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Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos.

Mir M, Stadler MR, Ortiz SA, Hannon CE, Harrison MM, Darzacq X, Eisen MB.

Elife. 2018 Dec 27;7. pii: e40497. doi: 10.7554/eLife.40497.


Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy.

Mir M, Reimer A, Stadler M, Tangara A, Hansen AS, Hockemeyer D, Eisen MB, Garcia H, Darzacq X.

Methods Mol Biol. 2018;1814:541-559. doi: 10.1007/978-1-4939-8591-3_32.


Convergent evolution of gene expression in two high-toothed stickleback populations.

Hart JC, Ellis NA, Eisen MB, Miller CT.

PLoS Genet. 2018 Jun 13;14(6):e1007443. doi: 10.1371/journal.pgen.1007443. eCollection 2018 Jun.


Gene family innovation, conservation and loss on the animal stem lineage.

Richter DJ, Fozouni P, Eisen MB, King N.

Elife. 2018 May 31;7. pii: e34226. doi: 10.7554/eLife.34226.


The ecology of the Drosophila-yeast mutualism in wineries.

Quan AS, Eisen MB.

PLoS One. 2018 May 16;13(5):e0196440. doi: 10.1371/journal.pone.0196440. eCollection 2018.


Patterns of chromatin accessibility along the anterior-posterior axis in the early Drosophila embryo.

Haines JE, Eisen MB.

PLoS Genet. 2018 May 4;14(5):e1007367. doi: 10.1371/journal.pgen.1007367. eCollection 2018 May.


Rapid Global Spread of wRi-like Wolbachia across Multiple Drosophila.

Turelli M, Cooper BS, Richardson KM, Ginsberg PS, Peckenpaugh B, Antelope CX, Kim KJ, May MR, Abrieux A, Wilson DA, Bronski MJ, Moore BR, Gao JJ, Eisen MB, Chiu JC, Conner WR, Hoffmann AA.

Curr Biol. 2018 Mar 19;28(6):963-971.e8. doi: 10.1016/j.cub.2018.02.015. Epub 2018 Mar 8.


A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates.

Plouhinec JL, Medina-Ruiz S, Borday C, Bernard E, Vert JP, Eisen MB, Harland RM, Monsoro-Burq AH.

PLoS Biol. 2017 Oct 19;15(10):e2004045. doi: 10.1371/journal.pbio.2004045. eCollection 2017 Oct.


Atlas…t, patterns from every cell.

Stadler MR, Eisen MB.

Science. 2017 Oct 13;358(6360):172-173. doi: 10.1126/science.aap8493. No abstract available.


Dense Bicoid hubs accentuate binding along the morphogen gradient.

Mir M, Reimer A, Haines JE, Li XY, Stadler M, Garcia H, Eisen MB, Darzacq X.

Genes Dev. 2017 Sep 1;31(17):1784-1794. doi: 10.1101/gad.305078.117.


Patterns of Genome-Wide Diversity and Population Structure in the Drosophila athabasca Species Complex.

Wong Miller KM, Bracewell RR, Eisen MB, Bachtrog D.

Mol Biol Evol. 2017 Aug 1;34(8):1912-1923. doi: 10.1093/molbev/msx134.


Genome-wide measurement of spatial expression in patterning mutants of Drosophila melanogaster.

Combs PA, Eisen MB.

F1000Res. 2017 Jan 12;6:41. doi: 10.12688/f1000research.9720.1. eCollection 2017.


Stable Host Gene Expression in the Gut of Adult Drosophila melanogaster with Different Bacterial Mono-Associations.

Elya C, Zhang V, Ludington WB, Eisen MB.

PLoS One. 2016 Nov 29;11(11):e0167357. doi: 10.1371/journal.pone.0167357. eCollection 2016.


The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion.

Kao D, Lai AG, Stamataki E, Rosic S, Konstantinides N, Jarvis E, Di Donfrancesco A, Pouchkina-Stancheva N, Sémon M, Grillo M, Bruce H, Kumar S, Siwanowicz I, Le A, Lemire A, Eisen MB, Extavour C, Browne WE, Wolff C, Averof M, Patel NH, Sarkies P, Pavlopoulos A, Aboobaker A.

Elife. 2016 Nov 16;5. pii: e20062. doi: 10.7554/eLife.20062.


Oxygen changes drive non-uniform scaling in Drosophila melanogaster embryogenesis.

Kuntz SG, Eisen MB.

F1000Res. 2015 Oct 23;4:1102. doi: 10.12688/f1000research.7221.1. eCollection 2015.


Sex Bias and Maternal Contribution to Gene Expression Divergence in Drosophila Blastoderm Embryos.

Paris M, Villalta JE, Eisen MB, Lott SE.

PLoS Genet. 2015 Oct 20;11(10):e1005592. doi: 10.1371/journal.pgen.1005592. eCollection 2015 Oct.


Transcriptional Activation of the Zygotic Genome in Drosophila.

Harrison MM, Eisen MB.

Curr Top Dev Biol. 2015;113:85-112. doi: 10.1016/bs.ctdb.2015.07.028. Epub 2015 Aug 19. Review.


Ten Years of PLoS Computational Biology: A Decade of Appreciation and Innovation.

Bourne PE, Brenner SE, Eisen MB.

PLoS Comput Biol. 2015 Jun 24;11(6):e1004317. doi: 10.1371/journal.pcbi.1004317. eCollection 2015 Jun. No abstract available.


Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols.

Combs PA, Eisen MB.

PeerJ. 2015 Mar 26;3:e869. doi: 10.7717/peerj.869. eCollection 2015.


Saccharomyces cerevisiae mitochondria are required for optimal attractiveness to Drosophila melanogaster.

Schiabor KM, Quan AS, Eisen MB.

PLoS One. 2014 Dec 2;9(12):e113899. doi: 10.1371/journal.pone.0113899. eCollection 2014.


Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition.

Li XY, Harrison MM, Villalta JE, Kaplan T, Eisen MB.

Elife. 2014 Oct 14;3. doi: 10.7554/eLife.03737.


Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

Chen ZX, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, Clough E, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kim YA, Kovar CL, Lee SL, Li M, Malley JD, Malone JH, Mathew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Przytycka TM, Pu LL, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner CB, Worley KC, Wu YQ, Zou X, Cherbas P, Kellis M, Eisen MB, Piano F, Kionte K, Fitch DH, Sternberg PW, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs RA, Bickel PJ, Kopp A, Carninci P, Celniker SE, Oliver B, Richards S.

Genome Res. 2014 Jul;24(7):1209-23. doi: 10.1101/gr.159384.113.


Structural variation among wild and industrial strains of Penicillium chrysogenum.

Wong VL, Ellison CE, Eisen MB, Pachter L, Brem RB.

PLoS One. 2014 May 13;9(5):e96784. doi: 10.1371/journal.pone.0096784. eCollection 2014.


Drosophila embryogenesis scales uniformly across temperature in developmentally diverse species.

Kuntz SG, Eisen MB.

PLoS Genet. 2014 Apr 24;10(4):e1004293. doi: 10.1371/journal.pgen.1004293. eCollection 2014 Apr.


Sex-specific embryonic gene expression in species with newly evolved sex chromosomes.

Lott SE, Villalta JE, Zhou Q, Bachtrog D, Eisen MB.

PLoS Genet. 2014 Feb 13;10(2):e1004159. doi: 10.1371/journal.pgen.1004159. eCollection 2014 Feb.


Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression.

Paris M, Kaplan T, Li XY, Villalta JE, Lott SE, Eisen MB.

PLoS Genet. 2013;9(9):e1003748. doi: 10.1371/journal.pgen.1003748. Epub 2013 Sep 12.


Mice infected with low-virulence strains of Toxoplasma gondii lose their innate aversion to cat urine, even after extensive parasite clearance.

Ingram WM, Goodrich LM, Robey EA, Eisen MB.

PLoS One. 2013 Sep 18;8(9):e75246. doi: 10.1371/journal.pone.0075246. eCollection 2013.


Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

Combs PA, Eisen MB.

PLoS One. 2013 Aug 12;8(8):e71820. doi: 10.1371/journal.pone.0071820. eCollection 2013.


Improving transcriptome assembly through error correction of high-throughput sequence reads.

Macmanes MD, Eisen MB.

PeerJ. 2013 Jul 23;1:e113. doi: 10.7717/peerj.113. Print 2013.


An essential role for zygotic expression in the pre-cellular Drosophila embryo.

Ali-Murthy Z, Lott SE, Eisen MB, Kornberg TB.

PLoS Genet. 2013 Apr;9(4):e1003428. doi: 10.1371/journal.pgen.1003428. Epub 2013 Apr 4.


Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence.

Rands CM, Darling A, Fujita M, Kong L, Webster MT, Clabaut C, Emes RD, Heger A, Meader S, Hawkins MB, Eisen MB, Teiling C, Affourtit J, Boese B, Grant PR, Grant BR, Eisen JA, Abzhanov A, Ponting CP.

BMC Genomics. 2013 Feb 12;14:95. doi: 10.1186/1471-2164-14-95.


Dual functions of TAF7L in adipocyte differentiation.

Zhou H, Kaplan T, Li Y, Grubisic I, Zhang Z, Wang PJ, Eisen MB, Tjian R.

Elife. 2013 Jan 8;2:e00170. doi: 10.7554/eLife.00170.


Spatial promoter recognition signatures may enhance transcription factor specificity in yeast.

Lusk RW, Eisen MB.

PLoS One. 2013;8(1):e53778. doi: 10.1371/journal.pone.0053778. Epub 2013 Jan 8.


The enigmatic conservation of a Rap1 binding site in the Saccharomyces cerevisiae HMR-E silencer.

Teytelman L, Osborne Nishimura EA, Özaydin B, Eisen MB, Rine J.

G3 (Bethesda). 2012 Dec;2(12):1555-62. doi: 10.1534/g3.112.004077. Epub 2012 Dec 1.


DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila.

Fisher WW, Li JJ, Hammonds AS, Brown JB, Pfeiffer BD, Weiszmann R, MacArthur S, Thomas S, Stamatoyannopoulos JA, Eisen MB, Bickel PJ, Biggin MD, Celniker SE.

Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21330-5. doi: 10.1073/pnas.1209589110. Epub 2012 Dec 10.


A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.

Hu TT, Eisen MB, Thornton KR, Andolfatto P.

Genome Res. 2013 Jan;23(1):89-98. doi: 10.1101/gr.141689.112. Epub 2012 Aug 30.


Probing the informational and regulatory plasticity of a transcription factor DNA-binding domain.

Shultzaberger RK, Maerkl SJ, Kirsch JF, Eisen MB.

PLoS Genet. 2012;8(3):e1002614. doi: 10.1371/journal.pgen.1002614. Epub 2012 Mar 29.


The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus.

Scannell DR, Zill OA, Rokas A, Payen C, Dunham MJ, Eisen MB, Rine J, Johnston M, Hittinger CT.

G3 (Bethesda). 2011 Jun;1(1):11-25. doi: 10.1534/g3.111.000273. Epub 2011 Jun 1.


A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila.

Fowlkes CC, Eckenrode KB, Bragdon MD, Meyer M, Wunderlich Z, Simirenko L, Luengo Hendriks CL, Keränen SV, Henriquez C, Knowles DW, Biggin MD, Eisen MB, DePace AH.

PLoS Genet. 2011 Oct;7(10):e1002346. doi: 10.1371/journal.pgen.1002346. Epub 2011 Oct 27.


Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition.

Harrison MM, Li XY, Kaplan T, Botchan MR, Eisen MB.

PLoS Genet. 2011 Oct;7(10):e1002266. doi: 10.1371/journal.pgen.1002266. Epub 2011 Oct 20.


Control of embryonic stem cell lineage commitment by core promoter factor, TAF3.

Liu Z, Scannell DR, Eisen MB, Tjian R.

Cell. 2011 Sep 2;146(5):720-31. doi: 10.1016/j.cell.2011.08.005.


The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding.

Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD.

Genome Biol. 2011;12(4):R34. doi: 10.1186/gb-2011-12-4-r34. Epub 2011 Apr 7.


Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq.

Lott SE, Villalta JE, Schroth GP, Luo S, Tonkin LA, Eisen MB.

PLoS Biol. 2011 Feb 8;9(2):e1000590. doi: 10.1371/journal.pbio.1000590.


Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development.

Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB.

PLoS Genet. 2011 Feb 3;7(2):e1001290. doi: 10.1371/journal.pgen.1001290.


The fitness landscapes of cis-acting binding sites in different promoter and environmental contexts.

Shultzaberger RK, Malashock DS, Kirsch JF, Eisen MB.

PLoS Genet. 2010 Jul 29;6(7):e1001042. doi: 10.1371/journal.pgen.1001042.


Exploring the genetic basis of variation in gene predictions with a synthetic association study.

Levin TC, Glazer AM, Pachter L, Brem RB, Eisen MB.

PLoS One. 2010 Jul 29;5(7):e11645. doi: 10.1371/journal.pone.0011645.


Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data.

Rübel O, Ahern S, Bethel EW, Biggin MD, Childs H, Cormier-Michel E, Depace A, Eisen MB, Fowlkes CC, Geddes CG, Hagen H, Hamann B, Huang MY, Keränen SV, Knowles DW, Hendriks CL, Malik J, Meredith J, Messmer P, Prabhat, Ushizima D, Weber GH, Wu K.

Procedia Comput Sci. 2010 May;1(1):1757-1764.


Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species.

Bradley RK, Li XY, Trapnell C, Davidson S, Pachter L, Chu HC, Tonkin LA, Biggin MD, Eisen MB.

PLoS Biol. 2010 Mar 23;8(3):e1000343. doi: 10.1371/journal.pbio.1000343.

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