A comparative analysis of sequence composition in different lots of a phage display peptide library during amplification by Anders Wilgaard Sinkjaer, Ane Beth Sloth, Amanda Oester Andersen, Malte Jensen, Babak Bakhshinejad, Andreas Kjaer

“…The NGS datasets underwent a variety of bioinformatic analyses using Python and MATLAB scripts. …”
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Complete genome sequencing and probiotic characterization of promising lactic acid bacterial strains isolated from dairy products in Egyptian markets by Mostafa F. El-Hosseny, Mohamed G Seadawy, Mohammed O Abdel-Monem, Mervat G Hassan

“…Conclusion Three promising isolates underwent complete genome sequencing with high-throughput second generation technology followed by comprehensive bioinformatic analysis. The results showed that our isolates possess traits enabling resilience to antimicrobial effects and stress factors that might cause problems in the human gut. …”
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First report on comprehensive genomic analysis of a multidrug-resistant Enterobacter asburiae isolated from diabetic foot infection from Bangladesh by Md. Rafiul Islam, Spencer Mark Mondol, Md. Azad Hossen, Mst. Poli Khatun, Shahjada Selim, Amiruzzaman, Donald James Gomes, Md. Mizanur Rahaman

“…Through sophisticated genomic techniques encompassing whole genome sequencing and in-depth bioinformatic analyses, this research unveils a profound understanding of the isolate’s antimicrobial resistance patterns, virulence determinants, biosynthetic gene clusters, metabolic pathways and pathogenic potential. …”
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Novel biomarkers: the RUNX family as prognostic predictors in colorectal cancer by Yingting Liu, Yingting Liu, Yingting Liu, Junjun Chen, Junjun Chen, Junjun Chen, An Li, An Li, An Li, Yue Wu, Yue Wu, Yue Wu, Junwei Ge, Junwei Ge, Junwei Ge, Maoling Yuan, Maoling Yuan, Maoling Yuan, Bin Xu, Bin Xu, Bin Xu, Xiao Zheng, Xiao Zheng, Xiao Zheng, Lujun Chen, Lujun Chen, Lujun Chen, Jingting Jiang, Jingting Jiang, Jingting Jiang

“…Moreover, further bioinformatic analysis conducted utilizing the TISIDB and TIMER platforms demonstrated significant associations between the members of the RUNX family and immune-infiltrating cells, specifically diverse subpopulations of CD8+TILs. …”
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Deep eutectic solvent enhances antibacterial activity of a modular lytic enzyme against Acinetobacter baumannii by Aleksandra Maria Kocot, Tomasz Swebocki, Karolina Ciemińska, Adrianna Łupkowska, Małgorzata Kapusta, Dennis Grimon, Ewa Laskowska, Anna-Karina Kaczorowska, Tadeusz Kaczorowski, Rabah Boukherroub, Yves Briers, Magdalena Plotka

“…Abstract In this study, we evaluated the combined effect between MLE-15, a modular lytic enzyme composed of four building blocks, and reline, a natural deep eutectic solvent. The bioinformatic analysis allowed us to determine the spatial architecture of MLE-15, whose components were bactericidal peptide cecropin A connected via a flexible linker to the cell wall binding domain (CBD) of mesophilic 201ϕ2 − 1 endolysin and catalytic domain (EAD) of highly thermostable Ph2119 endolysin. …”
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Traces of Paleolithic expansion in the Nivkh gene pool based on data on autosomal SNP and Y chromosome polymorphism by V. N. Kharkov, N. A. Kolesnikov, L. V. Valikhova, A. A. Zarubin, A. L. Sukhomyasova, I. Yu. Khitrinskaya, V. A. Stepanov

“…The gene pool of the Nivkhs and other Far Eastern and Siberian populations was characterized using a genome-wide panel of autosomal single-nucleotide polymorphic markers and Y chromosome haplogroups. Bioinformatic processing of frequencies of autosomal SNPs, Y chromosome haplogroups and YSTR haplotypes showed that the Nivkh gene pool is very different from the other populations’. …”
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Analysis of Vaginal Microbiome in Women with or Without Episodes of Spontaneous Abortion in Eastern Nigeria by Felix Emele Emele, Prisca Onyeulor, Francisca Nwaokorie, Damian Asogwa

“…The samples were analyzed and interpreted by standard metagenomic and bioinformatic techniques. RESULTS: The following phyla were encountered in spontaneous abortion and non-spontaneous abortion, respectively: Firmicutes (69.4%, 94.9%), Actinobacteria (12.7%, 1.1%), Bacteroidetes (9.5%, 2.8%), Proteobacteria (7.9%, 0.3%), Chloroflexi (0.2%, 0.0%), Fusobacteria (0.2%, 0.0%), Tenericutes (0.02%, 1.0%). …”
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Screening and Whole-Genome Sequencing Analysis of Fructofuranose-Metabolizing Lactiplantibacillus plantarum 19M03 by SUN Daqing, QI He, DI Ziqing, GE Xianglin, HONG Qingping, DU Xinrui, YAO Yuxi, LI Hongfei

“…Then, the strain was subjected to whole-genome sequencing and its fructan metabolism mechanism was analyzed by using high-throughput sequencing and bioinformatic techniques. The sequencing results showed that the genome of strain 19M03 contained one chromosome and nine plasmids, with a total length of 3 246 316 bp, GC content of 44.53%, 3 084 coding genes, 66 tRNAs and 16 rRNAs. …”
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Clade-specific long-read sequencing increases the accuracy and specificity of the gyrB phylogenetic marker gene by Robert G. Nichols, Emily R. Davenport

“…We demonstrate both bioinformatically and analytically that these longer amplicons offer more sequence space for greater taxonomic resolution, lower off-target amplification rates, and lower error rates with PacBio CCS sequencing versus established short-read sequencing. …”
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The rapid detection of a neonatal unit outbreak of a wild-type Klebsiella variicola using decentralized Oxford Nanopore sequencing by Rhys T. White, Michelle Balm, Megan Burton, Samantha Hutton, Jamaal Jeram, Matthew Kelly, Donia Macartney-Coxson, Tanya Sinha, Henrietta Sushames, David J. Winter, Maxim G. Bloomfield

“…If transmission events are suspected, sequence data are transferred to the reference laboratory, the Institute for Environmental Science and Research (ESR) for high-resolution bioinformatic analysis. Results Within 48 h of notification isolates had been subcultured and sequenced. …”
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Cell-free supernatants from plant growth-promoting rhizobacteria Bacillus albus strains control Aspergillus flavus disease in peanut and maize seedlings by Lai Loi Trinh, Kim Ngoc Le, Hoang Anh Le Lam, Hoai Huong Nguyen

“…These were characterized using rapid chemical assays and ultra-high-performance liquid chromatography-electrospray ionization-quadrupole time-of-flight/mass spectrometry (UHPLC-ESI-QTOF/MS), combined with bioinformatic tools such as Global Natural Product Social Molecular Networking (GNPS) and Natural Products Atlas (NPAtlas). …”
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Sinomenine attenuates uremia vascular calcification by miR-143-5p by Fengyi Yu, Zhong Peng, Ning Gao, Zixu Tang, Zihao Liao, Song Zhao, Shuzhu Zhong, Gloria Umwiza, Hong Huang, Wei Long, Zhangxiu He

“…The miRNA sequencing revealed differentially expressed miRNAs in aortas and bioinformatic analysis assisted with miRNA screening. …”
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S100A13-driven interaction between pancreatic adenocarcinoma cells and cancer-associated fibroblasts promotes tumor progression through calcium signaling by Liuyuan Xia, Xin Guo, Dong Lu, Yixin Jiang, Xiaohui Liang, Yiwen Shen, Jiayi Lin, Lijun Zhang, Hongzhuan Chen, Jinmei Jin, Xin Luan, Weidong Zhang

“…While the roles of some S100 proteins have been extensively studied, others, such as S100A13, remain less well understood. Methods Bioinformatic analysis was employed to predict the pathogenic potential of CAFs and S100A13. …”
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IL-13 Augments Histone Demethylase JMJD2B/KDM4B Expression Levels, Activity, and Nuclear Translocation in Airway Fibroblasts in Asthma by Khuloud Bajbouj, Mahmood Y. Hachim, Rakhee K. Ramakrishnan, Huwaida Fazel, Jumana Mustafa, Shahed Alzaghari, Mahmoud Eladl, Jasmin Shafarin, Ronald Olivenstein, Qutayba Hamid

“…Its subcellular localization and tissue distribution were examined in bronchial fibroblasts as well as bronchial biopsies by immunofluorescence and immunohistochemical analysis, respectively. Results. Bioinformatic analysis revealed the differential expression of the histone demethylase JMJD2B/KDM4B, a well-known epigenetic modulator that leads to the demethylation of different lysine residues on histones, in IL-13-treated lung fibroblasts. …”
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Clinical Role of Epigenetics and Network Analysis in Eye Diseases: A Translational Science Review by Michele Lanza, Giuditta Benincasa, Dario Costa, Claudio Napoli

“…Network medicine is a molecular-bioinformatic approach analyzing gene-gene interactions that can perturb the human interactome. …”
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DNA hypomethylation-mediated upregulation of GADD45B facilitates airway inflammation and epithelial cell senescence in COPD by Yuan Zhan, Qian Huang, Zhesong Deng, Shanshan Chen, Ruonan Yang, Jiaheng Zhang, Yating Zhang, Maocuo Peng, Jixing Wu, Yiya Gu, Zhilin Zeng, Jungang Xie

“…Methods: Expressions of GADD45 family were evaluated by bioinformatic analysis combined with detections in clinical specimens. …”
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Genome-Wide Identification and Expression Analysis of the <i>CAMTA</i> Gene Family in Roses (<i>Rosa chinensis</i> Jacq.) by Wanyi Su, Yuzheng Deng, Xuejuan Pan, Ailing Li, Yongjie Zhu, Jitao Zhang, Siting Lu, Weibiao Liao

“…<i>CAMTA</i> gene family members were identified and bioinformatically analyzed to investigate their expression characteristics in plant hormonal responses. …”
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Investigating intra‐tumoural heterogeneity and microenvironment diversity in primary cardiac angiosarcoma through single‐cell RNA sequencing by Jingyuan Huo, Zhen Wang, Wenting Zhao, Miao Chen, Haoyang Li, Fengpu He, Xiao Tian, Yaqi Ma, Firyuza Husanova, Liang Ma, Yiming Ni, Hongda Ding, Weidong Li, Hongfei Xu

“…We used scRNA‐seq data from five normal cardiac tissue samples downloaded from public databases for comparative analyses. Bioinformatic analyses, including Cell Ranger, Seurat, Monocle2, hdWGCNA, SCENIC and NicheNet, were utilized to identify distinct cell populations, transcriptional patterns, and co‐regulating gene modules. …”
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Achievements and prospects of applying high-throughput sequencing techniques to potato genetics and breeding by I. V. Bykova, N. A. Shmakov, D. A. Afonnikov, A. V. Kochetov, E. K. Khlestkina

“…Optimization of existing bioinformatic tools to support these studies, taking into account potato genome organization peculiarities, are carried out. …”
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The complete mitochondrial genome of Gyrodactylus pseudorasborae (Platyhelminthes: Monogenea) with a phylogeny of Gyrodactylidae parasites by Xinyi Zeng, Ye Li, Yang Liu, Yaoying Chen, Yajing Liu, Mengwei Song, Tao Chen

“…The mitochondrial genome of G. pseudorasborae was amplified in six parts from a single parasite, sequenced using primer walking, annotated and analyzed using bioinformatic tools. Results The mitochondrial genome of G. pseudorasborae is 14,189 bp in length, containing 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and two major non-coding regions (NCR: NC1 and NC2). …”
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