SwePub
Sök i SwePub databas

  Utökad sökning

Träfflista för sökning "WFRF:(Pawitan Yudi) "

Sökning: WFRF:(Pawitan Yudi)

  • Resultat 1-10 av 41
  • [1]2345Nästa
Sortera/gruppera träfflistan
   
NumreringReferensOmslagsbildHitta
1.
  • Pernemalm, Maria, et al. (författare)
  • Quantitative Proteomics Profiling of Primary Lung Adenocarcinoma Tumors Reveals Functional Perturbations in Tumor Metabolism
  • 2013
  • Ingår i: Journal of Proteome Research. - The American Chemical Society (ACS). - 1535-3893. ; 12:9, s. 3934-3943
  • Tidskriftsartikel (refereegranskat)abstract
    • In this study, we have analyzed human primary lung adenocarcinoma tumors using global mass spectrometry to elucidate the biological mechanisms behind relapse post surgery. In total, we identified over 3000 proteins with high confidence. Supervised multivariate analysis was used to select 132 proteins separating the prognostic groups. Based on in-depth bioinformatics analysis, we hypothesized that the tumors with poor prognosis had a higher glycolytic activity and HIF activation. By measuring the bioenergetic cellular index of the tumors, we could detect a higher dependency of glycolysis among the tumors with poor prognosis. Further, we could also detect an up-regulation of HIF1 alpha mRNA expression in tumors with early relapse. Finally, we selected three proteins that were upregulated in the poor prognosis group (cathepsin D, ENO1, and VDAC1) to confirm that the proteins indeed originated from the tumor and not from a stromal or inflammatory component. Overall, these findings show how in-depth analysis of clinical material can lead to an increased understanding of the molecular mechanisms behind tumor progression.
  •  
2.
  • Sjölander, Arvid, et al. (författare)
  • Between-within models for survival analysis.
  • 2013
  • Ingår i: Statistics in Medicine. - Hoboken, USA : Wiley-Blackwell. - 0277-6715. ; 32:18, s. 3067-3076
  • Tidskriftsartikel (refereegranskat)abstract
    • A popular way to control for confounding in observational studies is to identify clusters of individuals (e.g., twin pairs), such that a large set of potential confounders are constant (shared) within each cluster. By studying the exposure-outcome association within clusters, we are in effect controlling for the whole set of shared confounders. An increasingly popular analysis tool is the between-within (BW) model, which decomposes the exposure-outcome association into a 'within-cluster effect' and a 'between-cluster effect'. BW models are relatively common for nonsurvival outcomes and have been studied in the theoretical literature. Although it is straightforward to use BW models for survival outcomes, this has rarely been carried out in practice, and such models have not been studied in the theoretical literature. In this paper, we propose a gamma BW model for survival outcomes. We compare the properties of this model with the more standard stratified Cox regression model and use the proposed model to analyze data from a twin study of obesity and mortality. We find the following: (i) the gamma BW model often produces a more powerful test of the 'within-cluster effect' than stratified Cox regression; and (ii) the gamma BW model is robust against model misspecification, although there are situations where it could give biased estimates.
  •  
3.
  • Alexeyenko, Andrey, et al. (författare)
  • Network enrichment analysis : extension of gene-set enrichment analysis to gene networks
  • 2012
  • Ingår i: BMC Bioinformatics. - 1471-2105 .- 1471-2105. ; 13, s. 226
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Background: Gene-set enrichment analyses (GEA or GSEA) are commonly used for biological characterization of an experimental gene-set. This is done by finding known functional categories, such as pathways or Gene Ontology terms, that are over-represented in the experimental set; the assessment is based on an overlap statistic. Rich biological information in terms of gene interaction network is now widely available, but this topological information is not used by GEA, so there is a need for methods that exploit this type of information in high-throughput data analysis. Results: We developed a method of network enrichment analysis (NEA) that extends the overlap statistic in GEA to network links between genes in the experimental set and those in the functional categories. For the crucial step in statistical inference, we developed a fast network randomization algorithm in order to obtain the distribution of any network statistic under the null hypothesis of no association between an experimental gene-set and a functional category. We illustrate the NEA method using gene and protein expression data from a lung cancer study. Conclusions: The results indicate that the NEA method is more powerful than the traditional GEA, primarily because the relationships between gene sets were more strongly captured by network connectivity rather than by simple overlaps.</p>
  •  
4.
  • Bachmann, Julie, et al. (författare)
  • Affinity Proteomics Reveals Elevated Muscle Proteins in Plasma of Children with Cerebral Malaria
  • 2014
  • Ingår i: PLoS Pathogens. - 1553-7366 .- 1553-7374. ; 10:4, s. e1004038
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Systemic inflammation and sequestration of parasitized erythrocytes are central processes in the pathophysiology of severe Plasmodium falciparum childhood malaria. However, it is still not understood why some children are more at risks to develop malaria complications than others. To identify human proteins in plasma related to childhood malaria syndromes, multiplex antibody suspension bead arrays were employed. Out of the 1,015 proteins analyzed in plasma from more than 700 children, 41 differed between malaria infected children and community controls, whereas 13 discriminated uncomplicated malaria from severe malaria syndromes. Markers of oxidative stress were found related to severe malaria anemia while markers of endothelial activation, platelet adhesion and muscular damage were identified in relation to children with cerebral malaria. These findings suggest the presence of generalized vascular inflammation, vascular wall modulations, activation of endothelium and unbalanced glucose metabolism in severe malaria. The increased levels of specific muscle proteins in plasma implicate potential muscle damage and microvasculature lesions during the course of cerebral malaria.</p>
  •  
5.
  • Bachmann, Julie, et al. (författare)
  • Affinity Proteomics Reveals Elevated Muscle Proteins in Plasma of Children with Cerebral Malaria
  • 2014
  • Ingår i: PLoS Pathogens. - 1553-7366 .- 1553-7374. ; 10:4, s. e1004038
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Systemic inflammation and sequestration of parasitized erythrocytes are central processes in the pathophysiology of severe Plasmodium falciparum childhood malaria. However, it is still not understood why some children are more at risks to develop malaria complications than others. To identify human proteins in plasma related to childhood malaria syndromes, multiplex antibody suspension bead arrays were employed. Out of the 1,015 proteins analyzed in plasma from more than 700 children, 41 differed between malaria infected children and community controls, whereas 13 discriminated uncomplicated malaria from severe malaria syndromes. Markers of oxidative stress were found related to severe malaria anemia while markers of endothelial activation, platelet adhesion and muscular damage were identified in relation to children with cerebral malaria. These findings suggest the presence of generalized vascular inflammation, vascular wall modulations, activation of endothelium and unbalanced glucose metabolism in severe malaria. The increased levels of specific muscle proteins in plasma implicate potential muscle damage and microvasculature lesions during the course of cerebral malaria.</p>
  •  
6.
  • Berndt, Sonja I., et al. (författare)
  • Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture
  • 2013
  • Ingår i: Nature Genetics. - Nature Publishing Group. - 1546-1718. ; 45:5, s. 501-512
  • Tidskriftsartikel (refereegranskat)abstract
    • Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.
  •  
7.
  • Berndt, Sonja I., et al. (författare)
  • Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture
  • 2013
  • Ingår i: Nature Genetics. - 1061-4036 .- 1546-1718. ; 45:5, s. 501-U69
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.</p>
  •  
8.
  • Berndt, Sonja I., et al. (författare)
  • Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture
  • 2013
  • Ingår i: Nature Genetics. - 1061-4036 .- 1546-1718. ; 45:5, s. 501-U69
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.</p>
  •  
9.
  • Berndt, Sonja I., et al. (författare)
  • Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture
  • 2013
  • Ingår i: Nature Genetics. - 1061-4036 .- 1546-1718. ; 45:5, s. 501-U69
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.</p>
  •  
10.
  • Demissie, Meaza, et al. (författare)
  • Unequal group variances in microarray data analyses
  • 2008
  • Ingår i: Bioinformatics. - 1367-4803 .- 1367-4811. ; 24:9, s. 1168-1174
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Motivation: In searching for differentially expressed (DE) genes in microarray data, we often observe a fraction of the genes to have unequal variability between groups. This is not an issue in large samples, where a valid test exists that uses individual variances separately. The problem arises in the small-sample setting, where the approximately valid Welch test lacks sensitivity, while the more sensitive moderated t-test assumes equal variance. Methods: We introduce a moderated Welch test (MWT) that allows unequal variance between groups. It is based on (i) weighting of pooled and unpooled standard errors and (ii) improved estimation of the gene-level variance that exploits the information from across the genes. Results: When a non-trivial proportion of genes has unequal variability, false discovery rate (FDR) estimates based on the standard t and moderated t-tests are often too optimistic, while the standard Welch test has low sensitivity. The MWT is shown to (i) perform better than the standard t, the standard Welch and the moderated t-tests when the variances are unequal between groups and (ii) perform similarly to the moderated t, and better than the standard t and Welch tests when the group variances are equal. These results mean that MWT is more reliable than other existing tests over wider range of data conditions. Availability: R package to perform MWT is available at http://www.meb.ki.se/similar to yudpaw Contact: yudi.pawitan@ki.se Supplementary information: Supplementary data are available at Bioinformatics online.</p>
  •  
Skapa referenser, mejla, bekava och länka
  • Resultat 1-10 av 41
  • [1]2345Nästa
Åtkomst
fritt online (8)
Typ av publikation
tidskriftsartikel (38)
annan publikation (1)
forskningsöversikt (1)
doktorsavhandling (1)
Typ av innehåll
refereegranskat (39)
övrigt vetenskapligt (2)
Författare/redaktör
Adami, Hans Olov (11)
Mucci, Lorelei A (10)
Johansson, Jan-Erik (9)
Andersson, Swen-Olof (8)
Andrén, Ove (8)
Holmberg, Lars, (7)
visa fler...
Ganna, Andrea (6)
Berndt, Sonja I (5)
Strachan, David P. (5)
Lind, Lars, (4)
Khaw, Kay-Tee (4)
Froguel, Philippe, (4)
Viikari, Jorma (4)
Kuh, Diana (4)
Chanock, Stephen J (4)
Ouwehand, Willem H. (4)
Soranzo, Nicole (4)
Amin, Najaf (4)
Teumer, Alexander (4)
Amouyel, Philippe (4)
Boomsma, Dorret I. (4)
Gudnason, Vilmundur (4)
Hofman, Albert (4)
Homuth, Georg (4)
Hottenga, Jouke-Jan (4)
Montgomery, Grant W. (4)
Psaty, Bruce M. (4)
Uitterlinden, Andre ... (4)
Van Duijn, Cornelia ... (4)
Martin, Nicholas G. (4)
Launer, Lenore J. (4)
Medland, Sarah E. (4)
Pedersen, Nancy (4)
Deloukas, Panos (4)
Wareham, Nicholas J (4)
Fall, Tove (4)
Bergh, Jonas (4)
Stancáková, Alena, (4)
Kuusisto, Johanna, (4)
Laakso, Markku, (4)
McCarthy, Mark I (4)
Tregouet, David Alex ... (4)
Shungin, Dmitry, (4)
Ridker, Paul M., (4)
Hu, Frank B., (4)
Chasman, Daniel I., (4)
Rose, Lynda M (4)
Langenberg, Claudia (4)
Boehnke, Michael (4)
Hamsten, Anders (4)
visa färre...
Lärosäte
Uppsala universitet (22)
Örebro universitet (8)
Kungliga Tekniska Högskolan (4)
Lunds universitet (3)
Karolinska Institutet (3)
Umeå universitet (2)
visa fler...
Linköpings universitet (2)
Göteborgs universitet (1)
visa färre...
Språk
Engelska (41)
Forskningsämne (UKÄ/SCB)
Medicin och hälsovetenskap (32)
Naturvetenskap (10)
Teknik (1)

År

 
pil uppåt Stäng

Kopiera och spara länken för att återkomma till aktuell vy