Zhen Shi, Ph.D. - Related publications

Biological Sciences in Dental Medicine Harvard University, Cambridge, MA, United States 
miRNA, C. elegans development and lifespan
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50 most relevant papers in past 60 days:
Year Citation  Score
2019 Akhtar MM, Micolucci L, Islam MS, Olivieri F, Procopio AD. A Practical Guide to miRNA Target Prediction. Methods in Molecular Biology (Clifton, N.J.). 1970: 1-13. PMID 30963484 DOI: 10.1007/978-1-4939-9207-2_1   
2019 Tomasello L, Cluts L, Croce CM. Experimental Validation of MicroRNA Targets: Mutagenesis of Binding Regions. Methods in Molecular Biology (Clifton, N.J.). 1970: 331-339. PMID 30963501 DOI: 10.1007/978-1-4939-9207-2_18   
2019 Ferreira LRP. MicroRNA Transcriptome Profiling in Heart of Trypanosoma cruzi-Infected Mice. Methods in Molecular Biology (Clifton, N.J.). 1955: 203-214. PMID 30868529 DOI: 10.1007/978-1-4939-9148-8_15   
2019 Guo Z, Cao Y. An lncRNA‑miRNA‑mRNA ceRNA network for adipocyte differentiation from human adipose‑derived stem cells. Molecular Medicine Reports. PMID 30896814 DOI: 10.3892/mmr.2019.10067   
2019 Huang G, Cao M, Huang Z, Xiang Y, Liu J, Wang Y, Wang J, Yang W. Small RNA-sequencing identified the potential roles of neuron differentiation and MAPK signaling pathway in dilated cardiomyopathy. Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie. 108826. PMID 30948207 DOI: 10.1016/j.biopha.2019.108826   
2019 Shu Y, Zhang H, Cai Q, Tang D, Wang G, Liu T, Lv B, Wu H. Integrated mRNA and miRNA expression profile analyses reveal the potential roles of sex-biased miRNA-mRNA pairs in gonad tissues of the Chinese concave-eared torrent frog (Odorrana tormota). Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. PMID 30964604 DOI: 10.1002/jez.b.22851   
2019 Xu P, Palmer LE, Lechauve C, Zhao G, Yao Y, Luan J, Vourekas A, Tan H, Peng J, Scheutz J, Mourelatos Z, Wu G, Weiss MJ, Paralkar VR. Regulation of gene expression by miR-144/451 during mouse erythropoiesis. Blood. PMID 30971389 DOI: 10.1182/blood.2018854604   
2019 Wang LX, Wan C, Dong ZB, Wang BH, Liu HY, Li Y. Integrative Analysis of Long Noncoding RNA (lncRNA), microRNA (miRNA) and mRNA Expression and Construction of a Competing Endogenous RNA (ceRNA) Network in Metastatic Melanoma. Medical Science Monitor : International Medical Journal of Experimental and Clinical Research. 25: 2896-2907. PMID 31004080 DOI: 10.12659/MSM.913881   
2019 Marranci A, D'Aurizio R, Vencken S, Mero S, Guzzolino E, Rizzo M, Pitto L, Pellegrini M, Chiorino G, Greene CM, Poliseno L. Systematic evaluation of the microRNAome through miR-CATCHv2.0 identifies positive and negative regulators of BRAF-X1 mRNA. Rna Biology. PMID 30929607 DOI: 10.1080/15476286.2019.1600934   
2019 Li P, Tian Q, Hu M, Li W, Zhang X, Zeng Y. Cloning, expression, and characterization of the zebrafish Dicer and Drosha enzymes. Biochemical and Biophysical Research Communications. PMID 31029426 DOI: 10.1016/j.bbrc.2019.04.122   
2019 Fung L, Guzman H, Sevrioukov E, Idica A, Park E, Bochnakian A, Daugaard I, Jury D, Mortazavi A, Zisoulis DG, Pedersen IM. miR-128 Restriction of LINE-1 (L1) Retrotransposition Is Dependent on Targeting hnRNPA1 mRNA. International Journal of Molecular Sciences. 20. PMID 31010097 DOI: 10.3390/ijms20081955   
2019 Pitchiaya S, Mourao MDA, Jalihal AP, Xiao L, Jiang X, Chinnaiyan AM, Schnell S, Walter NG. Dynamic Recruitment of Single RNAs to Processing Bodies Depends on RNA Functionality. Molecular Cell. PMID 30952514 DOI: 10.1016/j.molcel.2019.03.001   
2019 Tan Y, Ma Z, Jin Y, Zong R, Wu J, Ren Z. MicroRNA 4651 regulates nonsense-mediated mRNA decay by targeting SMG9 mRNA. Gene. PMID 30902786 DOI: 10.1016/j.gene.2019.03.031   
2019 Luo Q, Cui M, Deng Q, Liu J. Comprehensive analysis of differentially expressed profiles and reconstruction of a competing endogenous RNA network in papillary renal cell carcinoma. Molecular Medicine Reports. PMID 30957192 DOI: 10.3892/mmr.2019.10138   
2019 Nettersheim D, Berger D, Jostes S, Kristiansen G, Lochnit G, Schorle H. N6-Methyladenosine detected in RNA of testicular germ cell tumors is controlled by METTL3, ALKBH5, YTHDC1/F1/F2, and HNRNPC as writers, erasers, and readers. Andrology. PMID 30903744 DOI: 10.1111/andr.12612   
2019 Paul S, Singh M. RFCM3: Computational Method for Identification of miRNA-mRNA Regulatory Modules in Cervical Cancer. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 30990434 DOI: 10.1109/TCBB.2019.2910851   
2019 Li K, Wu Y, Yang H, Hong P, Fang X, Hu Y. H19/miR-30a/C8orf4 axis modulates the adipogenic differentiation process in human adipose tissue-derived mesenchymal stem cells. Journal of Cellular Physiology. PMID 31026067 DOI: 10.1002/jcp.28697   
2019 Bai Y, Long J, Liu Z, Lin J, Huang H, Wang D, Yang X, Miao F, Mao Y, Sang X, Zhao H. Comprehensive analysis of a ceRNA network reveals potential prognostic cytoplasmic lncRNAs involved in HCC progression. Journal of Cellular Physiology. PMID 30916406 DOI: 10.1002/jcp.28522   
2019 Xia X. RNA-Seq approach for accurate characterization of splicing efficiency of yeast introns. Methods (San Diego, Calif.). PMID 30926533 DOI: 10.1016/j.ymeth.2019.03.019   
2019 Bai H, Guo J, Chang C, Guo X, Xu C, Jin W. Comprehensive analysis of lncRNA-miRNA-mRNA during proliferative phase of rat liver regeneration. Journal of Cellular Physiology. PMID 30916358 DOI: 10.1002/jcp.28529   
2019 Shields EJ, Petracovici AF, Bonasio R. lncRedibly versatile: biochemical and biological functions of long noncoding RNAs. The Biochemical Journal. 476: 1083-1104. PMID 30971458 DOI: 10.1042/BCJ20180440   
2019 Guan BG, Cai XX. Abnormal sub-pathways competitively regulated by lncRNAs contribute to postmenopausal osteoporosis. Experimental and Therapeutic Medicine. 17: 2894-2900. PMID 30936959 DOI: 10.3892/etm.2019.7326   
2019 Wu Y, Chen H, Chen Y, Qu L, Zhang E, Wang Z, Wu Y, Yang R, Mao R, Lu C, Fan Y. HPV shapes tumor transcriptome by globally modifying the pool of RNA binding protein-binding motif. Aging. PMID 31039132 DOI: 10.18632/aging.101927   
2019 Hughes CK, Maalouf SW, Liu WS, Pate JL. Molecular profiling demonstrates modulation of immune cell function and matrix remodeling during luteal rescue†. Biology of Reproduction. PMID 30915454 DOI: 10.1093/biolre/ioz037   
2019 Sablok G, Yang K, Wen X. Protocols for miRNA Target Prediction in Plants. Methods in Molecular Biology (Clifton, N.J.). 1970: 65-73. PMID 30963488 DOI: 10.1007/978-1-4939-9207-2_5   
2019 Zhu C, Jin G, Fang P, Zhang Y, Feng X, Tang Y, Qi W, Song R. Maize pentatricopeptide repeat protein DEK41 affects cis-splicing of mitochondrial nad4 intron 3 and seed development. Journal of Experimental Botany. PMID 31020318 DOI: 10.1093/jxb/erz193   
2019 Yu CY, Kuo HC. The emerging roles and functions of circular RNAs and their generation. Journal of Biomedical Science. 26: 29. PMID 31027496 DOI: 10.1186/s12929-019-0523-z   
2019 Hodson DJ, Screen M, Turner M. RNA binding proteins in hematopoiesis and hematological malignancy. Blood. PMID 30967369 DOI: 10.1182/blood-2018-10-839985   
2019 Rennie W, Kanoria S, Liu C, Carmack CS, Lu J, Ding Y. Sfold Tools for MicroRNA Target Prediction. Methods in Molecular Biology (Clifton, N.J.). 1970: 31-42. PMID 30963486 DOI: 10.1007/978-1-4939-9207-2_3   
2019 Jones JL, Hofmann KB, Cowan AT, Temiakov D, Cramer P, Anikin M. Yeast mitochondrial protein Pet111p binds directly to two distinct targets in mRNA, suggesting a mechanism of translational activation. The Journal of Biological Chemistry. PMID 30910813 DOI: 10.1074/jbc.RA118.005355   
2019 Akat KM, Lee YA, Hurley A, Morozov P, Max KE, Brown M, Bogardus K, Sopeyin A, Hildner K, Diacovo TG, Neurath MF, Borggrefe M, Tuschl T. Detection of circulating extracellular mRNAs by modified small-RNA-sequencing analysis. Jci Insight. 5. PMID 30973829 DOI: 10.1172/jci.insight.127317   
2019 Liu X, Schuessler PJ, Sahoo A, Walker SE. Reconstitution and Analyses of RNA Interactions with Eukaryotic Translation Initiation Factors and Ribosomal Preinitiation Complexes. Methods (San Diego, Calif.). PMID 30926531 DOI: 10.1016/j.ymeth.2019.03.024   
2019 Golden CEM, Breen MS, Koro L, Sonar S, Niblo K, Browne A, Burlant N, Di Marino D, De Rubeis S, Baxter MG, Buxbaum JD, Harony-Nicolas H. Deletion of the KH1 Domain of Fmr1 Leads to Transcriptional Alterations and Attentional Deficits in Rats. Cerebral Cortex (New York, N.Y. : 1991). PMID 30877790 DOI: 10.1093/cercor/bhz029   
2019 Pervouchine D, Popov Y, Berry A, Borsari B, Frankish A, Guigó R. Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay. Nucleic Acids Research. PMID 30916337 DOI: 10.1093/nar/gkz193   
2019 Lee SH, Mayr C. Gain of Additional BIRC3 Protein Functions through 3'-UTR-Mediated Protein Complex Formation. Molecular Cell. PMID 30948266 DOI: 10.1016/j.molcel.2019.03.006   
2019 Liao SE, Kandasamy SK, Zhu L, Fukunaga R. DEAD-box RNA helicase Belle post-transcriptionally promotes gene expression in an ATPase activity-dependent manner. Rna (New York, N.Y.). PMID 30979781 DOI: 10.1261/rna.070268.118   
2019 Yan Y, Chen Z, Xiao Y, Wang X, Qian K. Long non-coding RNA SNHG6 is upregulated in prostate cancer and predicts poor prognosis. Molecular Biology Reports. PMID 30911973 DOI: 10.1007/s11033-019-04723-9   
2019 Garvin AJ, Khalaf AHA, Rettino A, Xicluna J, Butler L, Morris JR, Heery DM, Clarke NM. GSK3β-SCFFBXW7α mediated phosphorylation and ubiquitination of IRF1 are required for its transcription-dependent turnover. Nucleic Acids Research. PMID 30854564 DOI: 10.1093/nar/gkz163   
2019 Neumann A, Schindler M, Olofsson D, Wilhelmi I, Schürmann A, Heyd F. Genome-wide identification of alternative splicing events that regulate protein transport across the secretory pathway. Journal of Cell Science. PMID 30890649 DOI: 10.1242/jcs.230201   
2019 Rahman SK, Okazawa H, Chen YW. Frameshift PQBP-1 mutants K192S and R153S implicated in X-linked intellectual disability form stable dimers. Journal of Structural Biology. PMID 30951824 DOI: 10.1016/j.jsb.2019.04.003   
2019 Albaqami M, Laluk K, Reddy ASN. The Arabidopsis splicing regulator SR45 confers salt tolerance in a splice isoform-dependent manner. Plant Molecular Biology. PMID 30968308 DOI: 10.1007/s11103-019-00864-4   
2019 Catalá R, Carrasco-López C, Perea-Resa C, Hernández-Verdeja T, Salinas J. Emerging Roles of LSM Complexes in Posttranscriptional Regulation of Plant Response to Abiotic Stress. Frontiers in Plant Science. 10: 167. PMID 30873189 DOI: 10.3389/fpls.2019.00167   
2019 Liu X, Yao Z, Jin M, Namkoong S, Yin Z, Lee JH, Klionsky DJ. Dhh1 promotes autophagy-related protein translation during nitrogen starvation. Plos Biology. 17: e3000219. PMID 30973873 DOI: 10.1371/journal.pbio.3000219   
2019 Cherry PD, Peach SE, Hesselberth JR. Multiple decay events target mRNA during splicing to regulate the unfolded protein response. Elife. 8. PMID 30874502 DOI: 10.7554/eLife.42262   
2019 Zan XY, Li L. Construction of lncRNA-mediated ceRNA network to reveal clinically relevant lncRNA biomarkers in glioblastomas. Oncology Letters. 17: 4369-4374. PMID 30944630 DOI: 10.3892/ol.2019.10114   
2019 Mockly S, Seitz H. Inconsistencies and Limitations of Current MicroRNA Target Identification Methods. Methods in Molecular Biology (Clifton, N.J.). 1970: 291-314. PMID 30963499 DOI: 10.1007/978-1-4939-9207-2_16   
2019 Reinkemeier CD, Girona GE, Lemke EA. Designer membraneless organelles enable codon reassignment of selected mRNAs in eukaryotes. Science (New York, N.Y.). 363. PMID 30923194 DOI: 10.1126/science.aaw2644   
2019 Singh AK, Choudhury SR, De S, Zhang J, Kissane S, Dwivedi V, Ramanathan P, Petric M, Orsini L, Hebenstreit D, Brogna S. The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from gene loci. Elife. 8. PMID 30907728 DOI: 10.7554/eLife.41444   
2019 Santos DA, Shi L, Tu BP, Weissman JS. Cycloheximide can distort measurements of mRNA levels and translation efficiency. Nucleic Acids Research. PMID 30916348 DOI: 10.1093/nar/gkz205   
2019 Denichenko P, Mogilevsky M, Cléry A, Welte T, Biran J, Shimshon O, Barnabas GD, Danan-Gotthold M, Kumar S, Yavin E, Levanon EY, Allain FH, Geiger T, Levkowitz G, Karni R. Specific inhibition of splicing factor activity by decoy RNA oligonucleotides. Nature Communications. 10: 1590. PMID 30962446 DOI: 10.1038/s41467-019-09523-0