Andrew L. Ji
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View article: A single-cell spatial transcriptomic census of human skin anatomy
A single-cell spatial transcriptomic census of human skin anatomy Open
The skin is the largest human organ and a site of significant disease burden, yet its cellular and molecular organization across the body are largely undefined. Here, we construct a spatially-resolved single-cell atlas of 1.2 million cells…
View article: Signal processing and data acquisition system for the BTO detectors onboard COSI
Signal processing and data acquisition system for the BTO detectors onboard COSI Open
The energy range from a few hundred keV to a few MeV includes important probes such as nuclear gamma-rays and the 511 keV annihilation line. However, compared to X-rays and GeV/TeV gamma-rays, this range suffers from lower sensitivity by o…
View article: A basophil-fibroblast pro-inflammatory axis fuels type 2 skin inflammation
A basophil-fibroblast pro-inflammatory axis fuels type 2 skin inflammation Open
Chronic inflammatory skin diseases arise from dysregulated interactions between tissue-resident and infiltrating cells, the complexity of which hinders disease understanding and treatment. To address this, here, we present a single-cell sp…
View article: Glucose modulates IRF6 transcription factor dimerization to enable epidermal differentiation
Glucose modulates IRF6 transcription factor dimerization to enable epidermal differentiation Open
Non-energetic roles for glucose are largely unclear, as is the interplay between transcription factors (TFs) and ubiquitous biomolecules. Metabolomic analyses uncovered elevation of intracellular glucose during differentiation of diverse c…
View article: Surface Code Error Correction with Crosstalk Noise
Surface Code Error Correction with Crosstalk Noise Open
The design and performance analysis of quantum error correction (QEC) codes are often based on incoherent and independent noise models since it is easy to simulate. However, these models fail to capture realistic hardware noise sources, su…
View article: In vivo CRISPRi screen identified lncRNA portfolio crucial for cutaneous squamous cell carcinoma tumor growth
In vivo CRISPRi screen identified lncRNA portfolio crucial for cutaneous squamous cell carcinoma tumor growth Open
Cutaneous squamous cell carcinoma (cSCC) accounts for 20% of all skin cancer deaths globally, making it the second-highest subtype of skin cancer. The prevalence of cSCC in humans, as well as the poor capacity for an efficient prognosis, h…
View article: Type 1 innate lymphoid cells: a biomarker and therapeutic candidate in sarcoidosis
Type 1 innate lymphoid cells: a biomarker and therapeutic candidate in sarcoidosis Open
Sarcoidosis is an inflammatory disease characterized by immune cell-rich granulomas that form in multiple organs. In this issue of the JCI, Sati and colleagues used scRNA-seq and spatial transcriptomics of skin samples from patients with s…
View article: Molecular investigation of <i>Treponema pallidum</i> strains associated with ocular syphilis in the United States, 2016–2020
Molecular investigation of <i>Treponema pallidum</i> strains associated with ocular syphilis in the United States, 2016–2020 Open
Ocular syphilis is a serious complication of Treponema pallidum infection that can occur at any stage of syphilis and affect any eye structure. It remains unknown if certain T. pallidum strains are associated with ocular infections; theref…
View article: The Use of Single-Cell RNA-Sequencing and Spatial Transcriptomics in Understanding the Pathogenesis and Treatment of Skin Diseases
The Use of Single-Cell RNA-Sequencing and Spatial Transcriptomics in Understanding the Pathogenesis and Treatment of Skin Diseases Open
The development of multiomic profiling tools has rapidly expanded in recent years, along with their use in profiling skin tissues in various contexts, including dermatologic diseases. Among these tools, single-cell RNA-sequencing (scRNA-se…
View article: Additional file 1 of STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer
Additional file 1 of STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer Open
Additional file 1: Table S1. Somatic mutations in tumors from patient 4 and 6. Point mutations were called as described and annotated with the funcotator (v4.1.2.0) tool from genome analysis toolkit (see GATK (v4.1.2.0) for description of …
View article: Visualizing somatic alterations in spatial transcriptomics data of skin cancer
Visualizing somatic alterations in spatial transcriptomics data of skin cancer Open
Tools to visualize genetic alterations within tissues remain underdeveloped despite the growth of spatial transcriptomic technologies, which measure gene expression in different regions of tissues. Since genetic alterations can be detected…
View article: Glucose modulates transcription factor dimerization to enable tissue differentiation
Glucose modulates transcription factor dimerization to enable tissue differentiation Open
Glucose is a universal energy currency for living organisms, however, its non-energetic functions in processes such as differentiation are undefined. In epidermis, differentiating cells exhibit dynamic changes in gene expression 1–4 driven…
View article: Skin proteomic analysis of immune activation associated with regression of melanoma metastases induced by diphencyprone
Skin proteomic analysis of immune activation associated with regression of melanoma metastases induced by diphencyprone Open
To the Editor: Diphencyprone (DPCP), a hapten that causes delayed-type hypersensitivity reactions, has been used to treat warts, alopecia areata, and cutaneous metastases in melanoma patients.1Damian D.L. Saw R.P. Thompson J.F. Topical imm…
View article: The spatial landscape of clonal somatic mutations in benign and malignant tissue
The spatial landscape of clonal somatic mutations in benign and malignant tissue Open
Defining the transition from benign to malignant tissue is fundamental to improve early diagnosis of cancer. Here, we provide an unsupervised approach to study spatial genome integrity in situ to describe previously unidentified clonal rel…
View article: The spatial landscape of clonal somatic mutations in benign and malignant tissue
The spatial landscape of clonal somatic mutations in benign and malignant tissue Open
Defining the transition from benign to malignant tissue is fundamental to improve early diagnosis of cancer. Here, we provide an unsupervised approach to study spatial genome integrity in situ to gain molecular insight into clonal relation…
View article: Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma
Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma Open
(Cell 182, 497–514.e1–e22; July 23, 2020) As a result of human error, the spatial feature plot labeled ITGB1 in Figure 6G was instead a duplicate of the ITGA3 data just below it. Additionally, in Figure S4C, the order of some of the bar la…