Scientist, Bioinformatics

Scientist, Bioinformatics

Bridging the gap between Genomics and Data Science

Posts by Tags

10XGenomics

10plex

16s rRNA amplicon

Taxonomic and diversity profiling of the microbiome - 16S rRNA gene amplicon sequence data

1 minute read

Published:

The 16S ribosomal RNA (rRNA) gene of Bacteria codes for the RNA component of the 30S subunit. Different bacterial species have one to multiple copies of the 16S rRNA gene, and each with 9 hypervariable regions, V1-V9. High-throughput sequencing of 16S rRNA gene (a “marker gene”) amplicons has become a widely used method to study bacterial phylogeny and species classification.

ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput Sequencing)

ATAC-seq peak calling with MACS2

2 minute read

Published:

ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput Sequencing) is a next-generation sequencing approach for the analysis of open chromatin regions to assess the genome-wise chromatin accessibility.

Amazon Web Services

BWA

ATAC-seq peak calling with MACS2

2 minute read

Published:

ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput Sequencing) is a next-generation sequencing approach for the analysis of open chromatin regions to assess the genome-wise chromatin accessibility.

Bioinformatics

Kaplan-Meier Curve using R

3 minute read

Published:

The Kaplan-Meier curve is a powerful tool in survival analysis, commonly used to estimate the probability of an event—such as survival—at different time intervals. It provides a visual representation of the time it takes for an event to occur across a patient population. This method is especially useful in medical studies where understanding survival rates is key.

Annotation of genetic variants

4 minute read

Published:

Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.

Cell Ranger

Chromium Single Cell Gene Expression

Cluster Computing

DADA2

Taxonomic and diversity profiling of the microbiome - 16S rRNA gene amplicon sequence data

1 minute read

Published:

The 16S ribosomal RNA (rRNA) gene of Bacteria codes for the RNA component of the 30S subunit. Different bacterial species have one to multiple copies of the 16S rRNA gene, and each with 9 hypervariable regions, V1-V9. High-throughput sequencing of 16S rRNA gene (a “marker gene”) amplicons has become a widely used method to study bacterial phylogeny and species classification.

Emory University

Quantitative Proteomics: Aptamer-Based Protein Quantification

5 minute read

Published:

Quantitative proteomics is a cutting-edge approach for measuring protein levels in complex biological samples. One innovative method in this field is aptamer-based protein quantification. Aptamers, which are short, single-stranded DNA or RNA molecules, are engineered to specifically bind to target proteins with high precision.

Kaplan-Meier Curve using R

3 minute read

Published:

The Kaplan-Meier curve is a powerful tool in survival analysis, commonly used to estimate the probability of an event—such as survival—at different time intervals. It provides a visual representation of the time it takes for an event to occur across a patient population. This method is especially useful in medical studies where understanding survival rates is key.

Annotation of genetic variants

4 minute read

Published:

Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.

FastQC

Feature Barcoding

GATK

Genomic variants from RNA-Seq data

1 minute read

Published:

RNA-Seq allows the detection and quantification of known and rare RNA transcripts within a sample. In addition to differential expression and detection of novel transcripts, RNA-seq also supports the detection of genomic variation in expressed regions.

Genomics

Annotation of genetic variants

4 minute read

Published:

Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.

Genotypes

Annotation of genetic variants

4 minute read

Published:

Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.

HOMER

ATAC-seq peak calling with MACS2

2 minute read

Published:

ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput Sequencing) is a next-generation sequencing approach for the analysis of open chromatin regions to assess the genome-wise chromatin accessibility.

HTSeq

HUMAnN2

Taxonomic and functional profiling of the microbiome - whole genome shotgun metagenomics

1 minute read

Published:

This workflow consists of taxonomic and functional profiling of shotgun metagenomics sequencing (MGS) reads using MetaPhlAn2 and HUMAnN2, respectively. To perform taxonomic (phyla, genera or species level) profiling of the MGS data, the MetaPhlAn2 pipeline was run on a high performance multicore cluster computing environment.

Indel

Genomic variants from RNA-Seq data

1 minute read

Published:

RNA-Seq allows the detection and quantification of known and rare RNA transcripts within a sample. In addition to differential expression and detection of novel transcripts, RNA-seq also supports the detection of genomic variation in expressed regions.

Kaplan-Meier-curve

Kaplan-Meier Curve using R

3 minute read

Published:

The Kaplan-Meier curve is a powerful tool in survival analysis, commonly used to estimate the probability of an event—such as survival—at different time intervals. It provides a visual representation of the time it takes for an event to occur across a patient population. This method is especially useful in medical studies where understanding survival rates is key.

LFQ

MACS2

ATAC-seq peak calling with MACS2

2 minute read

Published:

ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput Sequencing) is a next-generation sequencing approach for the analysis of open chromatin regions to assess the genome-wise chromatin accessibility.

MS-based Proteomics

Quantitative Proteomics: Aptamer-Based Protein Quantification

5 minute read

Published:

Quantitative proteomics is a cutting-edge approach for measuring protein levels in complex biological samples. One innovative method in this field is aptamer-based protein quantification. Aptamers, which are short, single-stranded DNA or RNA molecules, are engineered to specifically bind to target proteins with high precision.

MS3 spectra

MatrixEqtl

RNA-Seq eQTL Analysis Pipeline: Uncovering Genetic Influences on Gene Expression

1 minute read

Published:

Understanding how genetic variations impact gene expression is crucial for uncovering the underlying mechanisms of complex traits and diseases. One powerful tool for this investigation is the expression quantitative trait locus (eQTL) analysis, which examines the relationship between genetic variants and genome-wide expression levels.

MaxQuant

MetaPhlAn2

Taxonomic and functional profiling of the microbiome - whole genome shotgun metagenomics

1 minute read

Published:

This workflow consists of taxonomic and functional profiling of shotgun metagenomics sequencing (MGS) reads using MetaPhlAn2 and HUMAnN2, respectively. To perform taxonomic (phyla, genera or species level) profiling of the MGS data, the MetaPhlAn2 pipeline was run on a high performance multicore cluster computing environment.

NGS

Annotation of genetic variants

4 minute read

Published:

Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.

OTU

Taxonomic and diversity profiling of the microbiome - 16S rRNA gene amplicon sequence data

1 minute read

Published:

The 16S ribosomal RNA (rRNA) gene of Bacteria codes for the RNA component of the 30S subunit. Different bacterial species have one to multiple copies of the 16S rRNA gene, and each with 9 hypervariable regions, V1-V9. High-throughput sequencing of 16S rRNA gene (a “marker gene”) amplicons has become a widely used method to study bacterial phylogeny and species classification.

Olink Proteomics

Quantitative Proteomics: Aptamer-Based Protein Quantification

5 minute read

Published:

Quantitative proteomics is a cutting-edge approach for measuring protein levels in complex biological samples. One innovative method in this field is aptamer-based protein quantification. Aptamers, which are short, single-stranded DNA or RNA molecules, are engineered to specifically bind to target proteins with high precision.

Perseus

Proteomics

Quantitative Proteomics

Quantitative Proteomics: Aptamer-Based Protein Quantification

5 minute read

Published:

Quantitative proteomics is a cutting-edge approach for measuring protein levels in complex biological samples. One innovative method in this field is aptamer-based protein quantification. Aptamers, which are short, single-stranded DNA or RNA molecules, are engineered to specifically bind to target proteins with high precision.

RNA-Seq

Genomic variants from RNA-Seq data

1 minute read

Published:

RNA-Seq allows the detection and quantification of known and rare RNA transcripts within a sample. In addition to differential expression and detection of novel transcripts, RNA-seq also supports the detection of genomic variation in expressed regions.

RNA-Seq eQTL Analysis Pipeline: Uncovering Genetic Influences on Gene Expression

1 minute read

Published:

Understanding how genetic variations impact gene expression is crucial for uncovering the underlying mechanisms of complex traits and diseases. One powerful tool for this investigation is the expression quantitative trait locus (eQTL) analysis, which examines the relationship between genetic variants and genome-wide expression levels.

RNASeq

SGE Cluster

SNP

Genomic variants from RNA-Seq data

1 minute read

Published:

RNA-Seq allows the detection and quantification of known and rare RNA transcripts within a sample. In addition to differential expression and detection of novel transcripts, RNA-seq also supports the detection of genomic variation in expressed regions.

SOMALogic

Quantitative Proteomics: Aptamer-Based Protein Quantification

5 minute read

Published:

Quantitative proteomics is a cutting-edge approach for measuring protein levels in complex biological samples. One innovative method in this field is aptamer-based protein quantification. Aptamers, which are short, single-stranded DNA or RNA molecules, are engineered to specifically bind to target proteins with high precision.

SPATIAL GENE EXPRESSION

STAR

Genomic variants from RNA-Seq data

1 minute read

Published:

RNA-Seq allows the detection and quantification of known and rare RNA transcripts within a sample. In addition to differential expression and detection of novel transcripts, RNA-seq also supports the detection of genomic variation in expressed regions.

Seurat

Single Cell

Single cell RNA-sequencing (scRNA-seq)

Space Ranger

Survival analysis

Kaplan-Meier Curve using R

3 minute read

Published:

The Kaplan-Meier curve is a powerful tool in survival analysis, commonly used to estimate the probability of an event—such as survival—at different time intervals. It provides a visual representation of the time it takes for an event to occur across a patient population. This method is especially useful in medical studies where understanding survival rates is key.

TMT

TMT 10plex

VCF

Annotation of genetic variants

4 minute read

Published:

Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.

VEP

Annotation of genetic variants

4 minute read

Published:

Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.

Variant calling

Annotation of genetic variants

4 minute read

Published:

Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.

Visium Spatial Gene Expression Solution

Vital

Kaplan-Meier Curve using R

3 minute read

Published:

The Kaplan-Meier curve is a powerful tool in survival analysis, commonly used to estimate the probability of an event—such as survival—at different time intervals. It provides a visual representation of the time it takes for an event to occur across a patient population. This method is especially useful in medical studies where understanding survival rates is key.

WGS

Annotation of genetic variants

4 minute read

Published:

Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.

aptamer-based proteomics

Quantitative Proteomics: Aptamer-Based Protein Quantification

5 minute read

Published:

Quantitative proteomics is a cutting-edge approach for measuring protein levels in complex biological samples. One innovative method in this field is aptamer-based protein quantification. Aptamers, which are short, single-stranded DNA or RNA molecules, are engineered to specifically bind to target proteins with high precision.

brightfield microscope image

cnv

Workflows for Discovering Copy Number Variations Using NGS Data.

less than 1 minute read

Published:

Copy number variations (CNVs) are genomic alterations that involve the gain or loss of specific regions of DNA. These variations can be inherited from parents or can arise de novo, and they play a significant role in neuropsychiatric disorders and cancers.

computing

Taxonomic and diversity profiling of the microbiome - 16S rRNA gene amplicon sequence data

1 minute read

Published:

The 16S ribosomal RNA (rRNA) gene of Bacteria codes for the RNA component of the 30S subunit. Different bacterial species have one to multiple copies of the 16S rRNA gene, and each with 9 hypervariable regions, V1-V9. High-throughput sequencing of 16S rRNA gene (a “marker gene”) amplicons has become a widely used method to study bacterial phylogeny and species classification.

Workflows for Discovering Copy Number Variations Using NGS Data.

less than 1 minute read

Published:

Copy number variations (CNVs) are genomic alterations that involve the gain or loss of specific regions of DNA. These variations can be inherited from parents or can arise de novo, and they play a significant role in neuropsychiatric disorders and cancers.

curation

discordant sex informaion

Quality control for GWAS studies

1 minute read

Published:

A crucial step in analyzing genome-wide association studies (GWAS) is identifying problematic subjects and markers. Quality control (QC) in GWAS involves removing unreliable markers and individuals, significantly enhancing the accuracy of results.

eQTL

RNA-Seq eQTL Analysis Pipeline: Uncovering Genetic Influences on Gene Expression

1 minute read

Published:

Understanding how genetic variations impact gene expression is crucial for uncovering the underlying mechanisms of complex traits and diseases. One powerful tool for this investigation is the expression quantitative trait locus (eQTL) analysis, which examines the relationship between genetic variants and genome-wide expression levels.

edgeR

RNA-Seq eQTL Analysis Pipeline: Uncovering Genetic Influences on Gene Expression

1 minute read

Published:

Understanding how genetic variations impact gene expression is crucial for uncovering the underlying mechanisms of complex traits and diseases. One powerful tool for this investigation is the expression quantitative trait locus (eQTL) analysis, which examines the relationship between genetic variants and genome-wide expression levels.

functional profiling

Taxonomic and functional profiling of the microbiome - whole genome shotgun metagenomics

1 minute read

Published:

This workflow consists of taxonomic and functional profiling of shotgun metagenomics sequencing (MGS) reads using MetaPhlAn2 and HUMAnN2, respectively. To perform taxonomic (phyla, genera or species level) profiling of the MGS data, the MetaPhlAn2 pipeline was run on a high performance multicore cluster computing environment.

genomics

Workflows for Discovering Copy Number Variations Using NGS Data.

less than 1 minute read

Published:

Copy number variations (CNVs) are genomic alterations that involve the gain or loss of specific regions of DNA. These variations can be inherited from parents or can arise de novo, and they play a significant role in neuropsychiatric disorders and cancers.

heterozygosity rate

Quality control for GWAS studies

1 minute read

Published:

A crucial step in analyzing genome-wide association studies (GWAS) is identifying problematic subjects and markers. Quality control (QC) in GWAS involves removing unreliable markers and individuals, significantly enhancing the accuracy of results.

htseq

RNA-Seq eQTL Analysis Pipeline: Uncovering Genetic Influences on Gene Expression

1 minute read

Published:

Understanding how genetic variations impact gene expression is crucial for uncovering the underlying mechanisms of complex traits and diseases. One powerful tool for this investigation is the expression quantitative trait locus (eQTL) analysis, which examines the relationship between genetic variants and genome-wide expression levels.

human complement

iBAC

isobaric labeling

label free quantitation

metagenomics

Taxonomic and functional profiling of the microbiome - whole genome shotgun metagenomics

1 minute read

Published:

This workflow consists of taxonomic and functional profiling of shotgun metagenomics sequencing (MGS) reads using MetaPhlAn2 and HUMAnN2, respectively. To perform taxonomic (phyla, genera or species level) profiling of the MGS data, the MetaPhlAn2 pipeline was run on a high performance multicore cluster computing environment.

microbiome

Taxonomic and diversity profiling of the microbiome - 16S rRNA gene amplicon sequence data

1 minute read

Published:

The 16S ribosomal RNA (rRNA) gene of Bacteria codes for the RNA component of the 30S subunit. Different bacterial species have one to multiple copies of the 16S rRNA gene, and each with 9 hypervariable regions, V1-V9. High-throughput sequencing of 16S rRNA gene (a “marker gene”) amplicons has become a widely used method to study bacterial phylogeny and species classification.

missingness

Quality control for GWAS studies

1 minute read

Published:

A crucial step in analyzing genome-wide association studies (GWAS) is identifying problematic subjects and markers. Quality control (QC) in GWAS involves removing unreliable markers and individuals, significantly enhancing the accuracy of results.

networks

plink

Quality control for GWAS studies

1 minute read

Published:

A crucial step in analyzing genome-wide association studies (GWAS) is identifying problematic subjects and markers. Quality control (QC) in GWAS involves removing unreliable markers and individuals, significantly enhancing the accuracy of results.

qiime2

Taxonomic and diversity profiling of the microbiome - 16S rRNA gene amplicon sequence data

1 minute read

Published:

The 16S ribosomal RNA (rRNA) gene of Bacteria codes for the RNA component of the 30S subunit. Different bacterial species have one to multiple copies of the 16S rRNA gene, and each with 9 hypervariable regions, V1-V9. High-throughput sequencing of 16S rRNA gene (a “marker gene”) amplicons has become a widely used method to study bacterial phylogeny and species classification.

runs of homozygosity

Quality control for GWAS studies

1 minute read

Published:

A crucial step in analyzing genome-wide association studies (GWAS) is identifying problematic subjects and markers. Quality control (QC) in GWAS involves removing unreliable markers and individuals, significantly enhancing the accuracy of results.

shotgun metagenomics sequencing

Taxonomic and functional profiling of the microbiome - whole genome shotgun metagenomics

1 minute read

Published:

This workflow consists of taxonomic and functional profiling of shotgun metagenomics sequencing (MGS) reads using MetaPhlAn2 and HUMAnN2, respectively. To perform taxonomic (phyla, genera or species level) profiling of the MGS data, the MetaPhlAn2 pipeline was run on a high performance multicore cluster computing environment.

tandem mass tag

taxonomic profiling

Taxonomic and functional profiling of the microbiome - whole genome shotgun metagenomics

1 minute read

Published:

This workflow consists of taxonomic and functional profiling of shotgun metagenomics sequencing (MGS) reads using MetaPhlAn2 and HUMAnN2, respectively. To perform taxonomic (phyla, genera or species level) profiling of the MGS data, the MetaPhlAn2 pipeline was run on a high performance multicore cluster computing environment.