19 Result(s)
within
Clifford A Meyer
Life Sciences
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Article
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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Article
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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Article
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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Article
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 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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Article
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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Article
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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Article
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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Article
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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Article
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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Article
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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Article
Open AccessA closer look into DNase I hypersensitivity
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Article
Open AccessCistrome: an integrative platform for transcriptional regulation studies
The increasing volume of ChIP-chip and ChIP-seq data being generated creates a challenge for standard, integrative and reproducible bioinformatics data analysis platforms. We developed a web-based application ...
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Article
PKA-dependent regulation of the histone lysine demethylase complex PHF2–ARID5B
Reversible histone methylation and demethylation are highly regulated processes that are crucial for chromatin reorganization and regulation of gene transcription in response to extracellular conditions. Howev...
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Article
Open AccessMM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data
The ChIP-chip and ChIP-seq techniques enable genome-wide map** of in vivo protein-DNA interactions and chromatin states. The cross-platform and between-laboratory variation poses a challenge to the comparison a...
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Protocol
ChIP-Chip: Algorithms for Calling Binding Sites
Genome-wide ChIP-chip assays of protein–DNA interactions yield large volumes of data requiring effective statistical analysis to obtain reliable results. Successful analysis methods need to be tailored to plat...
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Article
Open AccessModel-based Analysis of ChIP-Seq (MACS)
We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and use...
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Article
Open AccessExon expression profiling reveals stimulus-mediated exon use in neural cells
Neuronal cells respond to changes in intracellular calcium ([Ca2+]i) by affecting both the abundance and architecture of specific mRNAs. Although calcium-induced transcription and transcript variation have both b...
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Article
Open AccessGenomic map** of RNA polymerase II reveals sites of co-transcriptional regulation in human cells
Transcription by RNA polymerase II is regulated at many steps including initiation, promoter release, elongation and termination. Accumulation of RNA polymerase II at particular locations across genes can be i...
