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Items: 28

1.

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
2.

The single-cell transcriptional landscape of mammalian organogenesis.

Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ, Trapnell C, Shendure J.

Nature. 2019 Feb;566(7745):496-502. doi: 10.1038/s41586-019-0969-x. Epub 2019 Feb 20.

PMID:
30787437
3.

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.

4.

Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type.

Boldog E, Bakken TE, Hodge RD, Novotny M, Aevermann BD, Baka J, Bordé S, Close JL, Diez-Fuertes F, Ding SL, Faragó N, Kocsis ÁK, Kovács B, Maltzer Z, McCorrison JM, Miller JA, Molnár G, Oláh G, Ozsvár A, Rózsa M, Shehata SI, Smith KA, Sunkin SM, Tran DN, Venepally P, Wall A, Puskás LG, Barzó P, Steemers FJ, Schork NJ, Scheuermann RH, Lasken RS, Lein ES, Tamás G.

Nat Neurosci. 2018 Sep;21(9):1185-1195. doi: 10.1038/s41593-018-0205-2. Epub 2018 Aug 27.

5.

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.

PMID:
30078726
6.

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.

Cusanovich DA, Hill AJ, Aghamirzaie D, Daza RM, Pliner HA, Berletch JB, Filippova GN, Huang X, Christiansen L, DeWitt WS, Lee C, Regalado SG, Read DF, Steemers FJ, Disteche CM, Trapnell C, Shendure J.

Cell. 2018 Aug 23;174(5):1309-1324.e18. doi: 10.1016/j.cell.2018.06.052. Epub 2018 Aug 2.

PMID:
30078704
7.

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.

8.

The cis-regulatory dynamics of embryonic development at single-cell resolution.

Cusanovich DA, Reddington JP, Garfield DA, Daza RM, Aghamirzaie D, Marco-Ferreres R, Pliner HA, Christiansen L, Qiu X, Steemers FJ, Trapnell C, Shendure J, Furlong EEM.

Nature. 2018 Mar 22;555(7697):538-542. doi: 10.1038/nature25981. Epub 2018 Mar 14.

9.

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.

10.

Haplotype phasing of whole human genomes using bead-based barcode partitioning in a single tube.

Zhang F, Christiansen L, Thomas J, Pokholok D, Jackson R, Morrell N, Zhao Y, Wiley M, Welch E, Jaeger E, Granat A, Norberg SJ, Halpern A, C Rogert M, Ronaghi M, Shendure J, Gormley N, Gunderson KL, Steemers FJ.

Nat Biotechnol. 2017 Sep;35(9):852-857. doi: 10.1038/nbt.3897. Epub 2017 Jun 26.

PMID:
28650462
11.

Contiguity-Preserving Transposition Sequencing (CPT-Seq) for Genome-Wide Haplotyping, Assembly, and Single-Cell ATAC-Seq.

Christiansen L, Amini S, Zhang F, Ronaghi M, Gunderson KL, Steemers FJ.

Methods Mol Biol. 2017;1551:207-221. doi: 10.1007/978-1-4939-6750-6_12.

PMID:
28138849
12.

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.

13.

Massively multiplex single-cell Hi-C.

Ramani V, Deng X, Qiu R, Gunderson KL, Steemers FJ, Disteche CM, Noble WS, Duan Z, Shendure J.

Nat Methods. 2017 Mar;14(3):263-266. doi: 10.1038/nmeth.4155. Epub 2017 Jan 30.

14.

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.

15.

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.

16.

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.

17.

Highly parallel oligonucleotide purification and functionalization using reversible chemistry.

York KT, Smith RC, Yang R, Melnyk PC, Wiley MM, Turk CM, Ronaghi M, Gunderson KL, Steemers FJ.

Nucleic Acids Res. 2012 Jan;40(1):e4. doi: 10.1093/nar/gkr910. Epub 2011 Oct 29.

18.

Whole genome genotyping technologies on the BeadArray platform.

Steemers FJ, Gunderson KL.

Biotechnol J. 2007 Jan;2(1):41-9.

PMID:
17225249
19.

Whole-genome genotyping.

Gunderson KL, Steemers FJ, Ren H, Ng P, Zhou L, Tsan C, Chang W, Bullis D, Musmacker J, King C, Lebruska LL, Barker D, Oliphant A, Kuhn KM, Shen R.

Methods Enzymol. 2006;410:359-76. Review.

PMID:
16938560
20.

High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping.

Peiffer DA, Le JM, Steemers FJ, Chang W, Jenniges T, Garcia F, Haden K, Li J, Shaw CA, Belmont J, Cheung SW, Shen RM, Barker DL, Gunderson KL.

Genome Res. 2006 Sep;16(9):1136-48. Epub 2006 Aug 9.

21.

Whole-genome genotyping of haplotype tag single nucleotide polymorphisms.

Gunderson KL, Kuhn KM, Steemers FJ, Ng P, Murray SS, Shen R.

Pharmacogenomics. 2006 Jun;7(4):641-8.

PMID:
16768648
22.

Whole-genome genotyping with the single-base extension assay.

Steemers FJ, Chang W, Lee G, Barker DL, Shen R, Gunderson KL.

Nat Methods. 2006 Jan;3(1):31-3.

PMID:
16369550
23.

Illumina, Inc.

Steemers FJ, Gunderson KL.

Pharmacogenomics. 2005 Oct;6(7):777-82.

PMID:
16207153
24.

A genome-wide scalable SNP genotyping assay using microarray technology.

Gunderson KL, Steemers FJ, Lee G, Mendoza LG, Chee MS.

Nat Genet. 2005 May;37(5):549-54. Epub 2005 Apr 17.

PMID:
15838508
25.

A cross-reactive, class-selective enzymatic array assay.

Schauer CL, Steemers FJ, Walt DR.

J Am Chem Soc. 2001 Sep 26;123(38):9443-4. No abstract available.

PMID:
11562228
26.

High-density fiber-optic DNA random microsphere array.

Ferguson JA, Steemers FJ, Walt DR.

Anal Chem. 2000 Nov 15;72(22):5618-24.

PMID:
11101240
27.

Screening unlabeled DNA targets with randomly ordered fiber-optic gene arrays.

Steemers FJ, Ferguson JA, Walt DR.

Nat Biotechnol. 2000 Jan;18(1):91-4.

PMID:
10625399
28.

Water-Soluble Neutral Calix[4]arene-Lanthanide Complexes: Synthesis and Luminescence Properties.

Steemers FJ, Meuris HG, Verboom W, Reinhoudt DN, van Der Tol EB, Verhoeven JW.

J Org Chem. 1997 Jun 27;62(13):4229-4235.

PMID:
11671740

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