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96 peer-reviewed articles • 27,883 peer-reviewed citations • Sorted by year • Download PDF (PDF by citations)
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1The covariance environment defines cellular niches for spatial inference
Nature Biotechnology, 2024, 43, 269-280
19.762Citations (PDF)
2CellRank 2: unified fate mapping in multiview single-cell data
Nature Methods, 2024, 21, 1196-1205
13.1252Citations (PDF)
3REUNION: transcription factor binding prediction and regulatory association inference from single-cell multi-omics data
Bioinformatics, 2024, 40, i567-i575
3.28Citations (PDF)
4Age-related epithelial defects limit thymic function and regeneration
Nature Immunology, 2024, 25, 1593-1606
14.186Citations (PDF)
5Precursor central memory versus effector cell fate and naïve CD4+ T cell heterogeneity
Journal of Experimental Medicine, 2024, 221,
5.915Citations (PDF)
6The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1
Nature Cancer, 2024, 5, 1641-1659
15.276Citations (PDF)
7SEACells infers transcriptional and epigenomic cellular states from single-cell genomics data
Nature Biotechnology, 2023, 41, 1746-1757
19.7222Citations (PDF)
8STING inhibits the reactivation of dormant metastasis in lung adenocarcinoma
Nature, 2023, 616, 806-813
30.7243Citations (PDF)
9Cross-platform dataset of multiplex fluorescent cellular object image annotations
Scientific Data, 2023, 10,
3.816Citations (PDF)
10The scverse project provides a computational ecosystem for single-cell omics data analysis
Nature Biotechnology, 2023, 41, 604-606
19.7365Citations (PDF)
11An integrated cell atlas of the lung in health and disease
Nature Medicine, 2023, 29, 1563-1577
22.6807Citations (PDF)
12scKINETICS: inference of regulatory velocity with single-cell transcriptomics data
Bioinformatics, 2023, 39, i394-i403
3.229Citations (PDF)
13Conserved transcriptional connectivity of regulatory T cells in the tumor microenvironment informs new combination cancer therapy strategies
Nature Immunology, 2023, 24, 1020-1035
14.162Citations (PDF)
14Epigenetic plasticity cooperates with cell-cell interactions to direct pancreatic tumorigenesis
Science, 2023, 380,
26.1216Citations (PDF)
15Supervised discovery of interpretable gene programs from single-cell data
Nature Biotechnology, 2023, 42, 1084-1095
19.794Citations (PDF)
16CellRank for directed single-cell fate mapping
Nature Methods, 2022, 19, 159-170
13.1783Citations (PDF)
17Spatial CRISPR genomics identifies regulators of the tumor microenvironment
Cell, 2022, 185, 1223-1239.e20
23.4287Citations (PDF)
18Radiotherapy orchestrates natural killer cell dependent antitumor immune responses through CXCL8
Science Advances, 2022, 8,
8.1142Citations (PDF)
19Lymphatics act as a signaling hub to regulate intestinal stem cell activity
Cell Stem Cell, 2022, 29, 1067-1082.e18
11.6119Citations (PDF)
20Systematic Comparison of Pancreatic Ductal Adenocarcinoma Models Identifies a Conserved Highly Plastic Basal Cell State
Cancer Research, 2022, 82, 3549-3560
2.624Citations (PDF)
21Lineage plasticity in prostate cancer depends on JAK/STAT inflammatory signaling
Science, 2022, 377, 1180-1191
26.1363Citations (PDF)
22MACHETE identifies interferon-encompassing chromosome 9p21.3 deletions as mediators of immune evasion and metastasis
Nature Cancer, 2022, 3, 1367-1385
15.2120Citations (PDF)
23A gene–environment-induced epigenetic program initiates tumorigenesis
Nature, 2021, 590, 642-648
30.7315Citations (PDF)
24Fully defined human pluripotent stem cell-derived microglia and tri-culture system model C3 production in Alzheimer’s disease
Nature Neuroscience, 2021, 24, 343-354
11.2246Citations (PDF)
25A unified atlas of CD8 T cell dysfunctional states in cancer and infection
Molecular Cell, 2021, 81, 2477-2493.e10
8.6120Citations (PDF)
26Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung
Circulation, 2021, 144, 286-302
13.1471Citations (PDF)
27Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer
Cancer Cell, 2021, 39, 1479-1496.e18
28.4412Citations (PDF)
28Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy
Cell Reports, 2021, 37, 109992
4.460Citations (PDF)
29Cancer cells deploy lipocalin-2 to collect limiting iron in leptomeningeal metastasis
Science, 2020, 369, 276-282
26.1291Citations (PDF)
30Single-Cell Transcriptomics Reveals Early Emergence of Liver Parenchymal and Non-parenchymal Cell Lineages
Cell, 2020, 183, 702-716.e14
23.484Citations (PDF)
31Notch3 signaling promotes tumor cell adhesion and progression in a murine epithelial ovarian cancer model
PLoS ONE, 2020, 15, e0233962
1.512Citations (PDF)
32Lineage plasticity in cancer: a shared pathway of therapeutic resistance
Nature Reviews Clinical Oncology, 2020, 17, 360-371
54.3543Citations (PDF)
33Adult Human Glioblastomas Harbor Radial Glia-like Cells
Stem Cell Reports, 2020, 14, 338-350
3.071Citations (PDF)
34Regenerative lineages and immune-mediated pruning in lung cancer metastasis
Nature Medicine, 2020, 26, 259-269
22.6474Citations (PDF)
35L1CAM defines the regenerative origin of metastasis-initiating cells in colorectal cancer
Nature Cancer, 2020, 1, 28-45
15.2244Citations (PDF)
36Regenerative potential of prostate luminal cells revealed by single-cell analysis
Science, 2020, 368, 497-505
26.1303Citations (PDF)
37Tumor Analyses Reveal Squamous Transformation and Off-Target Alterations As Early Resistance Mechanisms to First-line Osimertinib in EGFR -Mutant Lung Cancer
Clinical Cancer Research, 2020, 26, 2654-2663
4.5377Citations (PDF)
38NCMP-05. DECODING THE IMMUNE SYSTEM RESPONSE TO LEPTOMENINGEAL METASTASIS
Neuro-Oncology, 2020, 22, ii124-ii124
0.90Citations (PDF)
39Concurrent RB1 and TP53 Alterations Define a Subset of EGFR-Mutant Lung Cancers at risk for Histologic Transformation and Inferior Clinical Outcomes
Journal of Thoracic Oncology, 2019, 14, 1784-1793
1.5410Citations (PDF)
40Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity
Cell, 2019, 179, 846-863.e24
23.4608Citations (PDF)
41Combination anti–CTLA-4 plus anti–PD-1 checkpoint blockade utilizes cellular mechanisms partially distinct from monotherapies
Proceedings of the National Academy of Sciences of the United States of America, 2019, 116, 22699-22709
5.2337Citations (PDF)
42Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation
Cell Stem Cell, 2019, 25, 682-696.e8
11.6170Citations (PDF)
43Engineering γδT cells limits tonic signaling associated with chimeric antigen receptors
Science Signaling, 2019, 12,
3.952Citations (PDF)
44Natural Genetic Variation Reveals Key Features of Epigenetic and Transcriptional Memory in Virus-Specific CD8 T Cells
Immunity, 2019, 50, 1202-1217.e7
16.658Citations (PDF)
45The emergent landscape of the mouse gut endoderm at single-cell resolution
Nature, 2019, 569, 361-367
30.7420Citations (PDF)
46Characterization of cell fate probabilities in single-cell data with Palantir
Nature Biotechnology, 2019, 37, 451-460
19.7885Citations (PDF)
47Negative Co-stimulation Constrains T Cell Differentiation by Imposing Boundaries on Possible Cell States
Immunity, 2019, 50, 1084-1098.e10
16.699Citations (PDF)
48Immune profiling of human tumors identifies CD73 as a combinatorial target in glioblastoma
Nature Medicine, 2019, 26, 39-46
22.6341Citations (PDF)
49Inflammatory signaling supports cancer cell growth within the leptomeninges (P2.6-024)
Neurology, 2019, 92,
0.70Citations (PDF)
50Chromosomal instability drives metastasis through a cytosolic DNA response
Nature, 2018, 553, 467-472
30.71,542Citations (PDF)
51PhenoGraph and viSNE facilitate the identification of abnormal T‐cell populations in routine clinical flow cytometric data
Cytometry Part B - Clinical Cytometry, 2018, 94, 744-757
1.435Citations (PDF)
52CD49b defines functionally mature Treg cells that survey skin and vascular tissues
Journal of Experimental Medicine, 2018, 215, 2796-2814
5.954Citations (PDF)
53Learning time-varying information flow from single-cell epithelial to mesenchymal transition data
PLoS ONE, 2018, 13, e0203389
1.523Citations (PDF)
54Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Exhausted CD8 T Cells
Immunity, 2018, 48, 1029-1045.e5
16.6320Citations (PDF)
55Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment
Cell, 2018, 174, 1293-1308.e36
23.41,970Citations (PDF)
56Recovering Gene Interactions from Single-Cell Data Using Data Diffusion
Cell, 2018, 174, 716-729.e27
23.41,821Citations (PDF)
57Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses
Cell, 2017, 169, 750-765.e17
23.41,176Citations (PDF)
58An Immune Atlas of Clear Cell Renal Cell Carcinoma
Cell, 2017, 169, 736-749.e18
23.4941Citations (PDF)
59Distinct Cellular Mechanisms Underlie Anti-CTLA-4 and Anti-PD-1 Checkpoint Blockade
Cell, 2017, 170, 1120-1133.e17
23.41,248Citations (PDF)
60Bayesian Inference for Single-cell Clustering and Imputing
Genomics and Computational Biology, 2017, 3, 46
0.944Citations (PDF)
61Wishbone identifies bifurcating developmental trajectories from single-cell data
Nature Biotechnology, 2016, 34, 637-645
19.7603Citations (PDF)
62PD-1 Blockade Expands Intratumoral Memory T Cells
Cancer Immunology Research, 2016, 4, 194-203
3.1382Citations (PDF)
63Detection of minimal residual disease in B lymphoblastic leukemia using viSNE
Cytometry Part B - Clinical Cytometry, 2015, 88, 294-304
1.446Citations (PDF)
64Scalable microfluidics for single-cell RNA printing and sequencing
Genome Biology, 2015, 16,
12.2135Citations (PDF)
65Context Sensitive Modeling of Cancer Drug Sensitivity
PLoS ONE, 2015, 10, e0133850
1.513Citations (PDF)
66Interferon α/β Enhances the Cytotoxic Response of MEK Inhibition in Melanoma
Molecular Cell, 2015, 57, 784-796
8.633Citations (PDF)
67Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands
Proceedings of the National Academy of Sciences of the United States of America, 2015, 112,
5.2272Citations (PDF)
68Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis
Cell, 2015, 162, 184-197
23.42,460Citations (PDF)
69Trajectories of cell-cycle progression from fixed cell populations
Nature Methods, 2015, 12, 951-954
13.1110Citations (PDF)
70Integration of Genomic Data Enables Selective Discovery of Breast Cancer Drivers
Cell, 2014, 159, 1461-1475
23.487Citations (PDF)
71Conditional density-based analysis of T cell signaling in single-cell data
Science, 2014, 346,
26.1223Citations (PDF)
72Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development
Cell, 2014, 157, 714-725
23.4956Citations (PDF)
73Single-cell mass cytometry of TCR signaling: Amplification of small initial differences results in low ERK activation in NOD mice
Proceedings of the National Academy of Sciences of the United States of America, 2014, 111, 16466-16471
5.253Citations (PDF)
74viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia
Nature Biotechnology, 2013, 31, 545-552
19.71,616Citations (PDF)
75Environmental Stresses Disrupt Telomere Length Homeostasis
PLoS Genetics, 2013, 9, e1003721
2.2104Citations (PDF)
76Genotype-Environment Interactions Reveal Causal Pathways That Mediate Genetic Effects on Phenotype
PLoS Genetics, 2013, 9, e1003803
2.284Citations (PDF)
77Mapping Differentiation under Mixed Culture Conditions Reveals a Tunable Continuum of T Cell Fates
PLoS Biology, 2013, 11, e1001616
3.196Citations (PDF)
78RHPN2 Drives Mesenchymal Transformation in Malignant Glioma by Triggering RhoA Activation
Cancer Research, 2013, 73, 5140-5150
2.656Citations (PDF)
79Normalization of mass cytometry data with bead standards
Cytometry Part A: the Journal of the International Society for Analytical Cytology, 2013, 83A, 483-494
1.6801Citations (PDF)
80Inference of modules associated to eQTLs
Nucleic Acids Research, 2012, 40, e98-e98
10.712Citations (PDF)
81Using systems and structure biology tools to dissect cellular phenotypes
Journal of the American Medical Informatics Association: JAMIA, 2012, 19, 171-175
3.36Citations (PDF)
82Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum
Science, 2011, 332, 687-696
26.12,322Citations (PDF)
83Modulatory profiling identifies mechanisms of small molecule-induced cell death
Proceedings of the National Academy of Sciences of the United States of America, 2011, 108,
5.2127Citations (PDF)
84An Integrated Approach to Uncover Drivers of Cancer
Cell, 2010, 143, 1005-1017
23.4473Citations (PDF)
85Learning Signaling Network Structures with Sparsely Distributed Data
Journal of Computational Biology, 2009, 16, 201-212
0.725Citations (PDF)
86Modularity and interactions in the genetics of gene expression
Proceedings of the National Academy of Sciences of the United States of America, 2009, 106, 6441-6446
5.258Citations (PDF)
87Harnessing gene expression to identify the genetic basis of drug resistance
Molecular Systems Biology, 2009, 5,
3.648Citations (PDF)
88Learning a Prior on Regulatory Potential from eQTL Data
PLoS Genetics, 2009, 5, e1000358
2.2191Citations (PDF)
89High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis
Nature Biotechnology, 2009, 27, 1173-1175
19.7390Citations (PDF)
90Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification
Proceedings of the National Academy of Sciences of the United States of America, 2006, 103, 14062-14067
5.2128Citations (PDF)
91Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
Nature Genetics, 2003, 34, 166-176
14.11,596Citations (PDF)
92Minreg: Inferring an active regulator set
Bioinformatics, 2002, 18, S258-S267
3.263Citations (PDF)
93Inferring subnetworks from perturbed expression profiles
Bioinformatics, 2001, 17, S215-S224
3.2432Citations (PDF)
94Using Bayesian Networks to Analyze Expression Data
Journal of Computational Biology, 2000, 7, 601-620
0.72,725Citations (PDF)
95The Human Cell Atlas
ELife, 0, 6,
1.02,374Citations (PDF)
96Transcriptomic Plasticity Is a Hallmark of Metastatic Pancreatic Cancer
Cancer Research, 0, 86, 1769-1796
2.63Citations (PDF)