Publications

  1. The maize W22 genome provides a foundation for functional genomics and transposon biology. Springer NM, Anderson SN, Andorf CM, Ahern KR, Bai F, Barad O, Barbazuk WB, Bass HW, Baruch K, Ben-Zvi G, Buckler ES, Bukowski R, Campbell MS, Cannon EKS, Chomet P, Dawe RK, Davenport R, Dooner HK, Du LH, Du C, Easterling KA, Gault C, Guan JC, Hunter CT, Jander G, Jiao Y, Koch KE, Kol G, Köllner TG, Kudo T, Li Q, Lu F, Mayfield-Jones D, Mei W, McCarty DR, Noshay JM, Portwood JL 2nd, Ronen G, Settles AM, Shem-Tov D, Shi J, Soifer I, Stein JC, Stitzer MC, Suzuki M, Vera DL, Vollbrecht E, Vrebalov JT, Ware D, Wei S, Wimalanathan K, Woodhouse MR, Xiong W, Brutnell TP. Nat Genet. 2018 Jul 30. doi: 10.1038/s41588-018-0158-0. [Epub ahead of print] PMID:30061736
  2. An hPSC-Derived Tissue-Resident Macrophage Model Reveals Differential Responses of Macrophages to ZIKV and DENV Infection. Lang J, Cheng Y, Rolfe A, Hammack C, Vera D, Kyle K, Wang J, Meissner TB, Ren Y, Cowan C, Tang H. Stem Cell Reports. 2018 Jun 27. pii: S2213-6711(18)30269-8. doi: 10.1016/j.stemcr.2018.06.006. [Epub ahead of print] PMID: 29983385
  3. Allele-specific control of replication timing and genome organization during development. Rivera-Mulia JC, Dimond A, Vera D, Trevilla-Garcia C, Sasaki T, Zimmerman J, Dupont C, Gribnau J, Fraser P, Gilbert DM. Genome Res. 2018 Jun;28(6):800-811. doi: 10.1101/gr.232561.117. Epub 2018 May 7. PMID: 29735606
  4. Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq. Marchal C, Sasaki T, Vera D, Wilson K, Sima J, Rivera-Mulia JC, Trevilla-García C, Nogues C, Nafie E, Gilbert DM. Nat Protoc. 2018 May;13(5):819-839. doi: 10.1038/nprot.2017.148. Epub 2018 Mar 29. PMID: 29599440
  5. Stability of Wake-Sleep Cycles Requires Robust Degradation of the PERIOD Protein. D'Alessandro M, Beesley S, Kim JK, Jones Z, Chen R, Wi J, Kyle K, Vera D, Pagano M, Nowakowski R, Lee C. Curr Biol. 2017 Nov 20;27(22):3454-3467.e8. doi: 10.1016/j.cub.2017.10.014. Epub 2017 Nov 2. PMID: 29103939
  6. SRSF shape analysis for sequencing data reveal new differentiating patterns. Wesolowski S, Vera D, Wu W. Comput Biol Chem. 2017 Oct;70:56-64. doi: 10.1016/j.compbiolchem.2017.07.004. Epub 2017 Jul 27. PMID: 28803038
  7. Modeling Dengue Virus-Hepatic Cell Interactions Using Human Pluripotent Stem Cell-Derived Hepatocyte-like Cells. Lang J, Vera D, Cheng Y, Tang H. Stem Cell Reports. 2016 Sep 13;7(3):341-354. doi: 10.1016/j.stemcr.2016.07.012. Epub 2016 Aug 18. PMID: 27546535
  8. Open chromatin reveals the functional maize genome. Rodgers-Melnick E, Vera DL, Bass HW, Buckler ES. Proc Natl Acad Sci U S A. 2016 May 31;113(22):E3177-84. doi: 10.1073/pnas.1525244113. Epub 2016 May 16. PMID: 27185945
  9. Genetic Dissection of Dual Roles for the Transcription Factor six7 in Photoreceptor Development and Patterning in Zebrafish. Sotolongo-Lopez M, Alvarez-Delfin K, Saade CJ, Vera DL, Fadool JM. PLoS Genet. 2016 Apr 8;12(4):e1005968. doi: 10.1371/journal.pgen.1005968. eCollection 2016 Apr. PMID: 27058886
  10. RNA helicase Belle/DDX3 regulates transgene expression in Drosophila. Lo PK, Huang YC, Poulton JS, Leake N, Palmer WH, Vera D, Xie G, Klusza S, Deng WM. Dev Biol. 2016 Apr 1;412(1):57-70. doi: 10.1016/j.ydbio.2016.02.014. Epub 2016 Feb 18. PMID: 26900887
  11. Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response. Sexton BS, Druliner BR, Vera DL, Avey D, Zhu F, Dennis JH. Oncotarget. 2016 Feb 9;7(6):6460-75. doi: 10.18632/oncotarget.6841. PMID: 26771136
  12. Comprehensive nucleosome mapping of the human genome in cancer progression. Druliner BR, Vera D, Johnson R, Ruan X, Apone LM, Dimalanta ET, Stewart FJ, Boardman L, Dennis JH. Oncotarget. 2016 Mar 22;7(12):13429-45. doi: 10.18632/oncotarget.6811. PMID: 26735342
  13. Stimulation of the Drosophila immune system alters genome-wide nucleosome occupancy. Ren Y, Vera DL, Hughes KA, Dennis JH. Genom Data. 2015 Jan 9;3:146-7. doi: 10.1016/j.gdata.2015.01.001. eCollection 2015 Mar. PMID: 26484165
  14. Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program. Dileep V, Ay F, Sima J, Vera DL, Noble WS, Gilbert DM. Genome Res. 2015 Aug;25(8):1104-13. doi: 10.1101/gr.183699.114. Epub 2015 May 20. PMID: 25995270
  15. Topologically associating domains are stable units of replication-timing regulation. Pope BD, Ryba T, Dileep V, Yue F, Wu W, : 10.1038/nature13986. PMID: 25409831Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, Stamatoyannopoulos JA, Taylor J, Hardison RC, Kahveci T, Ren B, Gilbert DM. Nature. 2014 Nov 20;515(7527):402-5. doi
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