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Items: 32

1.

High-Throughput Single-Cell Sequencing with Linear Amplification.

Yin Y, Jiang Y, Lam KG, Berletch JB, Disteche CM, Noble WS, Steemers FJ, Camerini-Otero RD, Adey AC, Shendure J.

Mol Cell. 2019 Aug 28. pii: S1097-2765(19)30618-5. doi: 10.1016/j.molcel.2019.08.002. [Epub ahead of print]

PMID:
31495564
2.

Integration of Single-Cell Genomics Datasets.

Adey AC.

Cell. 2019 Jun 13;177(7):1677-1679. doi: 10.1016/j.cell.2019.05.034.

PMID:
31199914
3.

The accessible chromatin landscape of the murine hippocampus at single-cell resolution.

Sinnamon JR, Torkenczy KA, Linhoff MW, Vitak SA, Mulqueen RM, Pliner HA, Trapnell C, Steemers FJ, Mandel G, Adey AC.

Genome Res. 2019 May;29(5):857-869. doi: 10.1101/gr.243725.118. Epub 2019 Apr 1.

PMID:
30936163
4.

Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion.

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.

Genome Res. 2019 Mar;29(3):367-382. doi: 10.1101/gr.239830.118. Epub 2019 Jan 25.

5.

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 CJ, Liang J, Nan X, Dai MS, Adey A, Impey S, Sears RC.

Genes Dev. 2018 Nov 1;32(21-22):1398-1419. doi: 10.1101/gad.314377.118. Epub 2018 Oct 26.

6.

Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer.

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.

Nat Commun. 2018 Sep 19;9(1):3815. doi: 10.1038/s41467-018-05729-w.

7.

Joint profiling of chromatin accessibility and gene expression in thousands of single cells.

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.

Science. 2018 Sep 28;361(6409):1380-1385. doi: 10.1126/science.aau0730. Epub 2018 Aug 30.

8.

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.

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.

Mol Cell. 2018 Sep 6;71(5):858-871.e8. doi: 10.1016/j.molcel.2018.06.044. Epub 2018 Aug 2.

9.

Highly scalable generation of DNA methylation profiles in single cells.

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.

Nat Biotechnol. 2018 Jun;36(5):428-431. doi: 10.1038/nbt.4112. Epub 2018 Apr 9.

10.

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.

Methods Mol Biol. 2018;1708:105-122. doi: 10.1007/978-1-4939-7481-8_6.

PMID:
29224141
11.

Haplotype resolution at the single-cell level.

Adey AC.

Proc Natl Acad Sci U S A. 2017 Nov 21;114(47):12362-12364. doi: 10.1073/pnas.1717798114. Epub 2017 Nov 7. No abstract available.

12.

Comprehensive single-cell transcriptional profiling of a multicellular organism.

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.

Science. 2017 Aug 18;357(6352):661-667. doi: 10.1126/science.aam8940.

13.

Sequencing thousands of single-cell genomes with combinatorial indexing.

Vitak SA, Torkenczy KA, Rosenkrantz JL, Fields AJ, Christiansen L, Wong MH, Carbone L, Steemers FJ, Adey A.

Nat Methods. 2017 Mar;14(3):302-308. doi: 10.1038/nmeth.4154. Epub 2017 Jan 30.

14.

Recurrent somatic loss of TNFRSF14 in classical Hodgkin lymphoma.

Salipante SJ, Adey A, Thomas A, Lee C, Liu YJ, Kumar A, Lewis AP, Wu D, Fromm JR, Shendure J.

Genes Chromosomes Cancer. 2016 Mar;55(3):278-87. doi: 10.1002/gcc.22331. Epub 2015 Dec 9.

15.

Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.

Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, Steemers FJ, Trapnell C, Shendure J.

Science. 2015 May 22;348(6237):910-4. doi: 10.1126/science.aab1601. Epub 2015 May 7.

16.

Haplotype-resolved genome sequencing: experimental methods and applications.

Snyder MW, Adey A, Kitzman JO, Shendure J.

Nat Rev Genet. 2015 Jun;16(6):344-58. doi: 10.1038/nrg3903. Epub 2015 May 7. Review.

PMID:
25948246
17.

Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes.

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.

Genome Biol. 2014 Dec 3;15(12):530. doi: 10.1186/s13059-014-0530-z.

18.

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity.

Adey A, Kitzman JO, Burton JN, Daza R, Kumar A, Christiansen L, Ronaghi M, Amini S, Gunderson KL, Steemers FJ, Shendure J.

Genome Res. 2014 Dec;24(12):2041-9. doi: 10.1101/gr.178319.114. Epub 2014 Oct 19.

19.

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 JO, Vijayan K, Ronaghi M, Shendure J, Gunderson KL, Steemers FJ.

Nat Genet. 2014 Dec;46(12):1343-9. doi: 10.1038/ng.3119. Epub 2014 Oct 19.

20.

Decoding long nanopore sequencing reads of natural DNA.

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.

Nat Biotechnol. 2014 Aug;32(8):829-33. doi: 10.1038/nbt.2950. Epub 2014 Jun 25.

21.

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 BL, Certo MT, Baker D, Scharenberg AM.

Nucleic Acids Res. 2014 Feb;42(4):2591-601. doi: 10.1093/nar/gkt1224. Epub 2013 Nov 26.

22.

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 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.

J Mol Diagn. 2014 Jan;16(1):56-67. doi: 10.1016/j.jmoldx.2013.08.004. Epub 2013 Nov 2.

23.

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.

Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J.

Nat Biotechnol. 2013 Dec;31(12):1119-25. doi: 10.1038/nbt.2727. Epub 2013 Nov 3.

24.

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.

Nat Protoc. 2013 Oct;8(10):2022-32. doi: 10.1038/nprot.2013.118. Epub 2013 Sep 26.

PMID:
24071908
25.

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line.

Adey A, Burton JN, Kitzman JO, Hiatt JB, Lewis AP, Martin BK, Qiu R, Lee C, Shendure J.

Nature. 2013 Aug 8;500(7461):207-11. doi: 10.1038/nature12064.

26.

Capturing native long-range contiguity by in situ library construction and optical sequencing.

Schwartz JJ, Lee C, Hiatt JB, Adey A, Shendure J.

Proc Natl Acad Sci U S A. 2012 Nov 13;109(46):18749-54. doi: 10.1073/pnas.1202680109. Epub 2012 Oct 29.

27.

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

Adey A, Shendure J.

Genome Res. 2012 Jun;22(6):1139-43. doi: 10.1101/gr.136242.111. Epub 2012 Mar 30.

28.

Haplotype-resolved genome sequencing of a Gujarati Indian individual.

Kitzman JO, Mackenzie AP, Adey A, Hiatt JB, Patwardhan RP, Sudmant PH, Ng SB, Alkan C, Qiu R, Eichler EE, Shendure J.

Nat Biotechnol. 2011 Jan;29(1):59-63. doi: 10.1038/nbt.1740. Epub 2010 Dec 19. Erratum in: Nat Biotechnol. 2011 May;29(5):459.

29.

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition.

Adey A, Morrison HG, Asan, Xun X, Kitzman JO, Turner EH, Stackhouse B, MacKenzie AP, Caruccio NC, Zhang X, Shendure J.

Genome Biol. 2010;11(12):R119. doi: 10.1186/gb-2010-11-12-r119. Epub 2010 Dec 8.

30.

Whooping cough?

Adey AB.

Can Med Assoc J. 1980 Jun 7;122(11):1238. No abstract available.

31.

Isolation and partial characterization of plasma membranes bearing human fetal-associated antigens.

Akeson R, Goldblatt D, Adey A, Miyakawa J, Welch W, Weimer HE, Fahey JL.

Cancer Res. 1977 May;37(5):1468-75.

32.

The "Saturday night syndrome".

Adey AB.

Can Med Assoc J. 1969 Mar 15;100(11):539. No abstract available.

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