基因组生物学涵盖从基因组和后基因组角度研究的生物学和生物医学的所有领域。内容包括研究、新方法和软件工具，以及评论、意见和评论。涵盖的领域包括但不限于：序列分析；生物信息学；深入了解分子、细胞和有机体生物学；功能基因组学；表观基因组学；群体基因组学；蛋白质组学；比较生物学和进化论；系统和网络生物学；基因组编辑和工程；疾病基因组学；和临床基因组学。

Genome Biology covers all areas of biology and biomedicine studied from the perspectives of genomics and post-genomics. The content includes research articles, new methods and software tools, as well as reviews and opinions. The fields covered include, but are not limited to: sequence analysis; bioinformatics; in-depth studies of molecular, cellular, and organismal biology; functional genomics; epigenomics; population genomics; proteomics; comparative biology and evolution; systems and network biology; genome editing and engineering; disease genomics; and clinical genomics.

《Genome Biology》期刊涵盖了从基因组和后基因组的角度研究生物学和生物医学的各个领域。内容包括研究论文、新方法和软件工具，以及评论和意见。涉及的领域包括但不限于：序列分析、生物信息学、分子、细胞和有机体生物学的深入研究、功能基因组学、表观基因组学、群体基因组学、蛋白质组学、比较生物学和进化论、系统和网络生物学、基因组编辑和工程、疾病基因组学以及临床基因组学。

Genome Biology

CRISPR/Cas systems confer immunity against invading nucleic acids and phages in bacteria and archaea. CRISPR/Cas13a (known previously as C2c2) is a class 2 type VI-A ribonuclease capable of targeting and cleaving single-stranded RNA (ssRNA) molecules of the phage genome. Here, we employ CRISPR/Cas13a to engineer interference with an RNA virus, Turnip Mosaic Virus (TuMV), in plants. CRISPR/Cas13a produces interference against green fluorescent protein (GFP)-expressing TuMV in transient assays and stable overexpression lines of Nicotiana benthamiana. CRISPR RNA (crRNAs) targeting the HC-Pro and GFP sequences exhibit better interference than those targeting other regions such as coat protein (CP) sequence. Cas13a can also process pre-crRNAs into functional crRNAs. Our data indicate that CRISPR/Cas13a can be used for engineering interference against RNA viruses, providing a potential novel mechanism for RNA-guided immunity against RNA viruses and for other RNA manipulations in plants.

Rashid Aman

Zahir Ali

Haroon Butt

Ahmed Mahas

Fatimah Aljedaani

Muhammad Zuhaib Khan

Shouwei Ding

Magdy Mahfouz

Genome biology

Genome Biol

RNA virus interference via CRISPR/Cas13a system in plants

植物中通过CRISPR/Cas13a系统进行的RNA病毒干扰

Abstract Background AsCas12a and LbCas12a nucleases are reported to be promising tools for genome engineering with protospacer adjacent motif (PAM) TTTV as the optimal. However, the C-containing PAM (CTTV, TCTV, TTCV, etc.) recognition by Cas12a might induce extra off-target edits at these non-canonical PAM sites. Results Here, we identify a novel Cas12a nuclease CeCas12a from Coprococcus eutactus , which is a programmable nuclease with genome-editing efficiencies comparable to AsCas12a and LbCas12a in human cells. Moreover, CeCas12a is revealed to be more stringent for PAM recognition in vitro and in vivo followed by very low off-target editing rates in cells. Notably, CeCas12a renders less off-target edits located at C-containing PAM at multiple sites compared to LbCas12a and AsCas12a, as assessed by targeted sequencing methods. Conclusions Our study shows that CeCas12a nuclease is active in human cells and the stringency of PAM recognition could be an important factor shaping off-target editing in gene editing. Thus, CeCas12a provides a promising candidate with distinctive characteristics for research and therapeutic applications.

Peng Chen

Jin Zhou

Yibin Wan

Huan Liu

Yongzheng Li

Zhaoxin Liu

Hongjian Wang

Jun Lei

Kai Zhao

Yiliang Zhang

Yan Wang

Xinghua Zhang

Lei Yin

A Cas12a ortholog with stringent PAM recognition followed by low off-target editing rates for genome editing

一种具有严格PAM识别能力并伴随低脱靶编辑率的Cas12a同源基因编辑工具

Prasad Sarashetti

Josipa Lipovac

Filip Tomas

Mile Šikić

Jianjun Liu

Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references

评估高质量单倍型解析基因组创建稳健泛基因组参考所需的数据要求

Abstract Recent studies reveal that circular RNAs (circRNAs) are a novel class of abundant, stable and ubiquitous noncoding RNA molecules in animals. Comprehensive detection of circRNAs from high-throughput transcriptome data is an initial and crucial step to study their biogenesis and function. Here, we present a novel chiastic clipping signal-based algorithm, CIRI, to unbiasedly and accurately detect circRNAs from transcriptome data by employing multiple filtration strategies. By applying CIRI to ENCODE RNA-seq data, we for the first time identify and experimentally validate the prevalence of intronic/intergenic circRNAs as well as fragments specific to them in the human transcriptome.

Yuan Gao

Jinfeng Wang

Fangqing Zhao

CIRI: an efficient and unbiased algorithm for de novo circular RNA identification

CIRI：一种高效且无偏的从头环状RNA识别算法

The inherent similarities between natural language and biological sequences have inspired the use of large language models in genomics, but current models struggle to incorporate chromatin interactions or predict in unseen cellular contexts. To address this, we propose EpiGePT, a transformer-based model designed for predicting context-specific human epigenomic signals. By incorporating transcription factor activities and 3D genome interactions, EpiGePT outperforms existing methods in epigenomic signal prediction tasks, especially in cell-type-specific long-range interaction predictions and genetic variant impacts, advancing our understanding of gene regulation. A free online prediction service is available athttp://health.tsinghua.edu.cn/epigept.

Zijing Gao

Qiao Liu

Wanwen Zeng

Rui Jiang

Wing Hung Wong

EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics

EpiGePT：一种用于特定上下文人类表观基因组学的预训练transformer语言模型

Plasma cell-free DNA (cfDNA) is derived from cellular death in various tissues. Investigating the tissue origin of cfDNA through cell type deconvolution, we can detect changes in tissue homeostasis that occur during disease progression or in response to treatment. Consequently, cfDNA has emerged as a valuable noninvasive biomarker for disease detection and treatment monitoring. Although there are many methylation-based methods for cfDNA cell type deconvolution, a comprehensive and systematic evaluation of these methods has yet to be conducted.

Tongyue Sun

Jinqi Yuan

Yacheng Zhu

Jingqi Li

Shen Yang

Junpeng Zhou

Xinzhou Ge

Susu Qu

Wei Li

Jingyi Jessica Li

Yumei Li

Systematic evaluation of methylation-based cell type deconvolution methods for plasma cell-free DNA

基于甲基化的细胞类型反卷积方法在血浆游离DNA中的系统评估

We present GenomeDelta, a novel tool for identifying sample-specific sequences, such as recent transposable element (TE) invasions, without requiring a repeat library. GenomeDelta compares high-quality assemblies with short-read data to detect sequences absent from the short reads. It is applicable to both model and non-model organisms and can identify recent TE invasions, spatially heterogeneous sequences, viral insertions, and hotizontal gene transfers. GenomeDelta was validated with simulated and real data and used to discover three recent TE invasions in Drosophila melanogaster and a novel TE with geographic variation in Zymoseptoria tritici.

Riccardo Pianezza

Anna Haider

Robert Kofler

GenomeDelta: detecting recent transposable element invasions without repeat library

GenomeDelta：无需重复库即可检测近期转座子入侵

Transcription factors (TFs) bind regulatory genomic regions to orchestrate spatio-temporal expression of target genes. Global dissection of the cistrome is critical for elucidating transcriptional networks underlying complex agronomic traits in crops. Here, we generate a comprehensive genome-wide binding map for 148 TFs using DNA affinity purification sequencing in soybean. We find TF binding sites (TFBSs) exhibit elevated chromatin accessibility and contain more rare alleles than other genomic regions. Intriguingly, the methylation variations at TFBSs partially contribute to expression bias among whole genome duplication paralogs. Furthermore, we construct a soybean gene regulatory network (SoyGRN) by integrating TF-target interactions with diverse datasets encompassing gene expression, TFBS motifs, chromatin accessibility, and evolutionarily conserved regulation. SoyGRN comprises 2.44 million genome-wide interactions among 3188 TFs and 51,665 target genes. We successfully identify key TFs governing seed coat color and oil content and prioritize candidate genes within quantitative trait loci associated with various agronomic traits using SoyGRN. To accelerate utilization of SoyGRN, we develop an interactive webserver ( www.soytfbase.cn ) for soybean community to explore functional TFs involved in trait regulation. Overall, our study unravels intricate landscape of TF-target interactions in soybean and provides a valuable resource for dissecting key regulators for control of agronomic traits to accelerate soybean improvement.

Wu Jiao

Mangmang Wang

Yijian Guan

Wei Guo

Chang Zhang

Yuanchun Wei

Zhenwei Zhao

Hongyu Ma

Longfei Wang

Xinyu Jiang

Wenxue Ye

Dong Cao

Qingxin Song

Transcriptional regulatory network reveals key transcription factors for regulating agronomic traits in soybean

转录调控网络揭示大豆农艺性状调控的关键转录因子

Synthetic CRISPR-Cas9 gene drive has been developed to control harmful species. However, resistance to Cas9 gene drive can be acquired easily when DNA repair mechanisms patch up the genetic insults introduced by Cas9 and incorporate mutations to the sgRNA target. Although many strategies to reduce the occurrence of resistance have been developed so far, they are difficult to implement and not always effective. Here, Cas12f1, a recently developed CRISPR-Cas system with minimal potential for causing mutations within target sequences, has been explored as a potential platform for yielding low-resistance in gene drives. We construct Cas9 and Cas12f1 gene drives in a fast-replicating DNA virus, HSV1. Cas9 and Cas12f1 gene drives are able to spread among the HSV1 population with specificity towards their target sites, and their transmission among HSV1 viruses is not significantly affected by the reduced fitness incurred by the viral carriers. Cas12f1 gene drives spread similarly as Cas9 gene drives at high introduction frequency but transmit more slowly than Cas9 gene drives at low introduction frequency. However, Cas12f1 gene drives outperform Cas9 gene drives because they reach higher penetration and induce lower resistance than Cas9 gene drives in all cases. Due to lower resistance and higher penetration, Cas12f1 gene drives could potentially supplant Cas9 gene drives for population control.

Zhuangjie Lin

Qiaorui Yao

Keyuan Lai

Kehua Jiao

Xianying Zeng

Guanxiong Lei

Tongwen Zhang

Hongsheng Dai

Cas12f1 gene drives propagate efficiently in herpesviruses and induce minimal resistance

Cas12f1基因驱动在疱疹病毒中高效传播并引发最小抗性

Cloud computing allows storing the ever-growing genotype-phenotype datasets crucial for precision medicine. Due to the sensitive nature of this data and varied laws and regulations, additional security measures are needed to ensure data privacy. We develop SQUiD, a secure queryable database for storing and analyzing genotype-phenotype data. SQUiD allows storage and secure querying of data in a low-security, low-cost public cloud using homomorphic encryption in a multi-client setting. We demonstrate SQUiD's practical usability and scalability using synthetic and UK Biobank data.

Jacob Blindenbach

Jiayi Kang

Seungwan Hong

Caline Karam

Thomas Lehner

Gamze Gürsoy

SQUiD: ultra-secure storage and analysis of genetic data for the advancement of precision medicine

SQUiD：推进精准医学的超安全基因数据存储与分析

Abbreviation	Genome Biol
Journal Impact	10.26
Quartiles(Global)	GENETICS & HEREDITY(Q1)

ISSN	1465-6906, 1465-6914, 1474-7596, 1474-760X
h-index	301

Publication Information	Publisher: BioMed Central Ltd，Publishing cycle: ，Journal Type: journal，Open Access Journals: No
Basic data	Year of publication: 2000，Proportion of original research papers: 96.03%，Self Citation Rate:3.00%， Gold OA Rate: 99.41%
Average review cycle	网友分享经验：14 Weeks

Genome Biology

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