Impacts of host phylogeny, diet, and geography on the gut microbiome of rodents. by Sufia Akter Neha, John D Hanson, Jeremy E Wilkinson, Robert D Bradley, Caleb D Phillips

“…Colon samples were examined from rodents that were collected from 7 different localities in Texas and Oklahoma which were characterized using 16S rRNA gene amplicon sequencing targeting the V1-V3 variable regions. The microbiota of colon samples was largely dominated by the family Porphyromonadaceae (Parabacteriodes, Coprobacter) and herbivorous hosts harbored richer gut microbial communities than granivores and omnivores. …”
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Molecular Characterization of Wild and Cultivated Strawberry (Fragaria × ananassa) through DNA Barcode Markers by Awais Qarni, Khushi Muhammad, Abdul Wahab, Amir Ali, Chandni Khizar, Izhar Ullah, Abeer Kazmi, Tahira Sultana, Asma Hameed, Muhammad Younas, Mehdi Rahimi

“…The phylogenetic tree was constructed by using Fragaria current species sequences and reference sequences through the neighbor-joining method or maximum likelihood method. …”
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Meta-Omics Analyses of Conventional and Regenerative Fermented Vegetables: Is There an Impact on Health-Boosting Potential? by Kylene Guse, Qingqing Mao, Chi Chen, Andres Gomez

“…We profiled bacterial and fungal communities via 16S rRNA short-read (V4 region), long-read, and ITS2 sequencing, in tandem with untargeted metabolomics (LC-MS). …”
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Identification of therapeutic targets for Alzheimer’s Disease Treatment using bioinformatics and machine learning by ZhanQiang Xie, YongLi Situ, Li Deng, Meng Liang, Hang Ding, Zhen Guo, QinYing Xu, Zhu Liang, Zheng Shao

“…By integrating differential gene expression analysis, weighted gene co-expression network analysis, Mfuzz clustering, single-cell RNA sequencing, and machine learning algorithms including LASSO regression, SVM-RFE, and random forest, five hub genes related to AD, including PLCB1, NDUFAB1, KRAS, ATP2A2, and CALM3 were identified. …”
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Expressional Subpopulation of Cancers Determined by G64, a Co-regulated Module by Jae-Woong Min, Sun Shim Choi

“…Here, we investigated whether the G64 module genes were also expressed distinctively in different subpopulations of other cancers. RNA sequencing-based transcriptome data derived from 22 cancers, except LADC, were downloaded from The Cancer Genome Atlas (TCGA). …”
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Sequential Treatment with Activin and Hepatocyte Growth Factor Induces FOXM1 to Promote Colorectal Cancer Liver Metastasis by Hong Peng, Ting Ye, Lei Deng, Xiaofang Yang, Zheng Jiang, Jinjun Guo

“…HCT116 CRC cells were sequentially treated with activin and HGF and examined for migration and invasion in vitro and liver metastasis in vivo. RNA sequencing was performed to identify differentially expressed genes in response to activin and HGF. …”
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Non-native PGPB consortium consisting of Pseudomonas sp. G31 and Azotobacter sp. PBC2 promoted winter wheat growth and slightly altered the native bacterial community by J. Dobrzyński, I. Kulkova, Z. Jakubowska, B. Wróbel

“…For the metataxonomic study, Next-Generation Sequencing was performed using the Illumina NovaSeq 6000 system. …”
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Bacterial Infections across the Ants: Frequency and Prevalence of Wolbachia, Spiroplasma, and Asaia by Stefanie Kautz, Benjamin E. R. Rubin, Corrie S. Moreau

“…Bacterial endosymbionts are common across insects, but we often lack a deeper knowledge of their prevalence across most organisms. Next-generation sequencing approaches can characterize bacterial diversity associated with a host and at the same time facilitate the fast and simultaneous screening of infectious bacteria. …”
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Development of a high-throughput screening system for identification of novel reagents regulating DNA damage in human dermal fibroblasts by Bae Seunghee, An In-Sook, An Sungkwan

“…In the second step, we validated certain effective reagents identified in the first step by analyzing the cell cycle, evaluating cell death, and performing HPRT-DNA sequencing in DREAM-F cells treated with these reagents and UVB. …”
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Prefibrotic Myelofibrosis Presenting with Multiple Cerebral Embolic Infarcts and the Rare MPL W515S Mutation by Stephen E. Langabeer, Lisa Lee Tokar, Laura Kearney, Cathal O’Brien, Kowshika Thavarajah, Aisling Barrett, John McManus, Hilary O’Leary

“…Bone marrow biopsy showed evidence of prefibrotic myelofibrosis with targeted sequencing demonstrating the presence of the rare MPL W515S mutation. …”
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Isolation and Characterization of Diesel-Degrading Bacteria from Hydrocarbon-Contaminated Sites, Flower Farms, and Soda Lakes by Gessesse Kebede Bekele, Solomon Abera Gebrie, Eshetu Mekonen, Tekle Tafese Fida, Adugna Abdi Woldesemayat, Ebrahim M. Abda, Mesfin Tafesse, Fasil Assefa

“…Consequently, the partial 16S rRNA gene sequences revealed that the two most potent bacterial strains (AAUW23 and AAUG11) were Pseudomonas aeruginosa, while AAUG36 was Bacillus subtilis. …”
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Integrated gene expression and alternative splicing analysis in human and mouse models of Rett syndrome by Silvia Gioiosa, Silvia Gasparini, Carlo Presutti, Arianna Rinaldi, Tiziana Castrignanò, Cecilia Mannironi

“…To perform a comparative analysis of publicly available RNA sequencing (RNA-seq) studies and generate novel data resources for AS, we explored 100 human datasets and 130 mouse datasets from Mecp2-mutant models, processing data for gene expression and alternative splicing. …”
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Bacterial Colonization in the Airways and Intestines of Twin and Singleton Preterm Neonates: A Single-Center Study by Jiawei Yao, Tao Ai, Lei Zhang, Wei Tang, Zijin Chen, Yuedong Huang, Yinghong Fan

“…These specimens were analyzed using 16S rRNA deep sequencing to study the alpha and beta diversities and community structures of airway and intestinal bacteria and predict their metabolic functions. …”
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Alterations of the Gut Microbiome in Chinese Zhuang Ethnic Patients with Sepsis by Jieyang Yu, Hongping Li, Jingjie Zhao, Yanhua Huang, Chunlei Liu, Pengfei Yang, Dinggui Lu, Jian Song, Lingzhang Meng

“…Their gut microbial community profiles were analyzed by 16S rRNA gene sequencing using the Illumina MiSeq system. Results. …”
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Integrative analysis of SEPN1 in glioma: Prognostic roles, functional implications, and potential therapeutic interventions. by Zisong Wang, Danwen Wang, Xuanyu Wang, Yihang Xu, Yunhe Yuan, Yuxin Chen, Zhiqiang Li, Xiaoping Liu

“…SEPN1 in glioma was further examined using data from TCGA, CGGA, GEO, and ZN-GC cohorts, along with survival analysis, single-cell RNA sequencing analysis, and enrichment analysis. We developed an SEPN1-related risk score (SRS) based on SEPN1-related long non-coding RNAs and validated its prognostic value. …”
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Discontiguous recurrences of IDH-wildtype glioblastoma share a common origin with the initial tumor and are frequently hypermutated by Malcolm F. McDonald, Sricharan Gopakumar, Tareq A. Juratli, Ilker Y. Eyüpoglu, Ganesh Rao, Jacob J. Mandel, Ali Jalali

“…In our institutional database, we identified 22 patients with targeted exome sequencing of pairs of initial and recurrent IDH-wildtype glioblastoma. …”
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Study of Modern Human Evolution via Comparative Analysis with the Neanderthal Genome by Musaddeque Ahmed, Ping Liang

“…It has always been considered fascinating to compare the modern human genome with that of archaic humans to identify modern human-specific sequence variants and figure out those that made modern humans different from their predecessors or cousin species. …”
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Screening and Identification of Thermotolerant and Osmotolerant Bacillus amyloliquefaciens BKHE Isolated from Kinema of Eastern Nepal for Alkaline Protease Production by Gyanu Raj Pandey, Asmita Shrestha, Tika B. Karki, Shardul Neupane, Sabnam Ojha, Prashanna Koirala, Parash Mani Timilsina

“…The selected isolate was identified as Bacillus amyloliquefaciens BKHE based on 16S rRNA sequencing and phenotypic features. This bacterial strain was also found to be thermotolerant (confluent growth at 50°C) and salt tolerant up to 10% NaCl concentration. …”
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Transcriptome Analyses Reveal Lipid Metabolic Process in Liver Related to the Difference of Carcass Fat Content in Rainbow Trout (Oncorhynchus mykiss) by Guo Hu, Wei Gu, Peng Sun, Qingli Bai, Bingqian Wang

“…RNA-seq based whole transcriptome sequencing was performed to liver tissue of rainbow trout with high and low carcass fat content in this study. …”
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Short Reads Phasing to Construct Haplotypes in Genomic Regions That Are Associated with Body Mass Index in Korean Individuals by Kichan Lee, Seonggyun Han, Yeonjeong Tark, Sangsoo Kim

“…Here, we tried to make a haplotype catalog affecting body mass index (BMI) through an integrative analysis of previously published whole-genome next-generation sequencing (NGS) data of 7 representative Korean individuals and previously known Korean GWA signals. …”
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