Lista de obras - Martin J. Aryee - Dominio Público Uruguay

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

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

artículo científico publicado en 2012

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

artículo científico publicado en 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.

artículo científico publicado en 2012

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

artículo científico publicado en 2020

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

artículo científico publicado en 2014

Accurate genome-scale percentage DNA methylation estimates from microarray data

artículo científico publicado en 2010

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

artículo científico publicado en 2018

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

artículo científico publicado el 1 de noviembre de 2011

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

artículo científico publicado en 2011

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

artículo científico publicado en 2009

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

artículo científico publicado en 2010

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

artículo científico publicado en 2021

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

artículo científico publicado en 2020

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

artículo científico publicado en 2017

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

artículo científico publicado en 2019

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

artículo científico publicado en 2011

Comprehensive high-throughput arrays for relative methylation (CHARM)

artículo científico publicado en 2010

Comprehensive methylome map of lineage commitment from haematopoietic progenitors

artículo científico publicado en 2010

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing

artículo científico publicado en 2014

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

artículo científico publicado en 2013

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

artículo científico publicado en 2012

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

artículo científico publicado en 2020

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

artículo científico publicado en 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 ⬇️

artículo científico publicado el 21 de marzo de 2012

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

artículo científico publicado en 2009

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

artículo científico publicado en 2014

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

artículo científico publicado en 2017

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

artículo científico publicado en 2017

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

artículo científico publicado en 2011

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

artículo científico publicado en 2019

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

artículo científico publicado en 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

artículo científico publicado en 2015

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

artículo científico publicado en 2013

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

artículo científico publicado en 2014

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

artículo científico publicado el 3 de enero de 2012

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

artículo científico publicado en 2021

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

artículo científico publicado en 2019

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

artículo científico publicado en 2014

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 ⬇️

artículo científico publicado el 12 de abril de 2012

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

artículo científico publicado en 2022

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

artículo científico publicado en 2016

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

artículo científico publicado en 2013

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

artículo científico publicado en 2016

Identification of direction in gene networks from expression and methylation

artículo científico publicado en 2013

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

artículo científico publicado en 2015

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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2019

Lysine demethylase KDM4A associates with translation machinery and regulates protein synthesis

artículo científico publicado en 2015

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

artículo científico publicado en 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

artículo científico publicado en 2016

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

artículo científico publicado en 2014

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

artículo científico publicado en 2017

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

artículo científico publicado en 2016

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

artículo científico publicado en 2010

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

artículo científico publicado en 2020

Reply

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

Reversible switching between epigenetic states in honeybee behavioral subcastes

artículo científico publicado en 2012

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

artículo científico publicado en 2021

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

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

artículo científico publicado en 2019

Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer

artículo científico publicado en 2019

Subset quantile normalization using negative control features

artículo científico publicado en 2010

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

artículo científico publicado en 2016

The early pregnancy placenta foreshadows dna methylation alterations of solid tumors

artículo científico publicado en 2017

Therapeutic implications of GIPC1 silencing in cancer

artículo científico publicado en 2010

Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis

artículo científico publicado en 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

artículo científico publicado en 2018

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

artículo científico publicado en 2018

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

artículo científico publicado en 2012

Lista de obras de 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.

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

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.

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

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

Accurate genome-scale percentage DNA methylation estimates from microarray data

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

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

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

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

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

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

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

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

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

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

Comprehensive high-throughput arrays for relative methylation (CHARM)

Comprehensive methylome map of lineage commitment from haematopoietic progenitors

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Engineered CRISPR-Cas9 nucleases with altered PAM specificities

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

Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia

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

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

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

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

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

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

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

Genome-Wide DNA Methylation Scan in Major Depressive Disorder ⬇️

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

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

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

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

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

Identification of direction in gene networks from expression and methylation

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

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

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

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

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

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer

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

Lysine demethylase KDM4A associates with translation machinery and regulates protein synthesis

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

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

Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling

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

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

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

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

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

Preprocessing and Computational Analysis of Single-Cell Epigenomic Datasets

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

Reply

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

Reversible switching between epigenetic states in honeybee behavioral subcastes

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

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

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

Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer

Subset quantile normalization using negative control features

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