Kiko Garcia

Kiko Garcia's articles

Analytical Approaches and Applications of Whole Exome Sequencing (WES) in Oncology

Introduction Genomics has revolutionized cancer research, transforming the way we diagnose, treat, and monitor cancer. Among the powerful genetic analysis methods, Whole Exome Sequencing (WES) stands out as a cutting-edge technique that employs sequence capture technology to enrich DNA from the whole exome regions, enabling high-throughput sequencing. WES offers a simpler, more cost-effective, and efficient […]

Amplicon Sequencing Technology Unveils the Enigmas of Microbial Populations

Amplicon sequencing is a cutting-edge technique that involves sequencing PCR products or captured fragments of specific lengths, enabling the analysis of sequence variations. Among the diverse applications of this technology, the 16S rRNA gene has emerged as a fundamental tool for sequence-based bacterial analysis, boasting decades of significance. The process of 16S/18S/ITS amplicon sequencing entails […]

Application of Whole Plasmid Sequencing in Analyzing Drug Resistance Genes of Klebsiella pneumoniae

Klebsiella pneumoniae is a significant causative agent of hospital- and community-acquired infections, presenting with various clinical manifestations. Notably, the rapid spread of carbapenem-resistant K. pneumoniae (CRKP) has become a global threat, leading to high morbidity and mortality rates. In this context, researchers have employed high-throughput sequencing to investigate drug resistance mechanisms in this pathogen, particularly […]

Applications of Targeted Region Sequencing in Human Disease Studies and Clinical Care

Introduction to target region sequencing Since the introduction of Sanger sequencing in 1977, genetic sequencing has been greatly improved with costs simultaneously falling. With the ability to rapidly produce large volumes of sequencing data, next-generation sequencing (NGS) enables researchers to obtain whole genome or targeted regions of samples. Targeted region sequencing is preferred by researchers and clinical […]

The Methods of Whole Genome Sequencing

Overview of Whole Genome Sequencing The genome of each individual organism contains its entire genetic information. Whole genome sequencing technology can comprehensively and accurately analyze entire genomes, thereby breaking the information contained in it and revealing the complexity and diversity of the genome. The emergence of whole genome sequencing technology is a revolutionary advancement in all areas […]

Degradome Sequencing: Introduction, Features, Workflow, and Applications

What is Degradome Sequencing? MicroRNAs (miRNAs) are a class of small endogenous non-coding RNAs of about 22 nt in length, with hairpin structures as precursors, which are widely found in animal, plant and viral organisms. Numerous studies have shown that miRNAs are involved in a wide range of biological processes, including cell proliferation, apoptosis, differentiation, […]

Unraveling the Genetic Code: An Introduction to Genome-Wide Association Studies

Introduction to Genome-wide Association Studies A genome-wide association study is what the National Institutes of Health call “a study of common genetic variation across the whole human genome with the goal of finding genetic links to observable traits.”Even though family linkage studies and studies with tens of thousands of gene-based SNPs measure genetic variation across […]

Exploring the Potential of RNA-Seq in Various Fields

What is RNA-Seq? Regulation of gene expression is fundamental to linking genotypes with phenotypes. RNAs shape complex gene expression networks, which drive biological processes. An in-depth understanding of the underlying mechanisms of how to govern these complex gene expression networks is vital for the treatment of complex diseases such as cancer. Hybridization-based microarrays are used […]

Bioinformatics Analysis of Small RNA Sequencing

Small RNAs are important functional molecules in organisms, which have three main categories: microRNA (miRNA), small interfering RNA (siRNA), and piwi-interacting RNA (piRNA). They are less than 200 nt in length and are often not translated into proteins. Small RNA generally accomplishes RNA interference (RNAi) by forming the core of an RNA-protein complex (RNA-induced silencing […]

How Whole Exome Sequencing Works: Principles and Workflow Demystified

As the development of biological experimental technology, especially gene-sequencing technology, both laboratory and clinical researchers realize that genome sequencing is the best way to analyze the etiology, pathophysiology, treatment and prognosis of diseases. Researches further demonstrate that there are only 30 million base pairs of genes that contain essential information of proteins for human beings. […]

Evolutionary, Medical, and Clinical Applications of Whole Exome Sequencing

As we all know, proteins play important roles in human bodies since all physiologic events are related to the structural or mechanical functions of certain proteins. Studying the synthesis process of proteins is a way to study the etiology, pathophysiology, diagnosis, and treatment of certain diseases. The human genome contains approximately 3 billion base pairs […]

Navigating the Bioinformatics Workflow for Whole Exome Sequencing: A Step-by-Step Guide

Next-generation sequencing (NGS), which makes millions to billions of sequence reads at a fast rate, has greatly sped up genomics research. At the moment, Illumina, Ion Torrent/Life Technologies, 454/Roche, Pacific Bioscience, Nanopore, and GenapSys are all NGS platforms that can be used. They can produce reads of 100–10,000 bp in length, enabling sufficient coverage of […]

A Comprehensive Guide to CRISPR Screening and Sequencing: Methods, Applications, and Challenges

In competition with bacteriophages, bacteria and archaea have evolved unique ways of defending, which include the CRISPR/Cas systems and the immune systems of bacteria and archaea, which resist the invasion of foreign DNA or RNA and recognize the foreign invaders and cleave them for immune defense.   CRISPR/Cas systems are now useful research tools that […]

Bioinformatics Workflow for Whole Genome Sequencing

Whole genome sequencing (WGS) has the capacity to greatly enhance genomic knowledge and understand mysteries of life by utilizing the most advanced genetic sequencing technologies. WGS can be used for variant calling, genome annotation, phylogenetic analysis, reference genome construction, and more. WGS tries to cover the whole genome, but actually covers 95% of the genome with […]

Targeted Region Sequencing in Human Disease Studies and Clinical Care

Introduction to target region sequencing Since the introduction of Sanger sequencing in 1977, genetic sequencing has been greatly improved with costs simultaneously falling. With the ability to rapidly produce large volumes of sequencing data, next-generation sequencing (NGS) enables researchers to obtain whole genome or targeted regions of samples. Targeted region sequencing is preferred by researchers and clinical […]

Bioinformatics Analysis of Viral Metagenomic Sequencing

Viral metagenomics is the study of viruses in environmental and biological samples by utilizing next generation sequencing that generates very large data sets. Viral metagenomics analyzes viral sequences to deduce the impact of viruses on the environment of human health. Unlike amplicon sequencing, metagenomics obtains and investigates genetic material directly from environmental samples, which has led to a new […]

Applications of Metagenomics in Biotechnology and Health Care

Microbes are present almost everywhere. They play a vital role in cycling carbon, release important compounds, and may be associated with infectious diseases. Metagenomics is the culture-independent genomic research of microbial communities. Metagenomics presents a powerful tool to study prokaryotes and viruses in the environment via the analysis of their DNA obtained directly from environmental samples. This […]

Applications of 16S/18S/ITS Amplicon Sequencing

16S/18S/ITS amplicon sequencing has now been a well-established method. Due to its low cost, shorter cycle and low quality requirement of the sample, 16S/18S/ITS amplicon sequencing is widely used in the study of microorganisms. 16S/18S/ITS amplicon sequencing reveals the species of microorganisms in environmental samples and their differences, relative abundance, population structure and evolutionary relationships. It plays […]

Principles and Workflow of 16S/18S/ITS Amplicon Sequencing

16S/18S/ITS amplification sequencing uses the next/third generation sequencing platform and performs high throughput sequencing of PCR products from specific regions such as 16S rDNA/18S rDNA/ITS/ functional genes. It overcomes the disadvantage of some microorganisms that is difficult or impossible to culture, and obtains the information of microbial community structure, evolutionary relationships and microbial correlation with […]

Applications of Microbial Whole Genome Sequencing

Microorganisms widely exist in nature and are closely related to human life and production. They are generally divided into fungi, actinomycetes, bacteria, spirulina, rickettsia, chlamydia, mycoplasma and viruses. Microbial whole genome sequencing is an important tool for mapping genomes of novel organisms, finishing genomes of known organisms, or comparing genomes across multiple samples. Sequencing the entire microbial […]

Overview of Metatranscriptomic Sequencing: Principles, Workflow, and Applications

What is metatranscriptomic sequencing? Metatranscriptomic sequencing provides direct access to culturable and non-culturable microbial transcriptome information by large-scale, high-throughput sequencing of transcripts from all microbial communities in specific environmental samples. Metatranscriptomic sequencing offers an opportunity to randomly sequence mRNAs as a unit for understanding the regulation of complex processes in microbial communities. The study of the metatranscriptome […]

Introduction to Shotgun Metagenomics, From Sampling to Data Analysis

Metagenomics is the science that applies high-throughput sequencing technologies and bioinformatics tools to directly obtain the genetic content of a microbial community without the need to isolate and culture the individual microbial species. Metagenomics enables researchers not only to study the functional gene composition of microbial communities but also to conduct evolutionary research. Metagenomics has been […]

Bioinformatics Analysis of 16S rRNA Amplicon Sequencing

This article provides a brief introduction to good practices for the bioinformatics analysis of 16S rRNA sequencing by NGS (next-generation sequencing). The bioinformatics pipeline involves two main stages: the preprocessing of data (quality control) and quantification (including taxonomic profiling and predictive metagenomics profiling).   Preprocessing to eliminate uninformative data Removal of adapters, PCR primers, and […]

Bioinformatics Analysis of 16S rRNA Amplicon Sequencing

This article provides a brief introduction to good practices for the bioinformatics analysis of 16S rRNA sequencing by NGS (next-generation sequencing). The bioinformatics pipeline involves two main stages: the preprocessing of data (quality control) and quantification (including taxonomic profiling and predictive metagenomics profiling).   Preprocessing to eliminate uninformative data Removal of adapters, PCR primers, and […]

Applications of Metagenomics in Biotechnology and Health Care

Microbes are present almost everywhere. They play a vital role in cycling carbon, release important compounds, and may be associated with infectious diseases. Metagenomics is the culture-independent genomic research of microbial communities. Metagenomics presents a powerful tool to study prokaryotes and viruses in the environment via the analysis of their DNA obtained directly from environmental samples. This […]

Plasmid Detection and Complete Plasmid DNA Sequencing

Bacterial plasmids Bacterial plasmids are circular or linear double-stranded DNA molecules defined by their capability of autonomous replication in the hosts. They are critical sources for microbial evolution and genome innovation due to their ability to acquire foreign DNA sequences and transfer among bacteria and between distantly related organisms, like transferring from bacteria to eukaryotes […]

Dual RNA Sequencing: Definition and Principle, Workflow, and Applications

What is dual RNA sequencing? Understanding how pathogen induces disease requires the knowledge on which genes are expressed and how they are regulated during infection. RNA sequencing has been routinely used to analyze the gene expression of microbial pathogens. Apart from the standard mRNA sequencing, new methods are surging based on RNA-seq, mapping the post-transcriptional […]

Bioinformatics Analysis of Viral Metagenomic Sequencing

Viral metagenomics is the study of viruses in environmental and biological samples by utilizing next generation sequencing that generates very large data sets. Viral metagenomics analyzes viral sequences to deduce the impact of viruses on the environment of human health. Unlike amplicon sequencing, metagenomics obtains and investigates genetic material directly from environmental samples, which has […]

The Applications of Bioinformatics in Microbial Technology

Bioinformatics is a discipline developed on the basis of biology, mathematics and computer science. It effectively acquires and analyzes biological data such as nucleic acid sequences and protein structures, so as to conduct comprehensive and accurate biological analysis. Bioinformatics is an extremely important tool to study the microorganisms, which are widespread and highly varied.   […]

The Emergence of a New Force: Circular RNA

Circular RNAs are closed-loop single-stranded RNA (ssRNA) that are structurally specific, and produced by the back-splicing process. CircRNAs can exist independently of proteins and are unaffected by exonucleases, and are widely found in plant and animal cells to regulate gene expression.   Circular RNAs were first discovered by Sanger studying virus-like RNAs. And in 1991, […]

Introduction to DNA Methylation Analysis: From Wet Lab Experiments to Bioinformatics Analysis

Methylation is one of the most classical epigenetic modifications in eukaryotes. DNA methylation regulates gene expression and has important implications in both growth and disease-related research. DNA methylation affects the maturation of germ cells or embryonic cells subject to specific gene expression. It has also been widely studied and applied to track aging and various […]

When Respiratory Pathogen Metagenome Sequencing Meets Hybrid Capture Enrichment

Currently, the incidence of infectious diseases has increased globally, and the pathogens show a trend of diversification and complexity. Rapid and accurate pathogenic diagnosis, which enables early selection of sensitive anti-infective drugs or effective and targeted preventive and control measures, is the core of accurate prevention and treatment of infectious diseases. The epidemic of respiratory […]

Array-based Methylation Detection Explores the Mysteries of Cancer

Epigenetics is an emerging field of research that focuses on the effects of environmental factors, such as infections, pollutants, stress, and long-term drug exposure, on an individual's genome. Epigenetic changes do not alter the structure of DNA, but do alter the way DNA is modified. Thereby, those changes include DNA methylation, histone modifications and non-coding […]

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