Publications

Featured Publications:

Mulqueen RM, Pokholok D, Norberg S, Fields AJ, Sun D, Sinnamon JR, Torkenczy KA, Shendure J, Trapnell C, O’Roak BJ, Xia Z, Steemers FJ, Adey AC. Scalable and efficient single-cell DNA methylation sequencing by combinatorial indexing. Nature Biotechnology doi:10.1038/nbt.4112

Vitak SA, Torkenczy KA, Rosenkrantz JL, Fields AJ, Christiansen L, Wong MH, Carbone L, Steemers FJ, Adey A. Sequencing thousands of single-cell genomes with combinatorial indexing. Nature Methods. 2017 Jan 30. doi: 10.1038/nmeth.4154.

Other Publications:

Cao J, Packer JS, Ramani V, Cusanovich DA, Huynh C, Daza R, Qiu X, Lee C, Furlan SN, Steemers FJ, Adey A, Waterson RH, Trapnell C, Shendure J. Comprehensive single cell transcriptional profiling of a multicellular organism. Science. 2017 Aug 18; doi: 10.1126/science.aam8940

Salipante SJ, Adey A, Thomas A, Lee C, Liu YJ, Kumar A, Lewis AP, Wu D, Fromm JR, Shendure J. Recurrent somatic loss of TNFRSF14 in classical Hodgkin lymphoma. Genes Chromosomes Cancer. 2015 Dec 9. doi: 10.1002/gcc.22331.

Snyder MW, Adey A, Kitzman JO, Shendure J. Haplotype-resolved genome sequencing: experimental methods and applications. Nat Rev Genet. 2015 Jun;16(6):344-58.

Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, Steemers FJ, Trapnell C, Shendure J. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science. 2015 May 22;348(6237):910-4.

Kumar A, Boyle EA, Tokita M, Mikheev AM, Sanger MC, Girard E, Silber JR, Gonzalez-Cuyar LF, Hiatt JB, Adey A, Lee C, Kitzman JO, Born DE, Silbergeld DL, Olson JM, Rostomily RC, Shendure J. Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes. Genome Biol. 2014 Dec 3;15(12):530.

Adey A, Burton JN, Kitzman JO, Daza R, Patwardhan RP, Kumar A, Amini S, Steemers FJ, Shendure J. In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Res. 2014 19.

Amini S, Pushkarev D, Christiansen L, Royce T, Turk C, Pignatelli N, Adey A, Kitzman JO, Ronaghi M, Shendure J, Gunderson KL, Steemers FJ. Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nat Genet. 2014 Oct. 19:10.1038/ng.3119.

Laszlo AH, Derrington IM, Ross BC, Brinkerhoff H, Adey A, Nova IC, Craig JM, Langford KW, Samson JM, Daza R, Doering K, Shendure J, Gundlach JH. Decoding long nanopore sequencing reads of natural DNA. Nat Biotech. 2014 Jun 26;1038/nbt.2950.

Boissel SJ, Astrakhan A, Jarjour J, Adey A, Shendure J, Stoddard B, Certo M, Baker D, Scharenberg AM. megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering. Nucl Acid Res. 2013 Nov 26.

Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotech. 2013 Nov 3;10.1038/nbt.2727.

Pritchard CC, Salipante SJ, Koehler K, Smith C, Scroggins S, Wood B, Wu D, Lee MK, Dintzis D, Adey A, Liu Y, Eaton KD, Martins R, Stricker K, Margolin KA, Hoffman N, Churpek JE, Tait JE, King MC, Walsh T. Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens. J Mol Diag. 2013 Nov 1;S1525-1578(13)00217-1.

Wang Q, Gu L, Adey A, Radlwimmer B, Wang W, Hovestadt V, Bähr M, Wolf S, Shendure J, Eils R, Plass C, Weichenhan D. Tagmentation-based whole-genome bisulfite sequencing. Nat Protoc. 2013 Oct;8(10):2022-32.

Adey A, Burton JN, Kitzman JO, Hiatt JB, Lewis AP, Martin BK, Qiu R, Lee C, Shendure J. The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line. Nature. 2013 Aug 8;500(7461):207-11.

Schwartz JJ, Lee C, Hiatt JB, Adey A, Shendure J. Capturing native long-range contiguity by in situ library construction and optical sequencing. Proc Natl Acad Sci 2012 Nov 13;109(46):18749-54.

Adey A, Shendure J. Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing. Genome Res. 2012 Jun;22(6):1139-43.

Kitzman JO, Mackenzie AP, Adey A, Hiatt JB, Patwardhan RP, Sudmant PH, Ng SB, Alkan C, Qiu R, Eichler EE, Shendure J. Haplotype resolved genome sequencing of a Gujarati Indian individual. Nat Biotech. 2011 Jan;29(1):59-63.

Adey A, Morrison HG, Asan, Xun X, Kitzman JO, Turner EH, Stackhouse B, MacKenzie AP, Caruccio NC, Zhang X, Shendure J. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol. 2010;11(12):R119. Highly Accessed.

Preprints:

Mulqueen RM, Pokholok D, Norberg S, Fields AJ, Sun D, Torkenczy KA, Shendure J, Trapnell C, O’Roak BJ, Xia Z, Steemers FJ, Adey AC. Scalable and efficient single-cell DNA methylation sequencing by combinatorial indexing. 2017 June 28, doi: https://doi.org/10.1101/157230.

Pliner HA, Packer J, McFaline-Figueroa J, Cusanovich DA, Daza R, Srivatsan S, Qiu X, Jackson D, Minkina A, Adey A, Steemers FJ, Shendure J, Trapnell C. Chromatin accessibility dynamics of myogenesis at single cell resolution. bioRxiv. 2017 June 26, doi: https://doi.org/10.1101/155473.

Cao J, Packer JS, Ramani V, Cusanovich DA, Huynh C, Daza R, Qiu X, Lee C, Furlan SNSteemers FJ, Adey A, Waterston RH, Trapnell C, Shendure J. bioRxiv. February 2, 2017, doi: https://doi.org/10.1101/104844

Vitak SA, Torkenczy KA, Rosenkrantz JL, Fields AJ, Christiansen L, Wong MH, Carbone L, Steemers FJ, Adey A. Construction of thousands of single cell genome sequencing libraries using combinatorial indexing. bioRxiv. July 23, 2016, doi: http://dx.doi.org/10.1101/065482