{"id":13,"date":"2017-01-05T19:41:32","date_gmt":"2017-01-05T19:41:32","guid":{"rendered":"http:\/\/wordpress.uchospitals.edu\/basu-lab\/?page_id=13"},"modified":"2025-04-29T20:08:03","modified_gmt":"2025-04-29T20:08:03","slug":"publication","status":"publish","type":"page","link":"https:\/\/medpress.bsd.uchicago.edu\/basu-lab\/publication\/","title":{"rendered":"Publication"},"content":{"rendered":"

Y. Zhao, R. Zhou, Z. Mu, P. Carbonetto, X. Zhong, B. Xie, K. Luo, C. M. Cham, J. Koval, X. He, A. W. Dahl, X. Liu, E. B. Chang, A. Basu, S. Pott, Cell-type-resolved chromatin accessibility in the human intestine identifies complex regulatory programs and clarifies genetic associations in Crohn’s disease<\/em>, medRxiv (2024), https:\/\/doi.org\/10.1101\/2024.12.10.24318718<\/a><\/p>\n

R. Zhou, B. Xie, J. Liu, Y. Zhao, J. Koval, C. M. Cham, J. Pekow, C. Weber, E. B. Chang, A. Basu, Epithelia mediate inflammation with myeloid cells in Crohn\u0393\u00c7\u00d6s disease patients under treatment, bioRxiv (2025), https:\/\/doi.org\/10.1101\/2025.03.26.645552<\/a><\/p>\n

M. Weigert, Y. Li, L. Zhu, H. Eckart, P. Bajwa, R. Krishnan, S. Ackroyd, R. Lastra, A. Bilecz, A. Basu, E. Lengyel, M. Chen, “A cell atlas of the human fallopian tube throughout the menstrual cycle and menopause”, <\/em>Nature Communications<\/i> 16<\/b>, 372<\/span> (2025<\/span>)<\/a> (pdf<\/a>)<\/p>\n

Y. Zhao, R. Zhou, B. Xie, C. Y. Liu, M. Kalski, C. M. Cham, J. Koval, C. R. Weber, D. T. Rubin, M. Sogin, S. Crosson, J. Huang, A. Fiebig, S. Dalal, E. B. Chang, A. Basu, S. Pott*, “Multiomic analysis reveals cellular, transcriptomic and epigenetic changes in intestinal pouches of ulcerative colitis patients”, Nature Communications,<\/em> 16<\/strong>, 904 (2025)<\/a> (pdf<\/a>)<\/p>\n

B. Xie, S. Olalekan, R. Back, N. Ashitey, H. Eckart, A. Basu, \u0393\u00c7\u00a3Comparing the tumor microenvironment of solid tumors of different primary and metastatic ovarian cancer histotypes at single cell resolution\u0393\u00c7\u00a5, Frontiers<\/em><\/span> in Cell and Developmental Biology, Sec. Cell Adhesion and Migration<\/em>, 11<\/strong> (2023)<\/a> (pdf<\/a>)<\/p>\n

A. Selewa, K. Luo, M. Masney, L. Smith, C. Tang, H. Eckart, I. Moskowitz, A. Basu, X. He, S. Pott, “Single-cell genomics improves the discovery of risk variants and genes of cardiac traits”, Nature Communications<\/em>, 14<\/strong>, 4999 (2023)<\/a>, (pdf<\/a>)<\/p>\n

S. Baisiwala, S. Budhiraja, E. Perrault, A. Zolp, K. Nandoliya, J. Miska, L. Chen, C. Park, M. Saathoff, C. Dmello, J. Shireman, P. Lin, J. Duffy, I. Balyasnikova, J. David, C. Horbinski, S. Pott, A. Basu, A. Sonabend, A. Ahmed, “Ribonucleotide Reductase Regulatory Subunit M2 Drives Glioblastoma TMZ-Resistance through Modulation of dNTP Production”,<\/em> Science Advances<\/em>, 9<\/strong>, eade7236 (2023)<\/a>, (pdf<\/a>)<\/p>\n

P. V. K. Nittala, A. Hohreiter, E. R. Linhard, R. Dohn, S. Mishra, A. Konda, R. Divan, S. Guha, A. Basu, “Integration of silicon chip microstructures for in-line microbial cell lysis in soft microfluidics” Lab on a Chip<\/em>, 23<\/strong>, 2327-2340 (2023) <\/a>(pdf<\/a>)<\/p>\n

A. R. Haltom, W. E. Hassen, J. Hensel, J. Kim, H. Sugimoto, B. Li, K. M. McAndrews, M. R. Conner, M. L. Kirtley, X. Luo, B. Xie, O. V. Volpert, S. Olalekan, N. Maltsev, A. Basu, V. S. LeBleu, R. Kalluri, “Engineered exosomes targeting MYC reverse the proneural-mesenchymal transition and extend survival of glioblastoma” Extracellular Vesicle<\/em>, 1<\/strong>, 100014 (2022)<\/a>(pdf<\/a>)<\/p>\n

A. Moya-Rodr\u251c\u00a1guez, B. Xie, D. Cook, M. Klineberg, S. Nathan, M. Hammes, A. Basu, “Creating Patient-Specific Vein Models to Characterize Wall Shear Stress in Hemodialysis Population”, Computational and Structural Biotechnology Journal <\/em>, 20<\/strong>, 5729 (2022) <\/a>(pdf<\/a>)<\/p>\n

E. Lengyel, Y. Li, M. Weigert, L. Zhu, H. Eckart, M. Javellana, S. Ackroyd, J. Xiao, S. Olalekan, D. Glass, S. Iyer, A. J. Bilecz, R. Lastra, M. Chen, A. Basu, “A molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA and ATAC sequencing”, BioRXiv, doi: https:\/\/doi.org\/10.1101\/2022.08.04.502826 <\/em> <\/a> (pdf<\/a>); Cell Reports<\/em>, 41<\/strong>(12), 111838 (2022)<\/p>\n

A. Selewa, K. Luo, M. Wasney, L. Smith, C. Tang, H. Eckart, I. Moskowitz, A. Basu, X. He, S. Pott, “Single-cell genomics improves the discovery of risk variants and genes of cardiac traits”, MedRXiv,<\/em> https:\/\/doi.org\/10.1101\/2022.02.02.22270312 <\/a> (pdf<\/a>)<\/p>\n

R. Dohn, B. Xie, R. Back, A. Selewa, H. Eckart, R. Prusty Rao, A. Basu, “mDrop-seq: Massively parallel single-cell RNA-seq of Saccharomyces cerevisiae<\/em> and Candida albicans<\/em>“, Vaccines,<\/em> 10<\/strong>(1), 30 (2022)<\/a> (pdf<\/a>)<\/p>\n

V. Phan, M. van Gent, N. Drayman, A. Basu, M. U. Gack, S. Tay, “High-throughput RNA sequencing of paraformaldehyde-fixed single cells”, Nature Communications<\/em>, 12<\/strong>, 5636 (2021) <\/a> (pdf<\/a>)<\/p>\n

M. Hammes, A. Moya-Rodriguez, C. Bernstein, S. Nathan, R. Navuluri, A. Basu, “Computational modeling of the cephalic arch predicts hemodynamic profiles in patients with brachiocephalic fistula access receiving hemodialysis”, PLoS ONE<\/em>, 16<\/strong>(7): e0254016 (2021)<\/a> (pdf<\/a>)<\/p>\n

S. Olalekan, B. Xie, R. Back, H. Eckart, A. Basu, “Characterizing the tumor microenvironment of metastatic ovarian cancer by single cell transcriptomics”, Cell Reports<\/em>, 35<\/strong>, 109165 (2021) <\/a> (pdf<\/a>)<\/p>\n

M. Rowton, C. Perez-Cervantes, A. Rydeen, S. Hur, J. Jacobs-Li, N. Deng, E. Lu, A. Guzzetta, J. D. Steimle, A. Hoffmann, S. Lazarevic, X. H. Yang, C. Kim, S. Yu, H. Eckart, S. Iddir, M. Koska, E. Hanson, S. S. Chan, D. J. Garry, M. Kyba, A. Basu, K. Ikegami, S. Pott, I. P. Moskowitz, “Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages”,Developmental Cell<\/em>, 57<\/strong>, 2181 (2022) <\/a> (pdf<\/a>)<\/p>\n

A. Guzzetta, M. Koska, M. Rowton, J. Kweon, H. Hidalgo, H. Eckhart, A. Moon, A. Basu*, M. Bressan*, S. Pott*, I. Moskowitz*, “A Hedgehog-FGF signaling axis patterns anterior mesoderm during gastrulation”, PNAS,<\/em> 117<\/strong>, 15712 (2020) <\/a> (pdf<\/a>)<\/p>\n

A. Selewa, R. Dohn, H. Eckart, S. Lozano, B. Xie, E. Gauchat, R. Elorbany, K. Rhodes, J. Burnett, Y. Gilad, S. Pott, A. Basu, “Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation”, Scientific Reports,<\/i> 10<\/b>, 1535 (2020) (<\/a>pdf<\/a>)<\/a><\/p>\n

M. Hammes, R. L. McGill, A. Basu, T. Blicharski, K. Delaney, “Hemodynamic effects of hemodialyzer pump speed on arteriovenous fistulas”, Clinical Nephrology<\/em>, 91<\/strong>, 138 (2019)<\/a> (pdf)<\/p>\n

N. Habib*, I. Avraham-Davidi*, A. Basu*, T. Burks, K. Shekhar, M. Hofree, S. R. Choudhury, F. Aguet, E. Gelfand, K. Ardlie, D. A. Weitz, O. Rozenblatt-Rosen, F. Zhang & A. Regev, “Massively parallel single nucleus RNA -seq with DroNc-seq”, Nature Methods<\/em>, 955 (2017)<\/a> (pdf<\/a>)<\/p>\n

Y. Tao, A. Rotem, H. Zhang, C. B. Chang, A. Basu, A. O. Kolawole, S. A. Koehler, Y. Ren, J. S. Lin, J. M. Pipas, A. B. Feldman, C. E. Wobus and D. A. Weitz, “Rapid, targeted and culture-free viral infectivity assay in drop-based microfluidics”, Lab on a Chip<\/em>, 15<\/strong>, 3934 (2015) <\/span><\/a>(pdf<\/a>)<\/p>\n

E. Z. Macosko, A. Basu, R. Satija, J. Nemesh, K. Shekhar, M. Goldman, I. Tirosh, A. R. Bialas, N. Kamitaki, E. M. Martersteck, J. J. Trombetta, D. A. Weitz, J. R. Sanes, A. K. Shalek, A. Regev and S. A. McCarroll, “Highly Parallel Genome-Wide Expression Profiling of Individual Cells Using Nanoliter Droplets”, Cell<\/em>, 161<\/strong>, 1202 (2015) <\/a> (pdf<\/a>)<\/p>\n

A. Rotem, O. Ram, N. Shoresh, R. A. Sperling, M. Schnall-Levin, H. Zhang, A. Basu, B. E. Bernstein and D. A. Weitz, “High-Throughput Single-Cell Labeling (Hi-Scl) for Rna-Seq Using Drop-Based Microfluidics”, PLoS ONE<\/em>, 10<\/strong>, e0116328 (2015)<\/a> (pdf<\/a>)<\/p>\n

A. Basu, Y. Xu, T. Still, P. E. Arratia, Z. Zhang, K. N. Nordstrom, J. M. Rieser, J. P. Gollub, D.J. Durian and A. G. Yodh, “Rheology of Soft Colloids Across the Onset of Rigidity: Scaling Behavior, Thermal, and Non-thermal Responses”, Soft Matter<\/em>, 10<\/strong>(17), 3027 (2014) <\/a> (pdf<\/a>)<\/p>\n

A. Guha and A. Basu, “Role of rare earth oxide nanoparticles (CeO2 and La2O3) in suppressing the photobleaching of fluorescent organic dyes”, Journal of Fluorescence<\/em>, 24<\/strong>(3), 683 (2014)<\/a> (pdf<\/a>)<\/p>\n

Q. Wen, A. Basu, P. A. Janmey and A. G. Yodh, “Non-affine deformations in polymer hydrogels”, Soft Matter<\/em>, 8<\/strong>, 8039 (2012) <\/a> (pdf<\/a>)<\/p>\n

A. Basu, Q. Wen, X. Mao, T. C. Lubensky, P.A. Janmey and A. G. Yodh, “Non-affine displacements in flexible polymer networks”, Macromolecules<\/em>, 44,<\/strong> 1671 (2011) <\/a> (pdf<\/a>)<\/p>\n

K. N. Nordstrom, E. Verneuil, P. E. Arratia, A. Basu, Z. Zhang, A. G. Yodh, J. P. Gollub and D. J. Durian, “Microfluidic rheology of soft colloids above and below jamming”, Physical Review Letters<\/em>, 105<\/strong>, 175701 (2010)<\/a> (pdf<\/a>)<\/p>\n

Q. Wen, A. Basu, J. Winer, A. Yodh and P. Janmey, “Local and global deformations in a strain-stiffening fibrin gel”, New Journal of Physics<\/em>, 9<\/strong> 428 (2007)<\/a> (pdf<\/a>)<\/p>\n

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Y. Zhao, R. Zhou, Z. Mu, P. Carbonetto, X. Zhong, B. Xie, K. Luo, C. M. Cham, J. Koval, X. He, A. W. Dahl, X. Liu, E. B. Chang, A. Basu, S. Pott, Cell-type-resolved chromatin accessibility in the human intestine identifies complex regulatory programs and clarifies genetic associations in Crohn’s disease, medRxiv (2024), https:\/\/doi.org\/10.1101\/2024.12.10.24318718 R. … <\/p>\n

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