Clifford A. Meyer
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View article: LBA90 Prospective randomized phase II trial of 177Lutetium-PSMA therapy neoadjuvant to stereotactic ablative radiotherapy for recurrent oligo-metastatic hormone-sensitive prostate cancer (LUNAR NCT05496959)
LBA90 Prospective randomized phase II trial of 177Lutetium-PSMA therapy neoadjuvant to stereotactic ablative radiotherapy for recurrent oligo-metastatic hormone-sensitive prostate cancer (LUNAR NCT05496959) Open
View article: Expanding the DNA Motif Lexicon of the Transcriptional Regulatory Code
Expanding the DNA Motif Lexicon of the Transcriptional Regulatory Code Open
Transcriptional regulatory sequences in metazoans contain intricate combinations of transcription factor (TF) motifs. Stereospecific arrangements of simple motifs constitute composite elements (CEs) that enhance DNA-protein interaction spe…
View article: Informatics at the Frontier of Cancer Research
Informatics at the Frontier of Cancer Research Open
Digitized healthcare data, high-throughput profiling technologies, and data repositories have facilitated the emergence of a new era of cancer research. Each data stream requires specialized analysis methods for interpretation. The data-dr…
View article: Supplementary Data from Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer
Supplementary Data from Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer Open
Supplementary Data include: 1, Supplementary Methods: a detailed description of data processing, computational analysis, and web interface functions; 2, Supplementary References; 3, Supplementary Figures 1-6: Fig. S1: Cancer sample reclust…
View article: Supplementary Data from Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer
Supplementary Data from Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer Open
Supplementary Data include: 1, Supplementary Methods: a detailed description of data processing, computational analysis, and web interface functions; 2, Supplementary References; 3, Supplementary Figures 1-6: Fig. S1: Cancer sample reclust…
View article: Supplementary Video S1 from Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer
Supplementary Video S1 from Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer Open
Cistrome Cancer overview.
View article: Supplementary Video S1 from Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer
Supplementary Video S1 from Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer Open
Cistrome Cancer overview.
View article: Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation
Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation Open
View article: Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation
Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation Open
Summary Enteroendocrine cells (EECs), which secrete serotonin (enterochromaffin cells, EC) or a dominant peptide hormone, serve vital physiologic functions. As with any adult human lineage, the basis for terminal cell diversity remains obs…
View article: Cistrome Data Browser: integrated search, analysis and visualization of chromatin data
Cistrome Data Browser: integrated search, analysis and visualization of chromatin data Open
The Cistrome Data Browser is a resource of ChIP-seq, ATAC-seq and DNase-seq data from humans and mice. It provides maps of the genome-wide locations of transcription factors, cofactors, chromatin remodelers, histone post-translational modi…
View article: Multi-batch single-cell comparative atlas construction by deep learning disentanglement
Multi-batch single-cell comparative atlas construction by deep learning disentanglement Open
Cell state atlases constructed through single-cell RNA-seq and ATAC-seq analysis are powerful tools for analyzing the effects of genetic and drug treatment-induced perturbations on complex cell systems. Comparative analysis of such atlases…
View article: MetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment
MetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment Open
Recent advances in single-cell RNA sequencing have shown heterogeneous cell types and gene expression states in the non-cancerous cells in tumors. The integration of multiple scRNA-seq datasets across tumors can indicate common cell types …
View article: Figure S2 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Figure S2 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha Open
ESRRA inhibition induces antitumor immunity in vivo.
View article: Figure S16 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Figure S16 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha Open
Validation of bipotent regulators of angiogenesis or growth-suppressor.
View article: Figure S5 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Figure S5 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha Open
Robust in vivo antitumor elimination by ESRRA inhibition.
View article: Figure S9 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Figure S9 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha Open
ESRRAi does not affect CD8+T T-cells, and ESRRA activity increases post-immunotherapy in resistant tumors.
View article: Figure S13 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Figure S13 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha Open
Kaplan–Meier plots showing progression-free survival and overall survival differences for patients receiving anti-PD1 between the low-risk and high-risk groups defined by the median value of deepBTAS.
View article: Figure S2 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Figure S2 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha Open
ESRRA inhibition induces antitumor immunity in vivo.
View article: Figure S4 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Figure S4 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha Open
ESRRA inhibition correlated with immune infiltrations and proinflammatory signaling in patient tumors.
View article: Figure S14 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Figure S14 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha Open
Evaluation of bulk-BipotentR (BipotentR without single-cell sub-module).
View article: Figure S8 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Figure S8 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha Open
The effect of ESRRA inhibition on tumor microenvironments at single-cell resolutions.
View article: Figure S7 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Figure S7 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha Open
Energy metabolism and immune signaling by targeting ESRRA in vitro.
View article: Data from <i>BCOR</i> and <i>BCORL1</i> Mutations Drive Epigenetic Reprogramming and Oncogenic Signaling by Unlinking PRC1.1 from Target Genes
Data from <i>BCOR</i> and <i>BCORL1</i> Mutations Drive Epigenetic Reprogramming and Oncogenic Signaling by Unlinking PRC1.1 from Target Genes Open
Polycomb repressive epigenetic complexes are recurrently dysregulated in cancer. Unlike polycomb repressive complex 2 (PRC2), the role of PRC1 in oncogenesis and therapy resistance is not well-defined. Here, we demonstrate that highly recu…
View article: Figure S15 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Figure S15 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha Open
Evaluation of scRNA-BipotentR (BipotentR without bulk-tumor sub-module).
View article: Figure S14 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Figure S14 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha Open
Evaluation of bulk-BipotentR (BipotentR without single-cell sub-module).
View article: Supplementary Figure from <i>BCOR</i> and <i>BCORL1</i> Mutations Drive Epigenetic Reprogramming and Oncogenic Signaling by Unlinking PRC1.1 from Target Genes
Supplementary Figure from <i>BCOR</i> and <i>BCORL1</i> Mutations Drive Epigenetic Reprogramming and Oncogenic Signaling by Unlinking PRC1.1 from Target Genes Open
Supplementary Figure from BCOR and BCORL1 Mutations Drive Epigenetic Reprogramming and Oncogenic Signaling by Unlinking PRC1.1 from Target Genes
View article: Figure S19 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Figure S19 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha Open
Expression of markers of M1 and M2 in scRNA data of ESRRAi and Vehicle treated mice.
View article: Supplementary Notes from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Supplementary Notes from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha Open
We detailed a comparison of BipotentR with competing and alternative approaches in Supplementary notes 1, 2, 6, and 7. Supplementary Note 3-5 describes the in vitro findings of ESRRA, the potential clinical relevance of ESRRA across cancer…
View article: Figure S3 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Figure S3 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha Open
ESRRA inhibition is associated with immune infiltrations and proinflammatory signaling in patient tumors.
View article: Supplementary tables from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha
Supplementary tables from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha Open
S1: TFCRs of energy metabolism S2: Bipotent TFCRs S3: Log fold change of T-cell mediated killing upon knockout of OXPHOS genes S4: Log fold change of MHC-I protien expression upon knockout of OXPHOS genes S5: Bipotent TFCRs of angiogenesis…