Author details

Full Name

Clifford A Meyer

Affiliation

ORCID

Career Start Year

2005

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37433791	Multi-batch single-cell comparative atlas construction by deep learning disentanglement.		2023
37971305	Cistrome Data Browser: integrated search, analysisÂ and visualization of chromatin data.		2023
37149682	MetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment.		2023
36745048	Discovery of Targets for Immune-Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha.	Cancer Discov	2023
36688700	Cistrome Explorer: an interactive visual analysis tool for large-scale epigenomic data.	Bioinformatics	2023
35015684	BCOR and BCORL1 Mutations Drive Epigenetic Reprogramming and Oncogenic Signaling by Unlinking PRC1.1 from Target Genes.	Blood Cancer Discov	2022
35561684	Topical therapy for regression and melanoma prevention of congenital giant nevi.	Cell	2022
36130957	Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA.	Nat Commun	2022
36068320	MIRA: joint regulatory modeling of multimodal expression and chromatin accessibility in single cells.	Nature Methods	2022
34772935	Fast alignment and preprocessing of chromatin profiles with Chromap.	Nature Communications	2021
33589424	Therapeutically Increasing MHC-I Expression Potentiates Immune Checkpoint Blockade.	Cancer Discov	2021
33997789	CDK4/6 inhibition reprograms the breast cancer enhancer landscape by stimulating AP-1 transcriptional activity.	Nat Cancer	2021
33051080	Computational Approaches to Modeling Transcription Factor Activity and Gene Regulation.	Trends in Biochemical Sciences	2020
32374402	Hdac3 is an epigenetic inhibitor of the cytotoxicity program in CD8 T cells.	J Exp Med	2020
32424124	Determinants of transcription factor regulatory range.	Nature Communications	2020
32441763	Correction: Hdac3 is an epigenetic inhibitor of the cytotoxicity program in CD8 T cells.	J Exp Med	2020
32767996	Integrative analyses of single-cell transcriptome and regulome using MAESTRO.		2020
33059736	Clonal tracing reveals diverse patterns of response to immune checkpoint blockade.	Genome Biol	2020
31053864	Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks.	Nucleic Acids Research	2019
30462313	Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis.	Nucleic Acids Research	2019
29863497	ATR inhibition controls aggressive prostate tumors deficient in Y-linked histone demethylase KDM5D.	J Clin Invest	2018
29868757	Improved design and analysis of CRISPR knockout screens.	Bioinformatics	2018
28289232	Transcriptional landscape of the human cell cycle.	Proc Natl Acad Sci U S A	2017
29092931	Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer.	Cancer Res	2017
27789702	Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse.	Nucleic Acids Res	2017
27716038	ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.	BMC Bioinformatics	2016
26735014	Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer.	Nature	2016
27466232	Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles.	Genome Res	2016
27072482	High-dimensional genomic data bias correction and data integration using MANCIE.	Nat Commun	2016
26063738	Sequence determinants of improved CRISPR sgRNA design.	Genome Research	2015
26518695	Network analysis of gene essentiality in functional genomics experiments.	Genome Biol	2015
25223782	Identifying and mitigating bias in next-generation sequencing methods for chromatin biology.	Nature Reviews Genetics	2014
25344755	Cyclin C is a haploinsufficient tumour suppressor.	Nat Cell Biol	2014
24317252	Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification.	Nat Methods	2014
25103624	MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes.	Genome Biol	2014
24093963	A systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer.	BMC Genomics	2013
25411587	MULTIPLE TESTING OF LOCAL MAXIMA FOR DETECTION OF PEAKS IN CHIP-SEQ DATA.	Annals of Applied Statistics	2013
24263090	Target analysis by integration of transcriptome and ChIP-seq data with BETA.	Nat Protoc	2013
22495509	Computational inference of mRNA stability from histone modification and transcriptome profiles.	Nucleic Acids Research	2012
22508765	Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.	Genome Res	2012
22930692	Minireview: applications of next-generation sequencing on studies of nuclear receptor regulation and function.	Molecular Endocrinology	2012
22923299	GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.		2012
21859476	Cistrome: an integrative platform for transcriptional regulation studies.	Genome Biol	2011
20972221	CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data.	Nucleic Acids Research	2011
21284836	MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data.		2011
21532585	PKA-dependent regulation of the histone lysine demethylase complex PHF2-ARID5B.	Nature Cell Biology	2011
21551136	BINOCh: binding inference from nucleosome occupancy changes.	Bioinformatics	2011
21940749	A comprehensive view of nuclear receptor cancer cistromes.	Cancer Res	2011
20090754	Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen.	Nature	2010
21045080	Gene expression profiling of human breast tissue samples using SAGE-Seq.	Genome Res	2010