Publications by authors named "Martin Aryee"

80Publications

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

Biophys J 2020 Nov 22;119(9):1905-1916. Epub 2020 Sep 22.

Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts. Electronic address:

View Article and Find Full Text PDF
November 2020

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer.

Cell 2020 Sep 24;182(6):1474-1489.e23. Epub 2020 Aug 24.

Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA. Electronic address:

View Article and Find Full Text PDF
September 2020

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

Genome Biol 2020 Jul 22;21(1):179. Epub 2020 Jul 22.

Department of Biostatistics, Harvard University, Cambridge, MA, USA.

View Article and Find Full Text PDF
July 2020

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

Genome Biol 2019 12 23;20(1):295. Epub 2019 Dec 23.

Department of Biostatistics, Harvard University, Cambridge, MA, USA.

View Article and Find Full Text PDF
December 2019

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

Nat Biotechnol 2019 09 2;37(9):1041-1048. Epub 2019 Sep 2.

Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.

View Article and Find Full Text PDF
September 2019

Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis.

Cell Rep 2019 06;27(11):3228-3240.e7

Division of Hematology/Oncology, Boston Children's Hospital, and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:

View Article and Find Full Text PDF
June 2019

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

Nat Commun 2019 04 23;10(1):1903. Epub 2019 Apr 23.

Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA.

View Article and Find Full Text PDF
April 2019

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

Nature 2019 05 17;569(7756):433-437. Epub 2019 Apr 17.

Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.

View Article and Find Full Text PDF
May 2019

Reply.

Gastroenterology 2019 05 27;156(6):1933-1934. Epub 2019 Mar 27.

MGH Cancer Center, Harvard Medical School, Boston, Massachusetts.

View Article and Find Full Text PDF
May 2019

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

BMC Bioinformatics 2019 Mar 29;20(1):160. Epub 2019 Mar 29.

Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.

View Article and Find Full Text PDF
March 2019

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

Cell 2019 03 28;176(6):1325-1339.e22. Epub 2019 Feb 28.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

View Article and Find Full Text PDF
March 2019

Preprocessing and Computational Analysis of Single-Cell Epigenomic Datasets.

Methods Mol Biol 2019 ;1935:187-202

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.

View Article and Find Full Text PDF
June 2019

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

Nat Protoc 2018 11;13(11):2615-2642

Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.

View Article and Find Full Text PDF
November 2018

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

Gastroenterology 2018 12 13;155(6):2016-2018.e11. Epub 2018 Sep 13.

Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts. Electronic address:

View Article and Find Full Text PDF
December 2018

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

Nat Commun 2018 07 25;9(1):2905. Epub 2018 Jul 25.

Division of Genomics and Data Sciences, Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, 73104, OK, USA.

View Article and Find Full Text PDF
July 2018

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

Cell 2018 05 26;173(6):1535-1548.e16. Epub 2018 Apr 26.

Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94025, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA. Electronic address:

View Article and Find Full Text PDF
May 2018

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

Nat Methods 2018 04 30;15(4):238-239. Epub 2018 Mar 30.

Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.

View Article and Find Full Text PDF
April 2018

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

Nat Methods 2018 02;15(3):155-156

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.

View Article and Find Full Text PDF
February 2018

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

Bioinformatics 2018 02;34(4):672-674

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.

View Article and Find Full Text PDF
February 2018

The early pregnancy placenta foreshadows DNA methylation alterations of solid tumors.

Epigenetics 2017 09 24;12(9):793-803. Epub 2017 Nov 24.

f Massachusetts General Hospital and Harvard Medical School , Department of Pathology and Center for Cancer Research , Charlestown , Massachusetts , USA.

View Article and Find Full Text PDF
September 2017

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

Nat Methods 2017 Jun 1;14(6):607-614. Epub 2017 May 1.

Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.

View Article and Find Full Text PDF
June 2017

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

Mol Cell 2016 12;64(6):1088-1101

Massachusetts General Hospital Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA. Electronic address:

View Article and Find Full Text PDF
December 2016

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

Nat Biotechnol 2016 08 27;34(8):869-74. Epub 2016 Jun 27.

Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.

View Article and Find Full Text PDF
August 2016

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

Nat Biotechnol 2016 05;34(5):483

Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.

View Article and Find Full Text PDF
May 2016

Engineered CRISPR-Cas9 nucleases with altered PAM specificities.

Nature 2015 Jul 22;523(7561):481-5. Epub 2015 Jun 22.

1] Molecular Pathology Unit &Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [3] Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA.

View Article and Find Full Text PDF
July 2015

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

Methods 2015 Jul 23;83:118-27. Epub 2015 Apr 23.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, United States; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232, United States; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, United States. Electronic address:

View Article and Find Full Text PDF
July 2015

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

Cancer Discov 2015 Mar 6;5(3):255-63. Epub 2015 Jan 6.

Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts.

View Article and Find Full Text PDF
March 2015

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing.

Nat Methods 2015 Mar 2;12(3):230-2, 1 p following 232. Epub 2014 Nov 2.

1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [3] Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [4] Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.

View Article and Find Full Text PDF
March 2015

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

Genet Epidemiol 2014 Dec 22;38(8):714-21. Epub 2014 Sep 22.

Harvard University, Boston, Massachusetts, United States of America.

View Article and Find Full Text PDF
December 2014

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

Nat Biotechnol 2014 Jun 25;32(6):569-76. Epub 2014 Apr 25.

1] Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [2] Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [3] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [4] Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.

View Article and Find Full Text PDF
June 2014

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

Am J Hum Genet 2014 Apr 20;94(4):485-95. Epub 2014 Mar 20.

Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address:

View Article and Find Full Text PDF
April 2014

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

Bioinformatics 2014 May 28;30(10):1363-9. Epub 2014 Jan 28.

Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, Department of Biostatistics, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, Lieber Institute of Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe Street, Baltimore, MD 21205, USA, Department of Computer Science, University of Maryland, College Park, MD 20742, USA, Department of Epidemiology, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N Wolfe Street, Baltimore, MD 21205, USA and Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

View Article and Find Full Text PDF
May 2014

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

Nat Methods 2014 Mar 26;11(3):309-11. Epub 2014 Jan 26.

eScience Research Group, Microsoft Research, Los Angeles, California, USA.

View Article and Find Full Text PDF
March 2014

Identification of direction in gene networks from expression and methylation.

BMC Syst Biol 2013 Nov 1;7:118. Epub 2013 Nov 1.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.

View Article and Find Full Text PDF
November 2013

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

PLoS One 2013 4;8(9):e72788. Epub 2013 Sep 4.

Instituto de Investigacion Nutricional, Lima, Peru ; US Navy Medical Research Unit 6, Callao, Peru ; School of Medicine, Universidad Peruana de Ciencias Aplicadas, Lima, Peru.

View Article and Find Full Text PDF
April 2014

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

Epigenetics 2013 Mar 20;8(3):290-302. Epub 2013 Feb 20.

The Mood Disorders Center, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

View Article and Find Full Text PDF
March 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.

Authors:
Stephen S Lim Theo Vos Abraham D Flaxman Goodarz Danaei Kenji Shibuya Heather Adair-Rohani Markus Amann H Ross Anderson Kathryn G Andrews Martin Aryee Charles Atkinson Loraine J Bacchus Adil N Bahalim Kalpana Balakrishnan John Balmes Suzanne Barker-Collo Amanda Baxter Michelle L Bell Jed D Blore Fiona Blyth Carissa Bonner Guilherme Borges Rupert Bourne Michel Boussinesq Michael Brauer Peter Brooks Nigel G Bruce Bert Brunekreef Claire Bryan-Hancock Chiara Bucello Rachelle Buchbinder Fiona Bull Richard T Burnett Tim E Byers Bianca Calabria Jonathan Carapetis Emily Carnahan Zoe Chafe Fiona Charlson Honglei Chen Jian Shen Chen Andrew Tai-Ann Cheng Jennifer Christine Child Aaron Cohen K Ellicott Colson Benjamin C Cowie Sarah Darby Susan Darling Adrian Davis Louisa Degenhardt Frank Dentener Don C Des Jarlais Karen Devries Mukesh Dherani Eric L Ding E Ray Dorsey Tim Driscoll Karen Edmond Suad Eltahir Ali Rebecca E Engell Patricia J Erwin Saman Fahimi Gail Falder Farshad Farzadfar Alize Ferrari Mariel M Finucane Seth Flaxman Francis Gerry R Fowkes Greg Freedman Michael K Freeman Emmanuela Gakidou Santu Ghosh Edward Giovannucci Gerhard Gmel Kathryn Graham Rebecca Grainger Bridget Grant David Gunnell Hialy R Gutierrez Wayne Hall Hans W Hoek Anthony Hogan H Dean Hosgood Damian Hoy Howard Hu Bryan J Hubbell Sally J Hutchings Sydney E Ibeanusi Gemma L Jacklyn Rashmi Jasrasaria Jost B Jonas Haidong Kan John A Kanis Nicholas Kassebaum Norito Kawakami Young-Ho Khang Shahab Khatibzadeh Jon-Paul Khoo Cindy Kok Francine Laden Ratilal Lalloo Qing Lan Tim Lathlean Janet L Leasher James Leigh Yang Li John Kent Lin Steven E Lipshultz Stephanie London Rafael Lozano Yuan Lu Joelle Mak Reza Malekzadeh Leslie Mallinger Wagner Marcenes Lyn March Robin Marks Randall Martin Paul McGale John McGrath Sumi Mehta George A Mensah Tony R Merriman Renata Micha Catherine Michaud Vinod Mishra Khayriyyah Mohd Hanafiah Ali A Mokdad Lidia Morawska Dariush Mozaffarian Tasha Murphy Mohsen Naghavi Bruce Neal Paul K Nelson Joan Miquel Nolla Rosana Norman Casey Olives Saad B Omer Jessica Orchard Richard Osborne Bart Ostro Andrew Page Kiran D Pandey Charles D H Parry Erin Passmore Jayadeep Patra Neil Pearce Pamela M Pelizzari Max Petzold Michael R Phillips Dan Pope C Arden Pope John Powles Mayuree Rao Homie Razavi Eva A Rehfuess Jürgen T Rehm Beate Ritz Frederick P Rivara Thomas Roberts Carolyn Robinson Jose A Rodriguez-Portales Isabelle Romieu Robin Room Lisa C Rosenfeld Ananya Roy Lesley Rushton Joshua A Salomon Uchechukwu Sampson Lidia Sanchez-Riera Ella Sanman Amir Sapkota Soraya Seedat Peilin Shi Kevin Shield Rupak Shivakoti Gitanjali M Singh David A Sleet Emma Smith Kirk R Smith Nicolas J C Stapelberg Kyle Steenland Heidi Stöckl Lars Jacob Stovner Kurt Straif Lahn Straney George D Thurston Jimmy H Tran Rita Van Dingenen Aaron van Donkelaar J Lennert Veerman Lakshmi Vijayakumar Robert Weintraub Myrna M Weissman Richard A White Harvey Whiteford Steven T Wiersma James D Wilkinson Hywel C Williams Warwick Williams Nicholas Wilson Anthony D Woolf Paul Yip Jan M Zielinski Alan D Lopez Christopher J L Murray Majid Ezzati Mohammad A AlMazroa Ziad A Memish

Lancet 2012 Dec;380(9859):2224-60

Institute for Health Metrics and Evaluation, Seattle, WA 98121, USA.

View Article and Find Full Text PDF
December 2012

Reversible switching between epigenetic states in honeybee behavioral subcastes.

Nat Neurosci 2012 Oct 16;15(10):1371-3. Epub 2012 Sep 16.

Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

View Article and Find Full Text PDF
October 2012

Genome-wide DNA methylation scan in major depressive disorder.

PLoS One 2012 12;7(4):e34451. Epub 2012 Apr 12.

Department of Pediatrics, Stanley Division of Developmental Neurovirology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America.

View Article and Find Full Text PDF
December 2012

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

BMC Public Health 2012 Mar 21;12:220. Epub 2012 Mar 21.

Johns Hopkins Bloomberg School of Public Health, Department of International Health, Baltimore, MD 21205, USA.

View Article and Find Full Text PDF
March 2012

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

Bioinformatics 2012 Mar 13;28(5):726-8. Epub 2012 Jan 13.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA, USA.

View Article and Find Full Text PDF
March 2012

Estimating diarrhea mortality among young children in low and middle income countries.

PLoS One 2012 3;7(1):e29151. Epub 2012 Jan 3.

Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America.

View Article and Find Full Text PDF
May 2012

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

Nat Biotechnol 2011 Nov 27;29(12):1117-9. Epub 2011 Nov 27.

Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

View Article and Find Full Text PDF
November 2011

Therapeutic implications of GIPC1 silencing in cancer.

PLoS One 2010 Dec 30;5(12):e15581. Epub 2010 Dec 30.

Functional Genomics and Computational Biology Group, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States America.

View Article and Find Full Text PDF
December 2010

Subset quantile normalization using negative control features.

J Comput Biol 2010 Oct;17(10):1385-95

Center for Statistical Sciences and Department of Community Health, Brown University, Providence, Rhode Island 02912, USA.

View Article and Find Full Text PDF
October 2010

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

Biostatistics 2011 Apr 21;12(2):197-210. Epub 2010 Sep 21.

Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University and Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21231, USA.

View Article and Find Full Text PDF
April 2011

Comprehensive methylome map of lineage commitment from haematopoietic progenitors.

Nature 2010 Sep 15;467(7313):338-42. Epub 2010 Aug 15.

Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N. Wolfe St., Baltimore, Maryland 21205, USA.

View Article and Find Full Text PDF
September 2010

Comprehensive high-throughput arrays for relative methylation (CHARM).

Curr Protoc Hum Genet 2010 Apr;Chapter 20:Unit 20.1.1-19

Department of Medicine, Johns Hopkins University School of Medicine, Center for Epigenetics, Baltimore, Maryland, USA.

View Article and Find Full Text PDF
April 2010

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

BMC Bioinformatics 2009 Dec 10;10:409. Epub 2009 Dec 10.

Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, Massachusetts 02115, USA.

View Article and Find Full Text PDF
December 2009

An optimized predictive strategy for interactome mapping.

J Proteome Res 2008 Sep 22;7(9):4089-94. Epub 2008 Jul 22.

Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, Massachusetts 02115, USA.

View Article and Find Full Text PDF
September 2008