CATS: a bioinformatic tool for automated Cas9 nucleases activity comparison in clinically relevant contexts by Ettore Rocchi, Ettore Rocchi, Federico Magnani, Federico Magnani, Gastone Castellani, Gastone Castellani, Antonio Carusillo, Martina Tarozzi, Martina Tarozzi

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Left ventricular noncompaction associated with titin-truncating variants in the TTN gene by Yu. A. Vakhrushev, T. I. Vershinina, P. A. Fedotov, A. A. Kozyreva, A. M. Kiselev, Yu. V. Fomicheva, E. S. Vasichkina, T. M. Pervunina, A. A. Kostareva

“…Causal role of TTN-truncating variants in development of cardiomyopathies and, in particular, left ventricular noncompaction, requires a comprehensive clinical, segregation and bioinformatic analysis using international databases and the use of bioinformatics software.…”
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Assessment of the new Next Generation Sequencing (NGS) tools to identify genes associated with tolerance to water deficit in sugarcane by John Jaime Riascos Arcos, Héctor Fabio Espitia Navarro, Jershon López Gerena

“…Each library was sequenced using NGS methodologies (Illumina-RNA-Seq) and data were analyzed using specialized bioinformatics software. Among the genes that were observed as differentially expressed it was possible to identify orthologs of those previously associated with tolerance for the traits of interest. …”
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Screening of VHL mutation in different types of kidney cancer in patients of West Bengal (India) by Vishal Jalan, Ravi Prakash Yadav, Madhusudan Das, Dilip Kumar Pal

“…The effect of these Single nucleotide polymorphism SNPs/mutations on VHL function were predicted by various bioinformatics software and it was found that rs1399097617 C>T, rs5030830 T>C, and rs1553620326 G>C are disease-causing. …”
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Information and characteristics of EST-SNP loci in grape (Vitis vinifera L.) by LI Meng, GUO Da-long, LIU Chong-huai, ZHANG Guo-hai, HOU Xiao-gai

“…Aiming to mine candidate single nucleotide polymorphism (SNP) loci by aligning homologous expressed sequence tags (EST) using bioinformatics software, 42 493 EST sequences were retrieved from different tissues of nine different grape genotypes in NCBI dbEST database and assembled into 6 126 contigs by CAP3 software, then candidate SNP loci of the contigs were screened by QualitySNP software. …”
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Discovery of potential ovarian cancer biomarkers using low molecular weight blood plasma proteome profiling by mass spectrometry by V. E. Shevchenko, N. E. Arnotskaya, E. V. Ogorodnikova, N. R. Pogosyan, A. N. Gritsay, K. I. Zhordania

“…The given approach included three basic components: pre-preparation of samples, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and bioinformatics software for mass spectral data process- ing. …”
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Modern Bioinformatics Solutions Used for Genetic Data Analysis by Ya. A. Kibirev, A. V. Kuznetsovskiy, S. G. Isupov, I. V. Darmov

“…The key factor that largely determines the effectiveness of the genetic analysis methods used is  the competent use of the necessary bioinformatics software utilities. Standard stages of primary genetic data analysis  are assessment of the quality control, data preprocessing, mapping to a reference genome or de novo genome assembly,  genome annotation, typing and identification of significant genetic determinants (resistance to antibacterial drugs,  pathogenicity factors, etc.), phylogenetic analysis. …”
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Specificity protein 1 initiates epithelial-mesenchymal transition of circulating tumor cells to inhibit metastasis in prostate cancer by Mei Yang, Lin Jie Li, Guo Ping Qiu, Hui Liu, Fei Gao

“…The EMT regulators were analyzed by bioinformatics software. Specificity protein 1 (SP1) was overexpressed in PC3 cells by lentiviral transfection. …”
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Subcellular localization and expression analysis of MlSOC1 genes during flower bud differentiation period in Magnolia liliflora by XUAN Lingjuan, CHENG Shaoyu, DAI Mengyi, WANG Zhuowei, SHEN Yamei

“…In order to clarify the mechanism of SOC1 in the process of flower formation in Magnolia liliflora, two SOC1 genes were screened out based on the transcriptome data in M. sinostellata, and the complete coding regions of these two SOC1 genes were obtained by homologous gene cloning. The bioinformatics software was used to analyze the information of these two genes, and the expression patterns in different flower bud differentiation periods were verified by real-time fluorescence quantitative polymerase chain reaction (qRT-PCR). …”
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PVT1 affects growth of glioma microvascular endothelial cells by negatively regulating miR-186 by Yawen Ma, Ping Wang, Yixue Xue, Chengbin Qu, Jian Zheng, Xiaobai Liu, Jun Ma, Yunhui Liu

“…We also found that PVT1 overexpression upregulated the expression of the autophagy-related proteins Atg7 and Beclin1, which induced protective autophagy. Bioinformatics software and dual-luciferase system analysis confirmed that PVT1 acts by targeting miR-186. …”
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Novel candidate genes may be possible predisposing factors revealed by whole exome sequencing in familial esophageal squamous cell carcinoma by Narjes Forouzanfar, Ancha Baranova, Saman Milanizadeh, Alireza Heravi-Moussavi, Amir Jebelli, Mohammad Reza Abbaszadegan

“…Genomic DNA was extracted and whole exome sequencing performed to generate information about genetic variants in the coding regions. Bioinformatics software applications were utilized to exploit statistical algorithms to demonstrate protein structure and variants conservation. …”
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Prediction of hub genes in pulpal inflammation and regeneration using autoencoders and a generative AI approach by Pradeep K. Yadalam, Jogikalmat Krithikadatta, Prabhu M. Natarajan, Carlos M. Ardila

“…Differential gene expression analysis was performed on data from the accession number GSE255672 using the GEO2R tool and Cytoscape, a bioinformatics software platform. A protein-protein interaction network was constructed using gene ontology annotations to identify key genes and subnetworks. …”
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Cloning, sequence and expression analysis of two SOC1 genes from Anthurium by MA Guangying, ZHU Kaiyuan, SHI Xiaohua, ZOU Qingcheng, LIU Huichun, ZHAN Jing, TIAN Danqing

“…Preliminary analysis of their characteristics, structure, and potential function were performed through bioinformatics software, combined with multiple sequence alignment and phylogenetic tree construction. …”
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Enable, empower, succeed: a bioinformatics workshop Harnessing open web-based tools for surveillance of bacterial antimicrobial resistance by Luria Leslie Founou, Opeyemi U. Lawal, Armando Djiyou, Erkison Ewomazino Odih, Daniel Gyamfi Amoako, Stephane Fadanka, Mabel Kamweli Aworh, Sindiswa Lukhele, Dusanka Nikolic, Alice Matimba, Raspail Carrel Founou

“…The workshop introduced participants to basic next-generation sequencing concepts, data file formats used in bacterial genomics, data sharing procedures and considerations, as well as the use of web-based bioinformatics software to analyse genomic data, including in silico prediction of AMR, phylogenetics analyses, and a quick introduction to Linux© command line. …”
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Case Report: Phenotypic heterogeneity within an NF1 family: assessment of the pathogenicity of a de novo c.6640dupA shift mutation and a splice variant with an epilepsy phenotype by Sijing Ren, Sijing Ren, Sijing Ren, Yanling Wang, Xinhua Tong, Xiaoyu Wu, Xiaoyu Wu, Huan Yan, Huan Yan, Qing-Xia Kong, Qing-Xia Kong, Qing-Xia Kong

“…The identified genes were validated using Sanger sequencing, and alterations in the tertiary structural physicochemical properties of the mutant proteins were analyzed using AlphaFold2 bioinformatics software.ResultsWe identified two mutation sites in the NF1 gene of the patient. …”
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Relationship between IGF2a intron 3 single nucleotide polymorphisms and growth performance of Cyprinus carpio by Su Shengyan, Dong Zaijie, Zhu Wenbin, Yuan Xinhua

“…FFRC strain carp were analyzed by sequence and bioinformatics’ software. The relationships between SNP detected and FFRC strain carp growth traits were also analyzed by SAS 8.0.In the present study, DNA sequence (468 bp) of common carp IGF2a intron 3 was isolated and 4 SNPs in common carp IGF2a were found and named by their location. …”
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Screening and identification of protein 29 of Echinococcus granulosus interacting molecules by Zailing Shang, Fei Qiao, Yaning Li, Xuelin Ma, Mingxia Wang, Wenji Yang, Tianyu He, Haixia Ma, Yana Wang, Yana Wang

“…In this study, we identified the interacting molecules of Eg.P29 for foundation to exploring the function of Eg.P29 in E. granulosus metacestode.MethodsSome basic information about Eg.P29 through bioinformatics software. A total of 50 molecules interacting with Eg.P29 were screened by three immunoprecipitation-combined liquid chromatography-tandem mass spectrometry intersections. …”
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Benchmarking 16S rRNA Gene-Based Approaches to Bacterial Taxonomy Assignment Based on Amplicon Sequencing With Illumina and Oxford Nanopore by Carmen Hoffbeck, Danielle M. R. L. Middleton, Nicola J. Nelson, Michael W. Taylor

“…Research investigating the microbial community of an ecosystem or animal can involve a range of methodologies, including sequencing technology, bioinformatic software and taxonomy database. Researchers may utilise short-read sequencing on Illumina MiSeq or long-read sequencing on platforms like Oxford Nanopore to obtain different research outcomes, for example, enhanced identification of microbes at species or strain level with Nanopore. …”
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Hazelnut allergome overview and Cor a gRNAs identification by Ciro Gianmaria Amoroso, Giuseppe Andolfo

“…User-friendly web tools include limited reference genomes to design CRISPR-Cas9 gRNAs, while bioinformatic software for custom analysis require advanced command-line skills. …”
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