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List of works by Martin J. Aryee

A (fire)cloud-based DNA methylation data preprocessing and quality control platform

A DNA hypermethylation module for the stem/progenitor cell signature of cancer.

scientific article published on 5 March 2012

A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression

scientific article published on 20 February 2013

A comparative risk assessment of burden of disease and injury attributable to 67 risk factors and risk factor clusters in 21 regions, 1990-2010: a systematic analysis for the Global Burden of Disease Study 2010.

scientific article published in December 2012

A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing

scientific article published on 01 June 2020

A novel method for detecting association between DNA methylation and diseases using spatial information

scientific article

Accurate genome-scale percentage DNA methylation estimates from microarray data

scientific article

Activities and specificities of CRISPR/Cas9 and Cas12a nucleases for targeted mutagenesis in maize

scientific article published on 22 July 2018

Adaptation of the CHARM DNA methylation platform for the rat genome reveals novel brain region-specific differences ⬇️

scientific article published on November 1, 2011

Alterations in nucleolar structure and gene expression programs in prostatic neoplasia are driven by the MYC oncogene

scientific article

An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation).

scientific article

Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangements

scientific article published on 4 July 2010

Augmenting and directing long-range CRISPR-mediated activation in human cells

scientific article published on 05 August 2021

Author Correction: Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model

scientific article published on 22 July 2020

CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets

scientific article

CRISPR DNA base editors with reduced RNA off-target and self-editing activities

scientific article published on 02 September 2019

Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences

scientific article

Comprehensive high-throughput arrays for relative methylation (CHARM)

scientific article published on 01 April 2010

Comprehensive methylome map of lineage commitment from haematopoietic progenitors

scientific article

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing

scientific article

DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases

scientific article published on January 2013

DNA methylation shows genome-wide association of NFIX, RAPGEF2 and MSRB3 with gestational age at birth

scientific article

Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization

scientific article published on 22 September 2020

Defining CRISPR-Cas9 genome-wide nuclease activities with CIRCLE-seq

scientific article published in November 2018

Detection and Analysis of Circulating Epithelial Cells in Liquid Biopsies From Patients With Liver Disease

scientific article published on 13 September 2018

Diarrhea incidence in low- and middle-income countries in 1990 and 2010: a systematic review ⬇️

scientific article published on March 21, 2012

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

scientific article

Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing

scientific article

Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing.

scientific article

Diverse repetitive element RNA expression defines epigenetic and immunologic features of colon cancer

scientific article published on 09 February 2017

Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells

scientific article

Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility

scientific article published on 24 June 2019

EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma

scientific article published on 30 October 2014

EWSR1-ATF1 dependent 3D connectivity regulates oncogenic and differentiation programs in Clear Cell Sarcoma

scientific article published on 27 April 2022

Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing

article

Engineered CRISPR-Cas9 nucleases with altered PAM specificities

scientific article

Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks

scientific article published in Nature Communications

Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia

scientific article published on 15 May 2019

Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis

scientific article

Epigenome-wide association studies without the need for cell-type composition

scientific article

Estimating Diarrhea Mortality among Young Children in Low and Middle Income Countries ⬇️

scientific article published on January 3, 2012

Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells

scientific article published on 06 May 2021

Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model

scientific article published on 23 December 2019

GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases

scientific article

GeMes, clusters of DNA methylation under genetic control, can inform genetic and epigenetic analysis of disease

scientific article published on 20 March 2014

Genome-Wide DNA Methylation Scan in Major Depressive Disorder ⬇️

scientific article published on April 12, 2012

Genome-wide DNA methylation patterns reveal clinically relevant predictive and prognostic subtypes in human osteosarcoma

scientific article published on 08 March 2022

Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells.

scientific article published on 27 June 2016

Global causes of diarrheal disease mortality in children <5 years of age: a systematic review

scientific article

High levels of AAV vector integration into CRISPR-induced DNA breaks

scientific article published on 30 September 2019

High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis

scientific article

Identification of direction in gene networks from expression and methylation

scientific article

In vivo CRISPR editing with no detectable genome-wide off-target mutations

scientific article published in Nature

Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer

scientific article published on 23 April 2015

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

scientific article published on 25 April 2018

Interrogation of human hematopoiesis at single-cell and single-variant resolution

scholarly article published 28 January 2018

Interrogation of human hematopoiesis at single-cell and single-variant resolution

scientific article published on 11 March 2019

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer

scientific article published on 18 August 2020

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

scientific article published on 28 February 2019

Lysine demethylase KDM4A associates with translation machinery and regulates protein synthesis

scientific article published on 6 January 2015

MET Exon 14 Skipping in Non-Small Cell Lung Cancer.

scientific article published on 28 March 2016

Magnetic Resonance Spectroscopy-based Metabolomic Biomarkers for Typing, Staging, and Survival Estimation of Early-Stage Human Lung Cancer

scientific article published on 16 July 2019

Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling

scientific article published on 12 August 2020

Meta-Analysis With a Continuous Covariate That Is Differentially Categorized Across Studies

scientific article published on 10 February 2016

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

scientific article

OTX2 Activity at Distal Regulatory Elements Shapes the Chromatin Landscape of Group 3 Medulloblastoma

scientific article published on 17 February 2017

Open-source guideseq software for analysis of GUIDE-seq data.

scientific article

Personalized epigenomic signatures that are stable over time and covary with body mass index

scientific article

Preprocessing and Computational Analysis of Single-Cell Epigenomic Datasets

scientific article published on 01 January 2019

Publisher Correction: Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing

scientific article published on 15 June 2020

Reply

Response to "Unexpected mutations after CRISPR-Cas9 editing in vivo"

Reversible switching between epigenetic states in honeybee behavioral subcastes

scientific article

STAG2 loss rewires oncogenic and developmental programs to promote metastasis in Ewing sarcoma

scientific article published on 01 June 2021

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data

Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM

scientific article published on 23 April 2019

Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer

scientific article published on 30 May 2019

Subset quantile normalization using negative control features

scientific article

Survival in Quiescence Requires the Euchromatic Deployment of Clr4/SUV39H by Argonaute-Associated Small RNAs

scientific article published on December 2016

The early pregnancy placenta foreshadows dna methylation alterations of solid tumors

scientific article published on 5 July 2017

Therapeutic implications of GIPC1 silencing in cancer

scientific article

Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis

scientific article published on 01 June 2019

Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors

scientific article published on 17 April 2019

diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data

scientific article

hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data

scientific article published on 01 February 2018

nEASE: a method for gene ontology subclassification of high-throughput gene expression data.

scientific article

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