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Dissecting the human leptomeninges at single-cell resolution

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CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis

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Single-cell transcriptomics and epigenomics unravel the role of monocytes in neuroblastoma bone marrow metastasis

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Single-cell transcriptomic and chromatin dynamics of the human brain in PTSD

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Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology

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Fetal brain response to maternal inflammation requires microglia

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Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha

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Integrated single-cell transcriptomics of cerebrospinal fluid cells in treatment-naïve multiple sclerosis

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Single-cell chromatin accessibility and transposable element landscapes reveal shared features of tissue-residing immune cells

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Microbial signals in primary and metastatic brain tumors

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Cellxgene VIP unleashes full power of interactive visualization and integrative analysis of scRNA-seq, spatial transcriptomics, and multiome dataPreprint

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Collagen signaling and matrix stiffness regulate multipotency in glandular epithelial stem cells in mice

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Recommendations of scRNA-seq Differential Gene Expression Analysis Based on Comprehensive Benchmarking

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Single-nucleus RNA sequencing demonstrates an autosomal dominant Alzheimer’s disease profile and possible mechanisms of disease protection

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Modeling type 1 diabetes progression using machine learning and single-cell transcriptomic measurements in human islets

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Transcriptomic and spatial dissection of human ex vivo right atrial tissue reveals proinflammatory microvascular changes in ischemic heart disease

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Single-nucleus multi-omics of Parkinson’s disease reveals a glutamatergic neuronal subtype susceptible to gene dysregulation via alteration of transcriptional networks

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Targeting Piezo1 channel to alleviate intervertebral disc degeneration

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Mature and migratory dendritic cells promote immune infiltration and response to anti-PD-1 checkpoint blockade in metastatic melanoma

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Amygdala–liver signalling orchestrates glycaemic responses to stress

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An autoimmune transcriptional circuit drives FOXP3 + regulatory T cell dysfunction

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Single-cell sequencing reveals cellular landscape alterations in the airway mucosa of patients with pulmonary long COVID

Gerayeli, F. V., Park, H. Y., Milne, S. B., Li, X., Yang, C. X., Tuong, J., Eddy, R. L., Vahedi, S. M., Guinto, E., Cheung, C. Y., et al. (2024) · European Respiratory Journal · doi:10.1183/13993003.01947-2023 · Cited by 22 · see citing works

Allele-specific analysis reveals exon- and cell-type-specific regulatory effects of Alzheimer’s disease-associated genetic variants

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Single-cell analysis of chromatin and expression reveals age- and sex-associated alterations in the human heart

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Systematic analysis of cellular cross-talk reveals a role for SEMA6D-TREM2 regulating microglial function in Alzheimer’s disease

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Single-cell anatomical analysis of human hippocampus and entorhinal cortex uncovers early-stage molecular pathology in Alzheimer’s diseasePreprint

Dávila-Velderrain, J., Mathys, H., Mohammadi, S., Ruzicka, B., Jiang, X., Ng, A. P., Bennett, D. A., Tsai, L., & Kellis, M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.01.450715 · Cited by 19 · see citing works

Transcriptomic profiling after B cell depletion reveals central and peripheral immune cell changes in multiple sclerosis

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The microbial metabolite desaminotyrosine protects against graft-versus-host disease via mTORC1 and STING-dependent intestinal regeneration

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A systematic comparison of novel and existing differential analysis methods for CyTOF data

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Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies

Guo, X., Ning, J., Chen, Y., Liu, G., Zhao, L., Fan, Y., & Sun, S. (2023) · Briefings in Functional Genomics · doi:10.1093/bfgp/elad011 · Cited by 18 · see citing works

Best practices for differential accessibility analysis in single-cell epigenomics

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Single-nucleus RNA-seq identifies one galanin neuronal subtype in mouse preoptic hypothalamus activated during recovery from sleep deprivation

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Association of ten VEGF family genes with Alzheimer's disease endophenotypes at single cell resolution

Wu, Y., Libby, J. B., Dumitrescu, L. C., Jager, P. L. D., Menon, V., Schneider, J. A., Bennett, D. A., & Hohman, T. J. (2024) · Alzheimer s & Dementia · doi:10.1002/alz.14419 · Cited by 14 · see citing works

A single-cell multiomic analysis identifies molecular and gene-regulatory mechanisms dysregulated in developing Down syndrome neocortex

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4R-tau seeding activity reveals molecular subtypes in progressive supranuclear palsy

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Single-cell analysis reveals lasting immunological consequences of influenza infection and respiratory immunization in the pig lung

Muir, A., Paudyal, B., Schmidt, S., Sedaghat-Rostami, E., Chakravarti, S., Villanueva-Hernández, S., Moffat, K., Polo, N., Angelopoulos, N., Schmidt, A. P., et al. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1011910 · Cited by 13 · see citing works

Molecular and cellular processes disrupted in the early postnatal Down syndrome prefrontal cortex

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A phenotypic brain organoid atlas and biobank for neurodevelopmental disorders

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Recurrent patterns of TOP1-mediated neuronal genomic damage shared by major neurodegenerative disorders

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Pseudobulk with proper offsets has the same statistical properties as generalized linear mixed models in single-cell case-control studies

Lee, H., & Han, B. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae498 · Cited by 11 · see citing works

Coupling of response biomarkers between tumor and peripheral blood in patients undergoing chemoimmunotherapy

Chin, W. L., Cook, A., Chee, J., Principe, N., Hoang, T. S., Kidman, J., Hmon, K. P. W., Yeow, Y. L., Jones, M. E., Hou, R., et al. (2024) · Cell Reports Medicine · doi:10.1016/j.xcrm.2024.101882 · Cited by 11 · see citing works

A rat liver cell atlas reveals intrahepatic myeloid heterogeneity

Pouyabahar, D., Chung, S., Pezzutti, O. I., Perciani, C. T., Wang, X., Ma, X., Jiang, C., Camat, D., Chung, T., Sekhon, M., et al. (2023) · iScience · doi:10.1016/j.isci.2023.108213 · Cited by 11 · see citing works

4R-Tau seeding activity unravels molecular subtypes in patients with Progressive Supranuclear PalsyPreprint

Martínez-Valbuena, I., Lee, S., Santamaría, E., Fernández‐Irigoyen, J., Forrest, S. L., Li, J., Tanaka, H., Couto, B., Reyes, N. G. D., Qamar, S. H., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.28.559953 · Cited by 11 · see citing works

Dynamic changes of the immune microenvironment in the development of gastric cancer caused by inflammation

Gan, S., Li, C., Hou, R., Tian, G., Zhao, Y., Ren, D., Zhou, W., Zhao, F. L., Lv, K., & Yang, J. (2024) · Molecular Therapy Oncology · doi:10.1016/j.omton.2024.200849 · Cited by 10 · see citing works

A landscape of the genetic and cellular heterogeneity in Alzheimer diseasePreprint

Brase, L., You, S., Albanus, R. D., Del‐Aguila, J. L., Dai, Y., Novotny, B. C., Soriano‐Tárraga, C., Dykstra, T., Fernández, M. V., Budde, J., et al. (2021) · medRxiv · doi:10.1101/2021.11.30.21267072 · Cited by 10 · see citing works

Differential Expression Analysis for Spatially Correlated DataPreprint

Vasconcelos, A. G., McGuire, D., Simon, N., Danaher, P. J., & Shojaie, A. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.02.606405 · Cited by 10 · see citing works

Chromatin accessibility provides a window into the genetic etiology of human brain disease

Bendl, J. M., Fullard, J. F., Girdhar, K., Dong, P., Kosoy, R., Zeng, B., Hoffman, G. E., & Roussos, P. (2025) · Trends in Genetics · doi:10.1016/j.tig.2025.01.001 · Cited by 9 · see citing works

Integrative single-cell and spatial transcriptome analysis reveals the functions of TREM2high macrophages and infarct border dynamics post-myocardial infarction

Xiong, T., Chen, Y., Liu, C., Li, Y., Zhang, Y., & Chang, Q. (2025) · Molecular and Cellular Biochemistry · doi:10.1007/s11010-025-05317-9 · Cited by 9 · see citing works

Microglial States Are Susceptible to Senescence and Cholesterol Dysregulation in Alzheimer's Disease

Li, B., Wang, S., Kerman, B. E., Hugo, C., Shwab, E. K., Shu, C., Chiba‐Falek, O., Arvanitakis, Z., & Yassine, H. N. (2025) · Aging Cell · doi:10.1111/acel.70189 · Cited by 9 · see citing works

4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy

Cha, J., Kim, C. G., Sim, N. S., Kim, G., Son, W., Kim, D., Jung, Y., Hong, H. J., Lee, H. B., Kim, J., et al. (2025) · Cell Reports Medicine · doi:10.1016/j.xcrm.2025.102408 · Cited by 14 · see citing works

Exploring cellular heterogeneity: single-cell and spatial transcriptomics of Alzheimer's disease brains and iPSC-derived microglia

Garg, A., Vo, S., de Souza, I. D., Brant, A. C., Brase, L., Aladyeva, E., Albanus, R. D., Nallapu, A., Fu, H., & Harari, O. (2025) · Alzheimer s Research & Therapy · doi:10.1186/s13195-025-01944-y · Cited by 11 · see citing works

scViewer: An Interactive Single-Cell Gene Expression Visualization Tool

Patil, A. R., Kumar, G., Zhou, H., & Warren, L. L. (2023) · Cells · doi:10.3390/cells12111489 · Cited by 9 · see citing works

Detecting Fear-Memory-Related Genes from Neuronal scRNA-seq Data by Diverse Distributions and Bhattacharyya Distance

Zhang, S., Xie, L., Cui, Y., Carone, B. R., & Chen, Y. (2022) · Biomolecules · doi:10.3390/biom12081130 · Cited by 9 · see citing works

Using individual barcodes to increase quantification power of massively parallel reporter assays

Keukeleire, P., Rosen, J. D., Göbel-Knapp, A., Salomon, K., Schubach, M., & Kircher, M. (2025) · BMC Bioinformatics · doi:10.1186/s12859-025-06065-9 · Cited by 8 · see citing works

scRNASequest: an ecosystem of scRNA-seq analysis, visualization, and publishing

Li, K., Sun, Y. H., Ouyang, Z., Negi, S., Gao, Z., Zhu, J., Wang, W., Chen, Y., Piya, S., Hu, W., et al. (2023) · BMC Genomics · doi:10.1186/s12864-023-09332-2 · Cited by 8 · see citing works

Single-cell eQTL mapping in yeast reveals a tradeoff between growth and reproduction

Boocock, J., Alexander, N., Tapia, L. A., Walter-McNeill, L., Patel, S. P., Munugala, C., Bloom, J. S., & Kruglyak, L. (2025) · eLife · doi:10.7554/elife.95566.3 · Cited by 7 · see citing works

Single-cell RNA-seq reveals the metabolic status of immune cells response to immunotherapy in triple-negative breast cancer

Liu, P.-W., Lin, J., Hou, R., Cai, Z., Gong, Y., He, P., & Yang, J. (2024) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2024.107926 · Cited by 7 · see citing works

A multi-omics and cell type-specific characterization of the ventral striatum in human cocaine use disorder

Zillich, E., Artioli, A., Rossetti, A. C., Avetyan, D., Belschner, H., Frank, J., Stein, F., Schwarz, J., Mechawar, N., Turecki, G., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115332 · Cited by 6 · see citing works

miRglmm: a generalized linear mixed model of isomiR-level counts improves estimation of miRNA-level differential expression and uncovers variable differential expression between isomiRs

Baran, A. M., Patil, A. H., Aparicio‐Puerta, E., Jun, S.-H., Halushka, M. K., & McCall, M. N. (2025) · Genome biology · doi:10.1186/s13059-025-03549-y · Cited by 6 · see citing works

Intercellular signaling and synaptic deconstruction uncovered by single-cell and spatial transcriptomics in an AD tauopathy model

Ji, J. X., Giles, B. L., Bhattacharjee, S., Kautzmann, M.-A. I., Masson, A. P., Carmo, S. D., Cuello, A. C., & Bazan, N. G. (2025) · Communications Biology · doi:10.1038/s42003-025-08959-z · Cited by 6 · see citing works

Four-dimensional molecular mapping from a spatial snapshot reveals the dynamics of hair follicle organogenesis

Asami, S., Yin, C., Fan, J., Garza, L. A., & Kalhor, R. (2026) · Cell · doi:10.1016/j.cell.2026.06.014 · Cited by 6 · see citing works

Root Causal Inference from Single Cell RNA Sequencing with the Negative Binomial

Strobl, E. V. (2023) · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) · doi:10.1145/3584371.3612972 · Cited by 6 · see citing works

Computational single cell oncology: state of the art

Paas-Oliveros, E., Lemus, E. H., & de Anda‐Jáuregui, G. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1256991 · Cited by 6 · see citing works

Single‐cell landscape of sex‐specific drivers of Alzheimer's disease

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Single-cell atlas of the developing Down syndrome brain cortex

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Systems Analysis of Immune Changes after B-cell Depletion in Autoimmune Multiple SclerosisPreprint

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Identification of a therapeutic threshold for AAV-STXBP1 gene therapy in a rodent model of STXBP1 developmental and epileptic encephalopathy

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Lactate metabolism links reactive microglia, amyloid pathology, and Aβ dynamics

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Sex differences in progressive multiple sclerosis brain gene expression in oligodendrocytes and OPCs

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Hippocampus Glutathione S Reductase Potentially Confers Genetic Resilience to Cognitive Decline in the AD-BXD Mouse PopulationPreprint

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Elucidating early intestinal stem cell response to bacterial infectionPreprint

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Single-cell RNA-sequencing reveals adventitial fibroblast alterations during mouse atherosclerosis

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Aging, Rather than Genotype, Is the Principal Contributor to Differential Gene Expression Within Targeted Replacement APOE2, APOE3, and APOE4 Mouse Brain

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Differential expression analysis for spatially correlated data using smiDE

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An inflammasome-driven differentiation program in intestinal stem cells protects against Salmonella infection

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Efficient differential expression analysis of large-scale single-cell transcriptomics data using Dreamlet

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Recommendations of scRNA-seq Differential Gene Expression Analysis Based on Comprehensive Benchmarking

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A deep generative model for gene expression profiles from single-cell RNA sequencingPreprint

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A deep generative model for single-cell RNA sequencing with application to detecting differentially expressed genesPreprint

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