Andrew Adey

Assistant Professor

  • 2509 Citations
  • 20 h-Index
20102019

Research output per year

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Research Output

2019

High-Throughput Single-Cell Sequencing with Linear Amplification

Yin, Y., Jiang, Y., Lam, K. W. G., Berletch, J. B., Disteche, C. M., Noble, W. S., Steemers, F. J., Camerini-Otero, R. D., Adey, A. C. & Shendure, J., Nov 21 2019, In : Molecular Cell. 76, 4, p. 676-690.e10

Research output: Contribution to journalArticle

3 Scopus citations

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

4 Scopus citations

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
5 Scopus citations

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
2 Scopus citations
2018

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

34 Scopus citations

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., Aswani, A. J., Wang, N. J., Califano, A., Lewis, M. T., Tomlin, C. J., Spellman, P. T., Adey, A., Gray, J. W. & 1 others, Sears, R. C., Dec 1 2018, In : Nature communications. 9, 1, 3815.

Research output: Contribution to journalArticle

22 Scopus citations

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

42 Scopus citations

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

2 Scopus citations

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

75 Scopus citations

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

13 Scopus citations

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

2017

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

213 Scopus citations

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

1 Scopus citations

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

69 Scopus citations
2016

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

16 Scopus citations
2015

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 journalReview article

77 Scopus citations

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

306 Scopus citations
2014

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., Aug 2014, In : Nature biotechnology. 32, 8, p. 829-833 5 p.

Research output: Contribution to journalArticle

220 Scopus citations

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

29 Scopus citations

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

76 Scopus citations

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

53 Scopus citations

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 1 2014, In : Nucleic acids research. 42, 4, p. 2591-2601 11 p.

Research output: Contribution to journalArticle

110 Scopus citations

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 1 2014, In : Journal of Molecular Diagnostics. 16, 1, p. 56-67 12 p.

Research output: Contribution to journalArticle

162 Scopus citations
2013

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 1 2013, In : Nature biotechnology. 31, 12, p. 1119-1125 7 p.

Research output: Contribution to journalArticle

265 Scopus citations

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 1 2013, In : Nature protocols. 8, 10, p. 2022-2032 11 p.

Research output: Contribution to journalArticle

58 Scopus citations

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., Aug 19 2013, In : Nature. 500, 7461, p. 207-211 5 p.

Research output: Contribution to journalArticle

167 Scopus citations
2012

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

5 Scopus citations

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

Adey, A. & Shendure, J., Jun 1 2012, In : Genome Research. 22, 6, p. 1139-1143 5 p.

Research output: Contribution to journalArticle

67 Scopus citations
2011

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 1 2011, In : Nature biotechnology. 29, 5, 1 p.

Research output: Contribution to journalComment/debate

1 Scopus citations

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 1 2011, In : Nature biotechnology. 29, 1, p. 59-64 6 p.

Research output: Contribution to journalArticle

169 Scopus citations
2010

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

243 Scopus citations