List of works - Aaron Lun

A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division

scientific article published on 15 April 2020

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.

scientific article

Acetylation of the Cd8 Locus by KAT6A Determines Memory T Cell Diversity.

scientific article published on September 2016

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

scientific article published on 02 April 2018

COMRADES determines in vivo RNA structures and interactions

scientific article published on 10 September 2018

Detection and removal of barcode swapping in single-cell RNA-seq data

scientific article published in Nature Communications

Detection and removal of barcode swapping in single-cell RNA-seq data

scholarly article published 16 August 2017

Distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

EGF-mediated induction of Mcl-1 at the switch to lactation is essential for alveolar cell survival

scientific article

FluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry ⬇️

scientific article published on August 20, 2012

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline

scientific article

Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development.

scientific article

Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments.

scientific article published on 20 May 2016

Mass trees: a new phylogenetic approach and algorithm to chart evolutionary history with mass spectrometry.

scientific article published on 21 May 2013

No counts, no variance: allowing for loss of degrees of freedom when assessing biological variability from RNA-seq data.

scientific article

Orchestrating Single-Cell Analysis with Bioconductor

Orchestrating single-cell analysis with Bioconductor

scientific article published on 02 December 2019

Polycomb repressive complex 2 (PRC2) suppresses Eμ-myc lymphoma.

scientific article

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.

scientific article

Publisher Correction: Orchestrating single-cell analysis with Bioconductor

scientific article published on 01 February 2020

RUNX2 Mediates Plasmacytoid Dendritic Cell Egress from the Bone Marrow and Controls Viral Immunity.

scientific article published on 13 April 2016

Repression of Igf1 expression by Ezh2 prevents basal cell differentiation in the developing lung

scientific article

Senescence-induced endothelial phenotypes underpin immune-mediated senescence surveillance

scientific article published in 2022

Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis

scientific article published on 01 July 2018

Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis

T cell cytolytic capacity is independent of initial stimulation strength

scholarly article by Arianne C Richard et al published 16 July 2018 in Nature Immunology

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations.

scientific article published on 06 April 2016

Transcriptome and H3K27 tri-methylation profiling of Ezh2-deficient lung epithelium

scientific article

beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types.

scientific article published on 3 May 2018

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data

scientific article published on 19 August 2015

iSEE: Interactive SummarizedExperiment Explorer.

scientific article published on 14 June 2018

List of works by Aaron Lun

A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.

Acetylation of the Cd8 Locus by KAT6A Determines Memory T Cell Diversity.

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

COMRADES determines in vivo RNA structures and interactions

Detection and removal of barcode swapping in single-cell RNA-seq data

Detection and removal of barcode swapping in single-cell RNA-seq data

Distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

EGF-mediated induction of Mcl-1 at the switch to lactation is essential for alveolar cell survival

FluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry ⬇️

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline

Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development.

Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments.

Mass trees: a new phylogenetic approach and algorithm to chart evolutionary history with mass spectrometry.

No counts, no variance: allowing for loss of degrees of freedom when assessing biological variability from RNA-seq data.

Orchestrating Single-Cell Analysis with Bioconductor

Orchestrating single-cell analysis with Bioconductor

Polycomb repressive complex 2 (PRC2) suppresses Eμ-myc lymphoma.

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.

Publisher Correction: Orchestrating single-cell analysis with Bioconductor

RUNX2 Mediates Plasmacytoid Dendritic Cell Egress from the Bone Marrow and Controls Viral Immunity.

Repression of Igf1 expression by Ezh2 prevents basal cell differentiation in the developing lung

Senescence-induced endothelial phenotypes underpin immune-mediated senescence surveillance

Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis

Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis

T cell cytolytic capacity is independent of initial stimulation strength

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations.

Transcriptome and H3K27 tri-methylation profiling of Ezh2-deficient lung epithelium

beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types.

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data

iSEE: Interactive SummarizedExperiment Explorer.