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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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Article
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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Article
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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Article
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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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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Article
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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Article
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
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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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
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
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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
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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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...
