49 Result(s)
within
Clifford A Meyer
English
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Article
Open AccessMulti-batch single-cell comparative atlas construction by deep learning disentanglement
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. Compar...
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Open AccessMetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment
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 c...
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Open AccessIntrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA
Genome-wide profiling of chromatin accessibility by DNase-seq or ATAC-seq has been widely used to identify regulatory DNA elements and transcription factor binding sites. However, enzymatic DNA cleavage exhibi...
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MIRA: joint regulatory modeling of multimodal expression and chromatin accessibility in single cells
Rigorously comparing gene expression and chromatin accessibility in the same single cells could illuminate the logic of how coupling or decoupling of these mechanisms regulates fate commitment. Here we present...
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Open AccessFast alignment and preprocessing of chromatin profiles with Chromap
As sequencing depth of chromatin studies continually grows deeper for sensitive profiling of regulatory elements or chromatin spatial structures, aligning and preprocessing of these sequencing data have become...
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CDK4/6 inhibition reprograms the breast cancer enhancer landscape by stimulating AP-1 transcriptional activity
Pharmacologic inhibitors of cyclin-dependent kinases 4 and 6 (CDK4/6) were designed to induce cancer cell cycle arrest. Recent studies have suggested that these agents also exert other effects, influencing can...
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Cistrome Data Browser and Toolkit: analyzing human and mouse genomic data using compendia of ChIP-seq and chromatin accessibility data
The Cistrome Data Browser (DB) at the website (cistrome.org/db) provides about 56,000 published human and mouse ChIP-seq, DNase-seq, and ATAC-seq chromatin profiles, which we have processed using uniform analy...
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Open AccessIntegrative analyses of single-cell transcriptome and regulome using MAESTRO
We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO), a comprehensive open-source computational workflow (http://github.com/liulab-dfci/MAESTRO)...
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Open AccessDeterminants of transcription factor regulatory range
Characterization of the genomic distances over which transcription factor (TF) binding influences gene expression is important for inferring target genes from TF chromatin immunoprecipitation followed by seque...
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Open AccessLisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data
We developed Lisa (http://lisa.cistrome.org/) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the i...
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Open AccessChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline
Transcription factor binding, histone modification, and chromatin accessibility studies are important approaches to understanding the biology of gene regulation. ChIP-seq and DNase-seq have become the standard...
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Open AccessHigh-dimensional genomic data bias correction and data integration using MANCIE
High-dimensional genomic data analysis is challenging due to noises and biases in high-throughput experiments. We present a computational method matrix analysis and normalization by concordant information enha...
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Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer
BET inhibitors that target bromodomain chromatin readers such as BRD4 are being explored as potential therapeutics in cancer; here triple-negative breast cancer cell lines are shown to respond to BET inhibitor...
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Identifying and mitigating bias in next-generation sequencing methods for chromatin biology
In next-generation sequencing (NGS) chromatin profiling experiments technical artefacts may be introduced at any stage, most importantly in fragmenting DNA, se...
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Cyclin C is a haploinsufficient tumour suppressor
Cyclin C was cloned as a growth-promoting G1 cyclin, and was also shown to regulate gene transcription. Here we report that in vivo cyclin C acts as a haploinsufficient tumour suppressor, by controlling Notch1 on...
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Open AccessMethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes
We propose a statistical algorithm MethylPurify that uses regions with bisulfite reads showing discordant methylation levels to infer tumor purity from tumor samples alone. MethylPurify can identify differenti...
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Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification
Detailed analysis of DNase-seq protocols reveals the importance of choosing the right enzyme concentration and fragment length and cautions that many transcription factor footprints may represent cutting bias.
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Target analysis by integration of transcriptome and ChIP-seq data with BETA
The combination of ChIP-seq and transcriptome analysis is a compelling approach to unravel the regulation of gene expression. Several recently published methods combine transcription factor (TF) binding and ge...
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Open AccessA systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer
The epithelial-to-mesenchymal transition is an important mechanism in cancer metastasis. Although transcription factors including SNAIL, SLUG, and TWIST1 regulate the epithelial-to-mesenchymal transition, othe...
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Open AccessA closer look into DNase I hypersensitivity
