The heterogeneity of NOTCH1 to tumor immune infiltration in pan-cancer by XiaoJun Duan, Rihan Wu, Mingyang Zhang, Kexin Li, Lei Yu, Huirong Sun, Xingxia Hao, Changshan Wang

“…In this study, the data originated from the Genotype-Tissue Expression (GTEx) and the Cancer Genome Atlas (TCGA) databases were input into multiple online bioinformatic tools to study the characteristics of NOTCH1 in pan-cancer. …”
Get full text

Importance of appropriate genome information for the design of mating type primers in black and yellow morel populations by Melissa Cravero, Aaron J. Robinson, Patrick Hilpisch, Patrick S. Chain, Saskia Bindschedler, Pilar Junier

“…To evaluate the design and theoretical performance of these primers we performed a thorough bioinformatic investigation, including the detection of the MAT region in publicly available Morchella genomes and in-silico PCR analyses. …”
Get full text

The Underlying Molecular Basis and Mechanisms of Venous Thrombosis in Patients with Osteomyelitis: A Data-Driven Analysis by Peisheng Chen, Yinhuan Liu, Xiaofeng Lin, Bin Yu, Bin Chen, Fengfei Lin

“…This is the first data-mining study to explore shared signatures between OM and VTE by the integrated bioinformatic approach, which can help uncover potential biomarkers and therapeutic targets of OM-related VTE.…”
Get full text

Cannabidiol Ameliorates Doxorubicin-Induced Myocardial Injury via Activating Hippo Pathway by Dong T, Li J, Liang X, Wang W, Chen M, Yang G, Wu D

“…Western blotting was used to investigate the regulatory effects of CBD on the Hippo and apoptosis-related pathways.Results: Bioinformatic analysis suggested that the Hippo pathway was a crucial pathway involved in DOX-induced myocardial injury. …”
Get full text

Glutamine missense suppressor transfer RNAs inhibit polyglutamine aggregation by Rasangi Tennakoon, Teija M.I. Bily, Farah Hasan, Sunidhi Syal, Aaron Voigt, Tugce B. Balci, Kyle S. Hoffman, Patrick O’Donoghue

Get full text

Comparative genomics analyses of Actinobacteriota identify Golgi phosphoprotein 3 (GPP34) as a widespread ancient protein family associated with sponge symbiosis by Cláudia Ferreira, Ilia Burgsdorf, Tzipora Perez, Gustavo Ramírez, Maya Lalzar, Dorothée Huchon, Laura Steindler

Get full text

Functional Characterization of the <i>PoWHY1</i> Gene from <i>Platycladus orientalis</i> and Its Role in Abiotic Stress Tolerance in Transgenic <i>Arabidopsis thaliana</i> by Chun Ou, Zhiyu Dong, Xudong Zheng, Wenhui Cheng, Ermei Chang, Xiamei Yao

“…Here, the <i>PoWHY1</i> gene was analyzed bioinformatically using <i>P. orientalis</i> as study material, and the role of the gene against abiotic stress conditions in <i>Arabidopsis thaliana</i> was verified using transgenic technology. …”
Get full text

Genome-Wide Identification and Expression Analysis of bHLH-MYC Family Genes from Mustard That May Be Important in Trichome Formation by Jianzhong Li, Guoliang Li, Caishuo Zhu, Shaoxing Wang, Shifan Zhang, Fei Li, Hui Zhang, Rifei Sun, Lingyun Yuan, Guohu Chen, Xiaoyan Tang, Chenggang Wang, Shujiang Zhang

“…In this study, a total of 45 bHLH-MYC transcription factors were identified within the <i>Brassica juncea</i> genome, and a comprehensive series of bioinformatic analyses were conducted on their structures and properties: an examination of protein physicochemical properties, an exploration of conserved structural domains, an assessment of chromosomal positional distributions, an analysis of the conserved motifs, an evaluation of the gene structures, microsynteny analyses, three-dimensional structure prediction, and an analysis of sequence signatures. …”
Get full text

Development of delayed pulmonary toxicities and transcriptional changes in pre-existing interstitial lung disease mice after partial thoracic irradiation by Jiamei Fu, Xinglong Liu, Yuchuan Zhou, Shengnan Zhao, Liang Zeng, Yan Pan, Jianghong Zhang, Kevin M. Prise, Chunlin Shao, Yaping Xu

“…The histological phenotypes manifested exudative predominated DAD phase in the early phase and proliferating DAD pattern in the late phase. Bioinformatic analysis showed signaling pathways relevant to immune cell migration, epithelial cell development, and extracellular structure organization were commonly activated in different models. …”
Get full text

A concept of natural genome reconstruction. Part 2. Effect of extracellular double-stranded DNA fragments on hematopoietic stem cells by V. S. Ruzanova, S. G. Oshikhmina, A. S. Proskurina, G. S. Ritter, S. S. Kirikovich, E. V. Levites, Y. R. Efremov, T. V. Karamysheva, M. I. Meschaninova, A. L. Mamaev, O. S. Taranov, A. S. Bogachev, S. V. Sidorov, S. D. Nikonov, O. Y. Leplina, A. A. Ostanin, E. R. Chernykh, N. A. Kolchanov, E. V. Dolgova, S. S. Bogachev

“…It is known that the process of internalization of extracellular DNA fragments involves glycocalyx structures, which include glycoproteins/protein glycans, glycosylphosphatidylinositol-anchored proteins and scavenger receptors. The bioinformatic analysis conducted indicates that the main surface marker proteins of hematopoietic stem cells belong to the indicated groups of factors and contain specific DNA binding sites, including a heparin-binding domain and clusters of positively charged amino acid residues. …”
Get full text

Whole genome sequencing of a novel carrageenan-degrading bacterium Photobacterium rosenbergii and oligosaccharide preparation by Jing Chen, Jing Chen, Runmin Chen, Kit-Leong Cheong, Zhuo Wang, Rui Li, Xuejing Jia, Qiaoli Zhao, Xiaofei Liu, Bingbing Song, Saiyi Zhong, Saiyi Zhong

“…The pure culture of strain GDSX-4 was further subjected to bacterial genome sequencing assembly and bioinformatic analysis. Specifically, homology group cluster (COG) annotation, CAZy (carbohydrate-active enzyme) database annotation and CAZyme genome clusters (CGCs) annotation were utilized to identify potential polysaccharide degradation functions. …”
Get full text

Long non-coding RNA Malat1 modulates CXCR4 expression to regulate the interaction between induced neural stem cells and microglia following closed head injury by Qin Dong, Pengyu Chen, Wenqiao Qiu, Zhijun Yang, Yanteng Li, Yuhui Zhou, Lili Guo, Dan Zou, Ruxiang Xu, Mou Gao

“…Methods We performed bioinformatic analysis to detect the differentially expressed genes in iNSCs after co-cultured with LPS-activated microglia. …”
Get full text

Safeguarding and using global banana diversity: a holistic approach by Ines Van den houwe, Rachel Chase, Julie Sardos, Max Ruas, Els Kempenaers, Valentin Guignon, Sebastien Massart, Sebastien Carpentier, Bart Panis, Mathieu Rouard, Nicolas Roux

“…The evaluation of desirable agronomic traits inherent in Musa spp. are investigated by a high-throughput phenotyping platform, which helps breeding programs to select cultivars resistant or tolerant to biotic and abiotic stresses. Genomic and bioinformatic studies of several banana wild relatives greatly enhance our understanding of Musa genetic diversity, links to important phenotypic traits and bring new methods for management of the collection. …”
Get full text

Preliminary evidence of immune infiltration and neutrophil degranulation in peripheral blood of non-obese OSA patients related to cognitive decline by Qingqing Liu, Yanru Ou, Ting Liu, Yuming He, Xiangming Quan, Ruoyun Ouyang, Zhihui Shi

“…The differentially expressed genes were identified by bioinformatic analysis and confirmed by PCR. Imbalanced immune cell proportions were assessed by Cibersort. …”
Get full text

Tousled-like kinase loss confers PARP inhibitor resistance in BRCA1-mutated cancers by impeding non-homologous end joining repair by Min-ah Kim, Banseok Kim, Jihyeon Jeon, Jonghyun Lee, Hyeji Jang, Minjae Baek, Sang-Uk Seo, Dongkwan Shin, Anindya Dutta, Kyung Yong Lee

“…Cell viability assays were conducted to evaluate resistance to PARP inhibitors. Additionally, bioinformatic analyses of public databases were performed to investigate the association between TLK expression and BRCA1 status. …”
Get full text

Genetic predisposition to Behcet's disease mediated by a IL10RA enhancer polymorphism by Handan Tan, Zhenyu Zhong, Xiaojie Feng, Xiang Luo, Qingfeng Cao, Peizeng Yang

“…Methods: To analyse the genetic susceptibility to BD mediated by IL10RA causal polymorphisms, we performed a study on data from our previous genome-wide association studies (GWAS), the bioinformatic analysis of post-annotation of GWAS and relevant mechanism verification experiments, including chromatin immunoprecipitation, luciferase gene-reporter assay, electrophoretic mobility shift assays, and enzyme-linked immunosorbent assay. …”
Get full text

Low Frequency of MKRN3 and DLK1 Variants in Chinese Children with Central Precocious Puberty by Ting Chen, Linqi Chen, Haiying Wu, Rongrong Xie, Fengyun Wang, Xiuli Chen, Hui Sun, Fei Xiao

“…We also performed bioinformatic analysis to evaluate the impact of variants on MKRN3 protein structures, which showed that Ile357Met locates at the zinc-binding region (C3HC4 RING finger motif), while Glu380Lys is spatially extremely close to the C3HC4 RING finger, MKRN-specific Cys-His domain, and the third C3H1 zinc-finger motif region. …”
Get full text

Integrating rapamycin with novel PI3K/Akt/mTOR inhibitor microRNAs on NOTCH1-driven T-cell acute lymphoblastic leukemia (T-ALL) by Fateme Arjmand, Samaneh Shojaei, Mitra Khalili, Hossein Dinmohammadi, Behzad Poopak, Samira Mohammadi-Yeganeh, Yousef Mortazavi

“…This study aimed to investigate the combined effects of rapamycin and miRNAs in inhibiting the PI3K/AKT/mTOR pathway in T-ALL cells. Methods: Bioinformatic algorithms were used to find miRNAs that inhibit the PI3K/AKT/mTOR pathway. …”
Get full text

An ensemble machine learning-based performance evaluation identifies top In-Silico pathogenicity prediction methods that best classify driver mutations in cancer by Subrata Das, Vatsal Patel, Shouvik Chakravarty, Arnab Ghosh, Anirban Mukhopadhyay, Nidhan K. Biswas

“…Despite the presence of numerous bioinformatic algorithms for estimating mutation pathogenicity, there is significant variation in their assessments. …”
Get full text

IQUB mutation induces radial spoke 1 deficiency causing asthenozoospermia with normal sperm morphology in humans and mice by Tingwenyi Hu, Xiangrong Tang, Tiechao Ruan, Shunhua Long, Guicen Liu, Jing Ma, Xueqi Li, Ruoxuan Zhang, Guoning Huang, Ying Shen, Tingting Lin

“…Protein mass spectrometry, western blotting, and bioinformatic analyses were performed to identify critical components of mammalian RS1 to model its structure and explore the pathological mechanism of IQUB deficiency. …”
Get full text