The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species [0.03%]
奶牛泛基因组联盟：在全球奶牛品种及其他反刍动物种类中实现基因组组装的民主化和普及性
Timothy P L Smith,Derek M Bickhart,Didier Boichard et al.
Timothy P L Smith et al.
The Bovine Pangenome Consortium (BPC) is an international collaboration dedicated to the assembly of cattle genomes to develop a more complete representation of cattle genomic diversity. The goal of the BPC is to provide genome assemblies a...
Characterization of novel loci controlling seed oil content in Brassica napus by marker metabolite-based multi-omics analysis [0.03%]
基于标记代谢组多组学分析的大豆油分含量新位点的鉴定
Long Li,Zhitao Tian,Jie Chen et al.
Long Li et al.
Background: Seed oil content is an important agronomic trait of Brassica napus (B. napus), and metabolites are considered as the bridge between genotype and phenotype for physical traits. ...
Synergising single-cell resolution and 4sU labelling boosts inference of transcriptional bursting [0.03%]
单细胞分辨率和4sU标记的协同作用可提升转录爆发推断能力
David M Edwards,Philip Davies,Daniel Hebenstreit
David M Edwards
Despite the recent rise of RNA-seq datasets combining single-cell (sc) resolution with 4-thiouridine (4sU) labelling, analytical methods exploiting their power to dissect transcriptional bursting are lacking. Here, we present a mathematical...
Sebastian Schmidt,Shahbaz Khan,Jarno N Alanko et al.
Sebastian Schmidt et al.
We propose a polynomial algorithm computing a minimum plain-text representation of k-mer sets, as well as an efficient near-minimum greedy heuristic. When compressing read sets of large model organisms or bacterial pangenomes, with only a m...
Author Correction: INSERT-seq enables high-resolution mapping of genomically integrated DNA using Nanopore sequencing [0.03%]
作者勘误：INSERT-seq 使用纳米孔测序实现基因组整合DNA的高分辨率映射
Dimitrije Ivančić,Júlia Mir-Pedrol,Jessica Jaraba-Wallace et al.
Dimitrije Ivančić et al.
Published Erratum
Genome biology. 2023 Jun 9;24(1):137. DOI:10.1186/s13059-023-02979-w 2023
Yannis Nevers,Natasha M Glover,Christophe Dessimoz et al.
Yannis Nevers et al.
Background: In every living species, the function of a protein depends on its organization of structural domains, and the length of a protein is a direct reflection of this. Because every species evolved under different e...
Rui Yang,Arnav Das,Vianne R Gao et al.
Rui Yang et al.
Recent deep learning models that predict the Hi-C contact map from DNA sequence achieve promising accuracy but cannot generalize to new cell types and or even capture differences among training cell types. We propose Epiphany, a neural netw...
mutscan-a flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data [0.03%]
MutScan：一个用于有效分析变异效应多路复用测定数据的灵活的R软件包
Charlotte Soneson,Alexandra M Bendel,Guillaume Diss et al.
Charlotte Soneson et al.
Multiplexed assays of variant effect (MAVE) experimentally measure the effect of large numbers of sequence variants by selective enrichment of sequences with desirable properties followed by quantification by sequencing. mutscan is an R pac...
Kristoffer Sahlin,Thomas Baudeau,Bastien Cazaux et al.
Kristoffer Sahlin et al.
It has been over a decade since the first publication of a method dedicated entirely to mapping long-reads. The distinctive characteristics of long reads resulted in methods moving from the seed-and-extend framework used for short reads to ...
Pervasive tandem duplications and convergent evolution shape coral genomes [0.03%]
普遍的串联重复和趋同进化塑造珊瑚基因组
Benjamin Noel,France Denoeud,Alice Rouan et al.
Benjamin Noel et al.
Background: Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central...