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Items: 47

1.

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
2.

Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II.

Norman PJ, Norberg SJ, Guethlein LA, Nemat-Gorgani N, Royce T, Wroblewski EE, Dunn T, Mann T, Alicata C, Hollenbach JA, Chang W, Shults Won M, Gunderson KL, Abi-Rached L, Ronaghi M, Parham P.

Genome Res. 2017 May;27(5):813-823. doi: 10.1101/gr.213538.116. Epub 2017 Mar 30.

3.

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
4.

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.

5.

Subangstrom single-molecule measurements of motor proteins using a nanopore.

Derrington IM, Craig JM, Stava E, Laszlo AH, Ross BC, Brinkerhoff H, Nova IC, Doering K, Tickman BI, Ronaghi M, Mandell JG, Gunderson KL, Gundlach JH.

Nat Biotechnol. 2015 Oct;33(10):1073-5. doi: 10.1038/nbt.3357. Epub 2015 Sep 28.

6.

Very long haplotype tracts characterized at high resolution from HLA homozygous cell lines.

Norman PJ, Norberg SJ, Nemat-Gorgani N, Royce T, Hollenbach JA, Shults Won M, Guethlein LA, Gunderson KL, Ronaghi M, Parham P.

Immunogenetics. 2015 Sep;67(9):479-85. doi: 10.1007/s00251-015-0857-y. Epub 2015 Jul 22.

7.

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.

8.

Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationship to memory-cell development.

Smith EN, Ghia EM, DeBoever CM, Rassenti LZ, Jepsen K, Yoon KA, Matsui H, Rozenzhak S, Alakus H, Shepard PJ, Dai Y, Khosroheidari M, Bina M, Gunderson KL, Messer K, Muthuswamy L, Hudson TJ, Harismendy O, Barrett CL, Jamieson CH, Carson DA, Kipps TJ, Frazer KA.

Blood Cancer J. 2015 Apr 10;5:e303. doi: 10.1038/bcj.2015.14.

9.

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.

10.

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.

11.

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.

12.

High density DNA methylation array with single CpG site resolution.

Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, Delano D, Zhang L, Schroth GP, Gunderson KL, Fan JB, Shen R.

Genomics. 2011 Oct;98(4):288-95. doi: 10.1016/j.ygeno.2011.07.007. Epub 2011 Aug 2.

13.

Genome-wide assessment of imprinted expression in human cells.

Morcos L, Ge B, Koka V, Lam KC, Pokholok DK, Gunderson KL, Montpetit A, Verlaan DJ, Pastinen T.

Genome Biol. 2011;12(3):R25. doi: 10.1186/gb-2011-12-3-r25. Epub 2011 Mar 21.

14.

Deletion at fragile sites is a common and early event in Barrett's esophagus.

Lai LA, Kostadinov R, Barrett MT, Peiffer DA, Pokholok D, Odze R, Sanchez CA, Maley CC, Reid BJ, Gunderson KL, Rabinovitch PS.

Mol Cancer Res. 2010 Aug;8(8):1084-94. doi: 10.1158/1541-7786.MCR-09-0529. Epub 2010 Jul 20.

15.

Computational analysis of whole-genome differential allelic expression data in human.

Wagner JR, Ge B, Pokholok D, Gunderson KL, Pastinen T, Blanchette M.

PLoS Comput Biol. 2010 Jul 8;6(7):e1000849. doi: 10.1371/journal.pcbi.1000849.

16.

Global patterns of cis variation in human cells revealed by high-density allelic expression analysis.

Ge B, Pokholok DK, Kwan T, Grundberg E, Morcos L, Verlaan DJ, Le J, Koka V, Lam KC, Gagné V, Dias J, Hoberman R, Montpetit A, Joly MM, Harvey EJ, Sinnett D, Beaulieu P, Hamon R, Graziani A, Dewar K, Harmsen E, Majewski J, Göring HH, Naumova AK, Blanchette M, Gunderson KL, Pastinen T.

Nat Genet. 2009 Nov;41(11):1216-22. doi: 10.1038/ng.473. Epub 2009 Oct 18.

PMID:
19838192
17.

Genome-wide DNA methylation profiling using Infinium® assay.

Bibikova M, Le J, Barnes B, Saedinia-Melnyk S, Zhou L, Shen R, Gunderson KL.

Epigenomics. 2009 Oct;1(1):177-200. doi: 10.2217/epi.09.14.

18.

Identification of critical regions for clinical features of distal 10q deletion syndrome.

Yatsenko SA, Kruer MC, Bader PI, Corzo D, Schuette J, Keegan CE, Nowakowska B, Peacock S, Cai WW, Peiffer DA, Gunderson KL, Ou Z, Chinault AC, Cheung SW.

Clin Genet. 2009 Jul;76(1):54-62. doi: 10.1111/j.1399-0004.2008.01115.x. Epub 2009 Jun 22.

19.

Whole-genome genotyping on bead arrays.

Gunderson KL.

Methods Mol Biol. 2009;529:197-213. doi: 10.1007/978-1-59745-538-1_13.

PMID:
19381978
20.

Design of tag SNP whole genome genotyping arrays.

Peiffer DA, Gunderson KL.

Methods Mol Biol. 2009;529:51-61. doi: 10.1007/978-1-59745-538-1_4.

PMID:
19381970
21.

Single nucleotide polymorphism-based genome-wide chromosome copy change, loss of heterozygosity, and aneuploidy in Barrett's esophagus neoplastic progression.

Li X, Galipeau PC, Sanchez CA, Blount PL, Maley CC, Arnaudo J, Peiffer DA, Pokholok D, Gunderson KL, Reid BJ.

Cancer Prev Res (Phila). 2008 Nov;1(6):413-23. doi: 10.1158/1940-6207.CAPR-08-0121.

22.

Increased LIS1 expression affects human and mouse brain development.

Bi W, Sapir T, Shchelochkov OA, Zhang F, Withers MA, Hunter JV, Levy T, Shinder V, Peiffer DA, Gunderson KL, Nezarati MM, Shotts VA, Amato SS, Savage SK, Harris DJ, Day-Salvatore DL, Horner M, Lu XY, Sahoo T, Yanagawa Y, Beaudet AL, Cheung SW, Martinez S, Lupski JR, Reiner O.

Nat Genet. 2009 Feb;41(2):168-77. doi: 10.1038/ng.302. Epub 2009 Jan 11.

23.

Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation.

Milani L, Lundmark A, Nordlund J, Kiialainen A, Flaegstad T, Jonmundsson G, Kanerva J, Schmiegelow K, Gunderson KL, Lönnerholm G, Syvänen AC.

Genome Res. 2009 Jan;19(1):1-11. doi: 10.1101/gr.083931.108. Epub 2008 Nov 7.

24.

Delineation of the proximal 3q microdeletion syndrome.

Simovich MJ, Bland SD, Peiffer DA, Gunderson KL, Cheung SW, Yatsenko SA, Shinawi M.

Am J Med Genet A. 2008 Jul 1;146A(13):1729-35. doi: 10.1002/ajmg.a.32292. Review.

PMID:
18536049
25.

Mosaic tetrasomy 12p with triplication of 12p detected by array-based comparative genomic hybridization of peripheral blood DNA.

Powis Z, Kang SH, Cooper ML, Patel A, Peiffer DA, Hawkins A, Heidenreich R, Gunderson KL, Cheung SW, Erickson RP.

Am J Med Genet A. 2007 Dec 15;143A(24):2910-5.

PMID:
18000900
26.

Power to detect risk alleles using genome-wide tag SNP panels.

Eberle MA, Ng PC, Kuhn K, Zhou L, Peiffer DA, Galver L, Viaud-Martinez KA, Lawley CT, Gunderson KL, Shen R, Murray SS.

PLoS Genet. 2007 Oct;3(10):1827-37. Epub 2007 Aug 22.

27.

Characterization of de novo microdeletions involving 17q11.2q12 identified through chromosomal comparative genomic hybridization.

Brunetti-Pierri N, Grange DK, Ou Z, Peiffer DA, Peacock SK, Cooper ML, Eng PA, Lalani SR, Chinault AC, Gunderson KL, Craigen WJ, Cheung SW.

Clin Genet. 2007 Nov;72(5):411-9. Epub 2007 Oct 3.

PMID:
17916097
28.

Speech delay and autism spectrum behaviors are frequently associated with duplication of the 7q11.23 Williams-Beuren syndrome region.

Berg JS, Brunetti-Pierri N, Peters SU, Kang SH, Fong CT, Salamone J, Freedenberg D, Hannig VL, Prock LA, Miller DT, Raffalli P, Harris DJ, Erickson RP, Cunniff C, Clark GD, Blazo MA, Peiffer DA, Gunderson KL, Sahoo T, Patel A, Lupski JR, Beaudet AL, Cheung SW.

Genet Med. 2007 Jul;9(7):427-41.

PMID:
17666889
29.

Characterization of seed-specific benzoyloxyglucosinolate mutations in Arabidopsis thaliana.

Kliebenstein DJ, D'Auria JC, Behere AS, Kim JH, Gunderson KL, Breen JN, Lee G, Gershenzon J, Last RL, Jander G.

Plant J. 2007 Sep;51(6):1062-76. Epub 2007 Jul 25.

30.

Indel arrays: an affordable alternative for genotyping.

Salathia N, Lee HN, Sangster TA, Morneau K, Landry CR, Schellenberg K, Behere AS, Gunderson KL, Cavalieri D, Jander G, Queitsch C.

Plant J. 2007 Aug;51(4):727-37. Epub 2007 Jul 20.

31.

Deletion of 7q31.1 supports involvement of FOXP2 in language impairment: clinical report and review.

Lennon PA, Cooper ML, Peiffer DA, Gunderson KL, Patel A, Peters S, Cheung SW, Bacino CA.

Am J Med Genet A. 2007 Apr 15;143A(8):791-8. Review.

PMID:
17330859
32.

Whole genome genotyping technologies on the BeadArray platform.

Steemers FJ, Gunderson KL.

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

PMID:
17225249
33.

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
34.

Illumina universal bead arrays.

Fan JB, Gunderson KL, Bibikova M, Yeakley JM, Chen J, Wickham Garcia E, Lebruska LL, Laurent M, Shen R, Barker D.

Methods Enzymol. 2006;410:57-73. Review.

PMID:
16938546
35.

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.

36.

Highly parallel genomic assays.

Fan JB, Chee MS, Gunderson KL.

Nat Rev Genet. 2006 Aug;7(8):632-44. Review.

PMID:
16847463
37.

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
38.

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
39.

Illumina, Inc.

Steemers FJ, Gunderson KL.

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

PMID:
16207153
40.

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
41.

Highly parallel SNP genotyping.

Fan JB, Oliphant A, Shen R, Kermani BG, Garcia F, Gunderson KL, Hansen M, Steemers F, Butler SL, Deloukas P, Galver L, Hunt S, McBride C, Bibikova M, Rubano T, Chen J, Wickham E, Doucet D, Chang W, Campbell D, Zhang B, Kruglyak S, Bentley D, Haas J, Rigault P, Zhou L, Stuelpnagel J, Chee MS.

Cold Spring Harb Symp Quant Biol. 2003;68:69-78. No abstract available.

PMID:
15338605
42.

Decoding randomly ordered DNA arrays.

Gunderson KL, Kruglyak S, Graige MS, Garcia F, Kermani BG, Zhao C, Che D, Dickinson T, Wickham E, Bierle J, Doucet D, Milewski M, Yang R, Siegmund C, Haas J, Zhou L, Oliphant A, Fan JB, Barnard S, Chee MS.

Genome Res. 2004 May;14(5):870-7. Epub 2004 Apr 12.

43.
44.

Mutation detection by ligation to complete n-mer DNA arrays.

Gunderson KL, Huang XC, Morris MS, Lipshutz RJ, Lockhart DJ, Chee MS.

Genome Res. 1998 Nov;8(11):1142-53.

45.

Failure of the cystic fibrosis transmembrane conductance regulator to conduct ATP.

Reddy MM, Quinton PM, Haws C, Wine JJ, Grygorczyk R, Tabcharani JA, Hanrahan JW, Gunderson KL, Kopito RR.

Science. 1996 Mar 29;271(5257):1876-9.

PMID:
8596959
46.

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