Transcriptomic signatures of cold acclimated adipocytes reveal CXCL12 as a Brown autocrine and paracrine chemokine by Marina Agueda-Oyarzabal, Marie S. Isidor, Kaja Plucińska, Lars R. Ingerslev, Oksana Dmytriyeva, Patricia S.S. Petersen, Sara Laftih, Axel B. Pontoppidan, Jo B. Henningsen, Kaja Rupar, Erin L. Brown, Thue W. Schwartz, Romain Barrès, Zachary Gerhart-Hines, Camilla C. Schéele, Brice Emanuelli

“…For this, mRNA levels in mature adipocytes from mouse adipose depots were assessed using RNA sequencing upon chronic cold acclimation, and bioinformatic analysis was used to identify secreted factors. …”
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WWTR1-AS1 LncRNA as a Novel Potential Diagnostic and Prognostic Biomarker in Breast Cancer by Mohadese Safabakhsh, Sohrab Boozarpour, Kamran Ghaedi, Mina Lashkarboloki, Shaaban Ghalandarayeshi

“…In addition, these regulatory elements were related to three biological functions and 11 pathways. Finally, bioinformatic analysis identified lncRNA WWTR1-AS1 as having the highest node score involved in different mechanisms. …”
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Pangenome Analysis of Helicobacter pylori Isolates from Selected Areas of Africa Indicated Diverse Antibiotic Resistance and Virulence Genes by Biigba Yakubu, Edwin Moses Appiah, Andrews Frimpong Adu

“…As a result, this study compared the genomes of selected H. pylori isolates from selected areas of Africa and evaluated their virulence and antibiotic drug resistance, those that are highly pathogenic and are associated with specific clinical outcomes and those that are less virulent and rarely associated with clinical outcomes. 146 genomes of H. pylori isolated from selected locations of Africa were sampled, and bioinformatic tools such as Abricate, CARD RGI, MLST, Prokka, Roary, Phandango, Google Sheets, and iTOLS were used to compare the isolates and their antibiotic resistance or susceptibility. …”
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Islands of genomic stability in the face of genetically unstable metastatic cancer. by Kirsten Bowland, Jiaying Lai, Alyza Skaist, Yan Zhang, Selina Shiqing K Teh, Nicholas J Roberts, Elizabeth Thompson, Sarah J Wheelan, Ralph H Hruban, Rachel Karchin, Matthew H Bailey, Christine A Iacobuzio-Donahue, James R Eshleman

“…CRISPR-Cas9 PAM targets were determined by bioinformatic tumor-normal subtraction for each patient and verified in metastatic samples by high-depth capture-based sequencing.…”
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Physiology‐based pharmacokinetic model with relative transcriptomics to evaluate tissue distribution and receptor occupancy of anifrolumab by Pradeep Sharma, David W. Boulton, Lynn N. Bertagnolli, Weifeng Tang

“…A novel relative transcriptomics approach was employed to determine IFNAR1 expression in tissues (blood, skin, gastrointestinal tract, lungs, and muscle) using mRNA abundances from bioinformatic databases. The IFNAR1 expression and PBPK model were validated by testing their ability to predict clinical pharmacokinetics over a large dose range from different clinical scenarios after subcutaneous and intravenous anifrolumab dosing. …”
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Se-methylselenocysteine inhibits inflammatory response in an LPS-stimulated chicken HD11 macrophage-like cell model through the NFKB2 pathway by Min Yao, Binyu Wang, Zitong Li, Suqing Wu, Bingyu Zhao, Ning Sun, Huiping Xiao, Jianwu Wang, Guoping Liu, Tinghua Huang

“…RNA-seq identified 3,263 transcripts that exhibited a statistically significant differential expression between the SeMC-treated group and the control group and 1,344 transcripts that exhibited a statistically significant differential expression between the LPS + SeMC- and LPS-treated groups (FDR < 0.05, FDR > 1.5). The bioinformatic analysis identified six transcription factors (NFKB2, RFX2, E2F5, ETV5, BACH1, and E2F7) as potential candidate genes for transcriptome regulation in SeMC-treated HD11 cells. …”
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Identification of new candidate genes for the hereditary predisposition to uveal melanoma: IGCMU trial by Mélanie Godiveau, Mélanie Godiveau, Mélanie Godiveau, Angeline Ginzac, Angeline Ginzac, Angeline Ginzac, Yannick Bidet, Yannick Bidet, Flora Ponelle-Chachuat, Flora Ponelle-Chachuat, Maud Privat, Maud Privat, Xavier Durando, Xavier Durando, Xavier Durando, Xavier Durando, Mathias Cavaillé, Mathias Cavaillé, Mathis Lepage, Mathis Lepage

“…The primary objective is to identify novel candidate genes associated with hereditary cancer predisposition among UM patients. A several-step-bioinformatic analysis will be conducted to identify the genes of interest. …”
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RNA‐Binding Protein Hnrnpa1 Triggers Daughter Cardiomyocyte Formation by Promoting Cardiomyocyte Dedifferentiation and Cell Cycle Activity in a Post‐Transcriptional Manner by Chuling Li, Yijin Chen, Qiqi Chen, Haoxiang Huang, Michael Hesse, Yilin Zhou, Ming Jin, Yu Liu, Yifei Ruan, Xiang He, Guoquan Wei, Hao Zheng, Senlin Huang, Guojun Chen, Wangjun Liao, Yulin Liao, Yanmei Chen, Jianping Bin

“…By performing integrated bioinformatic analysis of snRNA‐seq data from neonatal and adult hearts, this study identified Hnrnpa1 as a potential RBP regulating CM DACCA. …”
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Propofol Ameliorates Microglia Activation by Targeting MicroRNA-221/222-IRF2 Axis by Xi Xiao, Yuanyuan Hou, Wei Yu, Sihua Qi

“…The biological roles and mechanisms of propofol in microglia activation were determined in BV2 cells and primary microglia. Bioinformatic analysis and luciferase reporter assay were used to confirm the regulatory role of miR-221/222 in Irf2 expression. …”
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Establishment and Validation of a Gene Signature-Based Prognostic Model to Improve Survival Prediction in Adrenocortical Carcinoma Patients by Xiaoqin Ge, Zhenzhen Liu, Xuehua Jiao, Xueyan Yin, Xiujie Wang, Gengxu Li

“…Using a series of bioinformatic and statistical approaches, a gene-expression signature was established and validated in two independent cohorts. …”
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Molecular Identification and Antimicrobial Potential of Streptomyces Species from Nepalese Soil by Karan Khadayat, Dawa Dindu Sherpa, Krishna Prakash Malla, Sunil Shrestha, Nabin Rana, Bishnu P. Marasini, Santosh Khanal, Binod Rayamajhee, Bibek Raj Bhattarai, Niranjan Parajuli

“…Streptomyces species were isolated on ISP4 media, and characterization was performed according to morphological similarity and 16S rRNA sequence similarity using bioinformatic tools. Ethyl acetate extracts of Streptomyces species were prepared, and the antimicrobial activity was carried out using agar well diffusion technique. …”
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Involvement of circRNAs in Proinflammatory Cytokines-Mediated β-Cell Dysfunction by Zhen Wang, Chao Deng, Ying Zheng

“…MicroRNA target prediction software and multiple bioinformatic approaches were used to predict the targeting genes of circRNAs and analyze possible functions of the circRNAs. …”
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circ_0075048 silencing regulates LCP1 to improve IL-1β-induced chondrocyte injury by binding with miR-663b by Pin Zhang, Ru Pei, Quanhu Shen

“…Human chondrocytes were stimulated with IL-1β to establish an in vitro OA model. Bioinformatic analysis was performed to identify target genes of circ_0075048. …”
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Proteomic characterization of molecular mechanisms of paraquat-induced lung injury in a mouse model by Yu Qing Zhou, Jin Jin Peng, Li Ping Shan, Wei Liu

“…Lung tissue components were assessed with tandem mass spectrometry tag technology, and differentially expressed proteins (DEPs) were bioinformatically analyzed and investigated with parallel reaction monitoring. …”
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An investigation of a hemophilia A female with heterozygous intron 22 inversion and skewed X chromosome inactivation by Xiaoyan Tan, Yi Yang, Xia Wu, Jing Zhu, Teng Wang, Huihui Jiang, Shu Chen, Shifeng Lou

“…Molecular genetic examinations, karyotype analysis, X-chromosome inactivation testing, and targeted bioinformatic analysis were used to identify potential genetic etiologies.ResultsThe proband exhibited a severe bleeding phenotype and was found to be a heterozygous carrier of an intron 22 inversion (Inv22) with a normal chromosomal karyotype. …”
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Problems with studying directional natural selection in humans by S. V. Mikhailova

“…The review describes the main methods for assessing directional selection in human populations. These include bioinformatic analysis of DNA sequences via detection of linkage disequilibrium and of deviations from the random distribution of frequencies of genetic variants, demographic and anthropometric studies based on a search for a correlation between fertility and phenotypic traits, genome-wide association studies on fertility along with genetic loci and polygenic risk scores, and a comparison of allele frequencies between generations (in modern samples and in those obtained from burials). …”
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The Major Prognostic Features of Nuclear Receptor NR5A2 in Infiltrating Ductal Breast Carcinomas by Li-Yun Chang, Li-Yu D. Liu, Don A. Roth, Wen-Hung Kuo, Hsiao-Lin Hwa, King-Jen Chang, Fon-Jou Hsieh

“…A supervised network analysis approach was used to build the NR5A-mediated transcriptional regulatory network. Other bioinformatic tools and statistical methods were utilized to confirm and extend results from the network analysis methodology. …”
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Metaproteomic portrait of the healthy human gut microbiota by Alessandro Tanca, Antonio Palomba, Giovanni Fiorito, Marcello Abbondio, Daniela Pagnozzi, Sergio Uzzau

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Overexpression of PAX8-AS1 Inhibits Malignant Phenotypes of Papillary Thyroid Carcinoma Cells via miR-96-5p/PKN2 Axis by Ping Zhou, Tongdao Xu, Hao Hu, Fei Hua

“…The expression of genes was detected by qRT-PCR. The bioinformatic analysis and luciferase reporter assay were used to confirm the binding relationship of PAX8-AS1 to miR-96-5p, and the targeting relationship of miR-96-5p to PKN2 was also predicted. …”
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Mesenchymal Stem Cells May Alleviate the Intervertebral Disc Degeneration by Reducing the Oxidative Stress in Nucleus Pulposus Cells by Yongzhao Zhao, Qian Xiang, Yunzhong Cheng, Jialiang Lin, Shuai Jiang, Weishi Li

“…Methods. A series of bioinformatic methods were used to calculate the oxidative stress score and autophagy score, identify the OSRDEGs, conduct the function enrichment analysis and protein-protein interaction (PPI) analysis, build the relevant competing endogenous RNA (ceRNA) regulatory networks, and explore the potential association between oxidative stress and autophagy in degenerative NPCs cocultured with MSCs. …”
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