Publications by authors named "Aaron McKenna"

43Publications

Emergence of Neuronal Diversity during Vertebrate Brain Development.

Neuron 2020 Dec 16;108(6):1058-1074.e6. Epub 2020 Oct 16.

Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA. Electronic address:

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December 2020

Recording development with single cell dynamic lineage tracing.

Development 2019 06 27;146(12). Epub 2019 Jun 27.

Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA

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June 2019

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data.

Cell Rep 2018 09;24(13):3607-3618

Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA; Morgridge Institute for Research, Madison, WI, USA. Electronic address:

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September 2018

A Review of the Effect of Management Practices on Prevalence in Poultry Farms.

Front Microbiol 2018 24;9:2002. Epub 2018 Aug 24.

Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom.

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August 2018

FlashFry: a fast and flexible tool for large-scale CRISPR target design.

BMC Biol 2018 07 5;16(1):74. Epub 2018 Jul 5.

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

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July 2018

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain.

Nat Biotechnol 2018 06 28;36(5):442-450. Epub 2018 Mar 28.

Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.

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June 2018

CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions.

Am J Hum Genet 2017 Aug 14;101(2):192-205. Epub 2017 Jul 14.

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA. Electronic address:

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August 2017

Whole-organism lineage tracing by combinatorial and cumulative genome editing.

Science 2016 Jul 26;353(6298):aaf7907. Epub 2016 May 26.

Department of Genome Sciences, University of Washington, Seattle, WA, USA. Howard Hughes Medical Institute, Seattle, WA, USA.

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July 2016

Genetic and clonal dissection of murine small cell lung carcinoma progression by genome sequencing.

Cell 2014 Mar;156(6):1298-1311

Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address:

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March 2014

Widespread genetic heterogeneity in multiple myeloma: implications for targeted therapy.

Cancer Cell 2014 Jan;25(1):91-101

Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address:

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January 2014

Landscape of genomic alterations in cervical carcinomas.

Nature 2014 Feb 25;506(7488):371-5. Epub 2013 Dec 25.

1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA [3] Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA [4].

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February 2014

Integrative and comparative genomic analysis of lung squamous cell carcinomas in East Asian patients.

J Clin Oncol 2014 Jan 9;32(2):121-8. Epub 2013 Dec 9.

Youngwook Kim, Ji-ae Yoon, Yoomi Lee, Yeong Kyung Yoo, and Keunchil Park, Samsung Medical Center, Samsung Biomedical Research Institute; Jong-Mu Sun, Hong Kwan Kim, Yong Soo Choi, Kwhanmien Kim, Young Mog Shim, Yoon-La Choi, Jhingook Kim, Jin Seok Ahn, Myung-Ju Ahn, and Keunchil Park, Samsung Medical Center, Sungkyunkwan University School of Medicine; Sukki Cho, Seoul National University Bundang Hospital, College of Medicine, Seoul National University, Seoul; In-Jae Oh, Kyu-Sik Kim, Sang-Yun Song, Kook-Ju Na, and Young-Chul Kim, Chonnam National University Hwasun Hospital, Jeonnam, Republic of Korea; Peter S. Hammerman, Jaegil Kim, Chandra Sekhar Pedamallu, Kristian Cibulskis, Michael S. Lawrence, Petar Stojanov, Scott L. Carter, Aaron McKenna, Chip Stewart, Andrey Y. Sivachenko, Gad Getz, and Matthew Meyerson, Broad Institute of Harvard and MIT, Cambridge; Matthew Meyerson, Harvard Medical School; Peter S. Hammerman and Chandra Sekhar Pedamallu, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital Cancer Center, Boston, MA; and Matthew D. Wilkerson and D. Neil Hayes, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC.

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January 2014

MAP kinase pathway alterations in BRAF-mutant melanoma patients with acquired resistance to combined RAF/MEK inhibition.

Cancer Discov 2014 Jan 21;4(1):61-8. Epub 2013 Nov 21.

1Department of Medical Oncology, Dana-Farber Cancer Institute; 2Department of Medicine, Brigham and Women's Hospital; 3Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston; 4Broad Institute of Harvard and MIT; and 5Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.

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January 2014

The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma.

Cancer Discov 2014 Jan 21;4(1):94-109. Epub 2013 Nov 21.

1Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School; 2Department of Pathology, Massachusetts General Hospital Cancer Center, Boston; 3Broad Institute of MIT and Harvard; 4Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts; 5Department of Dermatology, University Hospital, West German Cancer Center, University Duisburg-Essen, Essen; 6German Cancer Consortium (DKTK); 7Department of Dermatology, Heidelberg University Hospital, Heidelberg; 8Department of Dermatology and Allergy, Hannover Medical School, Hannover; 9Department of Dermatology, University of Wuerzburg, Wuerzburg; 10Department of Dermatology, Venerology and Allergology, University of Schleswig-Holstein Hospital, Kiel; 11Department of Dermatology and Allergology, Ludwig-Maximilian University, Munich; 12Department of Dermatology, Venerology and Allergy, Charité Universitätsmedizin Berlin, Humboldt University, Berlin; 13Department of Dermatology, University of Mainz, Mainz; 14University Medical Center, University of Tübingen, Tübingen, Germany; 15Department of Genome Sciences, University of Washington, Seattle, Washington; 16Department of Dermatology, University Hospital Zurich, Zurich, Switzerland; and 17First Department of Medicine, Medical School, University of Athens, Athens, Greece.

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January 2014

Integrative eQTL-based analyses reveal the biology of breast cancer risk loci.

Cell 2013 Jan;152(3):633-41

Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.

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January 2013

ContEst: estimating cross-contamination of human samples in next-generation sequencing data.

Bioinformatics 2011 Sep 29;27(18):2601-2. Epub 2011 Jul 29.

Genome Sequencing Analysis Program and Platform, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA.

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September 2011

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Genome Res 2010 Sep 19;20(9):1297-303. Epub 2010 Jul 19.

Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.

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September 2010