Published in Nature Biotechnology, 2026
Recommended citation: Yuzhou Chang, Hao Cheng, Mirage Modi, Guangyu Wang, Dong Xu, Qin Ma. (2026). "Tracing the rise of biomedical foundation models" Nature Biotechnology.
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Published in Cancer Research, 2026
Abstract Standard spatial proteomics (SP) pipelines for biomarker discovery have traditionally relied on cell segmentation followed by single-marker thresholding or rule-based mechanisms to assign cell phenotypes. However, this often suffers from a laborious process of manual annotations and neglects cell states cha…
Recommended citation: Andrew H. Song, Anurag Vaidya, Mohammed Shaban, Yuzhou Chang, Huaying Qiu, Yao Yu Yeo, Guillaume Jaume, W. L. K. Wu, et al.. (2026). "Abstract 4163: A general-purpose AI foundation model for spatial proteomics" Cancer Research.
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Published in Cell Reports Medicine, 2026
Classic Hodgkin lymphoma (cHL) is composed of rare malignant Hodgkin and Reed-Sternberg (HRS) cells within a T-cell-rich tumor microenvironment (TME). Epstein-Barr virus (EBV) is present in ∼25% of cases, but its contribution to pathogenesis and immunomodulation remains unclear due to technical barriers. Using compl…
Recommended citation: Yao Yu Yeo, Huaying Qiu, Yunhao Bai, Bokai Zhu, Yuzhou Chang, Fabio Iannelli, Stephanie Pei Tung Yiu, Jason Yeung, et al.. (2026). "Epstein-Barr virus orchestrates spatial reorganization and immunomodulation in the classic Hodgkin lymphoma tumor microenvironment" Cell Reports Medicine.
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Published in Cancer Discovery, 2026
Spatial transcriptomics and proteomics have enabled profound insights into tissue organization, yet these technologies remain largely disparate, and emerging same-slide multi-omics approaches are limited in plex, spatial resolution, signal retention, and integrative analytics. We introduce IN-situ DEtailed Phenotypi…
Recommended citation: Stephanie Pei Tung Yiu, Yuzhou Chang, Yao Yu Yeo, Huaying Qiu, Wenrui Wu, Hendrik A. Michel, Xiaojie Jin, Rongting Huang, et al.. (2026). "Same-Slide Spatial Multi-Omics Integration with IN-DEPTH Reveals Tumor Virus-Linked Spatial Reorganization of the Tumor Microenvironment" Cancer Discovery.
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Published in Molecular Neurodegeneration, 2026
Humanized APOE targeted-replacement (TR) mice are essential tools for studying apoE isoform effects in Alzheimer’s disease (AD) and other apoE-related disorders. Despite their widespread use, existing APOE mouse models, generated with different gene targeting strategies, have not been directly compared in terms of a…
Recommended citation: Na Wang, Gefei Yu, Zhen Wang, Alla Alnobani, Suren Jeevaratnam, Xue Zhang, Mehan McReynolds, Yuzhou Chang, et al.. (2026). "Molecular characterization of humanized APOE mouse models reveals source and genotype dependent differences" Molecular Neurodegeneration.
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Published in Immunity, 2025
T cell dysregulation, and mast cell enrichment. We identified key immune-epithelial interactions in tissue remodeling, particularly involving basal progenitor and tuft cells. A distinct basal cell trajectory was implicated in nasal polyp formation. Orthogonal validation with spatial transcriptomics from >100 individ…
Recommended citation: Guanrui Liao, Tsuguhisa Nakayama, Bokai Zhu, Ivan T. Lee, Jason Yeung, Yao Yu Yeo, Yuzhou Chang, Cankun Wang, et al.. (2025). "Multi-scaled transcriptomics of chronically inflamed nasal epithelium reveals immune-epithelial dynamics and tissue remodeling in nasal polyp formation" Immunity.
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Published in Neuro-Oncology, 2025
BACKGROUND: Glycoprotein A-repetitions predominant (GARP) is a cell surface non-signaling receptor for docking and activating latent transforming growth factor beta (LTGFβ) expressed by regulatory T cells, platelets, and tumor cells. In lung and breast cancers, its expression correlates with advanced stage and poor…
Recommended citation: Bill X. Wu, Daniel Kreatsoulas, Hakan Çam, Chelsea Bolyard, Yuzhou Chang, Jay K. Mandula, Parker W Welsh, Ziyu Wang, et al.. (2025). "Targeting TGFβ docking receptor glycoprotein A repetitions predominant (GARP) via novel chimeric antigen receptor (CAR)-T cell platform to treat glioblastoma" Neuro-Oncology.
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Published in Biology of Sex Differences, 2025
Bladder cancer (BC) remains a significant global health concern, with substantial sex and racial disparities in incidence, progression, and outcomes. BC is the sixth most common cancer among males and the seventeenth most common among females worldwide. Over 90% of BC cases are urothelial carcinoma (UC) with high de…
Recommended citation: Prakash Chaudhary, Biplab Singha, Hany Abdel-Hafiz, Maria Velegraki, Debasish Sundi, Swati Satturwar, Anil V. Parwani, Sergei I. Grivennikov, et al.. (2025). "Sex differences in bladder cancer: understanding biological and clinical implications" Biology of Sex Differences.
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Published in Alzheimer s & Dementia, 2024
BACKGROUND: Accumulation of the amyloid-β (Aβ) peptide into amyloid plaque is one of the key pathological markers of Alzheimer’s disease (AD). Apolipoprotein E (APOE) is known to modify AD risk and has been reported to influence Aβ accumulation in the brain in an isoform-dependent manner. ApoE can be produced by var…
Recommended citation: Na Wang, Sydney V. Doss, Yuzhou Chang, William Tauer, Yingxue Ren, Fangfang Qi, Guojun Bu, Chia‐Chen Liu, et al.. (2024). "Specific expression of APOE in astrocytes reduces Aβ accumulation and plaque‐related pathology in a mouse model of amyloidosis" Alzheimer s & Dementia.
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Published in Blood, 2024
Histologic transformation of follicular lymphoma (FL) to an aggressive lymphoma (transformed FL [tFL]) is a common disease complication associated with poor clinical outcomes. However, understanding of the mechanisms that drive FL transformation and the associated lymph node (LN) tumor microenvironment (TME) reorgan…
Recommended citation: Nicholas J. Haradhvala, Stephanie Pei Tung Yiu, Sam Sadigh, Laura Beckmann, Amber Pospistle, Stephanie Deng, Santiago Rivero, Yao Yu Yeo, et al.. (2024). "Cytokine-Linked Remodeling of the Immune Microenvironment Is a Hallmark of Transformation in Follicular Lymphoma" Blood.
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Published in Nature Communications, 2024
Spatial omics technologies decipher functional components of complex organs at cellular and subcellular resolutions. We introduce Spatial Graph Fourier Transform (SpaGFT) and apply graph signal processing to a wide range of spatial omics profiling platforms to generate their interpretable representations. This repre…
Recommended citation: Yuzhou Chang, Jixin Liu, Yi Jiang, Anjun Ma, Yao Yu Yeo, Qi Guo, Megan E. McNutt, Jordan E. Krull, et al.. (2024). "Graph Fourier transform for spatial omics representation and analyses of complex organs" Nature Communications.
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Published in Frontiers in Applied Mathematics and Statistics, 2024
Introduction: The advent of high throughput spatial transcriptomics (HST) has allowed for unprecedented characterization of spatially distinct cell communities within a tissue sample. While a wide range of computational tools exist for detecting cell communities in HST data, none allow for the characterization of co…
Recommended citation: Juan Xie, Kyeong Joo Jung, Carter Allen, Yuzhou Chang, Subhadeep Paul, Zihai Li, Qin Ma, Dongjun Chung. (2024). "Analysis of community connectivity in spatial transcriptomics data" Frontiers in Applied Mathematics and Statistics.
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Published in Journal of Clinical Investigation, 2024
Intratumoral Tregs are key mediators of cancer immunotherapy resistance, including anti-programmed cell death (ligand) 1 [anti-PD-(L)1] immune checkpoint blockade (ICB). The mechanisms driving Treg infiltration into the tumor microenvironment (TME) and the consequence on CD8+ T cell exhaustion remain elusive. Here,…
Recommended citation: Lei Zhou, Maria Velegraki, Yi Wang, Jay K. Mandula, Yuzhou Chang, Weiwei Liu, No‐Joon Song, Hyunwoo Kwon, et al.. (2024). "Spatial and functional targeting of intratumoral Tregs reverses CD8+ T cell exhaustion and promotes cancer immunotherapy" Journal of Clinical Investigation.
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Published in Computational and Structural Biotechnology Journal, 2024
The rapid growth of spatially resolved transcriptomics technology provides new perspectives on spatial tissue architecture. Deep learning has been widely applied to derive useful representations for spatial transcriptome analysis. However, effectively integrating spatial multi-modal data remains challenging. Here, w…
Recommended citation: Yu Lin, Yanchun Liang, Duolin Wang, Yuzhou Chang, Qin Ma, Yan Wang, Fei He, Dong Xu. (2024). "A contrastive learning approach to integrate spatial transcriptomics and histological images" Computational and Structural Biotechnology Journal.
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Published in Nature Communications, 2023
Identifying spatially variable genes (SVGs) is critical in linking molecular cell functions with tissue phenotypes. Spatially resolved transcriptomics captures cellular-level gene expression with corresponding spatial coordinates in two or three dimensions and can be used to infer SVGs effectively. However, current…
Recommended citation: Juexin Wang, Jinpu Li, Skyler T. Kramer, Li Su, Yuzhou Chang, Chunhui Xu, Michael T. Eadon, Krzysztof Kiryluk, et al.. (2023). "Dimension-agnostic and granularity-based spatially variable gene identification using BSP" Nature Communications.
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Published in Neuro-Oncology, 2023
BACKGROUND: Myeloid cells comprise up to 50% of the total tumor mass in glioblastoma (GBM) and have been implicated in promoting tumor progression and immunosuppression. Modulating the response of myeloid cells to the tumor has emerged as a promising new approach for cancer treatment. In this regard, we focus on the…
Recommended citation: Jiaying Zheng, Lingxiao Wang, Shunyi Zhao, Wenjing Zhang, Yuzhou Chang, Dale B. Bosco, Tao Huang, Aastha Dheer, et al.. (2023). "TREM2 mediates MHCII-associated CD4+ T-cell response against gliomas" Neuro-Oncology.
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Published in iScience, 2023
Bladder cancer (BLCA) is more common in men but more aggressive in women. Sex-based differences in cancer biology are commonly studied using a murine model with BLCA generated by N-butyl-N-(4-hydroxybutyl)-nitrosamine (BBN). While tumors in the BBN model have been profiled, these profiles provide limited information…
Recommended citation: Hany Abdel-Hafiz, Saravana Kumar Kailasam Mani, Wesley Huang, Kenneth Gouin, Yuzhou Chang, Tong Xiao, Qin Ma, Zihai Li, et al.. (2023). "Single-cell profiling of murine bladder cancer identifies sex-specific transcriptional signatures with prognostic relevance" iScience.
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Published in Nature Communications, 2023
Single-cell multi-omics (scMulti-omics) allows the quantification of multiple modalities simultaneously to capture the intricacy of complex molecular mechanisms and cellular heterogeneity. Existing tools cannot effectively infer the active biological networks in diverse cell types and the response of these networks…
Recommended citation: Anjun Ma, Xiaoying Wang, Jingxian Li, Cankun Wang, Tong Xiao, Yuntao Liu, Hao Cheng, Juexin Wang, et al.. (2023). "Single-cell biological network inference using a heterogeneous graph transformer" Nature Communications.
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Published in Food Science and Biotechnology, 2023
Recommended citation: Qizhang Li, Zerong Zhou, Cuiyu Hu, Xianbin Li, Yuzhou Chang, Yan Liu, Yuliang Wang, Xuanwei Zhou. (2023). "Recent advances of bioactive proteins/polypeptides in the treatment of breast cancer" Food Science and Biotechnology.
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Published in Genes & Diseases, 2022
Ribonucleotide reductase M2 (RRM2) is a small subunit in ribonucleotide reductases, which participate in nucleotide metabolism and catalyze the conversion of nucleotides to deoxynucleotides, maintaining the dNTP pools for DNA biosynthesis, repair, and replication. RRM2 performs a critical role in the malignant biolo…
Recommended citation: Zanwen Zuo, Zerong Zhou, Yuzhou Chang, Yan Liu, Yuping Shen, Qizhang Li, Lei Zhang. (2022). "Ribonucleotide reductase M2 (RRM2): Regulation, function and targeting strategy in human cancer" Genes & Diseases.
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Published in Acta Neuropathologica Communications, 2022
Human middle temporal gyrus (MTG) is a vulnerable brain region in early Alzheimer’s disease (AD), but little is known about the molecular mechanisms underlying this regional vulnerability. Here we utilize the 10 × Visium platform to define the spatial transcriptomic profile in both AD and control (CT) MTG. We identi…
Recommended citation: Shuo Chen, Yuzhou Chang, Liangping Li, Diana Acosta, Yang Li, Qi Guo, Cankun Wang, Emir Turkes, et al.. (2022). "Spatially resolved transcriptomics reveals genes associated with the vulnerability of middle temporal gyrus in Alzheimer’s disease" Acta Neuropathologica Communications.
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Published in Regular and Young Investigator Award Abstracts, 2022
Immune checkpoint blockade (ICB) targeting programed cell death protein 1 (PD-1) and its ligand has revolutionized cancer immunotherapy. Unfortunately, while some cancer patients experience robust and lasting remission following treatment, most fail to respond clinically. Accumulation of transfor…
Recommended citation: Anqi Li, Yuzhou Chang, No‐Joon Song, Xingjun Wu, Dongjun Chung, Brian Riesenberg, Maria Velegraki, Hyunwoo Kwon, et al.. (2022). "839 Selective targeting of GARP-LTGFß Axis in the tumor microenvironment augments PD-1 blockade via enhancing CD8+ T cell anti-tumor immunity" Regular and Young Investigator Award Abstracts.
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Published in Regular and Young Investigator Award Abstracts, 2022
It has been reported multiple times that exercise can prevent cancer development, help anti-tumor therapies, and lower relapse rate after successful cancer treatment. However, an underlying molecular mechanism for these beneficial effects remained elusive. Recent studies revealed that cytotoxic i…
Recommended citation: No‐Joon Song, Yuzhou Chang, Anqi Li, Yi Wang, Kelsi Reynolds, Kevin P. Weller, Chelsea Bolyard, Gang Xin, et al.. (2022). "1064 Exercise induced hormone irisin inhibits Integrin αv-TGF-β axis in tumor microenvironment to improve CD8+ T cell mediated tumor control" Regular and Young Investigator Award Abstracts.
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Published in Journal for ImmunoTherapy of Cancer, 2022
Background Immune checkpoint blockade (ICB) has revolutionized cancer immunotherapy. However, most patients with cancer fail to respond clinically. One potential reason is the accumulation of immunosuppressive transforming growth factor β (TGFβ) in the tumor microenvironment (TME). TGFβ drives cancer immune evasion…
Recommended citation: Anqi Li, Yuzhou Chang, No‐Joon Song, Xingjun Wu, Dongjun Chung, Brian Riesenberg, Maria Velegraki, Giuseppe D Giuliani, et al.. (2022). "Selective targeting of GARP-LTGFβ axis in the tumor microenvironment augments PD-1 blockade via enhancing CD8+ T cell antitumor immunity" Journal for ImmunoTherapy of Cancer.
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Published in Biometrics, 2022
High throughput spatial transcriptomics (HST) is a rapidly emerging class of experimental technologies that allow for profiling gene expression in tissue samples at or near single-cell resolution while retaining the spatial location of each sequencing unit within the tissue sample. Through analyzing HST data, we see…
Recommended citation: Carter Allen, Yuzhou Chang, Brian Neelon, Won Chang, Hang J. Kim, Zihai Li, Qin Ma, Dongjun Chung. (2022). "A Bayesian Multivariate Mixture Model for High Throughput Spatial Transcriptomics" Biometrics.
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Published in iScience, 2022
T cell dysfunction or exhaustion in the tumor microenvironment and summarize ongoing clinical efforts to determine the impact of androgen blockade on cancer immunotherapy. Finally, we outline a framework for future research in cancer biology and immuno-oncology, underscoring the importance of a holistic research app…
Recommended citation: Johanna M. Schafer, Tong Xiao, Hyunwoo Kwon, Katharine A. Collier, Yuzhou Chang, Hany Abdel-Hafiz, Chelsea Bolyard, Dongjun Chung, et al.. (2022). "Sex-biased adaptive immune regulation in cancer development and therapy" iScience.
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Published in Nature Neuroscience, 2022
Recommended citation: Mor Kenigsbuch, Pierre Bost, Shahar Halevi, Yuzhou Chang, Shuo Chen, Qin Ma, Renana Hajbi, Benno Schwikowski, et al.. (2022). "A shared disease-associated oligodendrocyte signature among multiple CNS pathologies" Nature Neuroscience.
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Published in Science Immunology, 2022
Sex bias exists in the development and progression of nonreproductive organ cancers, but the underlying mechanisms are enigmatic. Studies so far have focused largely on sexual dimorphisms in cancer biology and socioeconomic factors. Here, we establish a role for CD8 + T cell–dependent antitumor immunity in mediating…
Recommended citation: Hyunwoo Kwon, Johanna M. Schafer, No‐Joon Song, Satoshi Kaneko, Anqi Li, Tong Xiao, Anjun Ma, Carter Allen, et al.. (2022). "Androgen conspires with the CD8 + T cell exhaustion program and contributes to sex bias in cancer" Science Immunology.
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Published in Acta Neuropathologica, 2022
Recommended citation: Shuo Chen, Diana Acosta, Liangping Li, Jiawen Liang, Yuzhou Chang, Cankun Wang, Julie C. Fitzgerald, Cody Morrison, et al.. (2022). "Wolframin is a novel regulator of tau pathology and neurodegeneration" Acta Neuropathologica.
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Published in Journal of Hematology & Oncology, 2022
Abstract Background Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19) through direct lysis of infected lung epithelial cells, which releases damage-associated molecular patterns and induces a pro-inflammatory cytokine milieu causing systemic inflammation. Anti-vi…
Recommended citation: No‐Joon Song, Carter Allen, Anna E. Vilgelm, Brian Riesenberg, Kevin P. Weller, Kelsi Reynolds, Karthik B. Chakravarthy, Amrendra Kumar, et al.. (2022). "Treatment with soluble CD24 attenuates COVID-19-associated systemic immunopathology" Journal of Hematology & Oncology.
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Published in Computational and Structural Biotechnology Journal, 2022
Spatially resolved transcriptomics provides a new way to define spatial contexts and understand the pathogenesis of complex human diseases. Although some computational frameworks can characterize spatial context via various clustering methods, the detailed spatial architectures and functional zonation often cannot b…
Recommended citation: Yuzhou Chang, Fei He, Juexin Wang, Shuo Chen, Jingyi Li, Jixin Liu, Yang Yu, Li Su, et al.. (2022). "Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning" Computational and Structural Biotechnology Journal.
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Published in Alzheimer s & Dementia, 2021
Background In many neurodegenerative diseases including Alzheimer’s disease (AD), specific subpopulations of cells and brain regions are more sensitive to dysfunction and degeneration than others. For example, excitatory neurons in the layer 2/3 of middle temporal gyrus (MTG) is particularly vulnerable to degenerati…
Recommended citation: Shuo Chen, Yuzhou Chang, Liangping Li, Geidy E. Serrano, Thomas G. Beach, Karen Duff, Qin Ma, Hongjun Fu. (2021). "Spatial transcriptomics of human middle temporal gyrus reveals layer‐specific gene expression in early Alzheimer’s disease" Alzheimer s & Dementia.
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Published in Nature Communications, 2021
Single-cell RNA-sequencing (scRNA-Seq) is widely used to reveal the heterogeneity and dynamics of tissues, organisms, and complex diseases, but its analyses still suffer from multiple grand challenges, including the sequencing sparsity and complex differential patterns in gene expression. We introduce the scGNN (sin…
Recommended citation: Juexin Wang, Anjun Ma, Yuzhou Chang, Jianting Gong, Yuexu Jiang, Ren Qi, Cankun Wang, Hongjun Fu, et al.. (2021). "scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses" Nature Communications.
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Published in Bioinformatics, 2021
SUMMARY: Single-cell RNA-Seq (scRNA-Seq) data is useful in discovering cell heterogeneity and signature genes in specific cell populations in cancer and other complex diseases. Specifically, the investigation of condition-specific functional gene modules (FGM) can help to understand interactive gene networks and com…
Recommended citation: Yuzhou Chang, Carter Allen, Changlin Wan, Dongjun Chung, Chi Zhang, Zihai Li, Qin Ma. (2021). "IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis" Bioinformatics.
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Published in PMC, 2020
A group of genes controlled as a unit, usually by the same repressor or activator gene, is known as a regulon. The ability to identify active regulons within a specific cell type, i.e., cell-type-specific regulons (CTSR), provides an extraordinary opportunity to pinpoint crucial regulators and target genes responsib…
Recommended citation: Anjun Ma, Cankun Wang, Yuzhou Chang, Faith H. Brennan, Adam McDermaid, Bingqiang Liu, Chi Zhang, Phillip G. Popovich, et al.. (2020). "IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq" PMC.
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Published in Trends in biotechnology, 2020
Recommended citation: Anjun Ma, Adam McDermaid, Jennifer Xu, Yuzhou Chang, Qin Ma. (2020). "Integrative Methods and Practical Challenges for Single-Cell Multi-omics" Trends in biotechnology.
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Published in Nature Communications, 2018
Abstract Regulatory T (Treg) cells are essential for maintaining immune homeostasis and tolerance, but the mechanisms regulating the stability and function of Treg cells have not been fully elucidated. Here we show SUMO-specific protease 3 (SENP3) is a pivotal regulator of Treg cells that functions by controlling th…
Recommended citation: Xiaoyan Yu, Yimin Lao, Xiao-Lu Teng, Song Li, Yan Zhou, Feixiang Wang, Xinwei Guo, Siyu Deng, et al.. (2018). "SENP3 maintains the stability and function of regulatory T cells via BACH2 deSUMOylation" Nature Communications.
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Published in bioRxiv (Cold Spring Harbor Laboratory), 2026
Glycans regulate multiple physiological processes, including immune recognition and cancer progression. In disease, altered glycan landscapes are interpreted by human lectins. Functional glycan-lectin interactions are difficult to profile because glycans are not genome-encoded and their changes are poorly captured b…
Recommended citation: Ankit Basak, Carolina Ortiz-Cordero, Stephanie Pei Tung Yiu, Sidney Allison, Sarah Sweeting, Feng Shan, Yuzhou Evelyn Tong, Rajeev Chorghade, et al.. (2026). "Single-Cell and Spatial Methods for Multimodal Functional Glycan Profiling in Tissues" bioRxiv (Cold Spring Harbor Laboratory).
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Published in ArXiv.org, 2025
Foundation models have begun to transform image analysis by acting as pretrained generalist backbones that can be adapted to many tasks even when post-training data are limited, yet their impact on spatial proteomics, imaging that maps proteins at single-cell resolution, remains limited. Here, we introduce KRONOS, a…
Recommended citation: Muhammad Shaban, Yuzhou Chang, Huaying Qiu, Yao Yu Yeo, Song, Andrew H., Guillaume Jaume, Yuchen Wang, Luca L. Weishaupt, et al.. (2025). "A Foundation Model for Spatial Proteomics" ArXiv.org.
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Published in Research Square, 2025
Recommended citation: Dong Xu, Fei He, Ruixin Fei, Jordan E. Krull, Xinyu Zhang, Mingyue Gao, Li Su, Yibo Chen, et al.. (2025). "Harnessing the Power of Single Cell Large Language Models with Parameter Efficient Fine-Tuning using scPEFT" Research Square.
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Published in bioRxiv (Cold Spring Harbor Laboratory), 2024
The advent of spatial transcriptomics and spatial proteomics have enabled profound insights into tissue organization to provide systems-level understanding of diseases. Both technologies currently remain largely independent, and emerging same slide spatial multi-omics approaches are generally limited in plex, spatia…
Recommended citation: Yao Yu Yeo, Yuzhou Chang, Huaying Qiu, Stephanie Pei Tung Yiu, Hendrik A. Michel, Wenrui Wu, Xiaojie Jin, Shoko Kure, et al.. (2024). "Same-Slide Spatial Multi-Omics Integration Reveals Tumor Virus-Linked Spatial Reorganization of the Tumor Microenvironment" bioRxiv (Cold Spring Harbor Laboratory).
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Published in bioRxiv (Cold Spring Harbor Laboratory), 2024
Classic Hodgkin Lymphoma (cHL) is a tumor composed of rare malignant Hodgkin and Reed-Sternberg (HRS) cells nested within a T-cell rich inflammatory immune infiltrate. cHL is associated with Epstein-Barr Virus (EBV) in 25% of cases. The specific contributions of EBV to the pathogenesis of cHL remain largely unknown,…
Recommended citation: Yao Yu Yeo, Huaying Qiu, Yunhao Bai, Bokai Zhu, Yuzhou Chang, Jason Yeung, Hendrik A. Michel, Kyle Wright, et al.. (2024). "Epstein-Barr Virus Orchestrates Spatial Reorganization and Immunomodulation within the Classic Hodgkin Lymphoma Tumor Microenvironment" bioRxiv (Cold Spring Harbor Laboratory).
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Published in bioRxiv (Cold Spring Harbor Laboratory), 2023
Identifying spatially variable genes (SVGs) is critical in linking molecular cell functions with tissue phenotypes. Spatially resolved transcriptomics captures cellular-level gene expression with corresponding spatial coordinates in two or three dimensions and can be used to infer SVGs effectively. However, current…
Recommended citation: Juexin Wang, Jinpu Li, Skyler T. Kramer, Li Su, Yuzhou Chang, Chunhui Xu, Qin Ma, Dong Xu. (2023). "Dimension-agnostic and granularity-based spatially variable gene identification" bioRxiv (Cold Spring Harbor Laboratory).
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Published in bioRxiv (Cold Spring Harbor Laboratory), 2022
Abstract Tissue module (TM) is a spatially organized tissue region and executes specialized biological functions, recurring and varying at different tissue sites. However, the computational identification of TMs poses challenges due to their convoluted biological functions, poorly-defined molecular features, and var…
Recommended citation: Yuzhou Chang, Jixin Liu, Anjun Ma, Sizun Jiang, Jordan E. Krull, Yao Yu Yeo, Yang Liu, Scott J. Rodig, et al.. (2022). "Spatial omics representation and functional tissue module inference using graph Fourier transform" bioRxiv (Cold Spring Harbor Laboratory).
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Published in bioRxiv (Cold Spring Harbor Laboratory), 2022
High throughput spatial transcriptomics (HST) technologies provide unprecedented opportunity to identify spatially resolved cell sub-populations in tissue samples. However, existing methods preclude joint analysis of multiple HST samples, do not allow for differential abundance analysis (DAA), and ignore uncertainty…
Recommended citation: Hyeongseon Jeon, Carter Allen, José Antonio Ovando-Ricárdez, Yuzhou Chang, Lorena Rosas, Natalia-Del Pilar Vanegas, Hao Cheng, Juan Xie, et al.. (2022). "MAPLE: A Hybrid Framework for Multi-Sample Spatial Transcriptomics Data" bioRxiv (Cold Spring Harbor Laboratory).
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Published in bioRxiv (Cold Spring Harbor Laboratory), 2021
Abstract We present DeepMAPS (Deep learning-based Multi-omics Analysis Platform for Single-cell data) for biological network inference from single-cell multi-omics (scMulti-omics). DeepMAPS includes both cells and genes in a heterogeneous graph to simultaneously infer cell-cell, cell-gene, and gene-gene relations. T…
Recommended citation: Anjun Ma, Xiaoying Wang, Cankun Wang, Jingxian Li, Tong Xiao, Juexing Wang, Yang Li, Yun-Tao Liu, et al.. (2021). "DeepMAPS: Single-cell biological network inference using heterogeneous graph transformer" bioRxiv (Cold Spring Harbor Laboratory).
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Published in Research Square, 2021
Recommended citation: Shuo Chen, Yuzhou Chang, Liangping Li, Diana Acosta, Cody Morrison, Cankun Wang, Dominic Julian, Mark E. Hester, et al.. (2021). "Spatially resolved transcriptomics reveals gene signatures underlying the vulnerability of human middle temporal gyrus in Alzheimer's disease" Research Square.
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Published in bioRxiv (Cold Spring Harbor Laboratory), 2021
Abstract Alzheimer’s disease (AD) is pathologically characterized by amyloid beta (Aβ) plaques, neurofibrillary tangles (tau aggregates), and alterations in microglia, astrocytes and oligodendrocytes. The mesial temporal lobe is a vulnerable brain region in early AD; however, little is known about the transcriptome-…
Recommended citation: Shuo Chen, Yuzhou Chang, Liangping Li, Diana Acosta, Cody Morrison, Cankun Wang, Dominic Julian, Mark E. Hester, et al.. (2021). "Spatially resolved transcriptomics reveals unique gene signatures associated with human temporal cortical architecture and Alzheimer’s pathology" bioRxiv (Cold Spring Harbor Laboratory).
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Published in bioRxiv (Cold Spring Harbor Laboratory), 2021
Abstract High throughput spatial transcriptomics (HST) is a rapidly emerging class of experimental technologies that allow for profiling gene expression in tissue samples at or near single-cell resolution while retaining the spatial location of each sequencing unit within the tissue sample. Through analyzing HST dat…
Recommended citation: Carter Allen, Yuzhou Chang, Brian Neelon, Won Chang, Hang J. Kim, Zihai Li, Qin Ma, Dongjun Chung. (2021). "A Bayesian Multivariate Mixture Model for Spatial Transcriptomics Data" bioRxiv (Cold Spring Harbor Laboratory).
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Published in bioRxiv (Cold Spring Harbor Laboratory), 2020
ABSTRACT Single-cell RNA-sequencing (scRNA-Seq) is widely used to reveal the heterogeneity and dynamics of tissues, organisms, and complex diseases, but its analyses still suffer from multiple grand challenges, including the sequencing sparsity and complex differential patterns in gene expression. We introduce the s…
Recommended citation: Juexin Wang, Anjun Ma, Yuzhou Chang, Jianting Gong, Yuexu Jiang, Hongjun Fu, Cankun Wang, Ren Qi, et al.. (2020). "scGNN: a novel graph neural network framework for single-cell RNA-Seq analyses" bioRxiv (Cold Spring Harbor Laboratory).
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