Mapping the functional impact of non-coding regulatory elements in primary T cells through single-cell CRISPR screens
Drug targets with genetic evidence are expected to increase clinical success by at least twofold. Yet, translating disease-associated genetic variants into functional knowledge remains a fundamental challenge ... (Source: Genome Biology)
Source: Genome Biology - February 2, 2024 Category: Genetics & Stem Cells Authors: Celia Alda-Catalinas, Ximena Ibarra-Soria, Christina Flouri, Jorge Esparza Gordillo, Diana Cousminer, Anna Hutchinson, Bin Sun, William Pembroke, Sebastian Ullrich, Adam Krejci, Adrian Cortes, Alison Acevedo, Sunir Malla, Carl Fishwick, Gerard Drewes and Tags: Research Source Type: research
AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding
Protein function annotation has been one of the longstanding issues in biological sciences, and various computational methods have been developed. However, the existing methods suffer from a serious long-tail ... (Source: Genome Biology)
Source: Genome Biology - February 1, 2024 Category: Genetics & Stem Cells Authors: Lingyan Zheng, Shuiyang Shi, Mingkun Lu, Pan Fang, Ziqi Pan, Hongning Zhang, Zhimeng Zhou, Hanyu Zhang, Minjie Mou, Shijie Huang, Lin Tao, Weiqi Xia, Honglin Li, Zhenyu Zeng, Shun Zhang, Yuzong Chen & hellip; Tags: Method Source Type: research
Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc
Copy number alterations (CNAs) are among the most important genetic events in cancer, but their detection from sequencing data is challenging because of unknown sample purity, tumor ploidy, and general intra-t... (Source: Genome Biology)
Source: Genome Biology - January 31, 2024 Category: Genetics & Stem Cells Authors: Alice Antonello, Riccardo Bergamin, Nicola Calonaci, Jacob Househam, Salvatore Milite, Marc J. Williams, Fabio Anselmi, Alberto d ’Onofrio, Vasavi Sundaram, Alona Sosinsky, William C. H. Cross and Giulio Caravagna Tags: Method Source Type: research
RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci
Expansions of tandem repeats (TRs) cause approximately 60 monogenic diseases. We expect that the discovery of additional pathogenic repeat expansions will narrow the diagnostic gap in many diseases. A growing ... (Source: Genome Biology)
Source: Genome Biology - January 31, 2024 Category: Genetics & Stem Cells Authors: Sarah Fazal, Matt C. Danzi, Isaac Xu, Shilpa Nadimpalli Kobren, Shamil Sunyaev, Chloe Reuter, Shruti Marwaha, Matthew Wheeler, Egor Dolzhenko, Francesca Lucas, Stefan Wuchty, Mustafa Tekin, Stephan Z üchner and Vanessa Aguiar-Pulido Tags: Method Source Type: research
BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites
Pervasive usage of alternative promoters leads to the deregulation of gene expression in carcinogenesis and may drive the emergence of new genes in spermatogenesis. However, little is known regarding the mecha... (Source: Genome Biology)
Source: Genome Biology - January 31, 2024 Category: Genetics & Stem Cells Authors: Elena M. Pugacheva, Dharmendra Nath Bhatt, Samuel Rivero-Hinojosa, Md Tajmul, Liron Fedida, Emma Price, Yon Ji, Dmitri Loukinov, Alexander V. Strunnikov, Bing Ren and Victor V. Lobanenkov Tags: Research Source Type: research
deMULTIplex2: robust sample demultiplexing for scRNA-seq
Sample multiplexing enables pooled analysis during single-cell RNA sequencing workflows, thereby increasing throughput and reducing batch effects. A challenge for all multiplexing techniques is to link sample-... (Source: Genome Biology)
Source: Genome Biology - January 30, 2024 Category: Genetics & Stem Cells Authors: Qin Zhu, Daniel N. Conrad and Zev J. Gartner Tags: Method Source Type: research
Mosaic loss of Y chromosome is associated with aging and epithelial injury in chronic kidney disease
Mosaic loss of Y chromosome (LOY) is the most common chromosomal alteration in aging men. Here, we use single-cell RNA and ATAC sequencing to show that LOY is present in the kidney and increases with age and c... (Source: Genome Biology)
Source: Genome Biology - January 29, 2024 Category: Genetics & Stem Cells Authors: Parker C. Wilson, Amit Verma, Yasuhiro Yoshimura, Yoshiharu Muto, Haikuo Li, Nicole P. Malvin, Eryn E. Dixon and Benjamin D. Humphreys Tags: Research Source Type: research
Gene panel selection for targeted spatial transcriptomics
Targeted spatial transcriptomics hold particular promise in analyzing complex tissues. Most such methods, however, measure only a limited panel of transcripts, which need to be selected in advance to inform on... (Source: Genome Biology)
Source: Genome Biology - January 25, 2024 Category: Genetics & Stem Cells Authors: Yida Zhang, Viktor Petukhov, Evan Biederstedt, Richard Que, Kun Zhang and Peter V. Kharchenko Tags: Method Source Type: research
The unusual gene architecture of polyubiquitin is created by dual-specific splice sites
The removal of introns occurs through the splicing of a 5 ′ splice site (5′ss) with a 3′ splice site (3′ss). These two elements are recognized by distinct components of the spliceosome. However, introns in high... (Source: Genome Biology)
Source: Genome Biology - January 24, 2024 Category: Genetics & Stem Cells Authors: Chaorui Duan, Truman Mooney, Luke Buerer, Cory Bowers, Stephen Rong, Seong Won Kim, Alger M. Fredericks, Sean F. Monaghan and William G. Fairbrother Tags: Research Source Type: research
Quartet metabolite reference materials for inter-laboratory proficiency test and data integration of metabolomics profiling
Various laboratory-developed metabolomic methods lead to big challenges in inter-laboratory comparability and effective integration of diverse datasets. (Source: Genome Biology)
Source: Genome Biology - January 24, 2024 Category: Genetics & Stem Cells Authors: Naixin Zhang, Qiaochu Chen, Peipei Zhang, Kejun Zhou, Yaqing Liu, Haiyan Wang, Shumeng Duan, Yongming Xie, Wenxiang Yu, Ziqing Kong, Luyao Ren, Wanwan Hou, Jingcheng Yang, Xiaoyun Gong, Lianhua Dong, Xiang Fang & hellip; Tags: Research Source Type: research
FMRP-mediated spatial regulation of physiologic NMD targets in neuronal cells
In non-polarized cells, nonsense-mediated mRNA decay (NMD) generally begins during the translation of newly synthesized mRNAs after the mRNAs are exported to the cytoplasm. Binding of the FMRP translational re... (Source: Genome Biology)
Source: Genome Biology - January 23, 2024 Category: Genetics & Stem Cells Authors: Tatsuaki Kurosaki, Xavier Rambout and Lynne E. Maquat Tags: Review Source Type: research
Unraveling the phylogenomic diversity of Methanomassiliicoccales and implications for mitigating ruminant methane emissions
Methanomassiliicoccales are a recently identified order of methanogens that are diverse across global environments particularly the gastrointestinal tracts of animals; however, their metabolic capacities are d... (Source: Genome Biology)
Source: Genome Biology - January 23, 2024 Category: Genetics & Stem Cells Authors: Fei Xie, Shengwei Zhao, Xiaoxiu Zhan, Yang Zhou, Yin Li, Weiyun Zhu, Phillip B. Pope, Graeme T. Attwood, Wei Jin and Shengyong Mao Tags: Research Source Type: research
SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models
Genetic regulation of gene expression is a complex process, with genetic effects known to vary across cellular contexts such as cell types and environmental conditions. We developed SURGE, a method for unsuper... (Source: Genome Biology)
Source: Genome Biology - January 22, 2024 Category: Genetics & Stem Cells Authors: Benjamin J. Strober, Karl Tayeb, Joshua Popp, Guanghao Qi, M. Grace Gordon, Richard Perez, Chun Jimmie Ye and Alexis Battle Tags: Method Source Type: research
PICALO: principal interaction component analysis for the identification of discrete technical, cell-type, and environmental factors that mediate eQTLs
Expression quantitative trait loci (eQTL) offer insights into the regulatory mechanisms of trait-associated variants, but their effects often rely on contexts that are unknown or unmeasured. We introduce PICAL... (Source: Genome Biology)
Source: Genome Biology - January 22, 2024 Category: Genetics & Stem Cells Authors: Martijn Vochteloo, Patrick Deelen, Britt Vink, Ellen A. Tsai, Heiko Runz, Sergio Andreu-S ánchez, Jingyuan Fu, Alexandra Zhernakova, Harm-Jan Westra and Lude Franke Tags: Method Source Type: research
Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis
Centromeres load kinetochore complexes onto chromosomes, which mediate spindle attachment and allow segregation during cell division. Although centromeres perform a conserved cellular function, their underlyin... (Source: Genome Biology)
Source: Genome Biology - January 22, 2024 Category: Genetics & Stem Cells Authors: Joiselle B. Fernandes, Matthew Naish, Qichao Lian, Robin Burns, Andrew J. Tock, Fernando A. Rabanal, Piotr Wlodzimierz, Anette Habring, Robert E. Nicholas, Detlef Weigel, Raphael Mercier and Ian R. Henderson Tags: Research Source Type: research
