SiCLAT: simultaneous imaging of chromatin loops and active transcription in living cells by Xin Wan, Jie Kong, Xiaodi Hu, Lulu Liu, Yuanping Yang, Hu Li, Gaoao Liu, Xingchen Niu, Fengling Chen, Dan Zhang, Dahai Zhu, Yong Zhang

Get full text

RETRACTED ARTICLE: NR3C2 affects the proliferation and invasiveness of colon cancer cells through the Wnt/β-Catenin signaling pathway by Ke Nie, Zhong-Jiang He, Ling-Jun Kong

“…The relative role of NR3C2 were further predicted through bioinformatics methods and receiver operating characteristic (ROC) curve was used to evaluate the diagnostic value of NR3C2 in colon cancer. …”
Get full text

Increased TSPO alleviates neuropathic pain by preventing pyroptosis via the AMPK-PGC-1α pathway by Baolong Li, Kaiming Yu, Xiongyao Zhou, Jialu Sun, Le Qi, Weiye Li, Tuo Yang, Weizhen Li, Ningning Wang, Xiaosong Gu, Shusen Cui, Rangjuan Cao

“…Abstract Neuropathic pain poses a significant clinical challenge, largely due to the incomplete understanding of its molecular mechanisms, particularly the role of mitochondrial dysfunction. Bioinformatics analysis revealed that pyroptosis and inflammatory responses induced by spared nerve injury (SNI) in the spinal dorsal horn play a critical role in the initiation and persistence of neuropathic pain. …”
Get full text

Genes related to neural tube defects and glioblastoma by Rui Cao, Yurong Liu, Kaixin Wei, Ning Jin, Yuxiang Liang, Ruifang Ao, Weiwei Pan, Xiang Wang, Xiuwei Wang, Li Zhang, Jun Xie

“…To obtain genes related to both NTDs and GBM, as well as small molecule drugs with potential clinical application value. We performed bioinformatics analysis on transcriptome sequencing data of retinoic acid (RA)-induced NTDs mice, human NTDs samples and GBM samples. …”
Get full text

Abnormal ac4C modification in metabolic dysfunction associated steatotic liver cells by Xiqian Zhang, Yaxian Zheng, Jing Yang, Yan Yang, Qin He, Min Xu, Fangyi Long, Yujie Yang

“…We also identified 341 differentially expressed genes (DEGs), including 61 lncRNAs and 280 mRNAs, between control and MASLD model cells. Bioinformatics analysis showed that DEGs were significantly enriched in long-chain fatty acid biosynthetic process. …”
Get full text

Intelligent Electrochemical Sensing: A New Frontier in On-the-Fly Coffee Quality Assessment by Simone Grasso, Maria Vittoria Di Loreto, Alessandro Zompanti, Davide Ciarrocchi, Laura De Gara, Giorgio Pennazza, Luca Vollero, Marco Santonico

Get full text

Pathogenicity and Whole Genome Sequence Analysis of a Pseudorabies Virus Strain FJ-2012 Isolated from Fujian, Southern China by Xue-min Wu, Qiu-yong Chen, Ru-jing Chen, Yong-liang Che, Long-bai Wang, Chen-yan Wang, Shan Yan, Yu-tao Liu, Jin-sheng Xiu, Lun-jiang Zhou

“…We then conducted a few downstream bioinformatics analyses including phylogenetic analysis and pathogenic analysis and used the virus to infect 6 pseudorabies virus-free piglets. …”
Get full text

Genomic insights into multidrug-resistant Acinetobacter baumannii strains isolated from Dhaka, Bangladesh by Sadia Ferdous, K M Shayerul Abedin Shayer, Afia Anjum, Sabbir R. Shuvo, Ishrat Jabeen, Kristi Paul Hridi, A.K.M. Imrul Hassan, Md Imran Khan, Mohammad Fazle Alam Rabbi, Mahmud Hossain, Kazi Nadim Hasan, Sohidul Islam

Get full text

Unraveling nitrogen metabolism, cold and stress adaptation in polar Bosea sp. PAMC26642 through comparative genome analysis by Anamika Khanal, Anamika Khanal, So-Ra Han, So-Ra Han, So-Ra Han, Jun Hyuck Lee, Tae-Jin Oh, Tae-Jin Oh, Tae-Jin Oh, Tae-Jin Oh

“…Comparative genomic analysis was performed using various bioinformatics tools to compare Bosea sp. PAMC26642 with other strains of the same genus, emphasizing nitrogen metabolism and stress adaptability. …”
Get full text

Single nucleotide polymorphism rs110861313 in the intergenic region of chromosome 23 is associated with the development of leukosis in the Russian Black Pied cattle by R. B. Aitnazarov, E. V. Ignatieva, T. A. Agarkova, N. G. Dvoeglazov, N. A. Osipova, V. V. Khramtsov, N. S. Yudin

“…In this case, asymptomatic virus carriers can be considered a more suitable control than healthy animals that have not been in contact with the virus. According to bioinformatics analysis, resistance to BLV can be due to the presence of the transcription factor FOXM1 binding site in the region of rs110861313. …”
Get full text

The genome sequence of the Montseny horsehair worm, Gordionus montsenyensis sp. nov., a key resource to investigate Ecdysozoa evolution by Eleftheriadi, Klara, Guiglielmoni, Nadège, Salces-Ortiz, Judit, Vargas-Chavez, Carlos, Martínez-Redondo, Gemma I., Gut, Marta, Flot, Jean-François, Schmidt-Rhaesa, Andreas, Fernández, Rosa

Get full text

LURAP1L-AS1 long noncoding RNA promotes breast cancer progression and associates with poor prognosis by Radhakrishnan Vishnubalaji, Dania Awata, Nehad M. Alajez

“…RNA sequencing of LURAP1L-AS1-depleted cells revealed dysregulation of pathways related to cell proliferation, apoptosis, migration, and RNA processing. Bioinformatics analysis predicted LURAP1L-AS1 to function as a competitive endogenous RNA (ceRNA), sponging key microRNAs, such as miR-7a-5p, miR-101-3p, miR-181a-5p, and miR-27a-3p, thereby modulating oncogenes including EZH2, MCL1, and KRAS, which are linked to increased cancer cell survival, proliferation, and metastasis.In addition to its role in TNBC, correlation analysis using breast cancer patient datasets revealed a significant association between LURAP1L-AS1 and ESR1 expression, suggesting its broader impact across breast cancer subtypes. …”
Get full text

Comprehensive analysis of α2,3-sialyltransferases as prognostic biomarkers and immunotherapy targets in kidney renal clear cell carcinoma by Yuli Jian, Kangkang Yang, Jinjing Li, Ling Tang, Guang Zeng, Xiaoxin Sun, Xiao Yu, Abdullah Al-danakh, Qiwei Chen, Deyong Yang, Shujing Wang

“…In the study, through systematic bioinformatics analysis and experimental verification, we demonstrated that ST3Gal5 expression was elevated in tumor tissues of KIRC patients, correlating with poor prognosis, and ST3Gal1 was downregulated and associated with a better prognosis. …”
Get full text

Biodegradation of aflatoxin B1 by a novel mined aldo–keto reductase from Meyerozyma guilliermondii AF01 by Wan Zhang, Xiaojiao Chang, Yangying Han, Tiantian Li, Jianpeng Dou, Wen Du, Wenfu Wu, Wei Wang, Zhongjie Zhang, Changpo Sun

“…In this study, a potential degradation gene, MG2-4, was mined using a combination of bioinformatics and chemical approaches. The gene was heterologously expressed in Escherichia coli Rosetta DE3, and the recombinant protein, Mg aldo–keto reductase (AKR), reacted with AFB1 in vitro. …”
Get full text

<i>Botrytis cinerea</i> PMT4 Is Involved in <i>O</i>-Glycosylation, Cell Wall Organization, Membrane Integrity, and Virulence by Verónica Plaza, Alice Pasten, Luz A. López-Ramírez, Héctor M. Mora-Montes, Julia Rubio-Astudillo, Evelyn Silva-Moreno, Luis Castillo

“…The <i>PMT</i> family is grouped into <i>PMT1</i>, <i>PMT2</i>, and <i>PMT4</i> subfamilies. Using bioinformatics analysis within the <i>Botrytis cinerea</i> genome database, an ortholog to <i>Saccharomyces cerevisiae</i> Pmt4 and other fungal species was identified. …”
Get full text

Ameliorative effect of curcuminoids in liver fibrosis rat model via regulating GIPC1 gene and modulating MMP-8/TIMP-3 balance mediated by miR-483-5p by Rana Mostafa Adel, Sara Mostafa Kamal, Eman Adel Sherif, Sara Hatem El-shafiey

“…Surprisingly, significant upregulation in miRNA-483 expression was obtained in CURC-treated rats which consequentially enhanced MMP-8/TIMP-3 balance in the form of an elevation in MMP-8/reduction in TIMP-3 levels, along with confirming this novel pathway through conducting bioinformatics analysis. All these enhancements were mirrored in Annexin V/PI (Annexin V Propidium Iodide) assay as massive improvements in % of apoptotic and necrotic cells, plus, in H&E (hematoxylin and eosin) and Masson’s trichrome histopathological examinations that showed near to normal liver architecture with no collagen bands deposition. …”
Get full text

Collection of microorganisms of ICG SB RAS as a genetic resource for biotechnology by A. V. Bryanskaya, Y. E. Uvarova, A. S. Rozanov, N. M. Slynko, V. N. Shlyakhtun, K. V. Starostin, E. A. Demidov, E. V. Lazareva, O. P. Taran, S. E. Peltek

“…The value of the collection of microorganisms of the FRC ICG SB RAS as a genetic resource for biotechnology and bioengineering is determined not only by the species diversity of its strains, but also by a wide range of their area isolation and by the depth of their characterization using the widest arsenal of both classical and modern methods (including methods of genomics, proteomics, transcriptomics and bioinformatics).…”
Get full text

LIPUS promotes osteogenic differentiation of rat BMSCs and osseointegration of dental implants by regulating ITGA11 and focal adhesion pathway by Chao Liang, Yuqing Zhang, Yuwei Yan, Wei Geng, Jun Li, Xiu Liu

“…Results Our in vivo experimentations verified that LIPUS significantly increased new bone formation and osseointegration around the implant in rats. Bioinformatics analysis of RNA-seq data revealed that the upregulated genes in BMSCs after LIPUS treatment were significantly enriched in osteoblast differentiation-related functions and focal adhesion-related pathways. …”
Get full text

Evaluation of recombinant proteins <i>T. pallidum</i> Тр0163 and Тр0971 as antigens for the diagnosis of syphilis using enzyme immunoassay by Natalia V. Arbuzova, Marina V. Shpilevaya, Georgii L. Katunin, Oleg E. Kuznetsov, Nikita Yu. Nosov, Viсtoria S. Solomka

“…With the deciphering of the T. pallidum genome and the application of bioinformatics and immunoproteomics, many recombinant T. pallidum proteins have emerged that have been evaluated for their diagnostic value, some of which are used as diagnostic antigens in commercial tests. …”
Get full text

Integrated analyses uncover new features of atypical memory B cells and novel targets for intervention by Fuli Fan, Shubei Liu, Bin Wang, Xiaojian Song, Wei Wang

“…Functional characterization of AMB was performed with bioinformatics and CyTOF-based phenotyping. Alternation of AMB in systemic lupus erythematosus (SLE), rheumatoid arthritis (RA) and Sjögren's syndrome (SjS) was evaluated via bioinformatic approaches. …”
Get full text