Recent Works

  • PIASO: a single-cell omics toolkit for the selection of cell-type specific enhancers (in preparation)
  • ROEN: an Accurate and Efficient Normalization Method for single-cell RNA Sequencing Data (in preparation)
  • A Comprehensive Database of Genes Related to Repeat Expansion Diseases (in revision)
    It is a comprehensive manually-curated database that covers all reported repeat expansion diseases and also provides a list of predicted genes containing unstable tandem repeats that may cause diseases via abnormal repeat expansion by SVM and random forest.

Projects

  • Heterogeneous Network Representation Learning for Spatial Transcriptomics Data
    This work aims to incorporate gene expression profiles and spatial coordinates for cells during dimensionality reduction.
  • Integration of Multi-modal Single Cell Sequencing Data via Network Representation Learning
    This work aims to integrate different single-cell modalities, e.g., scRNA-seq data and scATAC-seq data.

Recent Publications

  • Strategies for arterial graft optimization at the single-cell level
    Zhan Hu#, Min Dai#, Yuan Chang#, Xiumeng Hua, Ningning Zhang, Xiao Chen, Yixuan Sheng, Zhenyu Xu, Hang Zhang, Yu Zhang, Hao Cui, Hao Jia, Xiu-Jie Wang*, Jiangping Song* Nature Cardiovascular Research, 2024

    Link

  • Allelic reprogramming of chromatin states in human early embryos
    Shenli Yuan#, Lei Gao#, Wenrong Tao#, Jianhong Zhan#, Gang Lu#, Jingye Zhang, Chuanxin Zhang, Lizhi Yi, Zhenbo Liu, Zhenzhen Hou, Min Dai, Han Zhao, Zi-Jiang Chen*, Jiang Liu*, Keliang Wu* National Science Review, 2024

    Link

  • Functional heterogeneity of Wnt-responsive and Hedgehog-responsive neural stem cells in the murine adult hippocampus
    Xing Luo, Min Dai, Min Wang, Xiu-Jie Wang, Weixiang Guo Developmental Cell, 2023

    Link

  • Pharmacological Perturbation of Mechanical Contractility Enables Robust Transdifferentiation of Human Fibroblasts into Neurons
    Zheng‐Quan He#, Yu‐Huan Li#, Gui‐Hai Feng#, Xue‐Wei Yuan#, Zong‐Bao Lu#, Min Dai, Yan‐Ping Hu, Ying Zhang, Qi Zhou*, Wei Li* Advanced Science, 2022

    Link

  • Accurate and fast cell marker gene identification with COSG
    Min Dai, Xiaobing Pei*, Xiu-Jie Wang* Briefings in Bioinformatics, 2022

    Link Preprint

  • Sequence Repetitiveness Quantification and de novo Repeat Detection by Weighted k-mer Coverage
    Cong Feng, Min Dai, Yongjing Liu, Ming Chen Briefings in Bioinformatics, 2020

    Link

Talks

  • Fast interpolation-based t-SNE for data visualization
    Journal Club, 20 May, 2021, IGDB, CAS, Beijng, China
  • Slides

  • Fasting Reduces Inflammation
    Journal Club, 7 Mar, 2021, IGDB, CAS, Beijng, China
  • Slides

  • Cell type-specific genetic regulation of gene expression across human tissues
    Journal Club, 7 Dec, 2020, IGDB, CAS, Beijng, China
  • Slides

  • Changes in regeneration-responsive enhancers shape regenerative capacities in vertebrates
    Journal Club, 9 Sep, 2020, IGDB, CAS, Beijng, China
  • Slides

  • Batch Correction of Single-cell Transcriptomics via SCANE
    International Student Workshop, 14 Nov, 2019, NAIST, Nara, Japan
  • Visualizing Data using t-SNE
    Journal Club, 22 Aug, 2019, IGDB, CAS, Beijng, China
  • The Pluripotent to Totipotent State Transition in Mouse Embryonic Stem Cells
    Journal Club, 20 June, 2019, IGDB, CAS, Beijng, China
  • Adjusting Batch Effects in RNA Sequencing Data
    Journal Club, 28 Feb, 2019, IGDB, CAS, Beijng, China
  • RNA Velocity of Single Cells
    Journal Club, 20 Dec, 2018, IGDB, CAS, Beijng, China
  • Slides

  • Challenges and Opportunities in Single Cell Sequencing
    Journal Club, 20 Dec, 2018, IGDB, CAS, Beijng, China
  • Cellular Automata, from Simple Rules to Great Complexity
    Future Science Salon, 29 June, 2018, IGDB, CAS, Beijng, China
  • Cellular Automaton
    Journal Club, 15 Mar, 2018, IGDB, CAS, Beijng, China
  • TGF-β Signaling through Cell Membrane to the Nucleus
    Journal Club, 30 Nov, 2017, IGDB, CAS, Beijng, China
  • Erasure of Genomic Imprints in Human Primordial Germ Cells
    Journal Club, 7 Sep, 2017, IGDB, CAS, Beijng, China

Skills

  • Programming Languages:
  • Python, R, Java, Shell, C#, JavaScript

  • Sequencing Data Anlaysis:
  • scRNA-seq, scATAC-seq, spatial transcriptomics, Snakemake, RNA-seq, ChIP-seq, Ribo-seq

  • Machine Learning:
  • Matrix Decomposition, Network Representation Learning, Dimensionality Reduction, Data Visualization

    Interests

  • Western Philosophy
  • Chinese Philosophy
  • Translation
  • Wresting
  • Classical Music