Intro
During my PhD at New York University, advised by Rahul Satija, my research focused on developing computational algorithms to learn the representation of single-cell data. I led the development of Seurat, now the most widely adopted platform in the field (>2.2M downloads). I created four core algorithms behind it: weighted nearest neighbor for multimodal clustering, reference mapping for automated cell-type annotation, bridge integration for cross-modality integration, and sketch integration for analysis across millions of cells.
To translate these innovations toward patients, I co-founded Neptune Bio after my PhD, a biotech startup focused on target identification for combination therapies. As head of data science, I built an iterative AI–Lab loop framework NAIAD that uses active learning to shrink the combinatorial search space and accelerate gene combination discovery.
I am now a postdoctoral fellow at the Edward Chang Lab at UCSF, where I work to decode human language at single-neuron resolution. By integrating in vivo single-neuron recordings, connectivity mapping, and spatial transcriptomics, I aim to build the first molecular-resolution map of language circuitry — advancing our understanding of the molecular and cellular mechanisms of human language.
Work Experience
| Position |
Institution |
Date |
| Post-doctoral |
UCSF |
2025- |
| Co-founder |
Neptune Bio |
2023- |
| Head of data science |
Neptune Bio |
2023-2025 |
| Post-doctoral |
New York Genome Center |
2023 |
Education
| Degree |
Institution |
Date |
| PhD, Computational Biology |
New York University |
2023 |
| MSc, Biological Sciences & Data Science |
Fordham University |
2017 |
| BSc, Biotechnology |
Dalian University of Technology, China |
2014 |
Publications
See the full list of publications on Google Scholar.
Selected Publications
* denotes co-first authorship; # denotes corresponding author.
Neuroscience
- Suresh V*, Wigdor E*, Hao Y*, Leonard R, Asfouri j, Griffiths M, Evans C, Yuan G, Rohani N, Weiss J, Dema C, Mukthar T, Lassen F, Schafer N, Dong S, Palmer D, Chang E, Sanders S, Nowakowski T. Molecular dynamics of Brodmann Area 22 in development and autism. bioRxiv. 2026
- Yuan G*, Suresh V*, Wigdor E*, Hao Y*, Leonard R, Steyert M, Griffiths M, Evans C, Rohani N, Weiss J, Lassen F, Schafer N, Dong S, Palmer D, Sanders S, Nowakowski T. Disruption of Cell-Type-Specific Molecular Programs of Medium Spiny Neurons in Autism. bioRxiv. 2025
Computational algorithms
- Qin J, Wessels HH, Fernandez-Granda C, Hao Y#. Active learning for efficient discovery of optimal combinatorial perturbations. ICML. 2025 (NAIAD)
- Hao Y, Stuart T, Kowalski MH, Choudhary S, Hoffman P, Hartman A, Srivastava A, Molla G, Madad S, Fernandez-Granda C, Satija R. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nature Biotechnology. 2023 (Seurat v5)
- Hao Y*, Hao S*, Andersen-Nissen E, Mauck WM, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M, Hoffman P, Stoeckius M, Papalexi E, Mimitou EP, Jaison J, Srivastava A, Stuart T, Fleming LM, Yeung B, Rogers AJ, McElrath JM, Blish CA, Gottardo R, Smibert P, Satija R. Integrated analysis of multimodal single-cell data. Cell. 2021 (Seurat v4)
- Hao Y*, Yang L, Neto A G, Amin M, Kelly D, Brown S, Branski R, Pei Z. HPViewer: Sensitive and specific genotyping of human papillomavirus in metagenomic DNA. Bioinformatics. 2018 (HPViewer)
- Stuart T*, Butler A*, Hoffman P, Hafemeister C, Papalexi E, Mauck III WM, Hao Y, Stoeckius M, Smibert P, Satija R. Comprehensive integration of single-cell data. Cell. 2019 (Seurat v3)
Technology development
- Wessels HH*, Méndez-Mancilla A*, Hao Y, Papalexi E, Mauck III WM, Lu L, Morris JA, Mimitou EP, Smibert P, Sanjana NE, Satija R. Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq. Nature Methods. 2022
- Mimitou EP, Lareau CA, Chen KY, Zorzetto-Fernandes AL, Hao Y, Takeshima Y, Luo W, Huang TS, Yeung BZ, Papalexi E, Thakore PI, Kibayashi T, Wing JB, Hata M, Satija R, Nazor KL, Sakaguchi S, Ludwig LS, Sankaran VG, Regev A, Smibert, P. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells. Nature Biotechnology. 2021
Immunology discovery
- Kedmi R, Najar TA, Mesa KR, Grayson A, Kroehling L, Hao Y, Hao S, Pokrovskii M, Xu M, Talbot J, Wang J, Germino J, Lareau CA, Satpathy AT, Anderson MS, Laufer TM, Aifantis I, Bartleson JM, Allen PM, Paidassi H, Gardner JM, Stoeckius M, Littman DR. A RORγt+ cell instructs gut microbiota-specific Treg cell differentiation. Nature. 2022
- Wu L, Hollinshead KE, Hao Y, Au C, Kroehling L, Ng C, Lin WY, Li D, Silva HM, Shin J, Lafaille JJ, Possemato R, Pacold M, Papagiannakopoulos T, Kimmelman A, Satija R, Littman DR. Niche-selective inhibition of pathogenic Th17 cells by targeting metabolic redundancy. Cell. 2020
Talks
2024
Spotlight presentation at Alexandria's Early-Stage Venture Summit, USA (June 2024)
2023
Invited talk at Models, Inference & Algorithms (MIA), Broad Institute, USA (Sept. 2023)
Invited talk at Single Cell Genomics Day, New York University, USA (Apr. 2023)
2022
Conference presentation at Centers of Excellence in Genomic Science (CEGS) annual meeting, Duke University, USA (Oct. 2022)
Conference presentation at Chan Zuckerberg Initiative Assembling Tissue References Workshop, San Francisco, USA (May 2022)
Invited talk at Genentech Monthly Single-Cell seminar, USA (May 2022)
Invited talk at New York Genome Center's Scientific Advisory Board meeting, New York Genome Center, USA (Apr. 2022)
Invited talk at Chan Zuckerberg Initiative Single-Cell Monthly Webinar, USA (Mar. 2022)
Invited talk at Single-Cell Genomics Day, New York University, USA (Mar. 2022)
Invited talk at MRC Weatherall Institute of Molecular Medicine Seminar, University of Oxford, UK (Jan. 2022)
2021
Invited talk at First author Forum, BioArt, China (Aug. 2021)
Invited talk at Front Line Genomics, UK (June 2021)
Invited talk at Chan Zuckerberg Initiative/National Institutes of Health Maps to Mechanism Symposium, USA (Apr. 2021)
2020
Conference presentation at Centers of Excellence in Genomic Science (CEGS) annual meeting, New York, USA (Oct. 2020)
Conference presentation at Biological Data Science, Cold Spring Harbor, USA (Aug. 2020)
Conference presentation at The Biology of Genomes, Cold Spring Harbor, USA (May 2020)
Invited talk at Single-Cell Genomics Day, New York University, USA (Jan. 2020)