Comprehensive Integration of Single-Cell Transcriptomic Data

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Lu, C., Kang, T., Zhang, J., Yang, K., Liu, Y., Song, K., Lin, Q., Dixit, D., Gimple, R. C., Zhang, Q., Shi, Z., Fan, X., Wu, Q., Li, D., Shan, D., Gao, J., Gu, D., You, H., Li, Y., … Wang, X. (2025). Combined targeting of glioblastoma stem cells of different cellular states disrupts malignant progression. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-58366-5
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Pita-Juarez, Y., Karagkouni, D., Kalavros, N., Melms, J. C., Niezen, S., Delorey, T. M., Essene, A. L., Brook, O. R., Pant, D., Skelton-Badlani, D., Naderi, P., Huang, P., Pan, L., Hether, T., Andrews, T. S., Ziegler, C. G. K., Reeves, J., Myloserdnyy, A., Chen, R., … Vlachos, I. S. (2025). A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients. Genome Biology, 26(1). https://doi.org/10.1186/s13059-025-03499-5
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Börner, K., Blood, P. D., Silverstein, J. C., Ruffalo, M., Satija, R., Teichmann, S. A., Pryhuber, G. J., Misra, R. S., Purkerson, J. M., Fan, J., Hickey, J. W., Molla, G., Xu, C., Zhang, Y., Weber, G. M., Jain, Y., Qaurooni, D., Kong, Y., … Herr, B. W. (2025). Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage. Nature Methods. https://doi.org/10.1038/s41592-024-02563-5
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Craig-Schapiro, R., Li, G., Chen, K., Gomez-Salinero, J. M., Nachman, R., Kopacz, A., Schreiner, R., Chen, X., Zhou, Q., Rafii, S., & Redmond, D. (2025). Single-cell atlas of human pancreatic islet and acinar endothelial cells in health and diabetes. Nature Communications, 16(1). https://doi.org/10.1038/s41467-024-55415-3
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Maurer, K., Park, C. Y., Mani, S., Borji, M., Raths, F., Gouin, K. H., Penter, L., Jin, Y., Zhang, J. Y., Shin, C., Brenner, J. R., Southard, J., Krishna, S., Lu, W., Lyu, H., Abbondanza, D., Mangum, C., Olsen, L. R., Lawson, M. J., … Azizi, E. (2025). Coordinated immune networks in leukemia bone marrow microenvironments distinguish response to cellular therapy. Science Immunology, 10(103). https://doi.org/10.1126/sciimmunol.adr0782
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Caron, D. P., Specht, W. L., Chen, D., Wells, S. B., Szabo, P. A., Jensen, I. J., Farber, D. L., & Sims, P. A. (2025). Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues. Cell Reports Methods, 5(1), 100938. https://doi.org/10.1016/j.crmeth.2024.100938
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Karaahmet, B., Duquesne, L., Sigalov, A., Yung, C. J., Kroshilina, A., Zhang, Y., Taga, M., & Klein, H. (2024). Spatial Transcriptomics Analysis Identifies Glial Signatures Spatially Associated with Neuritic Plaques in Human Post‐Mortem Brains. Alzheimer’s & Dementia, 20(S1). Portico. https://doi.org/10.1002/alz.087498
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Wu, Y., Dumitrescu, L. C., De Jager, P. L., Menon, V., Schneider, J. A., Bennett, D. A., & Hohman, T. J. (2024). Cell‐type specific contribution to sex differences in Alzheimer’s Disease revealed using single‐cell transcriptomes. Alzheimer’s & Dementia, 20(S1). Portico. https://doi.org/10.1002/alz.092518
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Jin, C., Wang, X., Yang, J., Kim, S., Hudgins, A. D., Gamliel, A., Pei, M., Contreras, D., Devos, M., Guo, Q., Vijg, J., Conti, M., Hoeijmakers, J., Campisi, J., Lobo, R., Williams, Z., Rosenfeld, M. G., & Suh, Y. (2024). Molecular and genetic insights into human ovarian aging from single-nuclei multi-omics analyses. Nature Aging. https://doi.org/10.1038/s43587-024-00762-5
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Shafighi, S., Geras, A., Jurzysta, B., Sahaf Naeini, A., Filipiuk, I., Ra̧czkowska, A., Toosi, H., Koperski, Ł., Thrane, K., Engblom, C., Mold, J. E., Chen, X., Hartman, J., Nowis, D., Carbone, A., Lagergren, J., & Szczurek, E. (2024). Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-53374-3
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Gu, J., Iyer, A., Wesley, B., Taglialatela, A., Leuzzi, G., Hangai, S., Decker, A., Gu, R., Klickstein, N., Shuai, Y., Jankovic, K., Parker-Burns, L., Jin, Y., Zhang, J. Y., Hong, J., Niu, X., Costa, J. A., Pezet, M. G., Chou, J., … Gaublomme, J. T. (2024). Mapping multimodal phenotypes to perturbations in cells and tissue with CRISPRmap. Nature Biotechnology. https://doi.org/10.1038/s41587-024-02386-x
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Kabeer, F., Tran, H., Andronescu, M., Singh, G., Lee, H., Salehi, S., Wang, B., Biele, J., Brimhall, J., Gee, D., Cerda, V., O’Flanagan, C., Algara, T., Kono, T., Beatty, S., Zaikova, E., Lai, D., Lee, E., … Moore, R. (2024). Single-cell decoding of drug induced transcriptomic reprogramming in triple negative breast cancers. Genome Biology, 25(1). https://doi.org/10.1186/s13059-024-03318-3
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Wang, Q., Antone, J., Alsop, E., Reiman, R., Funk, C., Bendl, J., Dudley, J. T., Liang, W. S., Karr, T. L., Roussos, P., Bennett, D. A., De Jager, P. L., Serrano, G. E., Beach, T. G., Van Keuren-Jensen, K., Mastroeni, D., Reiman, E. M., & Readhead, B. P. (2024). Single cell transcriptomes and multiscale networks from persons with and without Alzheimer’s disease. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-49790-0
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İş, Ö., Wang, X., Reddy, J. S., Min, Y., Yilmaz, E., Bhattarai, P., Patel, T., Bergman, J., Quicksall, Z., Heckman, M. G., Tutor-New, F. Q., Can Demirdogen, B., White, L., Koga, S., Krause, V., Inoue, Y., Kanekiyo, T., Cosacak, M. I., Nelson, N., … Ertekin-Taner, N. (2024). Gliovascular transcriptional perturbations in Alzheimer’s disease reveal molecular mechanisms of blood brain barrier dysfunction. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-48926-6
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Shannon, M. J., Eisman, S. E., Lowe, A. R., Sloan, T. F. W., & Mace, E. M. (2024). cellPLATO – an unsupervised method for identifying cell behaviour in heterogeneous cell trajectory data. Journal of Cell Science, 137(20). https://doi.org/10.1242/jcs.261887
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Ali, A. M., & Raza, A. (2024). scRNAseq and High-Throughput Spatial Analysis of Tumor and Normal Microenvironment in Solid Tumors Reveal a Possible Origin of Circulating Tumor Hybrid Cells. Cancers, 16(7), 1444. https://doi.org/10.3390/cancers16071444
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He, S., Jin, Y., Nazaret, A., Shi, L., Chen, X., Rampersaud, S., Dhillon, B. S., Valdez, I., Friend, L. E., Fan, J. L., Park, C. Y., Mintz, R. L., Lao, Y.-H., Carrera, D., Fang, K. W., Mehdi, K., Rohde, M., McFaline-Figueroa, J. L., Blei, D., … Azizi, E. (2024). Starfysh integrates spatial transcriptomic and histologic data to reveal heterogeneous tumor–immune hubs. Nature Biotechnology. https://doi.org/10.1038/s41587-024-02173-8
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Wu, X., & Zhang, H. (2024). Omics Approaches Unveiling the Biology of Human Atherosclerotic Plaques. The American Journal of Pathology, 194(4), 482–498. https://doi.org/10.1016/j.ajpath.2023.12.007
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Is, O., Wang, X., Reddy, J. S., Patel, T., Min, Y., Quicksall, Z., Heckman, M. G., Gao, J., Bergman, J., Da Mesquita, S. G. (Sandro D. M. F., Kizil, C., Bhattarai, P., Cosacak, M. I., Lee, A. J., Vardarajan, B. N., Mayeux, R., Koga, S., Kanekiyo, T., White, L. J., … Ertekin‐Taner, N. (2023). Gliovascular molecular alterations in Alzheimer’s disease: a cross‐tissue, cross‐species study. Alzheimer’s & Dementia, 19(S13). Portico. https://doi.org/10.1002/alz.073806
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Zhong, G., Choi, Y. A., & Shen, Y. (2023). VBASS enables integration of single cell gene expression data in Bayesian association analysis of rare variants. Communications Biology, 6(1). https://doi.org/10.1038/s42003-023-05155-9
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Green, G. S., Yang, H., Fujita, M., Taga, M., Regev, A., Menon, V., Bennett, D. A. A., Habib, N., & De Jager, P. L. (2023). Cellular dynamics across aged human brains uncover a multicellular cascade leading to Alzheimer’s disease. Alzheimer’s & Dementia, 19(S24). Portico. https://doi.org/10.1002/alz.083212
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Bhattarai, P., Cosacak, M. I., Lee, A. J., Yilmaz, E., Is, O., Wang, X., Vardarajan, B. N., Ertekin‐Taner, N., Mayeux, R., & Kizil, C. (2023). Functional investigation of the gliovascular niche‐related genes and their relevance to Alzheimer’s disease pathomechanisms in zebrafish. Alzheimer’s & Dementia, 19(S13). Portico. https://doi.org/10.1002/alz.073812
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Lopes, K. de P., Vialle, R. A., Green, G. S., Fujita, M., Wang, Y., Gaiteri, C., Menon, V., De Jager, P. L., Habib, N., Tasaki, S., & Bennett, D. A. A. (2023). Chasing the cell type‐specific molecular networks involved in Alzheimer’s Disease. Alzheimer’s & Dementia, 19(S12). Portico. https://doi.org/10.1002/alz.073444
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Wu, Y., Dumitrescu, L. C., De Jager, P. L., Menon, V., Schneider, J. A., Bennett, D. A. A., Petyuk, V. A., & Hohman, T. J. (2023). Single‐cell Transcriptomes Reveal Cell‐type Specific Roles of VEGF Family Genes in the Pathogenesis of Alzheimer’s Disease. Alzheimer’s & Dementia, 19(S12). Portico. https://doi.org/10.1002/alz.078447
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Chapman, O. S., Luebeck, J., Sridhar, S., Wong, I. T.-L., Dixit, D., Wang, S., Prasad, G., Rajkumar, U., Pagadala, M. S., Larson, J. D., He, B. J., Hung, K. L., Lange, J. T., Dehkordi, S. R., Chandran, S., Adam, M., Morgan, L., Wani, S., Tiwari, A., … Chavez, L. (2023). Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma. Nature Genetics, 55(12), 2189–2199. https://doi.org/10.1038/s41588-023-01551-3
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Mejia Saldarriaga, M., Unkenholz, C., Fein, J. A., Monge, J., Rosenbaum, C., Pearse, R., Mapara, M., Inghirami, G., Lentzsch, S., Reshef, R., Niesvizky, R., & Bustoros, M. (2023). Post CAR-T Peripheral Lymphocytosis and Its Kinetics Are a Potential Biomarker for Response and Immune Mediated Toxicities. Blood, 142(Supplement 1), 3341–3341. https://doi.org/10.1182/blood-2023-187832
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Rajbhandari, N., Hamilton, M., Quintero, C. M., Ferguson, L. P., Fox, R., Schürch, C. M., Wang, J., Nakamura, M., Lytle, N. K., McDermott, M., Diaz, E., Pettit, H., Kritzik, M., Han, H., Cridebring, D., Wen, K. W., Tsai, S., Goggins, M. G., Lowy, A. M., … Reya, T. (2023). Single-cell mapping identifies MSI+ cells as a common origin for diverse subtypes of pancreatic cancer. Cancer Cell, 41(11), 1989-2005.e9. https://doi.org/10.1016/j.ccell.2023.09.008
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Dugger, S. A., Dhindsa, R. S., Sampaio, G. D. A., Ressler, A. K., Rafikian, E. E., Petri, S., Letts, V. A., Teoh, J., Ye, J., Colombo, S., Peng, Y., Yang, M., Boland, M. J., Frankel, W. N., & Goldstein, D. B. (2023). Neurodevelopmental deficits and cell-type-specific transcriptomic perturbations in a mouse model of HNRNPU haploinsufficiency. PLOS Genetics, 19(10), e1010952. https://doi.org/10.1371/journal.pgen.1010952
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Chen, F., Köhler, M., Cucun, G., Takamiya, M., Kizil, C., Cosacak, M. I., & Rastegar, S. (2023). sox1a:eGFP transgenic line and single-cell transcriptomics reveal the origin of zebrafish intraspinal serotonergic neurons. IScience, 26(8), 107342. https://doi.org/10.1016/j.isci.2023.107342
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Touil, H., Roostaei, T., Calini, D., Diaconu, C., Epstein, S., Raposo, C., Onomichi, K., Thakur, K. T., Craveiro, L., Callegari, I., Bryois, J., Riley, C. S., Menon, V., Derfuss, T., De Jager, P. L., & Malhotra, D. (2023). A structured evaluation of cryopreservation in generating single-cell transcriptomes from cerebrospinal fluid. Cell Reports Methods, 3(7), 100533. https://doi.org/10.1016/j.crmeth.2023.100533
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Chen, Z., Zhang, B., Gong, F., Wan, L., & Ma, L. (2023). RobustTree: An adaptive, robust PCA algorithm for embedded tree structure recovery from single-cell sequencing data. Frontiers in Genetics, 14. https://doi.org/10.3389/fgene.2023.1110899
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Paquelet, G. E., Carrion, K., Lacefield, C. O., Zhou, P., Hen, R., & Miller, B. R. (2023). Protocol for in vivo imaging and analysis of brainstem neuronal activity in the dorsal raphe nucleus of freely behaving mice. STAR Protocols, 4(1), 102074. https://doi.org/10.1016/j.xpro.2023.102074
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Bukhari, S., Henick, B. S., Winchester, R. J., Lerrer, S., Adam, K., Gartshteyn, Y., Maniar, R., Lin, Z., Khodadadi-Jamayran, A., Tsirigos, A., Salvatore, M. M., Lagos, G. G., Reiner, S. L., Dallos, M. C., Mathew, M., Rizvi, N. A., & Mor, A. (2023). Single-cell RNA sequencing reveals distinct T cell populations in immune-related adverse events of checkpoint inhibitors. Cell Reports Medicine, 4(1), 100868. https://doi.org/10.1016/j.xcrm.2022.100868
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Limone, F., Guerra San Juan, I., Mitchell, J. M., Smith, J. L. M., Raghunathan, K., Meyer, D., Ghosh, S. D., Couto, A., Klim, J. R., Joseph, B. J., Gold, J., Mello, C. J., Nemesh, J., Smith, B. M., Verhage, M., McCarroll, S. A., Pietiläinen, O., Nehme, R., & Eggan, K. (2023). Efficient generation of lower induced motor neurons by coupling Ngn2 expression with developmental cues. Cell Reports, 42(1), 111896. https://doi.org/10.1016/j.celrep.2022.111896
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Lee, P. J., Benz, C. C., Blood, P., Börner, K., Campisi, J., Chen, F., Daldrup-Link, H., De Jager, P., Ding, L., Duncan, F. E., Eickelberg, O., Fan, R., Finkel, T., Furman, D., Garovic, V., Gehlenborg, N., Glass, C., … Yang, M. (2022). NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health. Nature Aging, 2(12), 1090–1100. https://doi.org/10.1038/s43587-022-00326-5
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Pandit, K., Petrescu, J., Cuevas, M., Stephenson, W., Smibert, P., Phatnani, H., & Maniatis, S. (2022). An open source toolkit for repurposing Illumina sequencing systems as versatile fluidics and imaging platforms. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-08740-w
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Sheng, J., Hod, E. A., Vlad, G., & Chavez, A. (2022). Quantifying protein abundance on single cells using split-pool sequencing on DNA-barcoded antibodies for diagnostic applications. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-04842-7
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Kabir, M. F., Karami, A. L., Cruz-Acuña, R., Klochkova, A., Saxena, R., Mu, A., Murray, M. G., Cruz, J., Fuller, A. D., Clevenger, M. H., Chitrala, K. N., Tan, Y., Keith, K., Madzo, J., Huang, H., Jelinek, J., Karakasheva, T., Hamilton, K. E., Muir, A. B., … Whelan, K. A. (2022). Single cell transcriptomic analysis reveals cellular diversity of murine esophageal epithelium. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-29747-x
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Ostkamp, P., Deffner, M., Schulte-Mecklenbeck, A., Wünsch, C., Lu, I.-N., Wu, G. F., Goelz, S., De Jager, P. L., Kuhlmann, T., Gross, C. C., Klotz, L., Meyer zu Hörste, G., Wiendl, H., Schneider-Hohendorf, T., & Schwab, N. (2022). A single-cell analysis framework allows for characterization of CSF leukocytes and their tissue of origin in multiple sclerosis. Science Translational Medicine, 14(673). https://doi.org/10.1126/scitranslmed.adc9778
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Peereboom, D., Lindsay, R., Badruddoja, M., Nabors, L. B., Kumthekar, P., Lieberman, F., Tran, D., Phuphanich, S., Schiff, D., Sherman, J., Butowski, N., Dunbar, E., Fink, K., Iwamoto, F., Moertel, C., Schulder, M., Walbert, T., Habboubi, N., Grzegorzewski, K., … Reardon, D. A. (2022). CTIM-29. PHASE 2 STUDY OF A NOVEL IMMUNOTHERAPY SL-701 IN ADULTS WITH RECURRENT GBM: IDENTIFICATION OF TREATMENT-INDUCED CD8+CD107A+ CD57+ PD-1- MEMORY T-CELLS THAT ARE ASSOCIATED WITH INCREASED SURVIVAL. Neuro-Oncology, 24(Supplement_7), vii67–vii67. https://doi.org/10.1093/neuonc/noac209.261
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Lakkis, J., Schroeder, A., Su, K., Lee, M. Y. Y., Bashore, A. C., Reilly, M. P., & Li, M. (2022). A multi-use deep learning method for CITE-seq and single-cell RNA-seq data integration with cell surface protein prediction and imputation. Nature Machine Intelligence, 4(11), 940–952. https://doi.org/10.1038/s42256-022-00545-w
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Miller, A. M., Szalontay, L., Bouvier, N., Hill, K., Ahmad, H., Rafailov, J., Lee, A. J., Rodriguez-Sanchez, M. I., Yildirim, O., Patel, A., Bale, T. A., Benhamida, J. K., Benayed, R., Arcila, M. E., Donzelli, M., Dunkel, I. J., Gilheeney, S. W., Khakoo, Y., Kramer, K., … Karajannis, M. A. (2022). Next-generation sequencing of cerebrospinal fluid for clinical molecular diagnostics in pediatric, adolescent and young adult brain tumor patients. Neuro-Oncology, 24(10), 1763–1772. https://doi.org/10.1093/neuonc/noac035
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Li, Z., Wang, D., Guo, W., Zhang, S., Chen, L., Zhang, Y.-H., Lu, L., Pan, X., Huang, T., & Cai, Y.-D. (2022). Identification of cortical interneuron cell markers in mouse embryos based on machine learning analysis of single-cell transcriptomics. Frontiers in Neuroscience, 16. https://doi.org/10.3389/fnins.2022.841145
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Cosacak, M. I., Bhattarai, P., De Jager, P. L., Menon, V., Tosto, G., & Kizil, C. (2022). Single Cell/Nucleus Transcriptomics Comparison in Zebrafish and Humans Reveals Common and Distinct Molecular Responses to Alzheimer’s Disease. Cells, 11(11), 1807. https://doi.org/10.3390/cells11111807
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