Differential LTR-retrotransposon dynamics across polyploidization, speciation, domestication, and improvement of cotton (Gossypium) [0.03%]
棉属多倍化、分化、驯化和改良过程中LTR反转录转座子的动态变化
Lucía Campos-Dominguez,Raúl Castanera,Corrinne E Grover et al.
Lucía Campos-Dominguez et al.
Background: Transposable elements are major components of plant genomes and major drivers of plant genome evolution. The cotton genus (Gossypium) is an excellent evolutionary model for polyploidization, speciation, domest...
CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets [0.03%]
CarpeDeam：一种古老的、受损严重的古DNA从头组装方法
Louis Kraft,Johannes Söding,Martin Steinegger et al.
Louis Kraft et al.
De novo assembly of ancient metagenomic datasets is a challenging task. Ultra-short fragment size and characteristic postmortem damage patterns of sequenced ancient DNA molecules leave current tools ill-equipped for ideal assembly. We prese...
Rational design of promoter editing confers multipathogen resistance in rice [0.03%]
理性设计启动子编辑使水稻具备广谱抗病性
Xinyu Han,Lei Yang,Fengdie Xia et al.
Xinyu Han et al.
Background: Fine-tuned gene expression rather than alterations in the protein-coding region of a gene is responsible for the optimal performance conferred by many elite alleles in crops. Lesion mimic mutants (LMMs), a typ...
Unlocking the regulatory code of RNA: launching the Human RNome Project [0.03%]
破解RNA调控代码：“人类RNOME项目”启动
International Human RNome Project Consortium
International Human RNome Project Consortium
The human RNome, the complete set of RNA molecules in human cells, arises through complex processing and includes diverse molecular species. While research traditionally focuses on four canonical nucleotide residues, the RNome, encompassing...
ParaMask: a new method to identify multicopy genomic regions, corrects major biases in whole-genome sequencing data [0.03%]
ParaMask：一种识别重复基因组区域的新方法，并校正全基因组测序数据中的主要偏差
Bastiaan Tjeng,Male Arimond,Helene Bråten Grindeland et al.
Bastiaan Tjeng et al.
Multicopy genomic regions are repeated sequences that can bias genomic analyses. Here, we present a method, ParaMask, to identify and filter multicopy regions in population-level genomic data of any species. The broad applicability of this ...
Identification of microprotein-coding intronic polyadenylation isoforms and function in genotoxic anticancer drug response [0.03%]
识别微蛋白编码内含子多聚腺苷酸化异构体及其在基因毒性抗癌药物反应中的功能
Alexandre Devaux,Iris Tanaka,Quentin Fouilleul et al.
Alexandre Devaux et al.
Background: Many transcript isoforms generated by intronic polyadenylation (IPA) encode isoforms of canonical proteins. Microproteins are an emerging class of small proteins translated from small open reading frames (sORF...
ParaRef: a decontaminated reference database for parasite detection in ancient and modern metagenomic datasets [0.03%]
ParaRef：一个用于古基因组和现代宏基因组数据寄生虫检测的去污染参考数据库
Jonas Niemann,Yuejiao Huang,Liam T Lanigan et al.
Jonas Niemann et al.
Shotgun metagenomics holds great potential for identifying parasite DNA in biological samples, but its effectiveness is limited by widespread contamination in publicly available reference genomes, which hinders accurate detection. In this s...
Author Correction: CpG island turnover events predict evolutionary changes in enhancer activity [0.03%]
作者更正：CpG岛周转事件可预测增强子活性的进化变化
Acadia A Kocher,Emily V Dutrow,Severin Uebbing et al.
Acadia A Kocher et al.
Published Erratum
Genome biology. 2025 Oct 22;26(1):363. DOI:10.1186/s13059-025-03834-w 2025
iNOME-seq: in vivo simultaneous genome-wide mapping of chromatin accessibility, nucleosome positioning, DNA-binding protein sites, and DNA methylation in Arabidopsis [0.03%]
iNOME-seq：在阿拉伯芥中同时进行染色体可接近性、核小体定位、DNA结合蛋白位点和DNA甲基化的全基因组测绘的体内方法
Nosheen Hussain,Ryan Merrit,Julia Engelhorn et al.
Nosheen Hussain et al.
We present iNOMe-seq, a novel method for in vivo simultaneous profiling of chromatin accessibility, nucleosome occupancy, DNA-binding protein sites, and DNA methylation in living tissues. iNOMe-seq utilizes an m5C methyltransferase to mark ...
Md Hassan Uz-Zaman,Howard Ochman
Md Hassan Uz-Zaman
Background: The birth of new genes from non-coding sequences has been postulated to be preceded by a proto-gene phase, in which a sequence is translated into protein but does not exhibit hallmarks of a clear function. Des...