Publications

Publications are also listed on Google Scholar. If you have difficulty accessing any of the papers listed here, please email Andrea for a copy.

2026

4 papers
  1. Kim D, Maziero M, Eckartt KA, DeJesus MA, Prensa GI, García Navarro A, Parker DR, Santucci P, Rock JM, Fossati A‡, The porin MspA is a phage-specific determinant of mycobacteriophage infection, bioRxiv (Preprint) (2026). (Preprint)
  2. Parker DR*, Ghosh S*, Dujiskova A*, Olinares PDB, Narrowe Danielsson S, Prensa GI, Kim D, Rosenberger FA, Elofsson A, Mann M, Campbell EA, Fossati A‡, Conserved mycobacteriophage protein uses structural mimicry to displace host initiation factors, bioRxiv (Preprint) (2026). (Preprint)
  3. Frommelt F, Uliana F, Aebersold R, Fossati A‡, Need for speed: Advances in the era of high throughput interaction proteomics, Molecular Omics 22(2) (2026). (PDF)
  4. Prensa GI, García Navarro A, Parker D, Fossati A‡, Exploring infection biology with mass spectrometry-based proteomics, Molecular Omics 22(2) (2026).

2025

4 papers
  1. 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 (2025).
  2. 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 (2025).
  3. 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 44(4), 654–667 (2025).
  4. 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 (2025).

2024

4 papers
  1. 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 the deconvolution of protein complexes, Nature Methods 21(4), 635–647 (2024).
  2. 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 (2024).
  3. 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 32(7), 1050–1058.e7 (2024).
  4. 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 (2024).

2023

6 papers
  1. 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 (2023).
  2. 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 (2023).
  3. 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, … Fossati A, … Towers GJ, Krogan NJ, SARS-CoV-2 variants evolve convergent strategies to remodel the host response, Cell 186(21), 4597–4614.e26 (2023).
  4. 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 (2023).
  5. 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 22(5), 1520–1536 (2023).
  6. Uliana F*, Ciuffa R*, Mishra R, Fossati A, Frommelt F, Keller S, Mehnert M, Birkeland ES, van Drogen F, Srejic N, Peter M, Tapon N, Aebersold R, Gstaiger M, Phosphorylation-linked complex profiling identifies assemblies required for Hippo signal integration, Molecular Systems Biology 19(4), e11024 (2023).

2022

3 papers
  1. 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 23(4), bbac239 (2022).
  2. Escalera A, Gonzalez-Reiche AS, Aslam S, Mena I, Laporte M, Pearl RL, Fossati A, … García-Sastre A, Aydillo T, Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission, Cell Host & Microbe 30(3), 373–387.e7 (2022).
  3. Thorne LG*, Bouhaddou M*, Reuschl AK*, Zuliani-Alvarez L*, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, … Krogan NJ, Evolution of enhanced innate immune evasion by SARS-CoV-2, Nature 602(7897), 487–495 (2022).

2021

5 papers
  1. 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 (2021).
  2. 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 (SEC-MS), Shotgun Proteomics: Methods and Protocols (Springer, Methods in Molecular Biology) 2259, 269–294 (2021).
  3. 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 (2021).
  4. Uliana F*, Vizovišek M*, Acquasaliente L, Ciuffa R, Fossati A, Frommelt F, Goetze S, Wollscheid B, Gstaiger M, De Filippis V, Auf dem Keller U, Aebersold R, Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen, Nature Communications 12, 1693 (2021).
  5. Gupta M*, Azumaya CM*, Moritz M*, Pourmal S*, Diallo A*, Merz GE*, Jang G*, Bouhaddou M, 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) (2021). (Preprint)

* equal contribution  ·  ‡ corresponding author