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Journal articles on the topic 'Cellular atlas'

Author: Grafiati

Published: 15 March 2025

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1

Hill, Matthew C., Zachary A. Kadow, Lele Li, Tien T. Tran, Joshua D. Wythe, and James F. Martin. "A cellular atlas of Pitx2-dependent cardiac development." Development 146, no. 12 (June 14, 2019): dev180398. http://dx.doi.org/10.1242/dev.180398.

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2

Srivastava, Sudhir, Paul D. Wagner, Shannon K. Hughes, and Sharmistha Ghosh. "PreCancer Atlas: Present and Future." Cancer Prevention Research 16, no. 7 (July 5, 2023): 379–84. http://dx.doi.org/10.1158/1940-6207.capr-22-0435.

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Abstract Precancer atlases have the potential to revolutionize how we think about the topographic and morphologic structures of precancerous lesions in relation to cellular, molecular, genetic, and pathophysiologic states. This mini review uses the Human Tumor Atlas Network (HTAN), established by the National Cancer Institute (NCI), to illustrate the construction of cellular and molecular three-dimensional atlases of human cancers as they evolve from precancerous lesions to advanced disease. We describe the collaborative nature of the network and the research to determine how and when premalignant lesions progress to invasive cancer, regress or obtain a state of equilibrium. We have attempted to highlight progress made by HTAN in building precancer atlases and discuss possible future directions. It is hoped that the lessons from our experience with HTAN will help other investigators engaged in the construction of precancer atlases to crystallize their thoughts on logistics, rationale, and implementation.

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McCampbell, Kristen K., Kristin N. Springer, and Rebecca A. Wingert. "Atlas of Cellular Dynamics during Zebrafish Adult Kidney Regeneration." Stem Cells International 2015 (2015): 1–19. http://dx.doi.org/10.1155/2015/547636.

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The zebrafish is a useful animal model to study the signaling pathways that orchestrate kidney regeneration, as its renal nephrons are simple, yet they maintain the biological complexity inherent to that of higher vertebrate organisms including mammals. Recent studies have suggested that administration of the aminoglycoside antibiotic gentamicin in zebrafish mimics human acute kidney injury (AKI) through the induction of nephron damage, but the timing and details of critical phenotypic events associated with the regeneration process, particularly in existing nephrons, have not been characterized. Here, we mapped the temporal progression of cellular and molecular changes that occur during renal epithelial regeneration of the proximal tubule in the adult zebrafish using a platform of histological and expression analysis techniques. This work establishes the timing of renal cell death after gentamicin injury, identifies proliferative compartments within the kidney, and documents gene expression changes associated with the regenerative response of proliferating cells. These data provide an important descriptive atlas that documents the series of events that ensue after damage in the zebrafish kidney, thus availing a valuable resource for the scientific community that can facilitate the implementation of zebrafish research to delineate the mechanisms that control renal regeneration.

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Kunst, Michael, Eva Laurell, Nouwar Mokayes, Anna Kramer, Fumi Kubo, António M. Fernandes, Dominique Förster, Marco Dal Maschio, and Herwig Baier. "A Cellular-Resolution Atlas of the Larval Zebrafish Brain." Neuron 103, no. 1 (July 2019): 21–38. http://dx.doi.org/10.1016/j.neuron.2019.04.034.

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5

Ding, Song‐Lin, Joshua J. Royall, Susan M. Sunkin, Lydia Ng, Benjamin A. C. Facer, Phil Lesnar, Angie Guillozet‐Bongaarts, et al. "Comprehensive cellular‐resolution atlas of the adult human brain." Journal of Comparative Neurology 524, no. 16 (September 15, 2016): 3127–481. http://dx.doi.org/10.1002/cne.24080.

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6

Ding, Song-Lin, Joshua J. Royall, Susan M. Sunkin, Lydia Ng, Benjamin A. C. Facer, Phil Lesnar, Angie Guillozet-Bongaarts, et al. "Comprehensive cellular-resolution atlas of the adult human brain." Journal of Comparative Neurology 524, no. 16 (September 15, 2016): Spc1. http://dx.doi.org/10.1002/cne.24097.

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7

Ding, Song-Lin, Joshua J. Royall, Susan M. Sunkin, Lydia Ng, Benjamin A. C. Facer, Phil Lesnar, Angie Guillozet-Bongaarts, et al. "Comprehensive cellular-resolution atlas of the adult human brain." Journal of Comparative Neurology 525, no. 2 (December 5, 2016): 407. http://dx.doi.org/10.1002/cne.24130.

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8

GÁL, V., J. HÁMORI, T. ROSKA, D. BÁLYA, ZS BOROSTYÁNKŐI, M. BRENDEL, K. LOTZ, et al. "RECEPTIVE FIELD ATLAS AND RELATED CNN MODELS." International Journal of Bifurcation and Chaos 14, no. 02 (February 2004): 551–84. http://dx.doi.org/10.1142/s0218127404009545.

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In this paper we demonstrate the potential of the cellular nonlinear/neural network paradigm (CNN) that of the analogic cellular computer architecture (called CNN Universal Machine — CNN-UM) in modeling different parts and aspects of the nervous system. The structure of the living sensory systems and the CNN share a lot of features in common: local interconnections ("receptive field architecture"), nonlinear and delayed synapses for the processing tasks, the potentiality of feedback and using the advantages of both the analog and logic signal-processing mode. The results of more than ten years of cooperative work of many engineers and neurobiologists have been collected in an atlas: what we present here is a kind of selection from these studies emphasizing the flexibility of the CNN computing: visual, tactile and auditory modalities are concerned.

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KHAW, P. T. "Atlas of Glaucoma." British Journal of Ophthalmology 83, no. 8 (August 1, 1999): 994d. http://dx.doi.org/10.1136/bjo.83.8.994d.

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10

Ffytche, T. J. "Atlas der Kontaktlinsenanpassung." British Journal of Ophthalmology 70, no. 1 (January 1, 1986): 80. http://dx.doi.org/10.1136/bjo.70.1.80.

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11

Toledo, Claudio A. B. "The Atlas of Chick Development." Journal of Chemical Neuroanatomy 25, no. 2 (February 2003): 149. http://dx.doi.org/10.1016/s0891-0618(03)00006-1.

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12

Eames, B., April DeLaurier, Bonnie Ullmann, Tyler R. Huycke, James T. Nichols, John Dowd, Marcie McFadden, Mark M. Sasaki, and Charles B. Kimmel. "FishFace: interactive atlas of zebrafish craniofacial development at cellular resolution." BMC Developmental Biology 13, no. 1 (2013): 23. http://dx.doi.org/10.1186/1471-213x-13-23.

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13

Carson, James P., Christina Thaller, and Gregor Eichele. "A transcriptome atlas of the mouse brain at cellular resolution." Current Opinion in Neurobiology 12, no. 5 (October 2002): 562–65. http://dx.doi.org/10.1016/s0959-4388(02)00356-2.

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14

Weistuch, Corey, Kevin Murgas, Ken Dill, Larry Norton, Joseph Deasy, and Allen Tannenbaum. "Abstract 6591: A universal atlas of cellular and oncogenic phenotypes." Cancer Research 83, no. 7_Supplement (April 4, 2023): 6591. http://dx.doi.org/10.1158/1538-7445.am2023-6591.

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Abstract Tumors and healthy tissues exhibit gene expression variability in many of the same pathways. We propose that these commonalities result from a performance trade-off between universal cellular phenotypes; each phenotype is defined by an orthogonal gene expression profile identified using unsupervised dimensionality reduction. Using two publicly available RNA-seq datasets (n=54 normal tissues; n=1504 cancer cell lines), we show that both healthy and cancerous cells occupy a trade-off between five canonical phenotypes: OxPhos, Warburg, Fibroblastic, Immune, and Growth. Each cell is assigned a phenotype score that, as we demonstrate, predicts differential drug sensitivities and mutational signatures, even among cancers of the same tissue type. Since these phenotype scores are defined using only healthy tissues, they can be generally applied to other diseases as well. Citation Format: Corey Weistuch, Kevin Murgas, Ken Dill, Larry Norton, Joseph Deasy, Allen Tannenbaum. A universal atlas of cellular and oncogenic phenotypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6591.

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15

Bhattacharya, Soumyaroop, Jacquelyn A. Myers, Cameron Baker, Minzhe Guo, Soula Danopoulos, Jason R. Myers, Gautam Bandyopadhyay, et al. "Single-Cell Transcriptomic Profiling Identifies Molecular Phenotypes of Newborn Human Lung Cells." Genes 15, no. 3 (February 26, 2024): 298. http://dx.doi.org/10.3390/genes15030298.

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While animal model studies have extensively defined the mechanisms controlling cell diversity in the developing mammalian lung, there exists a significant knowledge gap with regards to late-stage human lung development. The NHLBI Molecular Atlas of Lung Development Program (LungMAP) seeks to fill this gap by creating a structural, cellular and molecular atlas of the human and mouse lung. Transcriptomic profiling at the single-cell level created a cellular atlas of newborn human lungs. Frozen single-cell isolates obtained from two newborn human lungs from the LungMAP Human Tissue Core Biorepository, were captured, and library preparation was completed on the Chromium 10X system. Data was analyzed in Seurat, and cellular annotation was performed using the ToppGene functional analysis tool. Transcriptional interrogation of 5500 newborn human lung cells identified distinct clusters representing multiple populations of epithelial, endothelial, fibroblasts, pericytes, smooth muscle, immune cells and their gene signatures. Computational integration of data from newborn human cells and with 32,000 cells from postnatal days 1 through 10 mouse lungs generated by the LungMAP Cincinnati Research Center facilitated the identification of distinct cellular lineages among all the major cell types. Integration of the newborn human and mouse cellular transcriptomes also demonstrated cell type-specific differences in maturation states of newborn human lung cells. Specifically, newborn human lung matrix fibroblasts could be separated into those representative of younger cells (n = 393), or older cells (n = 158). Cells with each molecular profile were spatially resolved within newborn human lung tissue. This is the first comprehensive molecular map of the cellular landscape of neonatal human lung, including biomarkers for cells at distinct states of maturity.

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Fan, Lingzhong, Hai Li, Junjie Zhuo, Yu Zhang, Jiaojian Wang, Liangfu Chen, Zhengyi Yang, et al. "The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture." Cerebral Cortex 26, no. 8 (May 26, 2016): 3508–26. http://dx.doi.org/10.1093/cercor/bhw157.

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17

Pei, Jie, Lin Xiong, Shaoke Guo, Xingdong Wang, Yongfu La, Min Chu, Chunnian Liang, Ping Yan, and Xian Guo. "Single-Cell Transcriptomics Analysis Reveals a Cell Atlas and Cell Communication in Yak Ovary." International Journal of Molecular Sciences 24, no. 3 (January 17, 2023): 1839. http://dx.doi.org/10.3390/ijms24031839.

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Yaks (Bos grunniens) are the only bovine species that adapt well to the harsh high-altitude environment in the Qinghai-Tibetan plateau. However, the reproductive adaptation to the climate of the high elevation remains to be elucidated. Cell composition and molecular characteristics are the foundation of normal ovary function which determines reproductive performance. So, delineating ovarian characteristics at a cellular molecular level is conducive to elucidating the mechanism underlying the reproductive adaption of yaks. Here, the single-cell RNA-sequencing (scRNA-seq) was employed to depict an atlas containing different cell types with specific molecular signatures in the yak ovary. The cell types were identified on the basis of their specifically expressed genes and biological functions. As a result, a cellular atlas of yak ovary was established successfully containing theca cells, stromal cells, endothelial cells, smooth muscle cells, natural killer cells, macrophages, and proliferating cells. A cell-to-cell communication network between the distinct cell types was constructed. The theca cells were clustered into five subtypes based on their biological functions. Further, CYP11A1 was confirmed as a marker gene for the theca cells by immunofluorescence staining. Our work reveals an ovarian atlas at the cellular molecular level and contributes to providing insights into reproductive adaption in yaks.

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18

Crater, Jacqueline M., Daniel C. Dunn, Douglas F. Nixon, and Robert L. Furler O’Brien. "A History and Atlas of the Human CD4+ T Helper Cell." Biomedicines 11, no. 10 (September 23, 2023): 2608. http://dx.doi.org/10.3390/biomedicines11102608.

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CD4+ T cells have orchestrated and regulated immunity since the introduction of jawed vertebrates, yet our understanding of CD4+ T cell evolution, development, and cellular physiology has only begun to be unearthed in the past few decades. Discoveries of genetic diseases that ablate this cellular population have provided insight into their critical functions while transcriptomics, proteomics, and high-resolution microscopy have recently revealed new insights into CD4+ T cell anatomy and physiology. This article compiles historical, microscopic, and multi-omics data that can be used as a reference atlas and index to dissect cellular physiology within these influential cells and further understand pathologies like HIV infection that inflict human CD4+ T cells.

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19

DAMATO, B. "Atlas of Intraocular Tumours." British Journal of Ophthalmology 84, no. 7 (July 1, 2000): 805b—805. http://dx.doi.org/10.1136/bjo.84.7.805b.

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20

McLEOD, D. "Atlas of Vitreous Biomicroscopy." British Journal of Ophthalmology 85, no. 1 (January 1, 2001): 121d—121. http://dx.doi.org/10.1136/bjo.85.1.121d.

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21

Marsh, R. J. "Atlas of Clinical Ophthalmology." British Journal of Ophthalmology 70, no. 3 (March 1, 1986): 238. http://dx.doi.org/10.1136/bjo.70.3.238-a.

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22

Wilson, R. "Atlas of Ophthalmic Surgery." British Journal of Ophthalmology 73, no. 10 (October 1, 1989): 856. http://dx.doi.org/10.1136/bjo.73.10.856-a.

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23

Harrad, R. A. "Atlas of Ocular Motility." British Journal of Ophthalmology 75, no. 9 (September 1, 1991): 576. http://dx.doi.org/10.1136/bjo.75.9.576-c.

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24

Kim, Sohee, and Chuna Kim. "Transcriptomic Analysis of Cellular Senescence: One Step Closer to Senescence Atlas." Molecules and Cells 44, no. 3 (March 31, 2021): 136–45. http://dx.doi.org/10.14348/molcells.2021.2239.

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25

Wang, Lin, Jangham Jung, Husam Babikir, Karin Shamardani, Noriyuki Kasahara, Sabine Müller, and Aaron Diaz. "MEDB-59. A draft atlas of medulloblastoma cellular evolution under therapy." Neuro-Oncology 24, Supplement_1 (June 1, 2022): i120. http://dx.doi.org/10.1093/neuonc/noac079.433.

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Abstract How standard care shapes the cellular composition of recurrent medulloblastoma (MB), if therapy selects for specific tumor or immune cell types, is unknown. We report the pilot phase of our ongoing effort to profile human longitudinal MB specimens via single-cell transcriptomics and epigenetics. We profiled 11 diagnostic and eight recurrent specimens from 19 subjects via single-nucleus RNA sequencing (snRNA-seq), and four subjects via single-nucleus assay for transposase-accessible chromatin. Specimens from select subjects were also profiled to assess genome-wide enhancer activity via single-nucleus cleavage-under-targets and tagmentation. We found an upregulation of the DNA-damage response, RNA translation, WNT and NOTCH signaling in recurrent specimens. The percentages of stem-like cells increased by over two-fold at recurrence. We found that microglia and oligodendrocyte-lineage cells were the most abundant non-malignant tumor-associated cell types, representing 2%-10% of cells profiled. Microglia abundances were relatively stable across molecular subtypes, and when comparing primary to recurrent tumors. There was a moderate, but statistically significant, increase in oligodendrocyte abundance in SSH and WNT tumors, compared to Group 3/4 tumors. We compared gene expression in tumor cells with public snRNA-seq from developing human cerebella (PCW 9-21). Combined Group-3/4 cell analysis supports a common lineage hierarchy, with an enrichment for unipolar brush-cell and Purkinje-cell phenotypes found in Group-4 tumors. All Group-3/4 cases contained cycling cells expressing markers of PAX2+ interneuron progenitors, most cycling cells had this phenotype. All specimens contained populations of non-cycling granule-cell progenitor-like cells. We performed single-cell co-expression receptor/ligand analysis to infer paracrine signaling between tumor and non-malignant cell types. This identified both tumor cells and microglia as sources of growth factors, pro-inflammatory cytokines, and pro-apoptotic ligands. Non-malignant oligodendrocyte-lineage cells uniquely expressed IL6-family cytokines, pleiotrophin, and class-III semaphorins. These studies shed light on the cellular heterogeneity of MB and the effect of standard therapy in shaping composition at recurrence.

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26

Fogo, Agnes B., Mark A. Lusco, Behzad Najafian, and Charles E. Alpers. "AJKD Atlas of Renal Pathology: Cellular Variant of Focal Segmental Glomerulosclerosis." American Journal of Kidney Diseases 66, no. 2 (August 2015): e7. http://dx.doi.org/10.1053/j.ajkd.2015.06.002.

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27

Pisarev, A., E. Poustelnikova, M. Samsonova, and J. Reinitz. "FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution." Nucleic Acids Research 37, Database (January 1, 2009): D560—D566. http://dx.doi.org/10.1093/nar/gkn717.

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28

Macauley, M., and H. S. Mortveit. "An atlas of limit set dynamics for asynchronous elementary cellular automata." Theoretical Computer Science 504 (September 2013): 26–37. http://dx.doi.org/10.1016/j.tcs.2012.09.015.

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29

Kepple, Jessica, Simon Davis, Roman Fischer, and Katherine R. Bull. "Oxford Kidney Pathology Atlas: Single Cellular Profiling of Renal Biopsy Tissue." Journal of the American Society of Nephrology 34, no. 11S (November 2023): 963. http://dx.doi.org/10.1681/asn.20233411s1963b.

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30

Price, Colles, Kazuho Nishimura, Som Bandyopadhyay, Darrell Borger, and Russell Weiner. "Abstract LB331: Integrating multiple spatial transcriptomic and proteomic technologies to generate a cancer atlas to understand the tumor microenvironment." Cancer Research 84, no. 7_Supplement (April 5, 2024): LB331. http://dx.doi.org/10.1158/1538-7445.am2024-lb331.

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Abstract Deep single-cell genomics has provided a monumental leap in our understanding and categorical analysis of cancer cells and their unique molecular properties. With spatial platforms that preserve the tissue architecture, an emerging understanding of complex cell interactions and local environment influences is providing new perspectives for targeted therapies. Here we describe a comprehensive approach at profiling the tumor immune microenvironment across multiple solid malignancies to provide an atlas of tumor biology. To generate this atlas, we created a MERFISH panel of 500 genes representing over 40 cell phenotyping pathways and dozens of signaling pathways including chemokines, cytokines, interferon, and ligand-receptor interactions. This panel was used across 15 patients representing multiple solid malignancies. We also utilized the Immuno-Oncology focused Xenium panel to profile 16 different patients across the same indications. With the Xenium data we simultaneously assessed proteomic expression using a 16 plex panel focused on immuno-oncology targets and subsequently did H&E staining, allowing multiple -omic data collections within a single slide. After initial filtering and quality control this projects produced a total dataset with over 15 million cells and billions of transcripts. The 500 gene MERFISH panel revealed complex relationships between diverse cell types within the tumor microenvironment that was dependent on cellular location and surrounding area. While the presence of major immune cell types was observed in all cancer tissues, the ratio and spatial relationship to cancer cells differed between each tumor. Accordingly, we observed that differences in cellular composition of the microenvironment corresponded with associated changes in cellular signaling. Similarly, with Xenium we identified new spatial relationships between cancer and immune cells with their environment while confirming part of these relationships with subsequent immunofluorescence data. The H&E data provided an opportunity to overlay this data with standard pathological annotation. We further investigated how each cellular microneighborhood varied throughout the tumor and varied from patient. This comprehensive map of the tumor immune microenvironment is a deep cellular dive into cellular architecture. As this Cancer Atlas evolves this will drive the discovery of several new potential biological targets and cell types of interest. This will also be critical for the assessment of current cellular and drug therapies in preclinical and clinical models. This effort will continue with more patient samples across a greater number of disease indications and will include more technologies. We will also expand the development and implementation of analytical tools to maximum the knowledge and insights gained from this Atlas. Together, this will be a critical tool in the continuing fight against cancer. Citation Format: Colles Price, Kazuho Nishimura, Som Bandyopadhyay, Darrell Borger, Russell Weiner. Integrating multiple spatial transcriptomic and proteomic technologies to generate a cancer atlas to understand the tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB331.

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De Micheli, Andrea J., Jacob B. Swanson, Nathaniel P. Disser, Leandro M. Martinez, Nicholas R. Walker, David J. Oliver, Benjamin D. Cosgrove, and Christopher L. Mendias. "Single-cell transcriptomic analysis identifies extensive heterogeneity in the cellular composition of mouse Achilles tendons." American Journal of Physiology-Cell Physiology 319, no. 5 (November 1, 2020): C885—C894. http://dx.doi.org/10.1152/ajpcell.00372.2020.

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Tendon is a dense connective tissue that stores and transmits forces between muscles and bones. Cellular heterogeneity is increasingly recognized as an important factor in the biological basis of tissue homeostasis and disease, yet little is known about the diversity of cell types that populate tendon. To address this, we determined the heterogeneity of cell populations within mouse Achilles tendons using single-cell RNA sequencing. In assembling a transcriptomic atlas of Achilles tendons, we identified 11 distinct types of cells, including three previously undescribed populations of tendon fibroblasts. Prior studies have indicated that pericytes, which are found in the vasculature of tendons, could serve as a potential source of progenitor cells for adult tendon fibroblasts. Using trajectory inference analysis, we provide additional support for the notion that pericytes are likely to be at least one of the progenitor cell populations for the fibroblasts that compose adult tendons. We also modeled cell-cell interactions and identified previously undescribed ligand-receptor signaling interactions involved in tendon homeostasis. Our novel and interactive tendon atlas highlights previously underappreciated heterogeneity between and within tendon cell populations. The atlas also serves as a resource to further the understanding of tendon extracellular matrix assembly and maintenance and in the design of therapies for tendinopathies.

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32

Song, Liting, Shaojun Pan, Zichao Zhang, Longhao Jia, Wei-Hua Chen, and Xing-Ming Zhao. "STAB: a spatio-temporal cell atlas of the human brain." Nucleic Acids Research 49, no. D1 (September 25, 2020): D1029—D1037. http://dx.doi.org/10.1093/nar/gkaa762.

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Abstract The human brain is the most complex organ consisting of billions of neuronal and non-neuronal cells that are organized into distinct anatomical and functional regions. Elucidating the cellular and transcriptome architecture underlying the brain is crucial for understanding brain functions and brain disorders. Thanks to the single-cell RNA sequencing technologies, it is becoming possible to dissect the cellular compositions of the brain. Although great effort has been made to explore the transcriptome architecture of the human brain, a comprehensive database with dynamic cellular compositions and molecular characteristics of the human brain during the lifespan is still not available. Here, we present STAB (a Spatio-Temporal cell Atlas of the human Brain), a database consists of single-cell transcriptomes across multiple brain regions and developmental periods. Right now, STAB contains single-cell gene expression profiling of 42 cell subtypes across 20 brain regions and 11 developmental periods. With STAB, the landscape of cell types and their regional heterogeneity and temporal dynamics across the human brain can be clearly seen, which can help to understand both the development of the normal human brain and the etiology of neuropsychiatric disorders. STAB is available at http://stab.comp-sysbio.org.

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Feng, Xin, Lei Li, Eric J. Wagner, and Wei Li. "TC3A: The Cancer 3′ UTR Atlas." Nucleic Acids Research 46, no. D1 (October 9, 2017): D1027—D1030. http://dx.doi.org/10.1093/nar/gkx892.

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AbstractWidespread alternative polyadenylation (APA) occurs during enhanced cellular proliferation and transformation. Recently, we demonstrated that CFIm25-mediated 3′ UTR shortening through APA promotes glioblastoma tumor growth in vitro and in vivo, further underscoring its significance to tumorigenesis. Here, we report The Cancer 3′ UTR Atlas (TC3A), a comprehensive resource of APA usage for 10,537 tumors across 32 cancer types. These APA events represent potentially novel prognostic biomarkers and may uncover novel mechanisms for the regulation of cancer driver genes. TC3A is built on top of the now de facto standard cBioPortal. Therefore, the large community of existing cBioPortal users and clinical researchers will find TC3A familiar and immediately usable. TC3A is currently fully functional and freely available at http://tc3a.org.

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34

Kretzschmar, William A., Ilkka Juuso, and C. Thomas Bailey. "Computer Simulation of Dialect Feature Diffusion." Journal of Linguistic Geography 2, no. 1 (March 2014): 41–57. http://dx.doi.org/10.1017/jlg.2014.2.

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This paper describes the independent construction and implementation of two cellular automata that model dialect feature diffusion as the adaptive aspect of the complex system of speech. We show how a feature, once established, can spread across an area, and how the distribution of a dialect feature as it stands in Linguistic Atlas data could either spread or diminish. Cellular automata use update rules to determine the status of a feature at a given location with respect to the status of its neighboring locations. In each iteration all locations in a matrix are evaluated, and then the new status for each one is displayed all at once. Throughout hundreds of iterations, we can watch regional distributional patterns emerge as a consequence of these simple update rules. We validate patterns with respect to the linguistic distributions known to occur in the Linguistic Atlas Project.

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35

Aminoff,, Michael J. "Atlas of clinical neurology." Muscle & Nerve 21, no. 12 (December 1998): 1816. http://dx.doi.org/10.1002/(sici)1097-4598(199812)21:12<1816::aid-mus43>3.0.co;2-5.

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Dhoot, Dilsher S. "Gass' Atlas of Macular Diseases." British Journal of Ophthalmology 96, no. 10 (June 2, 2012): 1348.1–1348. http://dx.doi.org/10.1136/bjophthalmol-2012-301839.

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37

RESTORI, M. "Ophthalmic Ultrasound: a Diagnostic Atlas." British Journal of Ophthalmology 84, no. 8 (August 1, 2000): 936h—936. http://dx.doi.org/10.1136/bjo.84.8.936h.

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38

Chignell, A. "Atlas of the Peripheral Retina." British Journal of Ophthalmology 69, no. 7 (July 1, 1985): 555. http://dx.doi.org/10.1136/bjo.69.7.555.

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Marsh, R. J. "Atlas of the Ocular Fundus." British Journal of Ophthalmology 69, no. 7 (July 1, 1985): 556. http://dx.doi.org/10.1136/bjo.69.7.556.

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40

Graham, E. "A Colour Atlas of Allergy." British Journal of Ophthalmology 73, no. 11 (November 1, 1989): 935. http://dx.doi.org/10.1136/bjo.73.11.935.

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Falcon, M. G. "A Colour Atlas of Ophthalmology." British Journal of Ophthalmology 73, no. 7 (July 1, 1989): 583. http://dx.doi.org/10.1136/bjo.73.7.583.

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42

Lee, W. R. "Ocular Pathology: A Colour Atlas." British Journal of Ophthalmology 74, no. 2 (February 1, 1990): 128. http://dx.doi.org/10.1136/bjo.74.2.128-b.

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Karaiskos, Nikos, Mahdieh Rahmatollahi, Anastasiya Boltengagen, Haiyue Liu, Martin Hoehne, Markus Rinschen, Bernhard Schermer, et al. "A Single-Cell Transcriptome Atlas of the Mouse Glomerulus." Journal of the American Society of Nephrology 29, no. 8 (May 24, 2018): 2060–68. http://dx.doi.org/10.1681/asn.2018030238.

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Background Three different cell types constitute the glomerular filter: mesangial cells, endothelial cells, and podocytes. However, to what extent cellular heterogeneity exists within healthy glomerular cell populations remains unknown.Methods We used nanodroplet-based highly parallel transcriptional profiling to characterize the cellular content of purified wild-type mouse glomeruli.Results Unsupervised clustering of nearly 13,000 single-cell transcriptomes identified the three known glomerular cell types. We provide a comprehensive online atlas of gene expression in glomerular cells that can be queried and visualized using an interactive and freely available database. Novel marker genes for all glomerular cell types were identified and supported by immunohistochemistry images obtained from the Human Protein Atlas. Subclustering of endothelial cells revealed a subset of endothelium that expressed marker genes related to endothelial proliferation. By comparison, the podocyte population appeared more homogeneous but contained three smaller, previously unknown subpopulations.Conclusions Our study comprehensively characterized gene expression in individual glomerular cells and sets the stage for the dissection of glomerular function at the single-cell level in health and disease.

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Rosenke, Mona, Rick van Hoof, Job van den Hurk, Kalanit Grill-Spector, and Rainer Goebel. "A Probabilistic Functional Atlas of Human Occipito-Temporal Visual Cortex." Cerebral Cortex 31, no. 1 (September 24, 2020): 603–19. http://dx.doi.org/10.1093/cercor/bhaa246.

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Abstract Human visual cortex contains many retinotopic and category-specific regions. These brain regions have been the focus of a large body of functional magnetic resonance imaging research, significantly expanding our understanding of visual processing. As studying these regions requires accurate localization of their cortical location, researchers perform functional localizer scans to identify these regions in each individual. However, it is not always possible to conduct these localizer scans. Here, we developed and validated a functional region of interest (ROI) atlas of early visual and category-selective regions in human ventral and lateral occipito-temporal cortex. Results show that for the majority of functionally defined ROIs, cortex-based alignment results in lower between-subject variability compared to nonlinear volumetric alignment. Furthermore, we demonstrate that 1) the atlas accurately predicts the location of an independent dataset of ventral temporal cortex ROIs and other atlases of place selectivity, motion selectivity, and retinotopy. Next, 2) we show that the majority of voxel within our atlas is responding mostly to the labeled category in a left-out subject cross-validation, demonstrating the utility of this atlas. The functional atlas is publicly available (download.brainvoyager.com/data/visfAtlas.zip) and can help identify the location of these regions in healthy subjects as well as populations (e.g., blind people, infants) in which functional localizers cannot be run.

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Raddi, Gianmarco, Ana Beatriz F. Barletta, Mirjana Efremova, Jose Luis Ramirez, Rafael Cantera, Sarah A. Teichmann, Carolina Barillas-Mury, and Oliver Billker. "Mosquito cellular immunity at single-cell resolution." Science 369, no. 6507 (August 27, 2020): 1128–32. http://dx.doi.org/10.1126/science.abc0322.

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Hemocytes limit the capacity of mosquitoes to transmit human pathogens. Here we profile the transcriptomes of 8506 hemocytes of Anopheles gambiae and Aedes aegypti mosquito vectors. Our data reveal the functional diversity of hemocytes, with different subtypes of granulocytes expressing distinct and evolutionarily conserved subsets of effector genes. A previously unidentified cell type in An. gambiae, which we term “megacyte,” is defined by a specific transmembrane protein marker (TM7318) and high expression of lipopolysaccharide-induced tumor necrosis factor–α transcription factor 3 (LL3). Knockdown experiments indicate that LL3 mediates hemocyte differentiation during immune priming. We identify and validate two main hemocyte lineages and find evidence of proliferating granulocyte populations. This atlas of medically relevant invertebrate immune cells at single-cell resolution identifies cellular events that underpin mosquito immunity to malaria infection.

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Hawrylycz, Michael, Eitan S. Kaplan, Kyle J. Travaglini, Mariano I. Gabitto, Jeremy A. Miller, Lydia Ng, Jennie L. Close, et al. "SEA-AD is a multimodal cellular atlas and resource for Alzheimer’s disease." Nature Aging 4, no. 10 (October 14, 2024): 1331–34. http://dx.doi.org/10.1038/s43587-024-00719-8.

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Suoangbaji, Tina, Renwen Long, Irene Oi-Lin Ng, Loey Lung-Yi Mak, and Daniel Wai-Hung Ho. "LiverSCA 2.0: An Enhanced Comprehensive Cell Atlas for Human Hepatocellular Carcinoma and Intrahepatic Cholangiocarcinoma." Cancers 17, no. 5 (March 5, 2025): 890. https://doi.org/10.3390/cancers17050890.

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Background: Hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) are two distinct types of primary liver cancer (PLC) characterized by considerable extents of cellular and molecular heterogeneities. We recently developed a web-based cell atlas called LiverSCA that possesses a user-friendly interface and comprehensive functionalities. It facilitates the exploration of gene expression patterns, cellular compositions, and intercellular communication within the microenvironments of liver and PLC tumors. Methods: To further enhance the documentation of data pinpointing different phenotypes/subtypes of liver and PLC, we extended the catalog of LiverSCA with additional datasets, e.g., ICC and metabolic dysfunction-associated steatotic liver disease/steatosis (MASLD/MASH). Results: The current enhanced version of the LiverSCA cell atlas encompasses six phenotypes (normal, HBV-HCC, HCV-HCC, non-viral HCC, ICC, and MASH), 63 patients, and over 248,000 cells. Furthermore, we have incorporated comparative visualization methods that allow users to simultaneously examine and compare gene expression levels between two different phenotypes. Conclusions: We are committed to the continuous development of LiverSCA and envision that it will serve as a valuable resource to support researchers in convenient investigations into the cellular and molecular landscapes of liver and PLC.

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Zhu, Tianyu, Jacklyn Liu, Stephan Beck, Sun Pan, David Capper, Matt Lechner, Chrissie Thirlwell, Charles E. Breeze, and Andrew E. Teschendorff. "A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution." Nature Methods 19, no. 3 (March 2022): 296–306. http://dx.doi.org/10.1038/s41592-022-01412-7.

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AbstractBulk-tissue DNA methylomes represent an average over many different cell types, hampering our understanding of cell-type-specific contributions to disease development. As single-cell methylomics is not scalable to large cohorts of individuals, cost-effective computational solutions are needed, yet current methods are limited to tissues such as blood. Here we leverage the high-resolution nature of tissue-specific single-cell RNA-sequencing datasets to construct a DNA methylation atlas defined for 13 solid tissue types and 40 cell types. We comprehensively validate this atlas in independent bulk and single-nucleus DNA methylation datasets. We demonstrate that it correctly predicts the cell of origin of diverse cancer types and discovers new prognostic associations in olfactory neuroblastoma and stage 2 melanoma. In brain, the atlas predicts a neuronal origin for schizophrenia, with neuron-specific differential DNA methylation enriched for corresponding genome-wide association study risk loci. In summary, the DNA methylation atlas enables the decomposition of 13 different human tissue types at a high cellular resolution, paving the way for an improved interpretation of epigenetic data.

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Ulengin-Talkish, Idil, and Martha S. Cyert. "A cellular atlas of calcineurin signaling." Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, October 2022, 119366. http://dx.doi.org/10.1016/j.bbamcr.2022.119366.

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Costantini, Irene, Leah Morgan, Jiarui Yang, Yael Balbastre, Divya Varadarajan, Luca Pesce, Marina Scardigli, et al. "A cellular resolution atlas of Broca’s area." Science Advances 9, no. 41 (October 13, 2023). http://dx.doi.org/10.1126/sciadv.adg3844.

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Brain cells are arranged in laminar, nuclear, or columnar structures, spanning a range of scales. Here, we construct a reliable cell census in the frontal lobe of human cerebral cortex at micrometer resolution in a magnetic resonance imaging (MRI)–referenced system using innovative imaging and analysis methodologies. MRI establishes a macroscopic reference coordinate system of laminar and cytoarchitectural boundaries. Cell counting is obtained with a digital stereological approach on the 3D reconstruction at cellular resolution from a custom-made inverted confocal light-sheet fluorescence microscope (LSFM). Mesoscale optical coherence tomography enables the registration of the distorted histological cell typing obtained with LSFM to the MRI-based atlas coordinate system. The outcome is an integrated high-resolution cellular census of Broca’s area in a human postmortem specimen, within a whole-brain reference space atlas.

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