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Daniel Vera, Ph.D. - Publications

Affiliations: 
2014 Biological Science Florida State University, Tallahassee, FL, United States 
Area:
Genome regulation
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26 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Hu G, Grover CE, Vera DL, Lung PY, Girimurugan SB, Miller ER, Conover JL, Ou S, Xiong X, Zhu D, Li D, Gallagher JP, Udall JA, Sui X, Zhang J, et al. Evolutionary dynamics of chromatin structure and duplicate gene expression in diploid and allopolyploid cotton. Molecular Biology and Evolution. PMID 38758089 DOI: 10.1093/molbev/msae095  0.736
2022 Park M, Vera D, Kambrianda D, Gajjar P, Cadle-Davidson L, Tsolova V, El-Sharkawy I. Chromosome-level genome sequence assembly and genome-wide association study of Muscadinia rotundifolia reveal the genetics of 12 berry-related traits. Horticulture Research. PMID 35040982 DOI: 10.1093/hr/uhab011  0.432
2021 Savadel SD, Hartwig T, Turpin ZM, Vera DL, Lung PY, Sui X, Blank M, Frommer WB, Dennis JH, Zhang J, Bass HW. The native cistrome and sequence motif families of the maize ear. Plos Genetics. 17: e1009689. PMID 34383745 DOI: 10.1371/journal.pgen.1009689  0.747
2021 Cole L, Kurscheid S, Nekrasov M, Domaschenz R, Vera DL, Dennis JH, Tremethick DJ. Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells. Nature Communications. 12: 2524. PMID 33953180 DOI: 10.1038/s41467-021-22688-x  0.624
2020 Parvathaneni RK, Bertolini E, Shamimuzzaman M, Vera DL, Lung PY, Rice BR, Zhang J, Brown PJ, Lipka AE, Bass HW, Eveland AL. The regulatory landscape of early maize inflorescence development. Genome Biology. 21: 165. PMID 32631399 DOI: 10.1186/S13059-020-02070-8  0.713
2020 Vera DL, Seuylemezian A, Landry KS, Hendrickson R. Draft Genome Sequences of Six Strains Isolated from the InSight Spacecraft and Associated Surfaces Using Oxford Nanopore- and Illumina-Based Sequencing. Microbiology Resource Announcements. 9. PMID 32439680 DOI: 10.1128/MRA.01161-19  0.314
2020 Wheeler E, Brooks AM, Concia L, Vera D, Wear EE, LeBlanc C, Ramu U, Vaughn MW, Bass H, Martienssen R, Thompson WF, Hanley-Bowdoin L. Arabidopsis DNA replication initiates in intergenic, AT-rich open chromatin. Plant Physiology. PMID 32205451 DOI: 10.1104/Pp.19.01520  0.715
2018 Turpin ZM, Vera DL, Savadel SD, Lung PY, Wear EE, Mickelson-Young L, Thompson WF, Hanley-Bowdoin L, Dennis JH, Zhang J, Bass HW. Chromatin structure profile data from DNS-seq: Differential nuclease sensitivity mapping of four reference tissues of B73 maize ( L). Data in Brief. 20: 358-363. PMID 30175199 DOI: 10.1016/J.Dib.2018.08.015  0.755
2018 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, ... ... Vera DL, et al. The maize W22 genome provides a foundation for functional genomics and transposon biology. Nature Genetics. PMID 30061736 DOI: 10.1038/S41588-018-0158-0  0.761
2018 Rivera-Mulia JC, Dimond A, Vera D, Trevilla-Garcia C, Sasaki T, Zimmerman J, Dupont C, Gribnau J, Fraser P, Gilbert DM. Allele-specific control of replication timing and genome organization during development. Genome Research. PMID 29735606 DOI: 10.1101/Gr.232561.117  0.497
2018 Girimurugan SB, Liu Y, Lung PY, Vera DL, Dennis JH, Bass HW, Zhang J. iSeg: an efficient algorithm for segmentation of genomic and epigenomic data. Bmc Bioinformatics. 19: 131. PMID 29642840 DOI: 10.1186/S12859-018-2140-3  0.764
2018 Marchal C, Sasaki T, Vera D, Wilson K, Sima J, Rivera-Mulia JC, Trevilla-García C, Nogues C, Nafie E, Gilbert DM. Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq. Nature Protocols. 13: 819-839. PMID 29599440 DOI: 10.1038/Nprot.2017.148  0.493
2017 Wesolowski S, Vera D, Wu W. SRSF shape analysis for sequencing data reveal new differentiating patterns. Computational Biology and Chemistry. 70: 56-64. PMID 28803038 DOI: 10.1016/J.Compbiolchem.2017.07.004  0.502
2017 Sasaki T, Rivera-Mulia JC, Vera D, Zimmerman J, Das S, Padget M, Nakamichi N, Chang BH, Tyner J, Druker BJ, Weng AP, Civin CI, Eaves CJ, Gilbert DM. Stability of patient-specific features of altered DNA replication timing in xenografts of primary human acute lymphoblastic leukemia. Experimental Hematology. PMID 28433605 DOI: 10.1016/J.Exphem.2017.04.004  0.421
2016 Rodgers-Melnick E, Vera DL, Bass HW, Buckler ES. Open chromatin reveals the functional maize genome. Proceedings of the National Academy of Sciences of the United States of America. PMID 27185945 DOI: 10.1073/Pnas.1525244113  0.763
2016 Lo PK, Huang YC, Poulton JS, Leake N, Palmer WH, Vera D, Xie G, Klusza S, Deng WM. RNA helicase Belle/DDX3 regulates transgene expression in Drosophila. Developmental Biology. PMID 26900887 DOI: 10.1016/J.Ydbio.2016.02.014  0.305
2016 Sexton BS, Druliner BR, Vera DL, Avey D, Zhu F, Dennis JH. Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response. Oncotarget. PMID 26771136 DOI: 10.18632/Oncotarget.6841  0.822
2015 Druliner BR, Vera D, Johnson R, Ruan X, Apone LM, Dimalanta ET, Stewart FJ, Boardman L, Dennis JH. Comprehensive nucleosome mapping of the human genome in cancer progression. Oncotarget. PMID 26735342 DOI: 10.18632/Oncotarget.6811  0.819
2015 Ren Y, Vera DL, Hughes KA, Dennis JH. Stimulation of the Drosophila immune system alters genome-wide nucleosome occupancy. Genomics Data. 3: 146-7. PMID 26484165 DOI: 10.1016/J.Gdata.2015.01.001  0.699
2015 Ren Y, Vera DL, Hughes KA, Dennis JH. Stimulation of the Drosophila immune system alters genome-wide nucleosome occupancy Genomics Data. 3: 146-147. DOI: 10.1016/j.gdata.2015.01.001  0.638
2014 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, et al. Topologically associating domains are stable units of replication-timing regulation. Nature. 515: 402-5. PMID 25409831 DOI: 10.1038/Nature13986  0.602
2014 Vera DL, Madzima TF, Labonne JD, Alam MP, Hoffman GG, Girimurugan SB, Zhang J, McGinnis KM, Dennis JH, Bass HW. Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize. The Plant Cell. 26: 3883-93. PMID 25361955 DOI: 10.1105/Tpc.114.130609  0.799
2014 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. The spring-loaded genome: nucleosome redistributions are widespread, transient, and DNA-directed. Genome Research. 24: 251-9. PMID 24310001 DOI: 10.1101/Gr.160150.113  0.749
2013 Druliner BR, Fincher JA, Sexton BS, Vera DL, Roche M, Lyle S, Dennis JH. Chromatin patterns associated with lung adenocarcinoma progression Cell Cycle. 12: 1536-1543. PMID 23598721 DOI: 10.4161/Cc.24664  0.725
2013 Fincher JA, Vera DL, Hughes DD, McGinnis KM, Dennis JH, Bass HW. Genome-wide prediction of nucleosome occupancy in maize reveals plant chromatin structural features at genes and other elements at multiple scales Plant Physiology. 162: 1127-1141. PMID 23572549 DOI: 10.1104/Pp.113.216432  0.785
2011 Brown AN, Lauter N, Vera DL, McLaughlin-Large KA, Steele TM, Fredette NC, Bass HW. QTL Mapping and Candidate Gene Analysis of Telomere Length Control Factors in Maize (Zea mays L.). G3 (Bethesda, Md.). 1: 437-50. PMID 22384354 DOI: 10.1534/G3.111.000703  0.763
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