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Items: 1 to 20 of 36

1.

Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells.

Ohi Y, Qin H, Hong C, Blouin L, Polo JM, Guo T, Qi Z, Downey SL, Manos PD, Rossi DJ, Yu J, Hebrok M, Hochedlinger K, Costello JF, Song JS, Ramalho-Santos M.

Nat Cell Biol. 2011 May;13(5):541-9. doi: 10.1038/ncb2239. Epub 2011 Apr 17.

2.

A framework for variation discovery and genotyping using next-generation DNA sequencing data.

DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ.

Nat Genet. 2011 May;43(5):491-8. doi: 10.1038/ng.806. Epub 2011 Apr 10.

3.

Single-cell genomics.

Kalisky T, Quake SR.

Nat Methods. 2011 Apr;8(4):311-4. doi: 10.1038/nmeth0411-311.

PMID:
21451520
4.

Somatic coding mutations in human induced pluripotent stem cells.

Gore A, Li Z, Fung HL, Young JE, Agarwal S, Antosiewicz-Bourget J, Canto I, Giorgetti A, Israel MA, Kiskinis E, Lee JH, Loh YH, Manos PD, Montserrat N, Panopoulos AD, Ruiz S, Wilbert ML, Yu J, Kirkness EF, Izpisua Belmonte JC, Rossi DJ, Thomson JA, Eggan K, Daley GQ, Goldstein LS, Zhang K.

Nature. 2011 Mar 3;471(7336):63-7. doi: 10.1038/nature09805.

5.

Integrative genomics viewer.

Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP.

Nat Biotechnol. 2011 Jan;29(1):24-6. doi: 10.1038/nbt.1754. No abstract available.

6.

Dynamic changes in the copy number of pluripotency and cell proliferation genes in human ESCs and iPSCs during reprogramming and time in culture.

Laurent LC, Ulitsky I, Slavin I, Tran H, Schork A, Morey R, Lynch C, Harness JV, Lee S, Barrero MJ, Ku S, Martynova M, Semechkin R, Galat V, Gottesfeld J, Izpisua Belmonte JC, Murry C, Keirstead HS, Park HS, Schmidt U, Laslett AL, Muller FJ, Nievergelt CM, Shamir R, Loring JF.

Cell Stem Cell. 2011 Jan 7;8(1):106-18. doi: 10.1016/j.stem.2010.12.003.

7.

Chromatin signatures of the Drosophila replication program.

Eaton ML, Prinz JA, MacAlpine HK, Tretyakov G, Kharchenko PV, MacAlpine DM.

Genome Res. 2011 Feb;21(2):164-74. doi: 10.1101/gr.116038.110. Epub 2010 Dec 22.

8.

BMPs functionally replace Klf4 and support efficient reprogramming of mouse fibroblasts by Oct4 alone.

Chen J, Liu J, Yang J, Chen Y, Chen J, Ni S, Song H, Zeng L, Ding K, Pei D.

Cell Res. 2011 Jan;21(1):205-12. doi: 10.1038/cr.2010.172. Epub 2010 Dec 7.

9.

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.

Wang K, Li M, Hakonarson H.

Nucleic Acids Res. 2010 Sep;38(16):e164. doi: 10.1093/nar/gkq603. Epub 2010 Jul 3.

10.

Evolution of the mutation rate.

Lynch M.

Trends Genet. 2010 Aug;26(8):345-52. doi: 10.1016/j.tig.2010.05.003. Epub 2010 Jun 30.

11.

Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing.

Bell O, Schwaiger M, Oakeley EJ, Lienert F, Beisel C, Stadler MB, Schübeler D.

Nat Struct Mol Biol. 2010 Jul;17(7):894-900. doi: 10.1038/nsmb.1825. Epub 2010 Jun 20.

PMID:
20562853
12.

Expression in aneuploid Drosophila S2 cells.

Zhang Y, Malone JH, Powell SK, Periwal V, Spana E, Macalpine DM, Oliver B.

PLoS Biol. 2010 Feb 23;8(2):e1000320. doi: 10.1371/journal.pbio.1000320.

13.

Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis.

Hiratani I, Ryba T, Itoh M, Rathjen J, Kulik M, Papp B, Fussner E, Bazett-Jones DP, Plath K, Dalton S, Rathjen PD, Gilbert DM.

Genome Res. 2010 Feb;20(2):155-69. doi: 10.1101/gr.099796.109. Epub 2009 Dec 1.

14.

Mutational heterogeneity in human cancers: origin and consequences.

Salk JJ, Fox EJ, Loeb LA.

Annu Rev Pathol. 2010;5:51-75. doi: 10.1146/annurev-pathol-121808-102113. Review.

15.

Improved protocols for the illumina genome analyzer sequencing system.

Quail MA, Swerdlow H, Turner DJ.

Curr Protoc Hum Genet. 2009 Jul;Chapter 18:Unit 18.2. doi: 10.1002/0471142905.hg1802s62.

16.

VarScan: variant detection in massively parallel sequencing of individual and pooled samples.

Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L.

Bioinformatics. 2009 Sep 1;25(17):2283-5. doi: 10.1093/bioinformatics/btp373. Epub 2009 Jun 19.

17.

Cancer genome sequencing--an interim analysis.

Fox EJ, Salk JJ, Loeb LA.

Cancer Res. 2009 Jun 15;69(12):4948-50. doi: 10.1158/0008-5472.CAN-09-1231. Epub 2009 Jun 9.

18.

The Sequence Alignment/Map format and SAMtools.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup..

Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8.

19.

Fast and accurate short read alignment with Burrows-Wheeler transform.

Li H, Durbin R.

Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18.

20.

lacZ mouse embryonic fibroblasts detect both clastogens and mutagens.

Mahabir AG, Zwart E, Schaap M, van Benthem J, de Vries A, Hernandez LG, Hendriksen CF, van Steeg H.

Mutat Res. 2009 Jun 18;666(1-2):50-6. doi: 10.1016/j.mrfmmm.2009.04.005. Epub 2009 Apr 23.

PMID:
19393670

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