Identification and characterization of Faecalibacterium prophages rich in diversity-generating retroelements by Anastasia Gulyaeva, Lei Liu, Sanzhima Garmaeva, Marloes Kruk, Rinse K. Weersma, Hermie J. M. Harmsen, Alexandra Zhernakova

“…Here, we developed a bioinformatic approach to prophage identification that builds on prophage genomic properties, existing prophage-detecting software, and publicly available virome sequencing data. …”
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Genome-wide identification of short-chain dehydrogenases/reductases genes and functional characterization of ApSDR53C2 in melanin biosynthesis in Arthrinium phaeospermum by Jiao Liao, Yisi Wang, Han Liu, Sijia Liu, Peng Yan, Hang Chen, Shujiang Li, Shujiang Li

“…We have characterized the SDR family of A. pheospermum bioinformatically. Candidate ApSDRs screened by transcriptome sequencing were compared by qPCR experiments to obtain key ApSDRs that may play an important role in infestation and adversity resistance. …”
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A select inhibitor of MORC2 encapsulated by chimeric membranecoated DNA nanocage target alleviation TNBC progression by Xiaohan Su, Yunbo Luo, Yali Wang, Peng Qu, Jun Liu, Shiqi Han, Cui Ma, Shishan Deng, Qi Liang, Xiaowei Qi, Panke Cheng, Lingmi Hou

“…Triple-negative breast cancer (TNBC) is the most malignant type of breast cancer and lacks effective targeted therapeutic drugs, resulting in a high recurrence rate and worse outcome. In this study, bioinformatic analysis and a series of experiments demonstrated that MOCR2 was highly expressed in TNBC and closely associated with poor prognosis, indicating that MOCR2 may be a potential therapeutic target for TNBC. …”
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Reduced ATP turnover during hibernation in relaxed skeletal muscle by Cosimo De Napoli, Luisa Schmidt, Mauro Montesel, Laura Cussonneau, Samuele Sanniti, Lorenzo Marcucci, Elena Germinario, Jonas Kindberg, Alina Lynn Evans, Guillemette Gauquelin-Koch, Marco Narici, Fabrice Bertile, Etienne Lefai, Marcus Krüger, Leonardo Nogara, Bert Blaauw

“…Furthermore, using bioinformatical approaches and western blotting we find that phosphorylated myosin light chain, a known stimulator of basal myosin ATPase activity, is decreased in hibernating and disused muscles. …”
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A novel homozygous mutation of CFAP300 identified in a Chinese patient with primary ciliary dyskinesia and infertility by Zheng Zhou, Qi Qi, Wen-Hua Wang, Jie Dong, Juan-Juan Xu, Yu-Ming Feng, Zhi-Chuan Zou, Li Chen, Jin-Zhao Ma, Bing Yao

“…The proband had a PCD phenotype with laterality defects and immotile sperm flagella displaying a combined loss of the inner dynein arm (IDA) and outer dynein arm (ODA). Bioinformatic programs predicted that the mutation is deleterious. …”
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Genome-Wide Approach Identifies Natural Large-Fragment Deletion in ASFV Strains Circulating in Italy During 2023 by Claudia Torresi, Roberta Biccheri, Cesare Cammà, Carmina Gallardo, Maurilia Marcacci, Simona Zoppi, Barbara Secondini, Caterina Riverso, Alejandro Soler, Cristina Casciari, Michela Pela, Elisabetta Rossi, Claudia Pellegrini, Carmen Iscaro, Francesco Feliziani, Monica Giammarioli

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Exploratory analysis of molecular traits of the mitochondrial DNA of leafcutting ants to infer taxonomic characters towards an integrative taxonomy by Perpetua Ndubuisi Onyinyechi, Natália Martins Travenzoli, Maykon Passos Cristiano, Danon Clemes Cardoso

“…., 2020, Atta Fabricius, 1804 and Acromyrmex Mayr, 1865 as models to evaluate a mitochondrial genome fragment regularly applied in phylogenetic and evolutionary studies. Bioinformatic analysis revealed shared structural evidence between species that can serve as diagnostic characters, distinguishing them from other species and supporting the classification of the three genera of leafcutting ants. …”
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Transcriptional Profiling at High Temporal Resolution Reveals Robust Immune/Inflammatory Responses during Rat Sciatic Nerve Recovery by Lingyan Xing, Qiong Cheng, Guangbin Zha, Sheng Yi

“…We found that immune/inflammatory reactions not only occur in the acute injury but also remained activated over two weeks after injury. Detailed bioinformatic studies suggested that multiple immune/inflammatory pathways, including agranulocyte adhesion and diapedesis, granulocyte adhesion and diapedesis, IL-6 signaling, and IL-10 signaling, were sustained activated during nerve degeneration and regeneration. …”
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The Psu protein of phage satellite P4 inhibits transcription termination factor ρ by forced hyper-oligomerization by Daniela Gjorgjevikj, Naveen Kumar, Bing Wang, Tarek Hilal, Nelly Said, Bernhard Loll, Irina Artsimovitch, Ranjan Sen, Markus C. Wahl

“…Structure-guided mutagenesis in combination with growth, pull-down, and termination assays further delineated the functional ρ-Psu interfaces in vivo. Bioinformatic analyses revealed that Psu is associated with a wide variety of phage defense systems across Enterobacteriaceae, suggesting that Psu may regulate expression of anti-phage genes. …”
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Genomic evolution of SARS-CoV-2 in Morocco: Insights from whole genome sequences collected from 2020 to 2024 by Hamza GHAMMAZ, Marouane MELLOUL, Ahlam MBARKI, Mouhssine HEMLALI, Taha CHOUATI, Hicham EL ANNAZ, Nadia TOUIL, Mostafa ELOUENNASS, Khalid ENNIBI, Elmostafa EL FAHIME

“…A total of 2630 SARS-CoV-2 genome sequences were analyzed using bioinformatic tools such as Nextclade, followed by phylogenetic and statistical analyses. …”
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approach to calculate the transcript capacity by Young-Sup Lee, Kyung-Hye Won, Jae-Don Oh, Donghyun Shin

“…We expect that our analysis contributes to estimating TC in the diverse species and playing a benevolent role to the new bioinformatic analysis.…”
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Accelerating next generation sequencing data analysis: an evaluation of optimized best practices for Genome Analysis Toolkit algorithms by Karl R. Franke, Erin L. Crowgey

“…Additionally, the IBM POWER9 CPU performed well on bioinformatic workloads when tested with 10 different tools for alignment/mapping.…”
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Anticancer Ribosomally Synthesized and Post-Translationally Modified Peptides from Plants: Structures, Therapeutic Potential, and Future Directions by Hyeon-Jeong Hwang, Youngsang Nam, Chanhee Jang, Eun La Kim, Eun Seo Jang, Yeo Jin Lee, Seoung Rak Lee

“…By integrating traditional ethnobotanical knowledge with modern genomic and bioinformatic approaches, this study underscores the importance of plant RiPPs as a resource for developing innovative cancer treatments. …”
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Deciphering the Differences Between Epstein–Barr Virus‐Associated and Negative Gastric Cancer in the Prospect of CDKN2A Genomic Alterations and Lymphoid Infiltration by Fuda Xie, Bonan Chen, Yang Lyu, Peiyao Yu, Canbin Fang, Kam Tong Leung, Shouyu Wang, Dazhi Xu, Jun Yu, Kwok Wai Lo, Ka Fai To, Wei Kang

“…Functional potentials of EBV infection were predicted by bioinformatic enrichment analysis. Results CDKN2A genestayed intact in all EBV‐associated GC cases. …”
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THEORETICAL AND INSILCO PHARMACOKINETIC INVESTIGATIONS ON SOME PHENYL PIPERIDINE DERIVATIVES AS NOVEL ANTIDEPRESSANT AGENTS by Olasupo Sabitu Babatunde Babatunde, Adamu Uzairu, Gideon Adamu Shallangwa, Sani Uba

“… A theoretical bioinformatic investigation was carried out on some Inhibitors of serotonin transporter (SERT) of Phenyl piperidine derivatives using Density Functional Theory (DFT/B3LYP/6-31G*) at ground state with Spartan 14 V1.1.4 software in modeling the antipsychotic activity of the compounds. …”
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A single-cell RNA sequencing dataset of peripheral blood cells in long COVID patients on herbal therapy by Karolina Hanna Prazanowska, Tae-Hun Kim, Jung Won Kang, Young-Hee Jin, Sunoh Kwon, Su Bin Lim

“…To ensure the technical validity of our dataset, we implemented rigorous quality checks throughout stages of the study, including sample preparation, sequencing, and bioinformatic data analysis levels. This transcriptomic data may serve as a resource to deepen our insights into the role of herbal medicines in management of long COVID.…”
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The Impact of PPARγ Genetic Variants on IBD Susceptibility and IBD Disease Course by Jessica Mwinyi, Christa Grete-Wenger, Jyrki J. Eloranta, Gerd A. Kullak-Ublick

“…We determined genetic variants in the coding exons and flanking intronic sequences of the NR1C3 gene in 284 IBD patients and 194 controls and predicted NR1C3 haplotypes via bioinformatic analysis. We investigated whether certain NR1C3 variants are associated with susceptibility to IBD or its disease course. …”
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PathoGD: an integrative genomics approach to primer and guide RNA design for CRISPR-based diagnostics by Soo Jen Low, Matthew O’Neill, William J. Kerry, Natasha Wild, Marcelina Krysiak, Yi Nong, Francesca Azzato, Eileen Hor, Lewis Williams, George Taiaroa, Eike Steinig, Shivani Pasricha, Deborah A. Williamson

“…Here we present PathoGD, a bioinformatic pipeline for rapid and high-throughput design of RPA primers and gRNAs for CRISPR-Cas12a-based pathogen detection. …”
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Unveiling the endogenous CRISPR-Cas system in Pseudomonas aeruginosa PAO1. by Javier Alejandro Delgado-Nungaray, Luis Joel Figueroa-Yáñez, Eire Reynaga-Delgado, Ana Montserrat Corona-España, Orfil Gonzalez-Reynoso

“…Multidrug resistance in Pseudomonas aeruginosa, a high-priority pathogen per the World Health Organization, poses a global threat due to carbapenem resistance and limited antibiotic treatments. Using the bioinformatic tools CRISPRCasFinder, CRISPRCasTyper, CRISPRloci, and CRISPRImmunity, we analyzed the genome of P. aeruginosa PAO1 and revealed an orphan CRISPR system, suggesting it may be a remnant of a type IV system due to the presence of the DinG protein. …”
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Metagenomic Reveals the Role of Autochthonous <i>Debaryomyces hansenii</i> in the Fermentation and Flavor Formation of Dry Sausage by Qian Chen, Siyuan He, Mengtong Li, Yumeng Sui, Baohua Kong, Rongxin Wen

“…This study established a new insight into the metagenome-based bioinformatic effects of <i>D. hansenii</i> SH4 as a starter culture on the microbial synthesis of key volatile compounds in dry sausage.…”
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