List of works - Daniel J Gaffney

A map of transcriptional heterogeneity and regulatory variation in human microglia

scientific article published on 03 June 2021

A survey of best practices for RNA-seq data analysis

scientific article

AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation

scientific article published on 7 November 2013

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

scientific article

Activin/nodal signaling and NANOG orchestrate human embryonic stem cell fate decisions by controlling the H3K4me3 chromatin mark.

scientific article

Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants

Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes

scientific article published on 16 March 2020

Cell reprogramming shapes the mitochondrial DNA landscape

scientific article published on 02 September 2021

Common genetic variation drives molecular heterogeneity in human iPSCs

scientific article published on 10 May 2017

Controls of nucleosome positioning in the human genome.

scientific article

Correction: Gene expression and isoform variation analysis using Affymetrix exon arrays

article

Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs

scientific article published in Nature

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

scientific article

DNA sequence error rates in Genbank records estimated using the mouse genome as a reference

scientific article

Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis

scientific article

Dissecting the regulatory architecture of gene expression QTLs

scientific article published on 31 January 2012

Early maturation and distinct tau pathology in induced pluripotent stem cell-derived neurons from patients with MAPT mutations.

scientific article

Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals

scientific article

Epithelial IL-22RA1-mediated fucosylation promotes intestinal colonization resistance to an opportunistic pathogen

scientific article

Erratum to: A survey of best practices for RNA-seq data analysis

scientific article published on 26 August 2016

Erratum: Corrigendum: Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

scholarly article published in Nature Genetics

Evolutionary constraints in conserved nongenic sequences of mammals.

scientific article published on October 2005

Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data ⬇️

scientific article (publication date: 2012)

False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions

scientific article

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

scientific article published on 14 December 2015

Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents

scientific article

Genetic background drives transcriptional variation in human induced pluripotent stem cells

scientific article

Genomic selective constraints in murid noncoding DNA

scientific article

Global Properties and Functional Complexity of Human Gene Regulatory Variation ⬇️

scientific article published on May 30, 2013

High-resolution genetic mapping of putative causal interactions between regions of open chromatin.

scientific article published on 26 November 2018

Mapping and predicting gene-enhancer interactions

scientific article published on 01 December 2019

Molecular and functional variation in iPSC-derived sensory neurons.

scientific article

N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells

scientific article published on 16 December 2019

Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation

scientific article published on 04 March 2021

Quantifying the Slightly Deleterious Mutation Model of Molecular Evolution

article

Robust temporal map of human in vitro myelopoiesis using single-cell genomics

scientific article published on 24 May 2022

Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response.

scientific article

Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes

scientific article published on 04 May 2020

The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels

scientific article

The scale of mutational variation in the murid genome

scientific article published on 15 July 2005

Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription

scientific article published on 30 July 2015

Unexpected conserved non-coding DNA blocks in mammals.

scientific article published in August 2004

List of works by Daniel J Gaffney

A map of transcriptional heterogeneity and regulatory variation in human microglia

A survey of best practices for RNA-seq data analysis

AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

Activin/nodal signaling and NANOG orchestrate human embryonic stem cell fate decisions by controlling the H3K4me3 chromatin mark.

Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants

Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes

Cell reprogramming shapes the mitochondrial DNA landscape

Common genetic variation drives molecular heterogeneity in human iPSCs

Controls of nucleosome positioning in the human genome.

Correction: Gene expression and isoform variation analysis using Affymetrix exon arrays

Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

DNA sequence error rates in Genbank records estimated using the mouse genome as a reference

Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis

Dissecting the regulatory architecture of gene expression QTLs

Early maturation and distinct tau pathology in induced pluripotent stem cell-derived neurons from patients with MAPT mutations.

Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals

Epithelial IL-22RA1-mediated fucosylation promotes intestinal colonization resistance to an opportunistic pathogen

Erratum to: A survey of best practices for RNA-seq data analysis

Erratum: Corrigendum: Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

Evolutionary constraints in conserved nongenic sequences of mammals.

Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data ⬇️

False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents

Genetic background drives transcriptional variation in human induced pluripotent stem cells

Genomic selective constraints in murid noncoding DNA

Global Properties and Functional Complexity of Human Gene Regulatory Variation ⬇️

High-resolution genetic mapping of putative causal interactions between regions of open chromatin.

Mapping and predicting gene-enhancer interactions

Molecular and functional variation in iPSC-derived sensory neurons.

N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells

Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation

Quantifying the Slightly Deleterious Mutation Model of Molecular Evolution

Robust temporal map of human in vitro myelopoiesis using single-cell genomics

Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response.

Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes

The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels

The scale of mutational variation in the murid genome

Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription

Unexpected conserved non-coding DNA blocks in mammals.