Liquid –liquid phase separation of H3K27me3 reader BP1 regulates transcriptional repression
Bromo-adjacent homology-plant homeodomain domain containing protein 1 (BP1) is a reader of histone post-translational modifications in fungi. BP1 recognizes trimethylation of lysine 27 in histone H3 (H3K27me3)... (Source: Genome Biology)
Source: Genome Biology - March 11, 2024 Category: Genetics & Stem Cells Authors: Guangfei Tang, Haoxue Xia, Yufei Huang, Yuanwen Guo, Yun Chen, Zhonghua Ma and Wende Liu Tags: Research Source Type: research
Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
In rheumatoid arthritis (RA), the activation of T and B cell clones specific for self-antigens leads to the chronic inflammation of the synovium. Here, we perform an in-depth quantitative analysis of the seven... (Source: Genome Biology)
Source: Genome Biology - March 11, 2024 Category: Genetics & Stem Cells Authors: Adri à Aterido, María López-Lasanta, Francisco Blanco, Antonio Juan-Mas, María Luz García-Vivar, Alba Erra, Carolina Pérez-García, Simón Ángel Sánchez-Fernández, Raimon Sanmartí, Antonio Fernández-Nebro, Mercedes Alperi-López, Jesús Tornero Tags: Research Source Type: research
A comparison of methods for detecting DNA methylation from long-read sequencing of human genomes
Long-read sequencing can enable the detection of base modifications, such as CpG methylation, in single molecules of DNA. The most commonly used methods for long-read sequencing are nanopore developed by Oxfor... (Source: Genome Biology)
Source: Genome Biology - March 11, 2024 Category: Genetics & Stem Cells Authors: Brynja D. Sigurpalsdottir, Olafur A. Stefansson, Guillaume Holley, Doruk Beyter, Florian Zink, Marteinn Þ. Hardarson, Sverrir Þ. Sverrisson, Nina Kristinsdottir, Droplaug N. Magnusdottir, Olafur Þ. Magnusson, Daniel F. Gudbjartsson, Bjarni V. Halldorss Tags: Research Source Type: research
Joint analysis of mutational and transcriptional landscapes in human cancer reveals key perturbations during cancer evolution
Tumors are able to acquire new capabilities, including traits such as drug resistance and metastasis that are associated with unfavorable clinical outcomes. Single-cell technologies have made it possible to st... (Source: Genome Biology)
Source: Genome Biology - March 8, 2024 Category: Genetics & Stem Cells Authors: Jae-Won Cho, Jingyi Cao and Martin Hemberg Tags: Research Source Type: research
scAbsolute: measuring single-cell ploidy and replication status
Cancer cells often exhibit DNA copy number aberrations and can vary widely in their ploidy. Correct estimation of the ploidy of single-cell genomes is paramount for downstream analysis. Based only on single-ce... (Source: Genome Biology)
Source: Genome Biology - March 4, 2024 Category: Genetics & Stem Cells Authors: Michael P. Schneider, Amy E. Cullen, Justina Pangonyte, Jason Skelton, Harvey Major, Elke Van Oudenhove, Maria J. Garcia, Blas Chaves Urbano, Anna M. Piskorz, James D. Brenton, Geoff Macintyre and Florian Markowetz Tags: Method Source Type: research
Three near-complete genome assemblies reveal substantial centromere dynamics from diploid to tetraploid in Brachypodium genus
Centromeres are critical for maintaining genomic stability in eukaryotes, and their turnover shapes genome architectures and drives karyotype evolution. However, the co-evolution of centromeres from different ... (Source: Genome Biology)
Source: Genome Biology - March 4, 2024 Category: Genetics & Stem Cells Authors: Chuanye Chen, Siying Wu, Yishuang Sun, Jingwei Zhou, Yiqian Chen, Jing Zhang, James A. Birchler, Fangpu Han, Ning Yang and Handong Su Tags: Research Source Type: research
Early-life ruminal microbiome-derived indole-3-carboxaldehyde and prostaglandin D2 are effective promoters of rumen development
The function of diverse ruminal microbes is tightly linked to rumen development and host physiology. The system of ruminal microbes is an excellent model to clarify the fundamental ecological relationships amo... (Source: Genome Biology)
Source: Genome Biology - March 4, 2024 Category: Genetics & Stem Cells Authors: Daming Sun, Gaorui Bian, Kai Zhang, Ning Liu, Yuyang Yin, Yuanlong Hou, Fei Xie, Weiyun Zhu, Shengyong Mao and Junhua Liu Tags: Research Source Type: research
Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat
Tartary buckwheat, Fagopyrum tataricum, is a pseudocereal crop with worldwide distribution and high nutritional value. However, the origin and domestication history of this crop remain to be elucidated. (Source: Genome Biology)
Source: Genome Biology - February 27, 2024 Category: Genetics & Stem Cells Authors: Yuqi He, Kaixuan Zhang, Yaliang Shi, Hao Lin, Xu Huang, Xiang Lu, Zhirong Wang, Wei Li, Xibo Feng, Taoxiong Shi, Qingfu Chen, Junzhen Wang, Yu Tang, Mark A. Chapman, Mateja Germ, Zlata Luthar & hellip; Tags: Research Source Type: research
A comparison of marker gene selection methods for single-cell RNA sequencing data
The development of single-cell RNA sequencing (scRNA-seq) has enabled scientists to catalog and probe the transcriptional heterogeneity of individual cells in unprecedented detail. A common step in the analysi... (Source: Genome Biology)
Source: Genome Biology - February 26, 2024 Category: Genetics & Stem Cells Authors: Jeffrey M. Pullin and Davis J. McCarthy Tags: Research Source Type: research
scGIST: gene panel design for spatial transcriptomics with prioritized gene sets
A critical challenge of single-cell spatial transcriptomics (sc-ST) technologies is their panel size. Being based on fluorescence in situ hybridization, they are typically limited to panels of about a thousand... (Source: Genome Biology)
Source: Genome Biology - February 26, 2024 Category: Genetics & Stem Cells Authors: Mashrur Ahmed Yafi, Md. Hasibul Husain Hisham, Francisco Grisanti, James F. Martin, Atif Rahman and Md. Abul Hassan Samee Tags: Method Source Type: research
HiHo-AID2: boosting homozygous knock-in efficiency enables robust generation of human auxin-inducible degron cells
Recent developments in auxin-inducible degron (AID) technology have increased its popularity for chemogenetic control of proteolysis. However, generation of human AID cell lines is challenging, especially in h... (Source: Genome Biology)
Source: Genome Biology - February 26, 2024 Category: Genetics & Stem Cells Authors: Shiqian Li, Yafei Wang, Miesje van der Stoel, Xin Zhou, Shrinidhi Madhusudan, Kristiina Kanerva, Van Dien Nguyen, Nazli Eskici, Vesa M. Olkkonen, You Zhou, Taneli Raivio and Elina Ikonen Tags: Method Source Type: research
Precise fine-turning of GhTFL1 by base editing tools defines ideal cotton plant architecture
CRISPR/Cas-derived base editor enables precise editing of target sites and has been widely used for basic research and crop genetic improvement. However, the editing efficiency of base editors at different tar... (Source: Genome Biology)
Source: Genome Biology - February 26, 2024 Category: Genetics & Stem Cells Authors: Guanying Wang, Fuqiu Wang, Zhongping Xu, Ying Wang, Can Zhang, Yi Zhou, Fengjiao Hui, Xiyan Yang, Xinhui Nie, Xianlong Zhang and Shuangxia Jin Tags: Research Source Type: research
Rapid and sensitive detection of genome contamination at scale with FCS-GX
Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBI ’s Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant sequenc... (Source: Genome Biology)
Source: Genome Biology - February 26, 2024 Category: Genetics & Stem Cells Authors: Alexander Astashyn, Eric S. Tvedte, Deacon Sweeney, Victor Sapojnikov, Nathan Bouk, Victor Joukov, Eyal Mozes, Pooja K. Strope, Pape M. Sylla, Lukas Wagner, Shelby L. Bidwell, Larissa C. Brown, Karen Clark, Emily W. Davis, Brian Smith-White, Wratko Hlavin Tags: Method Source Type: research
SHARE-Topic: Bayesian interpretable modeling of single-cell multi-omic data
Multi-omic single-cell technologies, which simultaneously measure the transcriptional and epigenomic state of the same cell, enable understanding epigenetic mechanisms of gene regulation. However, noisy and sp... (Source: Genome Biology)
Source: Genome Biology - February 23, 2024 Category: Genetics & Stem Cells Authors: Nour El Kazwini and Guido Sanguinetti Tags: Method Source Type: research
CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete ed... (Source: Genome Biology)
Source: Genome Biology - February 22, 2024 Category: Genetics & Stem Cells Tags: Research Source Type: research
