Description
Under general supervision and as a team member, formulate and define system scope and objectives through research and fact-finding to develop or modify moderately complex applications. Additionally, support troubleshooting, problem identification and resolution. Duties include helping to write, modify, document, and test code and existing pipelines designed to process and analyze high-throughput sequence data. The position will require manipulation of enormous (up to 100 Gb) data files in the UNIX environment and using existing pipelines and custom scripts to post-process and interpret the results. Off-the-shelf packages and self-written code will also be necessary to generate images describing these results. To accomplish these goals, proficiency with R, Python, SAS, and SQL will be necessary. For data interpretation, the individual should also have statistical and data-mining proficiency.
ESSENTIAL FUNCTIONS
Data Acquisition & Processing: Download and process publicly available DNA and RNA sequence datasets. Manage patient-derived sequencing data from UH and results from wet lab experiments. Install packages and software on HPC as needed. (10%)
Bioinformatics Workflow Implementation: Conduct quality control (QC) using FastQC and preprocess sequencing data with Trimmomatic. Perform alignment of DNA sequences using BWA and RNA sequences using STAR. Apply GATK best practices for variant calling, generate VCF files, and manipulate sequencing data with SAMtools. Execute DNA signature analysis, SNP identification, epigenetic profiling, RNA expression analysis, and transcriptomics using appropriate computational tools. Perform microbiome analysis using Kraken2, BLAST, biobakery, cBioPortal, UCSC Genome Browser. (40%)
Advanced Genomic: Conduct pathway analysis using DAVID, GSEA (Gene Set Enrichment Analysis), limma, and other tools to interpret functional genomic impact. Perform drug response analysis using appropriate tools. (10%)
Data Visualization & Interpretation: Generate volcano plots using ggplot2 in R to highlight differential gene expression. Create heatmaps for expression clustering using ComplexHeatmap. Utilize advanced visualization techniques to illustrate genomic variation, RNA expression patterns, and epigenetic landscapes. (15%)
Perform machine learning (supervised and unsupervised) and statistical analysis (descriptive statistics, EDA, parametric and non-parametric statistical tests, fit prediction models, survival analysis using Kaplan Meier and Cox regressions) of processed data to interpret biological relevance. This will require the use of R packages and stand-alone programs. (16%)
NONESSENTIAL FUNCTIONS
Create quality images for papers and grant proposals. These images will be created using R, and PowerPoint. (5%)
Train undergraduates and other lab personnel as required. (3%)
Present in lab meetings. (1%)
CONTACTS
Department: Daily contact with department staff in consultation necessary for data analyses, code debugging, and code optimization.
University: Contact with department administrators to exchange information.
External: May have contact with outside consultants and representatives in consultation necessary for data analyses, code debugging, and code optimization.
Students: Interaction with graduate students in consultation necessary for data analyses, code debugging, and code optimization.
SUPERVISORY RESPONSIBILITIES
This position has no direct supervision of staff employees.
QUALIFICATIONS
Experience and Education: 2 years related experience and Associates degree in related field OR 0 years of experience and bachelor¿s degree in related field required.
REQUIRED SKILLS
Accountability/integrity, customer/quality focus, diversity/maturity, flexibility/receptivity, interpersonal relations, leadership/supervision, planning/organizing, problem solving, project management, self-development and teamwork.
Proficient in languages such as R, SAS, and Python.
Working knowledge of relational databases such as Oracle, includes SQL.
Operating systems such as Microsoft Windows and Unix.
Basic PC skills, general knowledge Microsoft Office products.
Basic SHELL script development.
Demonstrated history of successful support, education, and advocacy for all students, aligned with the values, mission, and messaging of the university, while adhering to the staff policy on conflict of commitment and interest.
Ability to meet consistent attendance.
Ability to interact with colleagues, supervisors and collaborators face to face.
WORKING CONDITIONS
General office environment. The employee will perform repetitive motion using computer mouse and keyboard to type. Limited manual dexterity required. Work requires negligible physical exertion. Little or no exposure to hazards.
Requirements
QUALIFICATIONS
Experience and Education: 2 years related experience and Associates degree in related field OR 0 years of experience and bachelor¿s degree in related field required.
