Publications

2023

Optimization-based decoding of Imaging Spatial Transcriptomics data
John P Bryan, Loïc Binan, Cai McCann, Yonina C Eldar, Samouil L Farhi, Brian Cleary
Bioinformatics 39 (6), btad362

Compressed Perturb-seq: highly efficient screens for regulatory circuits using random composite perturbations
Douglas Yao, Loic Binan, Jon Bezney, Brooke Simonton, Jahanara Freedman, Chris J Frangieh, Kushal K Dey, Kathryn Geiger-Schuller, Basak Eraslan, Alexander Gusev, Aviv Regev, Brian Cleary
bioRxiv, 2023.01. 23.525200

Compressed sensing for highly efficient imaging transcriptomics
Brian Cleary, Brooke Simonton, Jon Bezney, Evan Murray, Shahul Alam, Anubhav Sinha, Ehsan Habibi, Jamie Marshall, Eric S Lander, Fei Chen, Aviv Regev
Nature Biotechnology 39 (8), 936-942

Sparse Recovery Of Imaging Transcriptomics Data
John P Bryan, Brian Cleary, Samouil L Farhi, Yonina C Eldar
2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI), 802-806

Using viral load and epidemic dynamics to optimize pooled testing in resource-constrained settings
Brian Cleary, James A Hay, Brendan Blumenstiel, Maegan Harden, Michelle Cipicchio, Jon Bezney, Brooke Simonton, David Hong, Madikay Senghore, Abdul K Sesay, Stacey Gabriel, Aviv Regev, Michael J Mina
Science Translational Medicine

Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming
Geoffrey Schiebinger, Jian Shu, Marcin Tabaka, Brian Cleary, Vidya Subramanian, Aryeh Solomon, Joshua Gould, Siyan Liu, Stacie Lin, Peter Berube, Lia Lee, Jenny Chen, Justin Brumbaugh, Philippe Rigollet, Konrad Hochedlinger, Rudolf Jaenisch, Aviv Regev, Eric S Lander
Cell 176 (4), 928-943. e22