List of works - Kasper D. Hansen

"Gap hunting" to characterize clustered probe signals in Illumina methylation array data

scientific article

A ketogenic diet rescues hippocampal memory defects in a mouse model of Kabuki syndrome

scientific article published on 20 December 2016

Addressing the mean-correlation relationship in co-expression analysis

scientific article published on 30 March 2022

Advanced Paternal Age and Risk of Fetal Death: A Cohort Study

scientific article published on 01 December 2004

Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin

scientific article published on 16 April 2015

Analyzing whole genome bisulfite sequencing data from highly divergent genotypes

scientific article published on 01 November 2019

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

scientific article

Bacterial infection remodels the DNA methylation landscape of human dendritic cells

scientific article

Biases in Illumina transcriptome sequencing caused by random hexamer priming

scientific article

Cloud-scale RNA-sequencing differential expression analysis with Myrna

scientific article

Co-expression patterns define epigenetic regulators associated with neurological dysfunction

Coexpression patterns define epigenetic regulators associated with neurological dysfunction

scientific article published on 11 March 2019

Common DNA methylation alterations in multiple brain regions in autism.

scientific article

Computer mouse use predicts acute pain but not prolonged or chronic pain in the neck and shoulder

scientific article

Conservation of an RNA regulatory map between Drosophila and mammals

scientific article

Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses

scientific article published in February 2017

Corrigendum: Differential expression analysis of RNA-seq data at single-base resolution.

scientific article published in July 2014

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing

scientific article

DNA methylation is stable during replication and cell cycle arrest

scientific article

Differential expression analysis of RNA-seq data at single-base resolution

scientific article

Editor's note on Zheng et al. and Rahmani et al

scientific article published on 01 February 2017

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

scientific article (publication date: 18 February 2010)

Fertility pattern does not explain social gradient in breast cancer in denmark

scientific article published in September 2004

Functional normalization of 450k methylation array data improves replication in large cancer studies.

scientific article

Genome-wide association study identifies peanut allergy-specific loci and evidence of epigenetic mediation in US children

scientific article

Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila

scientific article

Histone deacetylase inhibition rescues structural and functional brain deficits in a mouse model of Kabuki syndrome

scientific article published on October 2014

Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits

scientific article published on 22 April 2021

Human methylome variation across Infinium 450K data on the Gene Expression Omnibus

scientific article published on 22 April 2021

Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive

scientific article

Improving Metabolic Health Through Precision Dietetics in Mice

scientific article published on 20 November 2017

Increased methylation variation in epigenetic domains across cancer types

scientific article published on 26 June 2011

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

scientific article published on 13 January 2022

Joint Bounding of Peaks Across Samples Improves Differential Analysis in Mass Spectrometry-Based Metabolomics.

scientific article published on 21 February 2017

Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization

scientific article published on 25 September 2013

Laser captured hepatocytes show association of butyrylcholinesterase gene loss and fibrosis progression in hepatitis C-infected drug users

scientific article

Linear models enable powerful differential activity analysis in massively parallel reporter assays

scientific article published on 12 March 2019

Linear models enable powerful differential activity analysis in massively parallel reporter assays

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

scientific article

Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability

scientific article published on 14 January 2019

Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species

scientific article

Orchestrating high-throughput genomic analysis with Bioconductor

scientific article

Precocious chondrocyte differentiation disrupts skeletal growth in Kabuki syndrome mice

scientific article published on 17 October 2019

Precocious neuronal differentiation and disrupted oxygen responses in Kabuki syndrome

scientific article published on 17 October 2019

Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array

Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi

scientific article

Public data and open source tools for multi-assay genomic investigation of disease

scientific article

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce

scientific article

Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data

scientific article

Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data

Removing technical variability in RNA-seq data using conditional quantile normalization

scientific article

Removing unwanted variation between samples in Hi-C experiments

Reproducible RNA-seq analysis using recount2.

scientific article

Reversible switching between epigenetic states in honeybee behavioral subcastes

scientific article

Sequencing technology does not eliminate biological variability

scientific article published on 11 July 2011

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

scientific article published on 23 November 2020

Social environment is associated with gene regulatory variation in the rhesus macaque immune system

scientific article published on 9 April 2012

Software for the Integration of Multiomics Experiments in Bioconductor

scientific article

Testing and Validation of Computational Methods for Mass Spectrometry

scientific article published on 9 November 2015

The Bioconductor channel in F1000Research

scientific article published on 10 July 2015

Transient Reduction of DNA Methylation at the Onset of Meiosis in Male Mice

Universal prediction of cell-cycle position using transfer learning

scientific article published on 31 January 2022

Use of census data for construction of fertility history for Danish women

scientific article

Whole-genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver

scientific article published on 13 October 2016

illuminaio: An open source IDAT parsing tool for Illumina microarrays

scientific article published on 04 December 2013

shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R.

scientific article

List of works by Kasper D. Hansen

"Gap hunting" to characterize clustered probe signals in Illumina methylation array data

A ketogenic diet rescues hippocampal memory defects in a mouse model of Kabuki syndrome

Addressing the mean-correlation relationship in co-expression analysis

Advanced Paternal Age and Risk of Fetal Death: A Cohort Study

Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin

Analyzing whole genome bisulfite sequencing data from highly divergent genotypes

Analyzing whole genome bisulfite sequencing data from highly divergent genotypes

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

Bacterial infection remodels the DNA methylation landscape of human dendritic cells

Biases in Illumina transcriptome sequencing caused by random hexamer priming

Cloud-scale RNA-sequencing differential expression analysis with Myrna

Co-expression patterns define epigenetic regulators associated with neurological dysfunction

Coexpression patterns define epigenetic regulators associated with neurological dysfunction

Common DNA methylation alterations in multiple brain regions in autism.

Computer mouse use predicts acute pain but not prolonged or chronic pain in the neck and shoulder

Conservation of an RNA regulatory map between Drosophila and mammals

Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses

Corrigendum: Differential expression analysis of RNA-seq data at single-base resolution.

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing

DNA methylation is stable during replication and cell cycle arrest

Differential expression analysis of RNA-seq data at single-base resolution

Editor's note on Zheng et al. and Rahmani et al

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

Fertility pattern does not explain social gradient in breast cancer in denmark

Functional normalization of 450k methylation array data improves replication in large cancer studies.

Genome-wide association study identifies peanut allergy-specific loci and evidence of epigenetic mediation in US children

Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila

Histone deacetylase inhibition rescues structural and functional brain deficits in a mouse model of Kabuki syndrome

Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits

Human methylome variation across Infinium 450K data on the Gene Expression Omnibus

Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive

Improving Metabolic Health Through Precision Dietetics in Mice

Increased methylation variation in epigenetic domains across cancer types

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

Joint Bounding of Peaks Across Samples Improves Differential Analysis in Mass Spectrometry-Based Metabolomics.

Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization

Laser captured hepatocytes show association of butyrylcholinesterase gene loss and fibrosis progression in hepatitis C-infected drug users

Linear models enable powerful differential activity analysis in massively parallel reporter assays

Linear models enable powerful differential activity analysis in massively parallel reporter assays

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability

Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species

Orchestrating high-throughput genomic analysis with Bioconductor

Precocious chondrocyte differentiation disrupts skeletal growth in Kabuki syndrome mice

Precocious neuronal differentiation and disrupted oxygen responses in Kabuki syndrome

Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array

Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi

Public data and open source tools for multi-assay genomic investigation of disease

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce

Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data

Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data

Removing technical variability in RNA-seq data using conditional quantile normalization

Removing unwanted variation between samples in Hi-C experiments

Reproducible RNA-seq analysis using recount2.

Reversible switching between epigenetic states in honeybee behavioral subcastes

Sequencing technology does not eliminate biological variability

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

Social environment is associated with gene regulatory variation in the rhesus macaque immune system

Software for the Integration of Multiomics Experiments in Bioconductor

Testing and Validation of Computational Methods for Mass Spectrometry

The Bioconductor channel in F1000Research

Transient Reduction of DNA Methylation at the Onset of Meiosis in Male Mice

Universal prediction of cell-cycle position using transfer learning

Use of census data for construction of fertility history for Danish women

Whole-genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver

illuminaio: An open source IDAT parsing tool for Illumina microarrays

shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R.