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Dec 30, 2024 | 
genomebiology.biomedcentral.com | Xiaoyang Chen |Keyi LI |Xiaoqing Wu |Zhen Li |Qun Jiang |Xuejian Cui | +3 more
To capture spatial accessibility pattern of each peak, Descart construct a spatial graph based on spatial locations of spots (can also be replaced by cells).
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Dec 18, 2024 | 
genomebiology.biomedcentral.com | Zijing Gao |Qiao Liu |Wanwen Zeng |Rui Jiang
We used three different datasets in the experiments. For chromatin accessible data, we downloaded DNase bam files across 129 human biosamples from ENCODE [21] project (Additional file 2: Table S6). We divided the human hg19 genome into 200-bp non-overlapping bins, and we assigned the label for each bin in each cell type. For the regression design, we pooled the bam files of multiple replicates for a cell type, and obtain the raw read count \({n}_{lk}\) for bin \(l\) in cell type \(k\).
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Oct 21, 2024 | 
mdpi.com | Guangyong Chen |Yiqun Zhang |Rui Jiang
All articles published by MDPI are made immediately available worldwide under an open access license. No special permission is required to reuse all or part of the article published by MDPI, including figures and tables. For articles published under an open access Creative Common CC BY license, any part of the article may be reused without permission provided that the original article is clearly cited. For more information, please refer to https://www.mdpi.com/openaccess.
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Jul 19, 2024 | 
science.org | Ruiyi Zhang |Aashish Gupta |Zhichao Lu |Min Zhu |Chenxing Wang |Rui Jiang | +10 more
AbstractAged patients often suffer poorer neurological recovery than younger patients after traumatic brain injury (TBI), but the mechanisms underlying this difference remain unclear. Here, we demonstrate abnormal myelopoiesis characterized by increased neutrophil and classical monocyte output but impaired nonclassical patrolling monocyte population in aged patients with TBI as well as in an aged murine TBI model.
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May 13, 2024 | 
analyticalsciencejournals.onlinelibrary.wiley.com | Deyu Li |Rui Jiang |Jun Li |Mechatronics Engineering
CONFLICT OF INTEREST STATEMENT The authors declare no conflicts of interest. Supporting Information Filename Description elps7986-sup-0001-SuppMat.docx164.2 KB Supporting Information Additional supporting information can be found online in the Supporting Information section at the end of this article. REFERENCES 1, , .
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Mar 13, 2024 | 
biorxiv.org | Xiaoyang Chen |Keyi LI |Rui Jiang |Zhen Li
AbstractRecent advances in spatial sequencing technologies enable simultaneous capture of spatial location and chromatin accessibility of cells within intact tissue slices. Identifying peaks that display spatial variation and cellular heterogeneity is the first and key analytic task for characterizing the spatial chromatin accessibility landscape of complex tissues.
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Feb 3, 2024 | 
biorxiv.org | Zijing Gao |Qiao Liu |Wanwen Zeng |Rui Jiang
AbstractThe inherent similarities between natural language and biological sequences have given rise to great interest in adapting the transformer-based large language models (LLMs) underlying recent breakthroughs in natural language processing (references), for applications in genomics.
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Oct 9, 2023 | 
genomebiology.biomedcentral.com | Wenhao Zhang |Rui Jiang |Shengquan Chen |Ying Wang
The scCAS data used in this study were derived from three main sources. The dataset of human mixed cell lines (HMC) was generated from a mixture of ten human cell lines using single-nucleus ATAC-seq [6]. The dataset of mouse forebrain (MF) was generated from the forebrain tissue of an 8-week-old adult mouse by single-nucleus ATAC-seq [19].
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Jul 26, 2023 | 
mdpi.com | Rui Jiang |Ping Guo
This is an early access version, the complete PDF, HTML, and XML versions will be available soon. Open AccessArticleby 1,2 and 1,2,* 1School of Law, Sun Yat-sen University, Guangzhou 510006, China2Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China*Author to whom correspondence should be addressed.
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Jul 18, 2023 | 
biorxiv.org | Zijing Gao |Qiao Liu |Wanwen Zeng |Rui Jiang
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