Gal Gilad,Teresa M Przytycka,Roded Sharan
Gal Gilad
Background: Mutational processes shape cancer genomes, leaving characteristic marks that are termed signatures. The level of activity of each such process, or its signature exposure, provides important information on the ...
Mahmudur Rahman Hera,Paul Medvedev,David Koslicki et al.
Mahmudur Rahman Hera et al.
Methods utilizing k-mers are widely used in bioinformatics, yet our understanding of their statistical properties under realistic mutation models remains incomplete. Previously, substitution-only mutation models have been considered to deri...
A k-mer-based estimator of the substitution rate between repetitive sequences [0.03%]
基于k-mer的重复序列替换率估计方法
Haonan Wu,Antonio Blanca,Paul Medvedev
Haonan Wu
Background: K-mer-based analysis of genomic data is ubiquitous, but the presence of repetitive k-mers continues to pose problems for the accuracy of many methods. For example, the Mash tool (Ondov et al 2016) can accurate...
Parvesh Barak,Daniel Gibney,Chirag Jain
Parvesh Barak
Error correction of long reads is an important initial step in genome assembly workflows. For organisms with ploidy greater than one, it is important to preserve haplotype-specific variation during read correction. This challenge has driven...
Marcos E González Laffitte,Tieu-Long Phan,Peter F Stadler
Marcos E González Laffitte
Chemical reaction databases typically report the molecular structures of reactant and product compounds, as well as their stoichiometry, but lack information, in particular, on the correspondence of reactant and product atoms. These atom-to...
Parsa Eskandar,Benedict Paten,Jouni Sirén
Parsa Eskandar
Pangenome graphs represent the genomic variation by encoding multiple haplotypes within a unified graph structure. However, efficient and lossless indexing of such structures remains challenging due to the scale and complexity of pangenomic...
Dolphyin: a combinatorial algorithm for identifying 1-Dollo phylogenies in cancer [0.03%]
用于在癌症中识别1- Dollo谱系的组合算法Dolphyin
Daniel W Feng,Mohammed El-Kebir
Daniel W Feng
Background: Several recent cancer phylogeny inference methods have used the k-Dollo evolutionary model for single-nucleotide variants, which requires a phylogeny T on binary sequencing data matrix B such that each variant...
Lukas Geis,Dennis Hecker,Martin Hoefer et al.
Lukas Geis et al.
Transcription factors (TFs) are essential players in the regulation of gene expression and thus have been the subject of interest in the context of diseases and the manipulation of specific cell functions or pathways. The complex interplay ...
Comparing the ability of embedding methods on metabolic hypergraphs for capturing taxonomy-based features [0.03%]
比较代谢超图的嵌入方法以捕获基于分类学的特征的能力
Mattia Cervellini,Blerina Sinaimeri,Catherine Matias et al.
Mattia Cervellini et al.
Background: Metabolic networks are complex systems that describe the biochemical reactions within an organism through pairwise interactions between chemical compounds. While this representation is widely used to study bio...
Pattern matching with Elastic-Degenerate strings and Elastic-Founder graphs [0.03%]
基于弹性退化字符串和建立者弹性的图形的模式匹配问题研究
Rocco Ascone,Giulia Bernardini,Alessio Conte et al.
Rocco Ascone et al.
Elastic Degenerate (ED) strings and Elastic Founder (EF) graphs, here collectively named variable strings, are two representations of acyclic components of pangenomes which extend the well-known notion of indeterminate string. Recent studie...