Ensemble learning-based predictor for driver synonymous mutation with sequence representation. by Chuanmei Bi, Yong Shi, Junfeng Xia, Zhen Liang, Zhiqiang Wu, Kai Xu, Na Cheng

“…Interestingly, while deep learning methods have shown promise in other fields, their DNA sequence representations do not significantly enhance the identification of driver synonymous mutations in this study. …”
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Application of internal transcribed spacer (ITS) sequences for identifying Anoectochilus setaceus Blume in Thanh Hoa, Vietnam by B. B. Thinh, L. D. Chac, L. T.M. Thu

“…Basically, this technique is based on the use of a DNA sequence (about 400–800 bp) as a standard to identify and determine the species relation of organisms quickly and accurately. …”
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Dynamic Circuit Specialisation for Key-Based Encryption Algorithms and DNA Alignment by Tom Davidson, Fatma Abouelella, Karel Bruneel, Dirk Stroobandt

“…Our final design is up to 2.80-times more efficient on cheaper FPGAs than the original DNA aligner when at least one DNA sequence is longer than 758 characters. Most sequences in DNA alignment are of the order 213.…”
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A new crustin-like gene from the redclaw crayfish Cherax quadricarinatus and its response to decapod iridescent virus 1 (DIV1) challenge by Xiaoying Hang, Jianbo Zheng, Fei Li

“…In this study, a novel crustin-like gene, Cqcarc1, was characterized from the redclaw crayfish Cherax quadricarinatus. The full-length cDNA sequence was 488 bp, and the open reading frame encoded 101 amino acids with a signal peptide in the N-terminus and a conserved WAP domain in the C-terminus. …”
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Tree polynomials identify a link between co-transcriptional R-loops and nascent RNA folding. by Pengyu Liu, Jacob Lusk, Nataša Jonoska, Mariel Vázquez

“…Recent research shows that DNA sequence and topology affect R-loops, yet it remains unclear how these and other factors contribute to R-loop formation. …”
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Immobilized Native Bacteria as a Tool for Bioremediation of Soils and Waters: Implementation and Modeling by C. Lobo, M. Sanchez, C. Garbi, E. Ferrer, M.J. Martinez-Iñigo, J.L. Allende, C. Martinez, L. Casasas, R. Alonso, A. Gibello, M. Martin

“…Based on 3,4-dihydroxyphenylacetate (3,4-DHPA) dioxygenase amino acid sequence and DNA sequence data for homologous genes, two different oligonucleotides were designed. …”
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Bioprospecting for Isoetes cangae Endophytes with Potential to Promote Plant Growth by Danielle Silveira Santos, Paula Veronesi Marinho Pontes, Analy Machado de Oliveira Leite, Aline Lemos Ferreira, Mariana de Souza, Thainá dos Santos Silva Araujo, Henrique Fragoso dos Santos, Guilherme Correa de Oliveira, José Augusto Bitencourt, Allysson Buraslan Cavalcanti, Rodrigo Lemes Martins, Francisco De Assis Esteves

“…The bioprospecting of potentially growth-promoting endophytes required the following steps to be taken: isolation of endophytic colonies, molecular identification by 16S rDNA sequence analysis, and evaluation of the bacterial potential for nitrogen fixation, production of indole acetic acid and siderophores, as well as phosphate solubilization and mineralization. …”
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Poly(A)-DG: A deep-learning-based domain generalization method to identify cross-species Poly(A) signal without prior knowledge from target species. by Yumin Zheng, Haohan Wang, Yang Zhang, Xin Gao, Eric P Xing, Min Xu

“…Identifying the cis-determinants of poly(A) signal (PAS) on the DNA sequence is the key to understand the mechanism of translation regulation and mRNA metabolism. …”
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Remodeling Intestinal Flora with Sleeve Gastrectomy in Diabetic Rats by Xiaofei Huang, Pan Weng, Huixin Zhang, Yingli Lu

“…The composition changes of intestinal flora were detected by 16S rDNA sequence analysis. Results. In diabetic rats, weight and fasting blood glucose decreased significantly after sleeve gastrectomy. …”
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Modern approaches to artificial gene synthesis: aspects of oligonucleotide synthesis, enzymatic assembly, sequence verification and error correction by G. Y. Shevelev, D. V. Pyshnyi

“…Thus, significant reduction in cost of DNA sequencing has provided an easy access to large amounts of data on the genetic sequences of various organisms, and decreased the price of the DNA sequence synthesis, which, analogous to Moore’s law, resulted in an opportunity to create a lot of potential genes without the time – consuming and labor – intensive traditional methods of molecular biology. …”
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Human SLC26A1 Gene Variants: A Pilot Study by Paul A. Dawson, Pearl Sim, David W. Mudge, David Cowley

“…To investigate the possible involvement of SAT1 in human urolithiasis, we screened the SLC26A1 gene in a cohort of 13 individuals with recurrent calcium oxalate urolithiasis, which is the commonest type. DNA sequence analyses showed missense mutations in seven patients: one individual was heterozygous R372H; 4 individuals were heterozygous Q556R; one patient was homozygous Q556R; and one patient with severe nephrocalcinosis (requiring nephrectomy) was homozygous Q556R and heterozygous M132T. …”
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Isolation and Characterization of Paracoccus sp. GSM2 Capable of Degrading Textile Azo Dye Reactive Violet 5 by Mallikarjun C. Bheemaraddi, Santosh Patil, Channappa T. Shivannavar, Subhashchandra M. Gaddad

“…A potential bacterial strain GSM2, capable of degrading an azo dye Reactive Violet 5 as a sole source of carbon, was isolated from textile mill effluent from Solapur, India. The 16S rDNA sequence and phenotypic characteristics indicated an isolated organism as Paracoccus sp. …”
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Phylogeny of Flavobacteria Group Isolated from Freshwater Using Multilocus Sequencing Analysis by Seyoung Mun, Jungnam Lee, Siwon Lee, Kyudong Han, Tae-Young Ahn

“…The genes were amplified by PCR and subjected to DNA sequencing. Based on the combined DNA sequence (4,412 bp) of the six housekeeping genes, we analyzed the phylogenetic relationship among the Flavobacterium species. …”
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Performance and limitations of linkage-disequilibrium-based methods for inferring the genomic landscape of recombination and detecting hotspots: a simulation study by Raynaud, Marie, Gagnaire, Pierre-Alexandre, Galtier, Nicolas

“…Population genomic approaches offer an attractive way to infer the population-scaled recombination rate ρ=4Ner using the linkage disequilibrium information contained in DNA sequence polymorphism data. Such methods have been used in a broad range of plant and animal species to build genome-wide recombination maps. …”
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The Intersection of Epigenetics and Senolytics in Mechanisms of Aging and Therapeutic Approaches by Daiana Burdusel, Thorsten R. Doeppner, Roxana Surugiu, Dirk M. Hermann, Denissa Greta Olaru, Aurel Popa-Wagner

“…Epigenetics refers to heritable changes in gene expression without altering the DNA sequence, with mechanisms like DNA methylation, histone modification, and non-coding RNA regulation playing critical roles in aging. …”
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Genetic Analysis of Sodium Channel Genes in Pediatric Epilepsy Patients of Pakistan by Aqsa Ashfaq, Tayyaba Saleem, Nadeem Sheikh, Hafsa Maqbool

“…The sequencing was performed, and the sequences were observed through BioEdit software for any change in DNA sequence. In our study, no polymorphism was observed in the studied SNPs except for rs2298771. …”
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The Impact of Epigenetics on the Pathophysiology of Type 2 Diabetes and Associated Nephropathic Complications by Amit Mukherjee, Tanusree Debbarman, Basu D. Banerjee, Sheelu S. Siddiqi

“…Epigenetics has emerged as a critical area of research, providing insights into how these factors can modify the expression and cellular behavior without altering the underlying DNA sequence. Various epigenetic mechanisms, including DNA methylation, histone modifications, chromatin remodeling, and non-coding RNA regulation, drive cell dysfunction, inflammation, and fibrosis, aggravating diabetes and its complications. …”
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Progress in plant genome sequencing: research directions by M. K. Bragina, D. A. Afonnikov, E. A. Salina

“…A comparison of the methods of targeted sequencing based on the use of the reference DNA sequence is accomplished.…”
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Investigation of genetic structure of various cat breeds by using d-loop polimorphism in turkey by Elif Yılmaz Şahin, Vahdettin Altunok, Ercan Kurar

“…In this study, the selection of 99 bç, a narrow location obtained from mtDNA sequence analysis is evaluated and in spite of a small number of samples the acquired statistical difference is significant.…”
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Targeting the epigenome with advanced delivery strategies for epigenetic modulators by Sonia Guha, Yogeswaran Jagadeesan, Murali Monohar Pandey, Anupama Mittal, Deepak Chitkara

“…By modulating the epigenetic status, the expression of genes can be regulated without any change in the DNA sequence itself. Epigenetic drugs exhibit promising therapeutic efficacy against several epigenetically originated diseases including several cancers, neurodegenerative diseases, metabolic disorders, cardiovascular disorders, and so forth. …”
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