Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue
We define and identify a new class of control genes for next-generation sequencing called total RNA expression genes (TREGs), which correlate with total RNA abundance in cell types of different sizes and trans... (Source: Genome Biology)
Source: Genome Biology - October 16, 2023 Category: Genetics & Stem Cells Authors: Louise A. Huuki-Myers, Kelsey D. Montgomery, Sang Ho Kwon, Stephanie C. Page, Stephanie C. Hicks, Kristen R. Maynard and Leonardo Collado-Torres Tags: Software Source Type: research
MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites
Malaria remains one of the deadliest infectious diseases. Transcriptional regulation effects of noncoding variants in this unusual genome of malaria parasites remain elusive. We developed a sequence-based, ab ... (Source: Genome Biology)
Source: Genome Biology - October 16, 2023 Category: Genetics & Stem Cells Authors: Chengqi Wang, Yibo Dong, Chang Li, Jenna Oberstaller, Min Zhang, Justin Gibbons, Camilla Valente Pires, Mianli Xiao, Lei Zhu, Rays H. Y. Jiang, Kami Kim, Jun Miao, Thomas D. Otto, Liwang Cui, John H. Adams and Xiaoming Liu Tags: Method Source Type: research
The evolution and mutational robustness of chromatin accessibility in Drosophila
The evolution of genomic regulatory regions plays a critical role in shaping the diversity of life. While this process is primarily sequence-dependent, the enormous complexity of biological systems complicates... (Source: Genome Biology)
Source: Genome Biology - October 16, 2023 Category: Genetics & Stem Cells Authors: Samuel Khodursky, Eric B. Zheng, Nicolas Svetec, Sylvia M. Durkin, Sigi Benjamin, Alice Gadau, Xia Wu and Li Zhao Tags: Research Source Type: research
Metagenome-wide analysis uncovers gut microbial signatures and implicates taxon-specific functions in end-stage renal disease
The gut microbiota plays a crucial role in regulating host metabolism and producing uremic toxins in patients with end-stage renal disease (ESRD). Our objective is to advance toward a holistic understanding of... (Source: Genome Biology)
Source: Genome Biology - October 12, 2023 Category: Genetics & Stem Cells Authors: Pan Zhang, Xifan Wang, Shenghui Li, Xuesen Cao, Jianzhou Zou, Yi Fang, Yiqin Shi, Fangfang Xiang, Bo Shen, Yixuan Li, Bing Fang, Yue Zhang, Ruochun Guo, Qingbo Lv, Liwen Zhang, Yufei Lu & hellip; Tags: Research Source Type: research
Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants
In several eukaryotes, DNA methylation occurs within the coding regions of many genes, termed gene body methylation (GbM). Whereas the role of DNA methylation on the silencing of transposons and repetitive DNA... (Source: Genome Biology)
Source: Genome Biology - October 12, 2023 Category: Genetics & Stem Cells Authors: Clara J. Williams, Dawei Dai, Kevin A. Tran, J. Grey Monroe and Ben P. Williams Tags: Research Source Type: research
Robust, scalable, and informative clustering for diverse biological networks
Clustering molecular data into informative groups is a primary step in extracting robust conclusions from big data. However, due to foundational issues in how they are defined and detected, such clusters are n... (Source: Genome Biology)
Source: Genome Biology - October 12, 2023 Category: Genetics & Stem Cells Authors: Chris Gaiteri, David R. Connell, Faraz A. Sultan, Artemis Iatrou, Bernard Ng, Boleslaw K. Szymanski, Ada Zhang and Shinya Tasaki Tags: Method Source Type: research
The landscape of cell-free mitochondrial DNA in liquid biopsy for cancer detection
Existing methods to detect tumor signal in liquid biopsy have focused on the analysis of nuclear cell-free DNA (cfDNA). However, non-nuclear cfDNA and in particular mitochondrial DNA (mtDNA) has been understud... (Source: Genome Biology)
Source: Genome Biology - October 12, 2023 Category: Genetics & Stem Cells Authors: Ymke van der Pol, Norbert Moldovan, Jip Ramaker, Sanne Bootsma, Kristiaan J. Lenos, Louis Vermeulen, Shahneen Sandhu, Idris Bahce, D. Michiel Pegtel, Stephen Q. Wong, Sarah-Jane Dawson, Dineika Chandrananda and Florent Mouliere Tags: Research Source Type: research
A fast non-parametric test of association for multiple traits
The increasing availability of multidimensional phenotypic data in large cohorts of genotyped individuals requires efficient methods to identify genetic effects on multiple traits. Permutational multivariate a... (Source: Genome Biology)
Source: Genome Biology - October 12, 2023 Category: Genetics & Stem Cells Authors: Diego Garrido-Mart ín, Miquel Calvo, Ferran Reverter and Roderic Guigó Tags: Method Source Type: research
scIBD: a self-supervised iterative-optimizing model for boosting the detection of heterotypic doublets in single-cell chromatin accessibility data
Application of the widely used droplet-based microfluidic technologies in single-cell sequencing often yields doublets, introducing bias to downstream analyses. Especially, doublet-detection methods for single... (Source: Genome Biology)
Source: Genome Biology - October 9, 2023 Category: Genetics & Stem Cells Authors: Wenhao Zhang, Rui Jiang, Shengquan Chen and Ying Wang Tags: Method Source Type: research
MCProj: metacell projection for interpretable and quantitative use of transcriptional atlases
We describe MCProj —an algorithm for analyzing query scRNA-seq data by projections over reference single-cell atlases. We represent the reference as a manifold of annotated metacell gene expression distribution... (Source: Genome Biology)
Source: Genome Biology - October 5, 2023 Category: Genetics & Stem Cells Authors: Oren Ben-Kiki, Akhiad Bercovich, Aviezer Lifshitz, Ofir Raz, Dror Brook and Amos Tanay Tags: Method Source Type: research
Genomic variant benchmark: if you cannot measure it, you cannot improve it
Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of sequencing technologies and analytical methods and highlight future ... (Source: Genome Biology)
Source: Genome Biology - October 5, 2023 Category: Genetics & Stem Cells Authors: Sina Majidian, Daniel Paiva Agustinho, Chen-Shan Chin, Fritz J. Sedlazeck and Medhat Mahmoud Tags: Review Source Type: research
HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing
DNA barcodes enable Oxford Nanopore sequencing to sequence multiple barcoded DNA samples on a single flow cell. DNA sequences with the same barcode need to be grouped together through demultiplexing. As the nu... (Source: Genome Biology)
Source: Genome Biology - October 5, 2023 Category: Genetics & Stem Cells Authors: Renmin Han, Junhai Qi, Yang Xue, Xiujuan Sun, Fa Zhang, Xin Gao and Guojun Li Tags: Method Source Type: research
GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation
Crop pangenomes made from individual cultivar assemblies promise easy access to conserved genes, but genome content variability and inconsistent identifiers hamper their exploration. To address this, we define... (Source: Genome Biology)
Source: Genome Biology - October 5, 2023 Category: Genetics & Stem Cells Authors: Bruno Contreras-Moreira, Shradha Saraf, Guy Naamati, Ana M. Casas, Sandeep S. Amberkar, Paul Flicek, Andrew R. Jones and Sarah Dyer Tags: Method Source Type: research
Large sample size and nonlinear sparse models outline epistatic effects in inflammatory bowel disease
Despite clear evidence of nonlinear interactions in the molecular architecture of polygenic diseases, linear models have so far appeared optimal in genotype-to-phenotype modeling. A key bottleneck for such mod... (Source: Genome Biology)
Source: Genome Biology - October 5, 2023 Category: Genetics & Stem Cells Authors: Nora Verplaetse, Antoine Passemiers, Adam Arany, Yves Moreau and Daniele Raimondi Tags: Research Source Type: research
CEGA: a method for inferring natural selection by comparative population genomic analysis across species
We developed maximum likelihood method for detecting positive selection or balancing selection using multilocus or genomic polymorphism and divergence data from two species. The method is especially useful for... (Source: Genome Biology)
Source: Genome Biology - October 3, 2023 Category: Genetics & Stem Cells Authors: Shilei Zhao, Lianjiang Chi and Hua Chen Tags: Method Source Type: research
