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Results: 1 to 20 of 75

1.

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak.

Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang PP, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Jalloh AA, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, Massally JL, Chapman SB, Bochicchio J, Murphy C, Nusbaum C, Young S, Birren BW, Grant DS, Scheiffelin JS, Lander ES, Happi C, Gevao SM, Gnirke A, Rambaut A, Garry RF, Khan SH, Sabeti PC.

Science. 2014 Sep 12;345(6202):1369-72. doi: 10.1126/science.1259657. Epub 2014 Aug 28.

PMID:
25214632
[PubMed - indexed for MEDLINE]
2.

Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes.

Melnikov A, Rogov P, Wang L, Gnirke A, Mikkelsen TS.

Nucleic Acids Res. 2014;42(14):e112. doi: 10.1093/nar/gku511. Epub 2014 Jun 9.

PMID:
24914046
[PubMed - in process]
Free Article
3.

Charting a dynamic DNA methylation landscape of the human genome.

Ziller MJ, Gu H, Müller F, Donaghey J, Tsai LT, Kohlbacher O, De Jager PL, Rosen ED, Bennett DA, Bernstein BE, Gnirke A, Meissner A.

Nature. 2013 Aug 22;500(7463):477-81. doi: 10.1038/nature12433. Epub 2013 Aug 7.

PMID:
23925113
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Cellular source and mechanisms of high transcriptome complexity in the mammalian testis.

Soumillon M, Necsulea A, Weier M, Brawand D, Zhang X, Gu H, Barthès P, Kokkinaki M, Nef S, Gnirke A, Dym M, de Massy B, Mikkelsen TS, Kaessmann H.

Cell Rep. 2013 Jun 27;3(6):2179-90. doi: 10.1016/j.celrep.2013.05.031. Epub 2013 Jun 20.

PMID:
23791531
[PubMed - indexed for MEDLINE]
Free Article
5.

Comparative analysis of RNA sequencing methods for degraded or low-input samples.

Adiconis X, Borges-Rivera D, Satija R, DeLuca DS, Busby MA, Berlin AM, Sivachenko A, Thompson DA, Wysoker A, Fennell T, Gnirke A, Pochet N, Regev A, Levin JZ.

Nat Methods. 2013 Jul;10(7):623-9. doi: 10.1038/nmeth.2483. Epub 2013 May 19. Erratum in: Nat Methods. 2014 Feb;11(2):210.

PMID:
23685885
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.

Shalek AK, Satija R, Adiconis X, Gertner RS, Gaublomme JT, Raychowdhury R, Schwartz S, Yosef N, Malboeuf C, Lu D, Trombetta JJ, Gennert D, Gnirke A, Goren A, Hacohen N, Levin JZ, Park H, Regev A.

Nature. 2013 Jun 13;498(7453):236-40. doi: 10.1038/nature12172. Epub 2013 May 19.

PMID:
23685454
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells.

Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES, Bernstein BE, Meissner A.

Cell. 2013 May 23;153(5):1149-63. doi: 10.1016/j.cell.2013.04.037. Epub 2013 May 9.

PMID:
23664763
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

The African coelacanth genome provides insights into tetrapod evolution.

Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Gamieldien J, Gnerre S, Gnirke A, Goldstone JV, Haerty W, Hahn ME, Hesse U, Hoffmann S, Johnson J, Karchner SI, Kuraku S, Lara M, Levin JZ, Litman GW, Mauceli E, Miyake T, Mueller MG, Nelson DR, Nitsche A, Olmo E, Ota T, Pallavicini A, Panji S, Picone B, Ponting CP, Prohaska SJ, Przybylski D, Saha NR, Ravi V, Ribeiro FJ, Sauka-Spengler T, Scapigliati G, Searle SM, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tabbaa D, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K.

Nature. 2013 Apr 18;496(7445):311-6. doi: 10.1038/nature12027.

PMID:
23598338
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing.

Kirby A, Gnirke A, Jaffe DB, Barešová V, Pochet N, Blumenstiel B, Ye C, Aird D, Stevens C, Robinson JT, Cabili MN, Gat-Viks I, Kelliher E, Daza R, DeFelice M, Hůlková H, Sovová J, Vylet'al P, Antignac C, Guttman M, Handsaker RE, Perrin D, Steelman S, Sigurdsson S, Scheinman SJ, Sougnez C, Cibulskis K, Parkin M, Green T, Rossin E, Zody MC, Xavier RJ, Pollak MR, Alper SL, Lindblad-Toh K, Gabriel S, Hart PS, Regev A, Nusbaum C, Kmoch S, Bleyer AJ, Lander ES, Daly MJ.

Nat Genet. 2013 Mar;45(3):299-303. doi: 10.1038/ng.2543. Epub 2013 Feb 10.

PMID:
23396133
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling.

Boyle P, Clement K, Gu H, Smith ZD, Ziller M, Fostel JL, Holmes L, Meldrim J, Kelley F, Gnirke A, Meissner A.

Genome Biol. 2012 Oct 3;13(10):R92. doi: 10.1186/gb-2012-13-10-r92.

PMID:
23034176
[PubMed - in process]
Free PMC Article
11.

A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals.

Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, Meldrim J, Ram O, Cheng C, Gnirke A, Fisher S, Friedman N, Wong B, Bernstein BE, Nusbaum C, Hacohen N, Regev A, Amit I.

Mol Cell. 2012 Sep 14;47(5):810-22. doi: 10.1016/j.molcel.2012.07.030. Epub 2012 Aug 30.

PMID:
22940246
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

DNA methylation dynamics during in vivo differentiation of blood and skin stem cells.

Bock C, Beerman I, Lien WH, Smith ZD, Gu H, Boyle P, Gnirke A, Fuchs E, Rossi DJ, Meissner A.

Mol Cell. 2012 Aug 24;47(4):633-47. doi: 10.1016/j.molcel.2012.06.019. Epub 2012 Jul 26.

PMID:
22841485
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Paired-end sequencing of Fosmid libraries by Illumina.

Williams LJ, Tabbaa DG, Li N, Berlin AM, Shea TP, Maccallum I, Lawrence MS, Drier Y, Getz G, Young SK, Jaffe DB, Nusbaum C, Gnirke A.

Genome Res. 2012 Nov;22(11):2241-9. doi: 10.1101/gr.138925.112. Epub 2012 Jul 16.

PMID:
22800726
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk.

Brinkman AB, Gu H, Bartels SJ, Zhang Y, Matarese F, Simmer F, Marks H, Bock C, Gnirke A, Meissner A, Stunnenberg HG.

Genome Res. 2012 Jun;22(6):1128-38. doi: 10.1101/gr.133728.111. Epub 2012 Mar 30.

PMID:
22466170
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

A unique regulatory phase of DNA methylation in the early mammalian embryo.

Smith ZD, Chan MM, Mikkelsen TS, Gu H, Gnirke A, Regev A, Meissner A.

Nature. 2012 Mar 28;484(7394):339-44. doi: 10.1038/nature10960.

PMID:
22456710
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.

Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, Nusbaum C, Birren BW, Gnirke A.

Genome Biol. 2012;13(3):R23. doi: 10.1186/gb-2012-13-3-r23.

PMID:
22455878
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay.

Melnikov A, Murugan A, Zhang X, Tesileanu T, Wang L, Rogov P, Feizi S, Gnirke A, Callan CG Jr, Kinney JB, Kellis M, Lander ES, Mikkelsen TS.

Nat Biotechnol. 2012 Feb 26;30(3):271-7. doi: 10.1038/nbt.2137.

PMID:
22371084
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Genomic distribution and inter-sample variation of non-CpG methylation across human cell types.

Ziller MJ, Müller F, Liao J, Zhang Y, Gu H, Bock C, Boyle P, Epstein CB, Bernstein BE, Lengauer T, Gnirke A, Meissner A.

PLoS Genet. 2011 Dec;7(12):e1002389. doi: 10.1371/journal.pgen.1002389. Epub 2011 Dec 8.

PMID:
22174693
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Hybrid selection for sequencing pathogen genomes from clinical samples.

Melnikov A, Galinsky K, Rogov P, Fennell T, Van Tyne D, Russ C, Daniels R, Barnes KG, Bochicchio J, Ndiaye D, Sene PD, Wirth DF, Nusbaum C, Volkman SK, Birren BW, Gnirke A, Neafsey DE.

Genome Biol. 2011 Aug 11;12(8):R73. doi: 10.1186/gb-2011-12-8-r73.

PMID:
21835008
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Full-length transcriptome assembly from RNA-Seq data without a reference genome.

Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A.

Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883.

PMID:
21572440
[PubMed - indexed for MEDLINE]
Free PMC Article

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