??Sawfish for SV Discovery, Pandagma: Pan-Gene Sets and Gene Families??, ??IMI-driver: Multi-Omics for Cancer Genes ??
Bioinformer Weekly Roundup
Stay Updated with the Latest in Bioinformatics!
Issue: 52 | Date: 30 August 2024
?? Welcome to the Bioinformer Weekly Roundup!
In this newsletter, we curate and bring you the most captivating stories, developments, and breakthroughs from the world of bioinformatics. Whether you're a seasoned researcher, a student, or simply curious about the intersection of biology and data science, we've got you covered. Subscribe now to stay ahead in the exciting realm of bioinformatics!
?? Featured Research
This study explores the 3D shapes of viral proteins to understand their biological functions[LM1]?. Using computational tools, researchers predicted the structures of nearly 70,000 viral proteins, revealing new insights into how viruses evade immune systems.
This research investigates the morphology, genome, and metabolic activity of uncultured magnetotactic Nitrospirota bacteria at the single-cell level. Using advanced techniques, the study provides insights into their CO2 fixation and NO3? reduction capabilities.
This study examines how branched-chain amino acids (BCAA) influence diabetic cardiomyopathy (DCM) through microbiota-liver-heart interactions. It highlights the role of FGF21 in mediating these effects and suggests potential therapeutic strategies.
This research compares methods for studying phage communities in bee guts. It finds that viromes and total metagenomes capture different components, suggesting the need for both approaches to fully understand phage diversity.
This research identifies shifts in gene expression profiles linked to ovarian cancer. Using dataset GSE54388, differentially expressed genes (DEGs) were found between ovarian surface epithelium and tumour samples. Analysis revealed 186 overlapping genes, with 10 identified as hub genes potentially involved in preventing ovarian cancer.
This study constructs a co-expression network using gene expression data from GSE55092 and GSE50006 to analyse chronic lymphocytic leukemia (CLL) and HBV-associated hepatocellular carcinoma (HCC). It identifies 314 common differentially expressed genes (DEGs) and 10 potential hub genes. The research also explores protein-drug interactions and survival analysis.
This study analyses integrated single-cell and bulk RNA-seq data to understand OSCC. It highlights the role of mitophagy-related genes (MRGs) in NK cells and develops a prognostic model using 12 genes linked to mitochondrial autophagy. The model aids in predicting patient outcomes and suggests potential targeted therapies for OSCC.
This study investigates the effects of ribociclib, a CDK4/6 inhibitor, on breast cancer cells. Ribociclib inhibits cell growth in a dose- and time-dependent manner. It decreases the mRNA expression of CDK6 and MYH10, increases CDON expression, and raises miR-141 levels after 72 hours of treatment.
??? Latest Tools
The research introduces TIANA, a deep learning framework that uses attention mechanisms to infer transcription factor cooperativities from distal sequence data. TIANA identifies co-occurring motifs, offering improved interpretability in regulatory element analysis.
Source code is available here.
This paper presents PRONTO-TK, a Python-based toolkit with a user-friendly GUI for protein function prediction using Gene Ontology terms. It simplifies the use of deep learning architectures for protein annotation, making complex analyses accessible to researchers with minimal programming experience.
Source code is available here.
The study introduces Eliater, a Python package designed to estimate the effect of upstream molecule perturbations on downstream molecules in biomolecular networks. It utilizes network data and perturbation inputs to provide quantitative effect estimates, demonstrated through a case study on the E. coli transcriptional regulatory network.
Source code is available here.
This article introduces Pandagma, a set of workflows designed to identify and compare pan-gene sets and gene families in eukaryotic genomes. It works on the challenges like whole-genome duplications and varying annotation qualities using homology, synteny, and synonymous change rates.
Source code is available here.
The study introduces SmCCNet 2.0, an advanced machine learning tool for integrating single or multiple omics data with phenotypes to reconstruct specific multi-omics networks. This version has user-friendly setup, supporting both manual and automatic configurations.
Source code is available here.
领英推荐
Sawfish is a tool for calling structural variants from high-quality long reads, incorporating haplotype modeling to enhance accuracy. It is tested against benchmarks for various SV sizes and coverage levels, and also in joint-genotyping scenarios.
Source code is available here.
The study presents IMI-driver, a model that integrates multi-omics data across eight biological networks to identify cancer driver genes. By applying Multi-view Collaborative Network Embedding, IMI-driver embeds gene regulation into a low-dimensional space, showing improved performance in predicting cancer drivers.
Source code is available here.
?? Community News
Researchers have developed AINU, an AI tool that uses high-resolution imaging to differentiate between cancerous and normal cells and detect early viral infections. This technology, detailed in Nature Machine Intelligence, could lead to effective disease diagnostics.
The study reported that certain Salmonella strains exhibit resistance to antibiotics. This resistance is due to a mechanism involving DNA repair. Specifically, the study observed that the activation of stress responses leads to the repair of DNA double-stranded breaks, which contributes to antibiotic persistence.
The research identifies novel proteins that could be targeted by future cancer drugs. By combining two protein analysis methods, the researchers mapped over 300 cancer-linked proteins and their small molecule binding sites, highlighting a target protein involved in cancer cell division.
Scientists at Washington University in St. Louis have discovered that certain species of purple bacteria can produce bioplastics more efficiently. Through genetic engineering, they enhanced the bacteria’s ability to create polyhydroxyalkanoates (PHAs), offering a sustainable alternative to petroleum-based plastics.
The research investigates how bacteriophages regulate anti-CRISPR responses to counter bacteria. This understanding may aid in fine-tuning the response and using phages to manage antibiotic-resistant bacteria.
?? Upcoming Events
The EMBL Conference ‘The Next Generation in Infection Biology’ offers postdoctoral scientists an opportunity showcases their groundbreaking research and connect with top European institutions specializing in infection biology. It covers topics such as Pathogen biology, Anti-infectives, Computational methods and analyses for infection.
?? Educational Corner
The blog post introduces Apache Parquet, a columnar file format for efficiently storing and processing large datasets. It covers key features like columnar storage, metadata structure, and compression techniques, and contrasts Parquet with traditional formats such as CSV and JSON, noting its benefits for analytical queries and data optimization.
This article outlines the GATK Best Practices for pre-processing data, including mapping reads, marking duplicates, and recalibrating base quality scores to prepare BAM files for variant discovery. It highlights tools like BWA, MarkDuplicatesSpark, and BaseRecalibrator and offers tips for optimizing these processes.
?? Connect with Us
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