Join the Neugebauer Lab
We are actively recruiting undergraduate researchers to join our lab. If you are interested, please submit a 1 page resume and a 1-2 paragraph statement describing why you would like to work with us to email@example.com. We are most interested in students who are able to commit to at least two full years of research. Below are some current projects in the lab that you could work on together with a mentor.
Tucker has identified a new putative splicing regulator in budding yeast (it’s a secret). You could follow up this hypothesis, using biochemistry and molecular biology.
Kirsten is using RNA sequencing to study the regulation of splicing kinetics during erythropoiesis. You can use the CRISPR/Cas system to generate cell lines that serve as disease models for red blood cells.
Tara is an expert in single molecule RNA sequencing and bioinformatic analysis. We have great data! You could make more data or work on generating analysis tools.
Spinal Muscular Atrophy (SMA) is a fatal childhood neurodegenerative disease, caused by the loss of a protein involved in splicing. You can investigate splicing regulation in a zebrafish model of SMA with Dahyana.
Dahyana and Edward are taking several approaches to identify the proteins and RNAs present in nuclear Cajal bodies. Ask how you can you can get involved by using mass spectrometry and fluorescence microscopy!
Students interested in doing a PhD with us should apply to the BBS track within the Yale Graduate School of Arts and Sciences. If you would like to do a rotation with us, please email Karla directly at firstname.lastname@example.org. Below are some open questions that rotation students could work on.
How do environmental conditions affect complex machineries in living cells? It turns out all sorts of environmental stresses (e.g. heat, oxidative stress, osmotic stress) as well as cancer, viral infections and cause changes in gene expression that are not fully understood. What are the underlying molecular mechanisms and cellular consequences of these phenomena? We are investigating the coupling between transcription and RNA processing steps (e.g. splicing and polyadenylation) by analyzing nascent RNA. In your rotation project, you could investigate the stress of your choice! As a reference, check out Herzel et al. Note that you could use budding or fission yeast, human tissue culture cells, or zebrafish embryos to test your stress!
We use a combination of emerging sequencing technologies to analyze nascent RNA and determine splicing kinetics. This involves both short (Illumina) and long (Oxford Nanopore) read sequencing of nascent RNA, which reveals splicing precursors, intermediates and products as transcription proceeds (the 3’ end indicates the position of Pol II). Each gene has a unique kinetic signature. As a reference, check out Carrillo Oesterreich et al. 2016 We have used machine learning to generate predictions about splicing regulation, but there are so many other approaches to explore! We would be interested in modeling and curve fitting approaches that allow us to test the effects of mutations.