Hi! I am a Principal Scientist in the department of Cell and Tissue Genomics - Oncology at Genentech. My work spans functional genomics, gene regulation and high-content screens to understand health and disease mechanisms. I want to understand how cells make decisions about their cell states, and how we can bias these away from disease states, especially in the context of acquired drug resistance in cancer.

In my postdoc, I worked with Aviv Regev, focusing on using Perturb-seq single-cell screening technologies to study cancer drivers, including coding variants in cancer (in collaboration with Jesse Boehm and JT Neal), and chromatin remodeling complexes (in collaboration with Cigall Kadoch, Jordan Otto and Alex Wu).

I received my PhD from Stanford University (Department of Genetics) in 2018, co-advised by Anshul Kundaje and Michael Snyder, and collaborating with Michael Bassik's lab. In my research, I combined machine learning with experiments to understand non-coding genetic variation in the context of how our genome folds in 3D space, how we can perturb the 3D genome and how this affects gene regulation.

I completed my undergrad studies in Computer Science and Molecular Biology at MIT in 2012, where I worked in Ernest Fraenkel's group to study drug resistance in pancreatic cancer. Previously, I spent the first 2 years of my undergrad degree at Mount Holyoke College where I took my first steps towards systems biology.

MAIN PAPERS

Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens [data] [code]

Molecular Cell, 2023 

Otto J. E*., Ursu O.*,  Wu A. P.*,  Winter E. B.,  Cuoco M. S.,  Ma S., Qian K.,  Michel B. C., Buenrostro J. D., Berger B.,  Regev A., Kadoch C.

* Co-first author 

Massively parallel phenotyping of coding variants in cancer with Perturb-seq [data] [code]

Nature Biotechnology, 2022

Ursu O.*, Neal JT*, Shea E, Thakore P., Jerby-Arnon L., Nguyen L., Dionne D., Diaz C., Bauman J., Mosaad M., Fagre C., Lo A., McSharry M., Giacomelli A., Huong Ly S., Rozenblatt-Rosen O., Hahn W., Aguirre A., Berger A., Regev A., Boehm J.

* Co-first author 

• Research highlight in Broad Institute News

GenomeDISCO: A concordance score for chromosome conformation capture experiments using random walks on contact map graphs [code: GenomeDISCO]

Bioinformatics, 2018

Ursu O, Boley N, Taranova M, Wang R, Yardimci G, Noble W and A. Kundaje

• Voted in the top reading list for 2017-2018 at the RECOMB/ISCB Regulatory Systems Genomics 2019 conference

Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens [data] [code]

PLoS ONE, 2017

Ursu O., Gosline SJC, Beeharry N., Fink L., Bhattacharjee V., Huang S-S C., Zhou Y, Yen T and E. Fraenkel 

Genetic control of chromatin states in humans involves local and distal chromosomal interactions [data] [code]

Cell, 2015

Grubert F.*, Zaugg J.*, Kasowski M.*, Ursu O*, Spacek D., Martin A., Greenside P., Srivas R., Phanstiel D., Pekowska A., Heidari N., Euskirchen G., Huber W., Pritchard J., Bustamante C., Steinmetz L., Kundaje A. and M. Snyder

* Co-first author

• Research highlight in Cell and Nature Reviews Genetics

ADDITIONAL PAPERS

Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements 

Nature Communications, 2019

Tycko J.*, Wainberg M.*, Marinov G. K.*, Ursu O., Hess G. T., Ego B., Aradhana, Li A., Truong A., Trevino A. E., Spees K., Yao D., Kaplow I., Greenside P. G., Morgens D., Phanstiel D., Snyder M. P., Bintu L., Greenleaf W. J., Kundaje A. and M. C. Bassik 

Measuring the reproducibility and quality of Hi-C data 

Genome Biology, 2019

Yardimci G., Ozadam H., Sauria M., Ursu O., Yan KK., Yang T., Chakraborty A., Kaul A., Lajoie B., Song F., Zhan Y., Ay F., Gerstein M., Kundaje A., Li Q., Taylor J., Yue F., Dekker J., Noble W.

Network modelling of topological domains using Hi-C data 

Annals of Applied Statistics, 2019

Wang Y. X. R., Sarkar P., Ursu O., Kundaje A and P. J. Bickel

Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens 

Nature Communications, 2017

Morgens D, Wainberg M, Boyle E, Ursu O, Araya C, Tsui K, Haney M, Hess G, Han K, Jeng E, Li A, Snyder M, Greenleaf W, Kundaje A and M Bassik

Unsupervised Learning from Noisy Networks with Applications to Hi-C Data

Advances In Neural Information Processing Systems, 2016

Wang B., Zhu J., Pourshafeie A., Ursu O., Batzoglou S. and A. Kundaje

SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets

Integrative Biology, 2012

Gosline SJC, Spencer SJ, Ursu O, Fraenkel E

MORE FUN STUFF

Here is my sister and favourite person in the world: Raluca Ursu

Here is my cat