Synthesis, Structure, and Anticancerous Properties of Silver Complexes by Shraddha Shukla, A. P. Mishra

“…The completion of the human genome sequence and its subsequent improvements in the sequence data are important steps to fully comprehend cancer cell biology. …”
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Spaced Seed Data Structures for De Novo Assembly by Inanç Birol, Justin Chu, Hamid Mohamadi, Shaun D. Jackman, Karthika Raghavan, Benjamin P. Vandervalk, Anthony Raymond, René L. Warren

“…De novo assembly of the genome of a species is essential in the absence of a reference genome sequence. Many scalable assembly algorithms use the de Bruijn graph (DBG) paradigm to reconstruct genomes, where a table of subsequences of a certain length is derived from the reads, and their overlaps are analyzed to assemble sequences. …”
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Genome resequencing and genome-wide polymorphisms in mosquito vectors Aedes aegypti and Aedes albopictus from south India by Preeti Acharya, Upasana Shyamsunder Singh, Veeramanoharan Rajamannar, Mayilsamy Muniaraj, Binata Nayak, Aparup Das

“…This study reports for the first time a high coverage genome sequence data of an Indian Ae. albopictus mosquito. …”
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Biofilm removal mediated by Salmonella phages from chicken-related sources by Zhenzhen Ning, Lingling Zhang, Linlin Cai, Xinglian Xu, Ying Chen, Huhu Wang

“…In this work, 21 Salmonella phages were isolated from a chicken farm and slaughter plant and the phage (CW1) with the broadest spectrum was characterized. Complete genome sequence analysis revealed that the genomes of phage CW1 is composed of 41763 bp with 58 open reading frames (ORFs) and a holin-endolysin system and it does not encode any virulence or lysogeny. …”
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Crop pangenomes by A. Yu. Pronozin, M. K. Bragina, E. A. Salina

“…Progress in genome sequencing, assembly and analysis allows for a deeper study of agricultural plants’ chromosome structures, gene identif ication and annotation. …”
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The emerging roles of aberrant alternative splicing in glioma by Reda Ben Mrid, Sara El Guendouzi, Marco Mineo, Rachid El Fatimy

“…AS is a process that produces, from a single genomic sequence, several mature messenger RNAs. Splicing of pre-messenger RNAs concerns at least 95% of transcripts and constitutes an important mechanism in gene expression regulation. …”
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Population Genomics Reveals Elevated Inbreeding and Accumulation of Deleterious Mutations in White Raccoon Dogs by Yinping Tian, Yu Lin, Yue Ma, Jiayi Li, Sunil Kumar Sahu, Jiale Fan, Chen Lin, Zhiang Li, Minhui Shi, Fengping He, Lianduo Bai, Yuan Fu, Zhangwen Deng, Huabing Guo, Haimeng Li, Qiye Li, Yanchun Xu, Tianming Lan, Zhijun Hou, Yanling Xia, Shuhui Yang

“…By analyzing and comparing whole-genome sequencing data from 20 white raccoon dogs and 38 normal raccoon dogs, we detected an increased occurrence of loss-of-function (LoF) mutations in white raccoon dogs compared with normal raccoon dogs. …”
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EFFECT OF FLANKING SEQUENCES ON THE ACCURACY OF THE RECOGNITION OF TRANSCRIPTION FACTOR BINDING SITES by T. M. Khlebodarova, D. Yu. Oshchepkov, V. G. Levitsky, O. A. Podkolodnaya, E. V. Ignatieva, E. A. Ananko, I. L. Stepanenko, N. A. Kolchanov

“…The detected features of in vitro selected TF binding sites impose constraints on their use in the development of computer-assisted methods of the recognition of candidate sites in genomic sequences.…”
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Faster model-based estimation of ancestry proportions by Santander, Cindy G., Refoyo Martinez, Alba, Meisner, Jonas

“…The ADMIXTURE software is a widely used model-based approach to account for population stratification, however, it struggles with convergence issues and does not scale to modern human datasets or the large number of variants in whole-genome sequencing data. Likelihood-free approaches optimize a least square objective and have gained popularity in recent years due to their scalability. …”
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The role of artificial intelligence and machine learning in predicting and combating antimicrobial resistance by Hazrat Bilal, Muhammad Nadeem Khan, Sabir Khan, Muhammad Shafiq, Wenjie Fang, Rahat Ullah Khan, Mujeeb Ur Rahman, Xiaohui Li, Qiao-Li Lv, Bin Xu

“…AI/ML models can use various data sources, such as clinical information, genomic sequences, microbiome insights, and epidemiological data for predicting AMR outbreaks. …”
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Global biogeography and projection of antimicrobial toxin genes by Ya Liu, Yu Geng, Yiru Jiang, Jingyu Sun, Peng Li, Yue-zhong Li, Zheng Zhang

“…Conclusions Our study provides baseline information on the global distribution of antimicrobial toxins by combining community samples, genome sequences, and environmental constraints. Our results highlight the natural environment as a reservoir of antimicrobial toxins, advance the understanding of the global distribution of these antimicrobial weapons, and aid their application in clinical, agricultural, and industrial fields. …”
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De Novo Sequencing and Characterization of the Transcriptome of Dwarf Polish Wheat (Triticum polonicum L.) by Yi Wang, Chao Wang, Xiaolu Wang, Fan Peng, Ruijiao Wang, Yulin Jiang, Jian Zeng, Xing Fan, Houyang Kang, Lina Sha, Haiqin Zhang, Xue Xiao, Yonghong Zhou

“…Aligning this transcriptome against draft wheat genome released by the International Wheat Genome Sequencing Consortium (IWGSC), 57,331 (75.42%) unigenes, including 26,122 AB-specific and 2,622 D-specific unigenes, were mapped on A, B, and/or D genomes. …”
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Genome analysis and prevalence of SARS-CoV-2 Indonesian variants and the correlation with the outbreak timeline by Maria Prevyolita Indra Muliawan, Timotius Christopher Tantokusumo, Amalda Siti Anisa, Kholis Abdurachim Audah

“…Methods: We analyzed whole genome sequences of SARS-CoV-2 wild type and variants isolated from Indonesian samples, sourced from GenBank and the GISAID EpiCoV database. …”
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Unraveling the genetic connections for mitochondrial DNA control region and breast cancer susceptibility by Namra Khalid, Muhammad Umer Khan, Raima Rehman, Shamsa Kanwal, Tazeen Zahid, Muhammad Usman Ghani, Ayesha Iftikhar, Qurban Ali, Muhammad Arshad Javed

“…The study reveals a significant abundance of haplogroup M in breast cancer cases by analyzing breast cancer patients and healthy controls through mitochondrial control region genome sequencing (p < 0.001). Increased frequencies of haplogroups M, H, and R in patients compared to controls suggest their potential role in breast cancer susceptibility. …”
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Metabolic Blockade-Based Genome Mining of <i>Malbranchea circinata</i> SDU050: Discovery of Diverse Secondary Metabolites by Hu Yang, Xiaowei Luo, Zhuo Shang, Kunlong Li, Jian Cai, Yingying Chen, Longchao Xin, Jianhua Ju

“…<i>Malbranchea circinata</i> SDU050, a fungus derived from deep-sea sediment, is a prolific producer of diverse secondary metabolites. Genome sequencing revealed the presence of at least 69 biosynthetic gene clusters (BGCs), including 30 encoding type I polyketide synthases (PKSs). …”
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Adaptive evolution of SARS-CoV-2 during a persistent infection for 521 days in an immunocompromised patient by Hanno Schmidt, Lea Schick, Jürgen Podlech, Angélique Renzaho, Bettina Lieb, Stefan Diederich, Thomas Hankeln, Bodo Plachter, Oliver Kriege

“…Virus samples from five time points were submitted to whole genome sequencing. Between the first detection of SARS-CoV-2 infection and its clearance, the patient’s virus population acquired 34 amino acid substitutions and 8 deletions in coding regions. …”
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Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome by Gary Xie, Shannon L. Johnson, Karen W. Davenport, Mathumathi Rajavel, Torsten Waldminghaus, John C. Detter, Patrick S. Chain, Shanmuga Sozhamannan

“…Here, we describe the genomic characterization of strains that are an exception to the two chromosome rules: naturally occurring single-chromosome V. cholerae. Whole genome sequence analyses of NSCV1 and NSCV2 (natural single-chromosome vibrio) revealed that the Chr1 and Chr2 fusion junctions contain prophages, IS elements, and direct repeats, in addition to large-scale chromosomal rearrangements such as inversions, insertions, and long tandem repeats elsewhere in the chromosome compared to prototypical two chromosome V. cholerae genomes. …”
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Successful Traceability of Wildlife Samples Contributes to Wildlife Conservation: A Case Study of Tracing the Snub-Nosed Monkey (<i>Rhinopithecus</i> spp.) by Xibo Wang, Ying Shen, Yang Teng, Ruifeng Wu, Shuhao Liu, Jilai Zhao, Can Hu, Ming Li, Huijuan Pan, Jiwei Qi

“…This pipeline has been applied to the whole-genome sequence (WGS) data of China’s flagship species, the snub-nosed monkey (<i>Rhinopithecus</i> spp.). …”
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Improving genomic prediction accuracy of pig reproductive traits based on genotype imputation using preselected markers with different imputation platforms by J. Sun, J. Wei, Y. Pan, M. Cao, X. Li, J. Xiao, G. Yang, T. Yu

“…In this study, the imputation from 80 k Single Nucleotide Polymorphism chip data of 832 Large White pigs to whole-genome sequencing genotypes was performed by Swine Imputation Server, Pig Haplotypes Reference Panel (PHARP), Animal Genotype Imputation Database and 1k-pig-genomes four thousand-pig imputation panels. …”
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Central Role of Gimap5 in Maintaining Peripheral Tolerance and T Cell Homeostasis in the Gut by Mehari Endale, H. Ibrahim Aksoylar, Kasper Hoebe

“…Specifically, genome-wide (GWAS) and also next-generation sequencing (NGS)—including whole exome or genome sequencing—have uncovered a large number of susceptibility loci that predispose to autoimmune diseases and/or the two phenotypes of IBD. …”
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