatic pipelines, with many dedicated tools available. Many of these tools produce in output k-mer count tables containing both k-mers and counts, easily reaching tens of GB. Furthermore, such tables do not support efficient random-access queries in general.
Shibuya, Yoshihiro +2 more
openaire +7 more sources