Admixture influences the genetic architecture of DNA methylation in a wild primate hybrid zone [0.03%]
杂交带中杂交对野生灵长类动物DNA甲基化的遗传结构的影响
Tauras P Vilgalys,Jordan A Anderson,Arielle S Fogel et al.
Tauras P Vilgalys et al.
Background: Hybrid zones play a central role in evolutionary biology because they serve as natural laboratories for studying how traits and taxa diverge. Changes in gene regulation make important contributions to this pro...
Shilpa Rao,Aden Y Le,Logan Persyn et al.
Shilpa Rao et al.
Background: Translational buffering refers to the regulation of ribosome occupancy to offset the effects of transcriptional variation. While previous studies have primarily investigated translational buffering in yeast un...
RIMap-RISC: a transcriptome-wide database of structurally modeled human microRNA interactions [0.03%]
RIMap-RISC：结构建模的人类microRNA互作转录组数据库
Simon Chasles,Zakary Gaillard-Duchassin,Jordan Quenneville et al.
Simon Chasles et al.
RIMap-RISC is a web-accessible database for transcriptome-wide modeling of human microRNA (miRNA) targeting. It computes plausible transcript-miRNA interactions and records their position, duplex secondary structure, free energy, site class...
Yang Liu,Lu Zhou,Xiawei Du et al.
Yang Liu et al.
Background: The surge in single-cell omics data exposes limitations in traditional, manually defined analysis workflows. AI agents offer a paradigm shift, enabling adaptive planning, executable code generation, traceable ...
iPepGen: a modular, immunopeptidogenomic analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates [0.03%]
iPepGen：一种模块化免疫肽基因组分析管线，用于发现、验证和优先处理癌症肽新抗原候选物
Subina Mehta,Reid Wagner,Katherine T Do et al.
Subina Mehta et al.
Characterizing tumor-specific neoantigen peptides, derived from genomic or transcriptomic aberrations and presented to the immune system, is critical for immuno-oncology studies. To this end, the modular iPepGen immunopeptidogenomics pipeli...
A systematic benchmark of high-accuracy PacBio long-read RNA sequencing for transcript-level quantification [0.03%]
高精度PacBio长读RNA测序进行转录本水平定量的系统基准研究
David Wissel,Madison M Mehlferber,Khue M Nguyen et al.
David Wissel et al.
Background: The assembly of fragmented RNA-sequencing reads into complete transcripts is error-prone, particularly for genes with complex splicing, resulting in ambiguity in transcript discovery and quantification. PacBio...
Reducing demographic bias in biomedical machine learning for cancer detection using cfDNA methylation [0.03%]
使用cfDNA甲基化减少生物医学机器学习中用于癌症检测的人口统计学偏差
Shuo Li,Weihua Zeng,Wenyuan Li et al.
Shuo Li et al.
Background: Machine learning models in biomedical research are often hindered by demographic imbalances in clinical datasets, leading to biased predictions that disadvantage minority populations. Existing bias-correction ...
Integrating scRNA-seq and snRNA-seq with spatial transcriptomics to unlock the xylem puzzle [0.03%]
结合空间转录组学整合scRNA-seq和snRNA-seq解析木质部的奥秘
Mingke Wei,Jo-Wei Allison Hsieh,Jr-Fong Dang et al.
Mingke Wei et al.
Background: Xylem development is a dynamic, continuous process fundamental to secondary growth in woody plants and to biomass accumulation on earth. While single-cell RNA sequencing (scRNA-seq) enables reconstruction of e...
krepp: a k-mer-based maximum pseudo-likelihood method for estimating read distances and genome-wide phylogenetic placement [0.03%]
基于k-mer的读距离估计和全基因组系统发育置位的最大伪似然法 KrePP
Ali Osman Berk Şapcı,Siavash Mirarab
Ali Osman Berk Şapcı
Comparing each sequencing read in a sample to a reference database is a fundamental step in wide-ranging applications. Results of these comparisons can enable phylogenetic characterization. However, phylogenetic placement is currently only ...
Decoding human tRNA modifications and crosstalk by enhanced single-read analysis [0.03%]
增强的单读数分析破解人类tRNA修饰及互作关系
Mahdi Assari,Brandon J Chew,Mohammad Amin Bayat Tork et al.
Mahdi Assari et al.
Background: Transfer RNA (tRNA) modifications play important roles in regulating gene expression and protein synthesis, yet their dynamic interplay remains elusive. The human tRNAome contains approximately 40 modification...