Lexanomics Blog

Generative AI uncovering drug-omics assocations in type 2 Diabetes

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Generative AI has garnered significant attention in bioinformatics. Techniques like Generative Adversarial Networks (GANs) and Variational Autoencoders (VAEs) are at the…

The impact of coffee consumption in the human gut microbiome

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Coffee, one of the world’s most consumed beverages, is not just a source of caffeine; it’s also linked to a range of health benefits, such as reducing mortality and lowering…

Insulin molecule with an on and off button

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Managing diabetes effectively requires precise control of blood glucose levels, typically achieved through insulin therapy. However, conventional insulin treatments can lead…

Base editing screens define the genetic landscape of cancer drug resistance mechanisms

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Recent advancements in cancer research have focused on understanding the genetic mechanisms that contribute to drug resistance in cancer therapies. Using CRISPR base editing…

Diego M. Coelho

Multikingdom and functional gut microbiota markers for autism spectrum disorder

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The gut microbiome’s role in health, especially in autism spectrum disorder (ASD), is gaining increasing attention. Research shows that children with ASD may have distinct…

Diego G. Teixeira

The gut microbiome influences microglial populations

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The relationship between the gut microbiome and the neural function and behavior has been widely explored in the past years, specially after the development of metagenomics…

Using mitochondrial genetics to improve clonal tracing with single-cell mtDNA data

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Mitochondrial DNA (mtDNA) is highly useful for clonal tracing, which tracks the lineage and growth of cells within an organism. Due to its high mutation rate and unique…

Diego M. Coelho

Using 16S rDNA and metagenomic sequencing technology to analyze the fecal microbiome of children with avoidant/restrictive food intake disorder

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The gut microbiome, an essential component for maintaining overall health, is shaped by various factors including genetics, diet, and lifestyle. While substantial research…

Human microbiome alterations during spaceflight

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Spaceflight missions have contributed to the advancement of a plentitude of areas, however, little is known about how the human body and its associated microbiome respond to…

Phylogenomics and the rise of the angiosperms

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Angiosperms, or flowering plants, represent one of the most diverse and ecologically dominant groups of plants on Earth. Check out what a high resolution phylogenetic tree…

Convert database identifiers with `biomaRt` R package

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BioMart is an integral part of the Ensembl project, and it was designed to facilitate the access and retrieval of biological data. With BioMart, users can easily extract…

Are you a good or a bad guy? Identifying malignant cells using Numbat

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Distinguishing malignant cells in a single-cell project can be a very time-consuming task. Particularly, malignant cells are heterogeneous and often display misleading…

Yet another tip for speeding up DEG analysis on Seurat

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Not long ago, we discussed ways to speed up differential expression analysis in single-cell datasets.

A link between the brain and the immune system

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The brain and the immune system are intricately connected, with recent research uncovering many pathways through which they interact. For example, The blood-brain barrier…

gnomAD: 1,000,000 individuals variation reference

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From time to time, large consortiums release valuable datasets to the public. gnomAD is one such example. Following the release of gnomAD’s exome and genome data, a new…

Diego M. Coelho

How non-coding variants can explain developmental disorders

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Coding variants, especially single-nucleotide variants, are genetic alterations occurring within the coding region of the genes. They are widely studied in human genomics…

Comparison of Metagenomics and Metatranscriptomics Tools: A Guide to Making the Right Choice

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Bioinformatics is an area where new analytical methods, tools, and pipelines are constantly emerging. Therefore, knowing which tools are most appropriate for your data is…

Improving single-cell projects: Generative models for data imputation

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In the previous post, we mentioned how deep-learning and generative approaches are revolutionizing genomics and single-cell studies.

scGPT: A foundation model for single-cell genomics that got it! (The Right Stuff).

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Generative pre-trained models are the new cool kid on the block 😎 that no one can ignore anymore. Usage of this new approach have tremendous impact in a broad amount of…

Gut microbiome composition: link between sports performance and protein absorption?

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Proteins are the building blocks of nutrition, indispensable for bone and muscle metabolism. Adequate intake not only maintains health but also bolsters sports performance.…

Population genetics meets immunotherapy

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Arguably, the immune system displays one of the highest complexities of any biological process in evolution. In humans, its ability to respond to pathogens spans multiple…

How much does it cost a Bioinformatician? - Asking ChatGPT

bioinformatics

Some time ago, I became curious about the gross salary range for bioinformaticians across various countries in Europe and North America. While browsing through platforms…

Diego M. Coelho

An automatic and biological-driven approach for defining “roots” on Monocle3

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There are many reasons why a researcher wants to perform pseudotime analysis on single-cell datasets, including but not limited to cellular differentiation, developmental…

Clinical application of bronchoalveolar lavage fluid metagenomics next-generation sequencing in cancer patients with severe pneumonia

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Severe pneumonia presents a significant challenge for cancer patients, often complicating timely and accurate diagnosis of underlying pathogens. Conventional diagnostic…

Creating a PPI network from a list of differentially expressed genes

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Suppose that we have a set of differentially expressed genes (DEG) from RNA-Seq data and their corresponding log2FoldChanges. Let’s create a protein-protein interaction…

Basic taxonomic classification of long and short reads with Kraken2

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The taxonomic classification of reads from sequencing experiments has become a common task for most computational biology and bioinformatics projects. To facilitate this…

Redefining the treponemal history through pre-Columbian genomes from Brazil

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It’s no secret that human migration dynamics are one of the primary factors responsible for the introduction of infectious agents to different parts of the planet.…

Parallelization tips on Seurat

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For the series on basic, but useful tips on single-cell analysis. We want to introduce parallelization using future for Seurat.

Cholesin: a new hormone discovered for controlling cholesterol levels in humans

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Energy metabolism is one of the most fascinating and complex subjects in human metabolism. For example, cholesterol metabolism involves many different hormones and has a…

The butterfly effect: lncRNAs in the evolutionists’ sights

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evolution

lncRNA

Flying insects have been starring the study of evolution. The story of how moths with darker color increased frequency in contrast to light color moths in the highly…

Data interoperability for single-cell analysis

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Seurat is undoubtedly the most used package for single-cell analysis. However, the single-cell field has changed towards new programming languages and packages (e.g.…

Unveiling the Beginning of the Pandemic: The Transformative Role of Meta-Transcriptomics in Pathogen Identification

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The year 2020 will forever be remembered as the starting point of the COVID-19 pandemic, declared by the World Health Organization. A revolution in the speed of information…

Why to sequence the DNA?

bioinfo-trends

sequencing-technologies

There are many different DNA sequencing technologies, all of them with their potentialities. However, do you know some of the main use cases for DNA sequencing?

Jumping genetic element getting in the way of primates tail evolution

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It is of common knowledge that humans and monkeys share great similarities regarding their genomes. And, if most monkeys have tails, what happend to ours? This is the…

Analysing the cell transcriptional profile at the single-cell resolution

bioinfo-trends

sequencing-technologies

Single-cell RNA-seq analysis is a powerful technique used in biology and medicine to study the gene expression of individual cells within a population. Single-cell gene…

A new look into microorganisms by the lens of metagenomics

bioinfo-trends

sequencing-technologies

Have you ever heard that a great percentage of our body composition comes from the microorganisms living with us? Recent research suggests a 1:1 ratio for the number of…

Are you aware about RNA sequencing analysis?

bioinfo-trends

sequencing-technologies

Sequencing technologies have revolutionized our understanding of human and other organisms’ biology. By having access to the transcriptome, one can have insights about the…