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Daniel Luis Vera, Ph.D.

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Schultz MB, Vera D, Sinclair DA. Can artificial intelligence identify effective COVID-19 therapies? EMBO Mol Med. 2020 08 07; 12(8):e12817. PMID: 32569446.
    Citations:    
  2. 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 Biol. 2020 Jul 06; 21(1):165. PMID: 32631399.
    Citations:    
  3. 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. Microbiol Resour Announc. 2020 May 21; 9(21). PMID: 32439680.
    Citations:    
  4. Wheeler E, Brooks AM, Concia L, Vera DL, Wear EE, LeBlanc C, Ramu U, Vaughn MW, Bass HW, Martienssen RA, Thompson WF, Hanley-Bowdoin L. Arabidopsis DNA Replication Initiates in Intergenic, AT-Rich Open Chromatin. Plant Physiol. 2020 05; 183(1):206-220. PMID: 32205451.
    Citations:    
  5. Donovan M, Lynch MDJ, Mackey CS, Platt GN, Washburn BK, Vera DL, Trickey DJ, Charles TC, Wang Z, Jones KM. Metagenome-Assembled Genome Sequences of Five Strains from the Microtus ochrogaster (Prairie Vole) Fecal Microbiome. Microbiol Resour Announc. 2020 Jan 09; 9(2). PMID: 31919172.
    Citations:    
  6. 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 (Zea mays L). Data Brief. 2018 Oct; 20:358-363. PMID: 30175199.
    Citations:    
  7. 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, 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. The maize W22 genome provides a foundation for functional genomics and transposon biology. Nat Genet. 2018 09; 50(9):1282-1288. PMID: 30061736.
    Citations:    Fields:    
  8. Lang J, Cheng Y, Rolfe A, Hammack C, Vera D, Kyle K, Wang J, Meissner TB, Ren Y, Cowan C, Tang H. An hPSC-Derived Tissue-Resident Macrophage Model Reveals Differential Responses of Macrophages to ZIKV and DENV Infection. Stem Cell Reports. 2018 08 14; 11(2):348-362. PMID: 29983385.
    Citations:    Fields:    
  9. 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 Res. 2018 06; 28(6):800-811. PMID: 29735606.
    Citations: 1     Fields:    Translation:AnimalsCells
  10. 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. 2018 04 11; 19(1):131. PMID: 29642840.
    Citations: 1     Fields:    Translation:HumansAnimals
  11. 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. Nat Protoc. 2018 05; 13(5):819-839. PMID: 29599440.
    Citations: 2     Fields:    
  12. D'Alessandro M, Beesley S, Kim JK, Jones Z, Chen R, Wi J, Kyle K, Vera D, Pagano M, Nowakowski R, Lee C. Stability of Wake-Sleep Cycles Requires Robust Degradation of the PERIOD Protein. Curr Biol. 2017 Nov 20; 27(22):3454-3467.e8. PMID: 29103939.
    Citations:    Fields:    Translation:AnimalsCells
  13. Wesolowski S, Vera D, Wu W. SRSF shape analysis for sequencing data reveal new differentiating patterns. Comput Biol Chem. 2017 Oct; 70:56-64. PMID: 28803038.
    Citations:    Fields:    
  14. 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. Exp Hematol. 2017 07; 51:71-82.e3. PMID: 28433605.
    Citations: 5     Fields:    Translation:HumansAnimalsCells
  15. Lang J, Vera D, Cheng Y, Tang H. Modeling Dengue Virus-Hepatic Cell Interactions Using Human Pluripotent Stem Cell-Derived Hepatocyte-like Cells. Stem Cell Reports. 2016 09 13; 7(3):341-354. PMID: 27546535.
    Citations: 4     Fields:    Translation:HumansCells
  16. Rodgers-Melnick E, Vera DL, Bass HW, Buckler ES. Open chromatin reveals the functional maize genome. Proc Natl Acad Sci U S A. 2016 May 31; 113(22):E3177-84. PMID: 27185945.
    Citations: 21     Fields:    Translation:AnimalsCells
  17. Sotolongo-Lopez M, Alvarez-Delfin K, Saade CJ, Vera DL, Fadool JM. Genetic Dissection of Dual Roles for the Transcription Factor six7 in Photoreceptor Development and Patterning in Zebrafish. PLoS Genet. 2016 Apr; 12(4):e1005968. PMID: 27058886.
    Citations: 4     Fields:    Translation:AnimalsCells
  18. 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. 2016 Mar 22; 7(12):13429-45. PMID: 26735342.
    Citations: 4     Fields:    Translation:HumansCells
  19. 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. Dev Biol. 2016 Apr 01; 412(1):57-70. PMID: 26900887.
    Citations: 2     Fields:    Translation:Animals
  20. 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. 2016 Feb 09; 7(6):6460-75. PMID: 26771136.
    Citations: 1     Fields:    Translation:HumansCells
  21. Dileep V, Ay F, Sima J, Vera DL, Noble WS, Gilbert DM. Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program. Genome Res. 2015 Aug; 25(8):1104-13. PMID: 25995270.
    Citations: 29     Fields:    Translation:AnimalsCells
  22. Ren Y, Vera DL, Hughes KA, Dennis JH. Stimulation of the Drosophila immune system alters genome-wide nucleosome occupancy. Genom Data. 2015 Mar; 3:146-7. PMID: 26484165.
    Citations:    
  23. 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. Topologically associating domains are stable units of replication-timing regulation. Nature. 2014 Nov 20; 515(7527):402-5. PMID: 25409831.
    Citations: 164     Fields:    Translation:HumansAnimalsCells
  24. 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. Plant Cell. 2014 Oct; 26(10):3883-93. PMID: 25361955.
    Citations: 21     Fields:    Translation:AnimalsCells
  25. 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 Res. 2014 Feb; 24(2):251-9. PMID: 24310001.
    Citations: 13     Fields:    Translation:HumansCells
  26. Druliner BR, Fincher JA, Sexton BS, Vera DL, Roche M, Lyle S, Dennis JH. Chromatin patterns associated with lung adenocarcinoma progression. . 2013 May 15; 12(10):1536-43. PMID: 23598721.
    Citations: 6     Fields:    Translation:HumansCells
  27. 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 Physiol. 2013 Jun; 162(2):1127-41. PMID: 23572549.
    Citations: 12     Fields:    Translation:HumansAnimalsCells
  28. 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). 2011 Nov; 1(6):437-50. PMID: 22384354.
    Citations: 4     Fields:    
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.