Protocadherin 20 maintains intestinal barrier function to protect against Crohn ’s disease by targeting ATF6
Intestinal barrier dysfunction plays a central role in the pathological onset of Crohn ’s disease. We identify the cadherin superfamily member protocadherin 20 (PCDH20) as a crucial factor in Crohn’s disease. H... (Source: Genome Biology)
Source: Genome Biology - July 5, 2023 Category: Genetics & Stem Cells Authors: Shanshan Huang, Zhuo Xie, Jing Han, Huiling Wang, Guang Yang, Manying Li, Gaoshi Zhou, Ying Wang, Lixuan Li, Li Li, Zhirong Zeng, Jun Yu, Minhu Chen and Shenghong Zhang Tags: Research Source Type: research
Characterization of large-scale genomic differences in the first complete human genome
The first telomere-to-telomere (T2T) human genome assembly (T2T-CHM13) release is a milestone in human genomics. The T2T-CHM13 genome assembly extends our understanding of telomeres, centromeres, segmental dup... (Source: Genome Biology)
Source: Genome Biology - July 4, 2023 Category: Genetics & Stem Cells Authors: Xiangyu Yang, Xuankai Wang, Yawen Zou, Shilong Zhang, Manying Xia, Lianting Fu, Mitchell R. Vollger, Nae-Chyun Chen, Dylan J. Taylor, William T. Harvey, Glennis A. Logsdon, Dan Meng, Junfeng Shi, Rajiv C. McCoy, Michael C. Schatz, Weidong Li & hellip; Tags: Research Source Type: research
An Atlas of Variant Effects to understand the genome at nucleotide resolution
Sequencing has revealed hundreds of millions of human genetic variants, and continued efforts will only add to this variant avalanche. Insufficient information exists to interpret the effects of most variants,... (Source: Genome Biology)
Source: Genome Biology - July 3, 2023 Category: Genetics & Stem Cells Authors: Douglas M. Fowler, David J. Adams, Anna L. Gloyn, William C. Hahn, Debora S. Marks, Lara A. Muffley, James T. Neal, Frederick P. Roth, Alan F. Rubin, Lea M. Starita and Matthew E. Hurles Tags: Correspondence Source Type: research
Efficient and versatile multiplex prime editing in hexaploid wheat
Prime editing is limited by low efficiency in plants. Here, we develop an upgraded engineered plant prime editor in hexaploid wheat, ePPEplus, by introducing a V223A substitution into reverse transcriptase in ... (Source: Genome Biology)
Source: Genome Biology - June 29, 2023 Category: Genetics & Stem Cells Authors: Pei Ni, Yidi Zhao, Ximeng Zhou, Zehua Liu, Zhengwei Huang, Zhongfu Ni, Qixin Sun and Yuan Zong Tags: Method Source Type: research
RAD21 is the core subunit of the cohesin complex involved in directing genome organization
The ring-shaped cohesin complex is an important factor for the formation of chromatin loops and topologically associating domains (TADs) by loop extrusion. However, the regulation of association between cohesi... (Source: Genome Biology)
Source: Genome Biology - June 28, 2023 Category: Genetics & Stem Cells Authors: Yuao Sun, Xin Xu, Wenxue Zhao, Yu Zhang, Keyang Chen, Yongzheng Li, Xiaotian Wang, Mengling Zhang, Boxin Xue, Wanting Yu, Yingping Hou, Chaobin Wang, Wei Xie, Cheng Li, Daochun Kong, Shu Wang & hellip; Tags: Research Source Type: research
ExplaiNN: interpretable and transparent neural networks for genomics
Deep learning models such as convolutional neural networks (CNNs) excel in genomic tasks but lack interpretability. We introduce ExplaiNN, which combines the expressiveness of CNNs with the interpretability of... (Source: Genome Biology)
Source: Genome Biology - June 27, 2023 Category: Genetics & Stem Cells Authors: Gherman Novakovsky, Oriol Fornes, Manu Saraswat, Sara Mostafavi and Wyeth W. Wasserman Tags: Method Source Type: research
Human papillomavirus integration transforms chromatin to drive oncogenesis
Human papillomavirus (HPV) drives almost all cervical cancers and up to 70% of head and neck cancers. Frequent integration into the host genome occurs predominantly in tumorigenic types of HPV. We hypothesize ... (Source: Genome Biology)
Source: Genome Biology - June 27, 2023 Category: Genetics & Stem Cells Authors: Mehran Karimzadeh, Christopher Arlidge, Ariana Rostami, Mathieu Lupien, Scott V. Bratman and Michael M. Hoffman Tags: Research Source Type: research
Panhematopoietic RNA barcoding enables kinetic measurements of nucleate and anucleate lineages and the activation of myeloid clones following acute platelet depletion
Platelets and erythrocytes constitute over 95% of all hematopoietic stem cell output. However, the clonal dynamics of HSC contribution to these lineages remains largely unexplored. (Source: Genome Biology)
Source: Genome Biology - June 27, 2023 Category: Genetics & Stem Cells Authors: Edyta E. Wojtowicz, Jayna J. Mistry, Vladimir Uzun, Charlotte Hellmich, Anita Scoones, Desmond W. Chin, Laura M. Kettyle, Francesca Grasso, Allegra M. Lord, David J. Wright, Graham J. Etherington, Petter S. Woll, Mirjam E. Belderbos, Kristian M. Bowles, C Tags: Research Source Type: research
Universal chromatin state annotation of the mouse genome
A large-scale application of the “stacked modeling” approach for chromatin state discovery previously provides a single “universal” chromatin state annotation of the human genome based jointly on data from many c... (Source: Genome Biology)
Source: Genome Biology - June 27, 2023 Category: Genetics & Stem Cells Authors: Ha Vu and Jason Ernst Tags: Short Report Source Type: research
Transcriptome- and proteome-wide association studies nominate determinants of kidney function and damage
The pathophysiological causes of kidney disease are not fully understood. Here we show that the integration of genome-wide genetic, transcriptomic, and proteomic association studies can nominate causal determi... (Source: Genome Biology)
Source: Genome Biology - June 26, 2023 Category: Genetics & Stem Cells Authors: Pascal Schlosser, Jingning Zhang, Hongbo Liu, Aditya L. Surapaneni, Eugene P. Rhee, Dan E. Arking, Bing Yu, Eric Boerwinkle, Paul A. Welling, Nilanjan Chatterjee, Katalin Susztak, Josef Coresh and Morgan E. Grams Tags: Research Source Type: research
DCATS: differential composition analysis for flexible single-cell experimental designs
Differential composition analysis — the identification of cell types that have statistically significant changes in abundance between multiple experimental conditions — is one of the most common tasks in singl... (Source: Genome Biology)
Source: Genome Biology - June 26, 2023 Category: Genetics & Stem Cells Authors: Xinyi Lin, Chuen Chau, Kun Ma, Yuanhua Huang and Joshua W. K. Ho Tags: Method Source Type: research
Engineered circular guide RNAs boost CRISPR/Cas12a- and CRISPR/Cas13d-based DNA and RNA editing
The CRISPR/Cas12a and CRISPR/Cas13d systems are widely used for fundamental research and hold great potential for future clinical applications. However, the short half-life of guide RNAs (gRNAs), particularly ... (Source: Genome Biology)
Source: Genome Biology - June 23, 2023 Category: Genetics & Stem Cells Authors: Xin Zhang, Xinlong Wang, Jie Lv, Hongxin Huang, Jiahong Wang, Ma Zhuo, Zhihong Tan, Guanjie Huang, Jiawei Liu, Yuchen Liu, Mengrao Li, Qixiao Lin, Lian Li, Shufeng Ma, Tao Huang, Ying Lin & hellip; Tags: Research Source Type: research
CATI: an efficient gene integration method for rodent and primate embryos by MMEJ suppression
The efficiency of homology-directed repair (HDR) plays a crucial role in the development of animal models and gene therapy. We demonstrate that microhomology-mediated end-joining (MMEJ) constitutes a substanti... (Source: Genome Biology)
Source: Genome Biology - June 23, 2023 Category: Genetics & Stem Cells Authors: Hongyu Chen, Xingchen Liu, Lanxin Li, Qingtong Tan, Shiyan Li, Li Li, Chunyang Li, Jiqiang Fu, Yong Lu, Yan Wang, Yidi Sun, Zhen-Ge Luo, Zongyang Lu, Qiang Sun and Zhen Liu Tags: Method Source Type: research
VarID2 quantifies gene expression noise dynamics and unveils functional heterogeneity of ageing hematopoietic stem cells
Variability of gene expression due to stochasticity of transcription or variation of extrinsic signals, termed biological noise, is a potential driving force of cellular differentiation. Utilizing single-cell ... (Source: Genome Biology)
Source: Genome Biology - June 23, 2023 Category: Genetics & Stem Cells Authors: Reyna Edith Rosales-Alvarez, Jasmin Rettkowski, Josip Stefan Herman, Gabrijela Dumbovi ć, Nina Cabezas-Wallscheid and Dominic Grün Tags: Method Source Type: research
scTour: a deep learning architecture for robust inference and accurate prediction of cellular dynamics
Despite the continued efforts, a batch-insensitive tool that can both infer and predict the developmental dynamics using single-cell genomics is lacking. Here, I present scTour, a novel deep learning architect... (Source: Genome Biology)
Source: Genome Biology - June 23, 2023 Category: Genetics & Stem Cells Authors: Qian Li Tags: Method Source Type: research
