Yuhan Hao

Computational algorithms

• Qin J, Wessels HH, Fernandez-Granda C, Hao Y#. Active learning for efficient discovery of optimal gene combinations in the combinatorial perturbation space. NeurIPS AIDrugX workshop. 2024 (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

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i = 0;

while (!deck.isInOrder()) {
    print 'Iteration ' + i;
    deck.shuffle();
    i++;
}

print 'It took ' + i + ' iterations to sort the deck.';

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