Martin Aryee

Martin Aryee

UNVERIFIED PROFILE

Are you Martin Aryee?   Register this Author

Register author
Martin Aryee

Martin Aryee

Publications by authors named "Martin Aryee"

Are you Martin Aryee?   Register this Author

73Publications

2829Reads

31Profile Views

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

Authors:
Julian Grünewald Ronghao Zhou Sowmya Iyer Caleb A Lareau Sara P Garcia Martin J Aryee J Keith Joung

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

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/s41587-019-0236-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6730565PMC
September 2019

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

Authors:
Killian S Hanlon Benjamin P Kleinstiver Sara P Garcia Mikołaj P Zaborowski Adrienn Volak Stefan E Spirig Alissa Muller Alexander A Sousa Shengdar Q Tsai Niclas E Bengtsson Camilla Lööv Martin Ingelsson Jeffrey S Chamberlain David P Corey Martin J Aryee J Keith Joung Xandra O Breakefield Casey A Maguire Bence György

Nat Commun 2019 Sep 30;10(1):4439. Epub 2019 Sep 30.

Department of Neurobiology, Harvard Medical School, Boston, MA, 02115, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/s41467-019-12449-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769011PMC
September 2019

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

Authors:
Caleb A Lareau Fabiana M Duarte Jennifer G Chew Vinay K Kartha Zach D Burkett Andrew S Kohlway Dmitry Pokholok Martin J Aryee Frank J Steemers Ronald Lebofsky Jason D Buenrostro

Nat Biotechnol 2019 08 24;37(8):916-924. Epub 2019 Jun 24.

Broad Institute of MIT and Harvard, Cambridge, MA, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/s41587-019-0147-6DOI Listing
August 2019

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

Authors:
Yannick Berker Lindsey A Vandergrift Isabel Wagner Li Su Johannes Kurth Andreas Schuler Sarah S Dinges Piet Habbel Johannes Nowak Eugene Mark Martin J Aryee David C Christiani Leo L Cheng

Sci Rep 2019 Jul 16;9(1):10319. Epub 2019 Jul 16.

Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, 02114, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/s41598-019-46643-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6635503PMC
July 2019

Preprocessing and Computational Analysis of Single-Cell Epigenomic Datasets.

Authors:
Caleb Lareau Divy Kangeyan Martin J Aryee

Methods Mol Biol 2019 ;1935:187-202

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1007/978-1-4939-9057-3_13DOI Listing
June 2019

Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer.

Authors:
Matteo Ligorio Srinjoy Sil Jose Malagon-Lopez Linda T Nieman Sandra Misale Mauro Di Pilato Richard Y Ebright Murat N Karabacak Anupriya S Kulkarni Ann Liu Nicole Vincent Jordan Joseph W Franses Julia Philipp Johannes Kreuzer Niyati Desai Kshitij S Arora Mihir Rajurkar Elad Horwitz Azfar Neyaz Eric Tai Neelima K C Magnus Kevin D Vo Chittampalli N Yashaswini Francesco Marangoni Myriam Boukhali Jackson P Fatherree Leah J Damon Kristina Xega Rushil Desai Melissa Choz Francesca Bersani Adam Langenbucher Vishal Thapar Robert Morris Ulrich F Wellner Oliver Schilling Michael S Lawrence Andrew S Liss Miguel N Rivera Vikram Deshpande Cyril H Benes Shyamala Maheswaran Daniel A Haber Carlos Fernandez-Del-Castillo Cristina R Ferrone Wilhelm Haas Martin J Aryee David T Ting

Cell 2019 Jun 30;178(1):160-175.e27. Epub 2019 May 30.

Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA. Electronic address:

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1016/j.cell.2019.05.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6697165PMC
June 2019

Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis.

Authors:
Leif S Ludwig Caleb A Lareau Erik L Bao Satish K Nandakumar Christoph Muus Jacob C Ulirsch Kaitavjeet Chowdhary Jason D Buenrostro Narla Mohandas Xiuli An Martin J Aryee Aviv Regev Vijay G Sankaran

Cell Rep 2019 Jun;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

Download full-text PDF

 Source
http://dx.doi.org/10.1016/j.celrep.2019.05.046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6579117PMC
June 2019

Reply.

Authors:
Irun Bhan Martin Aryee David T Ting

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

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1053/j.gastro.2019.03.042DOI Listing
May 2019

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

Authors:
Julian Grünewald Ronghao Zhou Sara P Garcia Sowmya Iyer Caleb A Lareau Martin J Aryee J Keith Joung

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

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/s41586-019-1161-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6657343PMC
May 2019

Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia.

Authors:
Federico Gaiti Ronan Chaligne Hongcang Gu Ryan M Brand Steven Kothen-Hill Rafael C Schulman Kirill Grigorev Davide Risso Kyu-Tae Kim Alessandro Pastore Kevin Y Huang Alicia Alonso Caroline Sheridan Nathaniel D Omans Evan Biederstedt Kendell Clement Lili Wang Joshua A Felsenfeld Erica B Bhavsar Martin J Aryee John N Allan Richard Furman Andreas Gnirke Catherine J Wu Alexander Meissner Dan A Landau

Nature 2019 May 15;569(7757):576-580. Epub 2019 May 15.

New York Genome Center, New York, NY, USA.

View Article

Download full-text PDF

 Source
http://www.nature.com/articles/s41586-019-1198-z
Publisher Site
http://dx.doi.org/10.1038/s41586-019-1198-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6533116PMC
May 2019

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

Authors:
Jacob C Ulirsch Caleb A Lareau Erik L Bao Leif S Ludwig Michael H Guo Christian Benner Ansuman T Satpathy Vinay K Kartha Rany M Salem Joel N Hirschhorn Hilary K Finucane Martin J Aryee Jason D Buenrostro Vijay G Sankaran

Nat Genet 2019 04 11;51(4):683-693. Epub 2019 Mar 11.

Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/s41588-019-0362-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441389PMC
April 2019

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

Authors:
Huidong Chen Luca Albergante Jonathan Y Hsu Caleb A Lareau Giosuè Lo Bosco Jihong Guan Shuigeng Zhou Alexander N Gorban Daniel E Bauer Martin J Aryee David M Langenau Andrei Zinovyev Jason D Buenrostro Guo-Cheng Yuan Luca Pinello

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

Download full-text PDF

 Source
http://dx.doi.org/10.1038/s41467-019-09670-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478907PMC
April 2019

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

Authors:
Benjamin P Kleinstiver Alexander A Sousa Russell T Walton Y Esther Tak Jonathan Y Hsu Kendell Clement Moira M Welch Joy E Horng Jose Malagon-Lopez Irene Scarfò Marcela V Maus Luca Pinello Martin J Aryee J Keith Joung

Nat Biotechnol 2019 03 11;37(3):276-282. Epub 2019 Feb 11.

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/s41587-018-0011-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6401248PMC
March 2019

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

Authors:
Leif S Ludwig Caleb A Lareau Jacob C Ulirsch Elena Christian Christoph Muus Lauren H Li Karin Pelka Will Ge Yaara Oren Alison Brack Travis Law Christopher Rodman Jonathan H Chen Genevieve M Boland Nir Hacohen Orit Rozenblatt-Rosen Martin J Aryee Jason D Buenrostro Aviv Regev Vijay G Sankaran

Cell 2019 Mar 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

Download full-text PDF

 Source
https://linkinghub.elsevier.com/retrieve/pii/S00928674193005
Publisher Site
http://dx.doi.org/10.1016/j.cell.2019.01.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6408267PMC
March 2019

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

Authors:
Divy Kangeyan Andrew Dunford Sowmya Iyer Chip Stewart Megan Hanna Gad Getz Martin J Aryee

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

Download full-text PDF

 Source
http://dx.doi.org/10.1186/s12859-019-2750-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6440105PMC
March 2019

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

Authors:
Keunsub Lee Yingxiao Zhang Benjamin P Kleinstiver Jimmy A Guo Martin J Aryee Jonah Miller Aimee Malzahn Scott Zarecor Carolyn J Lawrence-Dill J Keith Joung Yiping Qi Kan Wang

Plant Biotechnol J 2019 02 22;17(2):362-372. Epub 2018 Jul 22.

Crop Bioengineering Center, Iowa State University, Ames, IA, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1111/pbi.12982DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6320322PMC
February 2019

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

Authors:
Irun Bhan Kelly Mosesso Lipika Goyal Julia Philipp Mark Kalinich Joseph W Franses Melissa Choz Rahmi Oklu Mehmet Toner Shyamala Maheswaran Daniel A Haber Andrew X Zhu Raymond T Chung Martin Aryee David T Ting

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

Download full-text PDF

 Source
http://dx.doi.org/10.1053/j.gastro.2018.09.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347478PMC
December 2018

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

Authors:
Cicera R Lazzarotto Nhu T Nguyen Xing Tang Jose Malagon-Lopez Jimmy A Guo Martin J Aryee J Keith Joung Shengdar Q Tsai

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

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

View Article

Download full-text PDF

 Source
http://www.nature.com/articles/s41596-018-0055-0
Publisher Site
http://dx.doi.org/10.1038/s41596-018-0055-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6512799PMC
November 2018

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

Authors:
Pinar Akcakaya Maggie L Bobbin Jimmy A Guo Jose Malagon-Lopez Kendell Clement Sara P Garcia Mick D Fellows Michelle J Porritt Mike A Firth Alba Carreras Tania Baccega Frank Seeliger Mikael Bjursell Shengdar Q Tsai Nhu T Nguyen Roberto Nitsch Lorenz M Mayr Luca Pinello Mohammad Bohlooly-Y Martin J Aryee Marcello Maresca J Keith Joung

Nature 2018 09 12;561(7723):416-419. Epub 2018 Sep 12.

Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.

View Article

Download full-text PDF

 Source
http://www.nature.com/articles/s41586-018-0500-9
Publisher Site
http://dx.doi.org/10.1038/s41586-018-0500-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6194229PMC
September 2018

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

Authors:
Richard C Pelikan Jennifer A Kelly Yao Fu Caleb A Lareau Kandice L Tessneer Graham B Wiley Mandi M Wiley Stuart B Glenn John B Harley Joel M Guthridge Judith A James Martin J Aryee Courtney Montgomery Patrick M Gaffney

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

Download full-text PDF

 Source
http://www.nature.com/articles/s41467-018-05328-9
Publisher Site
http://dx.doi.org/10.1038/s41467-018-05328-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6060153PMC
July 2018

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

Authors:
Jason D Buenrostro M Ryan Corces Caleb A Lareau Beijing Wu Alicia N Schep Martin J Aryee Ravindra Majeti Howard Y Chang William J Greenleaf

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

Download full-text PDF

 Source
http://dx.doi.org/10.1016/j.cell.2018.03.074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989727PMC
May 2018

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

Authors:
Caleb A Lareau Kendell Clement Jonathan Y Hsu Vikram Pattanayak J Keith Joung Martin J Aryee Luca Pinello

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

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/nmeth.4541DOI Listing
April 2018

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

Authors:
Caleb A Lareau Martin J Aryee

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

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1093/bioinformatics/btx623DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860605PMC
February 2018

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

Authors:
Caleb A Lareau Martin J Aryee

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

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

View Article

Download full-text PDF

 Source
http://www.nature.com/articles/nmeth.4583
Publisher Site
http://dx.doi.org/10.1038/nmeth.4583DOI Listing
February 2018

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

Authors:
Qin Tang Sowmya Iyer Riadh Lobbardi John C Moore Huidong Chen Caleb Lareau Christine Hebert McKenzie L Shaw Cyril Neftel Mario L Suva Craig J Ceol Andre Bernards Martin Aryee Luca Pinello Iain A Drummond David M Langenau

J Exp Med 2017 Oct 6;214(10):2875-2887. Epub 2017 Sep 6.

Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1084/jem.20170976DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5626406PMC
October 2017

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

Authors:
Akpéli V Nordor Djamel Nehar-Belaid Sophie Richon David Klatzmann Dominique Bellet Virginie Dangles-Marie Thierry Fournier Martin J Aryee

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

Download full-text PDF

 Source
http://dx.doi.org/10.1080/15592294.2017.1342912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5739102PMC
September 2017

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

Authors:
Shengdar Q Tsai Nhu T Nguyen Jose Malagon-Lopez Ved V Topkar Martin J Aryee J Keith Joung

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

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/nmeth.4278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5924695PMC
June 2017

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

Authors:
Gaylor Boulay Mary E Awad Nicolo Riggi Tenley C Archer Sowmya Iyer Wannaporn E Boonseng Nikki E Rossetti Beverly Naigles Shruthi Rengarajan Angela Volorio James C Kim Jill P Mesirov Pablo Tamayo Scott L Pomeroy Martin J Aryee Miguel N Rivera

Cancer Discov 2017 03 17;7(3):288-301. Epub 2017 Feb 17.

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1158/2159-8290.CD-16-0844DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340587PMC
March 2017

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

Authors:
Niyati Desai Dipti Sajed Kshitij S Arora Alexander Solovyov Mihir Rajurkar Jacob R Bledsoe Srinjoy Sil Ramzi Amri Eric Tai Olivia C MacKenzie Mari Mino-Kenudson Martin J Aryee Cristina R Ferrone David L Berger Miguel N Rivera Benjamin D Greenbaum Vikram Deshpande David T Ting

JCI Insight 2017 02 9;2(3):e91078. Epub 2017 Feb 9.

Massachusetts General Hospital Cancer Center.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1172/jci.insight.91078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5291727PMC
February 2017

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

Authors:
Richard I Joh Jasbeer S Khanduja Isabel A Calvo Meeta Mistry Christina M Palmieri Andrej J Savol Shannan J Ho Sui Ruslan I Sadreyev Martin J Aryee Mo Motamedi

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

Download full-text PDF

 Source
http://dx.doi.org/10.1016/j.molcel.2016.11.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5180613PMC
December 2016

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

Authors:
David Gomez-Cabrero Malin Almgren Louise K Sjöholm Aase H Hensvold Mikael V Ringh Rakel Tryggvadottir Juha Kere Annika Scheynius Nathalie Acevedo Lovisa Reinius Margaret A Taub Carolina Montano Martin J Aryee Jason I Feinberg Andrew P Feinberg Jesper Tegnér Lars Klareskog Anca I Catrina Tomas J Ekström

Genome Med 2016 11 22;8(1):124. Epub 2016 Nov 22.

Center for Molecular Medicine at Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1186/s13073-016-0374-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120506PMC
November 2016

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

Authors:
Benjamin P Kleinstiver Shengdar Q Tsai Michelle S Prew Nhu T Nguyen Moira M Welch Jose M Lopez Zachary R McCaw Martin J Aryee J Keith Joung

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

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/nbt.3620DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4980201PMC
August 2016

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

Authors:
Shengdar Q Tsai Ved V Topkar J Keith Joung Martin J Aryee

Nat Biotechnol 2016 05;34(5):483

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/nbt.3534DOI Listing
May 2016

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

Authors:
Rebecca S Heist Hyo Sup Shim Shalini Gingipally Mari Mino-Kenudson Long Le Justin F Gainor Zongli Zheng Martin Aryee Junfeng Xia Peilin Jia Hailing Jin Zhongming Zhao William Pao Jeffrey A Engelman A John Iafrate

Oncologist 2016 Apr 28;21(4):481-6. Epub 2016 Mar 28.

Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1634/theoncologist.2015-0510DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4828128PMC
April 2016

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

Authors:
Jamie Perin Christa L Fischer Walker Robert E Black Martin J Aryee

Am J Epidemiol 2016 Mar 10;183(5):507-14. Epub 2016 Feb 10.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1093/aje/kwv140DOI Listing
March 2016

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

Authors:
Timothy D O'Brien Peilin Jia Junfeng Xia Uma Saxena Hailing Jin Huy Vuong Pora Kim Qingguo Wang Martin J Aryee Mari Mino-Kenudson Jeffrey A Engelman Long P Le A John Iafrate Rebecca S Heist William Pao Zhongming Zhao

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

Download full-text PDF

 Source
http://dx.doi.org/10.1016/j.ymeth.2015.04.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4509831PMC
July 2015

Engineered CRISPR-Cas9 nucleases with altered PAM specificities.

Authors:
Benjamin P Kleinstiver Michelle S Prew Shengdar Q Tsai Ved V Topkar Nhu T Nguyen Zongli Zheng Andrew P W Gonzales Zhuyun Li Randall T Peterson Jing-Ruey Joanna Yeh Martin J Aryee J Keith Joung

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

Download full-text PDF

 Source
http://dx.doi.org/10.1038/nature14592DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4540238PMC
July 2015

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

Authors:
Michael J Ziller Kasper D Hansen Alexander Meissner Martin J Aryee

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

Download full-text PDF

 Source
http://dx.doi.org/10.1038/nmeth.3152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344394PMC
March 2015

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

Authors:
Capucine Van Rechem Joshua C Black Myriam Boukhali Martin J Aryee Susanne Gräslund Wilhelm Haas Cyril H Benes Johnathan R Whetstine

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

Download full-text PDF

 Source
http://dx.doi.org/10.1158/2159-8290.CD-14-1326DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355328PMC
March 2015

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

Authors:
Shengdar Q Tsai Zongli Zheng Nhu T Nguyen Matthew Liebers Ved V Topkar Vishal Thapar Nicolas Wyvekens Cyd Khayter A John Iafrate Long P Le Martin J Aryee J Keith Joung

Nat Biotechnol 2015 Feb 16;33(2):187-197. Epub 2014 Dec 16.

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/nbt.3117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4320685PMC
February 2015

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

Authors:
Wai-Ki Yip Heide Fier Dawn L DeMeo Martin Aryee Nan Laird Christoph Lange

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

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1002/gepi.21851DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236268PMC
December 2014

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

Authors:
Nicolò Riggi Birgit Knoechel Shawn M Gillespie Esther Rheinbay Gaylor Boulay Mario L Suvà Nikki E Rossetti Wannaporn E Boonseng Ozgur Oksuz Edward B Cook Aurélie Formey Anoop Patel Melissa Gymrek Vishal Thapar Vikram Deshpande David T Ting Francis J Hornicek G Petur Nielsen Ivan Stamenkovic Martin J Aryee Bradley E Bernstein Miguel N Rivera

Cancer Cell 2014 Nov 30;26(5):668-681. Epub 2014 Oct 30.

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1016/j.ccell.2014.10.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4492343PMC
November 2014

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

Authors:
Shengdar Q Tsai Nicolas Wyvekens Cyd Khayter Jennifer A Foden Vishal Thapar Deepak Reyon Mathew J Goodwin Martin J Aryee J Keith Joung

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

Download full-text PDF

 Source
http://dx.doi.org/10.1038/nbt.2908DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090141PMC
June 2014

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

Authors:
Martin J Aryee Andrew E Jaffe Hector Corrada-Bravo Christine Ladd-Acosta Andrew P Feinberg Kasper D Hansen Rafael A Irizarry

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

Download full-text PDF

 Source
http://dx.doi.org/10.1093/bioinformatics/btu049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016708PMC
May 2014

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

Authors:
Claudio F Lanata Christa L Fischer-Walker Ana C Olascoaga Carla X Torres Martin J Aryee Robert E Black

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

Download full-text PDF

 Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072788PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3762858PMC
April 2014

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

Authors:
Yun Liu Xin Li Martin J Aryee Tomas J Ekström Leonid Padyukov Lars Klareskog Amy Vandiver Ann Zenobia Moore Toshiko Tanaka Luigi Ferrucci M Daniele Fallin Andrew P Feinberg

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

Download full-text PDF

 Source
https://linkinghub.elsevier.com/retrieve/pii/S00029297140006
Publisher Site
http://dx.doi.org/10.1016/j.ajhg.2014.02.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3980524PMC
April 2014

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

Authors:
James Zou Christoph Lippert David Heckerman Martin Aryee Jennifer Listgarten

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

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/nmeth.2815DOI Listing
March 2014

Identification of direction in gene networks from expression and methylation.

Authors:
David M Simcha Laurent Younes Martin J Aryee Donald Geman

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

Download full-text PDF

 Source
http://dx.doi.org/10.1186/1752-0509-7-118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4228359PMC
November 2013

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

Authors:
Jerry Guintivano Martin J Aryee Zachary A Kaminsky

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

Download full-text PDF

 Source
http://dx.doi.org/10.4161/epi.23924DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669121PMC
March 2013

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

Authors:
Yun Liu Martin J Aryee Leonid Padyukov M Daniele Fallin Espen Hesselberg Arni Runarsson Lovisa Reinius Nathalie Acevedo Margaret Taub Marcus Ronninger Klementy Shchetynsky Annika Scheynius Juha Kere Lars Alfredsson Lars Klareskog Tomas J Ekström Andrew P Feinberg

Nat Biotechnol 2013 Feb 20;31(2):142-7. Epub 2013 Jan 20.

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

View Article

Download full-text PDF

 Source
http://www.nature.com/articles/nbt.2487
Publisher Site
http://dx.doi.org/10.1038/nbt.2487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3598632PMC
February 2013

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

Authors:
Martin J Aryee Wennuan Liu Julia C Engelmann Philipp Nuhn Meltem Gurel Michael C Haffner David Esopi Rafael A Irizarry Robert H Getzenberg William G Nelson Jun Luo Jianfeng Xu William B Isaacs G Steven Bova Srinivasan Yegnasubramanian

Sci Transl Med 2013 Jan;5(169):169ra10

Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21231, USA.

View Article

Download full-text PDF

 Source
http://stm.sciencemag.org/cgi/doi/10.1126/scitranslmed.30052
Publisher Site
http://dx.doi.org/10.1126/scitranslmed.3005211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577373PMC
January 2013

Genome-wide DNA methylation scan in major depressive disorder.

Authors:
Sarven Sabunciyan Martin J Aryee Rafael A Irizarry Michael Rongione Maree J Webster Walter E Kaufman Peter Murakami Andree Lessard Robert H Yolken Andrew P Feinberg James B Potash

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

Download full-text PDF

 Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0034451PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3325245PMC
December 2012

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

Download full-text PDF

 Source
http://dx.doi.org/10.1016/S0140-6736(12)61766-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156511PMC
December 2012

Reversible switching between epigenetic states in honeybee behavioral subcastes.

Authors:
Brian R Herb Florian Wolschin Kasper D Hansen Martin J Aryee Ben Langmead Rafael Irizarry Gro V Amdam Andrew P Feinberg

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

Download full-text PDF

 Source
http://www.nature.com/articles/nn.3218
Publisher Site
http://dx.doi.org/10.1038/nn.3218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518384PMC
October 2012

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

Authors:
Christa L Fischer Walker Martin J Aryee Cynthia Boschi-Pinto Robert E Black

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

Download full-text PDF

 Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0029151PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3250411PMC
May 2012

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

Authors:
Hariharan Easwaran Sarah E Johnstone Leander Van Neste Joyce Ohm Tim Mosbruger Qiuju Wang Martin J Aryee Patrick Joyce Nita Ahuja Dan Weisenberger Eric Collisson Jingchun Zhu Srinivasan Yegnasubramanian William Matsui Stephen B Baylin

Genome Res 2012 May 5;22(5):837-49. Epub 2012 Mar 5.

The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins and the Johns Hopkins Medical Institutions, Baltimore, MD 21117, USA.

View Article

Download full-text PDF

 Source
http://genome.cshlp.org/content/early/2012/03/09/gr.131169.1
Web Search
http://genome.cshlp.org/cgi/doi/10.1101/gr.131169.111
Publisher Site
http://dx.doi.org/10.1101/gr.131169.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337430PMC
May 2012

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

Authors:
Thomas W Chittenden Eleanor A Howe Jennifer M Taylor Jessica C Mar Martin J Aryee Harold Gómez Razvan Sultana John Braisted Sarita J Nair John Quackenbush Chris Holmes

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

Download full-text PDF

 Source
http://bioinformatics.oxfordjournals.org/content/early/2012/
Web Search
http://bioinformatics.oxfordjournals.org/content/28/5/726.fu
Web Search
http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/bts011DOI Listing
March 2012

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

Authors:
Christa L Fischer Walker Jamie Perin Martin J Aryee Cynthia Boschi-Pinto Robert E Black

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

Download full-text PDF

 Source
http://dx.doi.org/10.1186/1471-2458-12-220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3323412PMC
March 2012

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

Authors:
Hwajin Lee Andrew E Jaffe Jason I Feinberg Rakel Tryggvadottir Shannon Brown Carolina Montano Martin J Aryee Rafael A Irizarry Julie Herbstman Frank R Witter Lynn R Goldman Andrew P Feinberg M Daniele Fallin

Int J Epidemiol 2012 Feb;41(1):188-99

Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1093/ije/dyr237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3304532PMC
February 2012

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

Authors:
Richard S Lee Kellie L K Tamashiro Martin J Aryee Peter Murakami Fayaz Seifuddin Brian Herb Yuqing Huo Michael Rongione Andrew P Feinberg Timothy H Moran James B Potash

Epigenetics 2011 Nov 1;6(11):1378-90. Epub 2011 Nov 1.

Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.4161/epi.6.11.18072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242812PMC
November 2011

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

Authors:
Kitai Kim Rui Zhao Akiko Doi Kitwa Ng Juli Unternaehrer Patrick Cahan Hongguang Huo Yuin-Han Loh Martin J Aryee M William Lensch Hu Li James J Collins Andrew P Feinberg George Q Daley

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

Download full-text PDF

 Source
http://dx.doi.org/10.1038/nbt.2052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357310PMC
November 2011

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

Authors:
Srinivasan Yegnasubramanian Zhijin Wu Michael C Haffner David Esopi Martin J Aryee Raghav Badrinath Tony L He James D Morgan Benilton Carvalho Qizhi Zheng Angelo M De Marzo Rafael A Irizarry William G Nelson

BMC Genomics 2011 Jun 13;12:313. Epub 2011 Jun 13.

Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

View Article

Download full-text PDF

 Source
http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
Publisher Site
http://dx.doi.org/10.1186/1471-2164-12-313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3124442PMC
June 2011

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

Authors:
Martin J Aryee Zhijin Wu Christine Ladd-Acosta Brian Herb Andrew P Feinberg Srinivasan Yegnasubramanian Rafael A Irizarry

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

Download full-text PDF

 Source
http://dx.doi.org/10.1093/biostatistics/kxq055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062148PMC
April 2011

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

Authors:
Cheryl M Koh Bora Gurel Siobhan Sutcliffe Martin J Aryee Denise Schultz Tsuyoshi Iwata Motohide Uemura Karen I Zeller Uzoma Anele Qizhi Zheng Jessica L Hicks William G Nelson Chi V Dang Srinivasan Yegnasubramanian Angelo M De Marzo

Am J Pathol 2011 Apr;178(4):1824-34

Department of Pathology, The Johns Hopkins University, School of Medicine, Baltimore, MD 21231 , USA.

View Article

Download full-text PDF

 Source
http://linkinghub.elsevier.com/retrieve/pii/S000294401100040
Publisher Site
http://dx.doi.org/10.1016/j.ajpath.2010.12.040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3078425PMC
April 2011

Therapeutic implications of GIPC1 silencing in cancer.

Authors:
Thomas W Chittenden Jane Pak Renee Rubio Hailing Cheng Kristina Holton Niall Prendergast Vladimir Glinskii Yi Cai Aedin Culhane Stefan Bentink Mathew Schwede Jessica C Mar Eleanor A Howe Martin Aryee Razvan Sultana Anthony A Lanahan Jennifer M Taylor Chris Holmes William C Hahn Jean J Zhao J Dirk Iglehart John Quackenbush

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

Download full-text PDF

 Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0015581PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3012716PMC
December 2010

Subset quantile normalization using negative control features.

Authors:
Zhijin Wu Martin J Aryee

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

Download full-text PDF

 Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3122888PMC
http://dx.doi.org/10.1089/cmb.2010.0049DOI Listing
October 2010

Comprehensive methylome map of lineage commitment from haematopoietic progenitors.

Authors:
Hong Ji Lauren I R Ehrlich Jun Seita Peter Murakami Akiko Doi Paul Lindau Hwajin Lee Martin J Aryee Rafael A Irizarry Kitai Kim Derrick J Rossi Matthew A Inlay Thomas Serwold Holger Karsunky Lena Ho George Q Daley Irving L Weissman Andrew P Feinberg

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

Download full-text PDF

 Source
http://dx.doi.org/10.1038/nature09367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956609PMC
September 2010

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

Authors:
Andrew P Feinberg Rafael A Irizarry Delphine Fradin Martin J Aryee Peter Murakami Thor Aspelund Gudny Eiriksdottir Tamara B Harris Lenore Launer Vilmundur Gudnason M Daniele Fallin

Sci Transl Med 2010 Sep;2(49):49ra67

Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1126/scitranslmed.3001262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137242PMC
September 2010

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

Authors:
Michael C Haffner Martin J Aryee Antoun Toubaji David M Esopi Roula Albadine Bora Gurel William B Isaacs G Steven Bova Wennuan Liu Jianfeng Xu Alan K Meeker George Netto Angelo M De Marzo William G Nelson Srinivasan Yegnasubramanian

Nat Genet 2010 Aug 4;42(8):668-75. Epub 2010 Jul 4.

Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/ng.613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3157086PMC
August 2010

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

Authors:
Christine Ladd-Acosta Martin J Aryee Jared M Ordway Andrew P Feinberg

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

Download full-text PDF

 Source
http://dx.doi.org/10.1002/0471142905.hg2001s65DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6353553PMC
April 2010

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

Authors:
Akiko Doi In-Hyun Park Bo Wen Peter Murakami Martin J Aryee Rafael Irizarry Brian Herb Christine Ladd-Acosta Junsung Rho Sabine Loewer Justine Miller Thorsten Schlaeger George Q Daley Andrew P Feinberg

Nat Genet 2009 Dec 1;41(12):1350-3. Epub 2009 Nov 1.

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/ng.471DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2958040PMC
December 2009

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

Authors:
Martin J Aryee José A Gutiérrez-Pabello Igor Kramnik Tapabrata Maiti John Quackenbush

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

Download full-text PDF

 Source
http://dx.doi.org/10.1186/1471-2105-10-409DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2801687PMC
December 2009

An optimized predictive strategy for interactome mapping.

Authors:
Martin J A Aryee John Quackenbush

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

Download full-text PDF

 Source
http://dx.doi.org/10.1021/pr700858eDOI Listing
September 2008