Pathogenesis of Helicobacter pylori-Related Gastroduodenal Diseases from Molecular Epidemiological Studies by Yoshio Yamaoka

“…Because genome wide analyses using whole-genome sequencing technology give a broad view of the genome of H. pylori, we hope that next-generation sequencers will enable us to efficiently investigate novel virulence factors.…”
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Metabolic Analysis of the Mode of Action and Mode of Resistance for Novobiocin in Staphylococcus aureus by Weile Xie, Dan Luo, Zhe Wang

“…Further metabolomic analysis revealed the function of the major mutation (in gyrB) in relation to the potential mechanism through which S. aureus responds to novobiocin. Through whole genome sequencing, three mutations of S. aureus in gyrB, potB, and fpgS were identified. …”
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Alu-Sc-mediated exonization generated a mitochondrial LKB1 gene variant found only in higher order primates by Ivan Tan, Sonia Chothani, Hong-Hwa Lim, Kong-Peng Lam

“…Analyses of putative exon 1b genomic sequences within the primate superfamily indicated that the exonization of LKB1/STK11 exon 1b was mediated by the conserved retrotransposable element Alu-Sc. …”
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Genomic and Drug Resistance Profile of Bovine Multidrug-Resistant <i>Escherichia coli</i> Isolated in Kazakhstan by Pavel G. Alexyuk, Andrey P. Bogoyavlenskiy, Yergali S. Moldakhanov, Kuralay S. Akanova, Adolat N. Manakbayeva, Timur Kerimov, Vladimir E. Berezin, Madina S. Alexyuk

“…While studying the prevalence and profile of antibiotic resistance among <i>E. coli</i> isolated from the feces of calves with signs of colibacillosis, a strain with a wide spectrum of drug resistance was isolated. Whole-genome sequencing, followed by bioinformatic processing and the annotation of genes of this strain, showed that the genome has a total length of 4,803,482 bp and contains 4986 genes, including 122 RNA genes. …”
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Short tandem repeats delineate gene bodies across eukaryotes by William B. Reinar, Anders K. Krabberød, Vilde O. Lalun, Melinka A. Butenko, Kjetill S. Jakobsen

“…These results suggest that the hypermutability inherent to STRs is canalized along the genome sequence and contributes to regulatory and eco-evolutionary dynamics in all eukaryotes.…”
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SP140L, an Evolutionarily Recent Member of the SP100 Family, Is an Autoantigen in Primary Biliary Cirrhosis by Mario Saare, Uku Hämarik, Rainis Venta, Marina Panarina, Chiara Zucchelli, Maire Pihlap, Anu Remm, Kai Kisand, Urve Toots, Kaidi Möll, Riina Salupere, Giovanna Musco, Raivo Uibo, Pärt Peterson

“…Here, we have characterized the SP100 family member SP140L. The genome sequence analysis showed the formation of SP140L gene through rearrangements of the two neighboring genes, SP100 and SP140, during the evolution of higher primates. …”
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Genomic analysis of three medieval parchments from German monasteries by Felix Heinrich, Henner Simianer, Jörg Bölling, Hedwig Röckelein, Christian Roos, Christian Reimer, Armin O. Schmitt

“…The source animal of the parchments could be identified as cattle and we compared their genome sequences with those of modern populations that are part of the 1000 Bull Genomes Project. …”
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Urinary Catheter Colonization by Multidrug-Resistant Cedecea neteri in Patient with Benign Prostatic Hyperplasia by Peter S. Ginn, Serina B. Tart, Stephen M. Sharkady, Dorothea K. Thompson

“…Analysis of whole genome sequence information for a representative C. neteri strain indicated the presence of multiple open reading frames with sequence similarity to β-lactamases, including a chromosome-encoded AmpC β-lactamase and metallo-β-lactamases, consistent with the resistance phenotype of this bacterium. …”
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Genome-wide association study and candidate gene identification for the cold tolerance at the seedling stage of rapeseed (Brassica napus L.) by Guangyu Wu, Yanda Zhou, Jingyi Zhang, Mengjie Gong, Lixi Jiang, Yang Zhu

“…These results suggested that variation in the genomic sequences of BnaA8.MYB60 caused the divergence of gene expression levels and functions on cold tolerance in rapeseed seedlings. …”
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Chromosome-level reference genome assembly of the gyrfalcon (Falco rusticolus) and population genomics offer insights into the falcon population in Mongolia by Farooq Omar Al-Ajli, Giulio Formenti, Olivier Fedrigo, Alan Tracey, Ying Sims, Kerstin Howe, Ikdam M. Al-Karkhi, Asmaa Ali Althani, Erich D. Jarvis, Sadequr Rahman, Qasim Ayub

“…Here, we generated a chromosome-level gyrfalcon reference genome using the Vertebrate Genomes Project (VGP) assembly pipeline. Using whole genome sequences of 49 falcons from different species and populations, including “Altai” falcons, we analyzed their population structure, admixture patterns, and demographic history. …”
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Classification of Complete Proteomes of Different Organisms and Protein Sets Based on Their Protein Distributions in Terms of Some Key Attributes of Proteins by Hao-Bo Guo, Yue Ma, Gerald A. Tuskan, Xiaohan Yang, Hong Guo

“…The existence of complete genome sequences makes it important to develop different approaches for classification of large-scale data sets and to make extraction of biological insights easier. …”
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A network medicine approach to investigating ME/CFS pathogenesis in severely ill patients: a pilot study by Li-Yuan Hung, Chan-Shuo Wu, Chia-Jung Chang, Peng Li, Kimberly Hicks, Joshua J. Dibble, Braxton Morrison, Chimere L. Smith, Ronald W. Davis, Wenzhong Xiao

“…By utilizing a network analysis on whole genome sequencing (WGS) data from the Severely Ill Patient Study (SIPS), we identified ME/CFS-associated proteins and delineated the corresponding network-level module, termed the SIPS disease module, together with its relevant pathways. …”
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Next-generation sequencing in soybean breeding and genetic research by M. T. Menkov, I. V. Rozanova, A. Ya. Evlash, E. K. Khlestkina

“…The first version of the soybean genome sequence, the G. max genome “Williams 82”, was presented in 2010, and this event significantly accelerated the study and development of genetic research on the crop. …”
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Lung Cancer Prediction Using Neural Network Ensemble with Histogram of Oriented Gradient Genomic Features by Emmanuel Adetiba, Oludayo O. Olugbara

“…The Voss DNA encoding was used to map the nucleotide sequences of mutated and normal genomes to obtain the equivalent numerical genomic sequences for training the selected classifiers. …”
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Investigating mobile element variations by statistical genetics by Shohei Kojima

“…We recently developed a variant caller that can accurately identify and genotype MEVs from biobank-scale short-read whole-genome sequencing (WGS) datasets and integrate them into statistical genetics. …”
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A CACTA-like transposon in the Anthocyanidin synthase 1 (Ans-1) gene is responsible for apricot fruit colour in the raspberry (Rubus idaeus) cultivar 'Varnes'. by Daniel James Sargent, Matteo Buti, Stefan Martens, Claudio Pugliesi, Kjersti Aaby, Dag Røen, Chandra Bhan Yadav, Felicidad Fernández Fernández, Muath Alsheikh, Jahn Davik, R Jordan Price

“…By performing RNASeq, we revealed differential expression patterns in the apricot-fruited 'Varnes' for genes in the anthocyanin biosynthesis pathway and following whole genome sequencing using long-read Oxford Nanopore Technologies sequencing, we identified a CACTA-like transposable element (TE) in the second exon of the Anthocyanidin synthase (Ans) gene that caused a truncated predicted ANS protein. …”
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Prospects for marker-associated selection in tomato <i>Solanum lycopersicum</i> L. by A. B. Shcherban

“…A separate chapter is devoted to the use of various types of DNA markers for constructing detailed genetic maps of the specified object, which, along with full-genome sequencing data, can be used to screen for genes responsible for breeding traits. …”
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Antioxidant and cytotoxic potentials of Streptomyces gilvigriseus MUSC 26T isolated from mangrove soil in Malaysia by Hooi-Leng Ser, Wai-Fong Yin, Kok-Gan Chan, Tahir Mehmood Khan, Bey-Hing Goh, Learn-Han Lee

“…By the same token, the availability of its genome sequence allows further investigation into the biosynthetic gene clusters responsible for the production of these compounds which could essentially accelerate its development as chemopreventive drug(s).…”
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Productive Entry Pathways of Human Rhinoviruses by Renate Fuchs, Dieter Blaas

“…Currently, complete or partial genome sequences of more than 150 human rhinovirus (HRV) isolates are known. …”
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AutoPVPrimer: A comprehensive AI-Enhanced pipeline for efficient plant virus primer design and assessment. by Abozar Ghorbani, Mahsa Rostami, Elham Ashrafi-Dehkordi, Pietro Hiram Guzzi

“…The pipeline uses Biopython to automatically retrieve different genomic sequences from the NCBI database to increase the robustness of the subsequent primer design. …”
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