Publications: Mr Cankut Cubuk

Er AG, Çubuk C, Durusu Tanrıöver M, Bağcı Bosi AT, Holyavkin C, Özışık L, Çakmak M, Uyaroğlu OA et al. ( 2024 ) . Influenza Surveillance Under the Shadow of COVID-19 Pandemic: Phylogenetic Analysis of Influenza A (H1N1)pdm09 Viruses in Türkiye in 2019-20 Season . Flora the Journal of Infectious Diseases and Clinical Microbiology vol. 29 , ( 4 ) 488 - 501 .

Iseppon F, Kanellopoulos AH, Tian N, Zhou J, Caan G, Chiozzi R, Thalassinos K, Çubuk C et al. ( 2024 ) . Sodium channels Nav1.7, Nav1.8 and pain; two distinct mechanisms for Nav1.7 null analgesia . Neurobiology of Pain vol. 16 ,

Bangash MA, Cubuk C, Iseppon F, Haroun R, Garcia C, Luiz AP, Arcangeletti M, Gossage SJ et al. ( 2024 ) . Analgesic targets identified in mouse sensory neuron somata and terminal pain translatomes . Cell Reports vol. 43 , ( 8 )

Çubuk C, Lau R, Cutillas P, Rajeeve V, John CR, Surace AEA, Hands R, Fossati-Jimack L et al. ( 2024 ) . Phosphoproteomic profiling of early rheumatoid arthritis synovium reveals active signalling pathways and differentiates inflammatory pathotypes . Arthritis Research & Therapy vol. 26 , ( 1 )

Corsiero E, Caliste M, Jagemann L, Fossati-Jimack L, Goldmann K, Cubuk C, Ghirardi GM, Prediletto E et al. ( 2024 ) . Autoimmunity to stromal-derived autoantigens in rheumatoid ectopic germinal centers exacerbates arthritis and affects clinical response . Journal of Clinical Investigation vol. 134 , ( 12 )

Nerviani A, Boutet M-A, Ghirardi GM, Goldmann K, Sciacca E, Rivellese F, Pontarini E, Prediletto E et al. ( 2024 ) . Axl and MerTK regulate synovial inflammation and are modulated by IL-6 inhibition in rheumatoid arthritis . Nature Communications vol. 15 , ( 1 )

Goldmann K, Spiliopoulou A, Iakovliev A, Plant D, Nair N, Cubuk C, Consortium TM, McKeigue P et al. ( 2024 ) . Expression quantitative trait loci analysis in rheumatoid arthritis identifies tissue specific variants associated with severity and outcome . Annals of the Rheumatic Diseases vol. 83 , ( 3 ) 288 - 299 .

Rivellese F, Nerviani A, Giorli G, Warren L, Jaworska E, Bombardieri M, Lewis MJ, Humby F et al. ( 2023 ) . Stratification of biological therapies by pathobiology in biologic-naive patients with rheumatoid arthritis (STRAP and STRAP-EU): two parallel, open-label, biopsy-driven, randomised trials . The Lancet Rheumatology vol. 5 , ( 11 ) e648 - e659 .

Yang Y-H, Cubuk C, Gauna DEC, Banchereau R, Kockx M, Rodriguez-Vida A, Martinez ID, Crabb S et al. ( 2023 ) . 2393P Ephrin signalling mediates resistance to programmed death ligand 1 (PD-L1) inhibition in urothelial carcinoma (UC) . Annals of Oncology vol. 34 ,

Pellegrinelli V, Figueroa-Juárez E, Samuelson I, U-Din M, Rodriguez-Fdez S, Virtue S, Leggat J, Çubuk C et al. ( 2023 ) . Defective extracellular matrix remodeling in brown adipose tissue is associated with fibro-inflammation and reduced diet-induced thermogenesis . Cell Reports vol. 42 , ( 6 )

Çubuk C, Loucera C, Peña-Chilet M, Dopazo J ( 2023 ) . Crosstalk between Metabolite Production and Signaling Activity in Breast Cancer . International Journal of Molecular Sciences vol. 24 , ( 8 )

Schmidt M, Sondermann JR, Gomez-Varela D, Çubuk C, Millet Q, Lewis MJ, Wood JN, Zhao J ( 2022 ) . Transcriptomic and proteomic profiling of NaV1.8-expressing mouse nociceptors . Frontiers in Molecular Neuroscience vol. 15 ,

Surace A, Sciacca E, Goldmann K, Rivellese F, Cubuk C, Giorli G, Fossati-Jimack L, Ahmed M et al. ( 2022 ) . OP0077 SYNOVIAL RNA-SEQ ANALYSIS OF THE R4RA TRIAL IDENTIFIES SIGNATURES OF TREATMENT RESISTANCE AND REFRACTORY STATE IN RHEUMATOID ARTHRITIS . Annals of the Rheumatic Diseases vol. 81 , 52 - 53 .

Rivellese F, Cubuk C, Surace A, Goldmann K, Sciacca E, Giorli G, Nerviani A, Fossati-Jimack L et al. ( 2022 ) . OP0085 CELL LINEAGE-SPECIFIC TRANSCRIPT DECONVOLUTION OF SYNOVIAL BIOPSIES FROM THE R4RA TRIAL IDENTIFIES CELL POPULATIONS ASSOCIATED WITH RESPONSE TO RITUXIMAB AND TOCILIZUMAB . Annals of the Rheumatic Diseases vol. 81 , 56 - 57 .

Prediletto E, Cubuk C, Pontarini E, Rivellese F, Nerviani A, Lucchesi D, Caliste M, Corsiero E et al. ( 2022 ) . POS0138 RHEUMATOID SYNOVIAL FIBROBLASTS DISPLAY IMPRINTED MEMORY OF THEIR SYNOVIAL ENDOTYPE WHICH CAN BE PLASTICALLY MODULATED BY B-CELLS CROSSTALK . Annals of the Rheumatic Diseases vol. 81 ,

Rivellese F, Surace AEA, Goldmann K, Sciacca E, Çubuk C, Giorli G, John CR, Nerviani A et al. ( 2022 ) . Rituximab versus tocilizumab in rheumatoid arthritis: synovial biopsy-based biomarker analysis of the phase 4 R4RA randomized trial . Nature Medicine vol. 28 , ( 6 ) 1256 - 1268 .

Micheroli R, Elhai M, Edalat S, Frank-Bertoncelj M, Bürki K, Ciurea A, MacDonald L, Kurowska-Stolarska M et al. ( 2022 ) . Role of synovial fibroblast subsets across synovial pathotypes in rheumatoid arthritis: a deconvolution analysis . RMD Open vol. 8 , ( 1 )

Rivellese F, Pontarini E, Cubuk C, Nerviani A, Fossati-Jimack L, Surace A, Sciacca E, Goldmann K et al. ( 2022 ) . Module Signatures of Synovial Single-cell States Identify Disease Phenotypes in Early Treatment-naive Rheumatoid Arthritis . ARTHRITIS & RHEUMATOLOGY . vol. 74 , 3345 - 3347 .

Prediletto E, Cubuk C, Pontarini E, Rivellese F, Nerviani A, Lucchesi D, Caliste M, Corsiero E et al. ( 2022 ) . Rheumatoid Synovial Fibroblasts Display Imprinted Memory of Their Synovial Endotype Which Can Be Plastically Modulated by B-cells Crosstalk . ARTHRITIS & RHEUMATOLOGY . vol. 74 , 1242 - 1244 .

Loong L, Cubuk C, Choi S, Allen S, Torr B, Garrett A, Loveday C, Durkie M et al. ( 2021 ) . Quantifying prediction of pathogenicity for within-codon concordance (PM5) using 7541 functional classifications of BRCA1 and MSH2 missense variants . Genetics in Medicine vol. 24 , ( 3 ) 552 - 563 .

Cubuk C, Garrett A, Choi S, King L, Loveday C, Torr B, Burghel GJ, Durkie M et al. ( 2021 ) . Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes . Genetics in Medicine vol. 23 , ( 11 ) 2096 - 2104 .

Rivellese F, Pontarini E, Fossati-Jimack L, Moura RA, Romão VC, Fonseca JE, Nerviani A, Cubuk C et al. ( 2021 ) . OP0011 INTEGRATION OF FLOW AND DIGITAL CYTOMETRY IN EARLY TREATMENT-NAÏVE RHEUMATOID ARTHRITIS IDENTIFIES DISTINCT IMMUNOPHENOTYPES IN PERIPHERAL BLOOD AND DISEASE TISSUE . Annals of the Rheumatic Diseases vol. 80 ,

Méndez-Salazar EO, Vázquez-Mellado J, Casimiro-Soriguer CS, Dopazo J, Çubuk C, Zamudio-Cuevas Y, Francisco-Balderas A, Martínez-Flores K et al. ( 2021 ) . Taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism . Molecular Medicine vol. 27 , ( 1 )

Rian K, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Esteban-Medina M, Alamo-Alvarez I, Peña-Chilet M et al. ( 2021 ) . Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data . Computational and Structural Biotechnology Journal vol. 19 , 2968 - 2978 .

Rian K, Esteban-Medina M, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Gunyel D, Ostaszewski M et al. ( 2021 ) . Mechanistic modeling of the SARS-CoV-2 disease map . BioData Mining vol. 14 , ( 1 )

Garrett A, Durkie M, Callaway A, Burghel GJ, Robinson R, Drummond J, Torr B, Cubuk C et al. ( 2020 ) . Combining evidence for and against pathogenicity for variants in cancer susceptibility genes: CanVIG-UK consensus recommendations . Journal of Medical Genetics vol. 58 , ( 5 ) 297 - 304 .

Cubuk C ( 2020 ) . Modeling Functional Modules Using Statistical and Machine Learning Methods .

Yang M, Petralia F, Li Z, Li H, Ma W, Song X, Kim S, Lee H et al. ( 2020 ) . Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics . Cell Systems

Çubuk C, Can FE, Peña-Chilet M, Dopazo J ( 2020 ) . Mechanistic Models of Signaling Pathways Reveal the Drug Action Mechanisms behind Gender-Specific Gene Expression for Cancer Treatments . Cells vol. 9 , ( 7 )

Garrett A, Callaway A, Durkie M, Cubuk C, Alikian M, Burghel GJ, Robinson R, Izatt L et al. ( 2020 ) . Cancer Variant Interpretation Group UK (CanVIG-UK): an exemplar national subspecialty multidisciplinary network . Journal of Medical Genetics vol. 57 , ( 12 ) 829 - 834 .

Petkevicius K, Virtue S, Bidault G, Jenkins B, Çubuk C, Morgantini C, Aouadi M, Dopazo J et al. ( 2019 ) . Accelerated phosphatidylcholine turnover in macrophages promotes adipose tissue inflammation in obesity . eLife vol. 8 ,

Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J et al. ( 2019 ) . Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen . Nature Communications vol. 10 , ( 1 )

Çubuk C, Hidalgo MR, Amadoz A, Rian K, Salavert F, Pujana MA, Mateo F, Herranz C et al. ( 2019 ) . Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models . npj Systems Biology and Applications vol. 5 , ( 1 )

Cubuk C, Hidalgo MR, Amadoz A, Pujana MA, Mateo F, Herranz C, Carbonell-Caballero J, Dopazo J ( 2018 ) . Gene expression integration into pathway modules reveals a pan-cancer metabolic landscape . Cancer Research vol. 78 , ( 21 )

Fourati S, Talla A, Mahmoudian M, Burkhart JG, Klén R, Henao R, Yu T, Aydın Z et al. ( 2018 ) . A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection . Nature Communications vol. 9 , ( 1 )

Hidalgo MR, Amadoz A, Çubuk C, Carbonell-Caballero J, Dopazo J ( 2018 ) . Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome . Biology Direct vol. 13 , ( 1 )

Amadoz A, Hidalgo MR, Çubuk C, Carbonell-Caballero J, Dopazo J ( 2018 ) . A comparison of mechanistic signaling pathway activity analysis methods . Brief Bioinform

Ferreira PG, Muñoz-Aguirre M, Reverter F, Sá Godinho CP, Sousa A, Amadoz A, Sodaei R, Hidalgo MR et al. ( 2018 ) . The effects of death and post-mortem cold ischemia on human tissue transcriptomes . Nature Communications vol. 9 , ( 1 )

Carbonell-Caballero J, Amadoz A, Alonso R, Hidalgo MR, Çubuk C, Conesa D, López-Quílez A, Dopazo J ( 2017 ) . Reference genome assessment from a population scale perspective: an accurate profile of variability and noise . Bioinformatics vol. 33 , ( 22 ) 3511 - 3517 .

Hidalgo MR, Cubuk C, Amadoz A, Salavert F, Carbonell-Caballero J, Dopazo J ( 2016 ) . High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes . Oncotarget vol. 5 , ( 0 ) 5160 - 5178 .

Salavert F, Hidago MR, Amadoz A, Çubuk C, Medina I, Crespo D, Carbonell-Caballero J, Dopazo J ( 2016 ) . Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models . Nucleic Acids Research vol. 44 , ( W1 ) w212 - w216 .

Sanghez V, Cubuk C, Sebastián-Leon P, Carobbio S, Dopazo J, Vidal-Puig A, Bartolomucci A ( 2016 ) . Chronic subordination stress selectively downregulates the insulin signaling pathway in liver and skeletal muscle but not in adipose tissue of male mice . Stress vol. 19 , ( 2 ) 214 - 224 .

Ergin K, Bozkurt G, Çubuk C, Aktaş S ( 2015 ) . Effect of Resveratrol on microRNA Profile and Apoptosis in HL-60 Leukemia and Raji Lymphoma Cells . Meandros Medical And Dental Journal vol. 16 , ( 3 ) 83 - 90 .

Razzoli M, Frontini A, Gurney A, Mondini E, Cubuk C, Katz LS, Cero C, Bolan PJ et al. ( 2015 ) . Stress-induced activation of brown adipose tissue prevents obesity in conditions of low adaptive thermogenesis . Molecular Metabolism vol. 5 , ( 1 ) 19 - 33 .

Alonso R, Salavert F, Garcia-Garcia F, Carbonell-Caballero J, Bleda M, Garcia-Alonso L, Sanchis-Juan A, Perez-Gil D et al. ( 2015 ) . Babelomics 5.0: functional interpretation for new generations of genomic data . Nucleic Acids Research vol. 43 , ( W1 ) w117 - w121 .

Diniz G, Aktas S, Cubuk C, Ortac R, Vergin C, Olgun N ( 2013 ) . Tissue Expression of MLH1, PMS2, MSH2, and MSH6 Proteins and Prognostic Value of Microsatellite Instability in Wilms Tumor: Experience of 45 Cases . Pediatric Hematology and Oncology vol. 30 , ( 4 ) 273 - 284 .

Ince D, Aktas S, Altun ZS, Cubuk C, Olgun N ( 2011 ) . EFFECT OF PHYTOCHEMICALS ON NEUROBLASTOMA AND METASTATIC POTENTIAL . PEDIATRIC BLOOD & CANCER . vol. 57 , 781 - 781 .

Diniz G, Aktas S, Cubuk C, Ortac R, Vergin C, Olgun N ( 2011 ) . MICROSATELLITE INSTABILITY IN WILMS TUMOR . PEDIATRIC BLOOD & CANCER . vol. 57 , 783 - 783 .

Aktas S, Ercetin P, Altun Z, Cubuk C, Olgun N ( 2011 ) . TUMOR METASTASIS GENES IN NEUROBLASTOMA STEM CELLS . PEDIATRIC BLOOD & CANCER . vol. 57 , 782 - 783 .