The University of Chicago Header Logo

Anindita Basu

TitleAssociate Professor
InstitutionUniversity of Chicago
DepartmentMedicine-Genetic Medicine
AddressChicago IL 60637
ORCID ORCID Icon0000-0001-9468-3727 Additional info
vCardDownload vCard

    Collapse Overview 
    Collapse overview
    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.
    Collapse webpage

    Collapse Biography 
    Collapse education and training
    Harvard University, Broad Institute, Cambridge, MAPost-doc10/2016Applied Physics, Genomics
    University of Pennsylvania, Philadelphia, PAPhD07/2012Physics
    University of Arkansas, Fayetteville, ARBS05/2004Physics; Computer Engineering

    Collapse Featured Content 
    Collapse Featured Videos

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Zhao Y, Zhou R, Xie B, Liu CY, Kalski M, Cham CM, Jiang Z, Koval J, Weber CR, Rubin DT, Sogin M, Crosson S, Chen M, Huang J, Fiebig A, Dalal S, Chang EB, Basu A, Pott S. Multiomic analysis reveals cellular, transcriptomic and epigenetic changes in intestinal pouches of ulcerative colitis patients. Nat Commun. 2025 Jan 21; 16(1):904. PMID: 39837850; PMCID: PMC11751449.
      Citations:    Fields:    Translation:HumansCells
    2. Zhao Y, Zhou R, Xie B, Liu CY, Kalski M, Cham CM, Koval J, Weber CR, Rubin DT, Sogin M, Crosson S, Huang J, Fiebig A, Dalal S, Chang EB, Basu A, Pott S, Zhao Y, Zhou R, Xie B, Liu CY, Kalski M, Cham CM, Jiang Z, Koval J, Weber CR, Rubin DT, Sogin M, Crosson S, Chen M, Huang J, Fiebig A, Dalal S, Chang EB, Basu A, Pott S, Zhao Y, Zhou R, Xie B, Liu CY, Kalski M, Cham CM, Jiang Z, Koval J, Weber CR, Rubin DT, Sogin M, Crosson S, Chen M, Huang J, Fiebig A, Dalal S, Chang EB, Basu A, Pott S. Multiomic analysis reveals cellular, transcriptomic and epigenetic changes in intestinal pouches of ulcerative colitis patients. medRxiv. 2025 Jan 09. PMID: 38014192; PMCID: PMC10680893.
      Citations:    
    3. Weigert M, Li Y, Zhu L, Eckart H, Bajwa P, Krishnan R, Ackroyd S, Lastra R, Bilecz A, Basu A, Lengyel E, Chen M. A cell atlas of the human fallopian tube throughout the menstrual cycle and menopause. Nat Commun. 2025 Jan 03; 16(1):372. PMID: 39753552; PMCID: PMC11698969.
      Citations:    Fields:    Translation:HumansCells
    4. Zhao Y, Zhou R, Mu Z, Carbonetto P, Zhong X, Xie B, Luo K, Cham CM, Koval J, He X, Dahl AW, Liu X, Chang EB, Basu A, Pott S. Cell-type-resolved chromatin accessibility in the human intestine identifies complex regulatory programs and clarifies genetic associations in Crohn's disease. medRxiv. 2024 Dec 11. PMID: 39711713; PMCID: PMC11661348.
      Citations:    
    5. Xie B, Olalekan S, Back R, Ashitey NA, Eckart H, Basu A. Exploring the tumor micro-environment in primary and metastatic tumors of different ovarian cancer histotypes. Front Cell Dev Biol. 2023; 11:1297219. PMID: 38328306; PMCID: PMC10847324.
      Citations: 1     
    6. Fiebig A, Schnizlein MK, Pena-Rivera S, Trigodet F, Dubey AA, Hennessy MK, Basu A, Pott S, Dalal S, Rubin D, Sogin ML, Eren AM, Chang EB, Crosson S. Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient. mBio. 2024 Jan 16; 15(1):e0283023. PMID: 38063424; PMCID: PMC10790697.
      Citations: 7     Fields:    Translation:HumansCells
    7. Fiebig A, Schnizlein MK, Pena-Rivera S, Trigodet F, Dubey AA, Hennessy M, Basu A, Pott S, Dalal S, Rubin D, Sogin ML, Murat Eren A, Chang EB, Crosson S. Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient. bioRxiv. 2023 Oct 17. PMID: 37214927; PMCID: PMC10197588.
      Citations:    
    8. Selewa A, Luo K, Wasney M, Smith L, Sun X, Tang C, Eckart H, Moskowitz IP, Basu A, He X, Pott S. Single-cell genomics improves the discovery of risk variants and genes of atrial fibrillation. Nat Commun. 2023 08 17; 14(1):4999. PMID: 37591828; PMCID: PMC10435551.
      Citations: 7     Fields:    Translation:HumansCells
    9. Perrault EN, Shireman JM, Ali ES, Lin P, Preddy I, Park C, Budhiraja S, Baisiwala S, Dixit K, James CD, Heiland DH, Ben-Sahra I, Pott S, Basu A, Miska J, Ahmed AU. Ribonucleotide reductase regulatory subunit M2 drives glioblastoma TMZ resistance through modulation of dNTP production. Sci Adv. 2023 05 19; 9(20):eade7236. PMID: 37196077; PMCID: PMC10191446.
      Citations: 7     Fields:    Translation:HumansCells
    10. Nittala PVK, Hohreiter A, Rosas Linhard E, Dohn R, Mishra S, Konda A, Divan R, Guha S, Basu A. Integration of silicon chip microstructures for in-line microbial cell lysis in soft microfluidics. Lab Chip. 2023 05 02; 23(9):2327-2340. PMID: 37083052; PMCID: PMC10259373.
      Citations: 4     Fields:    Translation:Animals
    11. Lengyel E, Li Y, Weigert M, Zhu L, Eckart H, Javellana M, Ackroyd S, Xiao J, Olalekan S, Glass D, Iyer S, Krishnan R, Bilecz AJ, Lastra R, Chen M, Basu A. A molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA and ATAC sequencing. Cell Rep. 2022 12 20; 41(12):111838. PMID: 36543131; PMCID: PMC11295111.
      Citations: 18     Fields:    Translation:HumansCells
    12. Haltom AR, Hassen WE, Hensel J, Kim J, Sugimoto H, Li B, McAndrews KM, Conner MR, Kirtley ML, Luo X, Xie B, Volpert OV, Olalekan S, Maltsev N, Basu A, LeBleu VS, Kalluri R. Engineered exosomes targeting MYC reverse the proneural-mesenchymal transition and extend survival of glioblastoma. Extracell Vesicle. 2022 Dec; 1. PMID: 37503329; PMCID: PMC10373511.
      Citations: 10     
    13. Xie B, Cook D, Klineberg M, Nathan S, Hammes M, Basu A, Moya-Rodríguez A. Creating patient-specific vein models to characterize wall shear stress in hemodialysis population. Comput Struct Biotechnol J. 2022; 20:5729-5739. PMID: 36382195; PMCID: PMC9619312.
      Citations: 1     
    14. Rowton M, Perez-Cervantes C, Hur S, Jacobs-Li J, Lu E, Deng N, Guzzetta A, Hoffmann AD, Stocker M, Steimle JD, Lazarevic S, Oubaha S, Yang XH, Kim C, Yu S, Eckart H, Koska M, Hanson E, Chan SSK, Garry DJ, Kyba M, Basu A, Ikegami K, Pott S, Moskowitz IP. Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages. Dev Cell. 2022 09 26; 57(18):2181-2203.e9. PMID: 36108627; PMCID: PMC10506397.
      Citations: 7     Fields:    Translation:AnimalsCells
    15. 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; PMCID: PMC8779198.
      Citations: 8     
    16. 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; PMCID: PMC8463713.
      Citations: 30     Fields:    Translation:HumansAnimalsCells
    17. 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; PMCID: PMC8279323.
      Citations: 3     Fields:    Translation:Humans
    18. 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.
      Citations: 73     Fields:    Translation:HumansCells
    19. 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; PMCID: PMC7523121.
      Citations:    
    20. 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; PMCID: PMC7354932.
      Citations: 20     Fields:    Translation:AnimalsCells
    21. 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; PMCID: PMC6992778.
      Citations: 47     Fields:    Translation:HumansCells
    22. 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.
      Citations: 2     Fields:    Translation:Humans
    23. Habib N, Avraham-Davidi I, Basu A, Burks T, Shekhar K, Hofree M, Choudhury SR, Gelfand E, Ardlie K, Weitz DA, Rozenblatt-Rosen O, Zhang F, Regev A, Aguet F. Massively parallel single-nucleus RNA-seq with DroNc-seq. Nat Methods. 2017 Oct; 14(10):955-958. PMID: 28846088; PMCID: PMC5623139.
      Citations: 472     Fields:    Translation:HumansAnimalsCells
    24. 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.
      Citations: 18     Fields:    Translation:AnimalsCells
    25. 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. PMID: 26000628; PMCID: PMC4441486.
      Citations: 31     Fields:    
    26. 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. PMID: 26000488; PMCID: PMC4481139.
      Citations: 3100     Fields:    Translation:Animals
    27. Chen J, Le S, Basu A, Chazin WJ, Yan J. Mechanochemical regulations of RPA's binding to ssDNA. Sci Rep. 2015 Mar 19; 5:9296. PMID: 25787788; PMCID: PMC4365408.
      Citations: 27     Fields:    Translation:Cells
    Basu's Networks
    Click the
    Explore
    buttons for more information and interactive visualizations!
    Concepts (112)
    Explore
    _
    Co-Authors (24)
    Explore
    _
    Similar People (60)
    Explore
    _
    Same Department Expand Description
    Explore
    _
    Physical Neighbors
    _