Akmuhammet Ashyralyyev,Zülal Bingöl,Begüm Filiz Öz et al.
Akmuhammet Ashyralyyev et al.
Efficient and consistent string processing is critical in the exponentially growing genomic data era. Locally Consistent Parsing (LCP) addresses this need by partitioning an input genome string into short, exactly matching substrings ("core...
Author Correction: Spatiotemporal transcriptomics reveals key gene regulation for grain yield and quality in wheat [0.03%]
Xiaohui Li,Yiman Wan,Dongzhi Wang et al.
Xiaohui Li et al.
Published Erratum
Genome biology. 2026 Apr 23;27(1):142. DOI:10.1186/s13059-026-04065-3 2026
Geometry-aware graph attention networks to explain single-cell chromatin states and gene expression with SEAGALL [0.03%]
Gabriele Malagoli,Patrick Hanel,Anna Danese et al.
Gabriele Malagoli et al.
High-throughput single-cell sequencing is widely used to study cell identity. We present SEAGALL (Single-cell Explainable Geometry-Aware Graph Attention Learning pipeLine), a deep learning method to quantify the impact of molecular features...
CrossFilt: a cross-species filtering tool that eliminates alignment bias in comparative genomics studies of primates [0.03%]
Kenneth A Barr,Yoav Gilad
Kenneth A Barr
Comparative functional genomic studies are often affected by biased read mapping across species due to inter-species differences in genome structure, sequence composition, and annotation quality. We developed CrossFilt, a filtering strategy...
Machine learning predictions surpass individual mRNAs as a proxy of single-cell protein expression [0.03%]
Josephine Fisher,Oliver Wood,Samuel Bullers et al.
Josephine Fisher et al.
Background: Expansive repositories of scRNA-seq data are now available. These are often analysed assuming that mRNA abundance reflects expression of the cognate protein. However, post-transcriptional/translational regulat...
Kailing Tu,Qilin Zhang,Yang Li et al.
Kailing Tu et al.
Somatic structural variations (SVs) are critical in cancer genomes, yet their detection from long-read sequencing remains challenging due to alignment errors in repetitive regions. We develop SVScope, leveraging full-length reads and local ...
Single-cell and spatial transcriptomics in Phragmites australis reveal the association of B chromosomes with plant invasiveness [0.03%]
Cui Wang,James Ord,Mengxiao Yan et al.
Cui Wang et al.
Background: Invasive plants pose a major threat to global biodiversity, yet the molecular and genomic mechanisms underlying their success remain poorly understood. Here, we investigate the invasion of the common reed Phra...
SpaNiche: spatial niche analysis to explore colocalization patterns and cellular interactions in spatial transcriptomics data [0.03%]
Siyuan Huang,Qinghua Ran,Junjie Tang et al.
Siyuan Huang et al.
We propose a computational framework for spatial niche analysis (SpaNiche) in spatial transcriptomics data to uncover colocalization patterns and infer potential ligand-receptor interactions. SpaNiche leverages graph-regularized joint non-n...
Jian Song,Amanda Momenzadeh,Hebin Liu et al.
Jian Song et al.
diaPASEF improves ion utilization and sensitivity by synchronizing quadrupole isolation with trapped ion mobility separation, making it suitable for single-cell proteomics. We present Full-DIA, a deep learning-driven software that enhances ...
Alison Harrod,Hugang Feng,Nagham Ghaddar et al.
Alison Harrod et al.
Background: G-quadruplex (G4) structures are secondary structures that can form in guanine-rich single stranded DNA sequences. These play important roles in biological processes such as regulation of gene expression but c...