Publications

Huang, A.Z., Prahl, L.S., Xu, K., Mauck, R.L., Hughes, A.J. (2024) Engineering kidney developmental trajectory using culture boundary conditions. BioRxiv.

Prahl*, L.S., Liu*, J., Viola*, J.M., Huang, A.Z., Chan, T.J., Hayward-Lara, G., Porter, C.M., Shi, C., Zhang, J., Hughes, A.J. (2024) Jamming of nephron-forming niches in the developing mouse kidney creates cyclical mechanical stresses. *Equal contribution. Nature Materials.

movie of two cell types condensing into a spheroid

Porter, C.M., Qian, G.C., Grindel, S.H., Hughes, A.J. (2024) Highly-parallel production of designer organoids by mosaic patterning of progenitors. Cell Systems, 15, 649-661.

Liu, J., Prahl, L.S., Huang, A., Hughes, A.J. (2024) Measurement of adhesion and traction of cells at high yield reveals an energetic ratchet operating during nephron condensation. PNAS, 121(39), e2404586121.

Davis*, S.N., Grindel*, S.H., Viola, J.M., Liu, G.Y., Liu, J., Qian, G., Porter, C.M., Hughes, A.J. (2023) Nephron progenitors rhythmically alternate between renewal and differentiation phases that synchronize with kidney branching morphogenesis. BioRxiv. *Equal contribution.

Viola, J.M., Liu, J., Huang, A., Grindel, S.H., Prahl, L.S., Hughes, A.J. (2023) Rho/ROCK activity tunes cell compartment segregation and differentiation in nephron-forming niches. BioRxiv.

Alibekova Long, M., Benman, W.K.J., Petrikas, N., Bugaj, L.J., Hughes, A.J. (2023) Enhancing single-cell western blotting sensitivity using diffusive analyte blotting and antibody conjugate amplification. Analytical Chemistry, 95, 17894-17902.

Prahl, L.S., Porter, C.M., Liu, J., Viola, J.M., Hughes, A.J. (2023) Independent control over cell patterning and adhesion on hydrogel substrates for tissue interface mechanobiology. iScience, 26, 106657.

Prahl, L.S., Viola, J.M., Liu, J., Hughes, A.J. (2023) The developing murine kidney actively negotiates geometric packing conflicts to avoid defects. Developmental Cell, 58(2), 110-120.

Viola, J.M., Porter, C.M., Gupta, A., Long, M., Prahl, L.S., Hughes, A.J. (2022) High-throughput assembly of compositionally controlled 3D cell communities for developmental engineering. Methods in Molecular Biology, 2805, 31-50.

Beck, L.E., Lee, J., Coté, C., Dunagin, M.C., Lukonin, I., Salla, N., Chang, M.K., Hughes, A.J., Mornin, J.D., Gartner, Z.J., Liberali, P., Raj, A. (2022) Systematically quantifying morphological features reveals constraints on organoid phenotypes. Cell Systems, 13, 1-14.

Whatever it is, the way you tell your story online can make all the difference.

Gupta, A., Lutolf, M.P., Hughes, A.J., Sonnen, K.F. (2021) Bioengineering in vitro models of embryonic development. Stem Cell Reports, 16, 1104-1116.

Daly*, A.C., Prendergast*, M.E., Hughes, A.J., Burdick, J.A. (2021) Bioprinting for the biologist. Cell, 184, 18-32. *Equal contribution.

Viola*, J.M., Porter*, C.M., Gupta, A., Alibekova, M., Prahl, L.S., Hughes, A.J. (2020) Guiding Cell Network Assembly Using Shape-Morphing Hydrogels. Advanced Materials, 361, 2002195. *Equal contribution.

News & Views: Gartner, Z.J., Hughes, A.J. (2019) Getting the measure of living biomaterials. Nature, 572, 38-39.

Hughes, A.J., Mornin, J.D., Biswas, S.K., Bauer, D.P., Bianco, S., Gartner, Z.J. (2018) Quanti.us: A Tool for Rapid, Flexible, Crowd-Based Annotation of Images. Nature Methods, 15(8), 587-590.

Nature Methods editorial & perspective.

Hughes, A.J., Coyle, M., Zhang, J., Miyazaki, H., Laurie, M., Chu, D., Vavrusova, Z., Schneider, R.A., Gartner, Z.J. (2018) Engineered tissue folding by mechanical compaction of the mesenchyme. Developmental Cell, 44(2), 165-178.

Perspectives & Press: Quanta, Science, Dev. Cell, Trends in Biotech.

Todhunter, M.E., Jee, N.Y., Hughes, A.J., Coyle, M.C., Cerchiari, A., Farlow, J., Garbe, J.C., LaBarge, M.A., Desai, T.A., Gartner, Z.J. (2015) Programmed synthesis of 3D tissues. Nature Methods, 12(10), 975–981.

Hughes, A.J., Spelke, D.P., Xu, Z., Kang, C.-C., Schaffer, D.V., Herr, A.E. (2014) Single-cell western blotting. Nature Methods, 11(7), 749–755.

Tentori, A.M., Hughes, A.J., Herr, A.E. (2013) Microchamber integration unifies distinct separation modes for two-dimensional electrophoresis. Analytical Chemistry, 85, 4538–4545.

Hughes, A.J., Herr, A.E. (2012) Microfluidic western blotting. PNAS, 109(52), 21450– 21455.

Hughes, A.J., Lin, R.K., Peehl, D.M., Herr, A.E. (2012) Microfluidic integration for automated targeted proteomic assays. PNAS, 109(16), 5972–5977.

Hughes, A.J., Tentori, A.M., Herr, A.E. (2012) Bistable isoelectric point photoswitching in green fluorescent proteins observed by dynamic immunoprobed isoelectric focusing. JACS, 134, 17582–17591.

Chen, X., Kapil, M.A., Hughes, A.J., Herr, A.E. (2011) Single-microchannel, multistep assay reports protein size and immunoaffinity. Analytical Chemistry, 83, 6573–6579.

Hughes, A.J., Herr, A.E. (2010) Quantitative enzyme activity determination with zeptomole sensitivity by microfluidic gradient-gel zymography. Analytical Chemistry, 82, 3803–3811.