Research
Our research so far has focused on building atlases, using these atlases, and designing quality standards for single cell analyses.
Here’s a list of the latest papers from the lab.
Highlighted
An integrated cell atlas of the human lung in health and disease
Cold Spring Harbor Laboratory
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11 Mar 2022
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doi:10.1101/2022.03.10.483747
Benchmarking atlas-level data integration in single-cell genomics
Nature Methods
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23 Dec 2021
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doi:10.1038/s41592-021-01336-8
All
2022
Probe set selection for targeted spatial transcriptomics
Cold Spring Harbor Laboratory
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17 Aug 2022
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doi:10.1101/2022.08.16.504115
Primary cilia and SHH signaling impairments in human and mouse models of Parkinson’s disease
Nature Communications
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16 Aug 2022
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doi:10.1038/s41467-022-32229-9
Alveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation
Frontiers in Immunology
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28 Jul 2022
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doi:10.3389/fimmu.2022.917232
Ketamine exerts its sustained antidepressant effects via cell-type-specific regulation of Kcnq2
Neuron
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01 Jul 2022
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doi:10.1016/j.neuron.2022.05.001
Ly6D+Siglec-H+ precursors contribute to conventional dendritic cells via a Zbtb46+Ly6D+ intermediary stage
Nature Communications
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16 Jun 2022
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doi:10.1038/s41467-022-31054-4
Ketamine exerts its sustained antidepressant effects via cell-type-specific regulation of Kcnq2.
Neuron
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31 May 2022
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pmid:35649415
Parkinson's disease motor symptoms rescue by CRISPRa‐reprogramming astrocytes into GABAergic neurons
EMBO Molecular Medicine
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04 Apr 2022
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doi:10.15252/emmm.202114797
An integrated cell atlas of the human lung in health and disease
Cold Spring Harbor Laboratory
·
11 Mar 2022
·
doi:10.1101/2022.03.10.483747
The discovAIR project: a roadmap towards the Human Lung Cell Atlas
European Respiratory Journal
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27 Jan 2022
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doi:10.1183/13993003.02057-2021
2021
Benchmarking atlas-level data integration in single-cell genomics
Nature Methods
·
23 Dec 2021
·
doi:10.1038/s41592-021-01336-8
SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis
Cell
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01 Dec 2021
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doi:10.1016/j.cell.2021.11.033
Diet-induced alteration of intestinal stem cell function underlies obesity and prediabetes in mice
Nature Metabolism
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22 Sep 2021
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doi:10.1038/s42255-021-00458-9
Mapping single-cell data to reference atlases by transfer learning
Nature Biotechnology
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30 Aug 2021
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doi:10.1038/s41587-021-01001-7
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.
Nature medicine
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02 Mar 2021
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pmid:33654293
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
Nature Medicine
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01 Mar 2021
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doi:10.1038/s41591-020-01227-z
2020
Query to reference single-cell integration with transfer learning
Cold Spring Harbor Laboratory
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16 Jul 2020
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doi:10.1101/2020.07.16.205997
RAAS blockade, kidney disease, and expression of ACE2, the entry receptor for SARS-CoV-2, in kidney epithelial and endothelial cells
Cold Spring Harbor Laboratory
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23 Jun 2020
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doi:10.1101/2020.06.23.167098
Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease
Cold Spring Harbor Laboratory
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30 May 2020
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doi:10.1101/2020.05.28.121541
Benchmarking atlas-level data integration in single-cell genomics
Cold Spring Harbor Laboratory
·
23 May 2020
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doi:10.1101/2020.05.22.111161
Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells
Cold Spring Harbor Laboratory
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20 Apr 2020
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doi:10.1101/2020.04.19.049254
2019
Current best practices in single‐cell RNA‐seq analysis: a tutorial
Molecular Systems Biology
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01 Jun 2019
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doi:10.15252/msb.20188746
2017
CommWalker: correctly evaluating modules in molecular networks in light of annotation bias
Bioinformatics
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03 Nov 2017
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doi:10.1093/bioinformatics/btx706