Inferring cell-type-specific causal gene regulatory networks during human neurogenesis
Genetic variation influences both chromatin accessibility, assessed in chromatin accessibility quantitative trait loci (caQTL) studies, and gene expression, assessed in expression QTL (eQTL) studies. Genetic v... (Source: Genome Biology)
Source: Genome Biology - May 30, 2023 Category: Genetics & Stem Cells Authors: Nil Ayg ün, Dan Liang, Wesley L. Crouse, Gregory R. Keele, Michael I. Love and Jason L. Stein Tags: Research Source Type: research
Genomic hallmarks and therapeutic implications of G0 cell cycle arrest in cancer
Therapy resistance in cancer is often driven by a subpopulation of cells that are temporarily arrested in a non-proliferative G0 state, which is difficult to capture and whose mutational drivers remain largely... (Source: Genome Biology)
Source: Genome Biology - May 23, 2023 Category: Genetics & Stem Cells Authors: Anna J. Wiecek, Stephen J. Cutty, Daniel Kornai, Mario Parreno-Centeno, Lucie E. Gourmet, Guidantonio Malagoli Tagliazucchi, Daniel H. Jacobson, Ping Zhang, Lingyun Xiong, Gareth L. Bond, Alexis R. Barr and Maria Secrier Tags: Research Source Type: research
Graph construction method impacts variation representation and analyses in a bovine super-pangenome
Several models and algorithms have been proposed to build pangenomes from multiple input assemblies, but their impact on variant representation, and consequently downstream analyses, is largely unknown. (Source: Genome Biology)
Source: Genome Biology - May 22, 2023 Category: Genetics & Stem Cells Authors: Alexander S. Leonard, Danang Crysnanto, Xena M. Mapel, Meenu Bhati and Hubert Pausch Tags: Research Source Type: research
SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors
Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) reveals chromatin accessibility across the genome. Currently, no method specifically detects differential chromatin accessibility. Here, Se... (Source: Genome Biology)
Source: Genome Biology - May 22, 2023 Category: Genetics & Stem Cells Authors: Wuming Gong, Nikita Dsouza and Daniel J. Garry Tags: Method Source Type: research
In silico methods for predicting functional synonymous variants
Single nucleotide variants (SNVs) contribute to human genomic diversity. Synonymous SNVs are previously considered to be “silent,” but mounting evidence has revealed that these variants can cause RNA and prote... (Source: Genome Biology)
Source: Genome Biology - May 22, 2023 Category: Genetics & Stem Cells Authors: Brian C. Lin, Upendra Katneni, Katarzyna I. Jankowska, Douglas Meyer and Chava Kimchi-Sarfaty Tags: Review Source Type: research
Profiling the immune epigenome across global cattle breeds
Understanding the variation between well and poorly adapted cattle breeds to local environments and pathogens is essential for breeding cattle with improved climate and disease-resistant phenotypes. Although c... (Source: Genome Biology)
Source: Genome Biology - May 22, 2023 Category: Genetics & Stem Cells Authors: Jessica Powell, Andrea Talenti, Andressa Fisch, Johanneke D. Hemmink, Edith Paxton, Philip Toye, Isabel Santos, Beatriz R. Ferreira, Tim K. Connelley, Liam J. Morrison and James G. D. Prendergast Tags: Research Source Type: research
SPUMONI 2: improved classification using a pangenome index of minimizer digests
Genomics analyses use large reference sequence collections, like pangenomes or taxonomic databases. SPUMONI 2 is an efficient tool for sequence classification of both short and long reads. It performs multi-cl... (Source: Genome Biology)
Source: Genome Biology - May 18, 2023 Category: Genetics & Stem Cells Authors: Omar Y. Ahmed, Massimiliano Rossi, Travis Gagie, Christina Boucher and Ben Langmead Tags: Software Source Type: research
Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications
Predicting the impact of coding and noncoding variants on splicing is challenging, particularly in non-canonical splice sites, leading to missed diagnoses in patients. Existing splice prediction tools are comp... (Source: Genome Biology)
Source: Genome Biology - May 17, 2023 Category: Genetics & Stem Cells Authors: Patricia J. Sullivan, Velimir Gayevskiy, Ryan L. Davis, Marie Wong, Chelsea Mayoh, Amali Mallawaarachchi, Yvonne Hort, Mark J. McCabe, Sarah Beecroft, Matilda R. Jackson, Peer Arts, Andrew Dubowsky, Nigel Laing, Marcel E. Dinger, Hamish S. Scott, Emily Oa Tags: Method Source Type: research
Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability
Computational methods represent the lifeblood of modern molecular biology. Benchmarking is important for all methods, but with a focus here on computational methods, benchmarking is critical to dissect importa... (Source: Genome Biology)
Source: Genome Biology - May 17, 2023 Category: Genetics & Stem Cells Authors: Anthony Sonrel, Almut Luetge, Charlotte Soneson, Izaskun Mallona, Pierre-Luc Germain, Sergey Knyazev, Jeroen Gilis, Reto Gerber, Ruth Seurinck, Dominique Paul, Emanuel Sonder, Helena L. Crowell, Imran Fanaswala, Ahmad Al-Ajami, Elyas Heidari, Stephan Schm Tags: Correspondence Source Type: research
Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data
Spatial transcriptomics maps gene expression across tissues, posing the challenge of determining the spatial arrangement of different cell types. However, spatial transcriptomics spots contain multiple cells. ... (Source: Genome Biology)
Source: Genome Biology - May 17, 2023 Category: Genetics & Stem Cells Authors: Agnieszka Geras, Shadi Darvish Shafighi, Kacper Domżał, Igor Filipiuk, Łukasz Rączkowski, Paulina Szymczak, Hosein Toosi, Leszek Kaczmarek, Łukasz Koperski, Jens Lagergren, Dominika Nowis and Ewa Szczurek Tags: Method Source Type: research
RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches
We present RabbitTClust, a fast and memory-efficient genome clustering tool based on sketch-based distance estimation. Our approach enables efficient processing of large-scale datasets by combining dimensional... (Source: Genome Biology)
Source: Genome Biology - May 17, 2023 Category: Genetics & Stem Cells Authors: Xiaoming Xu, Zekun Yin, Lifeng Yan, Hao Zhang, Borui Xu, Yanjie Wei, Beifang Niu, Bertil Schmidt and Weiguo Liu Tags: Software Source Type: research
Phenome-wide analyses identify an association between the parent-of-origin effects dependent methylome and the rate of aging in humans
The variation in the rate at which humans age may be rooted in early events acting through the genomic regions that are influenced by such events and subsequently are related to health phenotypes in later life... (Source: Genome Biology)
Source: Genome Biology - May 15, 2023 Category: Genetics & Stem Cells Authors: Chenhao Gao, Carmen Amador, Rosie M. Walker, Archie Campbell, Rebecca A. Madden, Mark J. Adams, Xiaomeng Bai, Ying Liu, Miaoxin Li, Caroline Hayward, David J. Porteous, Xueyi Shen, Kathryn L. Evans, Chris S. Haley, Andrew M. McIntosh, Pau Navarro & hellip Tags: Research Source Type: research
Publisher Correction: Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data
(Source: Genome Biology)
Source: Genome Biology - May 12, 2023 Category: Genetics & Stem Cells Authors: Yue You, Xueyi Dong, Yong Kiat Wee, Mhairi J. Maxwell, Monther Alhamdoosh, Gordon K. Smyth, Peter F. Hickey, Matthew E. Ritchie and Charity W. Law Tags: Publisher Correction Source Type: research
Cross-phyla protein annotation by structural prediction and alignment
Protein annotation is a major goal in molecular biology, yet experimentally determined knowledge is typically limited to a few model organisms. In non-model species, the sequence-based prediction of gene ortho... (Source: Genome Biology)
Source: Genome Biology - May 12, 2023 Category: Genetics & Stem Cells Authors: Fabian Ruperti, Nikolaos Papadopoulos, Jacob M. Musser, Milot Mirdita, Martin Steinegger and Detlev Arendt Tags: Research Source Type: research
Genetic basis of geographical differentiation and breeding selection for wheat plant architecture traits
Plant architecture associated with increased grain yield and adaptation to the local environments is selected during wheat (Triticum aestivum) breeding. The internode length of individual stems and tiller length ... (Source: Genome Biology)
Source: Genome Biology - May 12, 2023 Category: Genetics & Stem Cells Authors: Yangyang Liu, Kuocheng Shen, Changbin Yin, Xiaowan Xu, Xuchang Yu, Botao Ye, Zhiwen Sun, Jiayu Dong, Aoyue Bi, Xuebo Zhao, Daxing Xu, Zhonghu He, Xueyong Zhang, Chenyang Hao, Jianhui Wu, Ziying Wang & hellip; Tags: Research Source Type: research
