572.86
Genomics & Gene Editing
Sequencing, CRISPR and the regulatory genome.
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single-cell sequencing atlas
CRISPR gene editing
572.86
Sequencing, CRISPR and the regulatory genome.
Drawer contents
Filled from
Search threads
single-cell sequencing atlas
CRISPR gene editing
Yuqiao Liu, Siyu Yi, Hengchuang Yin, Wei Ju
Single-cell RNA sequencing profiles cellular heterogeneity at atlas scale, making automated annotation essential. However, target datasets often contain novel cell types missing from incomplete references. We present scOLAR, an ontology-guided open-set framework that learns prototypes over the Cell Ontology and uses…
Alessandra Fabrizi, Marta Valenti, Silvia Zacchino, Katia Russo + 3 more
Inherited genodermatoses are a heterogeneous group of rare monogenic disorders. Among these, epidermolysis bullosa (EB) and ichthyoses represent paradigmatic disorders characterized by severe skin fragility and hyperkeratosis, respectively, and impaired barrier function, often with profound effects on quality of life…
Negin Rahimzadeh, Samuel Morabito, Saniya Khullar, Zechuan Shi + 2 more
Interindividual heterogeneity in Alzheimer’s disease (AD) remains poorly understood, as disparate single-cell studies leave it unclear whether findings reflect shared architecture or dataset-specific idiosyncrasies. Here, we present panAD, a transcriptomic atlas of >3 million nuclei from 791 individuals across 13…
Masaki Kawamata, Satoshi Niwa, Atsushi Suzuki
CRISPR-Cas9 has revolutionised genome editing by enabling efficient and programmable modification of defined DNA sequences, with guide RNAs (gRNAs) serving as indispensable elements that direct Cas9 to specific genomic loci. Initially regarded as auxiliary components, gRNAs are now recognized as critical determinants…
Uzair Ahmed, Fausta Michnevičiūtė, Marius Vinogradovas, Eimina Dirvelytė-Valauskė + 2 more
Gene knockouts by CRISPR-Cas nucleases rely on targeted DNA cleavage and error-prone DNA repair: end-joining pathways can introduce insertions and deletions that assist in disrupting the coding sequence. However, only a fraction of edits achieves this, and an unfavorable array of repair outcomes typically requires…
Yuling Zhu, Yunfei Hu, Manfei Bella Xie, Haoran Qin + 7 more
Spatial transcriptomics enables the quantification of gene expression within its native tissue context, providing unprecedented insight into tissue architecture, cellular ecosystems, and local cell-cell interactions at regional and single-cell resolution. Accurate cell type annotation is a critical prerequisite for…
Brett Kiyota, Chaehyeon Lee, Haoyang Yao, Nozomu Yachie
The rapid expansion of single-cell genomic datasets has led to the compilation of biological resources comprising hundreds of millions of cells across tissues, developmental stages, and disease states. This has underscored the need for scalable and interpretable data representations that preserve the complex…
Jillian Cwycyshyn, Cooper Stansbury, Sarah Golts, Hyunsu Lee + 4 more
Title: Summary Direct reprogramming of human fibroblasts into hematopoietic stem cells (HSCs) offers a promising strategy for generating autologous cells to treat blood and immune disorders. Current protocols are limited by low efficiency and insufficient tools for evaluating reprogramming outcomes. Although functional…
Rafal Czapiewski, Michael Chiang, James Ding, Catherine Naughton + 3 more
Cell-to-cell transcriptional heterogeneity, or noise, is an intrinsic property of the transcriptome with implications for development, disease progression, and aging. Bulk RNA-seq masks this variability by averaging gene expression across cells, whereas single-cell RNA sequencing (scRNA-seq) resolves it. Nevertheless…
Weige Zhou, Xueying Fan, Lanxiang Li, Jianrong Zheng + 3 more
The rapid growth of single-cell and spatial omics has outpaced computational methods capable of unifying these data into a cohesive framework for tissue atlas construction and cross-sample analysis. A critical bottleneck lies in the inability of existing tools to co-embed cells from diverse technologies-spanning…
Quang Tri Le, Xuebo Zhao, Ping Yates, Henry W. Schmidt + 6 more
Plants adapted to saline coastal habitats provide valuable systems for understanding how natural selection reshapes stress-response programs, yet the cellular and molecular basis of this adaptation remains poorly resolved. Here, we generated a chromosome-scale reference genome and a single- nucleus transcriptomic atlas…
Sriwidodo Sriwidodo, Cecep Suhandi, Salsa Sagitasa, Belva Annora Alfita Davinali + 2 more
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) has emerged as a promising gene-editing platform for genetic disorders; however, its in vivo application remains limited by low delivery efficiency and biological barriers. Many CRISPR payloads fail to reach target…
Daniel E. Schäffer, Helen Kang, Ekin Deniz Aksu, Daniel Edelman + 1 more
Data from single-cell RNA sequencing (scRNA-seq) and the Assay for Transposase-Accessible Chromatin (scATAC-seq) are high-dimensional, sparse, and undesirably capture technical variability between experiments or batches. Many analysis methods thus seek to produce a low-dimensional cell-by-feature embedding space that…
Qingquan Xiao, Zhijin Tian, Luqi Weng, Kun Xu + 9 more
Despite the promise of DNA base editors for diverse genome editing applications, their utility remains constrained by off-target effects, which are exacerbated by short spacers in miniature systems and the large size of Cas9-derived editors, which impedes adeno-associated virus (AAV) delivery. Here, guided by…
Curtis Hart, Lovely Paul Solomon Devakumar, Khalid Saeed, Adam Spruce + 5 more
Precise temporal control of gene editing is essential for studying dynamic biological processes, interrogating essential gene function, and improving the interpretability of pooled perturbation screens. Cre-dependent single guide RNA (sgRNA) switches provide temporal regulation by coupling guide activation to…
Zuzanna Majewska, Grzegorz Jursza, Alicja Dolzblasz
Main Conclusion Our review illustrates how the dexamethasone-inducible LhGR/pOp system has been used across numerous tissues/organs and plant species, and summarizes the resources and inducer application procedures established to date. Abstract The establishment of groundbreaking molecular biology tools has enabled the…
Qiaochu Wang, Ahmed Saleh, Gundra Sivakrishna Rao, Ahmed M. Kazlak + 2 more
Compact CRISPR nucleases are attractive for therapeutic genome editing because their small coding sequences facilitate delivery by adeno-associated virus. Type II-D Cas9 (Cas9d) enzymes constitute the most compact Cas9 subtype, yet only a few orthologs have demonstrated mammalian genome-editing activity, leaving it…
Guoxia Wen, Jiaqi Li, Hanyu Wu, Jialing Fang + 9 more
To streamline the application of sequence-based DL methods in single-cell genomics, we established a two-layer CNN as our baseline model. We focus our benchmark on how data characteristics, hyperparameter optimization, and advanced model architectures impact performance across sequence-to-expression and…
Asfar Lathif Salaudeen, Trevor Shyiak, Carl G. de Boer
Virus-like particles (VLPs) enable transient, non-integrating delivery of CRISPR-Cas9 ribonucleoprotein cargo. Although VLPs have been reported for efficient DNA editing via base editors RNP delivery, the diversity of base editors tested as VLPs remains limited. We generated and benchmarked a panel of 12 base editors…
Mahalakshmi Mani, S. Poonguzhali, K. Baghyalakshmi
Rice is one of the most important food crops and feeds more than half of the world’s population. Enhancing grain quality is currently a highly important issue since consumers are now more concerned with the taste, appearance, and nutritional value of the grain. The quality of grain in rice is complex and regulated by a…
Antoine de Mathelin, Jeffrey F. Quinn, Christopher Tosh, Data Science TeamLab + 1 more
Assigning cell types to single-cell and spatial transcriptomic data remains inconsistent because marker gene knowledge is fragmented across thousands of individual studies. Here we present CellConsensus, a cell typing method built on a consensus corpus of marker genes aggregated from curated atlases (2,607 sources) and…
Yuanqing Yan, Diego Avella Patino, Yimeng Zhao, Xin Wu + 2 more
Myasthenia gravis (MG) presents a clinical challenge where autoantibody titers poorly predict disease severity, and thymectomy provides inconsistent benefits. We hypothesized that thymic B cells acquire survival mechanisms that bypass canonical tolerance checkpoints, enabling persistence independent of antigen-specific…
Maikel B.F. Steentjes, Gregory Ashe, Patricia Schöppl, Rahim Mehrabi + 1 more
Pseudocercospora fijiensis is the causal agent of Black Leaf Streak Disease (BLSD), also known as black Sigatoka, in banana. The disease affects many banana varieties, including the highly susceptible Cavendish banana that dominates global production and the export trade, and several cooking bananas that are a staple…
Mike Adam, Keri A. Drake, Naomi Pode-Shakked, Katherine VandenHeuvel + 2 more
While Wilms tumors commonly arise from renal precursor cells and maintain features of the developing kidney, recent studies have demonstrated substantial genetic, histologic, and molecular heterogeneity. To further investigate tumor variability as well as unifying features in tumor biology, we performed single-nucleus…