Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal
Hundreds of functional genomic screens have been performed across a diverse set of cancer contexts, as part of efforts such as the Cancer Dependency Map, to identify gene dependencies —genes whose loss of funct... (Source: Genome Biology)
Source: Genome Biology - August 23, 2023 Category: Genetics & Stem Cells Authors: J. Michael Krill-Burger, Joshua M. Dempster, Ashir A. Borah, Brenton R. Paolella, David E. Root, Todd R. Golub, Jesse S. Boehm, William C. Hahn, James M. McFarland, Francisca Vazquez and Aviad Tsherniak Tags: Research Source Type: research
GTM-decon: guided-topic modeling of single-cell transcriptomes enables sub-cell-type and disease-subtype deconvolution of bulk transcriptomes
We present Guided Topic Model for deconvolution (GTM-decon) to automatically infer cell-type-specific gene topic distributions from single-cell RNA-se... (Source: Genome Biology)
Source: Genome Biology - August 18, 2023 Category: Genetics & Stem Cells Authors: Lakshmipuram Seshadri Swapna, Michael Huang and Yue Li Tags: Method Source Type: research
Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture
The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and ... (Source: Genome Biology)
Source: Genome Biology - August 15, 2023 Category: Genetics & Stem Cells Authors: Jennifer R. S. Meadows, Jeffrey M. Kidd, Guo-Dong Wang, Heidi G. Parker, Peter Z. Schall, Matteo Bianchi, Matthew J. Christmas, Katia Bougiouri, Reuben M. Buckley, Christophe Hitte, Anthony K. Nguyen, Chao Wang, Vidhya Jagannathan, Julia E. Niskanen, Laur Tags: Research Source Type: research
BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens
MHC-I-associated peptides deriving from non-coding genomic regions and mutations can generate tumor-specific antigens, including neoantigens. Quantifying tumor-specific antigens ’ RNA expression in malignant an... (Source: Genome Biology)
Source: Genome Biology - August 15, 2023 Category: Genetics & Stem Cells Authors: Maria Virginia Ruiz Cuevas, Marie-Pierre Hardy, Jean-David Larouche, Anca Apavaloaei, Eralda Kina, Krystel Vincent, Patrick Gendron, Jean-Philippe Laverdure, Chantal Durette, Pierre Thibault, S ébastien Lemieux, Claude Perreault and Grégory Ehx Tags: Method Source Type: research
Predicting the impact of sequence motifs on gene regulation using single-cell data
The binding of transcription factors at proximal promoters and distal enhancers is central to gene regulation. Identifying regulatory motifs and quantifying their impact on expression remains challenging. Usin... (Source: Genome Biology)
Source: Genome Biology - August 15, 2023 Category: Genetics & Stem Cells Authors: Jacob Hepkema, Nicholas Keone Lee, Benjamin J. Stewart, Siwat Ruangroengkulrith, Varodom Charoensawan, Menna R. Clatworthy and Martin Hemberg Tags: Method Source Type: research
The CUT & RUN suspect list of problematic regions of the genome
Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is an increasingly popular technique to map genome-wide binding profiles of histone modifications, transcription factors, and co-factors. The ENCODE ... (Source: Genome Biology)
Source: Genome Biology - August 10, 2023 Category: Genetics & Stem Cells Authors: Anna Nordin, Gianluca Zambanini, Pierfrancesco Pagella and Claudio Cant ù Tags: Research Source Type: research
Maast: genotyping thousands of microbial strains efficiently
Existing single nucleotide polymorphism (SNP) genotyping algorithms do not scale for species with thousands of sequenced strains, nor do they account for conspecific redundancy. Here we present a bioinformatic... (Source: Genome Biology)
Source: Genome Biology - August 10, 2023 Category: Genetics & Stem Cells Authors: Zhou Jason Shi, Stephen Nayfach and Katherine S. Pollard Tags: Software Source Type: research
LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesis
Existing single-cell RNA sequencing (scRNA-seq) methods rely on reverse transcription (RT) and second-strand synthesis (SSS) to convert single-stranded RNA into double-stranded DNA prior to amplification, with... (Source: Genome Biology)
Source: Genome Biology - August 9, 2023 Category: Genetics & Stem Cells Authors: Jun Lyu and Chongyi Chen Tags: Method Source Type: research
Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome
Cumulative sequencing efforts have yielded enough genomes to construct pangenomes for dozens of bacterial species and elucidate intraspecies gene conservation. Given the diversity of organisms for which this i... (Source: Genome Biology)
Source: Genome Biology - August 8, 2023 Category: Genetics & Stem Cells Authors: Jason C. Hyun and Bernhard O. Palsson Tags: Research Source Type: research
3D organization of regulatory elements for transcriptional regulation in Arabidopsis
Although spatial organization of compartments and topologically associating domains at large scale is relatively well studied, the spatial organization of regulatory elements at fine scale is poorly understood... (Source: Genome Biology)
Source: Genome Biology - August 7, 2023 Category: Genetics & Stem Cells Authors: Li Deng, Qiangwei Zhou, Jie Zhou, Qing Zhang, Zhibo Jia, Guangfeng Zhu, Sheng Cheng, Lulu Cheng, Caijun Yin, Chao Yang, Jinxiong Shen, Junwei Nie, Jian-Kang Zhu, Guoliang Li and Lun Zhao Tags: Research Source Type: research
Cross-protein transfer learning substantially improves disease variant prediction
Genetic variation in the human genome is a major determinant of individual disease risk, but the vast majority of missense variants have unknown etiological effects. Here, we present a robust learning framewor... (Source: Genome Biology)
Source: Genome Biology - August 7, 2023 Category: Genetics & Stem Cells Authors: Milind Jagota, Chengzhong Ye, Carlos Albors, Ruchir Rastogi, Antoine Koehl, Nilah Ioannidis and Yun S. Song Tags: Research Source Type: research
Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning
We present RBPNet, a novel deep learning method, which predicts CLIP-seq crosslink count distribution from RNA sequence at single-nucleotide resolution. By training on up to a million regions, RBPNet achieves ... (Source: Genome Biology)
Source: Genome Biology - August 4, 2023 Category: Genetics & Stem Cells Authors: Marc Horlacher, Nils Wagner, Lambert Moyon, Klara Kuret, Nicolas Goedert, Marco Salvatore, Jernej Ule, Julien Gagneur, Ole Winther and Annalisa Marsico Tags: Method Source Type: research
BEDwARS: a robust Bayesian approach to bulk gene expression deconvolution with noisy reference signatures
Differential gene expression in bulk transcriptomics data can reflect change of transcript abundance within a cell type and/or change in the proportions of cell types. Expression deconvolution methods can help... (Source: Genome Biology)
Source: Genome Biology - August 3, 2023 Category: Genetics & Stem Cells Authors: Saba Ghaffari, Kelly J. Bouchonville, Ehsan Saleh, Remington E. Schmidt, Steven M. Offer and Saurabh Sinha Tags: Method Source Type: research
A syntelog-based pan-genome provides insights into rice domestication and de-domestication
Asian rice is one of the world ’s most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the ev... (Source: Genome Biology)
Source: Genome Biology - August 3, 2023 Category: Genetics & Stem Cells Authors: Dongya Wu, Lingjuan Xie, Yanqing Sun, Yujie Huang, Lei Jia, Chenfeng Dong, Enhui Shen, Chu-Yu Ye, Qian Qian and Longjiang Fan Tags: Research Source Type: research
Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes
RNA profiling technologies at single-cell resolutions, including single-cell and single-nuclei RNA sequencing (scRNA-seq and snRNA-seq, scnRNA-seq for short), can help characterize the composition of tissues a... (Source: Genome Biology)
Source: Genome Biology - August 1, 2023 Category: Genetics & Stem Cells Authors: Francisco Avila Cobos, Mohammad Javad Najaf Panah, Jessica Epps, Xiaochen Long, Tsz-Kwong Man, Hua-Sheng Chiu, Elad Chomsky, Evgeny Kiner, Michael J. Krueger, Diego di Bernardo, Luis Voloch, Jan Molenaar, Sander R. van Hooff, Frank Westermann, Selina Jans Tags: Research Source Type: research
