Our Faculty

Anindita Basu, PhD

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.

Harvard University, Broad Institute
Cambridge, MA
Post-doc - Applied Physics, Genomics
2016

University of Pennsylvania
Philadelphia, PA
PhD - Physics
2012

University of Arkansas
Fayetteville, AR
BS - Physics; Computer Engineering
2004

mDrop-Seq: Massively Parallel Single-Cell RNA-Seq of Saccharomyces cerevisiae and Candida albicans.
Dohn R, Xie B, Back R, Selewa A, Eckart H, Rao RP, Basu A. mDrop-Seq: Massively Parallel Single-Cell RNA-Seq of Saccharomyces cerevisiae and Candida albicans. Vaccines (Basel). 2021 Dec 27; 10(1).
PMID: 35062691

High-throughput RNA sequencing of paraformaldehyde-fixed single cells.
Phan HV, van Gent M, Drayman N, Basu A, Gack MU, Tay S. High-throughput RNA sequencing of paraformaldehyde-fixed single cells. Nat Commun. 2021 09 24; 12(1):5636.
PMID: 34561439

Computational modeling of the cephalic arch predicts hemodynamic profiles in patients with brachiocephalic fistula access receiving hemodialysis.
Hammes M, Moya-Rodriguez A, Bernstein C, Nathan S, Navuluri R, Basu A. Computational modeling of the cephalic arch predicts hemodynamic profiles in patients with brachiocephalic fistula access receiving hemodialysis. PLoS One. 2021; 16(7):e0254016.
PMID: 34260609

Characterizing the tumor microenvironment of metastatic ovarian cancer by single-cell transcriptomics.
Olalekan S, Xie B, Back R, Eckart H, Basu A. Characterizing the tumor microenvironment of metastatic ovarian cancer by single-cell transcriptomics. Cell Rep. 2021 05 25; 35(8):109165.
PMID: 34038734

Fixed single-cell RNA sequencing for understanding virus infection and host response.
Van Phan H, van Gent M, Drayman N, Basu A, Gack MU, Tay S. Fixed single-cell RNA sequencing for understanding virus infection and host response. bioRxiv. 2021 Jan 21.
PMID: 32995793

Hedgehog-FGF signaling axis patterns anterior mesoderm during gastrulation.
Guzzetta A, Koska M, Rowton M, Sullivan KR, Jacobs-Li J, Kweon J, Hidalgo H, Eckart H, Hoffmann AD, Back R, Lozano S, Moon AM, Basu A, Bressan M, Pott S, Moskowitz IP. Hedgehog-FGF signaling axis patterns anterior mesoderm during gastrulation. Proc Natl Acad Sci U S A. 2020 07 07; 117(27):15712-15723.
PMID: 32561646

Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation.
Selewa A, Dohn R, Eckart H, Lozano S, Xie B, Gauchat E, Elorbany R, Rhodes K, Burnett J, Gilad Y, Pott S, Basu A. Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation. Sci Rep. 2020 01 30; 10(1):1535.
PMID: 32001747

Hemodynamic effects of hemodialyzer pump speed on arteriovenous fistulas?.
Hammes M, McGill RL, Basu A, Blicharski T, Delaney K. Hemodynamic effects of hemodialyzer pump speed on arteriovenous fistulas?. Clin Nephrol. 2019 Mar; 91(3):138-146.
PMID: 30526815

Massively parallel single-nucleus RNA-seq with DroNc-seq.
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.
PMID: 28846088

Rapid, targeted and culture-free viral infectivity assay in drop-based microfluidics.
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.
PMID: 26304791

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