Archives of Advances in Biosciences

Velculescu VE, Zhang L, Vogelstein B,

Kinzler KW. Serial analysis of gene

expression. Science. 1995;270(5235):484-7. [DOI: 10.1126/science.270.5235.484]

Cai Y, Yu X, Hu S, Yu J. A brief review on the mechanisms of miRNA regulation. Genomics, proteomics & bioinformatics. 2009;7(4):147-54. [DOI: 10.1016/S1672-0229(08)60044-3]

Chen L, Heikkinen L, Wang C, Yang Y, Sun H, Wong G. Trends in the development of miRNA bioinformatics tools. Briefings in bioinformatics. 2019;20(5):1836-52. [DOI: 10.1093/bib/bby054 ]

. Jonas S, Izaurralde E. Towards a molecular understanding of microRNA-mediated gene silencing. Nature reviews genetics. 2015;16(7):421-33. [DOI: 10.1038/nrg3965]

Dexheimer PJ, Cochella L. MicroRNAs: From Mechanism to Organism. Front Cell Dev Biol. 2020;8:409. [DOI: 10.3389/fcell.2020.00409] [PMID] [PMCID]

Fugl A, Andersen CL. Epstein-Barr virus and its association with disease - a review of relevance to general practice. BMC Fam Pract. 2019;20(1):62. [DOI: 10.1186/s12875-019-0954-3] [PMID] [PMCID]

Smatti MK, Al-Sadeq DW, Ali NH, Pintus G, Abou-Saleh H, Nasrallah GK. Epstein-Barr Virus Epidemiology, Serology, and Genetic Variability of LMP-1 Oncogene Among Healthy Population: An Update. Front Oncol. 2018;8:211. [DOI: 10.3389/fonc.2018.00211] [PMID] [PMCID]

Pattle SB, Farrell PJ. The role of Epstein-Barr virus in cancer. Expert Opin Biol Ther. 2006;6(11):1193-205. [DOI: 10.1517/14712598.6.11.1193] [PMID]

Kutok JL, Wang F. Spectrum of Epstein-Barr virus-associated diseases. Annu Rev Pathol. 2006;1:375-404. [DOI: 10.1146/annurev.pathol.1.110304.100209] [PMID]

Jha HC, Pei Y, Robertson ES. Epstein-Barr Virus: Diseases Linked to Infection and Transformation. Front Microbiol. 2016;7:1602. [DOI: 10.3389/fmicb.2016.01602] [PMID] [PMCID]

Prasad A, Sharma N, Prasad M. Noncoding but Coding: Pri-miRNA into the Action. Trends Plant Sci. 2021;26(3):204-206. [DOI: 10.1016/j.tplants.2020.12.004 ] [PMID]

Krol J, Sobczak K, Wilczynska U, Drath M, Jasinska A, Kaczynska D, Krzyzosiak WJ. Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design. J Biol Chem. 2004;279(40):42230-9. [DOI: 10.1074/jbc.M404931200] [PMID]

Huang Y, Shen XJ, Zou Q, Wang SP, Tang SM, Zhang GZ. Biological functions of microRNAs: a review. J Physiol Biochem. 2011;67(1):129-39. [DOI:10.1007/s13105-010-0050-6] [PMID]

Gomes CP, Cho JH, Hood L, Franco OL, Pereira RW, Wang K. A review of computational tools in microRNA discovery. Frontiers in genetics. 2013;4:81. [DOI: 10.3389/fgene.2013.00081]

Tav C, Tempel S, Poligny L, Tahi F. miRNAFold: a web server for fast miRNA precursor prediction in genomes. Nucleic acids research. 2016;44(W1):W181-4. [DOI: 10.1093/nar/gkw459]

Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 2006;34:D140-4. [DOI: 10.1093/nar/gkj112] [PMID] [PMCID]

Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res. 2003;31(13):3429-31. [DOI: 10.1093/nar/gkg599] [PMID] [PMCID]

Wang X. miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA. 2008;14(6):1012-7. [DOI: 10.1261/rna.965408] [PMID] [PMCID]

Stelzer G, Dalah I, Stein TI, Satanower Y, Rosen N, Nativ N, Oz-Levi D, Olender T, Belinky F, Bahir I, Krug H. In-silico human genomics with GeneCards. Human genomics. 2011;5(6):1-9. [DOI: 10.1186/1479-7364-5-6-709]

Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T, Rattei T, et al. The dynamic genome of Hydra. Nature. 2010;464(7288):592-6. [DOI: 10.1038/nature08830] [PMID] [PMCID]

Hearn JP. The common marmoset (Callithrix jacchus). InReproduction in new world primates: new models in medical science.Springer. 1983: 181-215. [DOI: 10.1007/978-94-009-7322-0_6]

Yu Y, Wang J, Khaled W, Burke S, Li P, Chen X, Yang W, Jenkins NA, Copeland NG, Zhang S, Liu P. Bcl11a is essential for lymphoid development and negatively regulates p53. J Exp Med. 2012;209(13):2467-83. [DOI: 10.1084/jem.20121846] [PMID] [PMCID]

Satterwhite E, Sonoki T, Willis TG, Harder L, Nowak R, Arriola EL, Liu H, Price HP, Gesk S, Steinemann D, Schlegelberger B. The BCL11 gene family: involvement of BCL11A in lymphoid malignancies. Blood, The Journal of the American Society of Hematology. 2001;98(12):3413-20. [DOI: 10.1182/blood.v98.12.3413]

Tao H, Ma X, Su G, Yin J, Xie X, Hu C, Chen Z, Tan D, et al. BCL11A expression in acute myeloid leukemia. Leuk Res. 2016;41:71-5. [DOI: 10.1016/j.leukres.2015.12.001] [PMID]

Zhu H, He LY, Lin KS, Li C. Circular RNA cAGBL3 as an epithelial-mesenchymal transition trigger of liver cancer. American Society of Clinical Oncology.2016;34(15) [DOI: 10.1200/JCO.2016.34.15_suppl.e23245]

Zhou YY, Zou Y, Chen T, Wang HW, Han MF, Pi B, et al. KCTD9, a novel potassium channel related gene, was highly expressed in hepatic NK cells and T cells of fulminant hepatitis mice induced by MHV-3. Zhonghua Gan Zang Bing Za Zhi. 2011;19(11):833-7. [DOI: 10.3760/cma.j.issn.1007-3418.2011.11.010 ] [PMID]

Sleiman PM, Flory J, Imielinski M, Bradfield JP, Annaiah K, Willis-Owen SA et al. Variants of DENND1B associated with asthma in children. N Engl J Med. 2010;362(1):36-44. [DOI: 10.1056/NEJMoa0901867 ] [PMID]

Lagathu C, Christodoulides C, Virtue S, Cawthorn WP, Franzin C, Kimber WA, Dact1, a nutritionally regulated preadipocyte gene, controls adipogenesis by coordinating the Wnt/beta-catenin signaling network. Diabetes. 2009;58(3):609-19. [DOI: 10.2337/db08-1180] [PMID]

Austin S, Nowikovsky K. LETM1: essential for mitochondrial biology and cation homeostasis?. Trends in biochemical sciences. 2019;44(8):648-58. [DOI:10.1016/j.tibs.2019.04.002]

Osipovich AB, Gangula R, Vianna PG, Magnuson MA. Setd5 is essential for mammalian development and the co-transcriptional regulation of histone acetylation. Development. 2016;143(24):4595-4607. [DOI: 10.1242/dev.141465 ] [PMID] [PMCID]

Kurihara Y, Tokuriki M, Myojin R, Hori T, Kuroiwa A, Matsuda Y, Sakurai T, Kimura M, Hecht NB, Uesugi S. CPEB2, a novel putative translational regulator in mouse haploid germ cells. Biol Reprod. 2003;69(1):261-8. [DOI: 10.1095/biolreprod.103.015677 ] [PMID]

McIntyre RE, Nicod J, Robles-Espinoza CD, Maciejowski J, Cai N, Hill J,et al. A Genome-Wide Association Study for Regulators of Micronucleus Formation in Mice. G3 (Bethesda). 2016;6(8):2343-54. [DOI: 10.1534/g3.116.030767 ] [PMID] [PMCID]

Suryavathi V, Panneerdoss S, Wolkowicz MJ, Shetty J, Sherman NE, Flickinger CJ, Herr JC. Dynamic changes in equatorial segment protein 1 (SPESP1) glycosylation during mouse spermiogenesis.

Biology of reproduction. 2015;92(5):129-. [DOI: 10.1095/biolreprod.114.121095]

Dong X, Park S, Lin X, Copps K, Yi X, White MF. Irs1 and Irs2 signaling is essential for hepatic glucose homeostasis and systemic growth. J Clin Invest. 2006;116(1):101-14. [DOI: 10.1172/JCI25735 ] [PMID] [PMCID]

Feng L, Wang JT, Jin H, Qian K, Geng JG. SH3KBP1‐binding protein 1 prevents epidermal growth factor receptor degradation by the interruption of c‐Cbl‐CIN85 complex. Cell biochemistry and function. 2011;29(7):589-96. [DOI: 10.1002/cbf.1792]

Arnold MA, Kim Y, Czubryt MP, Phan D, McAnally J, Qi X, Shelton JM, Richardson JA, Bassel-Duby R, Olson EN. MEF2C transcription factor controls chondrocyte hypertrophy and bone development. Dev Cell. 2007;12(3):377-89. [DOI: 10.1016/j.devcel.2007.02.004] [PMID]

Shetty PB, Tang H, Tayo BO, Morrison AC, Hanis CL, Rao DC, et al.Variants in CXADR and F2RL1 are associated with blood pressure and obesity in African-Americans in regions identified through admixture mapping. J Hypertens. 2012;30(10):1970-6. [DOI: 10.1097/HJH.0b013e3283578c80 ] [PMID] [PMCID]

Søgaard R, Ljungstrøm T, Pedersen KA, Olesen SP, Jensen BS. KCNQ4 channels expressed in mammalian cells: functional characteristics and pharmacology. American Journal of Physiology-Cell Physiology. 2001;280(4):C859-66. [DOI:10.1152/ajpcell.2001.280.4.C859]

Sha J, Han Q, Chi C, Zhu Y, Pan J, Dong B, Huang Y, Xia W, Xue W. PRKAR2B promotes prostate cancer metastasis by activating Wnt/β‐catenin and inducing epithelial‐mesenchymal transition. Journal of cellular biochemistry. 2018;119(9):7319-27. [DOI: 10.1002/jcb.27030 ]

Cory S, Adams JM. The Bcl2 family: regulators of the cellular life-or-death switch. Nat Rev Cancer. 2002;2(9):647-56. [DOI: 10.1038/nrc883 ] [PMID]

Piazzon N, Maisonneuve C, Guilleret I, Rotman S, Constam DB. Bicc1 links the regulation of cAMP signaling in polycystic kidneys to microRNA-induced gene silencing. J Mol Cell Biol. 2012;4(6):398-408. [DOI: 10.1093/jmcb/mjs027] [PMID]

Takahashi Y, Koyanagi T, Suzuki Y, Saga Y, Kanomata N, Moriya T, Suzuki M, Sato Y. Vasohibin-2 expressed in human serous ovarian adenocarcinoma accelerates tumor growth by promoting angiogenesis. Mol Cancer Res. 2012;10(9):1135-46. [DOI:10.1158/1541-7786.mcr-12-0098-t] [PMID]

Kon S, Tanabe K, Watanabe T, Sabe H, Satake M. Clathrin dependent endocytosis of E-cadherin is regulated by the Arf6GAP isoform SMAP1. Exp Cell Res. 2008;314(7):1415-28. [DOI: 10.1016/j.yexcr.2007.11.006] [PMID]

van der Schoot V, de Munnik S, Venselaar H, Elting M, Mancini GMS, Ravenswaaij-Arts CMA, et al. Toward clinical and molecular understanding of pathogenic variants in the ZBTB18 gene. Mol Genet Genomic Med. 2018;6(3):393-400. [DOI: 10.1002/mgg3.387] [PMID] [PMCID]

Janssen B, Hohenadel D, Brinkkoetter P, Peters V, Rind N, Fischer C,et al. Carnosine as a protective factor in diabetic nephropathy: association with a leucine repeat of the carnosinase gene CNDP1. Diabetes. 2005;54(8):2320-7. [DOI: 10.2337/diabetes.54.8.2320] [PMID]

Sato K, Koyama T, Shichiri M. Biosynthesis and secretion of salusin-alpha from human cells. Peptides. 2008;29(12):2203-7. [DOI: 10.1016/j.peptides.2008.08.015 ] [PMID]

Istvánffy R, Vogt Weisenhorn DM, Floss T, Wurst W. Expression of neurochondrin in the developing and adult mouse brain. Dev Genes Evol. 2004;214(4):206-9. [DOI: 10.1007/s00427-004-0396-2] [PMID]

Gum JR Jr, Crawley SC, Hicks JW, Szymkowski DE, Kim YS. MUC17, a novel membrane-tethered mucin. Biochem Biophys Res Commun. 2002;291(3):466-75. [DOI: 10.1006/bbrc.2002.6475] [PMID]

Aruffo A, Stamenkovic I, Melnick M, Underhill CB, Seed B. CD44 is the principal cell surface receptor for hyaluronate. Cell. 1990;61(7):1303-13. [DOI: 10.1016/0092-8674(90)90694-a]

Magno L, Lessard CB, Martins M, Lang V, Cruz P, Asi Y,et al. Whiting PJ. Alzheimer's disease phospholipase C-gamma-2 (PLCG2) protective variant is a functional hypermorph. Alzheimers Res Ther. 2019;11(1):16. [DOI: 10.1186/s13195-019-0469-0] [PMID] [PMCID]

Siomi MC, Siomi H, Sauer WH, Srinivasan S, Nussbaum RL, Dreyfuss G. FXR1, an autosomal homolog of the fragile X mental retardation gene. EMBO J. 1995;14(11):2401-8. [DOI: 10.1002/j.1460-2075.1995.tb07237.x] [PMID] [PMCID]

Shiga A, Ishihara T, Miyashita A, Kuwabara M, Kato T, Watanabe N,et al. Alteration of POLDIP3 splicing associated with loss of function of TDP-43 in tissues affected with ALS. PLoS One. 2012;7(8):e43120. [DOI: 10.1371/journal.pone.0043120] [PMID] [PMCID]

Khan IM, Fisher RA, Johnson KJ, Bailey ME, Siciliano MJ, Kessling AM, Farrer M, Carritt B, Kamalati T, Buluwela L. The SON gene encodes a conserved DNA binding protein mapping to human chromosome 21. Ann Hum Genet. 1994;58(1):25-34. [DOI: 10.1111/j.1469-1809.1994.tb00723.x] [PMID]

Ramocki MB, Bartnik M, Szafranski P, Kołodziejska KE, Xia Z, Bravo J,et al. Recurrent distal 7q11.23 deletion including HIP1 and YWHAG identified in patients with intellectual disabilities, epilepsy, and neurobehavioral problems. Am J Hum Genet. 2010;87(6):857-65. [DOI: 10.1016/j.ajhg.2010.10.019]

Meeson AP, Shi X, Alexander MS, Williams RS, Allen RE, Jiang N, Adham IM, et al. Sox15 and Fhl3 transcriptionally coactivate Foxk1 and regulate myogenic progenitor cells. The EMBO journal. 2007;26(7):1902-12. [DOI: 10.1038/sj.emboj.7601635]

Ghanta KS, Li DQ, Eswaran J, Kumar R. Gene profiling of MTA1 identifies novel gene targets and functions. PLoS One. 2011;6(2):e17135. [DOI: 10.1371/journal.pone.0017135] [PMID] [PMCID]

Jiang R, Zhou Z, Liao Y, Yang F, Cheng Y, Huang J, Wang J, Chen H, Zhu T, Chao J. The emerging roles of a novel CCCH-type zinc finger protein, ZC3H4, in silica-induced epithelial to mesenchymal transition. Toxicol Lett. 2019;307:26-40. [DOI:10.1016/j.toxlet.2019.02.014] [PMID]

Al Eissa M, Fiorentino A, Sharp S, O’Brien NL, Giaroli G, Wolf K, Bass NJ, McQuillin A, Curtis D. Potential involvement of a CLSTN3 variant in susceptibility to schizophrenia. European Neuropsychopharmacology. 2016;2(26):S575-6. [DOI: 10.1016/S0924-977X(16)31635-2]

Wirtenberger, M., et al., Associations of genetic variants in the estrogen receptor coactivators PPARGC1A, PPARGC1B and EP300 with familial breast cancer. Carcinogenesis, 2006. 27(11): p. 2201-2208. [DOI: 10.1093/carcin/bgl067] [PMID]

Ikegami K, Mukai M, Tsuchida J, Heier RL, Macgregor GR, Setou M. TTLL7 is a mammalian beta-tubulin polyglutamylase required for growth of MAP2-positive neurites. J Biol Chem. 2006;281(41):30707-16. [DOI: 10.1074/jbc.M603984200] [PMID] [PMCID]

Shy ME, Jáni A, Krajewski K, Grandis M, Lewis RA, Li J, Shy RR, Balsamo J, Lilien J, Garbern JY, Kamholz J. Phenotypic clustering in MPZ mutations. Brain. 2004;127(Pt 2):371-84. [DOI: 10.1093/brain/awh048] [PMID]

Choi J, Zhou N, Busino L. KLHL6 is a tumor suppressor gene in diffuse large B-cell lymphoma. Cell Cycle. 2019;18(3):249-256. [DOI: 10.1080/15384101.2019.1568765 ] [PMID] [PMCID]

Chen Y, Wu H, Wang S, Koito H, Li J, Ye F, Hoang J, Escobar SS, Gow A, Arnett HA. The oligodendrocyte-specific G protein-coupled receptor GPR17 is a cell-intrinsic timer of myelination. Nat Neurosci. 2009;12(11):1398-406. [DOI: 10.1038/nn.2410 ] [PMID] [PMCID]

Keller A, Gröger L, Tschernig T, Solomon J, Laham O, Schaum N,et al. miRNATissueAtlas2: an update to the human miRNA tissue atlas. Nucleic Acids Res. 2022;50(D1):D211-D221. [DOI: 10.1093/nar/gkab808] [PMID] [PMCID]

Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol. 2006;2(4):e33. [DOI:10.1371/journal.pcbi.0020033] [PMID] [PMCID]

Carbone A, Gloghini A, Dotti G. EBV-associated lymphoproliferative disorders: classification and treatment. The oncologist. 2008;13(5):577-85. [DOI: 10.1634/theoncologist.2008-0036]

de Jesus O, Smith PR, Spender LC, Elgueta Karstegl C, Niller HH, Huang D, Farrell PJ. Updated Epstein-Barr virus (EBV) DNA sequence and analysis of a promoter for the BART (CST, BARF0) RNAs of EBV. J Gen Virol. 2003;84(Pt 6):1443-1450. [DOI: 10.1099/vir.0.19054-0] [PMID]

Williams DA. miRNA-embedded shRNAs for lineage-specific BCL11A knockdown and hemoglobin F induction.2015. [DOI: 10.1038/mt.2015.113]

Esrick EB, Lehmann LE, Biffi A, Achebe M, Brendel C, Ciuculescu MF, Daley H, MacKinnon B, Morris E, Federico A, Abriss D. Post-transcriptional genetic silencing of BCL11A to treat sickle cell disease. New England Journal of Medicine. 2021;384(3):205-15. [DOI: 10.1056/NEJMoa2029392]