Research publications

Rylaarsdam LE, Nichols RV, O’Connell BL, Kragness S, Yung JF, Saunders A, Mandel G, Adey AC. Early postnatal DNA methylation dynamics define neuronal subtypes and are disrupted by MECP2 loss. bioRxiv 2026.

Rylaarsdam LE, Skubi BW, Nichols RV, O'Connell BL, Kotnik JH, Coleman SD, Yardımcı GG, Adey AC. Single-cell DNA methylation analysis tool Amethyst resolves distinct non-CG methylation patterns in human astrocytes and oligodendrocytes. Commun Biol 2025;8(1):1468.

Nichols RV, Rylaarsdam LE, O'Connell BL, Shipony Z, Iremadze N, Acharya SN, Adey AC. Atlas-scale single-cell DNA methylation profiling with sciMETv3. Cell Genom 2025;5(1):100726.

Zhang H, Mulqueen RM, Iannuzo N, Farrera DO, Polverino F, Galligan JJ, Ledford JG, Adey AC, Cusanovich DA. txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility. Genome Biol 2024;25(1):78.

Acharya SN, Nichols RV, Rylaarsdam LE, O'Connell BL, Braun TP, Adey AC. sciMET-cap: high-throughput single-cell methylation analysis with a reduced sequencing burden. Genome Biol 2024;25(1):186.

Queitsch K, Moore TW, O'Connell BL, Nichols RV, Muschler JL, Keith D, Lopez C, Sears RC, Mills GB, Yardımcı GG, Adey AC. Accessible high-throughput single-cell whole-genome sequencing with paired chromatin accessibility. Cell Rep Methods 2023;3(11):100625.

O'Connell BL, Nichols RV, Pokholok D, Thomas J, Acharya SN, Nishida A, Thornton CA, Co M, Fields AJ, Steemers FJ, Adey AC. Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing. Genome Res 2023;33(2):208–217.

Nichols RV, O'Connell BL, Mulqueen RM, Thomas J, Woodfin AR, Acharya S, Mandel G, Pokholok D, Steemers FJ, Adey AC. High-throughput robust single-cell DNA methylation profiling with sciMETv2. Nat Commun 2022;13(1):7627.

Eksi SE, Chitsazan A, Sayar Z, Thomas GV, Fields AJ, Kopp RP, Spellman PT, Adey AC. Epigenetic loss of heterogeneity from low to high grade localized prostate tumours. Nat Commun 2021;12(1):7292.

Mulqueen RM, Pokholok D, O'Connell BL, Thornton CA, Zhang F, O'Roak BJ, Link J, Yardımcı GG, Sears RC, Steemers FJ, Adey AC. High-content single-cell combinatorial indexing. Nat Biotechnol 2021;39(12):1574–1580.

Thornton CA, Mulqueen RM, Torkenczy KA, Nishida A, Lowenstein EG, Fields AJ, Steemers FJ, Zhang W, McConnell HL, Woltjer RL, Mishra A, Wright KM, Adey AC. Spatially mapped single-cell chromatin accessibility. Nat Commun 2021;12(1):1274.

Sinnamon JR, Torkenczy KA, Linhoff MW, Vitak SA, Mulqueen RM, Pliner HA, Trapnell C, Steemers FJ, Mandel G, Adey AC. The accessible chromatin landscape of the murine hippocampus at single-cell resolution. Genome Res 2019;29(5):857–869.

Mulqueen RM, Pokholok D, Norberg SJ, Torkenczy KA, Fields AJ, Sun D, Sinnamon JR, Shendure J, Trapnell C, O'Roak BJ, Xia Z, Steemers FJ, Adey AC. Highly scalable generation of DNA methylation profiles in single cells. Nat Biotechnol 2018;36(5):428–431.

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. Nat Methods 2017;14(3):302–308.

Moore TW, Mohammed H, Adey AC, Yardımcı GG. Robust and generalizable CNV detection for single-cell sequencing assays. Nucleic Acids Res 2026;54(14):gkag636.

Hall ML, Quintal A, Acharya SN, Worme S, Nguyen TT, Schonrock Z, Tsuchiya M, Carlson HL, Pacentine IV, Shrestha SB, Macaraeg J, Armstrong R, Szczepanski N, Adler J, McGann J, Evans-Dutson S, Lusardi TA, O'Connell BL, Adey AC, Yardımcı GG, Maxson JE, Braun TP. Mutant ASXL1 Cooperates with MECOM and BRD4 to Drive Transcriptional Dysregulation in Human Hematopoiesis. Blood 2026:blood.2026034001.

Smith NR, Giske NR, Sengupta SK, Conley P, Swain JR, Nair A, Fowler KL, Klocke C, Yoo YJ, Anderson AN, Sanati N, Torkenczy K, Adey AC, Fischer JM, Wu G, Wong MH. Dual states of murine Bmi1-expressing intestinal stem cells drive epithelial development utilizing non-canonical Wnt signaling. Dev Cell 2025;60(16):2177–2191.e5.

Link JM, Eng JR, Pelz C, MacPherson-Hawthorne K, Worth PJ, Sivagnanam S, Keith DJ, Owen S, Langer EM, Grossblatt-Wait A, Salgado-Garza G, Creason AL, Protzek S, Egger J, Holly H, Heskett MB, Chin K, Kirchberger N, Betre K, Bucher E, Kilburn D, Hu Z, Munks MW, English IA, Tsuda M, Goecks J, Demir E, Adey AC, Kardosh A, Lopez CD, Sheppard BC, Guimaraes A, Brinkerhoff B, Morgan TK, Mills GB, Coussens LM, Brody JR, Sears RC. Ongoing replication stress tolerance and clonal T cell responses distinguish liver and lung recurrence and outcomes in pancreatic cancer. Nat Cancer 2025;6(1):123–144.

Bowman CL, Daniel CJ, Carlson EJ, Shah VM, Farrell AS, Kresse KM, Wang X, Lindley KA, Kuhn MR, MacPherson-Hawthorne K, Allen-Petersen BL, Eng J, Tsuda M, English IA, Pelz C, Amer A, Doe AR, Turnidge MA, Jenny ZP, Waugh T, Doha ZO, Kendsersky ND, Torkenczy K, Pelz KR, Fields AJ, Cohn GM, Dewson GS, Thoma MC, Amery TS, Sherman MH, Chin K, Agarwal A, Link JM, Sheppard BC, Adey AC, Sears RC, Langer EM. The Prolyl Isomerase PIN1 Affects Fibroblast Differentiation States and Cross-talk in Pancreatic Cancer. Cancer Res 2025;85(24):4899–4917.

De Rop FV, Hulselmans G, Flerin C, Soler-Vila P, Rafels A, Christiaens V, González-Blas CB, Marchese D, Caratù G, Poovathingal S, Rozenblatt-Rosen O, Slyper M, Luo W, Muus C, Duarte F, Shrestha R, Bagdatli ST, Corces MR, Mamanova L, Knights A, Meyer KB, Mulqueen R, Taherinasab A, Maschmeyer P, Pezoldt J, Lambert CLG, Iglesias M, Najle SR, Dossani ZY, Martelotto LG, Burkett Z, Lebofsky R, Martin-Subero JI, Pillai S, Sebé-Pedrós A, Deplancke B, Teichmann SA, Ludwig LS, Braun TP, Adey AC, Greenleaf WJ, Buenrostro JD, Regev A, Aerts S, Heyn H. Systematic benchmarking of single-cell ATAC-sequencing protocols. Nat Biotechnol 2024;42(6):916–926.

Ak Ç, Sayar Z, Thibault G, Burlingame EA, Kuykendall MJ, Eng J, Chitsazan A, Chin K, Adey AC, Boniface C, Spellman PT, Thomas GV, Kopp RP, Demir E, Chang YH, Stavrinides V, Eksi SE. Multiplex imaging of localized prostate tumors reveals altered spatial organization of AR-positive cells in the microenvironment. iScience 2024;27(9):110668.

Adey AC. Meet the author: Andrew Adey. Cell Rep Methods 2023;3(11):100648.

Ren T, Chen C, Danilov AV, Liu S, Guan X, Du S, Wu X, Sherman MH, Spellman PT, Coussens LM, Adey AC, Mills GB, Wu LY, Xia Z. Supervised learning of high-confidence phenotypic subpopulations from single-cell data. Nat Mach Intell 2023;5(5):528–541.

Romine KA, MacPherson K, Cho HJ, Kosaka Y, Flynn PA, Byrd KH, Coy JL, Newman MT, Pandita R, Loo CP, Scott J, Adey AC, Lind EF. BET inhibitors rescue anti-PD1 resistance by enhancing TCF7 accessibility in leukemia-derived terminally exhausted CD8+ T cells. Leukemia 2023;37(3):580–592.

Co M, Barnard RA, Jahncke JN, Grindstaff S, Fedorov LM, Adey AC, Wright KM, O'Roak BJ. Shared and Distinct Functional Effects of Patient-Specific Tbr1 Mutations on Cortical Development. J Neurosci 2022;42(37):7166–7181.

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. CRISPR J 2022;5(4):548–557.

Sun D, Guan X, Moran AE, Wu LY, Qian DZ, Schedin P, Dai MS, Danilov AV, Alumkal JJ, Adey AC, Spellman PT, Xia Z. Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data. Nat Biotechnol 2022;40(4):527–538.

Bates TA, Leier HC, Lyski ZL, McBride SK, Coulter FJ, Weinstein JB, Goodman JR, Lu Z, Siegel SAR, Sullivan P, Strnad M, Brunton AE, Lee DX, Adey AC, Bimber BN, O'Roak BJ, Curlin ME, Messer WB, Tafesse FG. Neutralization of SARS-CoV-2 variants by convalescent and BNT162b2 vaccinated serum. Nat Commun 2021;12(1):5135.

Emechebe U, Nelson JW, Alkayed NJ, Kaul S, Adey AC, Barnes AP. Age-dependent transcriptional alterations in cardiac endothelial cells. Physiol Genomics 2021;53(7):295–308.

Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jané-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe'er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH, Human Tumor Atlas Network. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Cell 2020;181(2):236–249.

Soza VL, Lindsley D, Waalkes A, Ramage E, Patwardhan RP, Burton JN, Adey A, Kumar A, Qiu R, Shendure J, Hall B. The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae). Genome Biol Evol 2019;11(12):3353–3371.

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. Mol Cell 2019;76(4):676–690.e10.

Su Y, Pelz C, Huang T, Torkenczy K, Wang X, Cherry A, Daniel CJ, Liang J, Nan X, Dai MS, Adey A, 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;32(21-22):1398–1419.

Cao J, Cusanovich DA, Ramani V, Aghamirzaie D, Pliner HA, Hill AJ, Daza RM, 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;361(6409):1380–1385.

Pliner HA, Packer JS, McFaline-Figueroa JL, Cusanovich DA, Daza RM, Aghamirzaie D, Srivatsan S, Qiu X, Jackson D, Minkina A, Adey AC, Steemers FJ, Shendure J, Trapnell C. Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data. Mol Cell 2018;71(5):858–871.e8.

Risom T, Langer EM, Chapman MP, Rantala J, Fields AJ, Boniface C, Alvarez MJ, Kendsersky ND, Pelz CR, 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. Nat Commun 2018;9(1):3815.

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. Comprehensive single-cell transcriptional profiling of a multicellular organism. Science 2017;357(6352):661–667.

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 2016;55(3):278–287.

Snyder MW, Adey A, Kitzman JO, Shendure J. Haplotype-resolved genome sequencing: experimental methods and applications. Nat Rev Genet 2015;16(6):344–358.

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;348(6237):910–914.

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;15(12):530.

Adey A, Kitzman JO, Burton JN, Daza R, Kumar A, Christiansen L, Ronaghi M, Amini S, Gunderson KL, Steemers FJ, Shendure J. In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Res 2014;24(12):2041–2049.

Amini S, Pushkarev D, Christiansen L, Kostem E, Royce T, Turk C, Pignatelli N, Adey A, Kitzman JO, Vijayan K, Ronaghi M, Shendure J, Gunderson KL, Steemers FJ. Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nat Genet 2014;46(12):1343–1349.

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 Biotechnol 2014;32(8):829–833.

Boissel S, Jarjour J, Astrakhan A, Adey A, Gouble A, Duchateau P, Shendure J, Stoddard BL, Certo MT, Baker D, Scharenberg AM. megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering. Nucleic Acids Res 2014;42(4):2591–2601.

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 Biotechnol 2013;31(12):1119–1125.

Pritchard CC, Salipante SJ, Koehler K, Smith C, Scroggins S, Wood B, Wu D, Lee MK, Dintzis S, Adey A, Liu Y, Eaton KD, Martins R, Stricker K, Margolin KA, Hoffman N, Churpek JE, Tait JF, 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 Diagn 2014;16(1):56–67.

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;8(10):2022–2032.

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;500(7461):207–211.

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 U S A 2012;109(46):18749–18754.

Adey A, Shendure J. Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing. Genome Res 2012;22(6):1139–1143.

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 Biotechnol 2011;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.

Mulqueen RM, Pokholok D, O’Connell BL, Thornton CA, Zhang F, O’Roak BJ, Link J, Yardmici GG, Sears RC, Steemers FJ, Adey AC. High-content single-cell combinatorial indexing. bioRxiv 2021.

Thornton CA, Mulqueen RM, Nishida A, Torkenczy KA, Lowenstein EG, Fields AJ, Steemers FJ, Zhang W, McConnell HL, Woltjer RL, Mishra A, Wright KM, Adey AC. Spatially mapped single-cell chromatin accessibility. bioRxiv 2019.

Torkenczy K, Langer E, Fields A, Turnidge M, Nishida A, Boniface C, Spellman P, Demir E, Gray J, Sears R, Adey A. Integrated Single-Cell Analysis Reveals Treatment-Induced Epigenetic Homogenization. SSRN 2020.

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.

Sun D, Guan X, Moran AE, Qian DZ, Schedin P, Adey A, Spellman PT, Xia Z. Phenotype-guided subpopulation identification from single-cell sequencing data. bioRxiv 2020.

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. bioRxiv 2019.

Sinnamon JR, Torkenczy KA, Linhoff MW, Vitak S, Pliner HA, Trapnell C, Steemers FJ, Mandel G, Adey AC. The accessible chromatin landscape of the hippocampus at single-cell resolution. bioRxiv 2018.

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. bioRxiv 2018.

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. bioRxiv 2017.

Pliner HA, Packer J, McFaline-Figueroa JL, 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.

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. Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing. bioRxiv 2017.

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 2016.