![]() ![]() Assisted other colleagues in the application of bioinformatic pipelines, script writing, and troubleshooting assisted in wet lab genomic assays.Host-microbe symbiosis/characterize microbial ecosystems.Involved in various projects using bioinformatics as tools for assessing microbiome fitness.Experience gained from Meta - proteomics.Experience in website development (wordpress/Drupal/CSS/HTML/MAMP ).Led undergraduates with the experimental design for Alzheimer s Disease diagnostic research project.Quantitative Proteomics and Bioinformatics Data analysis project collaborations.Grid-search tuning parameter optimization. ![]() Supervised Classification Clustering KNN/Louvain Community detection.Dimensional reduction techniques via Unsupervised Machine learning by t-distributed stochastic neighbor embedding (tsne).Non-metric Multidimensional Scaling, Principle Coordinate of Analysis (Bray-Curtis, Pearson, Euclidean, other distance metrics for Compositional Data Analysis of Multinomial data).Log ratio fold changes of differentially expressed proteins.Solid-Conservative Statistical testing with BH/BY p-value correction thresholds.Alpha/Beta Diversities (Chao1, Shannon, Simpson indexes).Bioedit/Jalview individual small sequence editing.GROMACS-OPEN MM/ CHARM-GUI Molecular simulations CLC Genomics Workbench (CLC Gx) is a powerful solution developed by scientists for scientists to analyze and visualize next generation sequencing (NGS) data.Phylogenetic Community Profiling ( BEAST/MEGA/UGENE).Illumina read Qualitiy filtration: Robert Edgar s USEARCH/UPARSE pipeline (16s,ITS), PandaSeq.Pathway Analysis and Gene Ontology: IPA, PANTHER, DAVID, SBML file format.Analysis of scalefree Networks for Co-regulation/Occurrence.R/python pipelines, QuiXoT, SanXoT, pRatio.GenBank/NCBI, Greengenes or Ribosomal Database Project (RDP), Uniprot, Interpro.Managing and analyzing Relational datasets.Python/UNIX/BASH/SQL script writing and creating wrappers for Pipeline source codes.Knowledge with Object - oriented language/Command line.R package experience but not limited to: phyloseq, DESeq2, gplots, ggplot2, Vegan, devtools, edited a version of heatmap.3, annheatmap2, igraph, microbiome, tidyverse, LIMMA/DEqMS, ROC, treeClust, WGCNA, RCircos, Seriate.Quantitative Insights into Microbial Ecology (QIIME). ![]()
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