Bio

I am a senior computational scientist and previously a postdoc in Prof. Gordon Fishell's lab at Harvard Medical School and the Broad Institute of MIT and Harvard. Previously, I finished my Ph.D. in Bioinformatics and B.S. in Bioinformatics in Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and Zhejiang University, respectively.

In order to unravel the molecular mechanisms regulating the spatiotemporal development and diverse function of cortex interneuron, I apply and develop computational methods to analyze multi-omics data. My research interests lie in the intersection of single cell data analysis, cortex development, machine learning and gene expression regulation. Additionally, I am fascinated with representation learning, and how cell states are synergistically regulated by both endogenous and exogenous signals.

• Emergene: Individual cell-based differential transcriptomic analysis across conditions (in preparation)

  GitHub

• PIASO: a single-cell omics toolkit for the selection of cell-type specific enhancers (in preparation)

  GitHub

• ZoneTalk for Spatial Ligand-Receptor Interaction Inference (in preparation)
• ROEN: an Accurate and Efficient Normalization Method for single-cell RNA Sequencing Data (in preparation)

• 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.

• Pyramidal neurons proportionately alter the identity and survival of specific cortical interneuron subtypes
  Sherry Jingjing Wu#, Min Dai#, Shang-Po Yang, Cai McCann, Yanjie Qiu, Giovanni J. Marrero, Jeffrey A. Stogsdill, Daniela J. Di Bella, Qing Xu, Samouil L. Farhi, Evan Z. Macosko, Fei Chen, and Gord Fishell bioRxiv, 2024

  Link

• An enhancer-AAV toolbox to target and manipulate distinct interneuron subtypes
  Elisabetta Furlanis#, Min Dai#, Brenda Leyva Garcia, Josselyn Vergara, Ana Pereira, Kenneth Pelkey, Thien Tran, Bram L. Gorissen, Anna Vlachos, Ariel Hairston, Shuhan Huang, Deepanjali Dwivedi, Sarah Du, Sara Wills, Justin McMahon, Anthony T. Lee, Edward F. Chang, Taha Razzaq, Ahmed Qazi, Geoffrey Vargish, Xiaoqing Yuan, Adam Caccavano, Steven Hunt, Ramesh Chittajallu, Nadiya McLean, Lauren Hewit, Emily Paranzino, Haley Rice, Alex C. Cummins, Anya Plotnikova, Arya Mohanty, Anne Claire Tangen, Jung Hoon Shin, Reza Azadi, Mark A.G. Eldridge, Veronica A. Alvarez, Bruno B. Averbeck, Mansour Alyahyay, Tania Reyes Vallejo, Mohammed Soheib, Lucas G. Vattino, Cathryn P. MacGregor, Emmie Banks, Viktor Janos Olah, Shovan Naskar, Sophie Hill, Sophie Liebergall, Rohan Badiani, Lili Hyde, Qing Xu, Kathryn C. Allaway, Ethan M. Goldberg, Tomasz J. Nowakowski, Soohyun Lee, Anne E. Takesian, Leena A. Ibrahim, Asim Iqbal, Chris J. McBain, Jordane Dimidschstein*, Gord Fishell*, Yating Wang* bioRxiv, 2024

  Link

• DRED: A Comprehensive Database of Genes Related to Repeat Expansion Diseases
  Qingqing Shi#, Min Dai#, Yingke Ma, Jun Liu, Xiuying Liu, Xiu-Jie Wang Genomics, Proteomics & Bioinformatics, 2024

  Link

• 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

• 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

Python, R, Java, Shell, C#, JavaScript

scRNA-seq, scATAC-seq, spatial transcriptomics, Snakemake, RNA-seq, ChIP-seq, Ribo-seq

Matrix Decomposition, Network Representation Learning, Dimensionality Reduction, Data Visualization

• dai@broadinstitute.org