Martin J. Aryee

发表

Identification of direction in gene networks from expression and methylation

Donald Geman, Laurent Younes, David M. Simcha, 2013, BMC Systems Biology.

Subset Quantile Normalization Using Negative Control Features

Zhijin Wu, Martin J. Aryee, M. Aryee, 2010, J. Comput. Biol..

Bioinformatics Applications Note Gene Expression Nease: a Method for Gene Ontology Subclassification of High-throughput Gene Expression Data

Eleanor Howe, John Quackenbush, Chris Holmes, 2022 .

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

Martin J. Aryee, Caleb A. Lareau, Jason D. Buenrostro, 2019, Nature Biotechnology.

Varying-Censoring Aware Matrix Factorization for Single Cell RNA-Sequencing

Rafael A. Irizarry, Stephanie C. Hicks, Martin J. Aryee, 2017, bioRxiv.

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

Rafael A. Irizarry, Andrew P. Feinberg, Martin J. Aryee, 2014, Bioinform..

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

John Quackenbush, Martin J. Aryee, Tapabrata Maiti, 2009, BMC Bioinformatics.

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

Andrew Dunford, Martin J. Aryee, Gad Getz, 2019, BMC Bioinformatics.

Aryeelab/Hichipper: Stable Version 7.0

Martin J. Aryee, Caleb A Lareau, Areyesq, 2017 .

hichipper: A preprocessing pipeline for assessing library quality and DNA loops from HiChIP data

Martin J. Aryee, Caleb A. Lareau, C. Lareau, 2017, bioRxiv.

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

Martin J. Aryee, Caleb A. Lareau, C. Lareau, 2016, bioRxiv.

Droplet-based combinatorial indexing for massive scale single-cell epigenomics

Martin J. Aryee, Caleb A Lareau, Jason D. Buenrostro, 2019, bioRxiv.

Data-driven polymer model for mechanistic exploration of diploid genome organization

Bradley E. Bernstein, Martin J. Aryee, Y. Qi, 2020, bioRxiv.

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

Martin J. Aryee, Robert E. Black, M. Aryee, 2012, PloS one.

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

Martin J. Aryee, Zachary A. Kaminsky, M. Aryee, 2013, Epigenetics.

Engineered CRISPR-Cas9 nucleases with altered PAM specificities

Martin J. Aryee, J. Keith Joung, Benjamin P. Kleinstiver, 2015, Nature.

A comprehensive methylome map of lineage commitment from hematopoietic progenitors

Irving L. Weissman, Rafael A. Irizarry, Andrew P. Feinberg, 2010, Nature.

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

Luca Pinello, Martin J. Aryee, J. Keith Joung, 2018, Nature Biotechnology.

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

Andrew P. Feinberg, George Q. Daley, James J. Collins, 2011, Nature Biotechnology.

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

Martin J. Aryee, Jianfeng Xu, William B. Isaacs, 2010, Nature Genetics.

Personalized Epigenomic Signatures That Are Stable Over Time and Covary with Body Mass Index

Rafael A. Irizarry, Andrew P. Feinberg, Martin J. Aryee, 2010, Science Translational Medicine.

Global Causes of Diarrheal Disease Mortality in Children <5 Years of Age: A Systematic Review

Martin J. Aryee, Robert E. Black, M. Aryee, 2013, PloS one.

Reversible switching between epigenetic states in honeybee behavioral subcastes

Andrew P. Feinberg, Martin J. Aryee, Ben Langmead, 2012, Nature Neuroscience.

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

Rafael A. Irizarry, Stephanie C. Hicks, Martin J. Aryee, 2019, Genome Biology.

Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis

Aviv Regev, Martin J. Aryee, Caleb A. Lareau, 2019, Cell reports.

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

Luigi Ferrucci, Xin Li, Martin J. Aryee, 2014, American journal of human genetics.

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

Martin J. Aryee, A. Feinberg, K. Hansen, 2014, Bioinform..

Epigenetic memory in induced pluripotent stem cells

Martin J. Aryee, Peter N. Murakami, A. Feinberg, 2010, Nature.

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

Martin J. Aryee, J. Joung, A. Iafrate, 2014, Nature Biotechnology.

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

Martin J. Aryee, Mathew J. Goodwin, J. Joung, 2014, Nature Biotechnology.

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

Martin J. Aryee, Peter N. Murakami, A. Feinberg, 2009, Nature Genetics.

DNA Methylation Alterations Exhibit Intraindividual Stability and Interindividual Heterogeneity in Prostate Cancer Metastases

Martin J. Aryee, Julia C. Engelmann, R. Irizarry, 2013, Science Translational Medicine.

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

Martin J. Aryee, D. Weisenberger, S. Baylin, 2011, Genome research.

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

Martin J. Aryee, Martin J Aryee, Caleb A Lareau, 2019, Nature Biotechnology.

EWS-FLI1 Utilizes Divergent Chromatin Remodeling Mechanisms to Directly Activate or Repress Enhancer Elements in Ewing Sarcoma

Martin J. Aryee, Shawn M. Gillespie, M. Rivera, 2014 .

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

Martin J. Aryee, Benjamin Haibe-Kains, M. Aryee, 2022, Communications Biology.

Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer

Martin J. Aryee, Linda T. Nieman, M. Lawrence, 2019, Cell.

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

Martin J. Aryee, Howard Y. Chang, Alicia N. Schep, 2018, Cell.

Lysine demethylase KDM4A associates with translation machinery and regulates protein synthesis.

Martin J. Aryee, C. Benes, M. Aryee, 2015, Cancer discovery.

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

Martin J. Aryee, M. Aryee, C. F. Fischer Walker, 2012, BMC Public Health.

Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in Rheumatoid Arthritis

Martin J. Aryee, A. Feinberg, J. Kere, 2013, Nature Biotechnology.

Gene clustering drives the transcriptional coherence of disparate biological processes in eukaryotes

Martin J. Aryee, Richard I. Joh, M. Lawrence, 2023, bioRxiv.

Personalized Epigenomic Signatures That Are Stable Over Time and Covary with Body Mass Index

Martin J. Aryee, Peter N. Murakami, A. Feinberg, 2010, Science Translational Medicine.

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

Shuigeng Zhou, Jihong Guan, Andrei Zinovyev, 2019, Nature Communications.

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

Martin J. Aryee, Martin J Aryee, Rafael A Irizarry, 2012, International journal of epidemiology.

Detection of allele-specific expression in spatial transcriptomics with spASE

Martin J. Aryee, Dylan M. Cable, Luli S. Zou, 2021, bioRxiv.

High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion dynamics

Martin J. Aryee, A. S. Hansen, Mital S. Bhakta, 2023, bioRxiv.

Therapeutic Implications of GIPC1 Silencing in Cancer

Martin J. Aryee, W. Hahn, John Quackenbush, 2010, PloS one.

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

Martin J. Aryee, R. Irizarry, B. Carvalho, 2011, BMC Genomics.

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

Martin J. Aryee, Carolyn J. Lawrence-Dill, J. Joung, 2018, Plant biotechnology journal.

CRISPR-Cas9 treatment partially restores amyloid-β 42/40 in human fibroblasts with the Alzheimer’s disease PSEN1 M146L mutation

Martin J. Aryee, J. Joung, V. Pattanayak, 2022, Molecular therapy. Nucleic acids.

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

Martin J. Aryee, Luli S. Zou, J. Joung, 2021, Nature Methods.

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

Martin J. Aryee, Jason D. Buenrostro, Vinay K. Kartha, 2018, Nature Genetics.

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

Martin J. Aryee, A. Feinberg, J. Kere, 2016, Genome Medicine.

The early pregnancy placenta foreshadows DNA methylation alterations of solid tumors

Martin J. Aryee, S. Richon, V. Dangles-Marie, 2017, Epigenetics.

The Early Pregnancy Human Placenta Shares Hypomethylation Patterns Characteristic of Solid Tumors

Martin J. Aryee, S. Richon, V. Dangles-Marie, 2017, bioRxiv.

Tumorigenesis and Neoplastic Progression Alterations in Nucleolar Structure and Gene Expression Programs in Prostatic Neoplasia Are Driven by the MYC Oncogene

Martin J. Aryee, K. Zeller, C. Dang, 2011 .

Epigenetic evolution and lineage histories of chronic lymphocytic leukemia

Martin J. Aryee, Rafael C. Schulman, Kevin Y. Huang, 2019, Nature.

Smart-RRBS for single-cell methylome and transcriptome analysis

Martin J. Aryee, Zachary D. Smith, A. Gnirke, 2021, Nature Protocols.

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

Martin J. Aryee, J. Mesirov, P. Tamayo, 2017, Cancer discovery.

Genome-Wide DNA Methylation Scan in Major Depressive Disorder

Martin J. Aryee, Peter N. Murakami, A. Feinberg, 2012, PloS one.

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

Martin J. Aryee, M. Rivera, Niyati T Desai, 2017, JCI insight.

Reverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer.

Martin J. Aryee, Linda T. Nieman, Jeffrey W. Clark, 2022, Cancer discovery.

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

Martin J. Aryee, D. Heckerman, J. Listgarten, 2014, Nature Methods.

Defining genome-wide CRISPR–Cas genome-editing nuclease activity with GUIDE-seq

Martin J. Aryee, J. Joung, A. Iafrate, 2021, Nature Protocols.

Global-scale CRISPR gene editor specificity profiling by ONE-seq identifies population-specific, variant off-target effects

Martin J. Aryee, Matthew C. Canver, David R. Liu, 2021, bioRxiv.

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

Martin J. Aryee, Martin J Aryee, J Keith Joung, 2018, Nature Protocols.

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

Martin J. Aryee, J. Joung, M. Firth, 2018, Nature.

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

Martin J. Aryee, Jason D. Buenrostro, Jacob C. Ulirsch, 2019, Cell.

Coverage recommendations for methylation analysis by whole genome bisulfite sequencing

Martin J. Aryee, Martin J Aryee, Alexander Meissner, 2014, Nature Methods.

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

Martin J. Aryee, Jonathan Y. Hsu, J. Joung, 2020, Nature Biotechnology.

Epigenetic clocks, aging, and cancer

Martin J. Aryee, Sarah E. Johnstone, B. Bernstein, 2022, Science.

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer

Martin J. Aryee, Luli S. Zou, Sarah E. Johnstone, 2020, Cell.

Abstract LB-174: A DNA hypermethylation module for the stem/progenitor cell signature of cancer

Martin J. Aryee, Sarah E. Johnstone, L. V. Neste, 2011 .

CRISPR adenine and cytosine base editors with reduced RNA off-target activities

Martin J. Aryee, C. Lareau, M. Aryee, 2019, bioRxiv.

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

Martin J. Aryee, Martin J Aryee, Caleb A Lareau, 2018, Nature Methods.

Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment

Philip S. Yu, Martin J. Aryee, Ramkumar Veppathur Mohan, 2022, Nature Genetics.

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

Martin J. Aryee, J. Joung, C. Lareau, 2019, Nature.

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

Martin J. Aryee, Andrej J. Savol, Richard I. Joh, 2016, Molecular cell.

Accurate genome-scale percentage DNA methylation estimates from microarray data.

Martin J. Aryee, A. Feinberg, R. Irizarry, 2011, Biostatistics.

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

Martin J. Aryee, Peter N. Murakami, A. Feinberg, 2011, Epigenetics.

Using the charm package to estimate DNA methylation levels and find differentially methylated regions

Martin J. Aryee, Peter N. Murakami, R. Irizarry, 2010 .

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

Martin J. Aryee, Alexander A. Sousa, J. Joung, 2019, Nature Communications.

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

Martin J. Aryee, P. Gaffney, C. Lareau, 2018, Nature Communications.

Integrative PTEN Enhancer Discovery Reveals a New Model of Enhancer Organization

Martin J. Aryee, K. Wood, Viraat Y. Goel, 2023, bioRxiv.

Highly connected 3D chromatin networks established by an oncogenic fusion protein shape tumor cell identity

Martin J. Aryee, M. Rivera, Nicolò Riggi, 2023, Science advances.

Polycomb-lamina antagonism partitions heterochromatin at the nuclear periphery

Martin J. Aryee, Sarah E. Johnstone, M. Aryee, 2022, Nature Communications.

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

Martin J. Aryee, M. Rivera, Nicolò Riggi, 2022, Nature Communications.

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

Martin J. Aryee, R. Young, S. Carr, 2021, Cancer cell.

Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling

Martin J. Aryee, Jason D. Buenrostro, Zachary D. Chiang, 2020, Nature Biotechnology.

DNA hypomethylation silences antitumor immune genes in early prostate cancer and CTCs

Martin J. Aryee, Ben S. Wittner, B. Wittner, 2023, Cell.

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

Martin J. Aryee, Martin J Aryee, J Keith Joung, 2016, Nature Biotechnology.

A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine expression profiles and plays a critical role in early Th1 cell fate specification.

Martin J. Aryee, C. Lareau, Seolkyoung Jung, 2024, Immunity.

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

Giosuè Lo Bosco, Martin J. Aryee, Jason D. Buenrostro, 2018, bioRxiv.

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

Martin J. Aryee, Martin J Aryee, Zachary R McCaw, 2016, Nature Biotechnology.

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

Martin J. Aryee, Zhongming Zhao, A. Iafrate, 2016, The oncologist.

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

Junfeng Xia, Peilin Jia, William Pao, 2015, Methods.

Genome-wide specificity profiles of CRISPR-Cas Cpf1 nucleases in human cells

Martin J. Aryee, Moira M. Welch, J. Joung, 2016, bioRxiv.

Distinguishing Autism Spectrum Disorders From Other Developmental Delays Using Blood RNASeq

Martin J. Aryee, J. Gregg, I. Hertz-Picciotto, 2013 .

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

Martin J. Aryee, J. Joung, M. Firth, 2018, bioRxiv.

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

Martin J. Aryee, Leo L. Cheng, E. Mark, 2019, Scientific Reports.

Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy.

Martin J. Aryee, N. Hacohen, Keren Yizhak, 2024, Nature immunology.

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

Martin J. Aryee, B. Bernstein, V. Hovestadt, 2021, Nature Biotechnology.

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

McKenzie L. Shaw, Martin J. Aryee, C. Ceol, 2017, The Journal of experimental medicine.