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Jonathan Hancock Dennis, Ph.D. - Publications

Affiliations: 
Biological Science Florida State University, Tallahassee, FL, United States 
Area:
Genome regulation
Website:
http://www.bio.fsu.edu/faculty-dennis.php
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33 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
2022 Benoit J, Sheikhbahaei MK, Dennis J. Chromatin dynamics: Nucleosome occupancy and sensitivity as determinants of gene expression and cell fate. Journal of Cancer Biology. 2: 51-55. PMID 36066918 DOI: 10.46439/cancerbiology.2.024  0.403
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  0.731
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  0.616
2020 Cole L, Dennis J. MNase Profiling of Promoter Chromatin in -Stimulated GM12878 Cells Reveals Dynamic and Response-Specific Nucleosome Architecture. G3 (Bethesda, Md.). PMID 32404364 DOI: 10.1534/G3.120.401266  0.494
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  0.746
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  0.734
2016 Pulivarthy SR, Lion M, Kuzu G, Matthews AG, Borowsky ML, Morris J, Kingston RE, Dennis JH, Tolstorukov MY, Oettinger MA. Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J recombination. Proceedings of the National Academy of Sciences of the United States of America. PMID 27698124 DOI: 10.1073/Pnas.1605543113  0.658
2016 Dang X, Singh A, Spetman BD, Nolan KD, Isaacs JS, Dennis JH, Dalton S, Marshall AG, Young NL. Label-Free Relative Quantitation of Isobaric and Isomeric Human Histone H2A and H2B Variants by Fourier Transform Ion Cyclotron Resonance Top-Down MS/MS. Journal of Proteome Research. PMID 27431976 DOI: 10.1021/Acs.Jproteome.6B00414  0.359
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  0.812
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  0.814
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  0.681
2015 Brown AN, Vied C, Dennis JH, Bhide PG. Nucleosome Repositioning: A Novel Mechanism for Nicotine- and Cocaine-Induced Epigenetic Changes. Plos One. 10: e0139103. PMID 26414157 DOI: 10.1371/Journal.Pone.0139103  0.487
2015 Lei I, West J, Yan Z, Gao X, Fang P, Dennis JH, Gnatovskiy L, Wang W, Kingston RE, Wang Z. BAF250a regulates nucleosome occupancy and histone modifications in priming embryonic stem cell differentiation. The Journal of Biological Chemistry. PMID 26070559 DOI: 10.1074/Jbc.M115.637389  0.642
2015 Fincher JA, Tyson GS, Dennis JH. DNA-Encoded Chromatin Structural Intron Boundary Signals Identify Conserved Genes with Common Function. International Journal of Genomics. 2015: 167578. PMID 25861617 DOI: 10.1155/2015/167578  0.794
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  0.556
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  0.592
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  0.801
2014 Sexton BS, Druliner BR, Avey D, Zhu F, Dennis JH. Changes in nucleosome occupancy occur in a chromosome specific manner. Genomics Data. 2: 114-116. PMID 25152865 DOI: 10.1016/J.Gdata.2014.06.006  0.749
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  0.762
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  0.736
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  0.776
2012 Takebayashi S, Dileep V, Ryba T, Dennis JH, Gilbert DM. Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding. Proceedings of the National Academy of Sciences of the United States of America. 109: 12574-9. PMID 22807480 DOI: 10.1073/Pnas.1207185109  0.379
2011 Lubelsky Y, Sasaki T, Kuipers MA, Lucas I, Le Beau MM, Carignon S, Debatisse M, Prinz JA, Dennis JH, Gilbert DM. Pre-replication complex proteins assemble at regions of low nucleosome occupancy within the Chinese hamster dihydrofolate reductase initiation zone. Nucleic Acids Research. 39: 3141-55. PMID 21148149 DOI: 10.1093/Nar/Gkq1276  0.422
2011 Druliner BR, Dennis JH. Abstract A36: Identification of chromatin-based patterns across lung cancer grades Cancer Prevention Research. 4. DOI: 10.1158/1940-6207.Prev-11-A36  0.728
2010 Fincher JA, Tyson G, Dennis JH. A computational exploration of gene regulation by nucleosome position 2010 Acm International Conference On Bioinformatics and Computational Biology, Acm-Bcb 2010. 469-471. DOI: 10.1145/1854776.1854860  0.766
2010 Zhang Y, Liu X, Fincher J, Dennis JH. DNA sequence feature selection for intrinsic nucleosome positioning signals using Adaboost 2010 Acm International Conference On Bioinformatics and Computational Biology, Acm-Bcb 2010. 386-389. DOI: 10.1145/1854776.1854836  0.775
2008 Gupta S, Dennis J, Thurman RE, Kingston R, Stamatoyannopoulos JA, Noble WS. Predicting human nucleosome occupancy from primary sequence. Plos Computational Biology. 4: e1000134. PMID 18725940 DOI: 10.1371/Journal.Pcbi.1000134  0.649
2007 Dennis JH, Fan HY, Reynolds SM, Yuan G, Meldrim JC, Richter DJ, Peterson DG, Rando OJ, Noble WS, Kingston RE. Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Genome Research. 17: 928-39. PMID 17568008 DOI: 10.1101/Gr.5636607  0.743
2005 Lee SA, Ndisang D, Patel C, Dennis JH, Faulkes DJ, D'Arrigo C, Samady L, Farooqui-Kabir S, Heads RJ, Latchman DS, Budhram-Mahadeo VS. Expression of the Brn-3b transcription factor correlates with expression of HSP-27 in cancer and is required for maximal activation of the HSP-27 promoter Cancer Research. 65: 3072-3080. PMID 15833836 DOI: 10.1158/0008-5472.Can-04-2865  0.471
2004 Samady L, Dennis J, Budhram-Mahadeo V, Latchman DS. Activation of CDK4 gene expression in human breast cancer cells by the Brn-3b POU family transcription factor. Cancer Biology & Therapy. 3: 317-23. PMID 14726699 DOI: 10.4161/Cbt.3.3.698  0.402
2002 Dennis JH, Budhram-Mahadeo V, Latchman DS. Functional interaction between Brn-3a and Src-1 co-activates Brn-3a-mediated transactivation Biochemical and Biophysical Research Communications. 294: 487-495. PMID 12051737 DOI: 10.1016/S0006-291X(02)00500-4  0.466
2001 Dennis JH, Budhram-Mahadeo V, Latchman DS. The Brn-3b POU family transcription factor regulates the cellular growth, proliferation, and anchorage dependence of MCF7 human breast cancer cells Oncogene. 20: 4961-4971. PMID 11526481 DOI: 10.1038/Sj.Onc.1204491  0.402
1997 Cox JM, Hayward MM, Sanchez JF, Gegnas LD, van der Zee S, Dennis JH, Sigler PB, Schepartz A. Bidirectional binding of the TATA box binding protein to the TATA box. Proceedings of the National Academy of Sciences of the United States of America. 94: 13475-80. PMID 9391050 DOI: 10.1073/Pnas.94.25.13475  0.567
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