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Kamzolas I, Koutsandreas T, Barker CG, Vathrakokoili Pournara A, Weston H, Vacca M, Papatheodorou I, Vidal-Puig A, Petsalaki E.

Preprint, 2025

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MAGELLAN: Automated Generation of Interpretable Computational Models for Biological Reasoning

Clarke MA, Barker CG, Sun Y, Roumeliotis TI, Choudhary JS, Fisher J.

Preprint, 2025

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Predicting Personalised Therapeutic Combinations in Non-Small Cell Lung Cancer Using <i>In Silico</i> Modelling

Clarke MA, Barker CG, Nicholls A, Handler MP, Pickard L, Shah A, Walter D, Braekeleer ED, Banerji U, Choudhary J, Ahmed S, McDermott U, Hannon GJ, Fisher J.

Preprint, 2025

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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

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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

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

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

Molecular & cellular proteomics : MCP, 2025

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

Pinheiro-de-Sousa I, Petsalaki E.

Nature protocols, 2025

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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

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Plasma from hypertensive pregnancy patients induce endothelial dysfunction even under atheroprotective shear stress.

Viana-Mattioli S, Fonseca-Alaniz MH, Pinheiro-de-Sousa I, Junior RR, Mastella MH, de Carvalho Cavalli R, Sandrim VC.

Scientific reports, 2025

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Lineage-specific patterns in the Moraceae family allow identification of convergent P450 enzymes involved in furanocoumarin biosynthesis.

Bouillé A, Larbat R, Kumari R, Olry A, Charles C, Nelson DR, Thornton J, Villard C, Hehn A.

The New phytologist, 2025

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Alleviating batch effects in cell type deconvolution with SCCAF-D.

Feng S, Huang L, Pournara AV, Huang Z, Yang X, Zhang Y, Brazma A, Shi M, Papatheodorou I, Miao Z.

Nature communications, 2024

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CATD: a reproducible pipeline for selecting cell-type deconvolution methods across tissues.

Vathrakokoili Pournara A, Miao Z, Beker OY, Nolte N, Brazma A, Papatheodorou I.

Bioinformatics advances, 2024

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Expression Atlas update: insights from sequencing data at both bulk and single cell level.

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Nucleic acids research, 2024

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ARID1A-induced transcriptional reprogramming rewires signalling responses to drug treatment in melanoma

Barker CG, Sharma S, Santos AM, Nikolakopoulos K, Velentzas AD, Völlmy FI, Minia A, Pliaka V, Altelaar M, Wright GJ, Alexopoulos LG, Stravopodis DJ, Petsalaki E.

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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

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

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

Bioinformatics (Oxford, England), 2024

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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

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Differential regulation of the proteome and phosphoproteome along the dorso-ventral axis of the early <i>Drosophila</i> 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

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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

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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

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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

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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

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PhosX: data-driven kinase activity inference from phosphoproteomics experiments

Lussana A, Petsalaki E.

Preprint, 2024

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In silico prediction of heme binding in proteins.

Marson NA, Gallio AE, Mandal SK, Laskowski RA, Raven EL.

The Journal of biological chemistry, 2024

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Interaction of Genetic Variants Activates Latent Metabolic Pathways in Yeast

Sasikumar S, Parkins ST, Sudarsan S, Sinha H.

Preprint, 2024

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Power analysis of cell-type deconvolution methods across tissues

Pournara AV, Miao Z, Beker O, Brazma A, Papatheodorou I.

Preprint, 2023

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CATD: A reproducible pipeline for selecting cell-type deconvolution methods across tissues

Pournara AV, Miao Z, Beker OY, Nolte N, Nolte N, Brazma A, Papatheodorou I.

Preprint, 2023

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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

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

Giudice G, Chen H, Petsalaki E.

Preprint, 2023

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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

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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

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Differential regulation of the proteome and phosphosproteome along the dorso-ventral axis of the early <i>Drosophila</i> embryo

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

Preprint, 2023

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Missing links in preeclampsia cell model systems of endothelial dysfunction.

Viana-Mattioli S, Fonseca-Alaniz MH, Pinheiro-de-Sousa I, Krieger JE, Sandrim VC.

Trends in molecular medicine, 2023

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The effects of pathogenic and likely pathogenic variants for inherited hemostasis disorders in 140 214 UK Biobank participants.

Stefanucci L, Collins J, Sims MC, Barrio-Hernandez I, Sun L, Burren OS, Perfetto L, Bender I, Callahan TJ, Fleming K, Guerrero JA, Hermjakob H, Martin MJ, Stephenson J, Paneerselvam K, Petrovski S, Porras P, Robinson PN, Wang Q, Watkins X, Frontini M, Laskowski RA, Beltrao P, Di Angelantonio E, Gomez K, Laffan M, Ouwehand WH, Mumford AD, Freson K, Carss K, Downes K, Gleadall N, Megy K, Bruford E, Vuckovic D.

Blood, 2023

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Genome-Scale Metabolic Modeling Identifies Causal Reactions Mediated by SNP-SNP Interactions Influencing Yeast Sporulation

Sasikumar S, Kumar S P, Bhatt N, Sinha H.

Preprint, 2023

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

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

Preprint, 2022

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Inter-gastruloid heterogeneity revealed by single cell transcriptomics time course: implications for organoid based perturbation studies

Rosen LU, Stapel LC, Argelaguet R, Barker CG, Yang A, Reik W, Marioni JC.

Preprint, 2022

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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

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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

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<i>In silico</i>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<i>ALMS1</i>and<i>BBS1</i>knockout models

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

Preprint, 2022

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

Sriraja LO, Werhli A, Petsalaki E.

Preprint, 2022

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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

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

Mihalic F, Simonetti L, Giudice G, Sander MR, Lindqvist R, Akprioro Peters MB, 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.

Preprint, 2022

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Mapping the Constrained Coding Regions in the Human Genome to Their Corresponding Proteins.

Hasenahuer MA, Sanchis-Juan A, Laskowski RA, Baker JA, Stephenson JD, Orengo CA, Raymond FL, Thornton JM.

Journal of molecular biology, 2022

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A structural biology community assessment of AlphaFold2 applications.

Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, Dunham AS, Burke D, Borkakoti N, Velankar S, Frost A, Basquin J, Lindorff-Larsen K, Bateman A, Kajava AV, Valencia A, Ovchinnikov S, Durairaj J, Ascher DB, Thornton JM, Davey NE, Stein A, Elofsson A, Croll TI, Beltrao P.

Nature structural & molecular biology, 2022

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PDBsum1: A standalone program for generating PDBsum analyses.

Laskowski RA.

Protein science : a publication of the Protein Society, 2022

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Mapping the Constrained Coding Regions in the human genome to their corresponding proteins

Hasenahuer MA, Sanchis-Juan A, Laskowski RA, Baker JA, Stephenson JD, Orengo CA, Raymond FL, Thornton JM.

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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

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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

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Transcription factors: Bridge between cell signaling and gene regulation.

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

Proteomics, 2021

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

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Preprint, 2021

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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

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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

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A photo-switchable yeast isocitrate dehydrogenase to control metabolic flux through the citric acid cycle

Chen H, Mulder L, Wijma HJ, Wabeke R, Losa JPVC, Rovetta M, de Leeuw TC, Millias-Argeitis A, Heinemann M.

Preprint, 2021

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PDBsum extras: SARS-CoV-2 and AlphaFold models.

Laskowski RA, Thornton JM.

Protein science : a publication of the Protein Society, 2021

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AlphaFold heralds a data-driven revolution in biology and medicine.

Thornton JM, Laskowski RA, Borkakoti N.

Nature medicine, 2021

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A structural biology community assessment of AlphaFold 2 applications

Akdel M, Pires DEV, Porta Pardo E, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Ruiz Serra V, Rodrigues CHM, Dunham AS, Burke D, Borkakoti N, Velankar S, Frost A, Lindorff-Larsen K, Valencia A, Ovchinnikov S, Durairaj J, Ascher DB, Thornton JM, Davey NE, Stein A, Elofsson A, Croll TI, Beltrao P.

Preprint, 2021

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A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases.

Magraner-Pardo L, Laskowski RA, Pons T, Thornton JM.

Scientific reports, 2021

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A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases and prostate cancer progression

Magraner-Pardo L, Laskowski RA, Pons T, Thornton JM.

Preprint, 2021

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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

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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

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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

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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

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

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

Preprint, 2020

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

Hosseini S, Wadie B, Petsalaki E.

Preprint, 2020

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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

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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

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Using protein interaction networks to identify cancer dependencies from tumor genome data

Horn H, Fagre C, Gupta A, Tsafou K, Fornelos N, Neal JT, Lage K.

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An automated protocol for modelling peptide substrates to proteases.

Ochoa R, Magnitov M, Laskowski RA, Cossio P, Thornton JM.

BMC bioinformatics, 2020

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Protein homeostasis imprinting across evolution

Koutsandreas T, Felden B, Chevet E, Chatziioannou A.

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iTRAQ-Based Global Phosphoproteomics Reveals Novel Molecular Differences Between <i>Toxoplasma gondii</i> 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

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Proteome-wide inference of protein kinase regulatory circuits

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

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

Sharma S, Petsalaki E.

Current opinion in genetics & development, 2019

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Proteomics and phosphoproteomics in precision medicine: applications and challenges.

Giudice G, Petsalaki E.

Briefings in bioinformatics, 2019

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VarSite: Disease variants and protein structure.

Laskowski RA, Stephenson JD, Sillitoe I, Orengo CA, Thornton JM.

Protein science : a publication of the Protein Society, 2019

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VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations.

Stephenson JD, Laskowski RA, Nightingale A, Hurles ME, Thornton JM.

Bioinformatics (Oxford, England), 2019

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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.

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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.

Application of CRISPR-Cas9 Based Genome-Wide Screening Approaches to Study Cellular Signalling Mechanisms.

Sharma S, Petsalaki E.

International journal of molecular sciences, 2018

doi:10.3390/ijms19040933.

A recombinant Fasciola gigantica 14-3-3 epsilon protein (rFg14-3-3e) modulates various functions of goat peripheral blood mononuclear cells.

Tian AL, Lu M, Calderón-Mantilla G, Petsalaki E, Dottorini T, Tian X, Wang Y, Huang SY, Hou JL, Li X, Elsheikha HM, Zhu XQ.

Parasites & vectors, 2018

doi:10.1186/s13071-018-2745-4.

Components of genetic associations across 2,138 phenotypes in the UK Biobank highlight novel adipocyte biology

Tanigawa Y, Li J, Justesen JM, Horn H, Aguirre M, DeBoever C, Chang C, Narasimhan B, Lage K, Hastie T, Park CY, Bejerano G, Ingelsson E, Rivas MA.

Preprint, 2018

doi:10.1101/442715.

Decoding the functional Fes kinase signaling network topology in a lymphocyte model

Helbig AO, Kofler M, Gish G, Sriraja L, Lorenzen K, Tucholska M, Zhang C, Roth FP, Pawson T, Colwill K, Petsalaki E.

Preprint, 2017

doi:10.1101/125088.

Systematic identification of phosphorylation-mediated protein interaction switches.

Betts MJ, Wichmann O, Utz M, Andre T, Petsalaki E, Minguez P, Parca L, Roth FP, Gavin AC, Bork P, Russell RB, Russell RB.

PLoS computational biology, 2017

doi:10.1371/journal.pcbi.1005462.

Expanding discovery from cancer genomes by integrating protein network analyses with in vivo tumorigenesis assays

Horn H, Lawrence MS, Chouinard CR, Shrestha Y, Hu JX, Worstell E, Shea E, Ilic N, Kim E, Kamburov A, Kashani A, Hahn WC, Campbell JD, Boehm JS, Getz G, Lage K.

Preprint, 2017

doi:10.1101/151977.

PDBsum: Structural summaries of PDB entries.

Laskowski RA, Jabłońska J, Pravda L, Vařeková RS, Thornton JM.

Protein science : a publication of the Protein Society, 2017

doi:10.1002/pro.3289.

Protein structure and phenotypic analysis of pathogenic and population missense variants in <i>STXBP1</i>.

Suri M, Evers JMG, Laskowski RA, O'Brien S, Baker K, Clayton-Smith J, Dabir T, Josifova D, Joss S, Kerr B, Kraus A, McEntagart M, Morton J, Smith A, Splitt M, Thornton JM, DDD Study, Wright CF.

Molecular genetics & genomic medicine, 2017

doi:10.1002/mgg3.304.

The ProFunc Function Prediction Server.

Laskowski RA.

Methods in molecular biology (Clifton, N.J.), 2017

doi:10.1007/978-1-4939-7015-5_7.

Structural analysis of pathogenic mutations in the DYRK1A gene in patients with developmental disorders.

Evers JM, Laskowski RA, Bertolli M, Clayton-Smith J, Deshpande C, Eason J, Elmslie F, Flinter F, Gardiner C, Hurst JA, Kingston H, Kini U, Lampe AK, Lim D, Male A, Naik S, Parker MJ, Price S, Robert L, Sarkar A, Straub V, Woods G, Thornton JM, DDD Study, Wright CF.

Human molecular genetics, 2017

doi:10.1093/hmg/ddw409.

Chopping and Changing: the Evolution of the Flavin-dependent Monooxygenases.

Mascotti ML, Juri Ayub M, Furnham N, Thornton JM, Laskowski RA.

Journal of molecular biology, 2016

doi:10.1016/j.jmb.2016.07.003.

Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis.

Jakubec D, Laskowski RA, Vondrasek J.

PloS one, 2016

doi:10.1371/journal.pone.0158704.

Rising levels of atmospheric oxygen and evolution of Nrf2.

Gacesa R, Dunlap WC, Barlow DJ, Laskowski RA, Long PF.

Scientific reports, 2016

doi:10.1038/srep27740.

BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization.

Ryu J, Lee M, Cha J, Laskowski RA, Ryu SE, Kim DS.

Nucleic acids research, 2016

doi:10.1093/nar/gkw368.

Protein Structure Databases.

Laskowski RA.

Methods in molecular biology (Clifton, N.J.), 2016

doi:10.1007/978-1-4939-3572-7_2.

Integrating population variation and protein structural analysis to improve clinical interpretation of missense variation: application to the WD40 domain.

Laskowski RA, Tyagi N, Johnson D, Joss S, Kinning E, McWilliam C, Splitt M, Thornton JM, Firth HV, DDD Study, Wright CF.

Human molecular genetics, 2016

doi:10.1093/hmg/ddv625.

A knowledge base for Vitis vinifera functional analysis.

Pulvirenti A, Giugno R, Distefano R, Pigola G, Mongiovi M, Giudice G, Vendramin V, Lombardo A, Cattonaro F, Ferro A.

BMC systems biology, 2015

doi:10.1186/1752-0509-9-s3-s5.

A global reference for human genetic variation.

1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR.

Nature, 2015

doi:10.1038/nature15393.

Large-Scale Quantitative Assessment of Binding Preferences in Protein-Nucleic Acid Complexes.

Jakubec D, Hostas J, Laskowski RA, Hobza P, Vondrásek J.

Journal of chemical theory and computation, 2015

doi:10.1021/ct501168n.

Proteins: interaction at a distance.

Laskowski RA, Thornton JM.

IUCrJ, 2015

doi:10.1107/s2052252515020217.

Representative Amino Acid Side-Chain Interactions in Protein-DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems.

Hostaš J, Jakubec D, Laskowski RA, Gnanasekaran R, Řezáč J, Vondrášek J, Hobza P.

Journal of chemical theory and computation, 2015

doi:10.1021/acs.jctc.5b00398.

BetaCavityWeb: a webserver for molecular voids and channels.

Kim JK, Cho Y, Lee M, Laskowski RA, Ryu SE, Sugihara K, Kim DS.

Nucleic acids research, 2015

doi:10.1093/nar/gkv360.

KinomeXplorer: an integrated platform for kinome biology studies.

Horn H, Schoof EM, Kim J, Robin X, Miller ML, Diella F, Palma A, Cesareni G, Jensen LJ, Linding R.

Nature methods, 2014

doi:10.1038/nmeth.2968.

CATH: comprehensive structural and functional annotations for genome sequences.

Sillitoe I, Lewis TE, Cuff A, Das S, Ashford P, Dawson NL, Furnham N, Laskowski RA, Lee D, Lees JG, Lehtinen S, Studer RA, Thornton J, Orengo CA.

Nucleic acids research, 2014

doi:10.1093/nar/gku947.

Anatomy of enzyme channels.

Pravda L, Berka K, Svobodová Vařeková R, Sehnal D, Banáš P, Laskowski RA, Koča J, Otyepka M.

BMC bioinformatics, 2014

doi:10.1186/s12859-014-0379-x.

PDBsum additions.

de Beer TA, Berka K, Thornton JM, Laskowski RA.

Nucleic acids research, 2013

doi:10.1093/nar/gkt940.

Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.

de Beer TA, Laskowski RA, Parks SL, Sipos B, Goldman N, Thornton JM.

PLoS computational biology, 2013

doi:10.1371/journal.pcbi.1003382.

LigSearch: a knowledge-based web server to identify likely ligands for a protein target.

de Beer TA, Laskowski RA, Duban ME, Chan AW, Anderson WF, Thornton JM.

Acta crystallographica. Section D, Biological crystallography, 2013

doi:10.1107/s0907444913022294.

The Ramachandran plot and protein structure validation

Laskowski RA, Furnham N, Thornton JM.

2013

doi:10.1142/9789814449144_0005.

The identification of short linear motif-mediated interfaces within the human interactome.

Weatheritt RJ, Luck K, Petsalaki E, Davey NE, Gibson TJ.

Bioinformatics (Oxford, England), 2012

doi:10.1093/bioinformatics/bts072.

Abstracting knowledge from the Protein Data Bank.

Furnham N, Laskowski RA, Thornton JM.

Biopolymers, 2012

doi:10.1002/bip.22107.

Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.

Furnham N, Sillitoe I, Holliday GL, Cuff AL, Laskowski RA, Orengo CA, Thornton JM.

PLoS computational biology, 2012

doi:10.1371/journal.pcbi.1002403.

FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.

Furnham N, Sillitoe I, Holliday GL, Cuff AL, Rahman SA, Laskowski RA, Orengo CA, Thornton JM.

Nucleic acids research, 2011

doi:10.1093/nar/gkr852.

LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.

Laskowski RA, Swindells MB.

Journal of chemical information and modeling, 2011

doi:10.1021/ci200227u.

Protein structure databases.

Laskowski RA.

Molecular biotechnology, 2011

doi:10.1007/s12033-010-9372-4.

WD40 proteins propel cellular networks.

Stirnimann CU, Petsalaki E, Russell RB, Russell RB, Müller CW.

Trends in biochemical sciences, 2010

doi:10.1016/j.tibs.2010.04.003.

Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins.

Berka K, Laskowski RA, Hobza P, Vondrášek J.

Journal of chemical theory and computation, 2010

doi:10.1021/ct100007y.

Visualization of macromolecular structures.

O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, Saibil HR, Schafferhans A, Wade RC, Westhof E, Olson AJ.

Nature methods, 2010

doi:10.1038/nmeth.1427.

Protein structure databases.

Laskowski RA.

Methods in molecular biology (Clifton, N.J.), 2010

doi:10.1007/978-1-60327-241-4_4.

On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins.

Kahraman A, Morris RJ, Laskowski RA, Favia AD, Thornton JM.

Proteins, 2010

doi:10.1002/prot.22633.

Accurate prediction of peptide binding sites on protein surfaces.

Petsalaki E, Stark A, García-Urdiales E, Russell RB, Russell RB.

PLoS computational biology, 2009

doi:10.1371/journal.pcbi.1000335.

Reflect: augmented browsing for the life scientist.

Pafilis E, O'Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, Schneider R.

Nature biotechnology, 2009

doi:10.1038/nbt0609-508.

Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures.

Berka K, Laskowski R, Riley KE, Hobza P, Vondrášek J.

Journal of chemical theory and computation, 2009

doi:10.1021/ct800508v.

Integrated Servers for Structure-Informed Function Prediction

Laskowski RA.

2009

doi:10.1007/978-1-4020-9058-5_10.

The fine details of evolution.

Laskowski RA, Thornton JM, Sternberg MJ.

Biochemical Society transactions, 2009

doi:10.1042/bst0370723.

The structural basis of allosteric regulation in proteins.

Laskowski RA, Gerick F, Thornton JM.

FEBS letters, 2009

doi:10.1016/j.febslet.2009.03.019.

WSsas: a web service for the annotation of functional residues through structural homologues.

Talavera D, Laskowski RA, Thornton JM.

Bioinformatics (Oxford, England), 2009

doi:10.1093/bioinformatics/btp116.

Peptide-mediated interactions in biological systems: new discoveries and applications.

Petsalaki E, Russell RB, Russell RB.

Current opinion in biotechnology, 2008

doi:10.1016/j.copbio.2008.06.004.

PDBsum new things.

Laskowski RA.

Nucleic acids research, 2008

doi:10.1093/nar/gkn860.

Understanding the molecular machinery of genetics through 3D structures.

Laskowski RA, Thornton JM.

Nature reviews. Genetics, 2008

doi:10.1038/nrg2273.

Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature.

Laskowski RA.

Bioinformatics (Oxford, England), 2007

doi:10.1093/bioinformatics/btm085.

Shape variation in protein binding pockets and their ligands.

Kahraman A, Morris RJ, Laskowski RA, Thornton JM.

Journal of molecular biology, 2007

doi:10.1016/j.jmb.2007.01.086.

Towards fully automated structure-based function prediction in structural genomics: a case study.

Watson JD, Sanderson S, Ezersky A, Savchenko A, Edwards A, Orengo C, Joachimiak A, Laskowski RA, Thornton JM.

Journal of molecular biology, 2007

doi:10.1016/j.jmb.2007.01.063.

A method for localizing ligand binding pockets in protein structures.

Glaser F, Morris RJ, Najmanovich RJ, Laskowski RA, Thornton JM.

Proteins, 2006

doi:10.1002/prot.20769.

Protein function prediction using local 3D templates.

Laskowski RA, Watson JD, Thornton JM.

Journal of molecular biology, 2005

doi:10.1016/j.jmb.2005.05.067.

ProFunc: a server for predicting protein function from 3D structure.

Laskowski RA, Watson JD, Thornton JM.

Nucleic acids research, 2005

doi:10.1093/nar/gki414.

Predicting protein function from sequence and structural data.

Watson JD, Laskowski RA, Thornton JM.

Current opinion in structural biology, 2005

doi:10.1016/j.sbi.2005.04.003.

PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids.

Laskowski RA, Chistyakov VV, Thornton JM.

Nucleic acids research, 2005

doi:10.1093/nar/gki001.

From protein structure to biochemical function?

Laskowski RA, Watson JD, Thornton JM.

Journal of structural and functional genomics, 2003

doi:10.1023/a:1026127927612.

Molecular basis of inherited diseases: a structural perspective.

Steward RE, MacArthur MW, Laskowski RA, Thornton JM.

Trends in genetics : TIG, 2003

doi:10.1016/s0168-9525(03)00195-1.

Target selection and determination of function in structural genomics.

Watson JD, Todd AE, Bray J, Laskowski RA, Edwards A, Joachimiak A, Orengo CA, Thornton JM.

IUBMB life, 2003

doi:10.1080/1521654031000123385.

Bioinformatics and protein design.

Laskowski RA, Chan AW.

Current pharmaceutical biotechnology, 2002

doi:10.2174/1389201023378157.

Who checks the checkers? Four validation tools applied to eight atomic resolution structures. EU 3-D Validation Network.

Journal of molecular biology, 1998

doi:10.1006/jmbi.1997.1526.

PROCHECK: a program to check the stereochemical quality of protein structures.

Laskowski RA, MacArthur MW, Moss DS, Thornton JM.

Journal of applied crystallography, 1993

doi:10.1107/s0021889892009944.