Nathan D. Trinklein, Ph.D. - Related publications

Affiliations: 
Stanford University, Palo Alto, CA 
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50 most relevant papers in past 60 days:
Year Citation  Score
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 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 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 Artigas-Jerónimo S, Villar M, Estrada-Peña A, Velázquez-Campoy A, Alberdi P, de la Fuente J. Function of cofactor Akirin2 in the regulation of gene expression in model human Caucasian neutrophil-like HL60 cells. Bioscience Reports. 41. PMID 34291801 DOI: 10.1042/BSR20211120   
2021 Artigas-Jerónimo S, Villar M, Estrada-Peña A, Velázquez-Campoy A, Alberdi P, de la Fuente J. Function of cofactor Akirin2 in the regulation of gene expression in model human Caucasian neutrophil-like HL60 cells. Bioscience Reports. PMID 34223621 DOI: 10.1042/BCJ20210294   
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 Mandla R, Jung C, Vedantham V. Transcriptional and Epigenetic Landscape of Cardiac Pacemaker Cells: Insights Into Cellular Specialization in the Sinoatrial Node. Frontiers in Physiology. 12: 712666. PMID 34335313 DOI: 10.3389/fphys.2021.712666   
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 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 Han M, Liu X, Zhang W, Wang M, Bu W, Chang C, Yu M, Li Y, Tian C, Yang X, Zhu Y, He F. TSMiner: a novel framework for generating time-specific gene regulatory networks from time-series expression profiles. Nucleic Acids Research. PMID 34313778 DOI: 10.1093/nar/gkab629   
2021 Han M, Liu X, Zhang W, Wang M, Bu W, Chang C, Yu M, Li Y, Tian C, Yang X, Zhu Y, He F. TSMiner: a novel framework for generating time-specific gene regulatory networks from time-series expression profiles. Nucleic Acids Research. PMID 34313778 DOI: 10.1093/nar/gkab629   
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 Zhu C, Li Z, Tang Y, Zhang L, Wen J, Wang Z, Su Y, Chen Y, Zhang H. TaWRKY10 plays a key role in the upstream of circadian gene TaLHY in wheat. Plant Science : An International Journal of Experimental Plant Biology. 310: 110973. PMID 34315591 DOI: 10.1016/j.plantsci.2021.110973   
2021 Zhu C, Li Z, Tang Y, Zhang L, Wen J, Wang Z, Su Y, Chen Y, Zhang H. TaWRKY10 plays a key role in the upstream of circadian gene TaLHY in wheat. Plant Science : An International Journal of Experimental Plant Biology. 310: 110973. PMID 34315591 DOI: 10.1016/j.plantsci.2021.110973   
2021 Mellis IA, Edelstein HI, Truitt R, Goyal Y, Beck LE, Symmons O, Dunagin MC, Linares Saldana RA, Shah PP, Pérez-Bermejo JA, Padmanabhan A, Yang W, Jain R, Raj A. Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro. Cell Systems. PMID 34352221 DOI: 10.1016/j.cels.2021.07.003   
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 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 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 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 Tan D, Chen R, Mo Y, Gu S, Ma J, Xu W, Lu X, He H, Jiang F, Fan W, Wang Y, Chen X, Huang W. Quantitative control of noise in mammalian gene expression by dynamic histone regulation. Elife. 10. PMID 34379055 DOI: 10.7554/eLife.65654   
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 Meschichi A, Ingouff M, Picart C, Mirouze M, Desset S, Gallardo F, Bystricky K, Picault N, Rosa S, Pontvianne F. ANCHOR: A Technical Approach to Monitor Single-Copy Locus Localization . Frontiers in Plant Science. 12: 677849. PMID 34295343 DOI: 10.3389/fpls.2021.677849   
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 Hung CH, Lee TL, Huang AY, Yang KC, Shyu YC, Wen SC, Lu MJ, Yuan S, Shen CJ. A Positive Regulatory Feedback Loop between EKLF/KLF1 and TAL1/SCL Sustaining the Erythropoiesis. International Journal of Molecular Sciences. 22. PMID 34360789 DOI: 10.3390/ijms22158024   
2021 Aviña-Padilla K, Ramírez-Rafael JA, Herrera-Oropeza GE, Muley VY, Valdivia DI, Díaz-Valenzuela E, García-García A, Varela-Echavarría A, Hernández-Rosales M. Evolutionary Perspective and Expression Analysis of Intronless Genes Highlight the Conservation of Their Regulatory Role. Frontiers in Genetics. 12: 654256. PMID 34306008 DOI: 10.3389/fgene.2021.654256   
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 Ding P, Sakai T, Shrestha RK, Perez NM, Guo W, Ngou BPM, He S, Liu C, Feng X, Zhang R, Vandepoele K, MacLean D, Jones JDG. Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. Journal of Experimental Botany. PMID 34387350 DOI: 10.1093/jxb/erab373   
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 Liu L, Zhao Q, Cheng C, Yi J, Sun H, Wang Q, Quan W, Xue Y, Sun L, Cong X, Zhang Y. Analysis of Bulk RNA Sequencing Data Reveals Novel Transcription Factors Associated With Immune Infiltration Among Multiple Cancers. Frontiers in Immunology. 12: 644350. PMID 34489925 DOI: 10.3389/fimmu.2021.644350   
2021 Olson AJ, Ware D. Ranked Choice Voting for Representative Transcripts with TRaCE. Bioinformatics (Oxford, England). PMID 34297055 DOI: 10.1093/bioinformatics/btab542   
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 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 Bene K, Halasz L, Nagy L. Transcriptional repression shapes the identity and function of tissue macrophages. Febs Open Bio. PMID 34358410 DOI: 10.1002/2211-5463.13269   
2021 Wang X, Yan J, Shen B, Wei G. Integrated Chromatin Accessibility and Transcriptome Landscapes of Doxorubicin-Resistant Breast Cancer Cells. Frontiers in Cell and Developmental Biology. 9: 708066. PMID 34395436 DOI: 10.3389/fcell.2021.708066   
2021 Qin J, Hu Y, Yao JC, Leung RWT, Zhou Y, Qin Y, Wang J. Cell fate conversion prediction by group sparse optimization method utilizing single-cell and bulk OMICs data. Briefings in Bioinformatics. PMID 34374760 DOI: 10.1093/bib/bbab311   
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 Baralle M, Romano M. Characterization of the human TARDBP gene promoter. Scientific Reports. 11: 10438. PMID 34002018 DOI: 10.1038/s41598-021-89973-z   
2021 Grabowicz IE, Wilczyński B, Kamińska B, Roura AJ, Wojtaś B, Dąbrowski MJ. The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes. Scientific Reports. 11: 15668. PMID 34341417 DOI: 10.1038/s41598-021-95009-3   
2021 Tan K, Song HW, Wilkinson MF. RHOX10 drives mouse spermatogonial stem cell establishment through a transcription factor signaling cascade. Cell Reports. 36: 109423. PMID 34289349 DOI: 10.1016/j.celrep.2021.109423   
2021 Liu X, Tang N, Xu F, Chen Z, Zhang X, Ye J, Liao Y, Zhang W, Kim SU, Wu P, Cao Z. SMRT and Illumina RNA sequencing reveal the complexity of terpenoid biosynthesis in Zanthoxylum armatum. Tree Physiology. PMID 34448876 DOI: 10.1093/treephys/tpab114   
2021 Tak YE, Horng JE, Perry NT, Schultz HT, Iyer S, Yao Q, Zou LS, Aryee MJ, Pinello L, Joung JK. Augmenting and directing long-range CRISPR-mediated activation in human cells. Nature Methods. PMID 34354266 DOI: 10.1038/s41592-021-01224-1   
2021 Ji Q, Zong X, Mao Y, Qian SB. A heat shock-responsive lncRNA acts as a HSF1-directed transcriptional brake via mA modification. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34131081 DOI: 10.1073/pnas.2102175118   
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 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 Zaynab M, Hussain A, Sharif Y, Fatima M, Sajid M, Rehman N, Yang X, Khan KA, Ghramh HA, Li S. Mitogen-Activated Protein Kinase Expression Profiling Revealed Its Role in Regulating Stress Responses in Potato (). Plants (Basel, Switzerland). 10. PMID 34371574 DOI: 10.3390/plants10071371   
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 Wang B, Gong S, Shao W, Han L, Li Z, Zhang Z, Zheng Y, Ouyang F, Ma Y, Xu W, Feng Y. Comprehensive analysis of pivotal biomarkers, immune cell infiltration and therapeutic drugs for steroid-induced osteonecrosis of the femoral head. Bioengineered. 12: 5971-5984. PMID 34488536 DOI: 10.1080/21655979.2021.1972081   
2021 Deng Y, Huang H, Rong Y, Hu S, Hu J, Hu B, He H, Li L, Wang J. Molecular characterization, expression profile and transcriptional regulation of the CYP19 gene in goose ovarian follicles. Gene. 145928. PMID 34455027 DOI: 10.1016/j.gene.2021.145928   
2021 Park J, Yim SS, Wang HH. High-Throughput Transcriptional Characterization of Regulatory Sequences from Bacterial Biosynthetic Gene Clusters. Acs Synthetic Biology. PMID 34288650 DOI: 10.1021/acssynbio.0c00639   
2021 Park J, Yim SS, Wang HH. High-Throughput Transcriptional Characterization of Regulatory Sequences from Bacterial Biosynthetic Gene Clusters. Acs Synthetic Biology. PMID 34288650 DOI: 10.1021/acssynbio.0c00639