Publications
Here is a list of all publications from our lab. Click here to see selected publications.
2025
Genomic analysis of progenitors in viral infection implicates glucocorticoids as suppressors of plasmacytoid dendritic cell generation
Proceedings of the National Academy of Sciences
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28 Apr 2025
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doi:10.1073/pnas.2410092122
Sensory input, sex and function shape hypothalamic cell type development
Nature
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05 Mar 2025
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doi:10.1038/s41586-025-08603-0
2024
A fast, scalable and versatile tool for analysis of single-cell omics data
Nature Methods
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08 Jan 2024
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doi:10.1038/s41592-023-02139-9
2023
Single-cell analysis of chromatin accessibility in the adult mouse brain
Nature
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13 Dec 2023
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doi:10.1038/s41586-023-06824-9
Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity
Proceedings of the National Academy of Sciences
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08 May 2023
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doi:10.1073/pnas.2210991120
2022
Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation
Cell Reports
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01 Nov 2022
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doi:10.1016/j.celrep.2022.111630
Systems-biology analysis of rheumatoid arthritis fibroblast-like synoviocytes implicates cell line-specific transcription factor function
Nature Communications
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20 Oct 2022
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doi:10.1038/s41467-022-33785-w
2021
A single-cell atlas of chromatin accessibility in the human genome
Cell
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01 Nov 2021
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doi:10.1016/j.cell.2021.10.024
An atlas of gene regulatory elements in adult mouse cerebrum
Nature
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06 Oct 2021
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doi:10.1038/s41586-021-03604-1
Cardiac cell type–specific gene regulatory programs and disease risk association
Science Advances
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14 May 2021
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doi:10.1126/sciadv.abf1444
Comprehensive analysis of single cell ATAC-seq data with SnapATAC
Nature Communications
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26 Feb 2021
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doi:10.1038/s41467-021-21583-9
2020
Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes
eLife
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09 Nov 2020
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doi:10.7554/elife.62522
Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss
Genetics
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01 Oct 2020
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doi:10.1534/genetics.120.303597
2019
Identification of DNA motifs that regulate DNA methylation
Nucleic Acids Research
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25 Jun 2019
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doi:10.1093/nar/gkz483
Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development
Science Advances
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01 Mar 2019
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doi:10.1126/sciadv.aav3262
Epigenomic analysis reveals DNA motifs regulating histone modifications in human and mouse
Proceedings of the National Academy of Sciences
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12 Feb 2019
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doi:10.1073/pnas.1813565116
Integrative analysis with expanded DNA methylation data reveals common key regulators and pathways in cancers
npj Genomic Medicine
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01 Feb 2019
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doi:10.1038/s41525-019-0077-8
2018
Bayesian Networks Predict Neuronal Transdifferentiation
G3 Genes|Genomes|Genetics
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01 Jul 2018
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doi:10.1534/g3.118.200401
Finding relevant biomedical datasets: the UC San Diego solution for the bioCADDIE Retrieval Challenge
Database
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01 Jan 2018
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doi:10.1093/database/bay017
2017
Runx3 programs CD8+ T cell residency in non-lymphoid tissues and tumours
Nature
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06 Dec 2017
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doi:10.1038/nature24993
Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation
Nature Immunology
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13 Mar 2017
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doi:10.1038/ni.3706
2016
Systematic identification of protein combinations mediating chromatin looping
Nature Communications
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27 Jul 2016
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doi:10.1038/ncomms12249
Constructing 3D interaction maps from 1D epigenomes
Nature Communications
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10 Mar 2016
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doi:10.1038/ncomms10812
2011
Signal-induced Brd4 release from chromatin is essential for its role transition from chromatin targeting to transcriptional regulation
Nucleic Acids Research
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02 Sep 2011
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doi:10.1093/nar/gkr698
Isolation and functional characterization of P-TEFb-associated factors that control general and HIV-1 transcriptional elongation
Methods
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01 Jan 2011
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doi:10.1016/j.ymeth.2010.04.005