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...
Genomic and epidemiological identification of Pseudomonas aeruginosa transmission chains and in hospital ICUs [0.03%]
利用基因组学和流行病学识别医院重症监护病房中恶臭假单胞菌的传播链
Lucia Graña-Miraglia,Xiaoyi Hu,Cheryl Volling et al.
Lucia Graña-Miraglia et al.
Background: Pseudomonas aeruginosa (PA) is an opportunistic pathogen that poses a significant threat to hospitalized patients, particularly in intensive care units (ICUs) due to its ability to contaminate the environment ...