Tim Nieuwenhuis

About Tim Nieuwenhuis

As a former computational biologist at Immunitas Therapeutics, I developed two internal R packages to streamline and optimize our team\'s workflows. The first package focused on single-cell RNA-seq data analysis, from dataset retrieval and annotation to target prioritization. This enabled us to respond faster to frequently asked questions from wet lab biologists and C-suite executives. The second package standardized and version controlled the biomarker analysis pipeline, specifically for the company\'s phase I/II clinical studies of the lead program.In addition, I collaborated closely with wet-lab and computational biologists to assist in developing a target identification engine incorporating external and internal datasets for rare immune cell types. This involved defining and implementing strategic analytical approaches, as well as presenting and justifying these approaches to external investors and scientific advisory board members.Prior to my work at Immunitas Therapeutics, I completed my PhD in which I studied sources of biological and technical variation found in different RNA sequencing platforms, with a focus on bulk sequencing. My analysis and insights on massive RNA-seq databases such as GTEx and TCGA led to the identification of previously unknown sources of sequencing contamination in bulk RNA sequencing and single-cell RNA sequencing. Additionally, I curated the first body-wide transcriptomic analysis of the Matrisome.Other notable projects included the development of the R Shiny App and Bioconductor package \"HPAStainR\", a tool that leveraged the public staining data of the Human Protein Atlas database to reveal protein enrichment in tissues and cell types. Furthermore, I collaborated with The Segars Lab by developing an analysis of The MarketScan Database, using insurance data records to perform an epidemiological observational study showing decreased risk of uterine fibroids development in hypertensive individuals who take ACE inhibitors.For further information please see my resume which is attached as a featured item.For a full list of my publications please go to my Google Scholar Page: & hl=enFor code related to the several projects mentioned above and personal projects as well, please go to: https://github.com/tnieuwe

Experience

1. Senior Scientist, Bioinformatics

   AstraZeneca

   Jul 2023 — Present · Waltham, MA, US

Education

• Dickinson College

  Bachelor of Science - BS, Biochemistry and Molecular Biology

• Kittatinny Regional HighSchool

  High School Diploma

• The Johns Hopkins University School of Medicine

  Doctor of Philosophy - PhD, Human Genetics

  2017