Author Correction: DNA methylation remodeling and the functional implication during male gametogenesis in rice [0.03%]
作者更正：DNA甲基化重塑及DNA甲基化在水稻雄配子发生过程中的功能分析
Xue Li,Bo Zhu,Yue Lu et al.
Xue Li et al.
Published Erratum
Genome biology. 2024 Jul 27;25(1):196. DOI:10.1186/s13059-024-03344-1 2024
SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models [0.03%]
SonicParanoid 2：基于机器学习和语言模型的快速、准确且全面的同源性推断方法
Salvatore Cosentino,Sira Sriswasdi,Wataru Iwasaki
Salvatore Cosentino
Accurate inference of orthologous genes constitutes a prerequisite for comparative and evolutionary genomics. SonicParanoid is one of the fastest tools for orthology inference; however, its scalability and accuracy have been hampered by tim...
Manish Goel,José A Campoy,Kristin Krause et al.
Manish Goel et al.
Background: Plant meristems are structured organs consisting of distinct layers of stem cells, which differentiate into new plant tissue. Mutations in meristematic layers can propagate into large sectors of the plant. How...
N6-methyladenosine writer METTL16-mediated alternative splicing and translation control are essential for murine spermatogenesis [0.03%]
N6-甲基腺苷书写物METTL16介导的可变剪接和翻译调控对小鼠精子发生至关重要
Qian Ma,Yiqian Gui,Xixiang Ma et al.
Qian Ma et al.
Background: The mitosis-to-meiosis switch during spermatogenesis requires dynamic changes in gene expression. However, the regulation of meiotic transcriptional and post-transcriptional machinery during this transition re...
A benchmark of computational methods for correcting biases of established and unknown origin in CRISPR-Cas9 screening data [0.03%]
校正CRISPR-Cas9筛选数据中已知和未知偏差的计算方法评估
Alessandro Vinceti,Raffaele M Iannuzzi,Isabella Boyle et al.
Alessandro Vinceti et al.
Background: CRISPR-Cas9 dropout screens are formidable tools for investigating biology with unprecedented precision and scale. However, biases in data lead to potential confounding effects on interpretation and compromise...
Single-cell decoding of drug induced transcriptomic reprogramming in triple negative breast cancers [0.03%]
三阴性乳腺癌单细胞药物转录重编的解码
Farhia Kabeer,Hoa Tran,Mirela Andronescu et al.
Farhia Kabeer et al.
Background: The encoding of cell intrinsic drug resistance states in breast cancer reflects the contributions of genomic and non-genomic variations and requires accurate estimation of clonal fitness from co-measurement of...
Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE [0.03%]
利用单细胞数据的邻域表示进行敏感差异表达分析的miloDE方法
Alsu Missarova,Emma Dann,Leah Rosen et al.
Alsu Missarova et al.
Single-cell RNA-sequencing enables testing for differential expression (DE) between conditions at a cell type level. While powerful, one of the limitations of such approaches is that the sensitivity of DE testing is dictated by the sensitiv...
Non-coding variants impact cis-regulatory coordination in a cell type-specific manner [0.03%]
非编码变异以细胞类型特异性的方式影响顺式调节协调作用
Olga Pushkarev,Guido van Mierlo,Judith Franziska Kribelbauer et al.
Olga Pushkarev et al.
Background: Interactions among cis-regulatory elements (CREs) play a crucial role in gene regulation. Various approaches have been developed to map these interactions genome-wide, including those relying on interindividua...
Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data [0.03%]
基于第三代测序数据的结构变异检测流程评估
Zhi Liu,Zhi Xie,Miaoxin Li
Zhi Liu
Background: Structural variation (SV) detection methods using third-generation sequencing data are widely employed, yet accurately detecting SVs remains challenging. Different methods often yield inconsistent results for ...
Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans [0.03%]
牛的表观遗传变异与人类相似
Wen-Jou Chang,Maria S Baker,Eleonora Laritsky et al.
Wen-Jou Chang et al.
Background: We recently identified ~ 10,000 correlated regions of systemic interindividual epigenetic variation (CoRSIVs) in the human genome. These methylation variants are amenable to population studies, as DNA methylat...