We are an interdisciplinary research group that combines expertise from physics, genomics, molecular biology and materials science to study complex biological systems with single cell resolution, at very high throughput, and in context of their native environments. We are jointly affiliated with the department of Medicine at UChicago and Center for Nanoscale Systems at ANL.
We develop and apply key technologies that allow single-cell epi-genomic and transcriptomic profiling of as many as 104-105 cells, including mammalian and microbial cells such as bacteria and yeasts, using microfluidics and next-gen sequencing, with applications in basic and translational research.
We also develop tools to study inter-cellular interactions in complex biological systems in context of environment, as well as physical and chemical techniques to systematically perturb them.
We expect our work will help create better taxonomy of cells in complex tissues, relate epi-genomics to transcription at a single cell level, and decipher inter-cellular interactions in healthy and diseased systems. This will help us understand systems-level cellular organization and function as part of complex biological environments.
Single Cell Analysis, Single Nucleus Analysis, Microfluidics, Device Design, Medical, Host Pathogen Interactions, High Throughput RNA Sequencing
Habib N, Avraham-Davidi I, Basu A, Burks T, Shekhar K, Hofree M, Choudhury SR, Aguet F, Gelfand E, Ardlie K, Weitz DA, Rozenblatt-Rosen O, Zhang F, Regev A. Massively parallel single-nucleus RNA-seq with DroNc-seq. Nat Methods. 2017 Oct; 14(10):955-958. View in: PubMed
Tao Y, Rotem A, Zhang H, Chang CB, Basu A, Kolawole AO, Koehler SA, Ren Y, Lin JS, Pipas JM, Feldman AB, Wobus CE, Weitz DA. Rapid, targeted and culture-free viral infectivity assay in drop-based microfluidics. Lab Chip. 2015 Oct 07; 15(19):3934-40. View in: PubMed
Rotem A, Ram O, Shoresh N, Sperling RA, Schnall-Levin M, Zhang H, Basu A, Bernstein BE, Weitz DA. High-Throughput Single-Cell Labeling (Hi-SCL) for RNA-Seq Using Drop-Based Microfluidics. PLoS One. 2015; 10(5):e0116328. View in: PubMed
Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas AR, Kamitaki N, Martersteck EM, Trombetta JJ, Weitz DA, Sanes JR, Shalek AK, Regev A, McCarroll SA. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell. 2015 May 21; 161(5):1202-1214. View in: PubMed