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Articles by Chenfei Wang
Genome-wide profiling of histone modifications and transcription factor binding at single-cell resolution by DeChIC-seq
Abstract Mapping of protein-DNA interactions at single-cell resolution remains a central challenge in epigenomics, particularly for transcription factors (TFs), whose sparse binding limits reliable detection. Here, we establish DeChIC-seq (DNA Deaminase-based Chromatin Immuno-Conversion sequencing), a conversion-based strategy that uses a protein A-DddAtox fusion to directly record protein-DNA interactions by inducing localized C-to-U conversions near antibody-bound chromatin.
Accurate, scalable and cross-platform cell identification for high-resolution spatial transcriptomics
Abstract Recent advances in spatial transcriptomics (ST) have brought unprecedented insights into cellular diversity and cell–cell interactions within their spatial context. High-resolution ST techniques, including barcoding-based and imaging-based platforms, have achieved remarkable subcellular resolution. However, precise cell segmentation remains a major challenge, hampering effective single-cell spatial analysis.
Commentary: Effect of acupuncture for poor ovarian response: a multicenter randomized controlled trial
A Commentary on Effect of acupuncture for poor ovarian response: a multicenter randomized controlled trial By Su C, Wang X, Liu X, Yang L, Su T, Wang H, Li Y, Zhao C, Zhang C, Xiang W, Tong G, Chen L, Zhao F, Xu H and Fang Y (2026). Front. Endocrinol. 17:1765527. doi: 10.3389/fendo.2026.1765527 We read with great interest the recent article by Su et al.
Investigating the effects and underlying mechanisms of glycosylation sites on the immunogenicity of COVID-19 vaccines
Abstract Glycosylation plays a pivotal role in modulating the structure and immunogenicity of viral antigens. Three glycosylation sites on the receptor-binding domain (RBD) of SARS-CoV-2, including N331, N343 (N-linked), and T323 (O-linked), are highly conserved and remain unchanged across multiple variant strains.
Effects of constant and incremental modes of music volume and odor concentration on vigilance
Abstract Introduction: Vigilance is critical in safety-critical domains, yet sustained attention often declines over time due to sensory adaptation. This study aimed to investigate whether dynamic incremental adjustments of music volume and odor concentration could counteract vigilance decrement more effectively than constant stimulation. Methods: A within-subjects design was adopted, in which 24 participants completed the Psychomotor Vigilance Task (PVT) under five experimental conditions.
HoloTrauma 3X Triadic AI Co reasoning for robot assisted emergency maxillofacial reconstruction
Abstract Maxillofacial trauma accounts for 8–12% of emergency department visits. Temporomandibular joint injuries and complex facial fractures are common causes of airway emergencies. Presently, no protocols exist to simultaneously evaluate airway patency, skeletal integrity, or occlusal function. We created HoloTrauma 3X, which uses vision-language models to comprehensively evaluate the occlusion-bone-airway triad in emergency settings.
Enterococcus faecalis Translocation in Sepsis: Fibrinolysis and Mitochondrial Dysfunction Drive Lung Injury
AVMA American Veterinary Medical Association CLP cecal ligation and puncture DAPI 4′,6-diamidino-2-phenylindole ELISA Enzyme-Linked Immunosorbent Assay HE haematoxylin and eosin IECs intestinal epithelial cells PAS periodic acid-Schiff ROS reactive oxygen species SD standard deviation 1 Introduction Sepsis is a life-threatening syndrome characterised by systemic inflammation and multi-organ failure [1-3], with acute lung injury (ALI) being a leading cause of mortality in severe cases [4, 5].
Cisformer: a scalable cross-modality generation framework for decoding transcriptional regulation at single-cell resolution - Genome Biology
To enable cross-dataset usages, Cisformer adopts a fixed gene or peak vocabulary. All input paired RNA-ATAC data are first mapped onto this unified vocabulary. Specifically, we constructed the vocabulary by retrieving human genes from the Ensembl genome database (https://www.ensembl.org) and CREs from the ENCODE project (https://screen.encodeproject.org). After filtering, we retained 38,244 genes and 1,033,239 CREs located on human autosomes to form the final vocabulary.
Non‐Viral Gene Delivery Systems: Current Advances and Therapeutic Applications
Conflict of Interests The authors declare no conflict of interest. References 1a) , , Nat. Rev. Mater. 2017, 2, 17056; b) , , , , Nat. Rev. Mater. 2021, 6, 1078–1094; c) , , , , , , Nat. Rev. Drug Discov. 2023, 22, 349–350. 2a) , , , , , Mol. Ther. 2021, 29, 442–463; b) , Drug Discov. Today 2019, 24, 949–954. 3, , , , , , , , , , , , , , , , , , , Nat. Med. 2022, 28, 780–788. 4, , , , , , J. Controlled Release 2022, 342, 241–279. 5, , , , , , , , , , , , , , , , , , , , Nat. Biotechnol. 2013, 31, 638–646. 6, , Acc.
Highly Branched Poly(β‐amino ester)s for Efficient mRNA Delivery and Nebulization Treatment of Silicosis
Conflict of Interest The authors declare no conflict of interest. Supporting Information Filename Description adma202414991-sup-0001-SuppMat.docx38 MB Supporting Information References 1a) , , , Nat. Rev. Drug Discovery 2014, 13, 759; b) , , , , , , , , , Chem. Soc. Rev. 2022, 51, 3828; c) , , Nat. Rev. Mater. 2017, 2, 17056. 2, , , , , , Nat. Struct. Mol. Biol. 2020, 27, 814. 3a) , , , Acc. Chem. Res. 2021, 54, 4283; b) , , , , Nat. Rev. Mater. 2021, 6, 1078. 4, , , , , , Nat. Rev. Drug Discovery 2023, 22, 349.
Integrated computational analysis identifies therapeutic targets with dual action in cancer cells and T cells
1Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100084, China 2Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100084, China 3School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China 4Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, Sichuan 610213, China 5Tsinghua-Peking Center for Life Sciences,...
Quantum Dots‐Engineered Flexible Hydrogel as Plant‐Wearable Sensor for on‐Site Profiling Dynamic Pesticide Degradation
Conflict of Interest The authors declare no conflict of interest. Supporting Information Filename Description adfm202423643-sup-0001-SuppMat.docx3.1 MB Supporting Information adfm202423643-sup-0002-VideoS1.mp45.9 MB Supplemental Video 1 adfm202423643-sup-0003-VideoS2.mp412.3 MB Supplemental Video 2 adfm202423643-sup-0004-VideoS3.mp423.6 MB Supplemental Video 3 References 1, , , , , , , , , , , , , Adv. Funct. Mater. 2024, 34, 2407336. 2, , , , , , , , , Adv. Funct. Mater. 2018, 28, 1803051. 3, , , , Adv.
Multi-omic profiling highlights factors associated with resistance to immuno-chemotherapy in non-small-cell lung cancer - Nature Genetics
Abstract Although immune checkpoint blockade (ICB) therapies have shifted the treatment paradigm for non-small-cell lung cancer (NSCLC), many patients remain resistant. Here we characterize the tumor cell states and spatial cellular compositions of the NSCLC tumor microenvironment (TME) by analyzing single-cell transcriptomes of 232,080 cells and spatially resolved transcriptomes of tumors from 19 patients before and after ICB–chemotherapy.
Facile Construction of Flame-Resistant and Thermal-Insulating Sodium Alginate Aerogel Incorporating N- and P-Elements
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MetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment - Nature Communications
Abstract Recent advances in single-cell RNA sequencing have shown heterogeneous cell types and gene expression states in the non-cancerous cells in tumors. The integration of multiple scRNA-seq datasets across tumors can indicate common cell types and states in the tumor microenvironment (TME). We develop a data driven framework, MetaTiME, to overcome the limitations in resolution and consistency that result from manual labelling using known gene markers.
TRPV1 regulates ApoE4-disrupted intracellular lipid homeostasis and decreases synaptic phagocytosis by microglia
Ovarian cancer occurs when abnormal cells in the ovaries or fallopian tubes grow uncontrollably, forming a mass (tumor). Treatment options for ovarian cancer depend on the type and stage of the disease. It may include a combination of surgery, chemotherapy, radiation therapy, or targeted therapies. The goals of ovarian cancer treatment are to remove the tumor(s), eliminate cancer cells in the body, and prevent a recurrence (return) of cancer.
Allele-specific H3K9me3 and DNA methylation co-marked CpG-rich regions serve as potential imprinting control regions in pre-implantation embryo - Nature Cell Biology
Abstract Parental DNA methylation and histone modifications undergo distinct global reprogramming in mammalian pre-implantation embryos, but the landscape of epigenetic crosstalk and its effects on embryogenesis are largely unknown.
Cyclic Poly(ß-amino ester)s with Enhanced Gene Transfection Activity Synthesized through Intra-molecular Cyclization
Cyclic Poly(ß-amino ester)s with Enhanced Gene Transfection Activity Synthesized through Intra-molecular Cyclization You have access to this article Please wait while we load your content... Something went wrong. Try again?
Fast alignment and preprocessing of chromatin profiles with Chromap
Abstract We present Chromap, an ultrafast method for aligning and preprocessing high throughput chromatin profiles. Chromap is comparable to BWA-MEM and Bowtie2 in alignment accuracy and is over 10 times faster than traditional workflows on bulk ChIP-seq / Hi-C profiles and than 10x Genomics' CellRanger v2.0.0 pipeline on single-cell ATAC-seq profiles.
Integrative analyses of single-cell transcriptome and regulome using MAESTRO
Chenfei Wang1,2 na1, Dongqing Sun3 na1, Xin Huang4, Changxin Wan3, Ziyi Li3, Ya Han3, Qian Qin3, Jingyu Fan3, Xintao Qiu2,5, Yingtian Xie2,5, Clifford A. Meyer1,2, Myles Brown2,5, Ming Tang1,2, Henry Long2,5, Tao Liu6 & X.
Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development
a, Scatterplots show the association tests between log2-transformed H3K27me3 / input ratio and DNA methylation level during pre-implantation embryos on specific LTR families. Different colors represent four major family of the LTRs, including ERVK, ERV1, MaLR and ERVL (two-sided association test, n = 7 biologically independent samples. The x-axis represents the Pearson's correlation coefficients and the y-axis represents P-value of the tests.
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