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Student Researcher Resume

SUMMARY:

  • Quantitative Insights into Microbial Ecology (QIIME)
  • R Project statistical software
  • 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
  • Knowledge with Object - oriented language/Command line
  • Python/UNIX/BASH/SQL script writing and creating wrappers for Pipeline source codes
  • Managing and analyzing Relational datasets
  • Genome & Proteome Database Usage:
  • GenBank/NCBI, Greengenes or Ribosomal Database Project (RDP), Uniprot, Interpro
  • Quantitative Proteomics Pipelines
  • Thermo Proteome Discoverer
  • Skyline
  • R/python pipelines, QuiXoT, SanXoT, pRatio
  • Qaigen s CLC Genomics Workbench
  • Analysis of scalefree Networks for Co-regulation/Occurrence
  • Pathway Analysis and Gene Ontology: IPA, PANTHER, DAVID, SBML file format.
  • Illumina read Qualitiy filtration: Robert Edgar s USEARCH/UPARSE pipeline (16s,ITS), PandaSeq
  • Phylogenetic Community Profiling (BEAST/MEGA/UGENE)
  • Molecular Modeling/Dynamics:
  • SwissDoc protein analysis
  • Visual Molecular Dynamics
  • UCSF Chimera
  • Marvin Sketch (Molecular drawing)
  • GROMACS-OPEN MM/ CHARM-GUI Molecular simulations
  • METAGENassist
  • Galaxy's (LDA Effect Size (LEfSe)
  • Bioedit/Jalview individual small sequence editing
  • Alpha/Beta Diversities (Chao1, Shannon, Simpson indexes)
  • Solid-Conservative Statistical testing with BH/BY p-value correction thresholds
  • Kruskal Wallis/ANOVA/PERMANOVA ect.
  • Post Hoc analysis: i.e. Dunn s Test
  • Log ratio fold changes of differentially expressed proteins
  • Non-metric Multidimensional Scaling, Principle Coordinate of Analysis (Bray-Curtis, Pearson, Euclidean, other distance metrics for Compositional Data Analysis of Multinomial data)
  • Missing value imputation
  • Dimensional reduction techniques via Unsupervised Machine learning by t-distributed stochastic neighbor embedding (tsne)
  • Supervised Classification Clustering KNN/Louvain Community detection
  • Grid-search tuning parameter optimization

WORK/RESEARCH EXPERIENCE:

Student Researcher

Confidential

Responsibilities:

  • Quantitative Proteomics and Bioinformatics Data analysis project collaborations.
  • Led undergraduates with the experimental design for Alzheimer s Disease diagnostic research project
  • Experience in website development (wordpress/Drupal/CSS/HTML/MAMP )
  • Experience gained from Meta - proteomics

Student Researcher

Confidential

Responsibilities:

  • Involved in various projects using bioinformatics as tools for assessing microbiome fitness
  • Host-microbe symbiosis/characterize microbial ecosystems.
  • Assisted other colleagues in the application of bioinformatic pipelines, script writing, and troubleshooting assisted in wet lab genomic assays.
  • Assisted in the Fungal (ITS) multivariate data analysis from Black (Rhizophora mangle) and Red Mangrove (Avicennia germinans) environmental samples

Student Researcher

Confidential

Responsibilities:

  • Predictive Molecular Simulations
  • Visual Molecular Dynamics

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