176 results on '"Tsoka S"'
Search Results
2. Novel drug-target interactions via link prediction and network embedding
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Amiri Souri, E., Laddach, R., Karagiannis, S. N., Papageorgiou, L. G., and Tsoka, S.
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- 2022
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3. Cancer Grade Model: a multi-gene machine learning-based risk classification for improving prognosis in breast cancer
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Amiri Souri, E., Chenoweth, A., Cheung, A., Karagiannis, S. N., and Tsoka, S.
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- 2021
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4. Analyzing the ENVI-met microclimate model’s performance and assessing cool materials and urban vegetation applications–A review
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Tsoka, S., Tsikaloudaki, A., and Theodosiou, T.
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- 2018
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5. Modeling the performance of cool pavements and the effect of their aging on outdoor surface and air temperatures
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Tsoka, S., Theodosiou, T., Tsikaloudaki, K., and Flourentzou, F.
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- 2018
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6. TIGIT blockade repolarizes AML-associated TIGIT(+) M2 macrophages to an M1 phenotype and increases CD47-mediated phagocytosis
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Brauneck, F., Fischer, B., Witt, M., Muschhammer, J., Oelrich, J., da Costa Avelar, P.H., Tsoka, S., Bullinger, L., Seubert, E., Smit, D.J., Bokemeyer, C., Ackermann, C., Wellbrock, J., Haag, F., and Fiedler, W.
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Cancer Research - Abstract
BACKGROUND: Leukemia-associated macrophages (LAMs) represent an important cell population within the tumor microenvironment, but little is known about the phenotype, function, and plasticity of these cells. The present study provides an extensive characterization of macrophages in patients with acute myeloid leukemia (AML). METHODS: The phenotype and expression of coregulatory markers were assessed on bone marrow (BM)-derived LAM populations, using multiparametric flow cytometry. BM and blood aspirates were obtained from patients with newly diagnosed acute myeloid leukemia (pAML, n=59), patients in long-term remission (lrAML, n=8), patients with relapsed acute myeloid leukemia (rAML, n=7) and monocyte-derived macrophages of the blood from healthy donors (HD, n=17). LAM subpopulations were correlated with clinical parameters. Using a blocking anti-T-cell immunoreceptor with Ig and ITIM domains (TIGIT) antibody or mouse IgG2a isotype control, we investigated polarization, secretion of cytokines, and phagocytosis on LAMs and healthy monocyte-derived macrophages in vitro. RESULTS: In pAML and rAML, M1 LAMs were reduced and the predominant macrophage population consisted of immunosuppressive M2 LAMs defined by expression of CD163, CD204, CD206, and CD86. M2 LAMs in active AML highly expressed inhibitory receptors such as TIGIT, T-cell immunoglobulin and mucin-domain containing-3 protein (TIM-3), and lymphocyte-activation gene 3 (LAG-3). High expression of CD163 was associated with a poor overall survival (OS). In addition, increased frequencies of TIGIT(+) M2 LAMs were associated with an intermediate or adverse risk according to the European Leukemia Network criteria and the FLT3 ITD mutation. In vitro blockade of TIGIT shifted the polarization of primary LAMs or peripheral blood-derived M2 macrophages toward the M1 phenotype and increased secretion of M1-associated cytokines and chemokines. Moreover, the blockade of TIGIT augmented the anti-CD47-mediated phagocytosis of AML cell lines and primary AML cells. CONCLUSION: Our findings suggest that immunosuppressive TIGIT(+) M2 LAMs can be redirected into an efficient effector population that may be of direct clinical relevance in the near future.
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- 2022
7. Influence of FLG loss-of-function mutations in host-microbe interactions during atopic skin inflammation
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Oláh, P., Szlávicz, E., Kuchner, M., Nemmer, J., Zeeuwen, P.L.J.M., Lefèvre-Utile, A., Fyhrquist, N., Prast-Nielsen, S., Skoog, T., Serra, A., Rodríguez, E., Raap, U., Meller, S., Gyulai, R., Hupé, P., Kere, J., Levi-Schaffer, F., Tsoka, S., Alexander, H., Nestle, F.O., Schröder, J.M., Weidinger, S., Bogaard, E. van den, Soumelis, V., Greco, D., Barker, J., Lauerma, A., Ranki, A., Andersson, B., Alenius, H., Homey, B., Oláh, P., Szlávicz, E., Kuchner, M., Nemmer, J., Zeeuwen, P.L.J.M., Lefèvre-Utile, A., Fyhrquist, N., Prast-Nielsen, S., Skoog, T., Serra, A., Rodríguez, E., Raap, U., Meller, S., Gyulai, R., Hupé, P., Kere, J., Levi-Schaffer, F., Tsoka, S., Alexander, H., Nestle, F.O., Schröder, J.M., Weidinger, S., Bogaard, E. van den, Soumelis, V., Greco, D., Barker, J., Lauerma, A., Ranki, A., Andersson, B., Alenius, H., and Homey, B.
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Item does not contain fulltext, BACKGROUND: Loss-of-function mutations in the filaggrin (FLG) gene directly alter skin barrier function and critically influence atopic inflammation. While skin barrier dysfunction, Th2-associated inflammation and bacterial dysbiosis are well-known characteristics of atopic dermatitis (AD), the mechanisms interconnecting genotype, transcriptome and microbiome remain largely elusive. OBJECTIVE: In-depth analysis of FLG genotype-associated skin gene expression alterations and host-microbe interactions in AD. METHODS: Multi-omics characterization of a cohort of AD patients carrying heterozygous loss-of-function mutations in the FLG gene (AD(Mut)) (n = 15), along with matched wild-type (AD(Wt)) patients and healthy controls. Detailed clinical characterization, microarray gene expression and 16 S rRNA-based microbial marker gene data were generated and analyzed. RESULTS: In the context of filaggrin dysfunction, the transcriptome was characterized by dysregulation of barrier function and water homeostasis, while the lesional skin of AD(Wt) demonstrated the specific upregulation of pro-inflammatory cytokines and T-cell proliferation. S. aureus dominated the microbiome in both patient groups, however, shifting microbial communities could be observed when comparing healthy with non-lesional AD(Wt) or AD(Mut) skin, offering the opportunity to identify microbe-associated transcriptomic signatures. Moreover, an AD core signature with 28 genes, including CCL13, CCL18, BTC, SCIN, RAB31 and PCLO was identified. CONCLUSIONS: Our integrative approach provides molecular insights for the concept that FLG loss-of-function mutations are a genetic shortcut to atopic inflammation and unravels the complex interplay between genotype, transcriptome and microbiome in the human holobiont.
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- 2022
8. Climate change impacts on heating and cooling energy demand in residential building units. Application in the city of Thessaloniki, Greece.
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Tsoka, S and Velikou, K
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- 2023
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9. Additional file 6 of Novel drug-target interactions via link prediction and network embedding
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Amiri Souri, E., Laddach, R., Karagiannis, S. N., Papageorgiou, L. G., and Tsoka, S.
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Quantitative Biology::Subcellular Processes ,Quantitative Biology::Biomolecules ,Computer Science::Computer Vision and Pattern Recognition ,Quantitative Biology::Molecular Networks - Abstract
Additional file 6: Figure S4. PCA plots. PCA of embedded vectors of proteins coloured according to protein type.
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- 2022
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10. Additional file 8 of Novel drug-target interactions via link prediction and network embedding
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Amiri Souri, E., Laddach, R., Karagiannis, S. N., Papageorgiou, L. G., and Tsoka, S.
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fungi - Abstract
Additional file 8: Figure S6. DTIs through docking. Molecular docking performed via SwissDock for novel predicted DTIs. (a) deltaG for the first 10 groups of molecules clustered by conformers similarity. (b) Binding locations with the lowest deltaG and all groups of conformers.
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- 2022
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11. Additional file 5 of Novel drug-target interactions via link prediction and network embedding
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Amiri Souri, E., Laddach, R., Karagiannis, S. N., Papageorgiou, L. G., and Tsoka, S.
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Additional file 5: Figure S3. Networks of drug and protein similarities. Topological representation of the DDS and PPS networks and PCA of drugs and targets based on embedded vectors.
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- 2022
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12. Additional file 1 of Novel drug-target interactions via link prediction and network embedding
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Amiri Souri, E., Laddach, R., Karagiannis, S. N., Papageorgiou, L. G., and Tsoka, S.
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Additional file 1: Related work. Related methods from literature. Summary of different embedding and similarity based methods for DTI prediction.
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- 2022
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13. Additional file 4 of Novel drug-target interactions via link prediction and network embedding
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Amiri Souri, E., Laddach, R., Karagiannis, S. N., Papageorgiou, L. G., and Tsoka, S.
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Additional file 4: Figure S2. Datasets and data splitting. Details of data types and data splitting in cross-validation.
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- 2022
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14. Additional file 3 of Novel drug-target interactions via link prediction and network embedding
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Amiri Souri, E., Laddach, R., Karagiannis, S. N., Papageorgiou, L. G., and Tsoka, S.
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Additional file 3: Figure S1. Data collection procedure. (a) Workflow to collect data from the ChEMBL database, (b) Scatter plot of the pChEMBL value of collected DTIs on a boxplot.
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- 2022
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15. Additional file 9 of Novel drug-target interactions via link prediction and network embedding
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Amiri Souri, E., Laddach, R., Karagiannis, S. N., Papageorgiou, L. G., and Tsoka, S.
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Additional file 9: Figure S7. Drug similarity heatmaps. Drug-drug similarity for drugs predicted to interact with (a) ADAM17 and (b) MMP14.
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- 2022
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16. Additional file 7 of Novel drug-target interactions via link prediction and network embedding
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Amiri Souri, E., Laddach, R., Karagiannis, S. N., Papageorgiou, L. G., and Tsoka, S.
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Additional file 7: Figure S5. ROC plots over the ten-fold five times cross-validation.
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- 2022
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17. Additional file 2 of Novel drug-target interactions via link prediction and network embedding
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Amiri Souri, E., Laddach, R., Karagiannis, S. N., Papageorgiou, L. G., and Tsoka, S.
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ComputingMethodologies_PATTERNRECOGNITION ,Data_MISCELLANEOUS - Abstract
Additional file 2: Datasets. Details about datasets used in this study are provided.
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- 2022
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18. Climate change and built environment - the role of urban greenery as a mitigation strategy in Greek urban areas
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Apostolopoulou, D, primary and Tsoka, S, additional
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- 2021
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19. Investigating the effect of summer night ventilation on the urban buildings’ thermal and energy performance using numerical approaches
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Tsoka, S, primary
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- 2021
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20. Finding community structures in complex networks using mixed integer optimisation
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Xu, G., Tsoka, S., and Papageorgiou, L. G.
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- 2007
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21. An immunologically relevant rodent model demonstrates safety of therapy using a tumour‐specific IgE
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Josephs, D. H., Nakamura, M., Bax, H. J., Dodev, T. S., Muirhead, G., Saul, L., Karagiannis, P., Ilieva, K. M., Crescioli, S., Gazinska, P., Woodman, N., Lombardelli, C., Kareemaghay, S., Selkirk, C., Lentfer, H., Barton, C., Canevari, S., Figini, M., Downes, N., Dombrowicz, D., Corrigan, C. J., Nestle, F. O., Jones, P. S., Gould, H. J., Blower, P. J., Tsoka, S., Spicer, J. F., and Karagiannis, S. N.
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AllergoOncology ,Receptors, IgE ,Tumor Necrosis Factor-alpha ,Immunoglobulin E ,Statistics, Nonparametric ,Rats ,Antibodies, Monoclonal, Murine-Derived ,Mice ,Treatment Outcome ,Experimental Allergy and Immunology ,Cell Line, Tumor ,Immunoglobulin G ,Neoplasms ,Models, Animal ,cancer ,Animals ,Humans ,Original Article ,rat ,Folate Receptor 1 ,IgE ,Immunotherapy ,ORIGINAL ARTICLES ,Protein Binding - Abstract
Background Designing biologically informative models for assessing the safety of novel agents, especially for cancer immunotherapy, carries substantial challenges. The choice of an in vivo system for studies on IgE antibodies represents a major impediment to their clinical translation, especially with respect to class‐specific immunological functions and safety. Fcε receptor expression and structure are different in humans and mice, so that the murine system is not informative when studying human IgE biology. By contrast, FcεRI expression and cellular distribution in rats mirror that of humans. Methods We are developing MOv18 IgE, a human chimeric antibody recognizing the tumour‐associated antigen folate receptor alpha. We created an immunologically congruent surrogate rat model likely to recapitulate human IgE‐FcεR interactions and engineered a surrogate rat IgE equivalent to MOv18. Employing this model, we examined in vivo safety and efficacy of antitumour IgE antibodies. Results In immunocompetent rats, rodent IgE restricted growth of syngeneic tumours in the absence of clinical, histopathological or metabolic signs associated with obvious toxicity. No physiological or immunological evidence of a “cytokine storm” or allergic response was seen, even at 50 mg/kg weekly doses. IgE treatment was associated with elevated serum concentrations of TNFα, a mediator previously linked with IgE‐mediated antitumour and antiparasitic functions, alongside evidence of substantially elevated tumoural immune cell infiltration and immunological pathway activation in tumour‐bearing lungs. Conclusion Our findings indicate safety of MOv18 IgE, in conjunction with efficacy and immune activation, supporting the translation of this therapeutic approach to the clinical arena.
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- 2018
22. IgE antibodies targeting a major melanoma antigen are more effective than IgG antibodies for tumour protection in a humanized melanoma model: o-14
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Karagiannis, P., Gilbert, A. E., Dodev, T., Josephs, D. H., Ali, N., Dafou, D., Ainali, C., Koers, A., Saul, L., Tsoka, S., Spicer, J., Gould, H. J., Beavil, A., Nestle, F. O., and Karagiannis, S. N.
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- 2012
23. Advancing sustainability in prefabricated buildings
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Tsikaloudaki, K G, primary, Theodosiou, T G, additional, Giarma, C S, additional, Kontoleon, K J, additional, Aravantinos, D G, additional, Tsoka, S P, additional, Tsirigoti, D C, additional, Chastas, P D, additional, and Karaoulis, A C, additional
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- 2020
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24. Building a new sustainable preconstructed building element
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Tsikaloudaki, K., primary, Theodosiou, T., additional, Giarma, C., additional, Kontoleon, K., additional, Aravantinos, D., additional, Tsoka, S., additional, Tsirigoti, D., additional, Karaoulis, A., additional, and Chastas, P., additional
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- 2020
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25. Assessing the effect of the urban morphology on the ambient air temperature of urban street canyons under different meteorological conditions. Application in residential areas of Thessaloniki, Greece
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Tsoka, S, primary, Tsikaloudaki, K, additional, Theodosiou, T, additional, and Bikas, D, additional
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- 2020
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26. Changes in serum somatostatin level and its association with calcium metabolism indicators in patients with gastroesophageal reflux disease and spinal injuries of degenerative-dystrophic and inflammatory genesis.
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Szircsak, Ye. S., Tsoka, S. A., and Filak, Ya. F.
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SERUM ,SOMATOSTATIN ,CALCIUM metabolism ,GASTROESOPHAGEAL reflux ,INFLAMMATION - Abstract
Background. The study of clinical features, factors and levels of various biologically active substances that may play an important role in the pathogenetic mechanism of gastroesophageal reflux disease (GERD) in combination with degenerative-dystrophic or inflammatory lesions of the spine, is an extremely important problem of the modern medical community. The purpose of the research is to determine the peculiarities of changes in the level of serum somatostatin (SST) and its relationship with calcium metabolism in patients with GERD and spine lesions of degenerative-dystrophic and inflammatory genesis. Materials and methods. 84 patients with spinal lesions of degenerative-dystrophic or inflammatory genesis in combination with GERD were examined. The examined patients with GERD were divided into two groups depending on the form of spine injury. Group I included 44 patients with osteochondrosis (OS) of the cervical and thoracic spine (SpA). Group II consisted of 40 patients with spinal arthritis. Results. There was a significant increase in the level of serum SST in both groups of the studied patients with GERD and spine injury of degenerative-dystrophic or inflammatory origin. At the same time, a more pronounced deviation from the norm was detected in group II of patients (increase up to (0.756 ± 0.027) pg/ml, p < 0.01). Determination of level 25(OH)D in serum indicates vitamin D3 deficiency in patients with GERD and OS (decrease to (23.35 ± 0.71) ng/ml, p < 0.05) and its deficiency in patients with SpA (decrease to (18.66 ± 0.52) ng/ml, p < 0.01). Serum 25(OH)D levels also decreased more markedly in the atypical clinical course of GERD in the examined patients. Conclusions. In patients with GERD with degenerative-dystrophic and inflammatory lesions of the spine, an increase in the level of serum SST was found with the most pronounced deviation from the norm in atypical manifestation of GERD. A correlation between SST and a decrease in the level of 25(OH)D and Ca
++ , mainly in patients with atypical clinical course of GERD, was established. [ABSTRACT FROM AUTHOR]- Published
- 2022
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27. Microbe-host interplay in atopic dermatitis and psoriasis
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Fyhrquist, N., Muirhead, G., Prast-Nielsen, S., Jeanmougin, M., Olah, P., Skoog, T., Jules-Clement, G., Feld, M., Barrientos-Somarribas, M., Sinkko, H., Bogaard, E.H.J. van den, Zeeuwen, P.L.J.M., Rikken, G., Schalkwijk, J., Niehues, H., Daubener, W., Eller, S.K., Alexander, H., Pennino, D., Suomela, S., Tessas, I., Lybeck, E., Baran, A.M., Darban, H., Gangwar, R.S., Gerstel, U., Jahn, K., Karisola, P., Yan, L., Hansmann, B., Katayama, S., Meller, S., Bylesjo, M., Hupe, P., Levi-Schaffer, F., Greco, D., Ranki, A., Schroder, J.M., Barker, J., Kere, J., Tsoka, S., Lauerma, A., Soumelis, V., Nestle, F.O., Homey, B., Andersson, B., Alenius, H., Fyhrquist, N., Muirhead, G., Prast-Nielsen, S., Jeanmougin, M., Olah, P., Skoog, T., Jules-Clement, G., Feld, M., Barrientos-Somarribas, M., Sinkko, H., Bogaard, E.H.J. van den, Zeeuwen, P.L.J.M., Rikken, G., Schalkwijk, J., Niehues, H., Daubener, W., Eller, S.K., Alexander, H., Pennino, D., Suomela, S., Tessas, I., Lybeck, E., Baran, A.M., Darban, H., Gangwar, R.S., Gerstel, U., Jahn, K., Karisola, P., Yan, L., Hansmann, B., Katayama, S., Meller, S., Bylesjo, M., Hupe, P., Levi-Schaffer, F., Greco, D., Ranki, A., Schroder, J.M., Barker, J., Kere, J., Tsoka, S., Lauerma, A., Soumelis, V., Nestle, F.O., Homey, B., Andersson, B., and Alenius, H.
- Abstract
Contains fulltext : 215275.pdf (publisher's version ) (Open Access), Despite recent advances in understanding microbial diversity in skin homeostasis, the relevance of microbial dysbiosis in inflammatory disease is poorly understood. Here we perform a comparative analysis of skin microbial communities coupled to global patterns of cutaneous gene expression in patients with atopic dermatitis or psoriasis. The skin microbiota is analysed by 16S amplicon or whole genome sequencing and the skin transcriptome by microarrays, followed by integration of the data layers. We find that atopic dermatitis and psoriasis can be classified by distinct microbes, which differ from healthy volunteers microbiome composition. Atopic dermatitis is dominated by a single microbe (Staphylococcus aureus), and associated with a disease relevant host transcriptomic signature enriched for skin barrier function, tryptophan metabolism and immune activation. In contrast, psoriasis is characterized by co-occurring communities of microbes with weak associations with disease related gene expression. Our work provides a basis for biomarker discovery and targeted therapies in skin dysbiosis.
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- 2019
28. New genetic loci link adipose and insulin biology to body fat distribution
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Shungin, D, Winkler, T, Croteau Chonka, D, Ferreira, T, Locke, A, Mägi, R, Strawbridge, R, Pers, T, Fischer, K, Justice, A, Workalemahu, T, Wu, J, Buchkovich, M, Heard Costa, N, Roman, T, Drong, A, Song, C, Gustafsson, S, Day, F, Esko, T, Fall, T, Kutalik, Z, Luan, J, Randall, J, Scherag, A, Vedantam, S, Wood, A, Chen, J, Fehrmann, R, Karjalainen, J, Kahali, B, Liu, C, Schmidt, E, Absher, D, Amin, N, Anderson, D, Beekman, M, Bragg Gresham, J, Buyske, S, Demirkan, A, Ehret, G, Feitosa, M, Goel, A, Jackson, A, Johnson, T, Kleber, M, Kristiansson, K, Mangino, M, Leach, I, Medina Gomez, C, Palmer, C, Pasko, D, Pechlivanis, S, Peters, M, Prokopenko, I, Stanca'Kova', A, Sung, Y, Tanaka, T, Teumer, A, Van Vliet Ostaptchouk, J, Yengo, L, Zhang, W, Albrecht, E, Ärnlöv, J, Arscott, G, Bandinelli, S, Barrett, A, Bellis, C, Bennett, A, Berne, C, Blüher, M, Böhringer, S, Bonnet, F, Böttcher, Y, Bruinenberg, M, Carba, D, Caspersen, I, Clarke, R, Daw, E, Deelen, J, Deelman, E, Delgado, G, Doney, A, Eklund, N, Erdos, M, Estrada, K, Eury, E, Friedrich, N, Garcia, M, Giedraitis, V, Gigante, B, Go, A, Golay, A, Grallert, H, Grammer, T, Gräsler, J, Grewal, J, Groves, C, Haller, T, Hallmans, G, Hartman, C, Hassinen, M, Hayward, C, Heikkilä, K, Herzig, K, Helmer, Q, Hillege, H, Holmen, O, Hunt, S, Isaacs, A, Ittermann, T, James, A, Johansson, I, Juliusdottir, T, Kalafati, I, Kinnunen, L, Koenig, W, Kooner, I, Kratzer, W, Lamina, C, Leander, K, Lee, N, Lichtner, P, Lind, L, Lindström, J, Lobbens, S, Lorentzon, M, Mach, F, Magnusson, P, Mahajan, A, Mcardle, W, Menni, C, Merger, S, Mihailov, E, Milani, L, Mills, R, Moayyeri, A, Monda, K, Mooijaart, S, Mühleisen, T, Mulas, A, Müller, G, Müller Nurasyid, M, Nagaraja, R, Nalls, M, Narisu, N, Glorioso, N, Nolte, I, Olden, M, Rayner, N, Renstrom, F, Ried, J, Robertson, N, Rose, L, Sanna, S, Scharnagl, H, Scholtens, S, Sennblad, B, Seufferlein, T, Sitlani, C, Smith, A, Stirrups, K, Stringham, H, Sundström, J, Swertz, M, Swift, A, Syvänen, A, Tayo, B, Thorand, B, Thorleifsson, G, Tomaschitz, A, Troffa, C, Van Oort, F, Verweij, N, Vonk, J, Waite, L, Wennauer, R, Wilsgaard, T, Wojczynski, M, Wong, A, Zhang, Q, Zhao, J, Brennan, E, Choi, M, Eriksson, P, Folkersen, L, Franco Cereceda, A, Gharavi, A, Hedman, A, Hivert, M, Huang, J, Kanoni, S, Karpe, F, Keildson, S, Kiryluk, K, Liang, L, Lifton, R, Ma, B, Mcknight, A, Mcpherson, R, Metspalu, A, Min, J, Moffatt, M, Montgomery, G, Murabito, J, Nicholson, G, Nyholt, D, Olsson, C, Perry, J, Reinmaa, E, Salem, R, Sandholm, N, Schadt, E, Scott, R, Stolk, L, Vallejo, E, Westra, H, Zondervan, K, Amouyel, P, Arveiler, D, Bakker, S, Beilby, J, Bergman, R, Blangero, J, Brown, M, Burnier, M, Campbell, H, Chakravarti, A, Chines, P, Claudi Boehm, S, Collins, F, Crawford, D, Danesh, J, De Faire, U, De Geus, E, Dörr, M, Erbel, R, Eriksson, J, Farrall, M, Ferrannini, E, Ferrières, J, Forouhi, N, Forrester, T, Franco, O, Gansevoort, R, Gieger, C, Gudnason, V, Haiman, C, Harris, T, Hattersley, A, Heliövaara, M, Hicks, A, Hingorani, A, Hoffmann, W, Hofman, A, Homuth, G, Humphries, S, Hyppönen, E, Illig, T, Jarvelin, M, Johansen, B, Jousilahti, P, Jula, A, Kaprio, J, Kee, F, Keinanen Kiukaanniemi, S, Kooner, J, Kooperberg, C, Kovacs, P, Kraja, A, Kumari, M, Kuulasmaa, K, Kuusisto, J, Lakka, T, Langenberg, C, Le Marchand, L, Lehtimäki, T, Lyssenko, V, Männistö, S, Marette, A, Matise, T, Mckenzie, C, Mcknight, B, Musk, A, Möhlenkamp, S, Morris, A, Nelis, M, Ohlsson, C, Oldehinkel, A, Ong, K, Palmer, L, Penninx, B, Peters, A, Pramstaller, P, Raitakari, O, Rankinen, T, Rao, D, Rice, T, Ridker, P, Ritchie, M, Rudan, I, Salomaa, V, Samani, N, Saramies, J, Sarzynski, M, Schwarz, P, Shuldiner, A, Staessen, J, Steinthorsdottir, V, Stolk, R, Strauch, K, Tönjes, A, Tremblay, A, Tremoli, E, Vohl, M, Völker, U, Vollenweider, P, Wilson, J, Witteman, J, Adair, L, Bochud, M, Boehm, B, Bornstein, S, Bouchard, C, Cauchi, S, Caulfield, M, Chambers, J, Chasman, D, Cooper, R, Dedoussis, G, Ferrucci, L, Froguel, P, Grabe, H, Hamsten, A, Hui, J, Hveem, K, Jöckel, K, Kivimaki, M, Kuh, D, Laakso, M, Liu, Y, März, W, Munroe, P, Njolstad, I, Oostra, B, Pedersen, N, Perola, M, Pe'Russe, L, Peters, U, Power, C, Quertermous, T, Rauramaa, R, Rivadeneira, F, Saaristo, T, Saleheen, D, Sinisalo, J, Slagboom, P, Snieder, H, Spector, T, Thorsteinsdottir, U, Stumvoll, M, Tuomilehto, J, Uitterlinden, A, Uusitupa, M, Van Der Harst, P, Veronesi, G, Walker, M, Wareham, N, Watkins, H, Wichmann, H, Abecasis, G, Assimes, T, Berndt, S, Boehnke, M, Borecki, I, Deloukas, P, Franke, L, Frayling, T, Groop, L, Hunter, D, Kaplan, R, O'Connell, J, Qi, L, Schlessinger, D, Strachan, D, Stefansson, K, Van Duijn, C, Willer, C, Visscher, P, Yang, J, Hirschhorn, J, Zillikens, M, Mccarthy, M, Speliotes, E, North, K, Fox, C, Barroso, I, Franks, P, Ingelsson, E, Heid, I, Loos, R, Cupples, L, Lindgren, C, Mohlke, K, Dastani, Z, Timpson, N, Yuan, X, Henneman, P, Kizer, J, Lyytikainen, L, Fuchsberger, C, Small, K, Coassin, 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- Abstract
Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, we conducted genome-wide association meta-analyses of waist and hip circumference-related traits in up to 224,459 individuals. We identified 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (WHRadjBMI) and an additional 19 loci newly associated with related waist and hip circumference measures (P<5×10-8). Twenty of the 49 WHRadjBMI loci showed significant sexual dimorphism, 19 of which displayed a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation, and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms.
- Published
- 2015
29. Genetic studies of body mass index yield new insights for obesity biology
- Author
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- Abstract
Obesity is heritable and predisposes to many diseases. To understand the genetic basis of obesity better, here we conduct a genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals. This analysis identifies 97 BMI-associated loci (P < 5 × 10-8), 56 of which are novel. Five loci demonstrate clear evidence of several independent association signals, and many loci have significant effects on other metabolic phenotypes. The 97 loci account for ∼2.7% of BMI variation, and genome-wide estimates suggest that common variation accounts for >20 % of BMI variation. Pathway analyses provide strong support for a role of the central nervous system in obesity susceptibility and implicate new genes and pathways, including those related to synaptic function, glutamate signalling, insulin secretion/action, energy metabolism, lipid biology and adipogenesis.
- Published
- 2015
30. A method to account for the urban microclimate on the creation of ‘typical weather year’ datasets for building energy simulation, using stochastically generated data
- Author
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Tsoka, S., primary, Tolika, K., additional, Theodosiou, T., additional, Tsikaloudaki, K., additional, and Bikas, D., additional
- Published
- 2018
- Full Text
- View/download PDF
31. Ventilated Facades: Requirements and Specifications Across Europe
- Author
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Bikas, D., primary, Tsikaloudaki, K., additional, Kontoleon, K.J., additional, Giarma, C., additional, Tsoka, S., additional, and Tsirigoti, D., additional
- Published
- 2017
- Full Text
- View/download PDF
32. Meta-Analysis of Genome-Wide Association Studies in African Americans Provides Insights into the Genetic Architecture of Type 2 Diabetes
- Author
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Ng, MCY, Shriner, D, Chen, BH, Li, J, Chen, WM, Guo, X, Liu, J, Bielinski, SJ, Yanek, LR, Nalls, MA, Comeau, ME, Rasmussen-Torvik, LJ, Jensen, RA, Evans, DS, Sun, YV, An, P, Patel, SR, Lu, Y, Long, J, Armstrong, LL, Wagenknecht, L, Yang, L, Snively, BM, Palmer, ND, Mudgal, P, Langefeld, CD, Keene, KL, Freedman, BI, Mychaleckyj, JC, Nayak, U, Raffel, LJ, Goodarzi, MO, Chen, YDI, Taylor, HA, Correa, A, Sims, M, Couper, DJ, Pankow, JS, Boerwinkle, E, Adeyemo, A, Doumatey, A, Chen, G, Mathias, RA, Vaidya, D, Singleton, AB, Zonderman, AB, Igo, RP, Sedor, JR, Zondervan, KT, Kabagambe, EK, Siscovick, DS, McKnight, B, Rice, K, Liu, Y, Hsueh, WC, Zhao, W, Bielak, LF, Kraja, A, Province, MA, Bottinger, EP, Gottesman, O, Cai, Q, Zheng, W, Blot, WJ, Lowe, WL, Pacheco, JA, Crawford, DC, Yang, TP, Wilk, A, Grundberg, E, Tsoka, S, Rich, SS, Hayes, MG, Shu, XO, and Loos, RJF
- Subjects
endocrine system diseases - Abstract
© 2014. Type 2 diabetes (T2D) is more prevalent in African Americans than in Europeans. However, little is known about the genetic risk in African Americans despite the recent identification of more than 70 T2D loci primarily by genome-wide association studies (GWAS) in individuals of European ancestry. In order to investigate the genetic architecture of T2D in African Americans, the MEta-analysis of type 2 DIabetes in African Americans (MEDIA) Consortium examined 17 GWAS on T2D comprising 8,284 cases and 15,543 controls in African Americans in stage 1 analysis. Single nucleotide polymorphisms (SNPs) association analysis was conducted in each study under the additive model after adjustment for age, sex, study site, and principal components. Meta-analysis of approximately 2.6 million genotyped and imputed SNPs in all studies was conducted using an inverse variance-weighted fixed effect model. Replications were performed to follow up 21 loci in up to 6,061 cases and 5,483 controls in African Americans, and 8,130 cases and 38,987 controls of European ancestry. We identified three known loci (TCF7L2, HMGA2 and KCNQ1) and two novel loci (HLA-B and INS-IGF2) at genome-wide significance (4.15×10−94
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- 2014
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33. New genetic loci link adipose and insulin biology to body fat distribution.
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ADIPOGen Consortium, CARDIOGRAMplusC4D Consortium, CKDGen Consortium, GEFOS Consortium, GENIE Consortium, International Endogene Consortium, LifeLines Cohort Study, MAGIC Investigators, MuTHER Consortium, PAGE Consortium, ReproGen Consortium, GLGC, ICBP, Dastani, Z., Hivert, MF., Timpson, N., Perry, JR., Yuan, X., Scott, RA., Henneman, P., Heid, IM., Kizer, JR., Lyytikainen, LP., Fuchsberger, C., Tanaka, T., Morris, AP., Small, K., Isaacs, A., Beekman, M., Coassin, S., Lohman, K., Qi, L., Kanoni, S., Pankow, JS., Uh, HW., Wu, Y., Bidulescu, A., Rasmussen-Torvik, LJ., Greenwood, CM., Ladouceur, M., Grimsby, J., Manning, AK., Liu, CT., Kooner, J., Mooser, VE., Vollenweider, P., Kapur, KA., Chambers, J., Wareham, NJ., Langenberg, C., Frants, R., Willemsvan-vanDijk, K., Oostra, BA., Willems, SM., Lamina, C., Winkler, T., Psaty, BM., Tracy, RP., Brody, J., Chen, I., Viikari, J., Kähönen, M., Pramstaller, PP., Evans, DM., St Pourcain, B., Sattar, N., Wood, A., Bandinelli, S., Carlson, OD., 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J.A., Steinthorsdottir, V., Stolk, R.P., Strauch, K., Tremblay, A., Vohl, M.C., Wilson, J.F., Witteman, J.C., Adair, L.S., Boehm, B.O., Bornstein, S.R., Bouchard, C., Cauchi, S., Caulfield, M.J., Chambers, J.C., Chasman, D.I., Cooper, R.S., Grabe, H.J., Jöckel, K.H., Munroe, P.B., Oostra, B.A., Palmer, C.N., Pedersen, N.L., Pérusse, L., Saaristo, T.E., Slagboom, P.E., Spector, T.D., Uitterlinden, A.G., Veronesi, G., Walker, M., Wareham, N.J., Wichmann, H.E., Abecasis, G.R., Assimes, T.L., Berndt, S.I., Borecki, I.B., Frayling, T.M., Groop, L.C., Hunter, D.J., Kaplan, R.C., O'Connell, J.R., Strachan, D.P., van Duijn, C.M., Willer, C.J., Visscher, P.M., Yang, J., Hirschhorn, J.N., Zillikens, M.C., McCarthy, M.I., Speliotes, E.K., North, K.E., Fox, C.S., Franks, P.W., Heid, I.M., Loos, R.J., Cupples, L.A., Morris, A.P., Lindgren, C.M., and Mohlke, K.L.
- Abstract
Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms.
- Published
- 2015
34. A systems model for immune cell interactions unravels the mechanism of inflammation in human skin
- Author
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Valeyev N., Hundhausen C., Umezawa Y., Kotov N., Williams G., Clop A., Ainali C., Ouzounis C., Tsoka S., and Nestle F.
- Abstract
Inflammation is characterized by altered cytokine levels produced by cell populations in a highly interdependent manner. To elucidate the mechanism of an inflammatory reaction, we have developed a mathematical model for immune cell interactions via the specific, dose-dependent cytokine production rates of cell populations. The model describes the criteria required for normal and pathological immune system responses and suggests that alterations in the cytokine production rates can lead to various stable levels which manifest themselves in different disease phenotypes. The model predicts that pairs of interacting immune cell populations can maintain homeostatic and elevated extracellular cytokine concentration levels, enabling them to operate as an immune system switch. The concept described here is developed in the context of psoriasis, an immune-mediated disease, but it can also offer mechanistic insights into other inflammatory pathologies as it explains how interactions between immune cell populations can lead to disease phenotypes. © 2010 Valeyev et al.
- Published
- 2010
35. Evaluation of annotation strategies using an entire genome sequence
- Author
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Iliopoulos, I. Tsoka, S. Andrade, M.A. Enright, A.J. Carroll, M. Poullet, P. Promponas, V. Liakopoulos, T. Palaios, G. Pasquier, C. Hamodrakas, S. Tamames, J. Yagnik, A.T. Tramontano, A. Devos, D. Blaschke, C. Valencia, A. Brett, D. Martin, D. Leroy, C. Rigoutsos, I. Sander, C. Ouzounis, C.A.
- Abstract
Motivation: Genome-wide functional annotation either by manual or automatic means has raised considerable concerns regarding the accuracy of assignments and the reproducibility of methodologies. In addition, a performance evaluation of automated systems that attempt to tackle sequence analyses rapidly and reproducibly is generally missing. In order to quantify the accuracy and reproducibility of function assignments on a genome-wide scale, we have re-annotated the entire genome sequence of Chlamydia trachomatis (serovar D), in a collaborative manner. Results: We have encoded all annotations in a structured format to allow further comparison and data exchange and have used a scale that records the different levels of potential annotation errors according to their propensity to propagate in the database due to transitive function assignments. We conclude that genome annotation may entail a considerable amount of errors, ranging from simple typographical errors to complex sequence analysis problems. The most surprising result of this comparative study is that automatic systems might perform as well as the teams of experts annotating genome sequences.
- Published
- 2003
36. A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
- Author
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DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium, Multiple Tissue Human Expression Resource (MUTHER) Consortium, Ahmadi, K.R., Ainali, C., Barrett, A., Bataille, V., Bell, J.T., Buil, A., Deloukas, P., Dermitzakis, E.T., Dimas, A.S., Durbin, R., Glass, D., Grundberg, E., Hassanali, N., Hedman, Å.K., Ingle, C., Knowles, D., Krestyaninova, M., Lindgren, C.M., Lowe, C.E., McCarthy, M.I., Meduri, E., di Meglio, P., Min, J.L., Montgomery, S.B., Nestle, F.O., Nica, A.C., Nisbet, J., O'Rahilly, S., Parts, L., Potter, S., Sekowska, M., Shin, S.Y., Small, K.S., Soranzo, N., Spector, T.D., Surdulescu, G., Travers, M.E., Tsaprouni, L., Tsoka, S., Wilk, A., Yang, T.P., Zondervan, K.T., Voight, B.F., Scott, L.J., Steinthorsdottir, V., Morris, A.P., Dina, C., Welch, R.P., Zeggini, E., Huth, C., Aulchenko, Y.S., Thorleifsson, G., McCulloch, L.J., Ferreira, T., Grallert, H., Amin, N., Wu, G., Willer, C.J., Raychaudhuri, S., McCarroll, S.A., Langenberg, C., Hofmann, O.M., Dupuis, J., Qi, L., Segrè, A.V., van Hoek, M., Navarro, P., Ardlie, K., Balkau, B., Benediktsson, R., Bennett, A.J., Blagieva, R., Boerwinkle, E., Bonnycastle, L.L., Boström, K.B., Bravenboer, B., Bumpstead, S., Burtt, N.P., Charpentier, G., Chines, P.S., Cornelis, M., Couper, D.J., Crawford, G., Doney, A.S., Elliott, K.S., Elliott, A.L., Erdos, M.R., Fox, C.S., Franklin, C.S., Ganser, M., Gieger, C., Grarup, N., Green, T., Griffin, S., Groves, C.J., Guiducci, C., Hadjadj, S., Herder, C., Isomaa, B., Jackson, A.U., Johnson, P.R., Jørgensen, T., Kao, W.H., Klopp, N., Kong, A., Kraft, P., Kuusisto, J., Lauritzen, T., Li, M., Lieverse, A., Lyssenko, V., Marre, M., Meitinger, T., Midthjell, K., Morken, M.A., Narisu, N., Nilsson, P., Owen, K.R., Payne, F., Perry, J.R., Petersen, A.K., Platou, C., Proença, C., Prokopenko, I., Rathmann, W., Rayner, N.W., Robertson, N.R., Rocheleau, G., Roden, M., Sampson, M.J., Saxena, R., Shields, B.M., Shrader, P., Sigurdsson, G., Sparsø, T., Strassburger, K., Stringham, H.M., Sun, Q., Swift, A.J., Thorand, B., Tichet, J., Tuomi, T., van Dam, R.M., van Haeften, T.W., van Herpt, T., van Vliet-Ostaptchouk, J.V., Walters, G.B., Weedon, M.N., Wijmenga, C., Witteman, J., Bergman, R.N., Cauchi, S., Collins, F.S., Gloyn, A.L., Gyllensten, U., Hansen, T., Hide, W.A., Hitman, G.A., Hofman, A., Hunter, D.J., Hveem, K., Laakso, M., Mohlke, K.L., Morris, A.D., Palmer, C.N., Pramstaller, P.P., Rudan, I., Sijbrands, E., Stein, L.D., Tuomilehto, J., Uitterlinden, A., Walker, M., Wareham, N.J., Watanabe, R.M., Abecasis, G.R., Boehm, B.O., Campbell, H., Daly, M.J., Hattersley, A.T., Hu, F.B., Meigs, J.B., Pankow, J.S., Pedersen, O., Wichmann, H.E., Barroso, I., Florez, J.C., Frayling, T.M., Groop, L., Sladek, R., Thorsteinsdottir, U., Wilson, J.F., Illig, T., Froguel, P., van Duijn, C.M., Stefansson, K., Altshuler, D., Boehnke, M., Manning, A.K., Hivert, M.F., Scott, R.A., Grimsby, J.L., Bouatia-Naji, N., Chen, H., Rybin, D., Liu, C.T., Bielak, L.F., Barnes, 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Jukema, J.W., Jula, A., Kaprio, J., Kardia, S.L., Keinanen-Kiukaanniemi, S., Kivimaki, M., Kolcic, I., Kovacs, P., Kumari, M., Kyvik, K.O., Lakka, T., Lannfelt, L., Lathrop, G.M., Launer, L.J., Leander, K., Li, G., Lind, L., Lindstrom, J., Lobbens, S., Loos, R.J., Luan, J., Mägi, R., Magnusson, P.K., Marmot, M., Meneton, P., Mooser, V., Miljkovic, I., O'Connell, J., Ong, K.K., Oostra, B.A., Palmer, L.J., Palotie, A., Peden, J.F., Pedersen, N.L., Pehlic, M., Peltonen, L., Penninx, B., Pericic, M., Perola, M., Perusse, L., Peyser, P.A., Polasek, O., Province, M.A., Räikkönen, K., Rauramaa, R., Rehnberg, E., Rice, K., Rotter, J.I., Ruokonen, A., Saaristo, T., Sabater-Lleal, M., Salomaa, V., Savage, D.B., Schwarz, P., Seedorf, U., Sennblad, B., Serrano-Rios, M., Shuldiner, A.R., Sijbrands, E.J., Siscovick, D.S., Smit, J.H., Smith, N.L., Smith, A.V., Stančáková, A., Stirrups, K., Stumvoll, M., Sun, Y.V., Tönjes, A., Trompet, S., Uitterlinden, A.G., Uusitupa, M., Vikström, M., Vitart, V., Vohl, M.C., Vollenweider, P., Waeber, G., Waterworth, D.M., Watkins, H., Wheeler, E., Widen, E., Wild, S.H., Willems, S.M., Willemsen, G., Witteman, J.C., Wright, A.F., Yaghootkar, H., Zelenika, D., Zemunik, T., Zgaga, L., DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium, Multiple Tissue Human Expression Resource (MUTHER) Consortium, Ahmadi, K.R., Ainali, C., Barrett, A., Bataille, V., Bell, J.T., Buil, A., Deloukas, P., Dermitzakis, E.T., Dimas, A.S., Durbin, R., Glass, D., Grundberg, E., Hassanali, N., Hedman, Å.K., Ingle, C., Knowles, D., Krestyaninova, M., Lindgren, C.M., Lowe, C.E., McCarthy, M.I., Meduri, E., di Meglio, P., Min, J.L., Montgomery, S.B., Nestle, F.O., Nica, A.C., Nisbet, J., O'Rahilly, S., Parts, L., Potter, S., Sekowska, M., Shin, S.Y., Small, K.S., Soranzo, N., Spector, T.D., Surdulescu, G., Travers, M.E., Tsaprouni, L., Tsoka, S., Wilk, A., Yang, T.P., Zondervan, K.T., Voight, B.F., Scott, L.J., Steinthorsdottir, V., Morris, A.P., Dina, C., Welch, R.P., Zeggini, E., Huth, C., Aulchenko, Y.S., Thorleifsson, G., McCulloch, L.J., Ferreira, T., Grallert, H., Amin, N., Wu, G., Willer, C.J., Raychaudhuri, S., McCarroll, S.A., Langenberg, C., Hofmann, O.M., Dupuis, J., Qi, L., Segrè, A.V., van Hoek, M., Navarro, P., Ardlie, K., Balkau, B., Benediktsson, R., Bennett, A.J., Blagieva, R., Boerwinkle, E., Bonnycastle, L.L., Boström, K.B., Bravenboer, B., Bumpstead, S., Burtt, N.P., Charpentier, G., Chines, P.S., Cornelis, M., Couper, D.J., Crawford, G., Doney, A.S., Elliott, K.S., Elliott, A.L., Erdos, M.R., Fox, C.S., Franklin, C.S., Ganser, M., Gieger, C., Grarup, N., Green, T., Griffin, S., Groves, C.J., Guiducci, C., Hadjadj, S., Herder, C., Isomaa, B., Jackson, A.U., Johnson, P.R., Jørgensen, T., Kao, W.H., Klopp, N., Kong, A., Kraft, P., Kuusisto, J., Lauritzen, T., Li, M., Lieverse, A., Lyssenko, V., Marre, M., Meitinger, T., Midthjell, K., Morken, M.A., Narisu, N., Nilsson, P., Owen, K.R., Payne, F., Perry, J.R., Petersen, A.K., Platou, C., Proença, C., Prokopenko, I., Rathmann, W., Rayner, N.W., Robertson, N.R., Rocheleau, G., Roden, M., Sampson, M.J., Saxena, R., Shields, B.M., Shrader, P., Sigurdsson, G., Sparsø, T., Strassburger, K., Stringham, H.M., Sun, Q., Swift, A.J., Thorand, B., Tichet, J., Tuomi, T., van Dam, R.M., van Haeften, T.W., van Herpt, T., van Vliet-Ostaptchouk, J.V., Walters, G.B., Weedon, M.N., Wijmenga, C., Witteman, J., Bergman, R.N., Cauchi, S., Collins, F.S., Gloyn, A.L., Gyllensten, U., Hansen, T., Hide, W.A., Hitman, G.A., Hofman, A., Hunter, D.J., Hveem, K., Laakso, M., Mohlke, K.L., Morris, A.D., Palmer, C.N., Pramstaller, P.P., Rudan, I., Sijbrands, E., Stein, L.D., Tuomilehto, J., Uitterlinden, A., Walker, M., Wareham, N.J., Watanabe, R.M., Abecasis, G.R., Boehm, B.O., Campbell, H., Daly, M.J., Hattersley, A.T., Hu, F.B., Meigs, J.B., Pankow, J.S., Pedersen, O., Wichmann, H.E., Barroso, I., Florez, J.C., Frayling, T.M., Groop, L., Sladek, R., Thorsteinsdottir, U., Wilson, J.F., Illig, T., Froguel, P., van Duijn, C.M., Stefansson, K., Altshuler, D., Boehnke, M., Manning, A.K., Hivert, M.F., Scott, R.A., Grimsby, J.L., Bouatia-Naji, N., Chen, H., Rybin, D., Liu, C.T., Bielak, L.F., Barnes, D., Cadby, G., Hottenga, J.J., Ingelsson, E., Johnson, T., Kanoni, S., Ladenvall, C., Lagou, V., Lahti, J., Lecoeur, C., Liu, Y., Martinez-Larrad, M.T., Montasser, M.E., Rasmussen-Torvik, L.J., Salo, P., Sattar, N., Shungin, D., Strawbridge, R.J., Tanaka, T., An, P., de Andrade, M., Andrews, J.S., Aspelund, T., Atalay, M., Aulchenko, Y., Bandinelli, S., Beckmann, J.S., Beilby, J.P., Bellis, C., Blangero, J., Boban, M., Boomsma, D.I., Borecki, I.B., Böttcher, Y., Bouchard, C., Brunner, E., Budimir, D., Carlson, O., Clarke, R., Corbatón-Anchuelo, A., Couper, D., de Faire, U., Dedoussis, G.V., Dimitriou, M., Egan, J.M., Eiriksdottir, G., Eriksson, J.G., Eury, E., Ferrucci, L., Ford, I., Forouhi, N.G., Franzosi, M.G., Franks, P.W., Galan, P., de Geus, E., Gigante, B., Glazer, N.L., Goel, A., Gudnason, V., Hallmans, G., Hamsten, A., Hansson, O., Harris, T.B., Hayward, C., Heath, S., Hercberg, S., Hicks, A.A., Hingorani, A., Hui, J., Hung, J., Jarvelin, M.R., Jhun, M.A., Johnson, P.C., Jukema, J.W., Jula, A., Kaprio, J., Kardia, S.L., Keinanen-Kiukaanniemi, S., Kivimaki, M., Kolcic, I., Kovacs, P., Kumari, M., Kyvik, K.O., Lakka, T., Lannfelt, L., Lathrop, G.M., Launer, L.J., Leander, K., Li, G., Lind, L., Lindstrom, J., Lobbens, S., Loos, R.J., Luan, J., Mägi, R., Magnusson, P.K., Marmot, M., Meneton, P., Mooser, V., Miljkovic, I., O'Connell, J., Ong, K.K., Oostra, B.A., Palmer, L.J., Palotie, A., Peden, J.F., Pedersen, N.L., Pehlic, M., Peltonen, L., Penninx, B., Pericic, M., Perola, M., Perusse, L., Peyser, P.A., Polasek, O., Province, M.A., Räikkönen, K., Rauramaa, R., Rehnberg, E., Rice, K., Rotter, J.I., Ruokonen, A., Saaristo, T., Sabater-Lleal, M., Salomaa, V., Savage, D.B., Schwarz, P., Seedorf, U., Sennblad, B., Serrano-Rios, M., Shuldiner, A.R., Sijbrands, E.J., Siscovick, D.S., Smit, J.H., Smith, N.L., Smith, A.V., Stančáková, A., Stirrups, K., Stumvoll, M., Sun, Y.V., Tönjes, A., Trompet, S., Uitterlinden, A.G., Uusitupa, M., Vikström, M., Vitart, V., Vohl, M.C., Vollenweider, P., Waeber, G., Waterworth, D.M., Watkins, H., Wheeler, E., Widen, E., Wild, S.H., Willems, S.M., Willemsen, G., Witteman, J.C., Wright, A.F., Yaghootkar, H., Zelenika, D., Zemunik, T., and Zgaga, L.
- Abstract
Recent genome-wide association studies have described many loci implicated in type 2 diabetes (T2D) pathophysiology and β-cell dysfunction but have contributed little to the understanding of the genetic basis of insulin resistance. We hypothesized that genes implicated in insulin resistance pathways might be uncovered by accounting for differences in body mass index (BMI) and potential interactions between BMI and genetic variants. We applied a joint meta-analysis approach to test associations with fasting insulin and glucose on a genome-wide scale. We present six previously unknown loci associated with fasting insulin at P < 5 × 10(-8) in combined discovery and follow-up analyses of 52 studies comprising up to 96,496 non-diabetic individuals. Risk variants were associated with higher triglyceride and lower high-density lipoprotein (HDL) cholesterol levels, suggesting a role for these loci in insulin resistance pathways. The discovery of these loci will aid further characterization of the role of insulin resistance in T2D pathophysiology.
- Published
- 2012
37. CAST: an iterative algorithm for the complexity analysis of sequence tracts
- Author
-
Promponas, VJ Enright, AJ Tsoka, S Kreil, DP Leroy, C and Hamodrakas, S Sander, C Ouzounis, CA
- Abstract
Motivation: Sensitive detection and masking of low-complexity regions in protein sequences. Filtered sequences can be used in sequence comparison without the risk of matching compositionally biased regions. The main advantage of the method over similar approaches is the selective masking of single residue types without affecting other possibly important, regions. Results: A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity. The detection of low-complexity regions is highly specific for single residue types. ft is shown that this approach is sufficient for masking database query sequences without generating false positives. The algorithm is benchmarked against widely available algorithms using the 210 genes of Plasmodium falciparum chromosome 2, a dataset known to contain a large number of low-complexity regions.
- Published
- 2000
38. Reproducibility in genome sequence annotation: the Plasmodium falciparum chromosome 2 case
- Author
-
Tsoka, S Promponas, V Ouzounis, CA
- Published
- 1999
39. Systembiologisch Netzwerkanalyse der Gen-Interaktion in der hepatozellulären Karzinogenese
- Author
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Bornschein, J, primary, Drozdov, I, additional, Wex, T, additional, Valeyev, N, additional, Tsoka, S, additional, and Malfertheiner, P, additional
- Published
- 2011
- Full Text
- View/download PDF
40. VLP concentration monitoring with the IAsys optical biosensor
- Author
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Tsoka, S., Gill, A., Hoare, M., and Brookman, J.L.
- Subjects
Biotechnology industry -- Product development ,Biotechnology industry ,Business - Abstract
Affinity Sensors' IAsys optical biosensor successfully performs real-time bioprocess monitoring of virus-like particles for rapid process optimization.
- Published
- 1999
41. CoGenT++: an extensive and extensible data environment for computational genomics
- Author
-
Goldovsky, L., primary, Janssen, P., additional, Ahren, D., additional, Audit, B., additional, Cases, I., additional, Darzentas, N., additional, Enright, A. J., additional, Lopez-Bigas, N., additional, Peregrin-Alvarez, J. M., additional, Smith, M., additional, Tsoka, S., additional, Kunin, V., additional, and Ouzounis, C. A., additional
- Published
- 2005
- Full Text
- View/download PDF
42. Functional Versatility and Molecular Diversity of the Metabolic Map of Escherichia coli
- Author
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Tsoka, S., primary
- Published
- 2001
- Full Text
- View/download PDF
43. Selective Flocculation and Precipitation for the Improvement of Virus-Like Particle Recovery from Yeast Homogenate
- Author
-
Tsoka, S., primary, Ciniawskyj, O.C., additional, Thomas, O.R.T., additional, Titchener-Hooker, N.J., additional, and Hoare, M., additional
- Published
- 2000
- Full Text
- View/download PDF
44. Virus-like particle analysis in yeast homogenate using a laser light-scattering assay
- Author
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Tsoka, S., primary, Holwill, I., additional, and Hoare, M., additional
- Published
- 1999
- Full Text
- View/download PDF
45. Sustainable prefabricated buildings: a holistic approach
- Author
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Tsikaloudaki Katerina, Theodosiou Theodore, Tsoka Stella, and Chastas Panagiotis
- Subjects
Energy conservation ,TJ163.26-163.5 ,Renewable energy sources ,TJ807-830 - Abstract
Although modern prefabricated buildings may offer many advantages, such as a significant reduction in cost and time, improved quality and accuracy in manufacture, easy dismantle and reuse of its components, etc., they have not gained the attention they deserve in the construction market yet. In this paper, a holistic approach for the formation of prefabricated buildings of advanced performance is presented. Within this context, a new, innovative prefabricated building element is developed, designed to exhibit optimized structural, hygrothermal, energy, acoustic, fire and environmental performance. The improved properties of the building element are ensured by the proper configuration of the layers that compose it with respect to the design objectives; for example, in order to support the heat storage and the control of indoor temperatures, the integration of PCMs in the element's layers is investigated. Furthermore, in order to indicate the contribution of the new building element to the sustainability of the overall construction, the performance of a building formulated with the new element is analyzed in terms of energy and environmental behaviour. The new building element and construction system are expected to systemize the prefabricated element's production, leading eventually to the improvement of the building quality, as well as to the reduction of time and cost of building's erection. In parallel, the new certified and optimized building performance will increase the share of prefabricated buildings in the Mediterranean countries, where housing needs are gradually growing, while at the same time, energy efficient and environmentally friendly construction will be promoted.
- Published
- 2022
- Full Text
- View/download PDF
46. Rapid monitoring of virus-like particles using an optical biosensor: A feasibility study
- Author
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Tsoka, S, primary, Gill, A, additional, Brookman, J.L, additional, and Hoare, M, additional
- Published
- 1998
- Full Text
- View/download PDF
47. Time temperatüre integration for chilled food shelf life monitoring using enzyme‐substrate systems
- Author
-
Tsoka, S., primary, Taoukis, P.S., additional, Christakopoulos, P., additional, Kekos, D., additional, and Macris, B.J., additional
- Published
- 1998
- Full Text
- View/download PDF
48. Selection of Chromatographic Protein Purification Operations Based on Physicochemical Propertiesa
- Author
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WATANABE, E., primary, TSOKA, S., additional, and ASENJO, J. A., additional
- Published
- 1994
- Full Text
- View/download PDF
49. CAST: an iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts.
- Author
-
Promponas, V J, Enright, A J, Tsoka, S, Kreil, D P, Leroy, C, Hamodrakas, S, Sander, C, and Ouzounis, C A
- Abstract
Sensitive detection and masking of low-complexity regions in protein sequences. Filtered sequences can be used in sequence comparison without the risk of matching compositionally biased regions. The main advantage of the method over similar approaches is the selective masking of single residue types without affecting other, possibly important, regions.
- Published
- 2000
- Full Text
- View/download PDF
50. Recent developments and future directions in computational genomics
- Author
-
Tsoka, S. and Ouzounis, C. A.
- Published
- 2000
- Full Text
- View/download PDF
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