Andrew Adey

Assistant Professor

  • 2083 Citations
  • 18 h-Index
20102019
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Research Output 2010 2019

  • 2083 Citations
  • 18 h-Index
  • 27 Article
  • 1 Chapter
  • 1 Comment/debate
  • 1 Short survey
2019
1 Citation (Scopus)

Integration of Single-Cell Genomics Datasets

Adey, A., Jun 13 2019, In : Cell. 177, 7, p. 1677-1679 3 p.

Research output: Contribution to journalShort survey

Genomics
RNA
Biological systems
Cells
Epigenomics
1 Citation (Scopus)

Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion

Daughtry, B. L., Rosenkrantz, J. L., Lazar, N. H., Fei, S. S., Redmayne, N., Torkenczy, K. A., Adey, A., Yan, M., Gao, L., Park, B., Nevonen, K. A., Carbone, L. & Chavez, S., Mar 1 2019, In : Genome Research. 29, 3, p. 367-382 16 p.

Research output: Contribution to journalArticle

Open Access
Blastomeres
Blastocyst
Primates
Chromosomes
Aneuploidy
1 Citation (Scopus)

The accessible chromatin landscape of the murine hippocampus at single-cell resolution

Sinnamon, J. R., Torkenczy, K. A., Linhoff, M. W., Vitak, S. A., Mulqueen, R. M., Pliner, H. A., Trapnell, C., Steemers, F. J., Mandel, G. & Adey, A., May 1 2019, In : Genome Research. 29, 5, p. 857-869 13 p.

Research output: Contribution to journalArticle

Open Access
Chromatin
Hippocampus
Transposases
Neurons
Pyramidal Cells
2018
13 Citations (Scopus)

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

Pliner, H. A., Packer, J. S., McFaline-Figueroa, J. L., Cusanovich, D. A., Daza, R. M., Aghamirzaie, D., Srivatsan, S., Qiu, X., Jackson, D., Minkina, A., Adey, A., Steemers, F. J., Shendure, J. & Trapnell, C., Sep 6 2018, In : Molecular Cell. 71, 5, p. 858-871.e8

Research output: Contribution to journalArticle

Cell Communication
Chromatin
Histone Code
Myoblasts
DNA
9 Citations (Scopus)

Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer

Risom, T., Langer, E. M., Chapman, M. P., Rantala, J., Fields, A. J., Boniface, C., Alvarez, M. J., Kendsersky, N. D., Pelz, C. R., Johnson-Camacho, K., Dobrolecki, L. E., Chin, K-Y., Aswani, A. J., Wang, N. J., Califano, A., Lewis, M. T., Tomlin, C. J., Spellman, P., Adey, A., Gray, J. & 1 others, Sears, R., Dec 1 2018, In : Nature Communications. 9, 1, 3815.

Research output: Contribution to journalArticle

plastic properties
breast
chromatin
Plasticity
drugs
30 Citations (Scopus)

Highly scalable generation of DNA methylation profiles in single cells

Mulqueen, R. M., Pokholok, D., Norberg, S. J., Torkenczy, K. A., Fields, A. J., Sun, D., Sinnamon, J. R., Shendure, J., Trapnell, C., O'Roak, B., Xia, Z., Steemers, F. J. & Adey, A., Jun 1 2018, In : Nature Biotechnology. 36, 5, p. 428-431 4 p.

Research output: Contribution to journalArticle

Methylation
DNA Methylation
Assays
Genes
Cells
1 Citation (Scopus)

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

Cao, J., Cusanovich, D. A., Ramani, V., Aghamirzaie, D., Pliner, H. A., Hill, A. J., Daza, R. M., McFaline-Figueroa, J. L., Packer, J. S., Christiansen, L., Steemers, F. J., Adey, A., Trapnell, C. & Shendure, J., Jan 1 2018, (Accepted/In press) In : Science.

Research output: Contribution to journalArticle

Chromatin
Joints
Gene Expression
Methylation
Dexamethasone
34 Citations (Scopus)

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

Cao, J., Cusanovich, D. A., Ramani, V., Aghamirzaie, D., Pliner, H. A., Hill, A. J., Daza, R. M., McFaline-Figueroa, J. L., Packer, J. S., Christiansen, L., Steemers, F. J., Adey, A., Trapnell, C. & Shendure, J., Sep 28 2018, In : Science. 361, 6409, p. 1380-1385 6 p.

Research output: Contribution to journalArticle

Chromatin
Joints
Gene Expression
Messenger RNA
Methylation
6 Citations (Scopus)

Post-translational modification localizes MYC to the nuclear pore basket to regulate a subset of target genes involved in cellular responses to environmental signals

Su, Y., Pelz, C., Huang, T., Torkenczy, K., Wang, X., Cherry, A., Daniel, C. J., Liang, J., Nan, X., Dai, M., Adey, A., Impey, S. & Sears, R., Nov 1 2018, In : Genes & development. 32, 21-22, p. 1398-1419 22 p.

Research output: Contribution to journalArticle

Nuclear Pore
Post Translational Protein Processing
Chromatin
Histone Code
Gene Expression

Tagmentation-based library preparation for low DNA input whole genome bisulfite sequencing

Weichenhan, D., Wang, Q., Adey, A., Wolf, S., Shendure, J., Eils, R. & Plass, C., Jan 1 2018, Methods in Molecular Biology. Humana Press Inc., Vol. 1708. p. 105-122 18 p. (Methods in Molecular Biology; vol. 1708).

Research output: Chapter in Book/Report/Conference proceedingChapter

Libraries
Genome
DNA
Transposases
Untranslated RNA
2017
147 Citations (Scopus)

Comprehensive single-cell transcriptional profiling of a multicellular organism

Cao, J., Packer, J. S., Ramani, V., Cusanovich, D. A., Huynh, C., Daza, R., Qiu, X., Lee, C., Furlan, S. N., Steemers, F. J., Adey, A., Waterston, R. H., Trapnell, C. & Shendure, J., Aug 18 2017, In : Science. 357, 6352, p. 661-667 7 p.

Research output: Contribution to journalArticle

RNA Sequence Analysis
Atlases
Chromatin Immunoprecipitation
Caenorhabditis elegans
Firearms
1 Citation (Scopus)

Haplotype resolution at the single-cell level

Adey, A., Nov 21 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 47, p. 12362-12364 3 p.

Research output: Contribution to journalComment/debate

Haplotypes
51 Citations (Scopus)

Sequencing thousands of single-cell genomes with combinatorial indexing

Vitak, S. A., Torkenczy, K. A., Rosenkrantz, J. L., Fields, A. J., Christiansen, L., Wong, M., Carbone, L., Steemers, F. J. & Adey, A., Feb 28 2017, In : Nature Methods. 14, 3, p. 302-308 7 p.

Research output: Contribution to journalArticle

Genes
Genome
Tumors
Tissue
Libraries
2016
14 Citations (Scopus)

Recurrent somatic loss of TNFRSF14 in classical Hodgkin lymphoma

Salipante, S. J., Adey, A., Thomas, A., Lee, C., Liu, Y. J., Kumar, A., Lewis, A. P., Wu, D., Fromm, J. R. & Shendure, J., Mar 1 2016, In : Genes Chromosomes and Cancer. 55, 3, p. 278-287 10 p.

Research output: Contribution to journalArticle

Hodgkin Disease
Reed-Sternberg Cells
Cell Line
Flow Cytometry
Carcinogenesis
2015
68 Citations (Scopus)

Haplotype-resolved genome sequencing: Experimental methods and applications

Snyder, M. W., Adey, A., Kitzman, J. O. & Shendure, J., May 18 2015, In : Nature Reviews Genetics. 16, 6, p. 344-358 15 p.

Research output: Contribution to journalArticle

Haplotypes
Genome
Clinical Medicine
Human Genome
Diploidy
252 Citations (Scopus)

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

Cusanovich, D. A., Daza, R., Adey, A., Pliner, H. A., Christiansen, L., Gunderson, K. L., Steemers, F. J., Trapnell, C. & Shendure, J., May 22 2015, In : Science. 348, 6237, p. 910-914 5 p.

Research output: Contribution to journalArticle

Chromatin
Atlases
Transcriptome
Genome
2014
203 Citations (Scopus)

Decoding long nanopore sequencing reads of natural DNA

Laszlo, A. H., Derrington, I. M., Ross, B. C., Brinkerhoff, H., Adey, A., Nova, I. C., Craig, J. M., Langford, K. W., Samson, J. M., Daza, R., Doering, K., Shendure, J. & Gundlach, J. H., 2014, In : Nature Biotechnology. 32, 8, p. 829-833 5 p.

Research output: Contribution to journalArticle

Nanopores
Decoding
DNA
Ions
Genes
27 Citations (Scopus)

Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes

Kumar, A., Boyle, E. A., Tokita, M., Mikheev, A. M., Sanger, M. C., Girard, E., Silber, J. R., Gonzalez-Cuyar, L. F., Hiatt, J. B., Adey, A., Lee, C., Kitzman, J. O., Born, D. E., Silbergeld, D. L., Olson, J. M., Rostomily, R. C. & Shendure, J., Dec 3 2014, In : Genome Biology. 15, 12, 530.

Research output: Contribution to journalArticle

High-Throughput Nucleotide Sequencing
neuroglia
tumor
Neuroglia
mutation
71 Citations (Scopus)

Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing

Amini, S., Pushkarev, D., Christiansen, L., Kostem, E., Royce, T., Turk, C., Pignatelli, N., Adey, A., Kitzman, J. O., Vijayan, K., Ronaghi, M., Shendure, J., Gunderson, K. L. & Steemers, F. J., Dec 11 2014, In : Nature Genetics. 46, 12, p. 1343-1349 7 p.

Research output: Contribution to journalArticle

Haplotypes
Genome
Human Genome
Libraries
DNA
42 Citations (Scopus)

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

Adey, A., Kitzman, J. O., Burton, J. N., Daza, R., Kumar, A., Christiansen, L., Ronaghi, M., Amini, S., Gunderson, K. L., Steemers, F. J. & Shendure, J., Dec 1 2014, In : Genome Research. 24, 12, p. 2041-2049 9 p.

Research output: Contribution to journalArticle

Transposases
Genome
In Vitro Techniques
Diptera
Libraries
106 Citations (Scopus)

MegaTALs: A rare-cleaving nuclease architecture for therapeutic genome engineering

Boissel, S., Jarjour, J., Astrakhan, A., Adey, A., Gouble, A., Duchateau, P., Shendure, J., Stoddard, B. L., Certo, M. T., Baker, D. & Scharenberg, A. M., Feb 2014, In : Nucleic Acids Research. 42, 4, p. 2591-2601 11 p.

Research output: Contribution to journalArticle

Genome
Endonucleases
DNA
Therapeutics
Research
149 Citations (Scopus)

Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens

Pritchard, C. C., Salipante, S. J., Koehler, K., Smith, C., Scroggins, S., Wood, B., Wu, D., Lee, M. K., Dintzis, S., Adey, A., Liu, Y., Eaton, K. D., Martins, R., Stricker, K., Margolin, K. A., Hoffman, N., Churpek, J. E., Tait, J. F., King, M. C. & Walsh, T., Jan 2014, In : Journal of Molecular Diagnostics. 16, 1, p. 56-67 12 p.

Research output: Contribution to journalArticle

Gene Rearrangement
Mutation
Neoplasms
Genes
High-Throughput Nucleotide Sequencing
2013
188 Citations (Scopus)

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

Burton, J. N., Adey, A., Patwardhan, R. P., Qiu, R., Kitzman, J. O. & Shendure, J., Dec 2013, In : Nature Biotechnology. 31, 12, p. 1119-1125 7 p.

Research output: Contribution to journalArticle

Chromosomes
Chromatin
Genes
Genome
Scaffolds
53 Citations (Scopus)

Tagmentation-based whole-genome bisulfite sequencing

Wang, Q., Gu, L., Adey, A., Radlwimmer, B., Wang, W., Hovestadt, V., Bähr, M., Wolf, S., Shendure, J., Eils, R., Plass, C. & Weichenhan, D., Oct 2013, In : Nature Protocols. 8, 10, p. 2022-2032 11 p.

Research output: Contribution to journalArticle

Genes
Genome
Methylation
DNA
Cytosine
155 Citations (Scopus)

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

Adey, A., Burton, J. N., Kitzman, J. O., Hiatt, J. B., Lewis, A. P., Martin, B. K., Qiu, R., Lee, C. & Shendure, J., 2013, In : Nature. 500, 7461, p. 207-211 5 p.

Research output: Contribution to journalArticle

Aneuploidy
HeLa Cells
Haplotypes
Papillomaviridae
Genome
2012
5 Citations (Scopus)

Capturing native long-range contiguity by in situ library construction and optical sequencing

Schwartz, J. J., Lee, C., Hiatt, J. B., Adey, A. & Shendure, J., Nov 13 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 46, p. 18749-18754 6 p.

Research output: Contribution to journalArticle

Libraries
High-Throughput Nucleotide Sequencing
Genomic Structural Variation
Technology
DNA Sequence Analysis
63 Citations (Scopus)

Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing

Adey, A. & Shendure, J., Jun 2012, In : Genome Research. 22, 6, p. 1139-1143 5 p.

Research output: Contribution to journalArticle

Genome
Transposases
DNA
Firearms
Libraries
2011
1 Citation (Scopus)

Erratum: Haplotype-resolved genome sequencing of a Gujarati Indian individual (Nature Biotechnology (2011) 29 (59-63))

Kitzman, J. O., MacKenzie, A. P., Adey, A., Hiatt, J. B., Patwardhan, R. P., Sudmant, P. H., Ng, S. B., Alkan, C., Qiu, R., Eichler, E. E. & Shendure, J., May 2011, In : Nature Biotechnology. 29, 5, p. 459 1 p.

Research output: Contribution to journalArticle

Biotechnology
Haplotypes
Genes
Genome
166 Citations (Scopus)

Haplotype-resolved genome sequencing of a Gujarati Indian individual

Kitzman, J. O., MacKenzie, A. P., Adey, A., Hiatt, J. B., Patwardhan, R. P., Sudmant, P. H., Ng, S. B., Alkan, C., Qiu, R., Eichler, E. E. & Shendure, J., Jan 2011, In : Nature Biotechnology. 29, 1, p. 59-64 6 p.

Research output: Contribution to journalArticle

Haplotypes
Genes
Genome
High-Throughput Nucleotide Sequencing
Firearms
2010
225 Citations (Scopus)

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

Adey, A., Morrison, H. G., Asan, Xun, X., Kitzman, J. O., Turner, E. H., Stackhouse, B., MacKenzie, A. P., Caruccio, N. C., Zhang, X. & Shendure, J., Dec 8 2010, In : Genome Biology. 11, 12, R119.

Research output: Contribution to journalArticle

transposition (genetics)
Firearms
Libraries
Exome
Transposases