GeneRAIN: multifaceted representation of genes via deep learning of gene expression networks [0.03%]
通过深度学习基因表达网络的基因多功能表示法(GeneRAIN)
Zheng Su,Mingyan Fang,Andrei Smolnikov et al.
Zheng Su et al.
We develop GeneRAIN, a suite of Transformer-based models that learn gene expression relationships from 410 K human bulk RNA-seq samples. Featuring a novel Binning-By-Gene normalization technique, our models capture diverse biological inform...
Regulation of heterosis-associated gene expression complementation in maize hybrids [0.03%]
调控玉米杂种优势相关基因表达互补的机制研究
Marion Pitz,Jutta A Baldauf,Hans-Peter Piepho et al.
Marion Pitz et al.
Background: Classical genetic concepts to explain heterosis attribute the superiority of F1-hybrids over their homozygous parents to the complementation of unfavorable by beneficial alleles (dominance) or to heterozygote ...
KEGNI: knowledge graph enhanced framework for gene regulatory network inference [0.03%]
基于知识图谱的基因调控网络推理框架
Pengxiao Li,Lin Li,Jingminjie Nan et al.
Pengxiao Li et al.
Inference of cell type-specific gene regulatory networks (GRNs) is a fundamental step in investigating complex regulatory mechanisms. Here, we present KEGNI (Knowledge graph-Enhanced Gene regulatory Network Inference), a knowledge-guided fr...
microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis [0.03%]
MicrobeTag：通过注释、丰富性检验和代谢互补性分析简化微生物网络解释
Haris Zafeiropoulos,Ermis Ioannis Michail Delopoulos,Andi Erega et al.
Haris Zafeiropoulos et al.
Microbial co-occurrence network inference is often hindered by low accuracy and tool dependency. We introduce microbetag, a comprehensive software ecosystem designed to annotate microbial networks. Nodes, representing taxa, are enriched wit...
Topsicle: a method for estimating telomere length from whole genome long-read sequencing data [0.03%]
一种从全基因组长读段测序数据估计端粒长度的方法
Linh Nguyen,Jae Young Choi
Linh Nguyen
Telomeres protect chromosome ends and their length varies significantly between organisms. Because telomere length variation is associated with various biomedical and eco-evolutionary phenotypes, many biological fields are interested in und...
Bruce Budowle,Kristen Mittelman,David Mittelman
Bruce Budowle
Dense single nucleotide polymorphism testing has revolutionized forensic science, helping solve decadesold, current and future cases by overcoming the limitations of traditional short tandem repeat profiling. By embracing innovations from f...
ScIsoX: a multidimensional framework for measuring isoform-level transcriptomic complexity in single cells [0.03%]
ScIsoX：单细胞中测量转录本异构体水平转录组复杂度的多维框架
Siyuan Wu,Ulf Schmitz
Siyuan Wu
Single-cell isoform analysis enables high-resolution characterization of transcript expression, yet analytical frameworks to systematically measure transcriptomic complexity are lacking. Here, we introduce ScIsoX, a computational framework ...
Jonas Scheid,Steffen Lemke,Naomi Hoenisch-Gravel et al.
Jonas Scheid et al.
Confident identification of human leukocyte antigen (HLA)-presented peptides is crucial for advancing cancer immunotherapy. We present MHCquant2, a scalable and modular Nextflow pipeline integrated into nf-core as a reproducible, portable, ...
Deciphering the sequence basis and application of transcriptional initiation regulation in plant genomes through deep learning [0.03%]
基于深度学习的植物基因组转录起始调控的序列解析及应用研究
Pengfei Gao,Lijie Lian,Wanjie Feng et al.
Pengfei Gao et al.
Background: Transcription initiation is a key checkpoint in plant gene regulation, yet the DNA features that determine where and the frequency of the genes start transcription remain unclear. ...
SIGEL: a context-aware genomic representation learning framework for spatial genomics analysis [0.03%]
SIGEL：一种用于空间组学分析的上下文感知基因组表示学习框架
Wenlin Li,Maocheng Zhu,Yucheng Xu et al.
Wenlin Li et al.
Spatial transcriptomics (ST) integrates spatial information into genomics, yet methods for generating spatially-informed gene representations are limited and computationally intensive. We present SIGEL, a cost-effective framework that deriv...