Publications
Here is a list of all publications from our lab. Click here to see selected publications.
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