??Erianin Derivative for Colorectal Cancer???, BCAT2: Cancer Biomarker??, R2R3-MYB in Apricot ??, Shiny ? for Python ??
Bioinformer Weekly Roundup
Stay Updated with the Latest in Bioinformatics!
Issue: 58 | Date: 18 October 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
The study investigates type 2 diabetes mellitus (T2D) with cognitive impairment and aging by analysing gene expression datasets related to T2D and Alzheimer’s disease. They identified differentially expressed genes (DEGs) and constructed a protein-protein interaction (PPI) network, highlighting six core genes: BCL6, TP53, HSP90AA1, CRYAB, IL1B, and DNAJB1.
This study evaluated circulating tumor DNA (ctDNA) in 69 metastatic uveal melanoma (MUM) patients treated with?Tebentafusp?using droplet digital PCR (ddPCR). Detectable?ctDNA?before treatment was associated with shorter survival, while a 90% reduction in?ctDNA?at 12 weeks correlated with longer survival. This underscores the value of?ddPCR-based?ctDNA?monitoring for assessing treatment response and prognosis in MUM.?
Data from?cBioPortal, TCGA,?GTEx, and RSEM were analysed for genetic alterations and expression patterns, while protein interactions were assessed using the Human Protein Atlas,?UniProt, and STRING. BCAT2 was often amplified and upregulated in various tumors, correlating with poor survival rates and influencing immune cell infiltration, particularly CD4+ T cells, CD8+ T cells, and Treg cells.
Genetic dissection of Meloidogyne incognita resistance genes based on VIGS functional analysis in Cucumis metuliferus | BMC Plant Biology
Scientists discover genes resistant to southern root-knot nematode, a devastating crop parasite in African horned melon. This study identified two potential resistance genes and a linked genetic region (QTL3.1), suggests that this may help for developing nematode-resistant cucumber cultivars.?
A recent study explored how ethoxy-erianin phosphate (EBTP) can inhibit angiogenesis in colorectal cancer. Researchers found that EBTP affects a specific pathway, which helps slow down the growth and spread of cancer cells.
Genome-wide identification, expression analysis of the?R2R3-MYB?gene family and their potential roles under cold stress in Prunus sibirica | BMC Genomics ?
A recent study examined R2R3-MYB gene family in prunus Siberian apricot, which is vulnerable to frost during flowering. Researchers identified 116 MYB genes and found that 37 of them have promoters responsive to cold stress. The study says that certain MYB genes are likely involved in plant's response to low temperatures and can provide insights to developing cold resistant varieties.?
This recent study investigated the roles of two nucleotides associated proteins, HupA and HupS in the soil bacterium Streptomyces coelicolor. Researchers found that both proteins are essential for growth, sporulation, and spore stability and they serve as global transcriptional regulators.
Whole genome analysis of?Pantoea?species identified from sepsis patients in selected Ethiopian referral hospitals: emerging pathogens | BMC Microbiology ?
The study reports the identification of emerging Pantoea species, including multidrug-resistant strains, from sepsis patients in Ethiopian referral hospitals. Using whole genome sequencing, P. dispersa, P. septica, and a novel Pantoea species were found, with most strains carrying multiple antimicrobial resistance genes.
This study explores the ribosome profiling landscape in yeast, highlighting the diversity of pervasive translation patterns, especially in noncoding regions. The study suggests that non-canonical translation signals provide valuable insights, emphasizing the need to consider them in proteogenomic research.
This study introduces ProEnd, a comprehensive database for identifying HbYX motif-containing proteins, which regulate proteasome activity, across various species. It talks about the evolutionary conservation and significance of HbYX motifs, including their prevalence in viral proteomes.
This recent study suggests that CDK1 plays a key role in regulating FOXM1, a protein important for self-renewal in epidermal stem cells. CDK1 phosphorylates FOXM1, helping it function better by stabilizing it and promoting its activity in the nucleus. In turn, FOXM1 increases CDK1 expression, creating a reinforcing loop that supports stem cell maintenance.
??? Latest Tools
Many statistical methods to identify Differential Accessibility (DA) regions have been developed but?for the DA analysis of single-cell epigenomics data no method has been agreed as most appropriate by the research community.?The study evaluated the statistical methods systematically and?assessed based on the accuracy, bias, robustness, and scalability of each method. Using the understanding from the assessment and following?the best practices,?the authors have developed Libra, an R package, for the DA analysis.
The study using extensive?Human Leucocyte Antigen (HLA) ligand datasets for training had come up with an interpretable deep learning framework called?ImmuneApp. The tool is aimed to improve the HLA-I epitope prediction and improve?immunopeptidomics?deconvolution.?
Source code is available?here.??
The study introduces?GraffiTE, an open-source pipeline, to analyse the insertion polymorphisms generated due to transposable elements which are ubiquitous mobile DNA sequences. The pipeline is configured to work on genome assemblies of both short and long read data.
Source code is available here.
A new computational tool?called?repDilPCR is?designed to improve the analysis of qPCR assays using the dilution-replicate experimental design.?The dilution-replicate design uses multiple linear regression of 3-point standard curves derived from experimental samples, eliminating the need for separate standard curves.?
BE-dataHIVE, is a?mySQL?database, developed to use as training dataset for?improving the model performance?to predict the base editing outcomes.?The database from five different studies?covers 460,000 gRNA target combinations and includes?melting temperatures, energy terms and multiple different data structures to help the machine learning researchers.
The database is available here.??
SurvBal?is an R package that help to analyse the microbiome balances in relation to censored time-to-event outcomes in microbiome profiling experiments. The R package supports?commonly used survival models such as?Cox proportional hazards, parametric survival models and to an extent Accelerate Failure Time (AFT) to report global balance of bacteria against the varying hazard or survival time.?
GIS-weigthed_LASSO?uses an integrative approach?in a single step?to select relevant features by combining weighted LASSO and prior biological knowledge. Using the prior biological knowledge, the scores according to biological relevance are assigned to each feature and thus improve biological interpretability of results upon selecting the features of importance.
Source code is available?here.
领英推荐
Transformer-based Analysis of Images of Tissue for Effective Remedy (TRAITER) uses deep learning approach for prognosis and diagnosis of Heart Failure (HF).?The likelihood to HF?and?potential for left ventricular reverse remodeling (LVRR)?from?cardiac tissue cell nuclear morphology images and?dual-stained images with cell nuclei and DNA damage markers are predicted in this approach by leveraging the image segmentation techniques and a Vison Transformer.
Source code is available?here.
?? Community News
A new computational pipeline has been developed to improve the design of personalized cancer vaccines. This method claims to tailor vaccines to individual patients by identifying unique tumor mutations, potentially enhancing the effectiveness of cancer immunotherapy.?
Researchers are using 3D?multiomics?to gain deeper insights into human brain development. This technique combines multiple layers of biological data, providing a detailed view of the molecular mechanisms that drive brain development and function.?
Targeting bacteria: Auxiliary metabolic genes expand understanding of phages and their reprogramming strategy |?PHYS.ORG?
Recent research has identified a previously unknown auxiliary metabolic gene in aquatic?phages, expanding our understanding of these bacterial predators. These auxiliary genes, originally from bacteria and hijacked by?phages, are not needed for new phage assembly but instead reprogram the host bacteria during infection.
Researchers have uncovered that early human development is influenced by DNA elements called transposons, rather than our genes. This discovery shifts our understanding, revealing that transposable elements (TEs) are crucial for the normal progression of human embryonic cells. Additionally, this research suggests that TEs could play significant roles in disease and have implications for fertility treatments and regenerative medicine.
A recent study has found that DNA polymerase, the enzyme responsible for DNA replication, operates in short bursts rather than a continuous stretch. This discovery challenges previous assumptions and offers new perspectives on the dynamics of DNA replication.?
A study from Brazil has identified new potential targets for treating visceral leishmaniasis, a severe parasitic disease. The research highlights specific molecular pathways that could be targeted to develop more effective therapies for this condition.?
Scientists have developed a new clinical model to predict hip fractures, which could significantly reduce mortality rates. This model uses patient-specific data to assess fracture risk, enabling early intervention and potentially improving patient outcomes.?
?? Upcoming Events
The?Nextflow?Summit 2024 in Barcelona, from October 28 to November 1, will feature foundational training, a hackathon, and a summit. Newcomers can attend training sessions, while those with?Nextflow?experience can join an?nf-core hackathon to work on specific tasks. The main summit will showcase the latest in workflow management and data orchestration.?
The course, scheduled for November 28, 2024, explores the role of small molecules in biological systems. Participants will learn about their binding interactions with macromolecular targets and impacts on biological pathways. The six-hour virtual workshop includes hands-on experience using EMBL-EBI tools to assess drug impacts.
This virtual conference on 14-15 Nov 2024 will feature late-stage postdoctoral scientists presenting research in infection biology. Participants will connect with leading European institutions and explore topics like pathogen biology, host genetics, and computational methods for infection analysis.
This hybrid conference at EMBL Heidelberg will explore the integration of advanced technologies and biological scales. Supported by the Bayer Foundation, the event will feature discussions from leaders in genomics, proteomics, and imaging. The conference aims to foster understanding of complex biological systems through quantitative and mechanistic models.?
?? Educational Corner
This blog delves into various coding practices that can greatly improve the performance of Shiny applications. It covers techniques for optimizing data loading, implementing caching strategies, utilizing asynchronous operations, and other methods to reduce loading and processing times, ensuring a smoother user experience.
This blog explores the concept of redirection in Linux, which enables users to alter the standard input and output devices when running commands. It introduces the fundamentals of redirection, highlighting how to use commands such as cat, sort, uniq, grep, wc, head, tail, and tee for efficient data manipulation.
This post highlights frequent errors in the field, such as misinterpreting genomic coordinates due to different indexing systems (0-based vs. 1-based), incorrect regular expressions, and mishandling complex file formats. It emphasizes the importance of understanding these pitfalls to ensure accurate data analysis and reproducibility.?
R package validation is the process of ensuring that the tools you use for data analysis consistently produce reliable, accurate, and reproducible results.?The software-based approach to validation treats R packages like any other software product, emphasizing solid software development practices throughout the entire Software Development Life Cycle (SDLC).
This?blog?will?guide?you?through?creating?custom?Shiny?modules?for?Python, featuring?two?examples?of?different?complexities.?Creating?custom?modules?in?Shiny for?Python?is?simple?enough and?will?provide?practical?insights?to?help?you seamlessly?integrate?custom?modules?into?your?projects.
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