Birney E - Search Results

1

Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel.

Leger A, Brettell I, Monahan J, Barton C, Wolf N, Kusminski N, Herder C, Aadepu N, Becker C, Gierten J, Hammouda OT, Hasel E, Lischik C, Lust K, Sokolova N, Suzuki R, Tavhelidse T, Thumberger T, Tsingos E, Watson P, Welz B, Naruse K, Loosli F, Wittbrodt J, Birney E, Fitzgerald T. Leger A, et al. Among authors: birney e. Genome Biol. 2022 Feb 21;23(1):58. doi: 10.1186/s13059-022-02602-4. Genome Biol. 2022. PMID: 35189951 Free PMC article.

2

The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates.

Ettwiller L, Paten B, Souren M, Loosli F, Wittbrodt J, Birney E. Ettwiller L, et al. Among authors: birney e. Genome Biol. 2005;6(12):R104. doi: 10.1186/gb-2005-6-12-r104. Epub 2005 Dec 2. Genome Biol. 2005. PMID: 16356267 Free PMC article.

3

Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation.

Ettwiller L, Paten B, Ramialison M, Birney E, Wittbrodt J. Ettwiller L, et al. Among authors: birney e. Nat Methods. 2007 Jul;4(7):563-5. doi: 10.1038/nmeth1061. Epub 2007 Jun 24. Nat Methods. 2007. PMID: 17589518

4

In vivo validation of a computationally predicted conserved Ath5 target gene set.

Del Bene F, Ettwiller L, Skowronska-Krawczyk D, Baier H, Matter JM, Birney E, Wittbrodt J. Del Bene F, et al. Among authors: birney e. PLoS Genet. 2007 Sep;3(9):1661-71. doi: 10.1371/journal.pgen.0030159. Epub 2007 Aug 1. PLoS Genet. 2007. PMID: 17892326 Free PMC article.

5

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Zerbino DR, Birney E. Zerbino DR, et al. Among authors: birney e. Genome Res. 2008 May;18(5):821-9. doi: 10.1101/gr.074492.107. Epub 2008 Mar 18. Genome Res. 2008. PMID: 18349386 Free PMC article.

6

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.

Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS. Boyle AP, et al. Among authors: birney e. Genome Res. 2011 Mar;21(3):456-64. doi: 10.1101/gr.112656.110. Epub 2010 Nov 24. Genome Res. 2011. PMID: 21106903 Free PMC article.

7

Efficient storage of high throughput DNA sequencing data using reference-based compression.

Hsi-Yang Fritz M, Leinonen R, Cochrane G, Birney E. Hsi-Yang Fritz M, et al. Among authors: birney e. Genome Res. 2011 May;21(5):734-40. doi: 10.1101/gr.114819.110. Epub 2011 Jan 18. Genome Res. 2011. PMID: 21245279 Free PMC article.

8

Analysis of variation at transcription factor binding sites in Drosophila and humans.

Spivakov M, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, Herrero J, Kellis M, Furlong EE, Birney E. Spivakov M, et al. Among authors: birney e. Genome Biol. 2012 Sep 28;13(9):R49. doi: 10.1186/gb-2012-13-9-r49. Genome Biol. 2012. PMID: 22950968 Free PMC article.

9

Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish.

Spivakov M, Auer TO, Peravali R, Dunham I, Dolle D, Fujiyama A, Toyoda A, Aizu T, Minakuchi Y, Loosli F, Naruse K, Birney E, Wittbrodt J. Spivakov M, et al. Among authors: birney e. G3 (Bethesda). 2014 Mar 20;4(3):433-45. doi: 10.1534/g3.113.008722. G3 (Bethesda). 2014. PMID: 24408034 Free PMC article.

10

ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy.

Barton C, Morganella S, Ødegård-Fougner Ø, Alexander S, Ries J, Fitzgerald T, Ellenberg J, Birney E. Barton C, et al. Among authors: birney e. PLoS Comput Biol. 2018 Mar 9;14(3):e1006002. doi: 10.1371/journal.pcbi.1006002. eCollection 2018 Mar. PLoS Comput Biol. 2018. PMID: 29522506 Free PMC article.

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