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...
Stable maternal proteins underlie distinct transcriptome, translatome, and proteome reprogramming during mouse oocyte-to-embryo transition [0.03%]
稳定的母源蛋白决定了小鼠卵子到胚胎转变过程中独特的转录组、翻译组和蛋白质组的重新编程
Hongmei Zhang,Shuyan Ji,Ke Zhang et al.
Hongmei Zhang et al.
Background: The oocyte-to-embryo transition (OET) converts terminally differentiated gametes into a totipotent embryo and is critically controlled by maternal mRNAs and proteins, while the genome is silent until zygotic g...
SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty [0.03%]
翘翘板：在推断不确定性情况下检测亚型水平的等位基因不平衡
Euphy Y Wu,Noor P Singh,Kwangbom Choi et al.
Euphy Y Wu et al.
Detecting allelic imbalance at the isoform level requires accounting for inferential uncertainty, caused by multi-mapping of RNA-seq reads. Our proposed method, SEESAW, uses Salmon and Swish to offer analysis at various levels of resolution...
Mapping genetic variants for nonsense-mediated mRNA decay regulation across human tissues [0.03%]
绘制无义介导的mRNA衰减调节在人类组织间的遗传变异图谱
Bo Sun,Liang Chen
Bo Sun
Background: Nonsense-mediated mRNA decay (NMD) was originally conceived as an mRNA surveillance mechanism to prevent the production of potentially deleterious truncated proteins. Research also shows NMD is an important po...
GreenHill: a de novo chromosome-level scaffolding and phasing tool using Hi-C [0.03%]
GreenHill：一种利用Hi-C从头进行染色体水平挂载和分型的工具
Shun Ouchi,Rei Kajitani,Takehiko Itoh
Shun Ouchi
Chromosome-level haplotype-resolved genome assembly is an important resource in molecular biology. However, current de novo haplotype assemblers require parental data or reference genomes and often fail to provide chromosome-level results. ...
Sayali Anil Alatkar,Daifeng Wang
Sayali Anil Alatkar
Multimodal measurements of single-cell sequencing technologies facilitate a comprehensive understanding of specific cellular and molecular mechanisms. However, simultaneous profiling of multiple modalities of single cells is challenging, an...
Tiago Maié,Marco Schmidt,Myriam Erz et al.
Tiago Maié et al.
DNA methylation signatures are usually based on multivariate approaches that require hundreds of sites for predictions. Here, we propose a computational framework named CimpleG for the detection of small CpG methylation signatures used for ...