Jessica Kaufman

Endicott College

I have been teaching for thirteen years and I am currently a Professor of Biotechnology and Bioengineering at Endicott College. I teach a wide variety of courses for Biology, Bioengineering, and Engineering majors including "Genes and Genomes Lab", "Bioinformatics", and "Engineering Physiology". I am interested in developing research-based projects for this classes to promote independent planning in lab and engage students to use advanced programming tools for biological data analysis.

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Resequencing of Commercial Microorganisms part of CUREnet:Institutes:Community College of Rhode island:Examples
Students choose a probiotic pill or product with labeling that indicates the species and strain of bacteria in the product. Products are chosen so that a high quality reference genome sequence is available on NCBI. After DNA isolation and library preparation, high-quality student samples are pooled for next-gen sequencing on an Illumina MiSeq. The following semester, students in the required bioinformatics course will analyze the FASTQ files from the NGS run with a simple variant call workflow on usegalaxy.org. Then, each student will use a R Shiny app developed for this CURE to convert the VCF output from Galaxy to a FASTA file for an assigned gene in the resequenced genome. Students will complete their research experience by submitting the FASTA file to the NCBI Nucleotide Database.