Bioinformatics

The research project deals with two different types of data for two separate analysis. The first analysis deals with normalised RNA-seq breast cancer data where machine learning techniques are used to classify and identify the biomarker of cancer. Second analysis deals with raw DNA methylated leukemia samples to determine the mutations.

102p runthenight04 02-02-2023 1 1   Download

Cellobiohydrolase (EC 3.2.1.91) is one of the important enzymes involved in cellulose hydrolysis. In this study, the gene sequences encoding cellobiohydrolase were extracted from the metagenome DNA data of microorganisms surrounding white-rot fungi in Cuc Phuong National Park based on the KEGG database. 73 ORFs encoding cellobiohydrolase were obtained, of which 15 ORFs contained complete genes, 6 ORFs with functional regions.

8p vineville 08-02-2023 1 1   Download

In this study, 23 GASA genes in common bean were identified and detailed bioinformatics analyzes were conducted at both gene and protein levels. Pvul-GASA proteins were categorized into three clusters, and a total of 13 duplication events (12 segmental and one tandem) were shown to play a role in the expansion of the GASA gene family in Phaseolus vulgaris L. The identified Pvul-GASAs have been shown to be linked to stress and hormone signaling pathways.

36p lyhuyenthu 31-01-2023 1 1   Download

In this paper, we show a detailed look at the barley XTH gene family, including detailed bioinformatics analyses of conserved protein motifs and structure, phylogenetic relationships, and a comparison of the expression patterns during germination and seedling growth using RT-qPCR and RNA-Seq analyses. Overall, there was a good correlation between RT-qPCR and RNA-Seq data for similar tissues. RNA-Seq data showed many different expression profile patterns, from broad, high level expression for some XTH genes to highly tissue specific patterns for others.

17p lyhuyenthu 31-01-2023 2 1   Download

This study aims to compare microRNA expression levels in wt and Bag-1 knockout (KO) MCF-7 breast cancer cells. hsa-miR-429 was selected as a potential miRNA in BAG-1KO MCF-7 cells because of the downregulation both in bioinformatics and validation qRT-PCR assay. According to predicted mRNA targets and functional enrichment analysis the ten hub proteins that are phosphatidylinositol4,5-biphosphate 3-kinase catalytic subunit alpha (PIK3CA), kinase insert domain receptor (KDR), GRB2 associated binding protein 1 (GAB1).

30p lyhuyenthu 31-01-2023 1 1   Download

Cancer is a disease in which abnormal cells grow uncontrollably and invade other tissues. Several types of cancer have various subtypes with different clinical and biological implications. Based on these differences, treatment methods need to be customized. The identification of distinct cancer subtypes is an important problem in bioinformatics, since it can guide future precision medicine applications. In order to design targeted treatments, bioinformatics methods attempt to discover common molecular pathology of different cancer subtypes.

17p lyhuyenthu 31-01-2023 1 1   Download

Peroxidases (PODs) have various physiological and biochemical roles in plant growth, development and stress response. The POD genes were identified in various plant species, but in passion fruit has not yet been thoroughly characterized. Here, we discovered 30 putative POD genes from the genome of Passiflora edulis Sims. For further elucidation, comprehensive bioinformatics analysis was utilized to determine the physicochemical properties, gene organization, conserved motifs, gene duplication and phylogenetic relationships of PePOD genes.

13p lyhuyenthu 31-01-2023 2 1   Download

Endometrial cancer is a common gynecological cancer with annually increasing incidence worldwide. However, the biomarkers that provide prognosis and progression for this disease remain elusive.

13p vihagrid 30-01-2023 3 2   Download

Pancreatic cancer (PC) is a highly lethal disease and an increasing cause of cancer-associated mortality worldwide. Interferon regulatory factors (IRFs) play vital roles in immune response and tumor cellular biological processes.

11p vihagrid 30-01-2023 6 2   Download

CesA and Csl gene families, which belong to the cellulose synthase gene superfamily, plays an important role in the biosynthesis of the plant cell wall. Although researchers have investigated this gene superfamily in several model plants, to date, no comprehensive analysis has been conducted in the common bean.

15p vihagrid 30-01-2023 3 2   Download

This study explored the key genes related to immune cell infiltration in endometriosis. Endometriosis is a benign gynecological condition characterized by the abnormal presence and growth of endometrial tissue outside the uterus.

16p vihagrid 30-01-2023 3 2   Download

Protein classification is a task of paramount importance in various fields of biology. Despite the great momentum of modern implementation of protein classification, machine learning techniques such as Random Forest and Neural Network could not always be used for several reasons: Data collection, unbalanced classification or labelling of the data.

18p vihagrid 30-01-2023 4 2   Download

Colitis-associated colon cancer (CAC) patients have a younger age of onset, more multiple lesions and invasive tumors than sporadic colon cancer patients. Early detection of CAC using endoscopy is challenging, and the incidence of septal colon cancer remains high.

13p vihagrid 30-01-2023 5 2   Download

The DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. To deal with the high amount of data generated by the high-throughput sequencing process, a bioinformatics workflow is required and the QIIME2 platform has emerged as one of the most reliable and commonly used.

14p vihagrid 30-01-2023 4 2   Download

It has been previously demonstrated that hyaluronan (HA) potentially regulates the initiation and propagation of bladder cancer (BLCA). HYAL3 encodes hyaluronidase and is a potential therapeutic target for BLCA. We aimed to explore the role that HYAL3 plays in BLCA pathogenesis.

17p vihagrid 30-01-2023 4 2   Download

The programmed cell death 1 (PD-1)/PD-1 ligand 1 (PD-L1) signaling pathway is significantly upregulated in influenza virus infection, which impairs the antiviral response. Blocking this signaling pathway may reduce the damage, lower the virus titer in lung tissue, and alleviate the symptoms of infection to promote recovery.

13p vihagrid 30-01-2023 5 2   Download

This study aimed to identify potential biomarkers, by means of bioinformatics, affecting the occurrence and development of septic shock. Methods: Download GSE131761 septic shock data set from NCBI geo database, including 33 control samples and 81 septic shock samples. GSE131761 and sequencing data were used to identify and analyze differentially expressed genes in septic shock patients and normal subjects.

13p vihagrid 30-01-2023 5 2   Download

Primary open-angle glaucoma (POAG) continues to be a poorly understood disease. Although there were multiple researches on the identification of POAG biomarkers, few studies systematically revealed the immune-related cells and immune infiltration of POAG.

16p vihagrid 30-01-2023 5 2   Download

Several studies have demonstrated the antitumor activity of rosiglitazone (RGZ) in cancer cells, including breast cancer cells. However, the molecular targets of RGZ in the inhibition of angiogenesis in breast cancer cells remain unclear.

17p vihagrid 30-01-2023 4 2   Download

The biology of colorectal cancer (CRC) is remained to be elucidated. Numerous genetic and epigenetic modifcations are in concert to create and progress CRC. DNA methylation as a principal epigenetic factor has gained increased attention and could be utilized for biological studies.

10p vihagrid 30-01-2023 3 2   Download