[HTML][HTML] Peptide absent sequences emerging in human cancers
Early diagnosis of cancer can significantly improve survival of cancer patients; however
sensitive and highly specific biomarkers for cancer detection are currently lacking for most …
sensitive and highly specific biomarkers for cancer detection are currently lacking for most …
Identification of the shortest species-specific oligonucleotide sequences
Despite the exponential increase in sequencing information driven by massively parallel
DNA sequencing technologies, universal and succinct genomic fingerprints for each …
DNA sequencing technologies, universal and succinct genomic fingerprints for each …
[HTML][HTML] kmerDB: a database encompassing the set of genomic and proteomic sequence information for each species
The decrease in sequencing expenses has facilitated the creation of reference genomes
and proteomes for an expanding array of organisms. Nevertheless, no established …
and proteomes for an expanding array of organisms. Nevertheless, no established …
Endhered patterns in matchings and RNA
C Biane, G Hampikian, S Kirgizov… - Journal of …, 2024 - liebertpub.com
An endhered (end-adhered) pattern is a subset of arcs in matchings, such that the
corresponding starting points are consecutive, and the same holds for the ending points …
corresponding starting points are consecutive, and the same holds for the ending points …
Nucleic quasi-primes: identification of the shortest unique oligonucleotide sequences in a species
Despite the exponential increase in sequencing information driven by massively parallel
DNA sequencing technologies, universal and succinct genomic fingerprints for each …
DNA sequencing technologies, universal and succinct genomic fingerprints for each …
[HTML][HTML] The topography of nullomer-emerging mutations and their relevance to human disease
Nullomers are short DNA sequences (11-18 base pairs) that are absent from a genome;
however, they can emerge due to mutations. Here, we characterize all possible putative …
however, they can emerge due to mutations. Here, we characterize all possible putative …
The determinants of the rarity of nucleic and peptide short sequences in nature
The prevalence of nucleic and peptide short sequences across organismal genomes and
proteomes has not been thoroughly investigated. We examined 45 785 reference genomes …
proteomes has not been thoroughly investigated. We examined 45 785 reference genomes …
Zimin patterns in genomes
N Chantzi, I Mouratidis… - arXiv preprint arXiv …, 2024 - arxiv.org
Zimin words are words that have the same prefix and suffix. They are unavoidable patterns,
with all sufficiently large strings encompassing them. Here, we examine for the first time the …
with all sufficiently large strings encompassing them. Here, we examine for the first time the …
Genomic and Transcriptomic Examination of Functional Elements and Absent Sequences
CSY Chan - 2024 - escholarship.org
Background: Genome-wide association studies have identified numerous disease-
associated variants, but a vast majority are located in non-coding regions, making it …
associated variants, but a vast majority are located in non-coding regions, making it …
[HTML][HTML] A survey of k-mer methods and applications in bioinformatics
The rapid progression of genomics and proteomics has been driven by the advent of
advanced sequencing technologies, large, diverse, and readily available omics datasets …
advanced sequencing technologies, large, diverse, and readily available omics datasets …