Publications – Petsalaki Group

A data-driven framework reconstructs the molecular continuum of human MASLD progression.

Kamzolas I, Koutsandreas T, Barker CG, Vathrakokoili Pournara A, Weston H, Fujiwara N, Hoshida Y, Anstee QM, Vacca M, Papatheodorou I, Vidal-Puig A, Petsalaki E.

Nature metabolism, 2026

doi:10.1038/s42255-026-01543-7.

Multi-omics and network propagation reveal latent innate immune programmes stratifying high-risk thrombotic primary antiphospholipid syndrome

Sasikumar S, Baltsiotis M, Verrou K, Rouni G, Sfikakis PP, Samiotaki M, Petsalaki E, Tektonidou MG.

Preprint, 2026

doi:10.64898/2026.06.26.26356680.

Biological Network Organization, Not Generic Graph Topology, Drives Graph-Based Gene Essentiality Prediction

Rahimi S, Bonner S, Afzal A, Milo M, Morrissey E, Petsalaki E.

Preprint, 2026

doi:10.64898/2026.06.30.735480.

The Potential of Digital Twins for Pediatric Rare Diseases.

Malik-Sheriff RS, Limdi A, Petsalaki E, Hermjakob H, McDonagh EM.

CPT: pharmacometrics & systems pharmacology, 2026

doi:10.1002/psp4.70234.

Genetic interactions, synthetic lethality and complexity in cancer vulnerability mapping-Insights and perspectives from the 2nd EuroDepMap symposium.

Proietti L, Beltrao P, Bruna A, Cortés-Ciriano I, Garnett MJ, Gonçalves E, Herranz-Ors C, Kaulich M, Lord CJ, Petsalaki E, Rad R, Ryan CJ, Savino A, Sesia D, Wessels L, Iorio F.

FEBS letters, 2026

doi:10.1002/1873-3468.70306.

Integrative multi-omics defines melanoma drug response networks and ARID1A-dependent resistance mechanisms.

Barker CG, Sharma S, Santos AM, Nikolakopoulos KS, Velentzas AD, Tormo-Garcia C, Sharma A, Völlmy FI, Minia A, Pliaka V, Clarke J, Altelaar M, Wright GJ, Alexopoulos LG, Stravopodis DJ, Petsalaki E.

Molecular systems biology, 2026

doi:10.1038/s44320-025-00183-5.

Endoglin as a BMP9 co-receptor in vascular endothelial cells: prodomain displacement and TGFBRII recruitment.

Guo J, Kostrzyńska K, Kamzolas I, Yang X, Thorikay M, De Bie E, Jones RJ, Brownstein A, Long L, Rhodes CJ, Lawrie A, Wilkins MR, Groeneveld E, Tong Z, Goumans MJ, Petsalaki E, Hong J, Toshner MR, Vidal-Puig A, Arthur HM, Li W.

Nature communications, 2025

doi:10.1038/s41467-025-67531-9.

Myelin-axon interface vulnerability in Alzheimer's disease revealed by subcellular proteomics and imaging of human and mouse brain.

Cai Y, Pinheiro-de-Sousa I, Slobodyanyuk M, Chen F, Huynh T, Kanyo J, Tang P, Fuentes LA, Braker A, Welch R, Huttner A, Tong L, Yuan P, Lam TT, Petsalaki E, Reimand J, Nairn AC, Grutzendler J.

Nature neuroscience, 2025

doi:10.1038/s41593-025-01973-8.

Comprehensive evaluation of phosphoproteomic-based kinase activity inference.

Müller-Dott S, Jaehnig EJ, Munchic KP, Jiang W, Yaron-Barir TM, Savage SR, Garrido-Rodriguez M, Johnson JL, Lussana A, Petsalaki E, Lei JT, Dugourd A, Krug K, Cantley LC, Mani DR, Zhang B, Saez-Rodriguez J.

Nature communications, 2025

doi:10.1038/s41467-025-59779-y.

Data-Driven Extraction of Human Kinase-Substrate Relationships From Omics Datasets.

Maier BD, Petursson B, Lussana A, Petsalaki E.

Molecular & cellular proteomics : MCP, 2025

doi:10.1016/j.mcpro.2025.100994.

Advancing cell-cell communication analysis from single-cell genomics data.

Pinheiro-de-Sousa I, Petsalaki E.

Nature protocols, 2025

doi:10.1038/s41596-025-01140-0.

Subcellular proteomics and iPSC modeling uncover reversible mechanisms of axonal pathology in Alzheimer's disease.

Cai Y, Kanyo J, Wilson R, Bathla S, Cardozo PL, Tong L, Qin S, Fuentes LA, Pinheiro-de-Sousa I, Huynh T, Sun L, Mansuri MS, Tian Z, Gan HR, Braker A, Trinh HK, Huttner A, Lam TT, Petsalaki E, Brennand KJ, Nairn AC, Grutzendler J.

Nature aging, 2025

doi:10.1038/s43587-025-00823-3.

Decoding MASLD Progression: A Molecular Trajectory-Based Framework for Modelling Disease Dynamics

Kamzolas I, Koutsandreas T, Barker CG, Vathrakokoili Pournara A, Weston H, Fujiwara N, Hoshida Y, Anstee QM, Vacca M, Papatheodorou I, Vidal-Puig A, Petsalaki E.

Preprint, 2025

doi:10.1101/2025.01.14.632908.

The Proteomics of T-Cell and Early T-Cell Precursor (ETP) Acute Lymphocytic Leukemia: Prognostic Patterns in Adult and Pediatric-ETP ALL.

Hoff FW, Sriraja L, Qiu Y, Jenkins GN, Teachey DT, Wood B, Devidas M, Shockley S, Loh ML, Petsalaki E, Kornblau SM, Horton TM.

Cancers, 2024

doi:10.3390/cancers16244241.

PhosX: data-driven kinase activity inference from phosphoproteomics experiments.

Lussana A, Müller-Dott S, Saez-Rodriguez J, Petsalaki E.

Bioinformatics (Oxford, England), 2024

doi:10.1093/bioinformatics/btae697.

Author Correction: Limited oxygen in standard cell culture alters metabolism and function of differentiated cells.

Tan J, Virtue S, Norris DM, Conway OJ, Yang M, Bidault G, Gribben C, Lugtu F, Kamzolas I, Krycer JR, Mills RJ, Liang L, Pereira C, Dale M, Shun-Shion AS, Baird HJ, Horscroft JA, Sowton AP, Ma M, Carobbio S, Petsalaki E, Murray AJ, Gershlick DC, Nathan JA, Hudson JE, Vallier L, Fisher-Wellman KH, Frezza C, Vidal-Puig A, Fazakerley DJ.

The EMBO journal, 2024

doi:10.1038/s44318-024-00230-1.

Differential regulation of the proteome and phosphoproteome along the dorso-ventral axis of the early Drosophila embryo.

Gomez JM, Nolte H, Vogelsang E, Dey B, Takeda M, Giudice G, Faxel M, Haunold T, Cepraga A, Zinzen RP, Krüger M, Petsalaki E, Wang YC, Leptin M.

eLife, 2024

doi:10.7554/elife.99263.

Comprehensive evaluation of phosphoproteomic-based kinase activity inference

Müller-Dott S, Jaehnig EJ, Munchic KP, Jiang W, Yaron-Barir TM, Savage SR, Garrido-Rodriguez M, Johnson JL, Lussana A, Petsalaki E, Lei JT, Dugourd A, Krug K, Cantley LC, Mani D, Zhang B, Saez-Rodriguez J.

Preprint, 2024

doi:10.1101/2024.06.27.601117.

An unbiased ranking of murine dietary models based on their proximity to human metabolic dysfunction-associated steatotic liver disease (MASLD).

Vacca M, Kamzolas I, Harder LM, Oakley F, Trautwein C, Hatting M, Ross T, Bernardo B, Oldenburger A, Hjuler ST, Ksiazek I, Lindén D, Schuppan D, Rodriguez-Cuenca S, Tonini MM, Castañeda TR, Kannt A, Rodrigues CMP, Cockell S, Govaere O, Daly AK, Allison M, Honnens de Lichtenberg K, Kim YO, Lindblom A, Oldham S, Andréasson AC, Schlerman F, Marioneaux J, Sanyal A, Afonso MB, Younes R, Amano Y, Friedman SL, Wang S, Bhattacharya D, Simon E, Paradis V, Burt A, Grypari IM, Davies S, Driessen A, Yashiro H, Pors S, Worm Andersen M, Feigh M, Yunis C, Bedossa P, Stewart M, Cater HL, Wells S, Schattenberg JM, Anstee QM, LITMUS Investigators, Tiniakos D, Perfield JW, Petsalaki E, Davidsen P, Vidal-Puig A.

Nature metabolism, 2024

doi:10.1038/s42255-024-01043-6.

phuEGO: A Network-Based Method to Reconstruct Active Signaling Pathways From Phosphoproteomics Datasets.

Giudice G, Chen H, Koutsandreas T, Petsalaki E.

Molecular & cellular proteomics : MCP, 2024

doi:10.1016/j.mcpro.2024.100771.

Limited oxygen in standard cell culture alters metabolism and function of differentiated cells.

Tan J, Virtue S, Norris DM, Conway OJ, Yang M, Bidault G, Gribben C, Lugtu F, Kamzolas I, Krycer JR, Mills RJ, Liang L, Pereira C, Dale M, Shun-Shion AS, Baird HJ, Horscroft JA, Sowton AP, Ma M, Carobbio S, Petsalaki E, Murray AJ, Gershlick DC, Nathan JA, Hudson JE, Vallier L, Fisher-Wellman KH, Frezza C, Vidal-Puig A, Fazakerley DJ.

The EMBO journal, 2024

doi:10.1038/s44318-024-00084-7.

PhosX: data-driven kinase activity inference from phosphoproteomics experiments

Lussana A, Petsalaki E.

Preprint, 2024

doi:10.1101/2024.03.22.586304.

Integrated systems biology approach identifies gene targets for endothelial dysfunction.

Pinheiro-de-Sousa I, Fonseca-Alaniz MH, Giudice G, Valadão IC, Modestia SM, Mattioli SV, Junior RR, Zalmas LP, Fang Y, Petsalaki E, Krieger JE.

Molecular systems biology, 2023

doi:10.15252/msb.202211462.

phuEGO: A network-based method to reconstruct active signalling pathways from phosphoproteomics datasets

Giudice G, Chen H, Petsalaki E.

Preprint, 2023

doi:10.1101/2023.08.07.552249.

Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs.

Mihalič F, Simonetti L, Giudice G, Sander MR, Lindqvist R, Peters MBA, Benz C, Kassa E, Badgujar D, Inturi R, Ali M, Krystkowiak I, Sayadi A, Andersson E, Aronsson H, Söderberg O, Dobritzsch D, Petsalaki E, Överby AK, Jemth P, Davey NE, Ivarsson Y.

Nature communications, 2023

doi:10.1038/s41467-023-38015-5.

Pan-Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival.

Sousa A, Dugourd A, Memon D, Petursson B, Petsalaki E, Saez-Rodriguez J, Beltrao P.

Molecular systems biology, 2023

doi:10.15252/msb.202110631.

Limited oxygen availability in standard cell culture alters metabolism and function in terminally-differentiated cells

Tan J, Virtue S, Norris DM, Conway OJ, Yang M, Gribben C, Lugtu F, Kamzolas I, Krycer JR, Mills RJ, Pereira C, Dale M, Shun-Shion AS, Baird HJM, Horscroft JA, Sowton AP, Ma M, Carobbio S, Petsalaki E, Murray AJ, Gershlick DC, Hudson JE, Vallier L, Fisher-Wellman KH, Frezza C, Vidal-Puig A, Fazakerley DJ.

Preprint, 2022

doi:10.1101/2022.11.29.516437.

In silico network-based screening reveals candidates for endothelial dysfunction therapy

Pinheiro-de-Sousa I, Giudice G, Fonseca-Alaniz MH, Modestia SM, Mattioli SV, Fang Y, Petsalaki E, Krieger JE.

Preprint, 2022

doi:10.1101/2022.11.17.516953.

Phosphoproteomic profiling highlights CDC42 and CDK2 as key players in the regulation of the TGF-β pathway in ALMS1 and BBS1 knockout models

Bea-Mascato B, Giudice G, Pinheiro-de-Sousa I, Solarat C, Petsalaki E, Valverde D.

Preprint, 2022

doi:10.1101/2022.11.04.514246.

Phosphoproteomics data-driven signalling network inference: does it work?

Sriraja LO, Werhli A, Petsalaki E.

Preprint, 2022

doi:10.1101/2022.09.07.506895.

Use of viral motif mimicry improves the proteome-wide discovery of human linear motifs.

Wadie B, Kleshchevnikov V, Sandaltzopoulou E, Benz C, Petsalaki E.

Cell reports, 2022

doi:10.1016/j.celrep.2022.110764.

Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.

Barker CG, Petsalaki E, Giudice G, Sero J, Ekpenyong EN, Bakal C, Petsalaki E.

Genome research, 2022

doi:10.1101/gr.276059.121.

Data-driven extraction of human kinase-substrate relationships from omics datasets

Maier BD, Petursson B, Lussana A, Petsalaki E.

Preprint, 2022

doi:10.1101/2022.01.15.476449.

Author Correction: Dynamic regulation of hypoxia-inducible factor-1α activity is essential for normal B cell development.

Burrows N, Bashford-Rogers RJM, Bhute VJ, Peñalver A, Ferdinand JR, Stewart BJ, Smith JEG, Deobagkar-Lele M, Giudice G, Connor TM, Inaba A, Bergamaschi L, Smith S, Tran MGB, Petsalaki E, Lyons PA, Espeli M, Huntly BJP, Smith KGC, Cornall RJ, Clatworthy MR, Maxwell PH.

Nature immunology, 2021

doi:10.1038/s41590-021-01036-7.

Transcription factors: Bridge between cell signaling and gene regulation.

Weidemüller P, Kholmatov M, Petsalaki E, Zaugg JB.

Proteomics, 2021

doi:10.1002/pmic.202000034.

Use of viral motif mimicry improves the proteome-wide discovery of human linear motifs

Wadie B, Kleshchevnikov V, Sandaltzopoulou E, Benz C, Petsalaki E.

Preprint, 2021

doi:10.1101/2021.06.25.449930.

Pan-Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival

Sousa A, Dugourd A, Memon D, Petursson B, Petsalaki E, Saez-Rodriguez J, Beltrao P.

Preprint, 2021

doi:10.1101/2021.06.09.447741.

Suppression of insulin-induced gene 1 (INSIG1) function promotes hepatic lipid remodelling and restrains NASH progression.

Azzu V, Vacca M, Kamzolas I, Hall Z, Leslie J, Carobbio S, Virtue S, Davies SE, Lukasik A, Dale M, Bohlooly-Y M, Acharjee A, Lindén D, Bidault G, Petsalaki E, Griffin JL, Oakley F, Allison MED, Vidal-Puig A.

Molecular metabolism, 2021

doi:10.1016/j.molmet.2021.101210.

Identification of phenotype-specific networks from paired gene expression-cell shape imaging data

Barker CG, Petsalaki E, Giudice G, Sero J, Ekpenyong EN, Bakal C, Petsalaki E.

Preprint, 2021

doi:10.1101/2021.02.11.430597.

Cell Surface Mechanics Gate Embryonic Stem Cell Differentiation.

Bergert M, Lembo S, Sharma S, Russo L, Milovanović D, Gretarsson KH, Börmel M, Neveu PA, Hackett JA, Petsalaki E, Diz-Muñoz A.

Cell stem cell, 2020

doi:10.1016/j.stem.2020.10.017.

CEN-tools: an integrative platform to identify the contexts of essential genes.

Sharma S, Dincer C, Weidemüller P, Wright GJ, Petsalaki E.

Molecular systems biology, 2020

doi:10.15252/msb.20209698.

Dynamic regulation of hypoxia-inducible factor-1α activity is essential for normal B cell development.

Burrows N, Bashford-Rogers RJM, Bhute VJ, Peñalver A, Ferdinand JR, Stewart BJ, Smith JEG, Deobagkar-Lele M, Giudice G, Connor TM, Inaba A, Bergamaschi L, Smith S, Tran MGB, Petsalaki E, Lyons PA, Espeli M, Huntly BJP, Smith KGC, Cornall RJ, Clatworthy MR, Maxwell PH.

Nature immunology, 2020

doi:10.1038/s41590-020-0772-8.

Prediction of Signed Protein Kinase Regulatory Circuits.

Invergo BM, Petursson B, Akhtar N, Bradley D, Giudice G, Hijazi M, Cutillas P, Petsalaki E, Beltrao P.

Cell systems, 2020

doi:10.1016/j.cels.2020.04.005.

CEN-tools: An integrative platform to identify the ‘contexts’ of essential genes

Sharma S, Dincer C, Weidemüller P, Wright GJ, Petsalaki E.

Preprint, 2020

doi:10.1101/2020.05.10.087668.

Chromosomal arrangement of synthetic lethal gene pairs: repulsion or attraction?

Hosseini S, Wadie B, Petsalaki E.

Preprint, 2020

doi:10.1101/2020.05.05.078626.

Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions.

Müller PM, Rademacher J, Bagshaw RD, Wortmann C, Barth C, van Unen J, Alp KM, Giudice G, Eccles RL, Heinrich LE, Pascual-Vargas P, Sanchez-Castro M, Brandenburg L, Mbamalu G, Tucholska M, Spatt L, Czajkowski MT, Welke RW, Zhang S, Nguyen V, Rrustemi T, Trnka P, Freitag K, Larsen B, Popp O, Mertins P, Gingras AC, Roth FP, Colwill K, Bakal C, Pertz O, Pawson T, Petsalaki E, Rocks O.

Nature cell biology, 2020

doi:10.1038/s41556-020-0488-x.

Phosphoproteomics identifies a bimodal EPHA2 receptor switch that promotes embryonic stem cell differentiation.

Fernandez-Alonso R, Bustos F, Budzyk M, Kumar P, Helbig AO, Hukelmann J, Lamond AI, Lanner F, Zhou H, Petsalaki E, Findlay GM.

Nature communications, 2020

doi:10.1038/s41467-020-15173-4.

iTRAQ-Based Global Phosphoproteomics Reveals Novel Molecular Differences Between Toxoplasma gondii Strains of Different Genotypes.

Wang ZX, Zhou CX, Calderón-Mantilla G, Petsalaki E, He JJ, Song HY, Elsheikha HM, Zhu XQ.

Frontiers in cellular and infection microbiology, 2019

doi:10.3389/fcimb.2019.00307.

Proteome-wide inference of protein kinase regulatory circuits

Invergo BM, Petursson B, Bradley D, Giudice G, Petsalaki E, Beltrao P.

Preprint, 2019

doi:10.1101/703157.

Large-scale datasets uncovering cell signalling networks in cancer: context matters.

Sharma S, Petsalaki E.

Current opinion in genetics & development, 2019

doi:10.1016/j.gde.2019.05.001.

Proteomics and phosphoproteomics in precision medicine: applications and challenges.

Giudice G, Petsalaki E.

Briefings in bioinformatics, 2019

doi:10.1093/bib/bbx141.

Allosteric Modulation of Binding Specificity by Alternative Packing of Protein Cores.

Ben-David M, Huang H, Sun MGF, Corbi-Verge C, Petsalaki E, Liu K, Gfeller D, Garg P, Tempel W, Sochirca I, Shifman JM, Davidson A, Min J, Kim PM, Sidhu SS.

Journal of molecular biology, 2018

doi:10.1016/j.jmb.2018.11.018.

The pervasive effects of recombinant Fasciola gigantica Ras-related protein Rab10 on the functions of goat peripheral blood mononuclear cells.

Tian AL, Lu M, Zhang FK, Calderón-Mantilla G, Petsalaki E, Tian X, Wang W, Huang SY, Li X, Elsheikha HM, Zhu XQ.

Parasites & vectors, 2018

doi:10.1186/s13071-018-3148-2.

Spatial Organization of Rho GTPase signaling by RhoGEF/RhoGAP proteins

Müller PM, Rademacher J, Bagshaw RD, Alp KM, Giudice G, Heinrich LE, Barth C, Eccles RL, Sanchez-Castro M, Brandenburg L, Mbamalu G, Tucholska M, Spatt L, Wortmann C, Czajkowski MT, Welke R, Zhang S, Nguyen V, Rrustemi T, Trnka P, Freitag K, Larsen B, Popp O, Mertins P, Bakal C, Gingras A, Pertz O, Roth FP, Colwill K, Pawson T, Petsalaki E, Rocks O.

Preprint, 2018

doi:10.1101/354316.