We aim to understand gene regulation by building broadly applicable computational tools to analyze high-throughput genomic assays. This approach works by carefully investigating the experimental design and developing data-driven models using computer science and high-dimensional statistics to advance biomedical discovery.
Our goal is to better understand how genes regulate each other and how disease disrupts gene networks. This goal is realized by developing software that enables us and others to analyze complex genomic datasets that sample the transcriptional landscape. With this mission in mind, we build models with insight of the experimental protocols and biological questions while utilizing and extending the latest theory of computer science and statistics.
Below are some representative tools that we developed in collaboration before the inception of the Pimentel lab.
sleuth is a transcript level differential expression analysis tool for RNA-Seq. It is different from most tools in that it incorporates the inferential variability from transcript abundance estimation.
sleuth also allows scientists to interactively explore their data using an R Shiny application which can be easily shared to encourage reproducibility and scientific sharing. A demo of this app can be found at the bear's lair.
We are currently looking for kind, curious, and ambitious researchers.
We will be looking for graduate student researchers to rotate starting early 2021. However, if there is a timing issue (e.g. your only available rotation is late 2020), please reach out.
Graduate students in our lab will be on collaborative teams with the goal of building generalizable software to solve complex problems in genomics. The goal and expectation is for each student to graduate with expertise in modeling and data analysis as well as expertise in an area of functional genomics.
The students we expect will thrive in our lab come from diverse backgrounds but are not limited to:
If you think you might be a good fit and are already at UCLA, please send Harold an email with your CV and research interests.
We currently have a position open jointly with Bogdan Pasaniuc. The job ad is here.
We are also open to co-advising postdoctoral researchers with other computational or experimental labs. An example might be an experimental postdoc with their own biological question for which there are no current analysis tools.
If interested, please send the following to Harold:
Unfortunately we are currently at capacity for undergrads. However, if you think that you might want to do some work in the lab in the future, please reach out so we can discuss.
We don’t have immediate plans to hire in other areas but if you think you are an exceptional fit, please email Harold your CV along with a short description of what you hope to accomplish by joining the lab.