Jennifer Knapp Ph.D. Email & Phone Number

Boston, MA, US

Cambridge, Massachusetts, United States

• Developed and analyzed a novel Phage ImmunoPrecipitation Sequencing (Phip-seq) pipeline
• Adapted and Implemented a Phage scATAC-seq (alternative approach to CITE-seq antibody protein recognition) pipeline and analysis methodology
• Analyzed TCR scRNA-seq from mouse and human systemic lupus erythematosus data as part of a collaborative team
• Analyzed scATAC-seq data from endobronchial brush samples from patients with asthma as part of a collaborative team
• Regularly presented results and participated in active scientific discussions in multi-disciplinary scientific program groups
• Served as subject matter expert for both biological and computational topics

Greater Denver Area

• Lead Bioinformatician for the Brian O'Connor Laboratory
• Genomics experimental design addressing biological questions
• Work in cross-functional environment to help coordinate clinical and laboratory goals for optimal experimental results
• Pipeline development for analysis of genomic experiments | single cell RNA-seq, ATAC-seq, ChIP-seq, RNA-seq, splicing analysis, SNP discovery
• Collaborate with the NJH Genomics Facility to provide specialized analysis of genomic data for a diverse group of customers/scientists. Participated in over 25 collaborations.
• Participate in study design, coordination, and data analysis.

Kansas City, Kansas

• Participated in a bioinformatics core to facilitate sequencing projects for KUMC faculty
• Experimental design of sequencing projects in a cross functional environment.
• Developed pipelines for sequencing data | RNA-seq, SNP discovery, ChIP-seq, metagenomics
• Results interpretation of data quality and biological meaning with pathway analysis
• Facilitated data storage management and delivery for KUMC’s sequencing core

Kansas City, Missouri

• Collaborative project with Dr. Kausik Si Genomic analysis of RNA binding protein (Pasilla/Nova) targets using the iClip protocol.
• Validated unexpected results using immunoprecipitation-PCR methods while adjusting biochemical conditions.

• Identifying developmental pathways disrupted by Hsp90 dependent polymorphisms in the Drosophila eye.
• Determined environmental conditions that influenced penetrance of the Drosophila deformed eye model to optimize crosses.
• Investigated genetic variation affecting the eye development of the deformed eye phenotype utilizing hundreds of available genetic stocks to perform crosses.
• Improved and maintained Drosophila stocks in multi-temperature environments.
• Wrote Grants to fund investigation of the deformed eye phenotype.

• Development of a Myogenin conditional allele for analysis of mouse adult skeletal muscle growth and repair.
• Designed and created the targeting construct for the conditional allele.
• Obtained mouse strains and maintained mouse colony for experimental needs.
• Designed crosses to generated experimental strains of mice.
• Wrote and summarized results in thesis and publications

Ashland, OR

• Analysis of polymorphisms in the mitochondrial genome between domestic and wild sheep
• Organized additional sample procurement to increase available spices samples

Seattle, WA

• Isolation of revertant alleles of the gene Unc-43 in C. Elegans
• Performed mutation inducing experiments
• Wrote and summarized all experimental results

Master Of Science (M.S.), Biotechnology W/ Bioinformatics

Doctor Of Philosophy (Ph.D.), Biomedical Sciences, Genes And Development

Bachelor Of Science (B.S.), Cell And Molecular Biology