# Publications

2018
Zhang, H. ; Cui, N. ; Cai, Y. ; Lei, F. ; Weitz, D. A. Single-cell sequencing leads a new era of proﬁling transcriptomic landscape. Journal of Bio-X Research 2018, 1 2-6. Publisher's VersionAbstract
Understanding the complexity of biological systems requires a comprehensive analysis of their cell populations. Ideally, this should be done at the single cell level, because bulk analysis of the full population obscured many critical details due to artifacts introduced by averaging. However, this has been technically challenging due to the cumbersome procedure, low throughput, and high costs of performing analysis on a single-cell basis. Excitingly, technical improvements in single-cell RNA sequencing are making it economically practical to proﬁle the transcriptomics of large populations of cells at the single-cell level, and have yielded numerous results that address important biological and medical questions. Further development of the technology and data analysis will signiﬁcantly beneﬁt the biomedical ﬁeld by unraveling the function of individual cells in their microenvironments and modeling their transcriptional dynamics.
Liu, E. Y. ; Jung, S. ; Weitz, D. A. ; Yi, H. ; Choi, C. - H. High-throughput double emulsion-based microfluidic production of hydrogel microspheres with tunable chemical functionalities toward biomolecular conjugation. Lab Chip 2018, 18, 323–334.
Klepac, D. ; Kostkova, H. ; Petrova, S. ; Chytil, P. ; Etrych, T. ; Kereiche, S. ; Raska, I. ; Weitz, D. A. ; Filippov, S. K. Interaction of spin-labeled HPMA-based nanoparticles with human blood plasma proteins – the introduction of protein-corona-free polymer nanomedicine. Nanoscale 2018, 10, 6194–6204.
Anbari, A. ; Chien, H. - T. ; Datta, S. S. ; Deng, W. ; Weitz, D. A. ; Fan, J. Microfluidic Model Porous Media: Fabrication and Applications. Small 2018, 14, 1703575.
Choi, C. - H. ; Lee, H. ; Weitz, D. A. Rapid Patterning of PDMS Microfluidic Device Wettability Using Syringe-Vacuum-Induced Segmented Flow in Nonplanar Geometry. ACS Appl. Mater. Interfaces 2018, 10, 3170–3174.
Wang, L. ; Xia, J. ; Li, J. ; Hagemann, T. L. ; Jones, J. R. ; Fraenkel, E. ; Weitz, D. A. ; Zhang, S. - C. ; Messing, A. ; Feany, M. B. Tissue and cellular rigidity and mechanosensitive signaling activation in Alexander disease. Nat. Commun. 2018, 9 1899.
Zhang, L. ; Chen, K. ; Zhang, H. ; Pang, B. ; Choi, C. - H. ; Mao, A. S. ; Liao, H. ; Utech, S. ; Mooney, D. J. ; Wang, H. ; et al. Microfluidic Templated Multicompartment Microgels for 3D Encapsulation and Pairing of Single Cells. Small 2018, 14, 1-8. Publisher's VersionAbstract
Controlled encapsulation and pairing of single cells within a confined 3D matrix can enable the replication of the highly ordered cellular structure of human tissues. Microgels with independently controlled compartments that can encapsulate cells within separately confined hydrogel matrices would provide precise control over the route of pairing single cells. Here, a one‐step microfluidic method is presented to generate monodisperse multicompartment microgels that can be used as a 3D matrix to pair single cells in a highly biocompatible manner. A method is presented to induce microgels formation on chip, followed by direct extraction of the microgels from oil phase, thereby avoiding prolonged exposure of the microgels to the oil. It is further demonstrated that by entrapping stem cells with niche cells within separate but adjacent compartments of the microgels, it can create complex stem cell niche microenvironments in a controlled manner, which can serve as a useful tool for the study of cell–cell interactions. This microfluidic technique represents a significant step toward high‐throughput single cells encapsulation and pairing for the study of intercellular communications at single cell level, which is of significant importance for cell biology, stem cell therapy, and tissue engineering.
Atia, L. ; Bi, D. ; Sharma, Y. ; Mitchel, J. A. ; Gweon, B. ; Koehler, S. A. ; DeCamp, S. J. ; Lan, B. ; Kim, J. H. ; Hirsch, R. ; et al. Geometric constraints during epithelial jamming. Nature Physics 2018. Publisher's VersionAbstract
As an injury heals, an embryo develops or a carcinoma spreads, epithelial cells systematically change their shape. In each of these processes cell shape is studied extensively whereas variability of shape from cell to cell is regarded most often as biological noise. But where do cell shape and its variability come from? Here we report that cell shape and shape variability are mutually constrained through a relationship that is purely geometrical. That relationship is shown to govern processes as diverse as maturation of the pseudostratified bronchial epithelial layer cultured from non-asthmatic or asthmatic donors, and formation of the ventral furrow in the Drosophila embryo. Across these and other epithelial systems, shape variability collapses to a family of distributions that is common to all. That distribution, in turn, is accounted for by a mechanistic theory of cell–cell interaction, showing that cell shape becomes progressively less elongated and less variable as the layer becomes progressively more jammed. These findings suggest a connection between jamming and geometry that spans living organisms and inert jammed systems, and thus transcends system details. Although molecular events are needed for any complete theory of cell shape and cell packing, observations point to the hypothesis that jamming behaviour at larger scales of organization sets overriding geometric constraints.
Edery, Y. ; Berg, S. ; Weitz, D. Surfactant Variations in Porous Media Localize Capillary Instabilities during Haines Jumps. Physical Review Letters 2018, 120. Publisher's VersionAbstract
We use confocal microscopy to measure velocity and interfacial tension between a trapped wetting phase with a surfactant and a flowing, invading nonwetting phase in a porous medium. We relate interfacial tension variations at the fluid-fluid interface to surfactant concentration and show that these variations localize the destabilization of capillary forces and lead to rapid local invasion of the nonwetting fluid, resulting in a Haines jump. These spatial variations in surfactant concentration are caused by velocity variations at the fluid-fluid interfaces and lead to localization of the Haines jumps even in otherwise very uniform pore structure and pressure conditions. Our results provide new insight into the nature of Haines jumps, one of the most ubiquitous and important instabilities in flow in porous media.
Zhang, H. ; Zhu, Y. ; Qu, L. ; Wu, H. ; Kong, H. ; Yang, Z. ; Chen, D. ; Mäkilä, E. ; Salonen, J. ; Santos, H. A. ; et al. Gold nanorods conjugated porous silicon nanoparticles encapsulated in calcium alginate nano hydrogels using microemulsion templates. Nano Letters 2018, 18, 1448-1453. Publisher's Version
Montessori, A. ; Lauricella, M. ; La Rocca, M. ; Succi, S. ; Stolovicki, E. ; Zibalt, R. ; Weitz, D. Regularized lattice Boltzmann multicomponent models for low capillary and Reynolds microfluidics flows. Computers & Fluids 2018, 167, 33-39. Publisher's VersionAbstract
We present a regularized version of the color gradient lattice Boltzmann (LB) scheme for the simulation of droplet formation in microfluidic devices of experimental relevance. The regularized version is shown to provide computationally efficient access to capillary number regimes relevant to droplet generation via microfluidic devices, such as flow-focusers and the more recent microfluidic step emulsifier devices.
Stolovicki, E. ; Ziblat, R. ; Weitz, D. A. Throughput enhancement of parallel step emulsifier devices by shear-free and efficient nozzle clearance. Lab on a Chip 2018, 132-138. Publisher's Version
2017
Kalinich, M. ; Bhan, I. ; Kwan, T. T. ; Miyamoto, D. T. ; Javaid, S. ; LiCausi, J. A. ; Milner, J. D. ; Hong, X. ; Goyal, L. ; Sil, S. ; et al. Abstract 1734: Absolute quantification of circulating tumor cell RNA enables high specificity detection of hepatocellular carcinoma. Cancer Res. 2017, 77, 1734.
Liber, S. R. ; Indech, G. ; van der Wee, E. B. ; Butenko, A. V. ; Kodger, T. E. ; Lu, P. J. ; Schofield, A. B. ; Weitz, D. A. ; van Blaaderen, A. ; Sloutskin, E. Axial Confocal Tomography of Capillary-Contained Colloidal Structures. Langmuir 2017, 33, 13343–13349.
Chen, D. ; Amstad, E. ; Zhao, C. - X. ; Cai, L. ; Fan, J. ; Chen, Q. ; Hai, M. ; Koehler, S. ; Zhang, H. ; Liang, F. ; et al. Biocompatible Amphiphilic Hydrogel–Solid Dimer Particles as Colloidal Surfactants. ACS Nano 2017, 11, 11978–11985.
Liu, J. ; Wang, N. \ddotu\elseü\fi}; Yu, L. - J. ; Karton, A. ; Li, W. ; Zhang, W. ; Guo, F. ; Hou, L. ; Cheng, Q. ; Jiang, L. ; et al. Bioinspired graphene membrane with temperature tunable channels for water gating and molecular separation. Nat. Commun. 2017, 8 2011.
Guo, M. ; Pegoraro, A. F. ; Mao, A. ; Zhou, E. H. ; Arany, P. R. ; Han, Y. ; Burnette, D. T. ; Jensen, M. H. ; Kasza, K. E. ; Moore, J. R. ; et al. Cell volume change through water efflux impacts cell stiffness and stem cell fate. Proc. Natl. Acad. Sci. U.S.A. 2017, 201705179.
Hu, Y. ; Mao, A. S. ; Desai, R. M. ; Wang, H. ; Weitz, D. A. ; Mooney, D. J. Controlled self-assembly of alginate microgels by rapidly binding molecule pairs. Lab Chip 2017, 17, 2481–2490.
Prodanovic, R. ; Ostafe, R. ; Kovacevic, G. ; Weitz, D. ; Fisher, R. DEVELOPMENT OF ULTRAHIGH-THROUGHPUT SCREENING PLATFORMS FOR DIRECTED EVOLUTION OF GLUCOSE OXIDASE. New Front. Chem. 2017, 26, S4\_OP2.
Chen, D. ; Zhao, C. - X. ; Lagoin, C. ; Hai, M. ; Arriaga, L. R. ; Koehler, S. ; Abbaspourrad, A. ; Weitz, D. A. Dispersing hydrophobic natural colourant $\beta$-carotene in shellac particles for enhanced stability and tunable colour. R. Soc. Open Sci. 2017, 4 170919.