| Year |
Citation |
Score |
| 2024 |
Zhang Z, Shafer A, Johnson-Camacho K, Adey A, Anur P, Brown KA, Conrad C, Crist R, Farris PE, Harrington CA, Marriott LK, Mitchell A, O'Roak B, Serrato V, Richards CS, et al. Novel recruitment approaches and operational results for a statewide population Cohort for cancer research: The Healthy Oregon Project. Journal of Clinical and Translational Science. 8: e32. PMID 38384895 DOI: 10.1017/cts.2024.9 |
0.59 |
|
| 2023 |
Adey AC. Meet the author: Andrew Adey. Cell Reports Methods. 3: 100648. PMID 37989084 DOI: 10.1016/j.crmeth.2023.100648 |
0.419 |
|
| 2023 |
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 Reports Methods. 100625. PMID 37918402 DOI: 10.1016/j.crmeth.2023.100625 |
0.462 |
|
| 2023 |
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, ... ... Adey AC, et al. Systematic benchmarking of single-cell ATAC-sequencing protocols. Nature Biotechnology. PMID 37537502 DOI: 10.1038/s41587-023-01881-x |
0.36 |
|
| 2023 |
O'Brien TD, Potter AB, Driscoll CC, Goh G, Letaw JH, McCabe S, Thanner J, Kulkarni A, Wong R, Medica S, Week T, Buitrago J, Larson A, Camacho KJ, Brown K, ... ... Adey A, et al. Population screening shows risk of inherited cancer and familial hypercholesterolemia in Oregon. American Journal of Human Genetics. PMID 37506692 DOI: 10.1016/j.ajhg.2023.06.014 |
0.611 |
|
| 2023 |
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. Biorxiv : the Preprint Server For Biology. PMID 37502923 DOI: 10.1101/2023.07.12.548718 |
0.389 |
|
| 2023 |
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 Research. PMID 36792372 DOI: 10.1101/gr.276655.122 |
0.306 |
|
| 2022 |
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. Nature Communications. 13: 7627. PMID 36494343 DOI: 10.1038/s41467-022-35374-3 |
0.332 |
|
| 2022 |
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 mutations on cortical development. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. PMID 35944998 DOI: 10.1523/JNEUROSCI.0409-22.2022 |
0.606 |
|
| 2022 |
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. The Crispr Journal. PMID 35833801 DOI: 10.1089/crispr.2021.0140 |
0.695 |
|
| 2021 |
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. Nature Biotechnology. PMID 34764492 DOI: 10.1038/s41587-021-01091-3 |
0.316 |
|
| 2021 |
Adey AC. Tagmentation-based single-cell genomics. Genome Research. 31: 1693-1705. PMID 34599003 DOI: 10.1101/gr.275223.121 |
0.429 |
|
| 2021 |
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, et al. Neutralization of SARS-CoV-2 variants by convalescent and BNT162b2 vaccinated serum. Nature Communications. 12: 5135. PMID 34446720 DOI: 10.1038/s41467-021-25479-6 |
0.569 |
|
| 2021 |
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. Nature Biotechnology. PMID 34226710 DOI: 10.1038/s41587-021-00962-z |
0.738 |
|
| 2021 |
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. Nature Communications. 12: 1274. PMID 33627658 DOI: 10.1038/s41467-021-21515-7 |
0.782 |
|
| 2019 |
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 Biology and Evolution. PMID 31702783 DOI: 10.1093/Gbe/Evz245 |
0.824 |
|
| 2019 |
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. PMID 31495564 DOI: 10.1016/J.Molcel.2019.08.002 |
0.714 |
|
| 2019 |
Adey AC. Integration of Single-Cell Genomics Datasets. Cell. 177: 1677-1679. PMID 31199914 DOI: 10.1016/J.Cell.2019.05.034 |
0.391 |
|
| 2019 |
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 Research. PMID 30936163 DOI: 10.1101/Gr.243725.118 |
0.79 |
|
| 2019 |
Daughtry BL, Rosenkrantz JL, Lazar NH, Fei SS, Redmayne N, Torkenczy KA, Adey A, Yan M, Gao L, Park B, Nevonen KA, Carbone L, Chavez SL. Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion. Genome Research. PMID 30683754 DOI: 10.1101/Gr.239830.118 |
0.78 |
|
| 2018 |
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 & Development. PMID 30366908 DOI: 10.1101/Gad.314377.118 |
0.758 |
|
| 2018 |
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, ... ... Adey A, et al. Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer. Nature Communications. 9: 3815. PMID 30232459 DOI: 10.1038/S41467-018-05729-W |
0.329 |
|
| 2018 |
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 (New York, N.Y.). PMID 30166440 DOI: 10.1126/Science.Aau0730 |
0.783 |
|
| 2018 |
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. Molecular Cell. PMID 30078726 DOI: 10.1016/J.Molcel.2018.06.044 |
0.769 |
|
| 2018 |
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. Nature Biotechnology. PMID 29644997 DOI: 10.1038/Nbt.4112 |
0.796 |
|
| 2018 |
Weichenhan D, Wang Q, Adey A, Wolf S, Shendure J, Eils R, Plass C. Tagmentation-Based Library Preparation for Low DNA Input Whole Genome Bisulfite Sequencing. Methods in Molecular Biology (Clifton, N.J.). 1708: 105-122. PMID 29224141 DOI: 10.1007/978-1-4939-7481-8_6 |
0.599 |
|
| 2017 |
Adey AC. Haplotype resolution at the single-cell level. Proceedings of the National Academy of Sciences of the United States of America. PMID 29114045 DOI: 10.1073/Pnas.1717798114 |
0.559 |
|
| 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. Science (New York, N.Y.). 357: 661-667. PMID 28818938 DOI: 10.1126/Science.Aam8940 |
0.783 |
|
| 2017 |
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. PMID 28135258 DOI: 10.1038/Nmeth.4154 |
0.824 |
|
| 2015 |
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. PMID 26650888 DOI: 10.1002/Gcc.22331 |
0.753 |
|
| 2015 |
Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, Steemers FJ, Trapnell C, Shendure J. Epigenetics. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science (New York, N.Y.). 348: 910-4. PMID 25953818 DOI: 10.1126/Science.Aab1601 |
0.793 |
|
| 2015 |
Snyder MW, Adey A, Kitzman JO, Shendure J. Haplotype-resolved genome sequencing: experimental methods and applications. Nature Reviews. Genetics. 16: 344-58. PMID 25948246 DOI: 10.1038/Nrg3903 |
0.808 |
|
| 2015 |
Snyder MW, Adey A, Kitzman JO, Shendure J. Haplotype-resolved genome sequencing: experimental methods and applications. Nature Reviews. Genetics. 16: 344-58. PMID 25948246 DOI: 10.1038/Nrg3903 |
0.808 |
|
| 2015 |
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. 348: 910-914. DOI: 10.1126/science.aab1601 |
0.762 |
|
| 2015 |
Laszlo AH, Derrington IM, Ross BC, Brinkerhoff H, Adey AC, Nova IC, Craig JM, Langford KW, Samson JM, Daza R, Doering K, Shendure J, Gundlach JH. Decoding Long Nanopore Reads of Bacteriophage Phi X 174 Biophysical Journal. 108: 630a. DOI: 10.1016/J.Bpj.2014.11.3425 |
0.586 |
|
| 2014 |
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, et al. Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes. Genome Biology. 15: 530. PMID 25608559 DOI: 10.1186/S13059-014-0530-Z |
0.773 |
|
| 2014 |
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, et al. Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes. Genome Biology. 15: 530. PMID 25608559 DOI: 10.1186/S13059-014-0530-Z |
0.773 |
|
| 2014 |
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 Research. 24: 2041-9. PMID 25327137 DOI: 10.1101/Gr.178319.114 |
0.834 |
|
| 2014 |
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. Nature Genetics. 46: 1343-9. PMID 25326703 DOI: 10.1038/Ng.3119 |
0.778 |
|
| 2014 |
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. Nature Genetics. 46: 1343-9. PMID 25326703 DOI: 10.1038/Ng.3119 |
0.778 |
|
| 2014 |
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. Nature Biotechnology. 32: 829-33. PMID 24964173 DOI: 10.1038/Nbt.2950 |
0.6 |
|
| 2014 |
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 Research. 42: 2591-2601. PMID 24285304 DOI: 10.1093/Nar/Gkt1224 |
0.566 |
|
| 2014 |
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, et al. Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens. The Journal of Molecular Diagnostics : Jmd. 16: 56-67. PMID 24189654 DOI: 10.1016/J.Jmoldx.2013.08.004 |
0.633 |
|
| 2014 |
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 Research. 24: 2041-2049. DOI: 10.1101/gr.178319.114 |
0.818 |
|
| 2014 |
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 Research. 24: 2041-2049. DOI: 10.1101/gr.178319.114 |
0.384 |
|
| 2014 |
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 Nature Biotechnology. 32: 829-833. DOI: 10.1038/nbt.2950 |
0.491 |
|
| 2013 |
Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions Nature Biotechnology. 31: 1119-1125. PMID 24185095 DOI: 10.1038/nbt.2727 |
0.315 |
|
| 2013 |
Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions Nature Biotechnology. 31: 1119-1125. PMID 24185095 DOI: 10.1038/Nbt.2727 |
0.812 |
|
| 2013 |
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. Nature Protocols. 8: 2022-32. PMID 24071908 DOI: 10.1038/Nprot.2013.118 |
0.562 |
|
| 2013 |
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. Nature Protocols. 8: 2022-32. PMID 24071908 DOI: 10.1038/Nprot.2013.118 |
0.562 |
|
| 2013 |
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. 500: 207-11. PMID 23925245 DOI: 10.1038/Nature12064 |
0.828 |
|
| 2013 |
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. 500: 207-11. PMID 23925245 DOI: 10.1038/Nature12064 |
0.828 |
|
| 2012 |
Schwartz JJ, Lee C, Hiatt JB, Adey A, Shendure J. Capturing native long-range contiguity by in situ library construction and optical sequencing Proceedings of the National Academy of Sciences of the United States of America. 109: 18749-18754. PMID 23112150 DOI: 10.1073/Pnas.1202680109 |
0.817 |
|
| 2012 |
Adey A, Shendure J. Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing Genome Research. 22: 1139-1143. PMID 22466172 DOI: 10.1101/Gr.136242.111 |
0.644 |
|
| 2011 |
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. Nature Biotechnology. 29: 59-63. PMID 21170042 DOI: 10.1038/Nbt.1740 |
0.824 |
|
| 2011 |
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. Nature Biotechnology. 29: 59-63. PMID 21170042 DOI: 10.1038/Nbt.1740 |
0.824 |
|
| 2011 |
Kitzman JO, MacKenzie AP, Adey A, Hiatt JB, Patwardhan RP, Sudmant PH, Ng SB, Alkan C, Qiu R, Eichler EE, Shendure J. Erratum: Haplotype-resolved genome sequencing of a Gujarati Indian individual Nature Biotechnology. 29: 459-459. DOI: 10.1038/Nbt0511-459C |
0.778 |
|
| 2010 |
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 Biology. 11. PMID 21143862 DOI: 10.1186/Gb-2010-11-12-R119 |
0.78 |
|
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