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Identification and Validation of a Prognostic Signature Based on Fibroblast Immune-related Genes to Predict the Prognosis and Therapeutic Response of renal clear cell carcinoma by Integrated Analysis of Single-Cell and Bulk RNA Sequencing Data

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Down-regulation of ATP8B2 in Foam Cells Inhibits Autophagic Flux and ox-LDL Degradation in Atherosclerosis

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Toti-N-glycan Recognition Enables Universal Multiplexed Single-Nucleus RNA Sequencing

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Using Cell Type–Specific Genes to Identify Cell-Type Transitions Between Different in vitro Culture Conditions

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Proliferative and quiescent human gastric cancer stem-like cells are associated with differential chemoresistance and patient mortalityPreprint

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Community Detection in a Weighted Directed Hypergraph Representation of Cell-to-cell Communication NetworksPreprint

Hou, R., SMALL, M. P., & Forrest, A. R. R. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.16.381566 · Cited by 1

Identification of Pathways and Genes Associated with Chemoradiotherapy in Locally Advanced Cervical CancerPreprint

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Absolute Scaling of Single-Cell Transcriptomes Reveals Pervasive Hypertranscription in Adult Stem and Progenitor CellsPreprint

Kim, Y., & Ramalho‐Santos, M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.13.472426 · Cited by 1

MiXcan: a Framework for Cell-Type-Specific Transcriptome-Wide Association Studies with an Application to Breast CancerPreprint

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Identification of Key Genes and Pathways associated with Chemotherapy and Radiotherapy Sensitivity in Locally Advanced Cervical CancerPreprint

Zhang, Z., Zhang, Y., Ma, Y., Xiang, S., Shen, J., Zhao, Y., Wu, X., Li, M., Yang, X., Kaboli, P. J., et al. (2020) · Research Square · doi:10.21203/rs.3.rs-120262/v1 · Cited by 1

A Statistical Framework to Identify Cell Types Whose Genetically Regulated Proportions are Associated with Complex DiseasesPreprint

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Adaptation to ex vivo culture drives human haematopoietic stem cell loss of repopulation capacity in a cell cycle independent mannerPreprint

Johnson, C. S., Sham, K., Belluschi, S., Wang, X., Lau, W. W. Y., Kaufmann, K. B., Krivdova, G., Calderbank, E. F., Mende, N., McLeod, J. L., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.17.516906 · Cited by 1

Transcriptional signals of dedifferentiation in human cancerPreprint

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Single-cell heterogeneity and dynamic evolution of Ph-like acute lymphoblastic leukemia patient with novel TPR-PDGFRB fusion genePreprint

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Amniotic Fluid Organoids As Personalized Tools For Real-Time Modeling Of The Developing FetusPreprint

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HIPSD&R-seq enables scalable genomic copy number and transcriptome profilingPreprint

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Landscape and functional repertoires of long noncoding RNAs in the pan-cancer tumor microenvironment using single-nucleus total RNA sequencingPreprint

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Idiosyncratic and generic single nuclei and spatial transcriptional patterns in papillary and anaplastic thyroid cancersPreprint

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Single-cell Landscape of Malignant Transition: Unraveling Cancer Cell-of-Origin and Heterogeneous Tissue MicroenvironmentPreprint

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Adversarial learning enables unbiased organism-wide cross-species alignment of single-cell RNA data at scalePreprint

Díaz-Mejía, J. J., Williams, E., Innes, B. T., Focsa, O., Mendonca, D., Singh, S., Nixon, A. M. L., Schuster, R., Buechler, M. B., Hinz, B., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.11.607498 · Cited by 1

A universal single-cell transcriptomics atlas of human lung decodes multiple pulmonary diseasesPreprint

Wu, F., Cai, W., Tang, H. C., Zheng, S., Zhang, H., Chen, Y., Han, Y., Zhou, D., Wang, R., Ye, M., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.17.628654 · Cited by 1

Single-cell resolution transcriptional atlases of aerial and subterranean pegs reveals auxin signaling associated with peg development in peanutPreprint

Jin, W., Xu, M., Huang, L., Zhou, Y., Xiao, Y., Zhong, W., Liang, Y., Zheng, Z., Li, H., Yu, Q., et al. (2025) · Research Square · doi:10.21203/rs.3.rs-5752647/v1 · Cited by 1

Asthma Exacerbations: Integrative Analysis of Mirna Activity in Using Single-cell Transcriptomics

Hadikhani, P., Yan, X., Chupp, G. L., Liu, Q., Ban, G., Piparia, S., McGeachie, M. J., Sharma, R., Weiss, S. T., Kho, A. T., et al. (2025) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/ajrccm.2025.211.abstracts.a7773 · Cited by 1

XChrom: A Cross‐Cell Chromatin Accessibility Prediction Model Integrating Genomic Sequence and Cellular Context

Miao, Y., Liang, X., Zhang, W., Han, D., Li, Y., & Wang, Z. (2026) · Advanced Science · doi:10.1101/2025.11.18.689149 · Cited by 1

GPTAnno: Ontology-tree-guided hierarchical cell type annotation based on GPT models for single-cell dataPreprint

Song, Y., Tang, M., Liu, Q., Wang, H., Li, Q., Zou, F., & Hou, W. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.27.690951 · Cited by 1

Identification of cell types associated with 14 brain phenotypes from more than 10 million single cellsPreprint

Phung, T. N., Seoane, S. L., Li, W.-P., Brouwer, R. M., & Posthuma, D. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.05.692533 · Cited by 1

Sexually dimorphic alternative splicing and its erosion following the loss of sex in stick insectsPreprint

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Integrated single-cell transcriptomic atlas of human gastric and colorectal tissues across diverse phenotypes

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H2O: A Foundation Model Bridging Histopathology to Spatial Multi-Omics ProfilingPreprint

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Placental molecular subtypes of severe preeclampsia reveal divergent aging trajectories and fetal growth outcomesPreprint

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Charting the human cell landscape

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Surveying the human single-cell landscape

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Single-cell analysis of mRNA splicing variants

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Fundamentals of extrachromosomal circular DNA in human cells - Genetic activities as regards cancer promotion alongside chromosomal DNA

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SPINT2 controls SARS-CoV-2 viral infection and is associated to disease severityPreprint

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Nucleocytoplasmic Transport of RNA-Binding Proteins Regulates Neural Stem Cell FatesPreprint

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EcTracker: Tracking and elucidating ectopic expression leveraging large-scale scRNA-seq studies

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Pan-cancer landscape of AID-related mutations, composite mutations and its potential role in the ICI responsePreprint

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miRSCAPE - Inferring miRNA expression in single-cell clustersPreprint

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