Publications

We study how phage proteins rewire bacterial systems and how to turn those mechanisms into smarter antimicrobials. Below are selected highlights; the full archive is grouped by year.

Highlights

Anti-restriction functions of injected phage proteins revealed by peeling back layers of bacterial immunity

Silas S, Carion H, Makarova KS, Sanchez Godinez D, Haniyur S, Volino L, Yee WX, Fossati A, Swaney D, Bocek M, Koonin EV, Bondy-Denomy J

Nature Communications (2025)

DOI

DIP-MS: ultra-deep interaction proteomics for deconvolution of protein complexes

Frommelt F*, Fossati A*, Uliana F, Wendt F, Xue P, Heusel M, Wollscheid B, Aebersold R, Ciuffa R, Gstaiger M

Nature Methods (2024)

DOI

Characterization of a lipid-based jumbo phage compartment as a hub for early phage infection

Mozumdar D, Fossati A, Stevenson E, Guan J, Nieweglowska E, Rao S, Agard D, Swaney DL, Bondy-Denomy J

Cell Host & Microbe (2024)

DOI

Next-generation proteomics for quantitative jumbophage–bacteria interaction mapping

Fossati A, Mozumdar D, Kokontis CY, Méndez-Moran M, Nieweglowska E, Pelin A, Li Y, Guo B, Krogan NJ, Agard DA, Bondy-Denomy J, Swaney DL

Nature Communications (2023)

DOI

All publications

2025

  • Fossati A, Wambi P, Jaganath D, Calderon R, Castro R, Mohapatra A, McKetney J, Luiz J, Nerurkar R, Nkereuwem E, Franke MF, Mousavian Z, Collins JM, Sigal GB, Segal MR, Kampman B, Wobudeya E, Cattamanchi A, Ernst JD, Zar HJ, Swaney DL. Plasma proteomics for biomarker discovery in childhood tuberculosis. Nature Communications 16:6657. doi:10.1038/s41467-025-46657-0
  • Silas S, Carion H, Makarova KS, Sanchez Godinez D, Haniyur S, Volino L, Yee WX, Fossati A, Swaney D, Bocek M, Koonin EV, Bondy-Denomy J. Anti-restriction functions of injected phage proteins revealed by peeling back layers of bacterial immunity. Nature Communications 16:7828. doi:10.1038/s41467-025-25678-x
  • Laman Trip DS, van Oostrum M, Memon D, Frommelt F, Baptista D, Panneerselvam K, Bradley G, Licata L, Hermjakob H, Orchard S, Trynka G, McDonagh EM, Fossati A, Aebersold R, Gstaiger M, Wollscheid B, Beltrao P. A tissue-specific atlas of protein–protein associations enables prioritization of candidate disease genes. Nature Biotechnology. doi:10.1038/s41587-025-02659-z
  • Mohammed* AM, Olwal* CO, Fossati* A, Nyakoe NK, Fabius JM, Gordon M, Polacco BJ, Swaney DL, Awandare GA, Krogan NJ, Bouhaddou M, Bediako Y. Malaria exposure remodels the plasma proteome of Ghanaian children. BMC Infectious Diseases 25:157. doi:10.1186/s12879-025-10495-4

2024

  • Frommelt F*, Fossati A*, Uliana F, Wendt F, Xue P, Heusel M, Wollscheid B, Aebersold R, Ciuffa R, Gstaiger M. DIP-MS: ultra-deep interaction proteomics for deconvolution of protein complexes. Nature Methods 21:211. doi:10.1038/s41592-024-02211-y
  • Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA. Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. Science 385(6706):eadl5763. doi:10.1126/science.adl5763
  • Mozumdar D, Fossati A, Stevenson E, Guan J, Nieweglowska E, Rao S, Agard D, Swaney DL, Bondy-Denomy J. Characterization of a lipid-based jumbo phage compartment as a hub for early phage infection. Cell Host & Microbe. doi:10.1016/j.chom.2024.05.016
  • Teuscher AC, Statzer C, Goyala A, Domenig SA, Schoen I, Hess M, Hofer AM, Fossati A, Vogel V, Göksel O, Aebersold R, Ewald CY. Longevity interventions modulate mechanotransduction and extracellular matrix homeostasis in C. elegans. Nature Communications 15:276. doi:10.1038/s41467-023-44409-2

2023

  • Fossati A, Mozumdar D, Kokontis CY, Méndez-Moran M, Nieweglowska E, Pelin A, Li Y, Guo B, Krogan NJ, Agard DA, Bondy-Denomy J, Swaney DL. Next-generation proteomics for quantitative jumbophage–bacteria interaction mapping. Nature Communications 14:5156. doi:10.1038/s41467-023-40724-w
  • Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP, Rezelj VV, Hardy A, Fossati A, Stevenson EJ, Sukerman E, Kim T, Penugonda S, Moreno E, Braberg H, … Krogan NJ. Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets. Nature Communications 14:6030. doi:10.1038/s41467-023-41442-z
  • Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, … Krogan NJ, Fossati A. SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell. doi:10.1016/j.cell.2023.08.026
  • Chen X, Haribowo AG, Baik AH, Fossati A, Stevenson E, Chen YR, Reyes NS, Peng T, Matthay MA, Traglia M, Pico AR, Jarosz DF, Buchwalter A, Ghaemmaghami S, Swaney DL, Jain IH. In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response. Science Advances 9(49):eadj4884. doi:10.1126/sciadv.adj4884
  • Bludau I*, Nicod C*, Martelli C*, Xue P, Heusel M, Fossati A, Uliana F, Frommelt F, Aebersold R, Collins BC. Rapid profiling of protein complex reorganization in perturbed systems. Journal of Proteome Research. doi:10.1021/acs.jproteome.3c00125
  • Uliana F*, Ciuffa R*, Mishra R, Fossati A, Frommelt F, Keller S, Mehnert M, van Drogen F, Peter M, Tapon N, Aebersold R, Gstaiger M. Phosphorylation-linked complex profiling identifies assemblies required for Hippo signal integration. Molecular Systems Biology 19:e11024. doi:10.15252/msb.202211024

2022

  • Sharma VS, Fossati A, Ciuffa R, Buljan M, Williams EG, Chen Z, Shao W, Pedrioli PGA, Purcell AW, Martínez MR, Song J, Manica M, Aebersold R, Li C. PCfun: a hybrid computational framework for systematic characterization of protein complex function. Briefings in Bioinformatics:bbac239. doi:10.1093/bib/bbac239
  • Escalera A, Gonzalez-Reiche AS, Aslam S, Mena I, Laporte M, Pearl RL, Fossati A, … García-Sastre A. Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission. Cell Host & Microbe 30(3):373–387.e7. doi:10.1016/j.chom.2022.01.006
  • Thorne LG*, Bouhaddou M*, Reuschl AK*, Zuliani-Alvarez L*, Polacco B, Pelin A, Batra J, Fossati A, … Krogan NJ. Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature 602:487–495. doi:10.1038/s41586-021-04352-y

2021

  • Fossati A*, Li C*, Uliana F, Wendt F, Frommelt F, Sykacek P, Heusel M, … Aebersold R. PCprophet: a framework for protein complex prediction and differential analysis using proteomic data. Nature Methods 18(5):520–527. doi:10.1038/s41592-021-01107-5
  • Fossati A, Frommelt F, Uliana F, Martelli C, Vizovišek M, Gillet L, Collins B, Gstaiger M, Aebersold R. System-wide profiling of protein complexes via size-exclusion chromatography–mass spectrometry. Shotgun Proteomics: Methods and Protocols (Springer, Methods in Molecular Biology). doi:10.1007/978-1-0716-1178-4_18
  • Fossati A, Richards AL, Chen KH, Jaganath D, Cattamanchi A, Ernst JD, Swaney DL. Toward comprehensive plasma proteomics by orthogonal protease digestion. Journal of Proteome Research 20(8):4031–4040. doi:10.1021/acs.jproteome.1c00357
  • Uliana F*, Vizovišek M*, Acquasaliente L, Ciuffa R, Fossati A, Frommelt F, Goetze S, Wollscheid B, Gstaiger M, Aebersold R. Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen. Nature Communications 12:1693. doi:10.1038/s41467-021-21754-8
  • Gupta M*, Azumaya CM*, Moritz M*, Pourmal S*, Diallo A*, Merz GE*, Jang G*, Fossati A, … Verba KA. CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. bioRxiv (Preprint). doi:10.1101/2021.05.10.443524