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Items: 14


Chromatin structure profile data from DNS-seq: Differential nuclease sensitivity mapping of four reference tissues of B73 maize (Zea mays L).

Turpin ZM, Vera DL, Savadel SD, Lung PY, Wear EE, Mickelson-Young L, Thompson WF, Hanley-Bowdoin L, Dennis JH, Zhang J, Bass HW.

Data Brief. 2018 Aug 10;20:358-363. doi: 10.1016/j.dib.2018.08.015. eCollection 2018 Oct.


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 Sep;50(9):1282-1288. doi: 10.1038/s41588-018-0158-0. Epub 2018 Jul 30.


iSeg: an efficient algorithm for segmentation of genomic and epigenomic data.

Girimurugan SB, Liu Y, Lung PY, Vera DL, Dennis JH, Bass HW, Zhang J.

BMC Bioinformatics. 2018 Apr 11;19(1):131. doi: 10.1186/s12859-018-2140-3.


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.


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.


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.


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.


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.


Topologically associating domains are stable units of replication-timing regulation.

Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas 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: 10.1038/nature13986.


Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize.

Vera DL, Madzima TF, Labonne JD, Alam MP, Hoffman GG, Girimurugan SB, Zhang J, McGinnis KM, Dennis JH, Bass HW.

Plant Cell. 2014 Oct;26(10):3883-93. doi: 10.1105/tpc.114.130609. Epub 2014 Oct 31.


The spring-loaded genome: nucleosome redistributions are widespread, transient, and DNA-directed.

Sexton BS, Avey D, Druliner BR, Fincher JA, Vera DL, Grau DJ, Borowsky ML, Gupta S, Girimurugan SB, Chicken E, Zhang J, Noble WS, Zhu F, Kingston RE, Dennis JH.

Genome Res. 2014 Feb;24(2):251-9. doi: 10.1101/gr.160150.113. Epub 2013 Dec 5.


Chromatin patterns associated with lung adenocarcinoma progression.

Druliner BR, Fincher JA, Sexton BS, Vera DL, Roche M, Lyle S, Dennis JH.

Cell Cycle. 2013 May 15;12(10):1536-43. doi: 10.4161/cc.24664. Epub 2013 Apr 17.


Genome-wide prediction of nucleosome occupancy in maize reveals plant chromatin structural features at genes and other elements at multiple scales.

Fincher JA, Vera DL, Hughes DD, McGinnis KM, Dennis JH, Bass HW.

Plant Physiol. 2013 Jun;162(2):1127-41. doi: 10.1104/pp.113.216432. Epub 2013 Apr 9.


QTL Mapping and Candidate Gene Analysis of Telomere Length Control Factors in Maize (Zea mays L.).

Brown AN, Lauter N, Vera DL, McLaughlin-Large KA, Steele TM, Fredette NC, Bass HW.

G3 (Bethesda). 2011 Nov;1(6):437-50. doi: 10.1534/g3.111.000703. Epub 2011 Nov 1.

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