Library size confounds biology in spatial transcriptomics data
Spatial molecular data has transformed the study of disease microenvironments, though, larger datasets pose an analytics challenge prompting the direct adoption of single-cell RNA-sequencing tools including no... (Source: Genome Biology)
Source: Genome Biology - April 18, 2024 Category: Genetics & Stem Cells Authors: Dharmesh D. Bhuva, Chin Wee Tan, Agus Salim, Claire Marceaux, Marie A. Pickering, Jinjin Chen, Malvika Kharbanda, Xinyi Jin, Ning Liu, Kristen Feher, Givanna Putri, Wayne D. Tilley, Theresa E. Hickey, Marie-Liesse Asselin-Labat, Belinda Phipson and Meliss Tags: Short Report Source Type: research
Characterizing glucokinase variant mechanisms using a multiplexed abundance assay
Amino acid substitutions can perturb protein activity in multiple ways. Understanding their mechanistic basis may pinpoint how residues contribute to protein function. Here, we characterize the mechanisms unde... (Source: Genome Biology)
Source: Genome Biology - April 16, 2024 Category: Genetics & Stem Cells Authors: Sarah Gersing, Thea K. Schulze, Matteo Cagiada, Amelie Stein, Frederick P. Roth, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen Tags: Research Source Type: research
Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods
Recent innovations in single-cell RNA-sequencing (scRNA-seq) provide the technology to investigate biological questions at cellular resolution. Pooling cells from multiple individuals has become a common strat... (Source: Genome Biology)
Source: Genome Biology - April 15, 2024 Category: Genetics & Stem Cells Authors: Drew Neavin, Anne Senabouth, Himanshi Arora, Jimmy Tsz Hang Lee, Aida Ripoll-Cladellas, Lude Franke, Shyam Prabhakar, Chun Jimmie Ye, Davis J. McCarthy, Marta Mel é, Martin Hemberg and Joseph E. Powell Tags: Method Source Type: research
Machine-learning analysis reveals an important role for negative selection in shaping cancer aneuploidy landscapes
Aneuploidy, an abnormal number of chromosomes within a cell, is a hallmark of cancer. Patterns of aneuploidy differ across cancers, yet are similar in cancers affecting closely related tissues. The selection p... (Source: Genome Biology)
Source: Genome Biology - April 15, 2024 Category: Genetics & Stem Cells Authors: Juman Jubran, Rachel Slutsky, Nir Rozenblum, Lior Rokach, Uri Ben-David and Esti Yeger-Lotem Tags: Research Source Type: research
Powerful and accurate detection of temporal gene expression patterns from multi-sample multi-stage single-cell transcriptomics data with TDEseq
We present a non-parametric statistical method called TDEseq that takes full advantage of smoothing splines basis functions to account for the dependence of multiple time points in scRNA-seq studies, and uses ... (Source: Genome Biology)
Source: Genome Biology - April 15, 2024 Category: Genetics & Stem Cells Authors: Yue Fan, Lei Li and Shiquan Sun Tags: Method Source Type: research
Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes
As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identif... (Source: Genome Biology)
Source: Genome Biology - April 15, 2024 Category: Genetics & Stem Cells Authors: Ling-Yi Wu, Yasas Wijesekara, Gon çalo J. Piedade, Nikolaos Pappas, Corina P. D. Brussaard and Bas E. Dutilh Tags: Research Source Type: research
Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies
In the metagenomic assembly of a microbial community, abundant species are often thought to assemble well given their deeper sequencing coverage. This conjuncture is rarely tested or evaluated in practice. We ... (Source: Genome Biology)
Source: Genome Biology - April 11, 2024 Category: Genetics & Stem Cells Authors: Xiaowen Feng and Heng Li Tags: Research Source Type: research
Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes
Unraveling bacterial gene function drives progress in various areas, such as food production, pharmacology, and ecology. While omics technologies capture high-dimensional phenotypic data, linking them to genom... (Source: Genome Biology)
Source: Genome Biology - April 11, 2024 Category: Genetics & Stem Cells Authors: Thomas Roder, Gr égory Pimentel, Pascal Fuchsmann, Mireille Tena Stern, Ueli von Ah, Guy Vergères, Stephan Peischl, Ola Brynildsrud, Rémy Bruggmann and Cornelia Bär Tags: Software Source Type: research
PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization
Inferring gene regulatory networks (GRNs) from single-cell data is challenging due to heuristic limitations. Existing methods also lack estimates of uncertainty. Here we present Probabilistic Matrix Factorizat... (Source: Genome Biology)
Source: Genome Biology - April 8, 2024 Category: Genetics & Stem Cells Authors: Claudia Skok Gibbs, Omar Mahmood, Richard Bonneau and Kyunghyun Cho Tags: Method Source Type: research
SuperCellCyto: enabling efficient analysis of large scale cytometry datasets
Advancements in cytometry technologies have enabled quantification of up to 50 proteins across millions of cells at single cell resolution. Analysis of cytometry data routinely involves tasks such as data inte... (Source: Genome Biology)
Source: Genome Biology - April 8, 2024 Category: Genetics & Stem Cells Authors: Givanna H. Putri, George Howitt, Felix Marsh-Wakefield, Thomas M. Ashhurst and Belinda Phipson Tags: Software Source Type: research
scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing
Single-cell ATAC-seq has emerged as a powerful approach for revealing candidate cis-regulatory elements genome-wide at cell-type resolution. However, current single-cell methods suffer from limited throughput ... (Source: Genome Biology)
Source: Genome Biology - April 8, 2024 Category: Genetics & Stem Cells Authors: Xuan Zhang, Alexandre P. Marand, Haidong Yan and Robert J. Schmitz Tags: Short Report Source Type: research
A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline
Although sequencing technologies have boosted the measurement of the genomic diversity of plant crops, it remains challenging to accurately genotype millions of genetic variants, especially structural variatio... (Source: Genome Biology)
Source: Genome Biology - April 8, 2024 Category: Genetics & Stem Cells Authors: Ze-Zhen Du, Jia-Bao He and Wen-Biao Jiao Tags: Research Source Type: research
Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement
DNA methylation is an essential epigenetic modification. However, its contribution to trait changes and diversity in the domestication of perennial fruit trees remains unknown. (Source: Genome Biology)
Source: Genome Biology - April 5, 2024 Category: Genetics & Stem Cells Authors: Bobo Song, Jinshan Yu, Xiaolong Li, Jiaming Li, Jing Fan, Hainan Liu, Weilin Wei, Lingchao Zhang, Kaidi Gu, Dongliang Liu, Kejiao Zhao and Jun Wu Tags: Research Source Type: research
Merit of integrating in situ transcriptomics and anatomical information for cell annotation and lineage construction in single-cell analyses of Populus
Cell type annotation and lineage construction are two of the most critical tasks conducted in the analyses of single-cell RNA sequencing (scRNA-seq). Four recent scRNA-seq studies of differentiating xylem prop... (Source: Genome Biology)
Source: Genome Biology - April 3, 2024 Category: Genetics & Stem Cells Authors: Ying-Lan Chen, Jo-Wei Allison Hsieh, Shang-Che Kuo, Chung-Ting Kao, Chia-Chun Tung, Jhong-He Yu, Tien-Hsien Chang, Chuan Ku, Jianbo Xie, Deqiang Zhang, Quanzi Li and Ying-Chung Jimmy Lin Tags: Correspondence Source Type: research
Response to: “Merit of integrating in situ transcriptomics and anatomical information for cell annotation and lineage construction in single-cell analyses of Populus”
(Source: Genome Biology)
Source: Genome Biology - April 3, 2024 Category: Genetics & Stem Cells Authors: Shaoming Liang, Yiling Li, Yang Chen, Heng Huang, Sijia Li, Yuanzhong Jiang and Tao Ma Tags: Correspondence Source Type: research
