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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