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Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity

Cell, 2012-04, Vol.149 (2), p.467-482

2012

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Nature biotechnology, 2010-05, Vol.28 (5), p.511-515

2010

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From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing

Genome research, 2014-03, Vol.24 (3), p.496-510

2014

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Dynamic DNA methylation across diverse human cell lines and tissues

Genome research, 2013-03, Vol.23 (3), p.555-567

2013

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The changing mouse embryo transcriptome at whole tissue and single-cell resolution

Nature (London), 2020-07, Vol.583 (7818), p.760-767

2020

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Single-Cell Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression during Reprogramming

Cell stem cell, 2015-01, Vol.16 (1), p.88-101

2015

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RNA editing in the human ENCODE RNA-seq data

Genome research, 2012-09, Vol.22 (9), p.1626-1633

2012

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Occupancy maps of 208 chromatin-associated proteins in one human cell type

Nature (London), 2020-07, Vol.583 (7818), p.720-728

2020

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Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq

Genome Biology, 2021-10, Vol.22 (1), p.286-28, Article 286

2021

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Systematic evaluation of factors influencing ChIP-seq fidelity

Nature methods, 2012-06, Vol.9 (6), p.609-614

2012

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Large-scale quality analysis of published ChIP-seq data

G3 : genes - genomes - genetics, 2014-02, Vol.4 (2), p.209-223

2014

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Genome-wide analysis reveals coating of the mitochondrial genome by TFAM

PloS one, 2013-08, Vol.8 (8), p.e74513-e74513

2013

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Evidence for site-specific occupancy of the mitochondrial genome by nuclear transcription factors

PloS one, 2014-01, Vol.9 (1), p.e84713-e84713

2014

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Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

Genome research, 2013-12, Vol.23 (12), p.2136-2148

2013

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Spatiometabolic Stratification of Shewanella oneidensis Biofilms

Applied and Environmental Microbiology, 2006-11, Vol.72 (11), p.7324-7330

2006

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Pitfalls of Mapping High-Throughput Sequencing Data to Repetitive Sequences: Piwi’s Genomic Targets Still Not Identified

Developmental cell, 2015-03, Vol.32 (6), p.765-771

2015

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High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation

Genome research, 2011-04, Vol.21 (4), p.566-577

2011

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Inviability of a DNA2 deletion mutant is due to the DNA damage checkpoint

Cell cycle (Georgetown, Tex.), 2011-05, Vol.10 (10), p.1690-1698

2011

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p62 overexpression in breast tumors and regulation by prostate-derived Ets factor in breast cancer cells

Oncogene, 2003-04, Vol.22 (15), p.2322-2333

2003

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ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Genome research, 2012-09, Vol.22 (9), p.1813-1831

2012

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Microglia in the Cerebral Cortex in Autism

Journal of autism and developmental disorders, 2012-12, Vol.42 (12), p.2569-2584

2012

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Assessment of transcript reconstruction methods for RNA-seq

Nature methods, 2013-12, Vol.10 (12), p.1177-1184

2013

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Mining gene expression data by interpreting principal components

BMC bioinformatics, 2006-04, Vol.7 (1), p.194-194, Article 194

2006

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Applicability of Tandem Affinity Purification MudPIT to Pathway Proteomics in Yeast

Molecular & cellular proteomics, 2004-03, Vol.3 (3), p.226-237

2004

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Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing

Dynamic DNA methylation across diverse human cell lines and tissues

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

Single-Cell Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression during Reprogramming

RNA editing in the human ENCODE RNA-seq data

Occupancy maps of 208 chromatin-associated proteins in one human cell type

Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq

Systematic evaluation of factors influencing ChIP-seq fidelity

Large-scale quality analysis of published ChIP-seq data

Genome-wide analysis reveals coating of the mitochondrial genome by TFAM

Evidence for site-specific occupancy of the mitochondrial genome by nuclear transcription factors

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

Spatiometabolic Stratification of Shewanella oneidensis Biofilms

Pitfalls of Mapping High-Throughput Sequencing Data to Repetitive Sequences: Piwi’s Genomic Targets Still Not Identified

High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation

Inviability of a DNA2 deletion mutant is due to the DNA damage checkpoint

p62 overexpression in breast tumors and regulation by prostate-derived Ets factor in breast cancer cells

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Microglia in the Cerebral Cortex in Autism

Assessment of transcript reconstruction methods for RNA-seq

Mining gene expression data by interpreting principal components

Applicability of Tandem Affinity Purification MudPIT to Pathway Proteomics in Yeast

A human embryonic limb cell atlas resolved in space and time

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