Genetic impacts on DNA methylation help elucidate regulatory genomic processes [0.03%]
基因对DNA甲基化的影响有助于阐明调控基因组过程
Sergio Villicaña,Juan Castillo-Fernandez,Eilis Hannon et al.
Sergio Villicaña et al.
Background: Pinpointing genetic impacts on DNA methylation can improve our understanding of pathways that underlie gene regulation and disease risk. Resul...
vamos: variable-number tandem repeats annotation using efficient motif sets [0.03%]
利用高效的动机集进行VANS可变数串联重复序列注释
Jingwen Ren,Bida Gu,Mark J P Chaisson
Jingwen Ren
Roughly 3% of the human genome is composed of variable-number tandem repeats (VNTRs): arrays of motifs at least six bases. These loci are highly polymorphic, yet current approaches that define and merge variants based on alignment breakpoin...
ISLET: individual-specific reference panel recovery improves cell-type-specific inference [0.03%]
ISLET：个体特异性参考面板恢复可改善细胞类型特异性推断
Hao Feng,Guanqun Meng,Tong Lin et al.
Hao Feng et al.
We propose a statistical framework ISLET to infer individual-specific and cell-type-specific transcriptome reference panels. ISLET models the repeatedly measured bulk gene expression data, to optimize the usage of shared information within ...
Observational Study
Genome biology. 2023 Jul 26;24(1):174. DOI:10.1186/s13059-023-03014-8 2023
Ireneusz Stolarek,Michal Zenczak,Luiza Handschuh et al.
Ireneusz Stolarek et al.
Background: The appearance of Slavs in East-Central Europe has been the subject of an over 200-year debate driven by two conflicting hypotheses. The first assumes that Slavs came to the territory of contemporary Poland no...
Predicting disease severity in metachromatic leukodystrophy using protein activity and a patient phenotype matrix [0.03%]
基于蛋白质活性和患者表型矩阵的元猫跳色白质营养不良疾病严重程度预测
Marena Trinidad,Xinying Hong,Steven Froelich et al.
Marena Trinidad et al.
Background: Metachromatic leukodystrophy (MLD) is a lysosomal storage disorder caused by mutations in the arylsulfatase A gene (ARSA) and categorized into three subtypes according to age of onset. The functional effect of...
Zhiheng Liu,Giovanni Quinones-Valdez,Ting Fu et al.
Zhiheng Liu et al.
Although long-read RNA-seq is increasingly applied to characterize full-length transcripts it can also enable detection of nucleotide variants, such as genetic mutations or RNA editing sites, which is significantly under-explored. Here, we ...
MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads [0.03%]
MSV：通过直接从读段推断并统一破裂端来揭示嵌套和复杂重排的模块化结构变异调用器
Markus Schmidt,Arne Kutzner
Markus Schmidt
Structural variant (SV) calling belongs to the standard tools of modern bioinformatics for identifying and describing alterations in genomes. Initially, this work presents several complex genomic rearrangements that reveal conceptual ambigu...
Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD [0.03%]
使用EMERALD从生物多样蛋白簇中敏感地推断安全对齐间隔区间的方法
Andreas Grigorjew,Artur Gynter,Fernando H C Dias et al.
Andreas Grigorjew et al.
Sequence alignments are the foundations of life science research, but most innovation so far focuses on optimal alignments, while information derived from suboptimal solutions is ignored. We argue that one optimal alignment per pairwise seq...
Identifying and quantifying isoforms from accurate full-length transcriptome sequencing reads with Mandalorion [0.03%]
利用Mandalorion从全长转录组测序读段中识别和量化异构体
Roger Volden,Kayla D Schimke,Ashley Byrne et al.
Roger Volden et al.
In this manuscript, we introduce and benchmark Mandalorion v4.1 for the identification and quantification of full-length transcriptome sequencing reads. It further improves upon the already strong performance of Mandalorion v3.6 used in the...
Comprehensive analysis of neoantigens derived from structural variation across whole genomes from 2528 tumors [0.03%]
来自2528个肿瘤的全基因组的结构变异衍生neo抗原的综合分析
Yang Shi,Biyang Jing,Ruibin Xi
Yang Shi
Background: Neoantigens are critical for anti-tumor immunity and have been long-envisioned as promising therapeutic targets. However, current neoantigen analyses mostly focus on single nucleotide variations (SNVs) and ind...