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Research
  1. Queen Mary University of London
  2. Research
  3. Publications

Publications: Mr Cankut Cubuk

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Schmidt M, Sondermann JR, Gomez-Varela D, Çubuk C, Millet Q, Lewis MJ, Wood JN, Zhao J ( 2022 ) . Transcriptomic and proteomic profiling of Na<inf>V</inf>1.8-expressing mouse nociceptors . Frontiers in Molecular Neuroscience vol. 15 ,
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 .
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 , ( Suppl 1 ) 296.1 - 29296 .
Loong L, Cubuk C, Choi S, Allen S, Torr B, Garrett A, Loveday C, Durkie M et al. ( 2022 ) . 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 .
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 )
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 )
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 )
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 , ( Suppl 1 ) 7.2 - 7.7 .
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 .
Garrett A, Durkie M, Callaway A, Burghel GJ, Robinson R, Drummond J, Torr B, Cubuk C et al. ( 2021 ) . 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 .
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 .
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 )
Rian K, Esteban-Medina M, Hidalgo M, Çubuk C, Falco M, Loucera C, Gunyel D, Ostaszewski M et al. ( 2020 ) . Mechanistic modeling of the SARS-CoV-2 disease map .
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 )
Petkevicius K, Virtue S, Bidault G, Jenkins B, Cubuk C, Morgantini C, Aouadi M, Dopazo J et al. ( 2019 ) . Accelerated phosphatidylcholine turnover in macrophages promotes adipose tissue inflammation in obesity . eLife vol. 8 ,
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 .
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 )
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 )
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 ) 6059 - 6072 .
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
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 ( 2017 ) . High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes . Oncotarget vol. 8 , ( 3 ) 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 , ( 1 ) 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 .
Razzoli M, Frontini A, Gurney A, Mondini E, Cubuk C, Katz LS, Cero C, Bolan PJ et al. ( 2016 ) . Stress-induced activation of brown adipose tissue prevents obesity in conditions of low adaptive thermogenesis . Molecular Metabolism vol. 5 , ( 1 ) 19 - 33 .
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 .
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 .
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