Scientist, Bioinformatics

Scientist, Bioinformatics

Bridging the gap between Genomics and Data Science

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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.

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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.

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.

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.

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.

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.

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.

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.

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publications

Signatures of somatic mutations and gene expression from p16INK4A positive head and neck squamous cell carcinomas (HNSCC).

Published in PLOS ONE, 2020

Cancer Genomics

Recommended citation: Nabil F. Saba NF*, Dinasarapu AR*, Magliocca KR, Dwivedi B, Seby S, Qin ZS, Patel M, Griffith CC, Wang X, El-Deiry M, Steuer CE, Kowalski J, Shin DM, Zwick ME, Chen ZG (2020). "Signatures of somatic mutations and gene expression from p16INK4A positive head and neck squamous cell carcinomas (HNSCC)." PLOS ONE 15(9): e0238497. https://doi.org/10.1371/journal.pone.0238497

Differential expression of striatal proteins in a mouse model of DOPA-responsive dystonia reveals shared mechanisms among dystonic disorders.

Published in Molecular Genetics and Metabolism, 2021

Neuroscience

Recommended citation: Briscione MA, Dinasarapu AR, Bagchi P, Donsante Y, Downs AM, Fan X, Hoehner J, Jinnah HA, Hess EJ (2021). "Differential expression of striatal proteins in a mouse model of DOPA-responsive dystonia reveals shared mechanisms among dystonic disorders." Molecular Genetics and Metabolism. 133(4):352-361. https://doi.org/10.1016/j.ymgme.2021.05.010

Combinatorial clinically driven blood biomarker functional genomics significantly enhances genotype-phenotype resolution and diagnostics in neuromuscular disease.

Published in medRxiv, 2021

Functional Genomics

Recommended citation: Chakravorty S, Berger L, Rufibach L, Gloster L, Emmons A, Shenoy S, Hegde M, Dinasarapu AR, Gibson G (2021) Combinatorial clinically driven blood biomarker functional genomics significantly enhances genotype-phenotype resolution and diagnostics in neuromuscular disease." medRxiv https://doi.org/10.1101/2021.01.14.21249850

Circulating integrin α4β7+ CD4 T cells are enriched for proliferative transcriptional programs in HIV infection.

Published in FEBS Letters, 2021

Infectious diseases

Recommended citation: Lakshmanappa YS, Roh JW, Rane NN, Dinasarapu AR , Tran DD, Velu VV, Sheth AN, Ofotokun I, Amara RR, Kelley CF, Waetjen EW, Iyer SS (2021) Circulating integrin α4β7+ CD4 T cells are enriched for proliferative transcriptional programs in HIV infection" FEBS Letters. 595(17):2257-2270. https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14163

Neuroinflammatory transcriptional programs induced in rhesus pre-frontal cortex white matter during acute SHIV infection.

Published in Journal of Neuroinflammation, 2022

Infectious diseases & Inflammation

Recommended citation: Hawes CE, Elizaldi SR, Beckman D, Diniz GB, Lakshmanappa YS, Ott S, Durbin-Johnson BP, Dinasarapu AR , Gompers AL, Morrison JH, Iyer SS (2022). Neuroinflammatory transcriptional programs induced in rhesus pre-frontal cortex white matter during acute SHIV infection. Journal of Neuroinflammation, 19, 250. https://jneuroinflammation.biomedcentral.com/articles/10.1186/s12974-022-02610-y

Anti-inflammatory effects of recreational marijuana in virally suppressed youth with HIV-1 are reversed by use of tobacco products in combination with marijuana.

Published in Retrovirology, 2022

Infectious diseases & Inflammation

Recommended citation: Yin L, Dinasarapu AR , Borkar SA, Chang KF, De Paris K, Kim-Chang JJ, Sleasman JW, Goodenow MM (2022) Anti-inflammatory effects of recreational marijuana in virally suppressed youth with HIV-1 are reversed by use of tobacco products in combination with marijuana" Retrovirology 19, 10 (2022) https://retrovirology.biomedcentral.com/articles/10.1186/s12977-022-00594-4

Chronic SIV-induced neuroinflammation disrupts CCR7+CD4+ T cell immunosurveillance in the rhesus macaque brain.

Published in Journal of Clinical Investigation, 2024

Infectious diseases & Inflammation

Recommended citation: Elizaldi SR, Hawes CE, Verma A, Shaan Lakshmanappa Y, Dinasarapu AR, Schlegel BT, Rajasundaram D, Li J, Durbin-Johnson BP, Ma ZM, Pal PB, Beckman D, Ott S, Raeman R, Lifson J, Morrison JH, Iyer SS (2024). Chronic SIV-induced neuroinflammation disrupts CCR7+CD4+ T cell immunosurveillance in the rhesus macaque brain. J Clin Invest. https://pubmed.ncbi.nlm.nih.gov/38470479/

Live-cell invasive phenotyping uncovers the ALK2/BMP6 iron homeostasis pathway as a therapeutic vulnerability in LKB1-mutant lung cancer.

Published in Cancer Research, 2024

Recommended citation: Koo J, Seong CS, Parker RE, Dwivedi B, Arthur RA, Dinasarapu AR, Johnston HR, Claussen H, Tucker-Burden C, Ramalingam SS, Fu H,Zhou W, Marcus AI, Gilbert-Ross M. (2023) Live-cell invasive phenotyping uncovers the ALK2/BMP6 iron homeostasis pathway as a therapeutic vulnerability in LKB1-mutant lung cancer" https://www.biorxiv.org/content/10.1101/2023.06.14.544941v1

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