Synthetic and Systems Biology - 2023

Volkel, K. D., Lin, K. N., Hook, P. W., Timp, W., Keung, A. J., & Tuck, J. M. (2023). FrameD: framework for DNA-based data storage design, verification, and validation. BIOINFORMATICS, 39(10). https://doi.org/10.1093/bioinformatics/btad572

Durmusoglu, D., Haller, D. J., Al’Abri, I. S., Day, K., Sands, C., Clark, A., … Crook, N. C. (2023, November 17). Programming Probiotics: Diet-responsive gene expression and colonization control in engineeredS. boulardii. https://doi.org/10.1101/2023.11.17.567539

Clark, A. S., Huayta, J., Morton, K. S., Meyer, J. N., & San-Miguel, A. (2023, August 23). Morphological hallmarks of dopaminergic neurodegeneration are associated with altered neuron function inCaenorhabditis elegans. https://doi.org/10.1101/2023.08.22.554364

Data for: Endogenous DAF-16 spatiotemporal activity quantitatively predicts lifespan extension induced by dietary restriction [Data set]. (2023). Dryad. https://doi.org/10.5061/dryad.vx0k6djwt

An unbiased, automated platform for scoring dopaminergic neurodegeneration in C. elegans [Data set]. (2023). Dryad. https://doi.org/10.5061/dryad.cvdncjt82

Clark, A. S., Kalmanson, Z., Morton, K., Hartman, J., Meyer, J., & San-Miguel, A. (2023). An unbiased, automated platform for scoring dopaminergic neurodegeneration in C. elegans. PLOS ONE. https://doi.org/10.1371/journal.pone.0281797

Gaudinier, A., Broeck, L. V., Moreno-Risueño, M., Rodriguez-Medina, J., Sozzani, R., & Brady, S. M. (2023, December 6). Quantitative Modeling of the Short-Term Response to Nitrogen Availability that Coordinates Early Events in Lateral Root Initiation. https://doi.org/10.1101/2023.12.05.570292

Mahatma, S., Broeck, L. V., Morffy, N., Staller, M. V., Strader, L. C., & Sozzani, R. (2023, March 22). Prediction and functional characterization of transcriptional activation domains. https://doi.org/10.1109/CISS56502.2023.10089768

Bennett, M. J., Brady, S. M., Dinneny, J. R., Helariutta, Y., & Sozzani, R. (2023, November 20). Obituary Philip N. Benfey (1953-2023). DEVELOPMENTAL CELL, Vol. 58, pp. 2413–2415. https://doi.org/10.1016/j.devcel.2023.10.013

Hornstein, E. D., & Sederoff, H. (2023, September 13). Back to the Future: Re-Engineering the Evolutionarily Lost Arbuscular Mycorrhiza Host Trait to Improve Climate Resilience for Agriculture. CRITICAL REVIEWS IN PLANT SCIENCES, Vol. 9. https://doi.org/10.1080/07352689.2023.2256093

Madison, I., Gillan, L., Peace, J., Gabrieli, F., Broeck, L., Jones, J. L., & Sozzani, R. (2023, August 23). Phosphate starvation: response mechanisms and solutions (D. Ort, Ed.). JOURNAL OF EXPERIMENTAL BOTANY, Vol. 8. https://doi.org/10.1093/jxb/erad326

Polak, R. E., & Keung, A. J. (2023). [Review of A molecular assessment of the practical potential of DNA-based computation]. CURRENT OPINION IN BIOTECHNOLOGY, 81. https://doi.org/10.1016/j.copbio.2023.102940

Broeck, L., Bhosale, D. K., Song, K., Lima, C. F., Ashley, M., Zhu, T., … Sozzani, R. (2023). Functional annotation of proteins for signaling network inference in non-model species. NATURE COMMUNICATIONS, 14(1). https://doi.org/10.1038/s41467-023-40365-z

Tam, R. W., & Keung, A. J. (2023). Profiling transcriptomic responses of human stem cell-derived medium spiny neuron-like cells to exogenous phasic and tonic neurotransmitters. MOLECULAR AND CELLULAR NEUROSCIENCE, 126. https://doi.org/10.1016/j.mcn.2023.103876

Karakis, V., Jabeen, M., Britt, J. W., Cordiner, A., Mischler, A., Li, F., … Rao, B. M. (2023). Laminin switches terminal differentiation fate of human trophoblast stem cells under chemically defined culture conditions. JOURNAL OF BIOLOGICAL CHEMISTRY, 299(5). https://doi.org/10.1016/j.jbc.2023.104650

Clark, A. S., Kalmanson, Z., Morton, K., Hartman, J., Meyer, J., & San-Miguel, A. (2023, February 3). An unbiased, automated platform for scoring dopaminergic neurodegeneration inC. elegans. https://doi.org/10.1101/2023.02.02.526781

Liu, C., Wang, S., Liu, Y., Wang, M., Fan, E., Liu, C., … Qu, G. (2023, May 4). Exceptionally high genetic variance of the doubled haploid (DH) population of poplar. JOURNAL OF FORESTRY RESEARCH, Vol. 5. https://doi.org/10.1007/s11676-023-01612-7

Beretta, V. M., Franchini, E., Din, I. U., Lacchini, E., Broeck, L., Sozzani, R., … Kater, M. M. (2023, April 21). The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice. PLANT JOURNAL, Vol. 4. https://doi.org/10.1111/tpj.16229

Charles, M., Edwards, B., Ravishankar, E., Calero, J., Henry, R., Rech, J., … Sederoff, H. (2023). Emergent molecular traits of lettuce and tomato grown under wavelength-selective solar cells. FRONTIERS IN PLANT SCIENCE, 14. https://doi.org/10.3389/fpls.2023.1087707

Han, L., Lee, J. B., Indermaur, E. W., & Keung, A. J. (2023). Chaetocin disrupts the SUV39H1-HP1 interaction independent of SUV39H1 methyltransferase activity. BIOCHEMICAL JOURNAL, 480(6), 421–432. https://doi.org/10.1042/BCJ20220528

Huayta, J., Crapster, J. P., & San-Miguel, A. (2023). Endogenous DAF-16 spatiotemporal activity quantitatively predicts lifespan extension induced by dietary restriction. COMMUNICATIONS BIOLOGY, 6(1). https://doi.org/10.1038/s42003-023-04562-2

Hornstein, E. D., Charles, M., Franklin, M., Edwards, B., Vintila, S., Kleiner, M., & Sederoff, H. (2023, March 7). Re-engineering a lost trait:IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss. https://doi.org/10.1101/2023.03.06.531368

Prodromou, R., Moore, B. D., Chu, W., Deal, H., San Miguel, A., Brown, A. C., … Menegatti, S. (2023, January 25). Molecular Engineering of Cyclic Azobenzene-Peptide Hybrid Ligands for the Purification of Human Blood Factor VIII via Photo-Affinity Chromatography. ADVANCED FUNCTIONAL MATERIALS, Vol. 1. https://doi.org/10.1002/adfm.202213881