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Author Details

Kai Tan
University of Pennsylvania
1999
75
33
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36255409Characterization of Leukemic Resistance to CD19-Targeted CAR T-cell Therapy through Deep Genomic Sequencing.Cancer Immunol Res2023
37536952RUNX1 is required in granulocyte-monocyte progenitors to attenuate inflammatory cytokine production by neutrophils.Genes Dev2023
36723808Integrating Single-Cell Methylome and Transcriptome Data with MAPLE.Methods Mol Biol2023
36747636RUNX1 is required in granulocyte-monocyte progenitors to attenuate inflammatory cytokine production by neutrophils.bioRxiv2023
34864916Single-cell multiomics reveals increased plasticity, resistant populations, and stem-cell-like blasts in KMT2A-rearranged leukemia.Blood2022
36084669LncRNA AC026401.3 interacts with OCT1 to intensify sorafenib and lenvatinib resistance by activating E2F2 signaling in hepatocellular carcinoma.Exp Cell Res2022
36113481Control of ribosomal RNA synthesis by hematopoietic transcription factors.Mol Cell2022
35245372Endothelial MEKK3-KLF2/4 signaling integrates inflammatory and hemodynamic signals during definitive hematopoiesis.Blood2022
33423324Dynamic Transcriptional and Epigenetic Changes Drive Cellular Plasticity in the Liver.Hepatology2021
33853780CytoTalk: De novo construction of signal transduction networks using single-cell transcriptomic data.Sci Adv2021
33569577RUNX-1 haploinsufficiency causes a marked deficiency of megakaryocyte-biased hematopoietic progenitor cells.Blood2021
33820778Integrative Bulk and Single-Cell Profiling of Premanufacture T-cell Populations Reveals Factors Mediating Long-Term Persistence of CAR T-cell Therapy.Cancer Discov2021
34675061Efficient hemogenic endothelial cell specification by RUNX1 is dependent on baseline chromatin accessibility of RUNX1-regulated TGFβ target genes.Genes Dev2021
34717611Analysis of multiple gene co-expression networks to discover interactions favoring CFTR biogenesis and οF508-CFTR rescue.BMC Med Genomics2021
34210682Network Analysis Reveals Synergistic Genetic Dependencies for Rational Combination Therapy in Philadelphia Chromosome-Like Acute Lymphoblastic Leukemia.Clin Cancer Res2021
33219054Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data.Genome Res2021
32127393Dissecting the Tumor-Immune Landscape in Chimeric Antigen Receptor T-cell Therapy: Key Challenges and Opportunities for a Systems Immunology Approach.Clin Cancer Res2020
31871269Mechanisms of Entrectinib Resistance in a Neuroblastoma Xenograft Model.Mol Cancer Ther2020
32832663Diverse noncoding mutations contribute to deregulation of cis-regulatory landscape in pediatric cancers.Sci Adv2020
32392346Developmental trajectory of prehematopoietic stem cell formation from endothelium.Blood2020
32312293scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data.Genome Biol2020
32499402Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells.Genes Dev2020
32208490Runx1 negatively regulates inflammatory cytokine production by neutrophils in response to Toll-like receptor signaling.Blood Adv2020
30606806H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification.Science2019
31851943Spatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells.Cell Rep2019
31488706A lineage-resolved molecular atlas of <i>C. elegans</i> embryogenesis at single-cell resolution.Science2019
31097707Optimal control nodes in disease-perturbed networks as targets for combination therapy.Nat Commun2019
31060596SCRABBLE: single-cell RNA-seq imputation constrained by bulk RNA-seq data.Genome Biol2019
30910956Risk variants disrupting enhancers of T<sub>H</sub>1 and T<sub>REG</sub> cells in type 1 diabetes.Proc Natl Acad Sci U S A2019
29282253Maturation of hematopoietic stem cells from prehematopoietic stem cells is accompanied by up-regulation of PD-L1.J Exp Med2018
30391350RUNX1 and the endothelial origin of blood.Exp Hematol2018
29472540Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility.Nat Commun2018
29453388Identifying noncoding risk variants using disease-relevant gene regulatory networks.Nat Commun2018
28844837Prostaglandin E1 and Its Analog Misoprostol Inhibit Human CML Stem Cell Self-Renewal via EP4 Receptor Activation and Repression of AP-1.Cell Stem Cell2017
29181104Recombinant human adenovirus-p53 improves the outcome of mid-late stage pancreatic cancer via arterial infusion.Oncol Lett2017
28912419Identifying topologically associating domains and subdomains by Gaussian Mixture model And Proportion test.Nat Commun2017
28588017CD27 marks murine embryonic hematopoietic stem cells and type II prehematopoietic stem cells.Blood2017
26950762Understanding transcriptional regulatory networks using computational models.Curr Opin Genet Dev2016
27986453CD8<sup>+</sup> T Cells Utilize Highly Dynamic Enhancer Repertoires and Regulatory Circuitry in Response to Infections.Immunity2016
27679570Correction: Functional screen identifies regulators of murine hematopoietic stem cell repopulation.J Exp Med2016
27515742EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types.Bioinformatics2016
273717234DGenome: a comprehensive database of chromatin interactions.Bioinformatics2016
26773050FLAGS: A Flexible and Adaptive Association Test for Gene Sets Using Summary Statistics.Genetics2016
26880577Functional screen identifies regulators of murine hematopoietic stem cell repopulation.J Exp Med2016
257886214DGenome: a comprehensive database of chromatin interactions.Bioinformatics2015
26165925Runx1 Deficiency Decreases Ribosome Biogenesis and Confers Stress Resistance to Hematopoietic Stem and Progenitor Cells.Cell Stem Cell2015
26083688Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks.PLoS Comput Biol2015
26214128A microfluidic device for epigenomic profiling using 100 cells.Nat Methods2015
24217919Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets.Nucleic Acids Res2014
25395663Inflammatory signaling regulates embryonic hematopoietic stem and progenitor cell production.Genes Dev2014
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Collaborators

Nancy A Speck
Perelman School of Medicine, University of Pennsylvania
Co-authored papers 14
Timothy Ravasi
Okinawa Institute of Science and Technology Graduate University
Co-authored papers 6
Gregory M Chen
University of Pennsylvania
Co-authored papers 5
Trey Ideker (CM4AI)
University of California San Diego
Co-authored papers 5
David M Barrett
Co-authored papers 4
Gary D Stormo
Washington University in St. Louis
Co-authored papers 4
Jesper Tegn??r
King Abdullah University of Science and Technology (KAUST)
Co-authored papers 3
Stephan A Grupp
Co-authored papers 3
Guolian Kang
Co-authored papers 2
Piero Carninci
RIKEN Center for Integrative Medical Sciences
Co-authored papers 2
David A Hume
Mater Research Institute-UQ, Translational Research Institute
Co-authored papers 2
Kengo Imamura
Co-authored papers 2
Colin Luo
University of California San Diego
Co-authored papers 2
Hoda Feizi
Co-authored papers 2
Erik van Nimwegen
University of Basel
Co-authored papers 2
Sean M Grimmond
The University of Melbourne
Co-authored papers 2
Alistair R R Forrest
RIKEN Center for Integrative Medical Sciences
Co-authored papers 2
Vladimir B Bajic
King Abdullah University of Science and Technology (KAUST)
Co-authored papers 2
Michihira Tagami
RIKEN Center for Integrative Medical Sciences
Co-authored papers 2
Ryoko Ishihara
National Institute of Animal Health
Co-authored papers 2
Mandeep Kaur
Post Graduate Institute of Medical Education and Research
Co-authored papers 2
Oliver Hofmann
University of Melbourne
Co-authored papers 2
Altuna Akalin
Berlin Institute for Medical Systems Biology
Co-authored papers 2
Hideya Kawaji
RIKEN Center for Integrative Medical Sciences
Co-authored papers 2
Kayoko Murakami
Co-authored papers 2
Sarah K Tasian
Co-authored papers 2
Rohan D Teasdale
The University of Queensland
Co-authored papers 2
Winston Hide
Harvard Medical School
Co-authored papers 2
Carsten O Daub
International Institute of Molecular and Cell Biology in Warsaw
Co-authored papers 2
Noriko Ninomiya
Japan Tobacco Inc.
Co-authored papers 2
Release 1.2