Jordan D. Irvin, Ph.D. - Related publications

Affiliations: 
2005 Pennsylvania State University, State College, PA, United States 
Area:
Biochemistry
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50 most relevant papers in past 60 days:
Year Citation  Score
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 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 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 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 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 Singh NP. Gene regulation: Context is everything. Current Biology : Cb. 31: R1115-R1117. PMID 34637709 DOI: 10.1016/j.cub.2021.08.064   
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 Xia B, Yanai I. Gene expression levels modulate germline mutation rates through the compound effects of transcription-coupled repair and damage. Human Genetics. PMID 34482438 DOI: 10.1007/s00439-021-02355-3   
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 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 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 Yu X, Martin PGP, Zhang Y, Trinidad JC, Xu F, Huang J, Thum KE, Li K, Zhao S, Gu Y, Wang X, Michaels SD. The BORDER family of negative transcription elongation factors regulates flowering time in Arabidopsis. Current Biology : Cb. PMID 34666004 DOI: 10.1016/j.cub.2021.09.074   
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 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 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 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   
2021 Duveau F, Vande Zande P, Metzger BP, Diaz CJ, Walker EA, Tryban S, Siddiq MA, Yang B, Wittkopp PJ. Mutational sources of -regulatory variation affecting gene expression in . Elife. 10. PMID 34463616 DOI: 10.7554/eLife.67806   
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 Pérez-Schindler J, Kohl B, Schneider-Heieck K, Leuchtmann AB, Henríquez-Olguín C, Adak V, Maier G, Delezie J, Sakoparnig T, Vargas-Fernández E, Karrer-Cardel B, Ritz D, Schmidt A, Hondele M, Jensen TE, et al. RNA-bound PGC-1α controls gene expression in liquid-like nuclear condensates. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34465622 DOI: 10.1073/pnas.2105951118   
2021 Giaimo BD, Friedrich T, Borggrefe T. A Comprehensive Toolbox to Analyze Enhancer-Promoter Functions. Methods in Molecular Biology (Clifton, N.J.). 2351: 3-22. PMID 34382181 DOI: 10.1007/978-1-0716-1597-3_1   
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 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 Chu YB, Li J, Jia P, Cui J, Zhang R, Kang X, Lv M, Zhang S. Irf1- and Egr1-activated transcription plays a key role in macrophage polarization: A multiomics sequencing study with partial validation. International Immunopharmacology. 99: 108072. PMID 34426111 DOI: 10.1016/j.intimp.2021.108072   
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 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 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 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 Vu BG, Stamnes MA, Li Y, Rogers PD, Moye-Rowley WS. The Candida glabrata Upc2A transcription factor is a global regulator of antifungal drug resistance pathways. Plos Genetics. 17: e1009582. PMID 34591857 DOI: 10.1371/journal.pgen.1009582   
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 Lozano R, Booth GT, Omar BY, Li B, Buckler ES, Lis JT, Del Carpio DP, Jannink JL. RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants. G3 (Bethesda, Md.). PMID 34499719 DOI: 10.1093/g3journal/jkab273   
2021 Zhang H, Lam J, Zhang D, Lan Y, Vermunt MW, Keller CA, Giardine B, Hardison RC, Blobel GA. CTCF and transcription influence chromatin structure re-configuration after mitosis. Nature Communications. 12: 5157. PMID 34453048 DOI: 10.1038/s41467-021-25418-5   
2021 Lauritsen I, Frendorf PO, Capucci S, Heyde SAH, Blomquist SD, Wendel S, Fischer EC, Sekowska A, Danchin A, Nørholm MHH. Temporal evolution of master regulator Crp identifies pyrimidines as catabolite modulator factors. Nature Communications. 12: 5880. PMID 34620864 DOI: 10.1038/s41467-021-26098-x   
2021 Pardo-Medina J, Gutiérrez G, Limón MC, Avalos J. The lncRNA Is a -Related Regulatory Element with Broad Effects on the Transcriptome. Non-Coding Rna. 7. PMID 34449676 DOI: 10.3390/ncrna7030046   
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 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 Habiba, Xu J, Gad AG, Luo Y, Fan C, Uddin JBG, Ul Ain N, Huang C, Zhang Y, Miao Y, Zheng X. Five Family Members Are Identified as Senescence-Related Genes in Rice by Reverse Genetics Approach. Frontiers in Plant Science. 12: 701529. PMID 34539694 DOI: 10.3389/fpls.2021.701529   
2021 McCann AJ, Lou J, Moustaqil M, Graus MS, Blum A, Fontaine F, Liu H, Luu W, Rudolffi-Soto P, Koopman P, Sierecki E, Gambin Y, Meunier FA, Liu Z, Hinde E, et al. A dominant-negative SOX18 mutant disrupts multiple regulatory layers essential to transcription factor activity. Nucleic Acids Research. PMID 34570228 DOI: 10.1093/nar/gkab820   
2021 Wang J, Wang Y, Zhang J, Ren Y, Li M, Tian S, Yu Y, Zuo Y, Gong G, Zhang H, Guo S, Xu Y. The NAC transcription factor ClNAC68 positively regulates sugar content and seed development in watermelon by repressing ClINV and ClGH3.6. Horticulture Research. 8: 214. PMID 34593776 DOI: 10.1038/s41438-021-00649-1   
2021 Xia S, Ventura IM, Blaha A, Sgromo A, Han S, Izaurralde E, Long M. Rapid Gene evolution in an ancient post-transcriptional and translational regulatory system compensates for meiotic X chromosomal inactivation. Molecular Biology and Evolution. PMID 34626117 DOI: 10.1093/molbev/msab296   
2021 Li J, Xie L, Tian X, Liu S, Xu D, Jin H, Song J, Dong Y, Zhao D, Li G, Li Y, Zhang Y, Zhang Y, Xia X, He Z, et al. TaNAC100 acts as an integrator of seed protein and starch synthesis conferring pleiotropic effects on agronomic traits in wheat. The Plant Journal : For Cell and Molecular Biology. PMID 34492155 DOI: 10.1111/tpj.15485   
2021 Markus BM, Boydston EA, Lourido S. CRISPR-Mediated Transcriptional Repression in Toxoplasma gondii. Msphere. e0047421. PMID 34643425 DOI: 10.1128/mSphere.00474-21   
2021 Dai Z, Ren J, Tong X, Hu H, Lu K, Dai F, Han MJ. The Landscapes of Full-Length Transcripts and Splice Isoforms as Well as Transposons Exonization in the Lepidopteran Model System, . Frontiers in Genetics. 12: 704162. PMID 34594358 DOI: 10.3389/fgene.2021.704162   
2021 Lucas T, Hafer TL, Zhang HG, Molotkova N, Kohwi M. Discrete cis-acting element regulates developmentally timed gene-lamina relocation and neural progenitor competence in vivo. Developmental Cell. PMID 34529940 DOI: 10.1016/j.devcel.2021.08.020   
2021 Liu K, Hu XR, Zhao LX, Wang Y, Deng Z, Tao M. Enhancing Ristomycin A Production by Overexpression of ParB-Like StrR Family Regulators Controlling the Biosynthesis Genes. Applied and Environmental Microbiology. 87: e0106621. PMID 34505824 DOI: 10.1128/AEM.01066-21   
2021 Chen X, Song B, Liu M, Qin L, Dong Z. Understanding the Role of Vib1 in Gene Expression during Cellulose Degradation. Journal of Fungi (Basel, Switzerland). 7. PMID 34436152 DOI: 10.3390/jof7080613   
2021 Magnusson R, Lubovac-Pilav Z. TFTenricher: a python toolbox for annotation enrichment analysis of transcription factor target genes. Bmc Bioinformatics. 22: 440. PMID 34530727 DOI: 10.1186/s12859-021-04357-4   
2021 Bergkessel M. Bacterial transcription during growth arrest. Transcription. 1-18. PMID 34486930 DOI: 10.1080/21541264.2021.1968761   
2021 Falavigna VDS, Severing E, Lai X, Estevan J, Farrera I, Hugouvieux V, Revers LF, Zubieta C, Coupland G, Costes E, Andrés F. Unraveling the role of MADS transcription factor complexes in apple tree dormancy. The New Phytologist. PMID 34480759 DOI: 10.1111/nph.17710   
2021 Chen Y, Wang W, Liu P, Lin A, Fan X, Wu C, Li N, Wei L, Wei D. The novel repressor Rce2 competes with Ace3 to regulate cellulase gene expression in the filamentous fungus Trichoderma reesei. Molecular Microbiology. PMID 34608686 DOI: 10.1111/mmi.14825