Current challenges and future of agricultural genomes to phenomes in the USA
Dramatic improvements in measuring genetic variation across agriculturally relevant populations (genomics) must be matched by improvements in identifying and measuring relevant trait variation in such populati... (Source: Genome Biology)
Source: Genome Biology - January 3, 2024 Category: Genetics & Stem Cells Authors: Christopher K. Tuggle, Jennifer L. Clarke, Brenda M. Murdoch, Eric Lyons, Nicole M. Scott, Bedrich Bene š, Jacqueline D. Campbell, Henri Chung, Courtney L. Daigle, Sruti Das Choudhury, Jack C. M. Dekkers, Joao R. R. Dórea, David S. Ertl, Max Feldman, Br Tags: Correspondence Source Type: research
Benchmarking differential abundance methods for finding condition-specific prototypical cells in multi-sample single-cell datasets
To analyze the large volume of data generated by single-cell technologies and to identify cellular correlates of particular clinical or experimental outcomes, differential abundance analyses are often applied.... (Source: Genome Biology)
Source: Genome Biology - January 3, 2024 Category: Genetics & Stem Cells Authors: Haidong Yi, Alec Plotkin and Natalie Stanley Tags: Research Source Type: research
Author Correction: Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression
(Source: Genome Biology)
Source: Genome Biology - January 2, 2024 Category: Genetics & Stem Cells Authors: Jizeng Jia, Yilin Xie, Jingfei Cheng, Chuizheng Kong, Meiyue Wang, Lifeng Gao, Fei Zhao, Jingyu Guo, Kai Wang, Guangwei Li, Dangqun Cui, Tiezhu Hu, Guangyao Zhao, Daowen Wang, Zhengang Ru and Yijing Zhang Tags: Author Correction Source Type: research
Response to Commentary: Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies
(Source: Genome Biology)
Source: Genome Biology - January 2, 2024 Category: Genetics & Stem Cells Authors: Shujun Ou, Ning Jiang, Candice N. Hirsch and Matthew B. Hufford Tags: Correspondence Source Type: research
Genetic effects of sequence-conserved enhancer-like elements on human complex traits
The vast majority of findings from human genome-wide association studies (GWAS) map to non-coding sequences, complicating their mechanistic interpretations and clinical translations. Non-coding sequences that ... (Source: Genome Biology)
Source: Genome Biology - January 2, 2024 Category: Genetics & Stem Cells Authors: Xiang Zhu, Shining Ma and Wing Hung Wong Tags: Research Source Type: research
Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network
Formation of tissue-specific transcriptional programs underlies multicellular development, including dorsoventral (DV) patterning of the Drosophila embryo. This involves interactions between transcriptional enhan... (Source: Genome Biology)
Source: Genome Biology - January 2, 2024 Category: Genetics & Stem Cells Authors: George Hunt, Roshan Vaid, Sergei Pirogov, Alexander Pfab, Christoph Ziegenhain, Rickard Sandberg, Johan Reimeg ård and Mattias Mannervik Tags: Research Source Type: research
FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases
The majority of disease-associated variants identified through genome-wide association studies are located outside of protein-coding regions. Prioritizing candidate regulatory variants and gene targets to iden... (Source: Genome Biology)
Source: Genome Biology - January 2, 2024 Category: Genetics & Stem Cells Authors: Charles E. Breeze, Eric Haugen, Mar ía Gutierrez-Arcelus, Xiaozheng Yao, Andrew Teschendorff, Stephan Beck, Ian Dunham, John Stamatoyannopoulos, Nora Franceschini, Mitchell J. Machiela and Sonja I. Berndt Tags: Method Source Type: research
ENGEP: advancing spatial transcriptomics with accurate unmeasured gene expression prediction
Imaging-based spatial transcriptomics techniques provide valuable spatial and gene expression information at single-cell resolution. However, their current capability is restricted to profiling a limited numbe... (Source: Genome Biology)
Source: Genome Biology - December 21, 2023 Category: Genetics & Stem Cells Authors: Shi-Tong Yang and Xiao-Fei Zhang Tags: Method Source Type: research
Benchmarking splice variant prediction algorithms using massively parallel splicing assays
Variants that disrupt mRNA splicing account for a sizable fraction of the pathogenic burden in many genetic disorders, but identifying splice-disruptive variants (SDVs) beyond the essential splice site dinucle... (Source: Genome Biology)
Source: Genome Biology - December 21, 2023 Category: Genetics & Stem Cells Authors: Cathy Smith and Jacob O. Kitzman Tags: Research Source Type: research
A super-pangenome of the North American wild grape species
Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability ... (Source: Genome Biology)
Source: Genome Biology - December 19, 2023 Category: Genetics & Stem Cells Authors: No é Cochetel, Andrea Minio, Andrea Guarracino, Jadran F. Garcia, Rosa Figueroa-Balderas, Mélanie Massonnet, Takao Kasuga, Jason P. Londo, Erik Garrison, Brandon S. Gaut and Dario Cantu Tags: Research Source Type: research
Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data
Spatial omics technologies can help identify spatially organized biological processes, but existing computational approaches often overlook structural dependencies in the data. Here, we introduce Smoother, a u... (Source: Genome Biology)
Source: Genome Biology - December 18, 2023 Category: Genetics & Stem Cells Authors: Jiayu Su, Jean-Baptiste Reynier, Xi Fu, Guojie Zhong, Jiahao Jiang, Rydberg Supo Escalante, Yiping Wang, Luis Aparicio, Benjamin Izar, David A. Knowles and Raul Rabadan Tags: Method Source Type: research
scNAT: a deep learning method for integrating paired single-cell RNA and T cell receptor sequencing profiles
Many deep learning-based methods have been proposed to handle complex single-cell data. Deep learning approaches may also prove useful to jointly analyze single-cell RNA sequencing (scRNA-seq) and single-cell ... (Source: Genome Biology)
Source: Genome Biology - December 18, 2023 Category: Genetics & Stem Cells Authors: Biqing Zhu, Yuge Wang, Li-Ting Ku, David van Dijk, Le Zhang, David A. Hafler and Hongyu Zhao Tags: Method Source Type: research
A time-resolved meta-analysis of consensus gene expression profiles during human T-cell activation
The coordinated transcriptional regulation of activated T-cells is based on a complex dynamic behavior of signaling networks. Given an external stimulus, T-cell gene expression is characterized by impulse and ... (Source: Genome Biology)
Source: Genome Biology - December 14, 2023 Category: Genetics & Stem Cells Authors: Michael Rade, Sebastian B öhlen, Vanessa Neuhaus, Dennis Löffler, Conny Blumert, Maximilian Merz, Ulrike Köhl, Susann Dehmel, Katherina Sewald and Kristin Reiche Tags: Research Source Type: research
Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets
Deconvolution of cell mixtures in “bulk” transcriptomic samples from homogenate human tissue is important for understanding disease pathologies. However, several experimental and computational challenges imped... (Source: Genome Biology)
Source: Genome Biology - December 14, 2023 Category: Genetics & Stem Cells Authors: Sean K. Maden, Sang Ho Kwon, Louise A. Huuki-Myers, Leonardo Collado-Torres, Stephanie C. Hicks and Kristen R. Maynard Tags: Review Source Type: research
Metabolic GWAS-based dissection of genetic basis underlying nutrient quality variation and domestication of cassava storage root
Metabolites play critical roles in regulating nutritional qualities of plants, thereby influencing their consumption and human health. However, the genetic basis underlying the metabolite-based nutrient qualit... (Source: Genome Biology)
Source: Genome Biology - December 14, 2023 Category: Genetics & Stem Cells Authors: Zehong Ding, Lili Fu, Bin Wang, Jianqiu Ye, Wenjun Ou, Yan Yan, Meiying Li, Liwang Zeng, Xuekui Dong, Weiwei Tie, Xiaoxue Ye, Jinghao Yang, Zhengnan Xie, Yu Wang, Jianchun Guo, Songbi Chen & hellip; Tags: Research Source Type: research
