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  1. CNVPipe: An enhanced pipeline for accurate analysis of copy number variation from whole-genome sequencing

    Article • May 2025, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  2. Single-cell transcriptomics reveals a compartmentalized antiviral interferon response in the nasal epithelium of mice

    Article • Journal of Virology, March 2025, ASM Journals

    Prof. Wenfei Jin

  3. Unveiling two distinct osteolineage cell populations linked to age-related osteoporosis in adult mice through integrative single-cell analyses

    Article • Cellular and Molecular Life Sciences, March 2025, Springer Science + Business Media

    Prof. Wenfei Jin

  4. Single-cell transcriptomic analysis of chondrocytes in cartilage and pathogenesis of osteoarthritis

    Article • Genes & Diseases, March 2025, Tsinghua University Press

    Prof. Wenfei Jin

  5. Graph-based Contrastive Learning Enables Unified Integration and Niche Transfer Across Single-Cell and Spatial Multi-Omics

    Article • February 2025, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  6. Protocol for mapping T cell activation using single-cell RNA-seq

    Article • STAR Protocols, December 2024, Elsevier

    Prof. Wenfei Jin

  7. A catalog of gene editing sites and genetic variations in editing sites in model organisms

    Article • BMC Genomics, November 2024, Springer Science + Business Media

    Prof. Wenfei Jin

  8. scMMO-atlas: a single cell multimodal omics atlas and portal for exploring fine cell heterogeneity and cell dynamics

    Article • Nucleic Acids Research, September 2024, Oxford University Press (OUP)

    Prof. Wenfei Jin

  9. Decreased GATA3 levels cause changed mouse cutaneous innate lymphoid cell fate, facilitating hair follicle recycling

    Article • Developmental Cell, July 2024, Elsevier

    Prof. Wenfei Jin

  10. Single cell analyses of cancer cells identified two regulatorily and functionally distinct categories in differentially expressed genes among tumor subclones

    Article • Heliyon, March 2024, Elsevier

    Prof. Wenfei Jin

  11. The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis

    Article • Nucleic Acids Research, February 2024, Oxford University Press (OUP)

    Prof. Wenfei Jin

  12. Sirpα on tumor-associated myeloid cells restrains antitumor immunity in colorectal cancer independent of its interaction with CD47

    Article • Nature Cancer, January 2024, Springer Science + Business Media

    Prof. Wenfei Jin

  13. The bone–liver interaction modulates immune and hematopoietic function through Pinch-Cxcl12-Mbl2 pathway

    Article • Cell Death and Differentiation, December 2023, Springer Science + Business Media

    Prof. Wenfei Jin

  14. Proline uptake promotes activation of lymphoid tissue inducer cells to maintain gut homeostasis

    Article • Nature Metabolism, October 2023, Springer Science + Business Media

    Prof. Wenfei Jin

  15. The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis

    Article • October 2023, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  16. Differentiation and migration of hematopoietic stem and progenitor cells cross multiple tissues

    Article • September 2023, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  17. Exploring the dynamics and influencing factors of CD4 T cell activation using single-cell RNA-seq

    Article • iScience, September 2023, Elsevier

    Prof. Wenfei Jin

  18. A fast and globally optimal solution for RNA-seq quantification

    Article • Briefings in Bioinformatics, August 2023, Oxford University Press (OUP)

    Prof. Wenfei Jin

  19. Progress in single-cell multimodal sequencing and multi-omics data integration

    Article • Biophysical Reviews, July 2023, Springer Science + Business Media

    Prof. Wenfei Jin

  20. Glucose-induced CRL4COP1-p53 axis amplifies glycometabolism to drive tumorigenesis

    Article • Molecular Cell, July 2023, Elsevier

    Prof. Wenfei Jin

  21. Single cell analyses of cancer cells identified two regulatorily and functionally distinct categories in differentially expressed genes among tumor subclones

    Article • April 2023, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  22. Anti-PD-1 therapy achieves favorable outcomes in HBV-positive non-liver cancer

    Article • Oncogenesis, April 2023, Springer Science + Business Media

    Prof. Wenfei Jin

  23. Mapping of alternative polyadenylation site usage at single-cell resolution

    Article • Proceedings of the National Academy of Sciences, December 2022, Proceedings of the National Academy of Sciences

    Prof. Wenfei Jin

  24. Dissecting Complex Traits Using Omics Data: A Review on the Linear Mixed Models and Their Application in GWAS

    Article • Plants, November 2022, MDPI AG

    Dr. Md. Alamin, Prof. Wenfei Jin

  25. ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells

    Article • Nature Chemical Biology, September 2022, Springer Science + Business Media

    Prof. Wenfei Jin

  26. Sensitive, flexible and modular single-cell multi-omics profiling with ISSAAC-seq

    Article • Nature Chemical Biology, September 2022, Springer Science + Business Media

    Prof. Wenfei Jin

  27. Dynamics, signals and influencing factors of CD4 T cell activation revealed by single cell RNA-seq

    Article • August 2022, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  28. Anti-PD1 therapy achieved better outcomes in non-liver cancer patients with HBV infection

    Article • August 2022, Research Square

    Prof. Wenfei Jin

  29. Single-Cell RNA Sequencing Unravels Upregulation of Immune Cell Crosstalk in Relapsed Pediatric Ependymoma

    Article • Frontiers in Immunology, June 2022, Frontiers

    Prof. Wenfei Jin

  30. Single-cell RNA Sequencing of Pediatric Ependymoma Unravels Subclonal Heterogeneity Associated with Patient Survival

    Article • March 2022, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  31. ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells

    Article • January 2022, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  32. Cross-Tissue Characterization of Heterogeneities of Mesenchymal Stem Cells and Their Differentiation Potentials

    Article • Frontiers in Cell and Developmental Biology, December 2021, Frontiers

    Prof. Wenfei Jin

  33. Reinvestigation of Classic T Cell Subsets and Identification of Novel Cell Subpopulations by Single-Cell RNA Sequencing

    Article • The Journal of Immunology, December 2021, The American Association of Immunologists

    Prof. Wenfei Jin

  34. Comprehensive mapping of the alternative polyadenylation site usage and its dynamics at single cell resolution

    Article • December 2021, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  35. A Comprehensive Characterization of Monoallelic Expression During Hematopoiesis and Leukemogenesis via Single-Cell RNA-Sequencing

    Article • Frontiers in Cell and Developmental Biology, October 2021, Frontiers

    Prof. Wenfei Jin

  36. A topology-preserving dimensionality reduction method for single-cell RNA-seq data using graph autoencoder

    Article • Scientific Reports, October 2021, Springer Science + Business Media

    Prof. Wenfei Jin

  37. The Tyrosine Kinase-Driven Networks of Novel Long Non-coding RNAs and Their Molecular Targets in Myeloproliferative Neoplasms

    Article • Frontiers in Cell and Developmental Biology, August 2021, Frontiers

    Prof. Wenfei Jin

  38. A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility

    Article • Nature Protocols, July 2021, Springer Science + Business Media

    Prof. Wenfei Jin

  39. Mesenchymal stem cell subpopulations and their heterogeneity of response to inductions revealed by single-cell RNA-seq

    Article • May 2021, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  40. Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis

    Article • March 2021, Springer Science + Business Media

    Prof. Wenfei Jin

  41. scGAE: topology-preserving dimensionality reduction for single-cell RNA-seq data using graph autoencoder

    Article • February 2021, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  42. Re-investigation of classic T cell subsets and identification of novel cell subpopulations by single-cell RNA sequencing

    Article • February 2021, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  43. Integrated decoding hematopoiesis and leukemogenesis using single-cell sequencing and its medical implication

    Article • Cell Discovery, January 2021, Springer Science + Business Media

    Prof. Wenfei Jin

  44. Kindlin-2 regulates skeletal homeostasis by modulating PTH1R in mice

    Article • Signal Transduction and Targeted Therapy, December 2020, Springer Science + Business Media

    Prof. Wenfei Jin

  45. Reclassification of classic T cell subsets and identification of novel cell types by single-cell RNA sequencing

    Article • October 2020, Research Square

    Prof. Wenfei Jin

  46. Single-Cell Transcriptome Analysis Reveals Six Subpopulations Reflecting Distinct Cellular Fates in Senescent Mouse Embryonic Fibroblasts

    Article • Frontiers in Genetics, August 2020, Frontiers

    Prof. Wenfei Jin

  47. Diploid genome architecture revealed by multi-omic data of hybrid mice

    Article • Genome Research, August 2020, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  48. Inhibition of Glycolysis in Pathogenic TH17 Cells through Targeting a miR -21–Peli1–c-Rel Pathway Prevents Autoimmunity

    Article • The Journal of Immunology, June 2020, The American Association of Immunologists

    Prof. Wenfei Jin

  49. The MicroRNA miR-22 Represses Th17 Cell Pathogenicity by Targeting PTEN-Regulated Pathways

    Article • ImmunoHorizons, June 2020, The American Association of Immunologists

    Prof. Wenfei Jin

  50. Integrated decoding hematopoiesis and leukemogenesis at single-cell resolution and its clinical implication

    Article • February 2020, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  51. Focal adhesion protein Kindlin-2 regulates bone homeostasis in mice

    Article • Bone Research, January 2020, Springer Science + Business Media

    Prof. Wenfei Jin

  52. H4K20me3 methyltransferase SUV420H2 shapes the chromatin landscape of pluripotent embryonic stem cells

    Article • Development, January 2020, The Company of Biologists

    Prof. Wenfei Jin

  53. Visualization of Single Cell RNA-Seq Data Using t-SNE in R

    Article • January 2020, Springer Science + Business Media

    Prof. Wenfei Jin

  54. Exploring the Changing Landscape of Cell-to-Cell Variation After CTCF Knockdown via Single Cell RNA-seq

    Article • December 2019, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  55. Exploring the changing landscape of cell-to-cell variation after CTCF knockdown via single cell RNA-seq

    Article • BMC Genomics, December 2019, Springer Science + Business Media

    Prof. Wenfei Jin

  56. Exploring the Changing Landscape of Cell-to-Cell Variation After CTCF Knockdown via Single Cell RNA-seq

    Article • November 2019, Research Square

    Prof. Wenfei Jin

  57. Exploring the Changing Landscape of Cell-to-Cell Variation After CTCF Knockdown via Single Cell RNA-seq

    Article • October 2019, Research Square

    Prof. Wenfei Jin

  58. Principles of 3D Nucleus Organization and Epigenetic Regulation in Diploid Genome Revealed by Multi-omic Data from Hybrid Mouse

    Article • September 2019, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  59. Accumulated degeneration of transcriptional regulation contributes to disease development and detrimental clinical outcomes of Alzheimer’s disease

    Article • September 2019, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  60. Sequences Dimensionality-Reduction by K-mer Substring Space Sampling Enables Effective Resemblance- and Containment-Analysis for Large-Scale omics-data

    Article • August 2019, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  61. Publisher Correction: Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing

    Article • Nature, November 2018, Springer Science + Business Media

    Prof. Wenfei Jin

  62. Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing

    Article • Nature, September 2018, Springer Science + Business Media

    Prof. Wenfei Jin

  63. Trac-looping measures genome structure and chromatin accessibility

    Article • Nature Chemical Biology, August 2018, Springer Science + Business Media

    Prof. Wenfei Jin

  64. Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells

    Article • Immunity, February 2018, Elsevier

    Prof. Wenfei Jin

  65. Deregulation of TGF-β1 signaling induces glycolysis by chromatin remodeling in pathogenic TH17 cells

    Article • November 2017, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  66. CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression

    Article • Molecular Cell, September 2017, Elsevier

    Prof. Wenfei Jin

  67. Genome-wide identification of histone H2A and histone variant H2A.Z-interacting proteins by bPPI-seq

    Article • BDJ, September 2017, Springer Science + Business Media

    Prof. Wenfei Jin

  68. Erratum to: Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3

    Article • February 2016, Springer Science + Business Media

    Prof. Wenfei Jin

  69. Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples

    Article • Nature, November 2015, Springer Science + Business Media

    Prof. Wenfei Jin

  70. Evaluating information content of SNPs for sample-tagging in re-sequencing projects

    Article • Scientific Reports, May 2015, Springer Science + Business Media

    Prof. Wenfei Jin

  71. A genome wide pattern of population structure and admixture in peninsular Malaysia Malays

    Article • The HUGO Journal, October 2014, Springer Science + Business Media

    Professor S. G. Tan, Prof. Wenfei Jin

  72. Y Chromosomes of 40% Chinese Descend from Three Neolithic Super-Grandfathers

    Article • PLOS One, August 2014, PLOS

    Prof. Wenfei Jin

  73. Copy number variations and genetic admixtures in three Xinjiang ethnic minority groups

    Article • European Journal of Human Genetics, July 2014, Springer Science + Business Media

    Prof. Wenfei Jin

  74. Distribution of ancestral chromosomal segments in admixed genomes and its implications for inferring population history and admixture mapping

    Article • European Journal of Human Genetics, November 2013, Springer Science + Business Media

    Prof. Wenfei Jin

  75. Association of Two Variants in SMAD7 with the Risk of Congenital Heart Disease in the Han Chinese Population

    Article • PLOS One, September 2013, PLOS

    Prof. Wenfei Jin

  76. A panel of ancestry informative markers to estimate and correct potential effects of population stratification in Han Chinese

    Article • European Journal of Human Genetics, May 2013, Springer Science + Business Media

    Prof. Wenfei Jin

  77. Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3

    Article • Genome Biology, January 2013, Springer Science + Business Media

    Prof. Wenfei Jin

  78. Exploring Population Admixture Dynamics via Empirical and Simulated Genome-wide Distribution of Ancestral Chromosomal Segments

    Article • The American Journal of Human Genetics, November 2012, Elsevier

    Prof. Wenfei Jin

  79. A systematic characterization of genes underlying both complex and Mendelian diseases

    Article • Human Molecular Genetics, December 2011, Oxford University Press (OUP)

    Prof. Wenfei Jin

  80. Genome-wide detection of natural selection in African Americans pre- and post-admixture

    Article • Genome Research, November 2011, Cold Spring Harbor Laboratory Press

    Prof. Wenfei Jin

  81. A Map of Copy Number Variations in Chinese Populations

    Article • PLOS One, November 2011, PLOS

    Prof. Wenfei Jin

  82. A Genome-Wide Search for Signals of High-Altitude Adaptation in Tibetans

    Article • Molecular Biology and Evolution, October 2010, Oxford University Press (OUP)

    Prof. Wenfei Jin

  83. Genomic Dissection of Population Substructure of Han Chinese and Its Implication in Association Studies

    Article • The American Journal of Human Genetics, December 2009, Elsevier

    Prof. Wenfei Jin

  84. Haplotype-Sharing Analysis Showing Uyghurs Are Unlikely Genetic Donors

    Article • Molecular Biology and Evolution, June 2009, Oxford University Press (OUP)

    Prof. Wenfei Jin