Publications
2024
Concepts and new developments in droplet-based single cell multi-omics
Trends in Biotechnology
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01 Aug 2024
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doi:10.1016/j.tibtech.2024.07.006
Artifacts in single-cell mitochondrial DNA mutation analyses misinform phylogenetic inference
Cold Spring Harbor Laboratory
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29 Jul 2024
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doi:10.1101/2024.07.28.605517
Distinct epigenomic landscapes underlie tissue-specific memory T cell differentiation
Immunity
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01 Jul 2024
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doi:10.1016/j.immuni.2024.06.014
Mitochondrial genetics through the lens of single-cell multi-omics
Nature Genetics
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01 Jul 2024
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doi:10.1038/s41588-024-01794-8
A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine expression profiles and plays a critical role in early Th1 cell fate specification
Immunity
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01 May 2024
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doi:10.1016/j.immuni.2024.04.007
Convergent epigenetic evolution drives relapse in acute myeloid leukemia
eLife
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22 Apr 2024
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doi:10.7554/eLife.93019
FOXO1 is a master regulator of memory programming in CAR T cells
Nature
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10 Apr 2024
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doi:10.1038/s41586-024-07300-8
Transcript-specific enrichment enables profiling rare cell states via scRNA-seq
Cold Spring Harbor Laboratory
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27 Mar 2024
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doi:10.1101/2024.03.27.587039
Regulation of immune signal integration and memory by inflammation-induced chromosome conformation
Cold Spring Harbor Laboratory
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04 Mar 2024
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doi:10.1101/2024.02.29.582872
2023
Latent human herpesvirus 6 is reactivated in CAR T cells
Nature
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08 Nov 2023
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doi:10.1038/s41586-023-06704-2
Multi-modal skin atlas identifies a multicellular immune-stromal community associated with altered cornification and specific T cell expansion in atopic dermatitis
Cold Spring Harbor Laboratory
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30 Oct 2023
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doi:10.1101/2023.10.29.563503
SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9
Cell
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01 Oct 2023
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doi:10.1016/j.cell.2023.09.002
Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells
Nature Genetics
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29 Jun 2023
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doi:10.1038/s41588-023-01433-8
Subtle cell states resolved in single-cell data
Nature Biotechnology
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17 May 2023
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doi:10.1038/s41587-023-01797-6
Codon affinity in mitochondrial DNA shapes evolutionary and somatic fitness
Cold Spring Harbor Laboratory
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23 Apr 2023
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doi:10.1101/2023.04.23.537997
Co-opting signalling molecules enables logic-gated control of CAR T cells
Nature
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08 Mar 2023
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doi:10.1038/s41586-023-05778-2
Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility
Nature Protocols
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15 Feb 2023
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doi:10.1038/s41596-022-00795-3
Concomitant Sequencing of Accessible Chromatin and Mitochondrial Genomes in Single Cells Using mtscATAC-Seq
Chromatin Accessibility
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01 Jan 2023
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doi:10.1007/978-1-0716-2899-7_14
Massively Parallel Profiling of Accessible Chromatin and Proteins with ASAP-Seq
Chromatin Accessibility
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01 Jan 2023
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doi:10.1007/978-1-0716-2899-7_13
The Impact of Genomic Variation on Function (IGVF) Consortium
arXiv
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01 Jan 2023
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doi:10.48550/arXiv.2307.13708
2022
Mitochondrial DNA Mutations as Natural Barcodes for Lineage Tracing of Murine Tumor Models
Cancer Research
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05 Dec 2022
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doi:10.1158/0008-5472.CAN-22-0275
BAF Complex Maintains Glioma Stem Cells in Pediatric H3K27M Glioma
Cancer Discovery
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11 Nov 2022
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doi:10.1158/2159-8290.CD-21-1491
Clonal expansion and epigenetic inheritance of long-lasting NK cell memory
Nature Immunology
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26 Oct 2022
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doi:10.1038/s41590-022-01327-7
Editorial: Lineage tracing, hematopoietic stem cell and immune cell dynamics
Frontiers in Immunology
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18 Oct 2022
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doi:10.3389/fimmu.2022.1062415
A RORγt+ cell instructs gut microbiota-specific Treg cell differentiation
Nature
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07 Sep 2022
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doi:10.1038/s41586-022-05089-y
Functional inference of gene regulation using single-cell multi-omics
Cell Genomics
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01 Sep 2022
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doi:10.1016/j.xgen.2022.100166
Advancing T cell–based cancer therapy with single-cell technologies
Nature Medicine
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01 Sep 2022
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doi:10.1038/s41591-022-01986-x
Runx3 drives a CD8+ T cell tissue residency program that is absent in CD4+ T cells
Nature Immunology
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26 Jul 2022
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doi:10.1038/s41590-022-01273-4
Congenital anemia reveals distinct targeting mechanisms for master transcription factor GATA1
Blood
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21 Apr 2022
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doi:10.1182/blood.2021013753
Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations
Nature Biotechnology
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24 Feb 2022
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doi:10.1038/s41587-022-01210-8
Functional dissection of inherited non-coding variation influencing multiple myeloma risk
Nature Communications
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10 Jan 2022
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doi:10.1038/s41467-021-27666-x
JAK inhibition in a patient with a STAT1 gain-of-function variant reveals STAT1 dysregulation as a common feature of aplastic anemia
Med
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01 Jan 2022
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doi:10.1016/j.medj.2021.12.003
2021
Spatial genomics enables multi-modal study of clonal heterogeneity in tissues
Nature
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15 Dec 2021
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doi:10.1038/s41586-021-04217-4
Longitudinal Single-Cell Dynamics of Chromatin Accessibility and Mitochondrial Mutations in Chronic Lymphocytic Leukemia Mirror Disease History
Cancer Discovery
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01 Dec 2021
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doi:10.1158/2159-8290.CD-21-0276
Charting the tumor antigen maps drawn by single-cell genomics
Cancer Cell
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01 Dec 2021
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doi:10.1016/j.ccell.2021.11.005
Single-cell multiomics defines tolerogenic extrathymic Aire-expressing populations with unique homology to thymic epithelium
Science Immunology
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26 Nov 2021
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doi:10.1126/sciimmunol.abl5053
Single-cell chromatin state analysis with Signac
Nature Methods
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01 Nov 2021
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doi:10.1038/s41592-021-01282-5
Integrated single-cell transcriptomics and epigenomics reveals strong germinal center–associated etiology of autoimmune risk loci
Science Immunology
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29 Oct 2021
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doi:10.1126/sciimmunol.abh3768
Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC
Nature Biotechnology
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21 Oct 2021
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doi:10.1038/s41587-021-01065-5
Transient dendritic cell activation diversifies the T cell response to acute infection
Cold Spring Harbor Laboratory
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27 Sep 2021
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doi:10.1101/2021.09.26.461821
Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells
Nature Biotechnology
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03 Jun 2021
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doi:10.1038/s41587-021-00927-2
STAG2 loss rewires oncogenic and developmental programs to promote metastasis in Ewing sarcoma
Cancer Cell
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01 Jun 2021
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doi:10.1016/j.ccell.2021.05.007
Distinct Foxp3 enhancer elements coordinate development, maintenance, and function of regulatory T cells
Immunity
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01 May 2021
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doi:10.1016/j.immuni.2021.04.005
2020
The SARS-CoV-2 RNA–protein interactome in infected human cells
Nature Microbiology
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21 Dec 2020
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doi:10.1038/s41564-020-00846-z
Single Cell Transcriptomics Implicate Novel Monocyte and T Cell Immune Dysregulation in Sarcoidosis
Frontiers in Immunology
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08 Dec 2020
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doi:10.3389/fimmu.2020.567342
Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin
Cell
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01 Nov 2020
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doi:10.1016/j.cell.2020.09.056
Purifying Selection against Pathogenic Mitochondrial DNA in Human T Cells
New England Journal of Medicine
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15 Oct 2020
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doi:10.1056/NEJMoa2001265
Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells
Nature
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14 Oct 2020
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doi:10.1038/s41586-020-2786-7
An old BATF’s new T-ricks
Nature Immunology
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28 Sep 2020
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doi:10.1038/s41590-020-0796-0
Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer
Cell
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01 Sep 2020
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doi:10.1016/j.cell.2020.07.030
Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations
Cell
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01 Sep 2020
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doi:10.1016/j.cell.2020.06.045
The Polygenic and Monogenic Basis of Blood Traits and Diseases
Cell
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01 Sep 2020
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doi:10.1016/j.cell.2020.08.008
Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling
Nature Biotechnology
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12 Aug 2020
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doi:10.1038/s41587-020-0645-6
Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma
Cancer Cell
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01 Aug 2020
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doi:10.1016/j.ccell.2020.06.006
ImmGen at 15
Nature Immunology
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23 Jun 2020
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doi:10.1038/s41590-020-0687-4
A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing
Nature Biotechnology
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01 Jun 2020
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doi:10.1038/s41587-020-0535-y
Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features
Nature Communications
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06 Mar 2020
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doi:10.1038/s41467-020-15022-4
Inference and effects of barcode multiplets in droplet-based single-cell assays
Nature Communications
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13 Feb 2020
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doi:10.1038/s41467-020-14667-5
Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation
Nature Genetics
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20 Jan 2020
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doi:10.1038/s41588-019-0568-7
2019
Longitudinal assessment of clonal mosaicism in human hematopoiesis via mitochondrial mutation tracking
Blood Advances
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16 Dec 2019
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doi:10.1182/bloodadvances.2019001196
Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations
Nature Genetics
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29 Nov 2019
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doi:10.1038/s41588-019-0538-0
Assessment of computational methods for the analysis of single-cell ATAC-seq data
Genome Biology
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18 Nov 2019
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doi:10.1186/s13059-019-1854-5
CRISPR DNA base editors with reduced RNA off-target and self-editing activities
Nature Biotechnology
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01 Sep 2019
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doi:10.1038/s41587-019-0236-6
Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility
Nature Biotechnology
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24 Jun 2019
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doi:10.1038/s41587-019-0147-6
Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis
Cell Reports
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01 Jun 2019
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doi:10.1016/j.celrep.2019.05.046
Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis
eLife
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09 May 2019
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doi:10.7554/eLife.44080
Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM
Nature Communications
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23 Apr 2019
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doi:10.1038/s41467-019-09670-4
Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors
Nature
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17 Apr 2019
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doi:10.1038/s41586-019-1161-z
Impaired human hematopoiesis due to a cryptic intronic GATA1 splicing mutation
Journal of Experimental Medicine
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26 Mar 2019
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doi:10.1084/jem.20181625
The ATPase module of mammalian SWI/SNF family complexes mediates subcomplex identity and catalytic activity–independent genomic targeting
Nature Genetics
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11 Mar 2019
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doi:10.1038/s41588-019-0363-5
Interrogation of human hematopoiesis at single-cell and single-variant resolution
Nature Genetics
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11 Mar 2019
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doi:10.1038/s41588-019-0362-6
Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics
Cell
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01 Mar 2019
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doi:10.1016/j.cell.2019.01.022
Heritability of fetal hemoglobin, white cell count, and other clinical traits from a sickle cell disease family cohort
American Journal of Hematology
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06 Feb 2019
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doi:10.1002/ajh.25421
The cis-Regulatory Atlas of the Mouse Immune System
Cell
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01 Feb 2019
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doi:10.1016/j.cell.2018.12.036
Preprocessing and Computational Analysis of Single-Cell Epigenomic Datasets
Methods in Molecular Biology
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01 Jan 2019
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doi:10.1007/978-1-4939-9057-3_13
2018
A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation
Nature Cell Biology
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05 Nov 2018
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doi:10.1038/s41556-018-0221-1
Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks
Nature Communications
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25 Jul 2018
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doi:10.1038/s41467-018-05328-9
Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation
Cell
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01 May 2018
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doi:10.1016/j.cell.2018.03.074
Transcript-indexed ATAC-seq for precision immune profiling
Nature Medicine
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23 Apr 2018
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doi:10.1038/S41591-018-0008-8
Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types
Nature Genetics
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01 Apr 2018
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doi:10.1038/s41588-018-0081-4
Response to “Unexpected mutations after CRISPR–Cas9 editing in vivo”
Nature Methods
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30 Mar 2018
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doi:10.1038/nmeth.4541
hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data
Nature Methods
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28 Feb 2018
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doi:10.1038/nmeth.4583
2017
Common genes associated with antidepressant response in mouse and man identify key role of glucocorticoid receptor sensitivity
PLOS Biology
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28 Dec 2017
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doi:10.1371/journal.pbio.2002690
A B Cell Regulome Links Notch to Downstream Oncogenic Pathways in Small B Cell Lymphomas
Cell Reports
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01 Oct 2017
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doi:10.1016/j.celrep.2017.09.066
diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data
Bioinformatics
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29 Sep 2017
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doi:10.1093/bioinformatics/btx623
Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing
Journal of Experimental Medicine
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06 Sep 2017
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doi:10.1084/jem.20170976
Confounding in ex vivo models of Diamond-Blackfan anemia
Blood
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31 Aug 2017
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doi:10.1182/blood-2017-05-783191
Polygenic risk assessment reveals pleiotropy between sarcoidosis and inflammatory disorders in the context of genetic ancestry
Genes & Immunity
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01 Mar 2017
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doi:10.1038/gene.2017.3
2016
The Integration of Epistasis Network and Functional Interactions in a GWAS Implicates RXR Pathway Genes in the Immune Response to Smallpox Vaccine
PLOS ONE
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11 Aug 2016
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doi:10.1371/journal.pone.0158016
An interaction quantitative trait loci tool implicates epistatic functional variants in an apoptosis pathway in smallpox vaccine eQTL data
Genes & Immunity
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07 Apr 2016
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doi:10.1038/gene.2016.15
2015
dcVar: a method for identifying common variants that modulate differential correlation structures in gene expression data
Frontiers in Genetics
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19 Oct 2015
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doi:10.3389/fgene.2015.00312
Fine mapping of chromosome 15q25 implicates ZNF 592 in neurosarcoidosis patients
Annals of Clinical and Translational Neurology
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31 Jul 2015
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doi:10.1002/acn3.229
Differential co-expression network centrality and machine learning feature selection for identifying susceptibility hubs in networks with scale-free structure
BioData Mining
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03 Feb 2015
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doi:10.1186/s13040-015-0040-x
2014
Network Theory for Data-Driven Epistasis Networks
Methods in Molecular Biology
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03 Nov 2014
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doi:10.1007/978-1-4939-2155-3_15
2013
Encore: Genetic Association Interaction Network Centrality Pipeline and Application to SLE Exome Data
Genetic Epidemiology
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05 Jun 2013
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doi:10.1002/gepi.21739