Michael S. Chimenti, Ph.D. Email & Phone Number

Cedar Rapids, Ia, Us

Iowa City, Iowa, United States

Helping the FBB team to develop an RNA-based liquid biopsy diagnostic for neurological disease and cancer. We aim to provide the first non-invasive and inexpensive alternative to an invasive lumbar puncture for (suspected) neurological disease patients. I am leveraging AWS cloud to build back-end infrastructure with S3, AWS Healthomics, Eventbridge, Cloudwatch, SageMaker, etc... I am also performing predictive modeling of RNA NGS data using tools like sPLS-DA and XG-boost.

Iowa City, Iowa Area

I lead a team of four bioinformaticians and a full-time system administrator in the Bioinformatics Core facility of the IIHG. I assist investigators by helping to find solutions to their bioinformatics challenges. I keep current on novel and emerging technologies and methods in genomics and bioinformatics, and work to develop those techniques and skills to support investigator research at the University of Iowa. I act as a liaison to the College of Medicine and University of Iowa research community for education and outreach about computational biology.

Iowa City, Iowa

I performed applied bioinformatics and computational biology within the Iowa Institute of Human Genetics (IIHG). Kinds of projects I worked on: Metagenomics studies of microbial populations Transcriptomics and gene expression studies Pharmacogenomics (PGX) panels for our CAP-certified clinical laboratoryCreating and developing bioinformatics training materials, including tutorial videos and lectures Recent projects I've worked on include: Metagenomic 16S amplicon and whole-genome shotgun (WGS) studies of the Upper Mississippi River sediment beds containing mussels. This work, which resulted in three manuscripts, made important contributions to the understanding of N-cycling and nitrification processes in the mussel bed. Collaboration with Craig Just and Ellen Black, Univ. of Iowa College of Engineering. Investigating the genetic basis for Vestibular Schwannomas (VS), a form of head/neck cancer. I contributed by running exome and whole-genome analysis pipelines to generate lists of potential somatic mutations. I calculated somatic mutational "signatures" from the data and showed relative abundances of the signatures within the tumors. I performed data analysis of genetic mutations in early- and late-stage tumors and showed genes in common, as well as differences. Expanding our pharmacogenomics panel with new genes for PGx screening. This involved researching and cataloging each gene's star alleles of interest and their constituent variants. I helped in validating that the pipeline could correctly detect the star alleles of interest with relevant PGx information. We also maintain this pipeline to CAP/CLIA standards of reporting and validation.

San Francisco

Computational and biophysical drug screening and development to discover novel small molecule inhibitors of a challenging target, p97 ATPase, for the treatment of Multiple Myeloma and other cancers. National Cancer Institute-funded collaboration with the UCSF Small Molecule Discovery Center.Virtual ligand screening to aid organic chemistry development routesI made correct computation predictions about the binding site and mode of our best ligands, providing critical guidance for ligand development My predictions were verified by cryo-EM structures that were subsequently published in Nature journals. I also used advanced structural NMR and labeling techniques to assess binding site configurations experimentallyAdvisors: Matt Jacobson, Mark Kelly, Michelle Arkin

San Francisco Bay Area

Collaborative study of pH sensing proteins in cytoskeleton dynamics and cell cycle checkpoint regulation. Biophysical and computational study of EB1 +TIP tracking protein interactions with human CLASP2.

Ph.D., Biophysics

Contributed novel large-scale biophysical datasets using structural NMR spectroscopy to aid the benchmarking and improvement.

Bachelor Of Science (B.S.) W/ Honors, Biochemistry

Activities and Societies: Honors Society; Jazz Band