2023

  • Chen, X., Haribowo, A. G., Baik, A. H., Fossati, A., Stevenson, E., Chen, Y. R., Reyes, N. S., Peng, T., Matthay, M. A., Traglia, M., Pico, A. R., Jarosz, D. F., Buchwalter, A., Ghaemmaghami, S., Swaney, D. L., & Jain, I. H. (2023). In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response. Science Advances, 9(49), eadj4884. https://doi.org/10.1126/sciadv.adj4884

  • Lin, Z., Schaefer, K., Lui, I., Yao, Z., Fossati, A. A., Swaney, D. L., Palar, A., Sali, A., & Wells, J. A. (2023). Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. BioRxiv, 2023.10.28.564055. https://doi.org/10.1101/2023.10.28.564055

  • Bouhaddou, M., Reuschl, A.-K., Polacco, B. J., Thorne, L. G., Ummadi, M. R., Ye, C., Rosales, R., Pelin, A., Batra, J., Jang, G. M., Xu, J., Moen, J. M., Richards, A. L., Zhou, Y., Harjai, B., Stevenson, E., Rojc, A., Ragazzini, R., Whelan, M. V. X., … Krogan, N. J. (2023). SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell, https://doi.org/10.1016/j.cell.2023.08.026.

  • Haas KM., McGregor MJ, Bouhaddou M., Polacco B., Kim EY., Nguyen TT., Newton BW., Urbanowski M., Kim H., Williams MAP., Rezelj VV., Hardy A., Fossati A. “Proteomic and Genetic Analyses of Influenza A Viruses Identify Pan-Viral Host Targets “, Nature Communications, 14(1), 6030. https://doi.org/10.1038/s41467-023-41442-z*.

  • Fossati, A., D. Mozumdar, C. Y Kokontis, E. S Nieweglowska, M. Mendez, A. Pelin, Y. Li, et al “Next-Generation Interaction Proteomics for Quantitative Jumbophage-Bacteria Interaction Mapping.” Nature Communication,14(1), 5156. https://doi.org/10.1038/s41467-023-40724-w.

  • Haas, K. M., McGregor, M. J., Bouhaddou, M., Polacco, B. J., Kim, E.-Y., Nguyen, T. T., Newton, B. W., Urbanowski, M., Kim, H., Williams, M. A. P., Rezelj, V. V, Hardy, A., Fossati, A., Stevenson, E. J., Sukerman, E., Kim, T., Penugonda, S., Moreno, E., Braberg, H., … Krogan, N. J. (2023). Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets. Nature Communications, 14(1), 6030. https://doi.org/10.1038/s41467-023-41442-z

  • Bludau*, I., C. Nicod*, C. Martelli*, P. Xue, M. Heusel, A. Fossati, F. Uliana, F. Frommelt, RA Aebersold, and Ben C Collins. “Rapid Profiling of Protein Complex Reorganization in Perturbed Systems.” Journal of Proteome Research, https://doi.org/10.1021/acs.jproteome.3c00125.

  • Frommelt*, F., A. Fossati*, F. Uliana, F. Wendt, P. Xue, M. Heusel, B. Wollscheid, RA Aebersold, R. Ciuffa, and M. Gstaiger. “DIP-MS: A Novel Ultra-Deep Interaction Proteomics for the Deconvolution of Protein Complexes.” bioRxiv, https://doi.org/10.1101/2023.03.22.533843.

  • Silas, S., Heloise C., KS Makarova, E. Laderman, D. Sanchez Godinez, M. Johnson, A. Fossati, et al. “Parallelized Screening of Virus Accessory Genes Reveals Diverse Defense and Counter-Defense Mechanisms.” bioRxiv, https://doi.org/10.1101/2023.04.06.535777.

  • Uliana*, F., Rodolfo Ciuffa*, Ranjan Mishra, A. Fossati, F. Frommelt, S. Keller, M. Mehnert, et al. “Phosphorylation-linked complex profiling identifies assemblies required for Hippo signal integration.” Molecular Systems Biology, https://doi.org/10.15252/msb.202211024.

2022

  • Teuscher, A., C. Statzer, A. Goyala, S. Domenig, I. Schoen, M. Hess, A. Hofer, et al. “Mechanotransduction coordinates extracellular matrix protein homeostasis promoting longevity in C. elegans.” bioRxiv, https://doi.org/10.1101/2022.08.30.505802.

  • Escalera, A., AS. Gonzalez-Reiche, S Aslam, I. Mena, M. Laporte, R. L. Pearl, A. Fossati, et al. “Mutations in SARS-CoV-2 Variants of Concern Link to Increased Spike Cleavage and Virus Transmission.” Cell Host & Microbe 30 (3): 373–387.e7, https://doi.org/10.1016/j.chom.2022.01.006.

  • Sharma, V. S, A. Fossati, R. Ciuffa, M. Buljan, E. G Williams, Z. Chen, W. Shao, et al. “PCfun: A Hybrid Computational Framework for Systematic Characterization of Protein Complex Function.” Briefings in Bioinformatics, June, bbac239, https://doi.org/10.1093/bib/bbac239.

  • Thorne*, LG., M. Bouhaddou*, AK. Reuschl*, L. Zuliani-Alvarez*, B. Polacco, A. Pelin, J Batra, et al. “Evolution of Enhanced Innate Immune Evasion by SARS-CoV-2.” Nature 602 (7897): 487–95, https://doi.org/10.1038/s41586-021-04352-y.

2021

  • Fossati, A., F. Frommelt, F. Uliana, C. Martelli, M. Vizovisek, L. Gillet, B. Collins, M. Gstaiger, and RA Aebersold. “System-Wide Profiling of Protein Complexes via Size Exclusion Chromatography–Mass SpectrometryMass Spectrometry (SEC–MS).” In Shotgun Proteomics: Methods and Protocols, edited by Mónica Carrera and Jesús Mateos, 269–94. New York, NY: Springer US, https://doi.org/10.1007/978-1-0716-1178-4_18.

  • Fossati, A., AL. Richards, KH. Chen, D. Jaganath, A. Cattamanchi, JD. Ernst, and DL. Swaney. “Toward Comprehensive Plasma Proteomics by Orthogonal Protease Digestion.” Journal of Proteome Research 20 (8): 4031–40, https://doi.org/10.1021/acs.jproteome.1c00357.

  • Fossati*, A., Chen Li*, F. Uliana, F. Wendt, F. Frommelt, P. Sykacek, M. Heusel, et al. “PCprophet: A Framework for Protein Complex Prediction and Differential Analysis Using Proteomic Data.” Nature Methods 18 (5): 520–27, https://doi.org/10.1038/s41592-021-01107-5.

  • Gupta*, M., CM. Azumaya*, M. Moritz*, S. Pourmal*, A. Diallo*, GE. Merz*, G. Jang*, et al. “CryoEM and AI Reveal a Structure of SARS-CoV-2 Nsp2, a Multifunctional Protein Involved in Key Host Processes.” bioRxiv, February. https://doi.org/10.1101/2021.05.10.443524.

  • Uliana, F.*, M.* Vizovišek, L. Acquasaliente, R. Ciuffa, A. Fossati, F. Frommelt, S. Goetze, et al. “Mapping Specificity, Cleavage Entropy, Allosteric Changes and Substrates of Blood Proteases in a High-Throughput Screen.” Nature Communications 12 (1): 1693, https://doi.org/10.1038/s41467-021-21754-8.