A translatome-transcriptome multi-omics gene regulatory network reveals the complicated functional landscape of maize [0.03%]
泛基因组转录组与翻译组联合分析绘制玉米复杂功能基因调控网络
Wanchao Zhu,Xinxin Miao,Jia Qian et al.
Wanchao Zhu et al.
Background: Maize (Zea mays L.) is one of the most important crops worldwide. Although sophisticated maize gene regulatory networks (GRNs) have been constructed for functional genomics and phenotypic dissection, a multi-o...
Iman Hajirasouliha,Stefan Semrau
Iman Hajirasouliha
The annual Genome Informatics conference was held at the Wellcome Genome Campus on September 21-23, 2022. The conference covered a remarkable range of topics of which we highlight a few in this report. ...
Shenghan Gao,Xiaofei Yang,Hongtao Guo et al.
Shenghan Gao et al.
Significant improvements in long-read sequencing technologies have unlocked complex genomic areas, such as centromeres, in the genome and introduced the centromere annotation problem. Currently, centromeres are annotated in a semi-manual wa...
Current sequence-based models capture gene expression determinants in promoters but mostly ignore distal enhancers [0.03%]
当前的序列模型能够捕获启动子中的基因表达特征，但忽略了远端增强子区域
Alexander Karollus,Thomas Mauermeier,Julien Gagneur
Alexander Karollus
Background: The largest sequence-based models of transcription control to date are obtained by predicting genome-wide gene regulatory assays across the human genome. This setting is fundamentally correlative, as those mod...
João Pedro de Magalhães
João Pedro de Magalhães
Ageing is inherent to all human beings, yet why we age remains a hotly contested topic. Most mechanistic explanations of ageing posit that ageing is caused by the accumulation of one or more forms of molecular damage. Here, I propose that w...
A role for heritable transcriptomic variation in maize adaptation to temperate environments [0.03%]
遗传转录本变异在玉米适应温带环境中的作用
Guangchao Sun,Huihui Yu,Peng Wang et al.
Guangchao Sun et al.
Background: Transcription bridges genetic information and phenotypes. Here, we evaluated how changes in transcriptional regulation enable maize (Zea mays), a crop originally domesticated in the tropics, to adapt to temper...
Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra [0.03%]
利用GenEra在动物、植物和真菌的重大进化过程中揭示基因家族创始事件
Josué Barrera-Redondo,Jaruwatana Sodai Lotharukpong,Hajk-Georg Drost et al.
Josué Barrera-Redondo et al.
We present GenEra ( https://github.com/josuebarrera/GenEra ), a DIAMOND-fueled gene-family founder inference framework that addresses previously raised limitations and biases in genomic phylostratigraphy, such as homology detection failure....
Evidence for the role of transcription factors in the co-transcriptional regulation of intron retention [0.03%]
转录因子在内含子滞留共转录调控中作用的证据
Fahad Ullah,Saira Jabeen,Maayan Salton et al.
Fahad Ullah et al.
Background: Alternative splicing is a widespread regulatory phenomenon that enables a single gene to produce multiple transcripts. Among the different types of alternative splicing, intron retention is one of the least ex...
Tian Zhang,Gregory R Keele,Isabela Gerdes Gyuricza et al.
Tian Zhang et al.
Background: Phosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling cascades. The abundance of a phosphorylated peptide (phosphopeptide) is dete...
NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule [0.03%]
NOMe-HiC：在同一DNA分子中联合分析遗传变异、DNA甲基化、染色质可及性和三维基因组
Hailu Fu,Haizi Zheng,Xiaoting Chen et al.
Hailu Fu et al.
Cis-regulatory elements are coordinated to regulate the expression of their targeted genes. However, the joint measurement of cis-regulatory elements' activities and their interactions in spatial proximity is limited by the current sequenci...