Research

I am a second-year PhD student in computer science at Princeton, advised by Barbara Engelhardt. Broadly, I am interested in machine learning methods motivated by scientific problems. My current work is in multimodal learning and generative modeling.

Previously, I worked as a research software engineer for Avi Ma'ayan at the Icahn School of Medicine at Mount Sinai, building tools for high-dimensional analysis of gene expression data.

As a self-taught programmer, I strongly support tech education as an inroad to economic opportunity. At Princeton, I volunteer for the Prison Teaching Initiative, where we are developing an accredited introductory computer science course to be offered at New Jersey state prisons. When I lived in New York, I volunteered for the Coalition for Queens by teaching programming to underserved communities.

Publications

  1. Fernandez, N., Gundersen, G., Rahman, A., Grimes, M., Rikova, K., Hornbeck, P., Ma'ayan, A. Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data (2017). Scientific Data. [pdf]
  2. Gundersen, G., Jagodnik, K., Woodland, H., Fernandez N., Sani, K., Dohlman, A., Man-Ung, P., Monteiro, C., Schlessinger, A., Ma'ayan, A. GEN3VA: aggregation and analysis of gene expression signatures from related studies (2016). BMC Bioinformatics. [pdf]
  3. Wang, Z. and 48 authors (Gundersen, G., author no. 5). Extraction and Analysis of Signatures from the Gene Expression Omnibus by the Crowd (2016). Nature Communications. [pdf]
  4. Kuleshov, M., Jones, M., Rouillard, A., Fernandez, N., Duan, Q., Wang, Z., Koplev, S., Jenkins, S., Jagodnik, K., Lachmann, A., McDermott, M., Monteiro, C., Gundersen, G., Ma'ayan, A. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update (2016). Nucleic Acids Research. [pdf]
  5. Rouillard, A., Gundersen, G., Fernandez, N., Wang, N., Monteiro, C., McDermott, M., Ma'ayan, A. The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins (2016). Database (Oxford). [pdf]
  6. Gundersen, G., Jones, M., Rouillard, A., Kou, Y., Monteiro, C., Feldmann, A., Hu, K., Ma'ayan, A. GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions (2015). Bioinformatics. [pdf]
  7. Gao, Y., Zorman, S., Gundersen, G., Xi, Z., Ma, L., Sirinakis, G., Rothman, J., Zhang, Y. Single Reconstituted Neuronal SNARE Complexes Zipper in Three Distinct Stages (2012). Science. [pdf, video]
  8. Zhang, Y., Sirinakis, G., Gundersen, G., Xi, Z., Gao, Y. DNA translocation of ATP-dependent chromatin remodeling factors revealed by high-resolution optical tweezers (2012). Methods Enzymol. [pdf]