Synthetic and Systems Biology - 2021

Thomas, H., Broeck, L. V., Spurney, R., Sozzani, R., & Frank, M. (2021, February 27). Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation. https://doi.org/10.1101/2021.02.26.433082

Broeck, L. V., Spurney, R. J., Fisher, A. P., Schwartz, M., Clark, N. M., Nguyen, T. T., … Sozzani, R. (2021). A hybrid model connecting regulatory interactions with stem cell divisions in the root. Quantitative Plant Biology. https://doi.org/10.1017/qpb.2021.1

Midkiff, D. F., & San-Miguel, A. (2021, December 16). Identifying C. elegans Lifespan Mutants by Screening for Early-Onset Protein Aggregation. https://doi.org/10.1101/2021.12.14.472506

Huayta, J., & San-Miguel, A. (2021, December 21). Endogenous DAF-16 Spatiotemporal Activity Quantitatively Predicts Lifespan Extension Induced by Dietary Restriction. https://doi.org/10.1101/2021.12.20.473576

Arulalan, K. S., Huayta, J., Stallrich, J. W., & San-Miguel, A. (2021). Antagonistic effects of chemical mixtures on the oxidative stress response are silenced by heat stress and reversed under dietary restriction. Exposome, 1(1). https://doi.org/10.1093/exposome/osab005

Arulalan, K. S., Huayta, J., Stallrich, J. W., & San-Miguel, A. (2021, March 19). Antagonistic effects of chemical mixtures on the oxidative stress response are silenced by heat stress and reversed under dietary restriction. https://doi.org/10.1101/2021.03.17.435857

Clark, A. S., Huayta, J., Arulalan, K. S., & San-Miguel, A. (2021). Microfluidic devices for imaging and manipulation of C. elegans. In Micro and Nano Systems for Biophysical Studies of Cells and Small Organisms (pp. 295–321). https://doi.org/10.1016/b978-0-12-823990-2.00013-1

Roszak, P., Heo, J.-O., Blob, B., Toyokura, K., Sugiyama, Y., Balaguer, M. A. de L., … Helariutta, Y. (2021). Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization. SCIENCE, 374(6575), 1577-+. https://doi.org/10.1126/science.aba5531

Lee, J. B., Caywood, L. M., Lo, J. Y., Levering, N., & Keung, A. J. (2021). Mapping the dynamic transfer functions of eukaryotic gene regulation. CELL SYSTEMS, 12(11), 1079-+. https://doi.org/10.1016/j.cels.2021.08.003

Waldman, A. C., Rao, B. M., & Keung, A. J. (2021). Mapping the residue specificities of epigenome enzymes by yeast surface display. CELL CHEMICAL BIOLOGY, 28(12), 1772-+. https://doi.org/10.1016/j.chembiol.2021.05.022

Wang, J., Chen, B., Ali, S., Zhang, T., Wang, Y., Zhang, H., … Zhang, Q. (2021, December 4). Epigenetic modification associated with climate regulates betulin biosynthesis in birch. JOURNAL OF FORESTRY RESEARCH, Vol. 12. https://doi.org/10.1007/s11676-021-01424-7

Hodgens, C., Akpa, B. S., & Long, T. A. (2021). [Review of Solving the puzzle of Fe homeostasis by integrating molecular, mathematical, and societal models]. CURRENT OPINION IN PLANT BIOLOGY, 64. https://doi.org/10.1016/j.pbi.2021.102149

Clark, N. M., Nolan, T. M., Wang, P., Song, G., Montes, C., Valentine, C. T., … Walley, J. W. (2021). Integrated omics networks reveal the temporal signaling events of brassinosteroid response in Arabidopsis. NATURE COMMUNICATIONS, 12(1). https://doi.org/10.1038/s41467-021-26165-3

Sen, D., Voulgaropoulos, A., & Keung, A. J. (2021). Effects of early geometric confinement on the transcriptomic profile of human cerebral organoids. BMC BIOTECHNOLOGY, 21(1). https://doi.org/10.1186/s12896-021-00718-2

Spurney, R., Schwartz, M., Gobble, M., Sozzani, R., & Broeck, L. (2021). Spatiotemporal Gene Expression Profiling and Network Inference: A Roadmap for Analysis, Visualization, and Key Gene Identification. MODELING TRANSCRIPTIONAL REGULATION, Vol. 2328, pp. 47–65. https://doi.org/10.1007/978-1-0716-1534-8_4

Mischler, A., Karakis, V., Mahinthakumar, J., Carberry, C. K., San Miguel, A., Rager, J. E., … Rao, B. M. (2021). Two distinct trophectoderm lineage stem cells from human pluripotent stem cells. JOURNAL OF BIOLOGICAL CHEMISTRY, 296. https://doi.org/10.1016/j.jbc.2021.100386

Li, Y., Li, X., Zhao, M.-H., Pang, Z.-Y., Wei, J.-T., Tigabu, M., … Zhao, X.-Y. (2021). [Review of An Overview of the Practices and Management Methods for Enhancing Seed Production in Conifer Plantations for Commercial Use]. HORTICULTURAE, 7(8). https://doi.org/10.3390/horticulturae7080252

Clark, A. S., & San-Miguel, A. (2021, August 11). A bioinspired, passive microfluidic lobe filtration system. LAB ON A CHIP, Vol. 21. https://doi.org/10.1039/d1lc00449b

San-Miguel, A. (2021, June 30). Optogenetics gets the worm. SCIENCE ROBOTICS, Vol. 6. https://doi.org/10.1126/scirobotics.abj3937

McDaniel, M., Flores, K. B., & Akpa, B. S. (2021, July 19). Predicting Inter-individual Variability During Lipid Resuscitation of Bupivacaine Cardiotoxicity in Rats: A Virtual Population Modeling Study. DRUGS IN R&D, Vol. 7. https://doi.org/10.1007/s40268-021-00353-4

Sen, D., Drobna, Z., & Keung, A. J. (2021). Evaluation of UBE3A antibodies in mice and human cerebral organoids. SCIENTIFIC REPORTS, 11(1). https://doi.org/10.1038/s41598-021-85923-x

Betegon-Putze, I., Mercadal, J., Bosch, N., Planas-Riverola, A., Marques-Bueno, M., Vilarrasa-Blasi, J., … Cano-Delgado, A. I. (2021). Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots. MOLECULAR SYSTEMS BIOLOGY, 17(6). https://doi.org/10.15252/msb.20209864

Tomek, K. J., Volkel, K., Indermaur, E. W., Tuck, J. M., & Keung, A. J. (2021). Promiscuous molecules for smarter file operations in DNA-based data storage. NATURE COMMUNICATIONS, 12(1). https://doi.org/10.1038/s41467-021-23669-w

Ravishankar, E., Charles, M., Xiong, Y., Henry, R., Swift, J., Rech, J., … Brendan T. O'Connor. (2021). Balancing crop production and energy harvesting in organic solar-powered greenhouses. CELL REPORTS PHYSICAL SCIENCE, 2(3). https://doi.org/10.1016/j.xcrp.2021.100381

Prodromou, R., Day, K. N., Saberi-Bosari, S., Schneible, J. D., Mabe, M. D., San Miguel, A., … Menegatti, S. (2021). Engineering Next Generation Cyclized Peptide Ligands for Light-Controlled Capture and Release of Therapeutic Proteins. ADVANCED FUNCTIONAL MATERIALS, 31(27). https://doi.org/10.1002/adfm.202101410

Schwartz, M. F., Peters, R., Hunt, A. M., Abdul-Matin, A.-K., Broeck, L., & Sozzani, R. (2021). [Review of Divide and Conquer: The Initiation and Proliferation of Meristems]. CRITICAL REVIEWS IN PLANT SCIENCES, 40(2), 147–156. https://doi.org/10.1080/07352689.2021.1915228

Orozco-Navarrete, B., Song, J., Casanal, A., Sozzani, R., Flors, V., Sanchez-Sevilla, J. F., … Valpuesta, V. (2021). Down-regulation of Fra a 1.02 in strawberry fruits causes transcriptomic and metabolic changes compatible with an altered defense response. HORTICULTURE RESEARCH, 8(1). https://doi.org/10.1038/s41438-021-00492-4

Matange, K., Tuck, J. M., & Keung, A. J. (2021). [Review of DNA stability: a central design consideration for DNA data storage systems]. NATURE COMMUNICATIONS, 12(1). https://doi.org/10.1038/s41467-021-21587-5

Smith, K. M., San-Miguel, A., & Hsiao, L. C. (2021). Local velocity of thermoresponsive colloidal gels in rate-driven flow. PHYSICS OF FLUIDS, 33(3). https://doi.org/10.1063/5.0042109

Annabi, N., Baker, M., Boettiger, A., Chakraborty, D., Chen, Y., Corbett, K. S., … Wang, J. (2021, March). Voices of biotech research. NATURE BIOTECHNOLOGY, Vol. 39, pp. 281–286. https://doi.org/10.1038/s41587-021-00847-1

Liu, C., Li, K., Wang, M., Fan, E., Yang, C., Wang, J., … Qu, G. (2021). Qu-2, a robust poplar suspension cell line for molecular biology. JOURNAL OF FORESTRY RESEARCH, 32(2), 733–740. https://doi.org/10.1007/s11676-020-01266-9