Scott D. Pope, Ph.D. - Related publications

Affiliations: 
2009 University of California, Los Angeles, Los Angeles, CA 
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Meléndez-Ramírez C, Cuevas-Diaz Duran R, Barrios-García T, Giacoman-Lozano M, López-Ornelas A, Herrera-Gamboa J, Estudillo E, Soto-Reyes E, Velasco I, Treviño V. Dynamic landscape of chromatin accessibility and transcriptomic changes during differentiation of human embryonic stem cells into dopaminergic neurons. Scientific Reports. 11: 16977. PMID 34417498 DOI: 10.1038/s41598-021-96263-1   
2021 Singh NP. Gene regulation: Context is everything. Current Biology : Cb. 31: R1115-R1117. PMID 34637709 DOI: 10.1016/j.cub.2021.08.064   
2021 Meiler A, Marchiano F, Haering M, Weitkunat M, Schnorrer F, Habermann BH. AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators. Scientific Reports. 11: 15463. PMID 34326396 DOI: 10.1038/s41598-021-94805-1   
2021 Goszczynski DE, Tinetti PS, Choi YH, Hinrichs K, Ross PJ. Genome activation in equine in vitro-produced embryos. Biology of Reproduction. PMID 34515744 DOI: 10.1093/biolre/ioab173   
2021 Gaudet P, Logie C, Lovering RC, Kuiper M, Lægreid A, Thomas PD. Gene Ontology representation for transcription factor functions. Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms. 194752. PMID 34461313 DOI: 10.1016/j.bbagrm.2021.194752   
2021 Sun J, Fahmi NA, Nassereddeen H, Cheng S, Martinez I, Fan D, Yong J, Zhang W. Computational Methods to Study Human Transcript Variants in COVID-19 Infected Lung Cancer Cells. International Journal of Molecular Sciences. 22. PMID 34575842 DOI: 10.3390/ijms22189684   
2021 Yang GH, Fontaine DA, Lodh S, Blumer JT, Roopra A, Davis DB. TCF19 Impacts a Network of Inflammatory and DNA Damage Response Genes in the Pancreatic β-Cell. Metabolites. 11. PMID 34436454 DOI: 10.3390/metabo11080513   
2021 Henderson S, Pullabhatla V, Hertweck A, de Rinaldis E, Herrero J, Lord GM, Jenner RG. The Th1 cell regulatory circuitry is largely conserved between human and mouse. Life Science Alliance. 4. PMID 34531288 DOI: 10.26508/lsa.202101075   
2021 Zhao K, Kong D, Jin B, Smolke CD, Rhee SY. A novel form of bivalent chromatin associates with rapid induction of camalexin biosynthesis genes in response to a pathogen signal in Arabidopsis. Elife. 10. PMID 34523419 DOI: 10.7554/eLife.69508   
2021 Sanson MA, Vega LA, Shah B, Regmi S, Cubria MB, Horstmann N, Shelburne SA, Flores AR. The LiaFSR transcriptome reveals an interconnected regulatory network in group A . Infection and Immunity. IAI0021521. PMID 34370508 DOI: 10.1128/IAI.00215-21   
2021 El-Sappah AH, Yan K, Huang Q, Islam MM, Li Q, Wang Y, Khan MS, Zhao X, Mir RR, Li J, El-Tarabily KA, Abbas M. Comprehensive Mechanism of Gene Silencing and Its Role in Plant Growth and Development. Frontiers in Plant Science. 12: 705249. PMID 34589097 DOI: 10.3389/fpls.2021.705249   
2021 Trevino AE, Müller F, Andersen J, Sundaram L, Kathiria A, Shcherbina A, Farh K, Chang HY, Pașca AM, Kundaje A, Pașca SP, Greenleaf WJ. Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution. Cell. PMID 34390642 DOI: 10.1016/j.cell.2021.07.039   
2021 Ruppert PM, Deng L, Hooiveld GJ, Hangelbroek RW, Zeigerer A, Kersten S. RNA sequencing reveals niche gene expression effects of beta-hydroxybutyrate in primary myotubes. Life Science Alliance. 4. PMID 34407998 DOI: 10.26508/lsa.202101037   
2021 Briggs P, Hunter AL, Yang SH, Sharrocks AD, Iqbal M. PEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals. F1000research. 10: 570. PMID 34504687 DOI: 10.12688/f1000research.53926.1   
2021 Huang X, Zhang X, Zong L, Gao Q, Zhang C, Wei R, Guan Y, Huang L, Zhang L, Lyu G, Tao W. Gene body methylation safeguards ribosomal DNA transcription by preventing PHF6-mediated enrichment of repressive histone mark H4K20me3. The Journal of Biological Chemistry. 101195. PMID 34520760 DOI: 10.1016/j.jbc.2021.101195   
2021 Thomas AL, Marsman J, Antony J, Schierding W, O'Sullivan JM, Horsfield JA. Transcriptional Regulation of : An Informatics Analysis. Genes. 12. PMID 34440349 DOI: 10.3390/genes12081175   
2021 Stec N, Doerfel K, Hills-Muckey K, Ettorre VM, Ercan S, Keil W, Hammell CM. An Epigenetic Priming Mechanism Mediated by Nutrient Sensing Regulates Transcriptional Output during C. elegans Development. Current Biology : Cb. 31: 809-826.e6. PMID 33357451 DOI: 10.1016/j.cub.2020.11.060   
2021 Xie CD, Wang B, Shen ZJ, Yao WY, Ao H, Li B, Pei Y, Zhou R. Validation of the Reference Genes for the Gene Expression Studies in Different Cell Lines of Pig. Biomed Research International. 2021: 5364190. PMID 34458368 DOI: 10.1155/2021/5364190   
2021 Galfrè SG, Morandin F, Pietrosanto M, Cremisi F, Helmer-Citterich M. COTAN: scRNA-seq data analysis based on gene co-expression. Nar Genomics and Bioinformatics. 3: lqab072. PMID 34396096 DOI: 10.1093/nargab/lqab072   
2021 Caba E, Sherman MD, Farizatto KLG, Alcira B, Wang HW, Giardina C, Shin DG, Sandefur CI, Bahr BA. Excitotoxic stimulation activates distinct pathogenic and protective expression signatures in the hippocampus. Journal of Cellular and Molecular Medicine. PMID 34414662 DOI: 10.1111/jcmm.16864   
2021 Wang L, Li JH, Huang HY, Wu Q. [Serial deletions of tandem reverse CTCF sites reveal balanced regulatory landscape of enhancers]. Yi Chuan = Hereditas. 43: 775-791. PMID 34413017 DOI: 10.16288/j.yczz.21-132   
2021 Luo Y, Wang G, Ren T, Zhang T, Chen H, Li Y, Yin X, Zhang Z, Sun Y. Screening of Host Genes Regulated by ID1 and ID3 Proteins During Foot-and-Mouth Disease Virus Infection. Virus Research. 198597. PMID 34648884 DOI: 10.1016/j.virusres.2021.198597   
2021 Dai Z, Li R, Hou Y, Li Q, Zhao K, Li T, Li MJ, Wu X. Inducible CRISPRa screen identifies putative enhancers. Journal of Genetics and Genomics = Yi Chuan Xue Bao. PMID 34531148 DOI: 10.1016/j.jgg.2021.06.012   
2021 Meurer L, Ferdman L, Belcher B, Camarata T. The SIX Family of Transcription Factors: Common Themes Integrating Developmental and Cancer Biology. Frontiers in Cell and Developmental Biology. 9: 707854. PMID 34490256 DOI: 10.3389/fcell.2021.707854   
2021 Channappa M, Sharma S, Kulshreshtha D, Singh K, Bhardwaj SC, Murugasamy S, Sindhu A, Vikas VK, Aggarwal R. Transcriptome profiling and differential gene expression analysis provides insights into 24-based resistance in wheat against . 3 Biotech. 11: 455. PMID 34631354 DOI: 10.1007/s13205-021-02972-9   
2021 Villarroel CA, Bastías M, Canessa P, Cubillos FA. Uncovering Divergence in Gene Expression Regulation in the Adaptation of Yeast to Nitrogen Scarcity. Msystems. 6: e0046621. PMID 34427519 DOI: 10.1128/mSystems.00466-21   
2021 Nair VD, Vasoya M, Nair V, Smith GR, Pincas H, Ge Y, Douglas CM, Esser KA, Sealfon SC. Differential analysis of chromatin accessibility and gene expression profiles identifies cis-regulatory elements in rat adipose and muscle. Genomics. 113: 3827-3841. PMID 34547403 DOI: 10.1016/j.ygeno.2021.09.013   
2021 Tooley JG, Catlin JP, Schaner Tooley CE. CREB-mediated transcriptional activation of NRMT1 drives muscle differentiation. Transcription. 1-17. PMID 34403304 DOI: 10.1080/21541264.2021.1963627   
2021 Wu Y, Kröller L, Miao B, Boekhoff H, Bauer AS, Büchler MW, Hackert T, Giese NA, Taipale J, Hoheisel JD. Promoter Hypermethylation Promotes the Binding of Transcription Factor NFATc1, Triggering Oncogenic Gene Activation in Pancreatic Cancer. Cancers. 13. PMID 34572796 DOI: 10.3390/cancers13184569   
2021 Bonetti A, Kwon AT, Arner E, Carninci P. Analysis of Enhancer-Promoter Interactions using CAGE and RADICL-Seq Technologies. Methods in Molecular Biology (Clifton, N.J.). 2351: 201-210. PMID 34382191 DOI: 10.1007/978-1-0716-1597-3_11   
2021 Graßhoff H, Müller-Fielitz H, Dogbevia GK, Körbelin J, Bannach J, Vahldieck CM, Kusche-Vihrog K, Jöhren O, Müller OJ, Nogueiras R, Prevot V, Schwaninger M. Short regulatory DNA sequences to target brain endothelial cells for gene therapy. Journal of Cerebral Blood Flow and Metabolism : Official Journal of the International Society of Cerebral Blood Flow and Metabolism. 271678X211039617. PMID 34427142 DOI: 10.1177/0271678X211039617   
2021 Zhang J, Le Gras S, Pouxvielh K, Faure F, Fallone L, Kern N, Moreews M, Mathieu AL, Schneider R, Marliac Q, Jung M, Berton A, Hayek S, Vidalain PO, Marçais A, et al. Sequential actions of EOMES and T-BET promote stepwise maturation of natural killer cells. Nature Communications. 12: 5446. PMID 34521844 DOI: 10.1038/s41467-021-25758-2   
2021 Fang Z, Zhao Z, Eapen V, Clarke RA. siRNA Mediate RNA Interference Concordant with Early On-Target Transient Transcriptional Interference. Genes. 12. PMID 34440463 DOI: 10.3390/genes12081290   
2021 Yi F, Hu J, Zhu X, Wang Y, Yu Q, Deng J, Huang X, Ma Y, Xie Y. Transcriptional Profiling of Human Peripheral Blood Mononuclear Cells Stimulated by PPE57 Identifies Characteristic Genes Associated With Type I Interferon Signaling. Frontiers in Cellular and Infection Microbiology. 11: 716809. PMID 34490145 DOI: 10.3389/fcimb.2021.716809   
2021 Ali H, Bhange D, Mehta K, Gohil Y, Prajapati HK, Byrareddy SN, Buch S, Ranga U. An emerging and variant viral promoter of HIV-1 subtype C exhibits low-level gene expression noise. Retrovirology. 18: 27. PMID 34538278 DOI: 10.1186/s12977-021-00572-2   
2021 Shi K, Zhu X, Wu J, Chen Y, Zhang J, Sun X. Centromere protein E as a novel biomarker and potential therapeutic target for retinoblastoma. Bioengineered. 12: 5950-5970. PMID 34482803 DOI: 10.1080/21655979.2021.1972080   
2021 Yang J, Li Q, Du W, Yao Y, Shen G, Jiang W, Pang Y. Genome-Wide Analysis of Glycoside Hydrolase Family 35 Genes and Their Potential Roles in Cell Wall Development in . Plants (Basel, Switzerland). 10. PMID 34451684 DOI: 10.3390/plants10081639   
2021 Wang L, Oh TG, Magida J, Estepa G, Obayomi SMB, Chong LW, Gatchalian J, Yu RT, Atkins AR, Hargreaves D, Downes M, Wei Z, Evans RM. Bromodomain containing 9 (BRD9) regulates macrophage inflammatory responses by potentiating glucocorticoid receptor activity. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34446564 DOI: 10.1073/pnas.2109517118   
2021 Payankaulam S, Hickey SL, Arnosti DN. Cell cycle expression of polarity genes features Rb targeting of Vang. Cells & Development. 169: 203747. PMID 34583062 DOI: 10.1016/j.cdev.2021.203747   
2021 Kumar S, Ruggles A, Logan S, Mazarakis A, Tyson T, Bates M, Grosse C, Reed D, Li Z, Grimwood J, Schmutz J, Saski C. Comparative Transcriptomics of Non-Embryogenic and Embryogenic Callus in Semi-Recalcitrant and Non-Recalcitrant Upland Cotton Lines. Plants (Basel, Switzerland). 10. PMID 34579308 DOI: 10.3390/plants10091775   
2021 Cuesta-Astroz Y, Gischkow Rucatti G, Murgas L, SanMartín CD, Sanhueza M, Martin AJM. Filtering of Data-Driven Gene Regulatory Networks Using as a Case Study. Frontiers in Genetics. 12: 649764. PMID 34394179 DOI: 10.3389/fgene.2021.649764   
2021 Winckers LA, Evelo CT, Willighagen EL, Kutmon M. Investigating the Molecular Processes behind the Cell-Specific Toxicity Response to Titanium Dioxide Nanobelts. International Journal of Molecular Sciences. 22. PMID 34502343 DOI: 10.3390/ijms22179432   
2021 Price EE, Rudra P, Norambuena J, Román-Rodríguez F, Boyd JM. Tools, strains, and strategies to effectively conduct anaerobic and aerobic transcriptional reporter screens and assays in . Applied and Environmental Microbiology. AEM0110821. PMID 34406831 DOI: 10.1128/AEM.01108-21   
2021 Kotarba G, Taracha-Wisniewska A, Miller M, Dabrowski M, Wilanowski T. Transcription factors Krüppel-like factor 4 and paired box 5 regulate the expression of the Grainyhead-like genes. Plos One. 16: e0257977. PMID 34570823 DOI: 10.1371/journal.pone.0257977   
2021 Li Z, Yang J, Peng J, Cheng Z, Liu X, Zhang Z, Bhadauria V, Zhao W, Peng YL. Transcriptional Landscapes of Long Non-coding RNAs and Alternative Splicing in Revealed by RNA-Seq. Frontiers in Plant Science. 12: 723636. PMID 34589103 DOI: 10.3389/fpls.2021.723636   
2021 Nussinov R, Zhang M, Maloney R, Jang H. Ras isoform-specific expression, chromatin accessibility, and signaling. Biophysical Reviews. 13: 489-505. PMID 34466166 DOI: 10.1007/s12551-021-00817-6   
2021 Chung H, Parkhurst CN, Magee EM, Phillips D, Habibi E, Chen F, Yeung BZ, Waldman J, Artis D, Regev A. Joint single-cell measurements of nuclear proteins and RNA in vivo. Nature Methods. 18: 1204-1212. PMID 34608310 DOI: 10.1038/s41592-021-01278-1   
2021 Zhao YP, Shen JL, Li WJ, Wu N, Chen C, Hou YX. Evolutionary and Characteristic Analysis of RING-DUF1117 E3 Ubiquitin Ligase Genes in Discerning the Role of GhRDUF4D in Resistance. Biomolecules. 11. PMID 34439811 DOI: 10.3390/biom11081145   
2021 Jiao F, Lin G, Yu J. Approximating gene transcription dynamics using steady-state formulas. Physical Review. E. 104: 014401. PMID 34412315 DOI: 10.1103/PhysRevE.104.014401   
2021 Luo G, Shen L, Zhao S, Li R, Song Y, Song S, Yu K, Yang W, Li X, Sun J, Wang Y, Gao C, Liu D, Zhang A. Genome-wide identification of seed storage protein gene regulators in wheat through coexpression analysis. The Plant Journal : For Cell and Molecular Biology. PMID 34634158 DOI: 10.1111/tpj.15538