Publication
B. Xie, S. Olalekan, R. Back, N. Ashitey, H. Eckart, A. Basu, “Comparing the tumor microenvironment of solid tumors of different primary and metastatic ovarian cancer histotypes at single cell resolution” (accepted, Frontiers in Cell and Developmental Biology) https://doi.org/10.1101/2023.10.07.561344
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, 14, 4999 (2023), (pdf)
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”, Science Advances, 9, eade7236 (2023), (pdf)
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, 23, 2327-2340 (2023) (pdf)
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, 1, 100014 (2022)(pdf)
A. Moya-Rodríguez, 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 , 20, 5729 (2022) (pdf)
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 (pdf); Cell Reports, 41(12), 111838 (2022)
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, https://doi.org/10.1101/2022.02.02.22270312 (pdf)
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 and Candida albicans“, Vaccines, 10(1), 30 (2022) (pdf)
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, 12, 5636 (2021) (pdf)
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, 16(7): e0254016 (2021) (pdf)
S. Olalekan, B. Xie, R. Back, H. Eckart, A. Basu, “Characterizing the tumor microenvironment of metastatic ovarian cancer by single cell transcriptomics”, Cell Reports, 35, 109165 (2021) (pdf)
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, 57, 2181 (2022) (pdf)
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, 117, 15712 (2020) (pdf)
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, 10, 1535 (2020) (pdf)
M. Hammes, R. L. McGill, A. Basu, T. Blicharski, K. Delaney, “Hemodynamic effects of hemodialyzer pump speed on arteriovenous fistulas”, Clinical Nephrology, 91, 138 (2019) (pdf)
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, 955 (2017) (pdf)
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, 15, 3934 (2015) (pdf)
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, 161, 1202 (2015) (pdf)
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, 10, e0116328 (2015) (pdf)
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, 10(17), 3027 (2014) (pdf)
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, 24(3), 683 (2014) (pdf)
Q. Wen, A. Basu, P. A. Janmey and A. G. Yodh, “Non-affine deformations in polymer hydrogels”, Soft Matter, 8, 8039 (2012) (pdf)
A. Basu, Q. Wen, X. Mao, T. C. Lubensky, P.A. Janmey and A. G. Yodh, “Non-affine displacements in flexible polymer networks”, Macromolecules, 44, 1671 (2011) (pdf)
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, 105, 175701 (2010) (pdf)
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, 9 428 (2007) (pdf)