• Genomics & Informatics
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• v.19 no.4
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• pp.40.1-40.11
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• 2021

Mutation signatures represent unique sequence footprints of somatic mutations resulting from specific DNA mutagenic and repair processes. However, their causal associations and the potential utility for genome research remain largely unknown. In this study, we performed PanCancer-scale correlative analyses to identify the genomic features associated with tumor mutation burdens (TMB) and individual mutation signatures. We observed that TMB was correlated with tumor purity, ploidy, and the level of aneuploidy, as well as with the expression of cell proliferation-related genes representing genomic covariates in evaluating TMB. Correlative analyses of mutation signature levels with genes belonging to specific DNA damage-repair processes revealed that deficiencies of NHEJ1 and ALKBH3 may contribute to mutations in the settings of APOBEC cytidine deaminase activation and DNA mismatch repair deficiency, respectively. We further employed a strategy to identify feature-driven, de novo mutation signatures and demonstrated that mutation signatures can be reconstructed using known causal features. Using the strategy, we further identified tumor hypoxia-related mutation signatures similar to the APOBEC-related mutation signatures, suggesting that APOBEC activity mediates hypoxia-related mutational consequences in cancer genomes. Our study advances the mechanistic insights into the TMB and signature-based DNA mutagenic and repair processes in cancer genomes. We also propose that feature-driven mutation signature analysis can further extend the categories of cancer-relevant mutation signatures and their causal relationships.

• The Journal of the Korea Contents Association
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• v.7 no.11
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• pp.94-101
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• 2007

We introduce the way to detect the mutation worm. We implemented the program that can generate signature using LCSeq(Longest Common Subsequence) technique in Suffix Tree studied as pattern recognition algorithm. We also showed the process to detect the mutation of CodeRed worm and Nimda worm and evaluated signatures generated by snort and LCSeq.

• Experimental and Molecular Medicine
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• v.50 no.11
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• pp.7.1-7.12
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• 2018

Recent findings from The Cancer Genome Atlas project have provided a comprehensive map of genomic alterations that occur in hepatocellular carcinoma (HCC), including unexpected mutations in apolipoprotein B (APOB). We aimed to determine the clinical significance of this non-oncogenetic mutation in HCC. An Apob gene signature was derived from genes that differed between control mice and mice treated with siRNA specific for Apob (1.5-fold difference; P < 0.005). Human gene expression data were collected from four independent HCC cohorts (n = 941). A prediction model was constructed using Bayesian compound covariate prediction, and the robustness of the APOB gene signature was validated in HCC cohorts. The correlation of the APOB signature with previously validated gene signatures was performed, and network analysis was conducted using ingenuity pathway analysis. APOB inactivation was associated with poor prognosis when the APOB gene signature was applied in all human HCC cohorts. Poor prognosis with APOB inactivation was consistently observed through cross-validation with previously reported gene signatures (NCIP A, HS, high-recurrence SNUR, and high RS subtypes). Knowledge-based gene network analysis using genes that differed between low-APOB and high-APOB groups in all four cohorts revealed that low-APOB activity was associated with upregulation of oncogenic and metastatic regulators, such as HGF, MTIF, ERBB2, FOXM1, and CD44, and inhibition of tumor suppressors, such as TP53 and PTEN. In conclusion, APOB inactivation is associated with poor outcome in patients with HCC, and APOB may play a role in regulating multiple genes involved in HCC development.

• The KIPS Transactions:PartC
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• v.10C no.6
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• pp.747-754
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• 2003

Thia paper suggests a milti user-authentication system comprises that DNA biometric informatiom, owner's RFID(Radio Frequency Identification) smartcard of hardware token, and PKI digital signqture of software. This system improved items proposed in [1] as follows : this mechanism provides one RFID smartcard instead of two user-authentication smartcard(the biometric registered seal card and the DNA personal ID card), and solbers user information exposure as RFID of low proce when the card is lost. In addition, this can be perfect multi user-autentication system to enable identification even in cases such as identical twins, the DNA collected from the blood of patient who has undergone a medical procedure involving blood replacement and the DNA of the blood donor, mutation in the DNA base of cancer cells and other cells. Therefore, the proposed system is applied to terminal log-on with RFID smart card that stores accurate digital DNA biometric information instead of present biometric user-authentication system with the card is lost, which doesn't expose any personal DNA information. The security of PKI digital signature private key can be improved because secure pseudo random number generator can generate infinite one-time pseudo randon number corresponding to a user ID to keep private key of PKI digital signature securely whenever authenticated users access a system. Un addition, this user-authentication system can be used in credit card, resident card, passport, etc. acceletating the use of biometric RFID smart' card. The security of proposed system is shown by statistical anaysis.

• Journal of Microbiology and Biotechnology
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• v.19 no.3
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• pp.217-228
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• 2009

Mobile genetic segments, or transposons, are also referred to as jumping genes as they can shift from one position in the genome to another, thus inducing a chromosomal mutation. According to the target site-specificity of the transposon during a transposition event, the result is either the insertion of a gene of interest at a specific chromosomal site, or the creation of knockout mutants. The former situation includes the integration of conjugative transposons via site-specific recombination, several transposons preferring a target site of a conserved AT-rich sequence, and Tn7 being site-specifically inserted at attTn7, the downstream of the essential glmS gene. The latter situation is exploited for random mutagenesis in many prokaryotes, including IS (insertion sequence) elements, mariner, Mu, Tn3 derivatives (Tn4430 and Tn917), Tn5, modified Tn7, Tn10, Tn552, and Ty1, enabling a variety of genetic manipulations. Randomly inserted transposons have been previously employed for a variety of applications such as genetic footprinting, gene transcriptional and translational fusion, signature-tagged mutagenesis (STM), DNA or cDNA sequencing, transposon site hybridization (TraSH), and scanning linker mutagenesis (SLM). Therefore, transposon-mediated genetic engineering is a valuable discipline for the study of bacterial physiology and pathogenesis in living hosts.