Publications

Featured Publications:

Thornton CA, Mulqueen RM, Torkenczy KA, Nishida A, Lowenstein EG, Fields AJ, Steemers FJ, Zhang W, McConnell H, Woltjer RL, Mishra A, Wright KM, Adey AC. Spatially-mapped single-cell chromatin accessibility. Nature Communications 2021. 12:1274. doi: 10.1038/s41467-021-21515-7

Sinnamon JR, Torkenczy KA, Linhoff MW, Vitak SA, Pliner HA, Trapnell C, Steemers FJ, Mandel G, Adey AC. The accessible chromatin landscape of the murine hippocampus at single-cell resolution. Genome Research. 2019 April 1. doi: 10.1101/gr.243725.

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:

Yin Y, Jiang Y, Lam KG, Berletch JB, Disteche CM, Noble WS, Steemers FJ, Camerini-Otero RD, Adey AC, Shendure J. High-Throughput single-cell sequencing with linear amplification. Molecular Cell. 2019 Aug 28. doi: 10.1016/j.molcel.2019.08.002.

Su Y, Pelz C, Huang T, Torkenczy KA, Wang X, Cherry A, Daniel CJ, Liang J, Nan X, Dai M, Adey AC, Impey S, Sears RC. Post-translational modification localizes MYC to the nuclear pore basket to regulate a subset of target genes involved in cellular responses to environmental signals. Genes & Dev. 2018. doi: 10.1101/gad.314377.118

Cao J, Cusanovich DA, Ramani V, Aghamirzaie D, Pliner HA, Hill AJ, Daza R, McFaline-Figueroa JL, Packer JS, Christiansen L, Steemers FJ, Adey AC, Trapnell C, Shendure J. Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science. 2018 Aug 30. doi: 10.1126/science.aau0730

Pliner HA, Packer J, McFaline-Figueroa J, Cusanovich DA, Daza R, Srivatsan S, Qiu X, Jackson D, Minkina A, Adey AC, Steemers FJ, Shendure J, Trapnell C. Chromatin accessibility dynamics of myogenesis at single cell resolution. Molecular Cell. 2018 Aug. 2; doi: 10.1016/j.molcel.2018.06.044

Risom T, Langer EM, Chapman MP, Rantala J, Fields AJ, Boniface C, Alvarez MJ, Kendersky ND, Pelz CP, Johnson-Camacho K, Dobrolecki LE, Chin K, Aswani AJ, Wang NJ, Califano A, Lewis MT, Tomlin CJ, Spellman PT, Adey A, Gray JW, Sears RC. Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer. Comms. 2018 In Press

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, O’Connell BL, Thornton CA, Zhang F, O’Roak BJ, Link J, Yardimci GG, Sears RC, Steemers FJ, Adey AC. High-content single-cell combinatorial indexing. bioRxiv, 2021 doi: https://doi.org/10.1101/2021.01.11.425995

Thornton CA, Mulqueen RM, Torkenczy KA, Lowenstein EG, Fields AJ, Steemers FJ, Wright KM, Adey AC. Spatially-mapped single-cell chromatin accessibility. 2019 Oct. 23. doi: https://doi.org/10.1101/815720

Torkenczy KA, Langer E, Fields AJ, Turnidge M, Nishida AR, Boniface C, Spellman P, Demir E, Gray J, Sears RC, Adey AC. Integrated Single-Cell Analysis Reveals Treatment-Induced Epigenetic Homogenization. Cell Sneak Peek Preprint 2020 doi: http://dx.doi.org/10.2139/ssrn.3687026

Mighell TL, Nishida A, O’Connell BL, Miller CV, Grindstaff S, Thornton CA, Adey AC, Doherty D, O’Roak BJ. Cas12a-Capture: a novel, low-cost, and scalable method for targeted sequencing. bioRxiv 2020. doi: https://doi.org/10.1101/2020.11.18.38887

Sun D, Guan X, Moran AE, Qian DZ, Schedin P, Adey AC, Spellman PT, Xia, Z. Phenotype-guided subpopulation identification from single-cell sequencing data. bioRxiv 2020. doi: https://doi.org/10.1101/2020.06.05.137240

Mulqueen RM, DeRosa BA, Thornton CA, Sayar Z, Torkenczy KA, Fields AJ, Wright KM, Nan X, Ramji R, Steemers FJ, O’Roak BJ, Adey AC. Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis. 2019 May 15, doi: https://doi.org/10.1101/637256

Sinnamon JR, Torkenczy KA, Linhoff MW, Vitak SA, Pliner HA, Trapnell C, Steemers FJ, Mandel G, Adey AC. The accessible chromatin landscape of the hippocampus at single-cell resolution. bioRxiv 2018 Sept. 4, doi: https://doi.org/10.1101/407668

Yin Y, Jiang Y, Berletch JB, Disteche CM, Noble WS, Steemers FJ, Adey AC, Shendure JA. High-throughput mapping of meiotic crossover and chromosome mis-segregation events in interspecific hybrid mice. 2018 June 12, doi: https://doi.org/10.1101/338053

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 SN, Steemers 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. Construct
ion of thousands of single cell genome sequencing libraries using combinatorial indexing. bioRxiv. July 23, 2016, doi: http://dx.doi.org/10.1101/065482