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Eda Yildirim, Ph.D. - Related publications

1998-2005 MCDB University of California, Los Angeles, Los Angeles, CA 
 2006-2014 Molecular Biology Harvard Medical School - Massachusetts General Hospital 
 2014- Cell Biology Duke Medical School, Durham, NC, United States 
Epigenetics; Cell biology
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Kim D, Hong SH, Han G, Cho C. Analysis of mouse male germ cell-specific or -predominant Tex13 family genes encoding proteins with transcriptional repressor activity. Molecular Biology Reports. PMID 33811575 DOI: 10.1007/s11033-021-06265-5   
2021 Yi C, Spitters TW, Al-Far EAA, Wang S, Xiong T, Cai S, Yan X, Guan K, Wagner M, El-Armouche A, Antos CL. A calcineurin-mediated scaling mechanism that controls a K-leak channel to regulate morphogen and growth factor transcription. Elife. 10. PMID 33830014 DOI: 10.7554/eLife.60691   
2021 Kwik M, Hainzl S, Oppelt J, Tichy B, Koller U, Bernardinelli E, Steiner M, Zara G, Nofziger C, Weis S, Paulmichl M, Dossena S, Patsch W, Soyal SM. Selective Activation of CNS and Reference Promoters Is Associated with Distinct Gene Programs Relevant for Neurodegenerative Diseases. International Journal of Molecular Sciences. 22. PMID 33804860 DOI: 10.3390/ijms22073296   
2021 Casas-Tintó S, Ferrús A. The haplolethality paradox of the wupA gene in Drosophila. Plos Genetics. 17: e1009108. PMID 33739971 DOI: 10.1371/journal.pgen.1009108   
2021 Wang L, Jia G, Jiang X, Cao S, Chen ZJ, Song Q. Altered chromatin architecture and gene expression during polyploidization and domestication of soybean. The Plant Cell. PMID 33730165 DOI: 10.1093/plcell/koab081   
2021 Choi J, Lysakovskaia K, Stik G, Demel C, Söding J, Tian TV, Graf T, Cramer P. Evidence for additive and synergistic action of mammalian enhancers during cell fate determination. Elife. 10. PMID 33770473 DOI: 10.7554/eLife.65381   
2021 Reed F, Larsuel ST, Mayday MY, Scanlon V, Krause DS. MRTFA: a critical protein in normal and malignant hematopoiesis and beyond. The Journal of Biological Chemistry. 100543. PMID 33722605 DOI: 10.1016/j.jbc.2021.100543   
2021 Wu B, Jiang X, Huang Y, Ying X, Zhang H, Liu B, Li Z, Qi D, Ji W, Cai X. Integrated Analysis of mRNA-mA-protein Profiles Reveals Novel Insights into the Mechanisms for Cadmium-induced Urothelial Transformation. Biomarkers : Biochemical Indicators of Exposure, Response, and Susceptibility to Chemicals. 1-23. PMID 33830842 DOI: 10.1080/1354750X.2021.1913513   
2021 He H, Yu F, Shen W, Chen K, Zhang L, Lou S, Zhang Q, Chen S, Yuan X, Jia X, Zhou Y. The Novel Key Genes of Non-obstructive Azoospermia Affect Spermatogenesis: Transcriptomic Analysis Based on RNA-Seq and scRNA-Seq Data. Frontiers in Genetics. 12: 608629. PMID 33732283 DOI: 10.3389/fgene.2021.608629   
2021 Zhang L, Zhao J, Bi H, Yang X, Zhang Z, Su Y, Li Z, Zhang L, Sanderson BJ, Liu J, Ma T. Bioinformatic analysis of chromatin organization and biased expression of duplicated genes between two poplars with a common whole-genome duplication. Horticulture Research. 8: 62. PMID 33750794 DOI: 10.1038/s41438-021-00494-2   
2021 Nuñez JK, Chen J, Pommier GC, Cogan JZ, Replogle JM, Adriaens C, Ramadoss GN, Shi Q, Hung KL, Samelson AJ, Pogson AN, Kim JYS, Chung A, Leonetti MD, Chang HY, et al. Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Cell. PMID 33838111 DOI: 10.1016/j.cell.2021.03.025   
2021 Wang Y, Lin W, Brown JE, Chen L, Pandak WM, Hylemon PB, Ren S. 25-hydroxycholesterol 3-sulfate is an endogenous ligand of DNA methyltransferases in hepatocytes. Journal of Lipid Research. 100063. PMID 33705741 DOI: 10.1016/j.jlr.2021.100063   
2021 Crespo NE, Torres-Bracero A, Renta JY, Desnick RJ, Cadilla CL. Expression Profiling Identifies TWIST2 Target Genes in Setleis Syndrome Patient Fibroblast and Lymphoblast Cells. International Journal of Environmental Research and Public Health. 18. PMID 33669496 DOI: 10.3390/ijerph18041997   
2021 He K, Zhang J, Liu J, Cui Y, Liu LG, Ye S, Ban Q, Pan R, Liu D. Functional genomics study of protein inhibitor of activated STAT1 in mouse hippocampal neuronal cells revealed by RNA sequencing. Aging. 13. PMID 33759814 DOI: 10.18632/aging.202749   
2021 Roy S, Huang B, Sinha N, Wang J, Sen A. Androgens regulate ovarian gene expression by balancing Ezh2-Jmjd3 mediated H3K27me3 dynamics. Plos Genetics. 17: e1009483. PMID 33784295 DOI: 10.1371/journal.pgen.1009483   
2021 Roy S, Huang B, Sinha N, Wang J, Sen A. Androgens regulate ovarian gene expression by balancing Ezh2-Jmjd3 mediated H3K27me3 dynamics. Plos Genetics. 17: e1009483. PMID 33784295 DOI: 10.1371/journal.pgen.1009483   
2021 Mayère C, Neirijnck Y, Sararols P, Rands CM, Stévant I, Kühne F, Chassot AA, Chaboissier MC, Dermitzakis ET, Nef S. Single-cell transcriptomics reveal temporal dynamics of critical regulators of germ cell fate during mouse sex determination. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 35: e21452. PMID 33749946 DOI: 10.1096/fj.202002420R   
2021 Kitajima K, Kawahira N, Lee S, Tamura K, Morishita Y, Ohtsuka D. Light-induced local gene expression in primary chick cell culture system. Development, Growth & Differentiation. PMID 33733477 DOI: 10.1111/dgd.12721   
2021 Tian Y, Smith-Bolton RK. Regulation of growth and cell fate during tissue regeneration by the two SWI/SNF chromatin-remodeling complexes of Drosophila. Genetics. 217: 1-16. PMID 33683366 DOI: 10.1093/genetics/iyaa028   
2021 Meng F, Zhao H, Zhu B, Zhang T, Yang M, Li Y, Han Y, Jiang J. Genomic Editing of Intronic Enhancers Unveils Their Role in Fine-Tuning Tissue-Specific Gene Expression in Arabidopsis thaliana. The Plant Cell. PMID 33764459 DOI: 10.1093/plcell/koab093   
2021 Booeshaghi AS, Pachter L. Normalization of single-cell RNA-seq counts by log(x + 1)* or log(1 + x). Bioinformatics (Oxford, England). PMID 33676365 DOI: 10.1093/bioinformatics/btab085   
2021 Zhou Y, Zhang X, Xiong S, Zeng X, Zhang X. Predicted gene 31453 (Gm31453) and the gene encoding carboxypeptidase A5 (Cpa5) are not essential for spermatogenesis and male fertility in the mouse. Reproduction, Fertility, and Development. PMID 33745502 DOI: 10.1071/RD20284   
2021 Jin XH, Zhang YF, Yuan YX, Han L, Zhang GP, Hu H. Isolation, characterization and transcriptome analysis of porcine deltacoronavirus strain HNZK-02 from Henan Province, China. Molecular Immunology. 134: 86-99. PMID 33740580 DOI: 10.1016/j.molimm.2021.03.006   
2021 Carreras D, Martinez-Moreno R, Pinsach-Abuin ML, Santafe MM, Gomà P, Brugada R, Scornik FS, Pérez GJ, Pagans S. Epigenetic Changes Governing Expression in Denervated Skeletal Muscle. International Journal of Molecular Sciences. 22. PMID 33803193 DOI: 10.3390/ijms22052755   
2021 Qiao Y, Zhang B, Liu Y. Identification of Potential Diagnostic Gene Targets for Pediatric Sepsis Based on Bioinformatics and Machine Learning. Frontiers in Pediatrics. 9: 576585. PMID 33748037 DOI: 10.3389/fped.2021.576585   
2021 Gordon MR, Zhu J, Qu V, Li R. A case of convergent-gene interference in the budding yeast knockout library causing chromosome instability. G3 (Bethesda, Md.). PMID 33724427 DOI: 10.1093/g3journal/jkab084   
2021 Gandhi S, Li Y, Tang W, Christensen JB, Urrutia HA, Vieceli FM, Piacentino ML, Bronner ME. A single-plasmid approach for genome editing coupled with long-term lineage analysis in chick embryos. Development (Cambridge, England). PMID 33688075 DOI: 10.1242/dev.193565   
2021 Kim GN, Sung YH. The Genetic Basis of Reporter Mouse Strains. Advances in Experimental Medicine and Biology. 1310: 551-564. PMID 33834450 DOI: 10.1007/978-981-33-6064-8_21   
2021 Garcia-Lozano M, Natarajan P, Levi A, Katam R, Lopez-Ortiz C, Nimmakayala P, Reddy UK. Altered chromatin conformation and transcriptional regulation in watermelon following genome doubling. The Plant Journal : For Cell and Molecular Biology. PMID 33788333 DOI: 10.1111/tpj.15256   
2021 Zhou Y, Sharpee TO. Hyperbolic geometry of gene expression. Iscience. 24: 102225. PMID 33748711 DOI: 10.1016/j.isci.2021.102225   
2021 Zhou Y, Sharpee TO. Hyperbolic geometry of gene expression. Iscience. 24: 102225. PMID 33748711 DOI: 10.1016/j.isci.2021.102225   
2021 Singh D, Yi SV. Enhancer pleiotropy, gene expression, and the architecture of human enhancer-gene interactions. Molecular Biology and Evolution. PMID 33749795 DOI: 10.1093/molbev/msab085   
2021 Hang D, Yan L, Shunchun L, Lei L, Juanyan W, Zhijie Z, Qichun P, Nan L, Xiangqian Z. Effect of extensin-like OsPEX1 on pollen fertility in rice. Yi Chuan = Hereditas. 43: 271-279. PMID 33724211 DOI: 10.16288/j.yczz.20-296   
2021 Rashid M, Shah SG, Verma T, Chaudhary N, Sukanya, Patel VB, Gera PB, Smoot D, Ashaktorab H, Dalal SN, Gupta S. Tumor-specific overexpression of histone gene, H3C14 in gastric cancer is mediated through EGFR-FOXC1 axis. Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms. 194703. PMID 33727172 DOI: 10.1016/j.bbagrm.2021.194703   
2021 Li F, Hu D, Dieter C, Ansong C, Sussel L, Orr G. Single Molecule-based FliFISH Validates Radial and Heterogeneous Gene Expression Patterns in Pancreatic Islet β Cells. Diabetes. PMID 33685924 DOI: 10.2337/db20-0802   
2021 Abbas F, Ke Y, Zhou Y, Yu Y, Waseem M, Ashraf U, Wang C, Wang X, Li X, Yue Y, Yu R, Fan Y. Genome-Wide Analysis Reveals the Potential Role of MYB Transcription Factors in Floral Scent Formation in . Frontiers in Plant Science. 12: 623742. PMID 33719296 DOI: 10.3389/fpls.2021.623742   
2021 Wang G, Xia B, Zhou M, Lv J, Zhao D, Li Y, Bu Y, Wang X, Cooke JP, Cao Q, Gyu Lee M, Zhang L, Chen K. MACMIC Reveals A Dual Role of CTCF in Epigenetic Regulation of Cell Identity Genes. Genomics, Proteomics & Bioinformatics. PMID 33677108 DOI: 10.1016/j.gpb.2020.10.008   
2021 Shehzad M, Zhou Z, Ditta A, Khan M, Cai X, Xu Y, Maqbool A, Khalofah A, Shaban M, Naeem M, Ansari MJ, Wang K, Liu F. Identification and characterization of genes related to salt stress tolerance within segregation distortion regions of genetic map in F2 population of upland cotton. Plos One. 16: e0247593. PMID 33770112 DOI: 10.1371/journal.pone.0247593   
2021 Mark KG, Rape M. Ubiquitin-dependent regulation of transcription in development and disease. Embo Reports. e51078. PMID 33779035 DOI: 10.15252/embr.202051078   
2021 Bhatia S, Kumar H, Mahajan M, Yadav S, Saini P, Yadav S, Sahu SK, Sundaram JK, Yadav RK. A cellular expression map of epidermal and subepidermal cell layer-enriched transcription factor genes integrated with the regulatory network in Arabidopsis shoot apical meristem. Plant Direct. 5: e00306. PMID 33748654 DOI: 10.1002/pld3.306   
2021 Tang D, Zhang Z, Zboril E, Wetzel MD, Xu X, Zhang W, Chen L, Liu Z. Pontin Functions as A Transcriptional Co-activator for Retinoic Acid-induced HOX Gene Expression. Journal of Molecular Biology. 166928. PMID 33713676 DOI: 10.1016/j.jmb.2021.166928   
2021 Liu J, Han J, Sharma A, Wai CM, Ming R, Yu Q. Transcriptional regulation of dosage compensation in Carica papaya. Scientific Reports. 11: 5854. PMID 33712672 DOI: 10.1038/s41598-021-85480-3   
2021 Zhang X, Lv S, Luo Z, Hu Y, Peng X, Lv J, Zhao S, Feng J, Huang G, Wan QL, Liu J, Huang H, Luan B, Wang D, Zhao X, et al. MiniCAFE, a CRISPR/Cas9-based compact and potent transcriptional activator, elicits gene expression in vivo. Nucleic Acids Research. PMID 33751124 DOI: 10.1093/nar/gkab174   
2021 Rodríguez-Gómez G, Paredes-Villa A, Cervantes-Badillo MG, Gómez-Sonora JP, Jorge-Pérez JH, Cervantes-Roldán R, León-Del-Río A. Tristetraprolin: A cytosolic regulator of mRNA turnover moonlighting as transcriptional corepressor of gene expression. Molecular Genetics and Metabolism. PMID 33795191 DOI: 10.1016/j.ymgme.2021.03.015   
2021 Elgaabari A, Miyawaki-Kuwakado A, Tomimatsu K, Wu Q, Tokunaga K, Izumi W, Suzuki T, Tatsumi R, Nakamura M. Epigenetic effects induced by the ectopic expression of Pax7 in 3T3-L1. Journal of Biochemistry. PMID 33729538 DOI: 10.1093/jb/mvab030   
2021 Keshavarz M, Tautz D. The imprinted lncRNA regulates sexual preference and the sex-specific brain transcriptome in mice. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33658376 DOI: 10.1073/pnas.2022172118   
2021 Hansen J, von Melchner H, Wurst W. Mutant non-coding RNA resource in mouse embryonic stem cells. Disease Models & Mechanisms. 14. PMID 33729986 DOI: 10.1242/dmm.047803   
2021 Akash, Parida AP, Srivastava A, Mathur S, Sharma AK, Kumar R. Identification, evolutionary profiling, and expression analysis of F-box superfamily genes under phosphate deficiency in tomato. Plant Physiology and Biochemistry : Ppb. 162: 349-362. PMID 33730620 DOI: 10.1016/j.plaphy.2021.03.002   
2021 Haellman V, Saxena P, Jiang Y, Fussenegger M. Rational design and optimization of synthetic gene switches for controlling cell-fate decisions in pluripotent stem cells. Metabolic Engineering. 65: 99-110. PMID 33744461 DOI: 10.1016/j.ymben.2021.03.009   
2021 Zhang B, Chen Z, Wang Y, Fan G, He X. Integrated bioinformatics analysis for the identification of key genes and signaling pathways in thyroid carcinoma. Experimental and Therapeutic Medicine. 21: 298. PMID 33717241 DOI: 10.3892/etm.2021.9729