Piero Carninci - Related publications

Affiliations: 
RIKEN Omics, Yokohama-shi, Kanagawa-ken, Japan 
Area:
genomics, RACE, EST
NOTE: We are testing a new system for identifying relevant work based on semantic analysis that identifies similarities between recently published papers and the current author's publications. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches.
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 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 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 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 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 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 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 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 Ahmed FF, Hossen MI, Sarkar MAR, Konak JN, Zohra FT, Shoyeb M, Mondal S. Genome-wide identification of DCL, AGO and RDR gene families and their associated functional regulatory elements analyses in banana (Musa acuminata). Plos One. 16: e0256873. PMID 34473743 DOI: 10.1371/journal.pone.0256873   
2021 Xu GF, Gong CC, Lyu H, Deng HM, Zheng SC. Dynamic transcriptome analysis of Bombyx mori embryonic development. Insect Science. PMID 34388292 DOI: 10.1111/1744-7917.12934   
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 Ramos ML, Park D, Lim J, Park J, Tran K, Garcia EJ, Green E. Adaptive local false discovery rate procedures for highly spiky data and their application RNA sequencing data of yeast SET4 deletion mutants. Biometrical Journal. Biometrische Zeitschrift. PMID 34320248 DOI: 10.1002/bimj.202000256   
2021 Ramos ML, Park D, Lim J, Park J, Tran K, Garcia EJ, Green E. Adaptive local false discovery rate procedures for highly spiky data and their application RNA sequencing data of yeast SET4 deletion mutants. Biometrical Journal. Biometrische Zeitschrift. PMID 34320248 DOI: 10.1002/bimj.202000256   
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 AbuQamar SF, El-Tarabily KA, Sham A. Co-expression Networks in Predicting Transcriptional Gene Regulation. Methods in Molecular Biology (Clifton, N.J.). 2328: 1-11. PMID 34251616 DOI: 10.1007/978-1-0716-1534-8_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 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 Olson AJ, Ware D. Ranked Choice Voting for Representative Transcripts with TRaCE. Bioinformatics (Oxford, England). PMID 34297055 DOI: 10.1093/bioinformatics/btab542   
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 Fan B, Han Y, Yang Y, Zhao X, Tang Y, Li X, Diao Y, Xu B. Transcriptomic analysis of ovarian signaling at the emergence of the embryo from obligate diapause in the American mink (Neovison vison). Animal Reproduction Science. 232: 106823. PMID 34390943 DOI: 10.1016/j.anireprosci.2021.106823   
2021 Zinani OQH, Keseroğlu K, Özbudak EM. Regulatory mechanisms ensuring coordinated expression of functionally related genes. Trends in Genetics : Tig. PMID 34376301 DOI: 10.1016/j.tig.2021.07.008   
2021 Lü BB, Wu GG, Sun Y, Zhang LS, Wu X, Jiang W, Li P, Huang YN, Wang JB, Zhao YC, Liu H, Song LL, Mo Q, Pan AH, Yang Y, et al. Comparative Transcriptome and Endophytic Bacterial Community Analysis of SH. Frontiers in Microbiology. 12: 682356. PMID 34354681 DOI: 10.3389/fmicb.2021.682356   
2021 Sant DW, Sinclair M, Mungall CJ, Schulz S, Zerbino D, Lovering RC, Logie C, Eilbeck K. Sequence ontology terminology for gene regulation. Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms. 194745. PMID 34389511 DOI: 10.1016/j.bbagrm.2021.194745   
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 Zhu D, Ge J, Guo S, Hou L, Shi R, Zhou X, Nie X, Wang X. Independent variations in genome-wide expression, alternative splicing, and DNA methylation in brain tissues among castes of the buff-tailed bumblebee, Bombus terrestris. Journal of Genetics and Genomics = Yi Chuan Xue Bao. PMID 34315685 DOI: 10.1016/j.jgg.2021.04.008   
2021 Zhu D, Ge J, Guo S, Hou L, Shi R, Zhou X, Nie X, Wang X. Independent variations in genome-wide expression, alternative splicing, and DNA methylation in brain tissues among castes of the buff-tailed bumblebee, Bombus terrestris. Journal of Genetics and Genomics = Yi Chuan Xue Bao. PMID 34315685 DOI: 10.1016/j.jgg.2021.04.008   
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 Kang DR, Zhu Y, Li SL, Ai PH, Khan MA, Ding HX, Wang Y, Wang ZC. Transcriptome analysis of differentially expressed genes in chrysanthemum RNA interference lines. Physiology and Molecular Biology of Plants : An International Journal of Functional Plant Biology. 27: 1455-1468. PMID 34366589 DOI: 10.1007/s12298-021-01022-1   
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 Xie S, Zeng Q, Ouyang S, Liang Y, Xiao C. Bioinformatics analysis of epigenetic and SNP-related molecular markers in systemic lupus erythematosus. American Journal of Translational Research. 13: 6312-6329. PMID 34306371   
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 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 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 An B, Kameda T, Imamura T. The evolutionary acquisition and mode of functions of promoter-associated non-coding RNAs (pancRNAs) for mammalian development. Essays in Biochemistry. PMID 34328174 DOI: 10.1042/EBC20200143   
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 Fischer EK, Hauber ME, Bell AM. Back to the basics? Transcriptomics offers integrative insights into the role of space, time and the environment for gene expression and behaviour. Biology Letters. 17: 20210293. PMID 34520681 DOI: 10.1098/rsbl.2021.0293   
2021 Sun Z, Wang X, Wang J, Wang J, Liu X, Huang R, Chen C, Deng M, Wang H, Han F. Key radioresistance regulation models and marker genes identified by integrated transcriptome analysis in nasopharyngeal carcinoma. Cancer Medicine. PMID 34432380 DOI: 10.1002/cam4.4228   
2021 Huang J, Zhang Q, He Y, Liu W, Xu Y, Liu K, Xian F, Li J, Hu J. Genome-Wide Identification, Expansion Mechanism and Expression Profiling Analysis of   Gene Family in Gramineae Crops. International Journal of Molecular Sciences. 22. PMID 34445464 DOI: 10.3390/ijms22168758   
2021 Mehranfard D, Perez G, Rodriguez A, Ladna JM, Neagra CT, Goldstein B, Carroll T, Tran A, Trivedi M, Speth RC. Alterations in Gene Expression of Renin-Angiotensin System Components and Related Proteins in Colorectal Cancer. Journal of the Renin-Angiotensin-Aldosterone System : Jraas. 2021: 9987115. PMID 34285715 DOI: 10.1155/2021/9987115   
2021 Decourty L, Malabat C, Frachon E, Jacquier A, Saveanu C. Investigation of RNA metabolism through large-scale genetic interaction profiling in yeast. Nucleic Acids Research. PMID 34358317 DOI: 10.1093/nar/gkab680   
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 Tu Z, Shen Y, Wen S, Liu H, Wei L, Li H. A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in . Frontiers in Plant Science. 12: 705321. PMID 34367224 DOI: 10.3389/fpls.2021.705321   
2021 Hajirnis N, Mishra RK. Homeotic Genes: Clustering, Modularity, and Diversity. Frontiers in Cell and Developmental Biology. 9: 718308. PMID 34458272 DOI: 10.3389/fcell.2021.718308   
2021 Kattupalli D, Srinivasan A, Soniya EV. A Genome-Wide Analysis of Pathogenesis-Related Protein-1 () Genes from Reveals Its Critical Role during Infection. Genes. 12. PMID 34208836 DOI: 10.3390/genes12071007   
2021 Zogopoulos VL, Saxami G, Malatras A, Angelopoulou A, Jen CH, Duddy WJ, Daras G, Hatzopoulos P, Westhead DR, Michalopoulos I. Coexpression Tool: a tool for gene coexpression analysis in . Iscience. 24: 102848. PMID 34381973 DOI: 10.1016/j.isci.2021.102848   
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 Na Z, Fan L, Wang X. Gene Signatures and Prognostic Values of N6-Methyladenosine Related Genes in Ovarian Cancer. Frontiers in Genetics. 12: 542457. PMID 34484284 DOI: 10.3389/fgene.2021.542457   
2021 Shih CH, Fay J. -regulatory variants affect gene expression dynamics in yeast. Elife. 10. PMID 34369376 DOI: 10.7554/eLife.68469