Bioinformation Newsletter
GeneSpectrum Life Sciences
Simplifying Genomics and Bioinformatics for a Better World!
Issue: 1 | Date: 16 May 2024
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??Research
Assessing the reliability of point mutation as data augmentation for deep learning with genomic data?
The study proposes a novel data augmentation technique for genomic data inspired by biology: point mutations. It aims to enhance the performance of deep neural networks (DNNs) in genomic tasks by simulating mutations in coding regions. The findings suggest that point mutation-based augmentation improves DNN performance, particularly in functions like translation initiation and splice site detection.
As single-cell RNA sequencing (scRNA-seq) technology advances, it offers insights into connections among individual cells, genes, and diseases. Clustering is commonly used for single-cell data analysis, but traditional methods are sensitive to noise. To address this, the Cauchy hyper-graph Laplacian non-negative matrix factorization (CHLNMF) is proposed. CHLNMF replaces Euclidean distance measurement with the Cauchy loss function to mitigate noise influence and incorporates hyper-graph constraints to capture high-order links among samples. The model is optimized using half-quadratic optimization. Evaluation of seven scRNA-seq datasets shows CHLNMF outperforms nine top methods, validating its effectiveness.
This study aimed to find biomarkers for metastasis and recurrence in colorectal cancer (CRC) by analyzing DNA methylation. Researchers created a model to predict CRC metastasis and identified 17 methylation sites linked to survival. They found that these patterns could predict metastasis, survival, and were related to the tumor immune microenvironment and response to immunotherapy. This work enhances our understanding of CRC and could improve treatment strategies.
???Tools
Commonly used next generation sequencing machines typically produce large amounts of short reads of a few hundred base-pairs in length. However, many downstream applications would generally benefit from longer reads. CAREx is a new MSA-based algorithm and software for producing pseudo-long reads from paired-end short read data.
BiSDL is a computational language for multicellular synthetic biology, representing spatiality and cellular dynamics in complex systems. It integrates high-level design with detailed modeling, aiding collaboration and the Design-Build-Test-Learn cycle. BiSDL compiles into Nets-Within-Nets (NWNs) models, simplifying complex system modeling. Case studies show BiSDL's ability to represent spatial interactions and cellular dynamics, making advanced tools more accessible and potentially transforming synthetic biology research.
CAIM is a new bioinformatics tool for accurate taxonomic profiling in metagenomic samples. It uses genome coverage to reduce false positives and offers precise abundance estimation. CAIM outperforms other tools on mock communities and can identify species markers in cancer patients, showing consistent performance across sequencing platforms.
领英推荐
??Learn
The blog examines the discovery of sex chromosome variations in a large cohort of men from the Million Veteran Program. It discusses the historical context and potential impact of screening for XXY and XYY conditions. The findings reveal many men with undiagnosed extra sex chromosomes, raising questions about the need and consequences of widespread genetic screening. Despite health associations, the blog highlights concerns about discrimination and ethical disclosure of genetic information. It calls for thoughtful consideration before implementing routine screening protocols.
This blog discusses how rare gene variants can offer insights into combatting Alzheimer's disease. It highlights three cases where specific gene mutations delay the onset or progression of the disease: the Christchurch mutation in the APOE gene, a gain-of-function mutation in the RELN gene, and a variant of the fibronectin gene. These findings suggest new therapeutic approaches for Alzheimer's based on targeting these genetic factors.?
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Attending Banaras Hindu University
6 个月Hello di i want to ask you something about bioinformatics , i am also a bioinformatic student . I got your linkdin i'd from Meenakshi mam. Please message me , because i tried to contact but your message option is locked.... Srinka Datta