An immunophenotype-coupled transcriptomic atlas of human hematopoietic progenitors. Nature Immunology. 2024; 25:703-715.
.Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy. Science Translational Medicine. 2024; 16:eade2886.
.Decision level integration of unimodal and multimodal single cell data with scTriangulate. Nature Communications. 2023; 14:406.
. .Retinoid X receptor promotes hematopoietic stem cell fitness and quiescence and preserves hematopoietic homeostasis. Blood. 2023; 141:592-608.
.Erythroblastic islands foster granulopoiesis in parallel to terminal erythropoiesis. Blood. 2022; 140:1621-1634.
.CellDrift: inferring perturbation responses in temporally sampled single-cell data. Briefings in Bioinformatics. 2022; 23.
.Bromodomain inhibition overcomes treatment resistance in distinct molecular subtypes of melanoma. Proceedings of the National Academy of Sciences of USA. 2022; 119:e2206824119.
.A census of the lung: CellCards from LungMAP. Developmental Cell. 2022; 57:112-145.e2.
.Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. Nature Communications. 2021; 12:6324.
.DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity. Briefings in Bioinformatics. 2021; 22.
.In situ mapping identifies distinct vascular niches for myelopoiesis. Nature. 2021; 590:457-462.
.Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers. Nature Communications. 2020; 11:6374.
.Protocol for Identification and Removal of Doublets with DoubletDecon. Star Protocols. 2020; 1:100085.
.Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF. Bioinformatics. 2020; 36:3773-3780.
.Mouse models of neutropenia reveal progenitor-stage-specific defects. Nature. 2020; 582:109-114.
.MBNL1 regulates essential alternative RNA splicing patterns in MLL-rearranged leukemia. Nature Communications. 2020; 11:2369.
.Asymmetrically Segregated Mitochondria Provide Cellular Memory of Hematopoietic Stem Cell Replicative History and Drive HSC Attrition. Cell Stem Cell. 2020; 26:420-430.e6.
.Unraveling bone marrow architecture. Nature Cell Biology. 2020; 22:5-6.
.cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes. Nucleic Acids Research (NAR). 2019; 47:e138.
.DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing Data. Cell Reports. 2019; 29:1718-1727.e8.
.Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia. Cancer Discovery. 2019; 9:1080-1101.
.U2AF1 mutations induce oncogenic IRAK4 isoforms and activate innate immune pathways in myeloid malignancies. Nature Cell Biology. 2019; 21:640-650.
.The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. Developmental Cell. 2019; 49:10-29.
.Investigating Cell Fate Decisions with ICGS Analysis of Single Cells. Methods in molecular biology (Clifton, N.J.). 2019; 1975:251-275.
.Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis. Nature Communications. 2018; 9:4906.
.The Human Cell Atlas bone marrow single-cell interactive web portal. Experimental Hematology. 2018; 68:51-61.
.SKI controls MDS-associated chronic TGF-β signaling, aberrant splicing, and stem cell fitness. Blood. 2018; 132:e24-e34.
.The Molecular Signature of Megakaryocyte-Erythroid Progenitors Reveals a Role for the Cell Cycle in Fate Specification. Cell Reports. 2018; 25:2083-2093.e4.
.Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. Nature Genetics. 2018; 50:699-707.
.Cross-platform single cell analysis of kidney development shows stromal cells express Gdnf. Developmental Biology. 2018; 434:36-47.
.2017; 130:770.
. Integrative Epigenetic and Single-Cell RNA-Seq Profiling of Human Hematopoietic Stem Cells Reveals Epigenetic Reprogramming of Enhancer and Regulatory Elements during Normal Aging. Blood.Granulocyte-Monocyte Progenitors and Monocyte-Dendritic Cell Progenitors Independently Produce Functionally Distinct Monocytes. Immunity. 2017; 47:890-902.e4.
.Transcriptomic and epigenomic differences in human induced pluripotent stem cells generated from six reprogramming methods. Nature Biomedical Engineering. 2017; 1:826-837.
.Molecular Characterization of Pediatric Restrictive Cardiomyopathy from Integrative Genomics. Scientific Reports. 2017; 7:39276.
.Single-cell analysis of mixed-lineage states leading to a binary cell fate choice. Nature. 2016; 537:698-702.
.Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium. Stem Cell Reports. 2016; 7:110-125.
.DNMT3A Haploinsufficiency Transforms FLT3ITD Myeloproliferative Disease into a Rapid, Spontaneous, and Fully Penetrant Acute Myeloid Leukemia. Cancer Discovery. 2016; 6:501-515.
.Systems biology evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity. BMC Medical Genomics. 2015; 8:67.
.The kSORT assay to detect renal transplant patients at high risk for acute rejection: results of the multicenter AART study. PLoS Medicine. 2014; 11:e1001759.
.Systems-level perspective of sudden infant death syndrome. Pediatric Research. 2014; 76:220-229.
.GO-Elite: a flexible solution for pathway and ontology over-representation. Bioinformatics. 2012; 28:2209-2210.
.AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Research (NAR). 2010; 38:W755-W762.
.Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Proceedings of the National Academy of Sciences of USA. 2010; 107:10514-10519.
.G(i)-coupled GPCR signaling controls the formation and organization of human pluripotent colonies. PloS one. 2009; 4:e7780.
.Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. PLoS Computational Biology. 2009; 5:e1000553.
.Identification of Spt5 target genes in zebrafish development reveals its dual activity in vivo. PloS one. 2008; 3:e3621.
.GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics. 2007; 8:217.
.Time- and exercise-dependent gene regulation in human skeletal muscle. Genome Biology: biology for the post-genomic era. 2003; 4:R61.
.MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biology: biology for the post-genomic era. 2003; 4:R7.
.GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nature Genetics. 2002; 31:19-20.
.Conditional expression of a Gi-coupled receptor causes ventricular conduction delay and a lethal cardiomyopathy. Proceedings of the National Academy of Sciences of USA. 2000; 97:4826-4831.
.RNA Isoforms as Broad Targets for Cancer Immunotherapy. DNA and Cell Biology. 2024; 43:363-368.
.Temporal dynamics and genomic programming of plasma cell fates. Nature Immunology. 2024; 25:1097-1109.
.An immunophenotype-coupled transcriptomic atlas of human hematopoietic progenitors. Nature Immunology. 2024; 25:703-715.
.LungMAP Portal Ecosystem: Systems-level Exploration of the Lung. American Journal of Respiratory Cell and Molecular Biology. 2024; 70:129-139.
.Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy. Science Translational Medicine. 2024; 16:eade2886.
.Sex-associated differences in frequencies and prognostic impact of recurrent genetic alterations in adult acute myeloid leukemia (Alliance, AMLCG). Leukemia. 2024; 38:45-57.
.Slow cycling and durable Flt3+ progenitors contribute to hematopoiesis under native conditions. The Journal of Experimental Medicine. 2024; 221.
.Guided construction of single cell reference for human and mouse lung. Nature Communications. 2023; 14:4566.
.Sinus venosus adaptation models prolonged cardiovascular disease and reveals insights into evolutionary transitions of the vertebrate heart. Nature Communications. 2023; 14:5509.
.Decision level integration of unimodal and multimodal single cell data with scTriangulate. Nature Communications. 2023; 14:406.
.Population-level single-cell genomics reveals conserved gene programs in systemic juvenile idiopathic arthritis. The Journal of Clinical Investigation. 2023; 133.
.2023; 142:837.
. Genomic Profiles and Associated Survival Prognosticators in Black Patients with Acute Myeloid Leukemia. Blood.Development of a Single-Neurosphere Culture to Assess Radiation Toxicity and Pre-Clinical Cancer Combination Therapy Safety. Cancers. 2023; 15.
.Repression of TRIM13 by chromatin assembly factor CHAF1B is critical for AML development. Blood Advances. 2023; 7:4822-4837.
.ThPOK is a critical multifaceted regulator of myeloid lineage development. Nature Immunology. 2023; 24:1295-1307.
.pyInfinityFlow: optimized imputation and analysis of high-dimensional flow cytometry data for millions of cells. Bioinformatics. 2023; 39.
.2023; 210:250.13.
. High-throughput workflow leveraging spectral flow cytometry and CITE-seq to characterize human bone marrow across race and gender. Journal of immunology (Baltimore, Md. : 1950).2023; 210:65.01.
. Th2 immune responses induced by helminth infection reprogram multilineage progenitors to produce successive waves of neutrophils, basophils, and eosinophils. Journal of immunology (Baltimore, Md. : 1950).2023; 210:65.05.
. Live bacterial ligands universally regulate mTOR activity but are not essential for homeostatic innate immunity. Journal of immunology (Baltimore, Md. : 1950).BAFF and APRIL counterregulate susceptibility to inflammation-induced preterm birth. Cell Reports. 2023; 42:112352.
. .Retinoid X receptor promotes hematopoietic stem cell fitness and quiescence and preserves hematopoietic homeostasis. Blood. 2023; 141:592-608.
.Ontogeny and function of the circadian clock in intestinal organoids. The EMBO Journal. 2022; 41:e106973.
.2022; 140:1234-1235.
. De Novo Germline DHX38 Variant Associated with Alternative Splicing of Multiple Transcripts in Iron-Related Pathways in a Patient with Atypical Congenital Dyserythropoietic Anemia with Ring Sideroblasts. Blood.2022; 140:1981-1982.
. Hematopoietic Flt3+ Multipotent Progenitors Are Organized in Discrete Functionally and Hierarchically Distinct Populations. Blood.2022; 140:2978-2979.
. TRIM13 Is a Novel Cell Cycle Hub Regulated By CHAF1B to Promote Acute Myeloid Leukemogenesis. Blood.2022; 140:9103-9104.
. Metallothionein 1 (MT1) Is Selectively Required for DNMT3A;NPM1-Mutant Acute Myeloid Leukemia Proliferation. Blood.2022; 140:936-939.
. Sex-Associated Differences in Frequencies and Outcome Prognostication of Recurrent Molecular Features in Adults with Acute Myeloid Leukemia (AML) (AMLCG, CALGB [Alliance]). Blood.2022; 140:2856.
. Identification and Isolation of Hematopoietic Stem Cells and Progenitors with Discrete Developmental Gene Expression Programs. Blood.2022; 140:9759-9760.
. Single-Cell Multiomics Reveal Hypomethylating Agent Partially Restores Hematopoiesis in a LR-MDS Patient at the Cost of Leukemic Transformation. Blood.Erythroblastic islands foster granulopoiesis in parallel to terminal erythropoiesis. Blood. 2022; 140:1621-1634.
.Fetal maturation revealed by amniotic fluid cell-free transcriptome in rhesus macaques. JCI insight. 2022; 7.
.Multiple Nf1 Schwann cell populations reprogram the plexiform neurofibroma tumor microenvironment. JCI insight. 2022; 7.
.CellDrift: inferring perturbation responses in temporally sampled single-cell data. Briefings in Bioinformatics. 2022; 23.
.Bromodomain inhibition overcomes treatment resistance in distinct molecular subtypes of melanoma. Proceedings of the National Academy of Sciences of USA. 2022; 119:e2206824119.
.The balance between protective and pathogenic immune responses to pneumonia in the neonatal lung is enforced by gut microbiota. Science Translational Medicine. 2022; 14:eabl3981.
.2022; 208:168.08.
. Developmental dynamics and genomic programming of GC-derived precursors that give rise to long lived plasma cells. Journal of immunology (Baltimore, Md. : 1950).A potent myeloid response is rapidly activated in the lungs of premature Rhesus macaques exposed to intra-uterine inflammation. Mucosal Immunology. 2022; 15:730-744.
.LAMP-5 is an essential inflammatory-signaling regulator and novel immunotherapy target for mixed lineage leukemia-rearranged acute leukemia. Haematologica: the hematology journal. 2022; 107:803-815.
.Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates. Science Translational Medicine. 2022; 14:eabl8574.
.Induced cell-autonomous neutropenia systemically perturbs hematopoiesis in Cebpa enhancer-null mice. Blood Advances. 2022; 6:1406-1419.
.A census of the lung: CellCards from LungMAP. Developmental Cell. 2022; 57:112-145.e2.
.2022; 111:s72.
. 3055 – METALLOTHIONEIN 1 (MT1) AS A TARGETABLE DEPENDENCY IN ACUTE MYELOID LEUKEMIA. Experimental Hematology.2022; 111:s35.
. 2007 – IDENTIFICATION AND ISOLATION OF HEMATOPOIETIC STEM CELLS AND PROGENITORS WITH DISCRETE DEVELOPMENTAL GENE EXPRESSION PROGRAMS. Experimental Hematology.2022; 111:s142.
. 3194 – LIVE BACTERIAL LIGANDS PROGRAM CORE HEMATOPOIETIC GENE EXPRESSION. Experimental Hematology.Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data. Star Protocols. 2021; 2:100989.
.GM-CSF Programs Hematopoietic Stem and Progenitor Cells During Candida albicans Vaccination for Protection Against Reinfection. Frontiers in Immunology. 2021; 12:790309.
.Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. Nature Communications. 2021; 12:6324.
.Progenitor translatome changes coordinated by Tsc1 increase perception of Wnt signals to end nephrogenesis. Nature Communications. 2021; 12:6332.
.DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity. Briefings in Bioinformatics. 2021; 22.
.2021; 2021.10.16.464640.
. scTriangulate, a game-theory based framework for optimal solutions of uni- and multimodal single-cell data.IFN-γ is essential for alveolar macrophage-driven pulmonary inflammation in macrophage activation syndrome. JCI insight. 2021; 6.
.Prevalence of Homologous Recombination Pathway Gene Mutations in Melanoma: Rationale for a New Targeted Therapeutic Approach. Journal of Investigative Dermatology. 2021; 141:2028-2036.e2.
.Coupled analysis of transcriptome and BCR mutations reveals role of OXPHOS in affinity maturation. Nature Immunology. 2021; 22:904-913.
.PKM2-dependent metabolic skewing of hepatic Th17 cells regulates pathogenesis of non-alcoholic fatty liver disease. Cell Metabolism. 2021; 33:1187-1204.e9.
.Pseudocell Tracer-A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination. PLoS Computational Biology. 2021; 17:e1008094.
.The Rhesus Macaque Serves As a Model for Human Lateral Branch Nephrogenesis. Journal of the American Society of Nephrology : JASN. 2021; 32:1097-1112.
.Cannabidiol Treatment Results in a Common Gene Expression Response Across Aggressive Cancer Cells from Various Origins. Cannabis and Cannabinoid Research. 2021; 6:148-155.
.In situ mapping identifies distinct vascular niches for myelopoiesis. Nature. 2021; 590:457-462.
.Short-term exposure to intermittent hypoxia leads to changes in gene expression seen in chronic pulmonary disease. eLife. 2021; 10.
.Differential transcriptome response to proton versus X-ray radiation reveals novel candidate targets for combinatorial PT therapy in lymphoma. Radiotherapy and Oncology. 2021; 155:293-303.
.Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers. Nature Communications. 2020; 11:6374.
.FOXO activity adaptation safeguards the hematopoietic stem cell compartment in hyperglycemia. Blood Advances. 2020; 4:5512-5526.
.Protocol for Identification and Removal of Doublets with DoubletDecon. Star Protocols. 2020; 1:100085.
.Combinatorial Single-Cell Analyses of Granulocyte-Monocyte Progenitor Heterogeneity Reveals an Early Uni-potent Neutrophil Progenitor. Immunity. 2020; 53:303-318.e5.
.Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF. Bioinformatics. 2020; 36:3773-3780.
.Mouse models of neutropenia reveal progenitor-stage-specific defects. Nature. 2020; 582:109-114.
.MBNL1 regulates essential alternative RNA splicing patterns in MLL-rearranged leukemia. Nature Communications. 2020; 11:2369.
.PHIP drives glioblastoma motility and invasion by regulating the focal adhesion complex. Proceedings of the National Academy of Sciences of USA. 2020; 117:9064-9073.
.Asymmetrically Segregated Mitochondria Provide Cellular Memory of Hematopoietic Stem Cell Replicative History and Drive HSC Attrition. Cell Stem Cell. 2020; 26:420-430.e6.
.Pbx4 limits heart size and fosters arch artery formation by partitioning second heart field progenitors and restricting proliferation. Development (Cambridge). 2020; 147.
.Unraveling bone marrow architecture. Nature Cell Biology. 2020; 22:5-6.
.