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Items: 14

1.

Longitudinal profiling of the lung microbiome in the AERIS study demonstrates repeatability of bacterial and eosinophilic COPD exacerbations.

Mayhew D, Devos N, Lambert C, Brown JR, Clarke SC, Kim VL, Magid-Slav M, Miller BE, Ostridge KK, Patel R, Sathe G, Simola DF, Staples KJ, Sung R, Tal-Singer R, Tuck AC, Van Horn S, Weynants V, Williams NP, Devaster JM, Wilkinson TMA; AERIS Study Group.

Thorax. 2018 May;73(5):422-430. doi: 10.1136/thoraxjnl-2017-210408. Epub 2018 Jan 31.

2.

Systematic Analysis of Drug Targets Confirms Expression in Disease-Relevant Tissues.

Kumar V, Sanseau P, Simola DF, Hurle MR, Agarwal P.

Sci Rep. 2016 Nov 8;6:36205. doi: 10.1038/srep36205.

3.

MLL1 is essential for the senescence-associated secretory phenotype.

Capell BC, Drake AM, Zhu J, Shah PP, Dou Z, Dorsey J, Simola DF, Donahue G, Sammons M, Rai TS, Natale C, Ridky TW, Adams PD, Berger SL.

Genes Dev. 2016 Feb 1;30(3):321-36. doi: 10.1101/gad.271882.115.

4.

Epigenetic (re)programming of caste-specific behavior in the ant Camponotus floridanus.

Simola DF, Graham RJ, Brady CM, Enzmann BL, Desplan C, Ray A, Zwiebel LJ, Bonasio R, Reinberg D, Liebig J, Berger SL.

Science. 2016 Jan 1;351(6268):aac6633. doi: 10.1126/science.aac6633.

5.

Sphingolipids, Transcription Factors, and Conserved Toolkit Genes: Developmental Plasticity in the Ant Cardiocondyla obscurior.

Schrader L, Simola DF, Heinze J, Oettler J.

Mol Biol Evol. 2015 Jun;32(6):1474-86. doi: 10.1093/molbev/msv039. Epub 2015 Feb 27.

6.

DNA methylation in social insects: how epigenetics can control behavior and longevity.

Yan H, Bonasio R, Simola DF, Liebig J, Berger SL, Reinberg D.

Annu Rev Entomol. 2015 Jan 7;60:435-52. doi: 10.1146/annurev-ento-010814-020803. Epub 2014 Oct 17. Review.

PMID:
25341091
7.

Eusocial insects as emerging models for behavioural epigenetics.

Yan H, Simola DF, Bonasio R, Liebig J, Berger SL, Reinberg D.

Nat Rev Genet. 2014 Oct;15(10):677-88. doi: 10.1038/nrg3787. Epub 2014 Sep 9. Review.

PMID:
25200663
8.

Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality.

Simola DF, Wissler L, Donahue G, Waterhouse RM, Helmkampf M, Roux J, Nygaard S, Glastad KM, Hagen DE, Viljakainen L, Reese JT, Hunt BG, Graur D, Elhaik E, Kriventseva EV, Wen J, Parker BJ, Cash E, Privman E, Childers CP, Muñoz-Torres MC, Boomsma JJ, Bornberg-Bauer E, Currie CR, Elsik CG, Suen G, Goodisman MA, Keller L, Liebig J, Rawls A, Reinberg D, Smith CD, Smith CR, Tsutsui N, Wurm Y, Zdobnov EM, Berger SL, Gadau J.

Genome Res. 2013 Aug;23(8):1235-47. doi: 10.1101/gr.155408.113. Epub 2013 May 1.

9.

Mechanisms and dynamics of orphan gene emergence in insect genomes.

Wissler L, Gadau J, Simola DF, Helmkampf M, Bornberg-Bauer E.

Genome Biol Evol. 2013;5(2):439-55. doi: 10.1093/gbe/evt009.

10.

A chromatin link to caste identity in the carpenter ant Camponotus floridanus.

Simola DF, Ye C, Mutti NS, Dolezal K, Bonasio R, Liebig J, Reinberg D, Berger SL.

Genome Res. 2013 Mar;23(3):486-96. doi: 10.1101/gr.148361.112. Epub 2012 Dec 3.

11.

The genomic impact of 100 million years of social evolution in seven ant species.

Gadau J, Helmkampf M, Nygaard S, Roux J, Simola DF, Smith CR, Suen G, Wurm Y, Smith CD.

Trends Genet. 2012 Jan;28(1):14-21. doi: 10.1016/j.tig.2011.08.005. Epub 2011 Oct 5. Review.

12.

Sniper: improved SNP discovery by multiply mapping deep sequenced reads.

Simola DF, Kim J.

Genome Biol. 2011 Jun 20;12(6):R55. doi: 10.1186/gb-2011-12-6-r55.

13.

Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus.

Vishnoi A, Sethupathy P, Simola D, Plotkin JB, Hannenhalli S.

Mol Biol Evol. 2011 Sep;28(9):2615-27. doi: 10.1093/molbev/msr085. Epub 2011 Apr 3.

14.

Heterochronic evolution reveals modular timing changes in budding yeast transcriptomes.

Simola DF, Francis C, Sniegowski PD, Kim J.

Genome Biol. 2010;11(10):R105. doi: 10.1186/gb-2010-11-10-r105. Epub 2010 Oct 22.

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