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1,396 results on '"Sterk, Peter"'

1. Prospective Detection of Early Lung Cancer in Patients With COPD in Regular Care by Electronic Nose Analysis of Exhaled Breath

Author

de Vries, Rianne, Farzan, Niloufar, Fabius, Timon, De Jongh, Frans H.C., Jak, Patrick M.C., Haarman, Eric G., Snoey, Erik, In ’T Veen, Johannes C.C.M., Dagelet, Yennece W.F., Maitland-Van Der Zee, Anke-Hilse, Lucas, Annelies, Van Den Heuvel, Michel M., Wolf-Lansdorf, Marguerite, Muller, Mirte, Baas, Paul, and Sterk, Peter J.

Published
2023
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2. The role of inflammation in anxiety and depression in the European U-BIOPRED asthma cohorts

Author

Hou, Ruihua, Ye, Gang, Cheng, Xiaojing, Shaw, Dominick E., Bakke, Per S., Caruso, Massimo, Dahlen, Barbro, Dahlen, Sven-Erik, Fowler, Stephen J., Horváth, Ildikó, Howarth, Peter, Krug, Norbert, Montuschi, Paolo, Sanak, Marek, Sandström, Thomas, Auffray, Charles, De Meulder, Bertrand, Sousa, Ana R., Adcock, Ian M., Fan Chung, Kian, Sterk, Peter J., Skipp, Paul J., Schofield, James, and Djukanović, Ratko

Published
2023
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3. Stratification of asthma by lipidomic profiling of induced sputum supernatant

Author

Brandsma, Joost, Schofield, James P.R., Yang, Xian, Strazzeri, Fabio, Barber, Clair, Goss, Victoria M., Koster, Grielof, Bakke, Per S., Caruso, Massimo, Chanez, Pascal, Dahlén, Sven-Erik, Fowler, Stephen J., Horváth, Ildikó, Krug, Norbert, Montuschi, Paolo, Sanak, Marek, Sandström, Thomas, Shaw, Dominick E., Chung, Kian Fan, Singer, Florian, Fleming, Louise J., Adcock, Ian M., Pandis, Ioannis, Bansal, Aruna T., Corfield, Julie, Sousa, Ana R., Sterk, Peter J., Sánchez-García, Rubén J., Skipp, Paul J., Postle, Anthony D., and Djukanović, Ratko

Published
2023
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7. Biomarker Predictors of Clinical Efficacy of the Anti-IgE Biologic Omalizumab in Severe Asthma in Adults: Results of the SoMOSA Study.

Author

Djukanović, Ratko, Brinkman, Paul, Kolmert, Johan, Gomez, Cristina, Schofield, James, Brandsma, Joost, Shapanis, Andy, Skipp, Paul J. S., Postle, Anthony, Wheelock, Craig, Dahlen, Sven-Erik, Sterk, Peter J., Brown, Thomas, Jackson, David J., Mansur, Adel, Pavord, Ian, Patel, Mitesh, Brightling, Christopher, Siddiqui, Salman, and Bradding, Peter

Subjects
OMALIZUMAB, ASTHMA, RECEIVER operating characteristic curves, WHEEZE, BIOLOGICALS, BIOMARKERS
Abstract

Background: The anti-IgE monoclonal antibody omalizumab is widely used for severe asthma. This study aimed to identify biomarkers that predict clinical improvement during 1 year of omalizumab treatment. Methods: One-year open-label Study of Mechanisms of action of Omalizumab in Severe Asthma (SoMOSA) involving 216 patients with severe (Global Initiative for Asthma step 4/5) uncontrolled atopic asthma (at least two severe exacerbations in the previous year) taking high-dose inhaled corticosteroids and long-acting β-agonists with or without maintenance oral corticosteroids. It had two phases: 0–16 weeks, to assess early clinical improvement by Global Evaluation of Therapeutic Effectiveness (GETE); and 16–52 weeks, to assess late responses based on ⩾50% reduction in exacerbations or mOCS dose. All participants provided samples (exhaled breath, blood, sputum, urine) before and after 16 weeks of omalizumab treatment. Measurements and Main Results: A total of 191 patients completed phase 1; 63% had early improvement. Of 173 who completed phase 2, 69% had reduced exacerbations by ⩾50% and 57% (37 of 65) taking mOCSs had reduced their dose by ⩾50%. The primary outcomes 2,3-dinor-11-β-PGF2α, GETE score, and standard clinical biomarkers (blood and sputum eosinophils, exhaled nitric oxide, serum IgE) did not predict either clinical response. Five volatile organic compounds and five plasma lipid biomarkers strongly predicted the ⩾50% reduction in exacerbations (receiver operating characteristic areas under the curve of 0.780 and 0.922, respectively) and early responses (areas under the curve of 0.835 and 0.949, respectively). In an independent cohort, gas chromatography/mass spectrometry biomarkers differentiated between severe and mild asthma. Conclusions: This is the first discovery of omics biomarkers that predict improvement in asthma with biologic agent treatment. Prospective validation and development for clinical use is justified. [ABSTRACT FROM AUTHOR]

Published
2024
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10. Asthma similarities across ProAR (Brazil) and U-BIOPRED (Europe) adult cohorts of contrasting locations, ethnicity and socioeconomic status

Author

Alcantara-Neves, N., Almeida, P.C.A., Amorim, L., Araujo, M.I., Barnes, K.C., Barreto, M.L., Belitardo, E., Bião-Lima, V., Cardoso, L., Camargos, P.A., Chatkin, J.M., Costa, R.S., Coelho, A.C.C., Cooper, P.J., Cruz, A.A., Cruz, C.S., Cunha, J., de Jesus, J.V., Fernandes, J., Franco, R.A., Gomes-Filho, I., Lima-Matos, A., Figueiredo, C.A., Lessa, M.A., Lins, L., Mello, L.M., Moura-Santos, P., Muniz, I.S., Paixao-Araujo, I., Pinheiro, G.P., Ponte, E.V., Rodrigues, L.C., Santana, C.V.N., Santos-Lima, G., Souza, T.M.O., Souza-Machado, A., Souza-Machado, C., Stelmach, R., Vasquez, V.S., Adcock, I.M., Ahmed, H., Auffray, C., Bakke, P., Baribaud, F., Bel, E.H., Bigler, J., Bisgaard, H., Boedigheimer, M.J., Bønnelykke, K., Brandsma, J., Brinkman, P., Bucchioni, E., Burg, D., Bush, A., Caruso, M., Chaiboonchoe, A., Chanez, P., Compton, C.H., Corfield, J., D'Amico, A., Dahlén, B., Dahlén, S.E., De Meulder, B., Djukanovic, R., Erpenbeck, V.J., Erzen, D., Fichtner, K., Fitch, N., Fleming, L.J., Formaggio, E., Fowler, S.J., Frey, U., Gahlemann, M., Geiser, T., Goss, V., Guo, Y.-K., Hashimoto, S., Haughney, J., Hedlin, G., Hekking, P.W., Higenbottam, T., Hohlfeld, J.M., Holweg, C., Horváth, I., Howarth, P., James, A.J., Knowles, R.G., Knox, A.J., Krug, N., Lefaudeux, D., Loza, M.J., Lutter, R., Manta, A., Masefield, S., Matthews, J.G., Mazein, A., Meiser, A., Middelveld, R.J.M., Miralpeix, M., Montuschi, P., Mores, N., Murray, C.S., Musial, J., Myles, D., Pahus, L., Pandis, I., Pavlidis, S., Postle, A., Powel, P., Praticò, G., Puig Valls, M., Rao, N., Roberts, A., Roberts, G., Rowe, A., Sandström, T., Schofield, J.P.R., Seibold, W., Selby, A., Shaw, D.E., Sigmund, R., Singer, F., Skipp, P.J., Sousa, A.R., Sterk, P.J., Sun, K., Thornton, B., van Aalderen, W.M., van Geest, M., Vestbo, J., Vissing, N.H., Wagener, A.H., Wagers, S.S., Weiszhart, Z., Wheelock, C.E., Wilson, S.J., Cruz, Alvaro A., Riley, John H., Bansal, Aruna T., Ponte, Eduardo V., Souza-Machado, Adelmir, Almeida, Paula C.A., Biao-Lima, Valmar, Davis, Maggie, Bates, Stewart, Adcock, Ian M., Sterk, Peter J., and Chung, Kian Fan

Published
2020
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13. IL-17–high asthma with features of a psoriasis immunophenotype

Author

Adcock, I.M., Ahmed, H., Auffray, C., Bakke, P., Bansal, A.T., Baribaud, F., Bates, S., Bel, E.H., Bigler, J., Bisgaard, H., Boedigheimer, M.J., Bønnelykke, K., Brandsma, J., Brinkman, P., Bucchioni, E., Burg, D., Bush, A., Caruso, M., Chaiboonchoe, A., Chanez, P., Chung, K.F., Compton, C.H., Corfield, J., D'Amico, A., Dahlen, S.E., De Meulder, B., Djukanovic, R., Erpenbeck, V.J., Erzen, D., Fichtner, K., Fitch, N., Fleming, L.J., Formaggio, E., Fowler, S.J., Frey, U., Gahlemann, M., Geiser, T., Guo, Y., Hashimoto, S., Haughney, J., Hedlin, G., Hekking, P.W., Higenbottam, T., Hohlfeld, J.M., Holweg, C., Horváth, I., Howarth, P., James, A.J., Knowles, R., Knox, A.J., Krug, N., Lefaudeux, D., Loza, M.J., Lutter, R., Manta, A., Masefield, S., Mazein, A., Meiser, A., Middelveld, R.J.M., Miralpeix, M., Montuschi, P., Mores, N., Murray, C.S., Musial, J., Myles, D., Pahus, L., Pandis, I., Pavlidis, S., Powell, P., Praticò, G., Rao, M. Puig N., Riley, J., Roberts, A., Roberts, G., Rowe, A., Sandström, T., Seibold, W., Selby, A., Shaw, D.E., Sigmund, R., Singer, F., Skipp, P.J., Sousa, A.R., Sterk, P.J., Sun, K., Thornton, B., van Aalderen, W.M., van Geest, M., Vestbo, J., Vissing, N.H., Wagener, A.H., Wagers, S.S., Weiszhart, Z., Wheelock, C.E., Wilson, S.J., Aliprantis, Antonios, Allen, David, Alving, Kjell, Badorrek, P., Balgoma, David, Ballereau, S., Barber, Clair, Batuwitage, Manohara Kanangana, Bautmans, A., Bedding, A., Behndig, A.F., Beleta, Jorge, Berglind, A., Berton, A., Bochenek, Grazyna, Braun, Armin, Campagna, D., Carayannopoulos, Leon, Casaulta, C., Chaleckis, Romanas, Dahlén, B., Davison, imothy, De Alba, Jorge, De Lepeleire, Inge, Dekker, Tamara, Delin, Ingrid, Dennison, P., Dijkhuis, Annemiek, Dodson, Paul, Draper, Aleksandra, Dyson, K., Edwards, Jessica, El Hadjam, L., Emma, Rosalia, Ericsson, Magnus, Faulenbach, C., Flood, Breda, Galffy, G., Gallart, Hector, Garissi, D., Gent, J., Gerhardsson de Verdier, M., Gibeon, D., Gomez, Cristina, Gove, Kerry, Gozzard, Neil, Guillmant-Farry, E., Henriksson, E., Hewitt, Lorraine, Hoda, U., Hu, Richard, Hu, Sile, Hu, X., Jeyasingham, E., Johnson, K., Jullian, N., Kamphuis, Juliette, Kennington, Erika J., Kerry, Dyson, Kerry, G., Klüglich, M., Knobel, Hugo, Kolmert, Johan, Konradsen, J.R., Kots, Maxim, Kretsos, Kosmas, Krueger, L., Kuo, Scott, Kupczyk, Maciej, Lambrecht, Bart, Lantz, A.-S., Larminie, Christopher, Larsson, L.X., Latzin, P., Lazarinis, N., Lemonnier, N., Lone-Latif, Saeeda, Lowe, L.A., Manta, Alexander, Marouzet, Lisa, Martin, Jane, Mathon, Caroline, McEvoy, L., Meah, Sally, Menzies-Gow, A., Metcalf, Leanne, Mikus, Maria, Monk, Philip, Naz, Shama, Nething, K., Nicholas, Ben, Nihlén, U., Nilsson, Peter, Niven, R., Nordlund, B., Nsubuga, S., Pacino, Antonio, Palkonen, Susanna, Pellet, J., Pennazza, Giorgio, Petrén, Anne, Pink, Sandy, Pison, C., Postle, Anthony, Rahman-Amin, Malayka, Ravanetti, Lara, Ray, Emma, Reinke, Stacey, Reynolds, Leanne, Riemann, K., Robberechts, Martine, Rocha, J.P., Rossios, C., Russell, Kirsty, Rutgers, Michael, Santini, G., Santoninco, Marco, Saqi, M., Schoelch, Corinna, Schofield, James P.R., Scott, S., Sehgal, N., Sjödin, Marcus, Smids, Barbara, Smith, Caroline, Smith, Jessica, Smith, Katherine M., Söderman, P., Sogbessan, A., Spycher, F., Staykova, Doroteya, Stephan, S., Stokholm, J., Strandberg, K., Sunther, M., Szentkereszty, M., Tamasi, L., Tariq, K., Thörngren, John-Olof, Thorsen, Jonathan, Valente, S., van de Pol, Marianne, van Drunen, C.M., Van Eyll, Jonathan, Versnel, Jenny, Vink, Anton, von Garnier, C., Vyas, A., Wald, Frans, Walker, Samantha, Ward, Jonathan, Wetzel, Kristiane, Wiegman, Coen, Williams, Siân, Yang, Xian, Yeyasingham, Elizabeth, Amgen, W. Yu, Zetterquist, W., Zolkipli, Z., Zwinderman, A.H., Östling, Jörgen, van Geest, Marleen, Jevnikar, Zala, Wilson, Susan, Lutter, Rene, Shaw, Dominick E., Bakke, Per S., Caruso, Massimo, Dahlen, Sven-Erik, Fowler, Stephen J., Horváth, Ildikó, Krug, Norbert, Montuschi, Paolo, Sanak, Marek, Sandström, Thomas, Sun, Kai, Pandis, Ioannis, Auffray, Charles, Sousa, Ana R., Guo, Yike, Adcock, Ian M., Howarth, Peter, Chung, Kian Fan, Bigler, Jeanette, Sterk, Peter J., Skipp, Paul J., Djukanović, Ratko, and Vaarala, Outi

Published
2019
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14. Modules, networks and systems medicine for understanding disease and aiding diagnosis

Author

Gustafsson, Mika, Nestor, Colm E, Zhang, Huan, Barabási, Albert-László, Baranzini, Sergio, Brunak, Sören, Chung, Kian Fan, Federoff, Howard J, Gavin, Anne-Claude, Meehan, Richard R, Picotti, Paola, Pujana, Miguel Ángel, Rajewsky, Nikolaus, Smith, Kenneth GC, Sterk, Peter J, Villoslada, Pablo, and Benson, Mikael

Subjects
Biological Sciences, Genetics, Biotechnology, Lung, Obesity, Aetiology, 2.1 Biological and endogenous factors, Generic health relevance, Good Health and Well Being, Clinical Sciences
Abstract

Many common diseases, such as asthma, diabetes or obesity, involve altered interactions between thousands of genes. High-throughput techniques (omics) allow identification of such genes and their products, but functional understanding is a formidable challenge. Network-based analyses of omics data have identified modules of disease-associated genes that have been used to obtain both a systems level and a molecular understanding of disease mechanisms. For example, in allergy a module was used to find a novel candidate gene that was validated by functional and clinical studies. Such analyses play important roles in systems medicine. This is an emerging discipline that aims to gain a translational understanding of the complex mechanisms underlying common diseases. In this review, we will explain and provide examples of how network-based analyses of omics data, in combination with functional and clinical studies, are aiding our understanding of disease, as well as helping to prioritize diagnostic markers or therapeutic candidate genes. Such analyses involve significant problems and limitations, which will be discussed. We also highlight the steps needed for clinical implementation.

Published
2014

15. Genomic Standards Consortium Projects

Author

Field, Dawn, Sterk, Peter, Kottmann, Renzo, De Smet, J Wim, Amaral-Zettler, Linda, Cochrane, Guy, Cole, James R, Davies, Neil, Dawyndt, Peter, Garrity, George M, Gilbert, Jack A, Glöckner, Frank Oliver, Hirschman, Lynette, Klenk, Hans-Peter, Knight, Rob, Kyrpides, Nikos, Meyer, Folker, Karsch-Mizrachi, Ilene, Morrison, Norman, Robbins, Robert, Gil, Inigo San, Sansone, Susanna, Schriml, Lynn, Tatusova, Tatiana, Ussery, Dave, Yilmaz, Pelin, White, Owen, Wooley, John, and Caporaso, Gregory

Subjects
Clinical Research, Genetics, Human Genome
Abstract

The Genomic Standards Consortium (GSC) is an open-membership community that was founded in 2005 to work towards the development, implementation and harmonization of standards in the field of genomics. Starting with the defined task of establishing a minimal set of descriptions the GSC has evolved into an active standards-setting body that currently has 18 ongoing projects, with additional projects regularly proposed from within and outside the GSC. Here we describe our recently enacted policy for proposing new activities that are intended to be taken on by the GSC, along with the template for proposing such new activities.

Published
2014

16. Stratification of asthma phenotypes by airway proteomic signatures

Author

Ahmed, H., Allen, D., Badorrek, P., Ballereau, S., Baribaud, F., Bedding, A., Behndig, A.F., Berglind, A., Berton, A., Bigler, J., Boedigheimer, M.J., Bønnelykke, K., Brinkman, P., Bush, A., Campagna, D., Casaulta, C., Chaiboonchoe, A., Davison, T., De Meulder, B., Delin, I., Dennison, P., Dodson, P., El Hadjam, L., Erzen, D., Faulenbach, C., Fichtner, K., Fitch, N., Formaggio, E., Gahlemann, M., Galffy, G., Garissi, D., Garret, T., Gent, J., Guillmant-Farry, E., Henriksson, E., Hoda, U., Hohlfeld, J.M., Hu, X., James, A., Johnson, K., Jullian, N., Kerry, G., Klüglich, M., Knowles, R., Konradsen, J.R., Kretsos, K., Krueger, L., Lantz, A.-S., Larminie, C., Latzin, P., Lefaudeux, D., Lemonnier, N., Lowe, L.A., Lutter, R., Manta, A., Mazein, A., McEvoy, L., Menzies-Gow, A., Mores, N., Murray, C.S., Nething, K., Nihlén, U., Niven, R., Nordlund, B., Nsubuga, S., Pellet, J., Pison, C., Praticò, G., Valls, M. Puig, Riemann, K., Rocha, J.P., Rossios, C., Santini, G., Saqi, M., Scott, S., Sehgal, N., Selby, A., Söderman, P., Sogbesan, A., Spycher, F., Stephan, S., Stokholm, J., Sunther, M., Szentkereszty, M., Tamasi, L., Tariq, K., Valente, S., van Aalderen, W.M., van Drunen, C.M., Van Eyll, J., Vyas, A., Yu, W., Zetterquist, W., Zolkipli, Z., Zwinderman, A.H., Schofield, James P.R., Burg, Dominic, Nicholas, Ben, Strazzeri, Fabio, Brandsma, Joost, Staykova, Doroteya, Folisi, Caterina, Bansal, Aruna T., Xian, Yang, Guo, Yike, Rowe, Anthony, Corfield, Julie, Wilson, Susan, Ward, Jonathan, Lutter, Rene, Shaw, Dominick E., Bakke, Per S., Caruso, Massimo, Dahlen, Sven-Erik, Fowler, Stephen J., Horváth, Ildikó, Howarth, Peter, Krug, Norbert, Montuschi, Paolo, Sanak, Marek, Sandström, Thomas, Sun, Kai, Pandis, Ioannis, Riley, John, Auffray, Charles, De Meulder, Bertrand, Lefaudeux, Diane, Sousa, Ana R., Adcock, Ian M., Chung, Kian Fan, Sterk, Peter J., Skipp, Paul J., and Djukanović, Ratko

Published
2019
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17. Identification and prospective stability of electronic nose (eNose)–derived inflammatory phenotypes in patients with severe asthma

Author

Brinkman, Paul, Wagener, Ariane H., Hekking, Pieter-Paul, Bansal, Aruna T., Maitland-van der Zee, Anke-Hilse, Wang, Yuanyue, Weda, Hans, Knobel, Hugo H., Vink, Teunis J., Rattray, Nicholas J., D'Amico, Arnaldo, Pennazza, Giorgio, Santonico, Marco, Lefaudeux, Diane, De Meulder, Bertrand, Auffray, Charles, Bakke, Per S., Caruso, Massimo, Chanez, Pascal, Chung, Kian F., Corfield, Julie, Dahlén, Sven-Erik, Djukanovic, Ratko, Geiser, Thomas, Horvath, Ildiko, Krug, Nobert, Musial, Jacek, Sun, Kai, Riley, John H., Shaw, Dominic E., Sandström, Thomas, Sousa, Ana R., Montuschi, Paolo, Fowler, Stephen J., and Sterk, Peter J.

Published
2019
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18. Epithelial IL-6 trans-signaling defines a new asthma phenotype with increased airway inflammation

Author

Adcock, I.M., Ahmed, H., Auffray, C., Bakke, P., Bansal, A.T., Baribaud, F., Bates, S., Bel, E.H., Bigler, J., Bisgaard, H., Boedigheimer, M.J., Bønnelykke, K., Brandsma, J., Brinkman, P., Bucchioni, E., Burg, D., Bush, A., Caruso, M., Chaiboonchoe, A., Chanez, P., Chung, F.K., Compton, C.H., Corfield, J., D'Amico, A., Dahlen, S.E., De Meulder, B., Djukanovic, R., Erpenbeck, V.J., Erzen, D., Fichtner, K., Fitch, N., Fleming, L.J., Formaggio, E., Fowler, S.J., Frey, U., Gahlemann, M., Geiser, T., Goss, V., Guo, Y., Hashimoto, S., Haughney, J., Hedlin, G., Hekking, P.W., Higenbottam, T., Hohlfeld, J.M., Holweg, C., Horváth, I., James, A.J., Knowles, R., Knox, A.J., Krug, N., Lefaudeux, D., Loza, M.J., Manta, A., Matthews, J.G., Mazein, A., Meiser, A., Middelveld, R.J.M., Miralpeix, M., Montuschi, P., Mores, N., Murray, C.S., Musial, J., Myles, D., Pahus, L., Pandis, I., Pavlidis, S., Postle, A., Powel, P., Praticò, G., Rao, N., Riley, J., Roberts, A., Roberts, G., Rowe, A., Sandström, T., Schofield, J.P.R., Seibold, W., Selby, A., Shaw, D.E., Sigmund, R., Singer, F., Skipp, P.J., Sousa, A.R., Sterk, P.J., Sun, K., Thornton, B., van Aalderen, W.M., van Geest, M., Vestbo, J., Vissing, N.H., Wagener, A.H., Wagers, S.S., Weiszhart, Z., Wheelock, C.E., Wilson, S.J., Jevnikar, Zala, Östling, Jörgen, Ax, Elisabeth, Calvén, Jenny, Thörn, Kristofer, Israelsson, Elisabeth, Öberg, Lisa, Singhania, Akul, Lau, Laurie C.K., Wilson, Susan J., Ward, Jonathan A., Chauhan, Anoop, Sousa, Ana R., De Meulder, Bertrand, Loza, Matthew J., Baribaud, Frédéric, Sterk, Peter J., Chung, Kian Fan, Sun, Kai, Guo, Yike, Adcock, Ian M., Payne, Debbie, Dahlen, Barbro, Chanez, Pascal, Shaw, Dominick E., Krug, Norbert, Hohlfeld, Jens M., Sandström, Thomas, Djukanovic, Ratko, James, Anna, Hinks, Timothy S.C., Howarth, Peter H., Vaarala, Outi, van Geest, Marleen, and Olsson, Henric

Published
2019
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19. Moderate-to-severe asthma in individuals of European ancestry: a genome-wide association study

Author

Shrine, Nick, Portelli, Michael A, John, Catherine, Soler Artigas, María, Bennett, Neil, Hall, Robert, Lewis, Jon, Henry, Amanda P, Billington, Charlotte K, Ahmad, Azaz, Packer, Richard J, Shaw, Dominick, Pogson, Zara E K, Fogarty, Andrew, McKeever, Tricia M, Singapuri, Amisha, Heaney, Liam G, Mansur, Adel H, Chaudhuri, Rekha, Thomson, Neil C, Holloway, John W, Lockett, Gabrielle A, Howarth, Peter H, Djukanovic, Ratko, Hankinson, Jenny, Niven, Robert, Simpson, Angela, Chung, Kian Fan, Sterk, Peter J, Blakey, John D, Adcock, Ian M, Hu, Sile, Guo, Yike, Obeidat, Maen, Sin, Don D, van den Berge, Maarten, Nickle, David C, Bossé, Yohan, Tobin, Martin D, Hall, Ian P, Brightling, Christopher E, Wain, Louise V, and Sayers, Ian

Published
2019
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21. Data-driven model links BMIz to gene expression in pediatric asthma

Author

Dandenault, Vincent, primary, Hachem, Nehme, additional, Adcock, Ian M, additional, Andersson, Lars I., additional, Auffray, Charles, additional, Chung, Fan K, additional, Dahlén, Sven-Erik, additional, De Meulder, Bertrand, additional, Djukanovic, Ratko, additional, Howarth, Peter, additional, Knowles, Richard G, additional, Krug, Norbert, additional, Roberts, Amanda, additional, Sousa, Ana R, additional, Sterk, Peter J., additional, Supple, David, additional, Rao, Navin, additional, Roberts, Graham, additional, Uddin, Mohib, additional, Wagers, Scott, additional, Maitland-Van Der Zee, Anke-Hilse, additional, and Longo, Cristina, additional

Published
2023
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22. Low levels of endogenous anabolic androgenic steroids in females with severe asthma taking corticosteroids

Author

Yasinska, Valentyna, primary, Gómez, Cristina, additional, Kolmert, Johan, additional, Ericsson, Magnus, additional, Pohanka, Anton, additional, James, Anna, additional, Andersson, Lars I., additional, Sparreman-Mikus, Maria, additional, Sousa, Ana R., additional, Riley, John H., additional, Bates, Stewart, additional, Bakke, Per S., additional, Zounemat Kermani, Nazanin, additional, Caruso, Massimo, additional, Chanez, Pascal, additional, Fowler, Stephen J., additional, Geiser, Thomas, additional, Howarth, Peter H., additional, Horváth, Ildikó, additional, Krug, Norbert, additional, Montuschi, Paolo, additional, Sanak, Marek, additional, Behndig, Annelie, additional, Shaw, Dominick E., additional, Knowles, Richard G., additional, Dahlén, Barbro, additional, Maitland-van der Zee, Anke-Hilse, additional, Sterk, Peter J., additional, Djukanovic, Ratko, additional, Adcock, Ian M., additional, Fan Chung, Kian, additional, Wheelock, Craig E., additional, Dahlén, Sven-Erik, additional, and Wikström Jonsson, Eva, additional

Published
2023
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24. Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012.

Author

Gilbert, Jack A, Bao, Yiming, Wang, Hui, Sansone, Susanna-Assunta, Edmunds, Scott C, Morrison, Norman, Meyer, Folker, Schriml, Lynn M, Davies, Neil, Sterk, Peter, Wilkening, Jared, Garrity, George M, Field, Dawn, Robbins, Robert, Smith, Daniel P, Mizrachi, Ilene, and Moreau, Corrie

Subjects
Genomic Observatories Network, Genomic Standards Consortium, fungal genomics, microbial metagenomics, microbiome, viral genomics, Biochemistry and Cell Biology, Genetics
Abstract

This report details the outcome of the 13(th) Meeting of the Genomic Standards Consortium. The three-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on March 5-7, 2012, and was hosted by the Beijing Genomics Institute. The meeting, titled From Genomes to Interactions to Communities to Models, highlighted the role of data standards associated with genomic, metagenomic, and amplicon sequence data and the contextual information associated with the sample. To this end the meeting focused on genomic projects for animals, plants, fungi, and viruses; metagenomic studies in host-microbe interactions; and the dynamics of microbial communities. In addition, the meeting hosted a Genomic Observatories Network session, a Genomic Standards Consortium biodiversity working group session, and a Microbiology of the Built Environment session sponsored by the Alfred P. Sloan Foundation.

Published
2012

25. The Genomic Standards Consortium.

Author

Field, Dawn, Amaral-Zettler, Linda, Cochrane, Guy, Cole, James R, Dawyndt, Peter, Garrity, George M, Gilbert, Jack, Glöckner, Frank Oliver, Hirschman, Lynette, Karsch-Mizrachi, Ilene, Klenk, Hans-Peter, Knight, Rob, Kottmann, Renzo, Kyrpides, Nikos, Meyer, Folker, San Gil, Inigo, Sansone, Susanna-Assunta, Schriml, Lynn M, Sterk, Peter, Tatusova, Tatiana, Ussery, David W, White, Owen, and Wooley, John

Subjects
Genomics, International Cooperation, Databases, Genetic, Metagenome, Human Genome, Genetics, Generic health relevance, Developmental Biology, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences
Abstract

A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic Standards Consortium (GSC), an open-membership organization that drives community-based standardization activities, Here we provide a short history of the GSC, provide an overview of its range of current activities, and make a call for the scientific community to join forces to improve the quality and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences.

Published
2011

26. Meeting report of the RNA Ontology Consortium January 8-9, 2011.

Author

Birmingham, Amanda, Clemente, Jose C, Desai, Narayan, Gilbert, Jack, Gonzalez, Antonio, Kyrpides, Nikos, Meyer, Folker, Nawrocki, Eric, Sterk, Peter, Stombaugh, Jesse, Weinberg, Zasha, Wendel, Doug, Leontis, Neocles B, Zirbel, Craig, Knight, Rob, and Laederach, Alain

Subjects
Biochemistry and Cell Biology, Genetics
Abstract

This report summarizes the proceedings of the structure mapping working group meeting of the RNA Ontology Consortium (ROC), held in Kona, Hawaii on January 8-9, 2011. The ROC hosted this workshop to facilitate collaborations among those researchers formalizing concepts in RNA, those developing RNA-related software, and those performing genome annotation and standardization. The workshop included three software presentations, extended round-table discussions, and the constitution of two new working groups, the first to address the need for better software integration and the second to discuss standardization and benchmarking of existing RNA annotation pipelines. These working groups have subsequently pursued concrete implementation of actions suggested during the discussion. Further information about the ROC and its activities can be found at http://roc.bgsu.edu/.

Published
2011

27. Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10.

Author

Glass, Elizabeth, Meyer, Folker, Gilbert, Jack A, Field, Dawn, Hunter, Sarah, Kottmann, Renzo, Kyrpides, Nikos, Sansone, Susanna, Schriml, Lynn, Sterk, Peter, White, Owen, and Wooley, John

Subjects
Biochemistry and Cell Biology, Genetics
Abstract

This report summarizes the proceedings of the 10th workshop of the Genomic Standards Consortium (GSC), held at Argonne National Laboratory, IL, USA. It was the second GSC workshop to have open registration and attracted over 60 participants who worked together to progress the full range of projects ongoing within the GSC. Overall, the primary focus of the workshop was on advancing the M5 platform for next-generation collaborative computational infrastructures. Other key outcomes included the formation of a GSC working group focused on MIGS/MIMS/MIENS compliance using the ISA software suite and the formal launch of the GSC Developer Working Group. Further information about the GSC and its range of activities can be found at http://gensc.org/.

Published
2010

28. Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9.

Author

Davidsen, Tanja, Madupu, Ramana, Sterk, Peter, Field, Dawn, Garrity, George, Gilbert, Jack, Glöckner, Frank Oliver, Hirschman, Lynette, Kolker, Eugene, Kottmann, Renzo, Kyrpides, Nikos, Meyer, Folker, Morrison, Norman, Schriml, Lynn, Tatusova, Tatiana, and Wooley, John

Subjects
Biochemistry and Cell Biology, Genetics
Abstract

This report summarizes the proceedings of the 9th workshop of the Genomic Standards Consortium (GSC), held at the J. Craig Venter Institute, Rockville, MD, USA. It was the first GSC workshop to have open registration and attracted over 90 participants. This workshop featured sessions that provided overviews of the full range of ongoing GSC projects. It included sessions on Standards in Genomic Sciences, the open access journal of the GSC, building standards for genome annotation, the M5 platform for next-generation collaborative computational infrastructures, building ties with the biodiversity research community and two discussion panels with government and industry participants. Progress was made on all fronts, and major outcomes included the completion of the MIENS specification for publication and the formation of the Biodiversity working group.

Published
2010

29. Oropharyngeal Microbiota Clusters in Children with Asthma/Wheeze Associate with Allergy, Blood Transcriptomic Immune Pathways and Exacerbations Risk

Author

Abdel-Aziz, Mahmoud I., primary, Thorsen, Jonathan, additional, Hashimoto, Simone, additional, Vijverberg, Susanne J H, additional, Neerincx, Anne H, additional, Brinkman, Paul, additional, van Aalderen, Wim, additional, Stokholm, Jakob, additional, Rasmussen, Morten Arendt, additional, Roggenbuck-Wedemeyer, Michael, additional, Vissing, Nadja H, additional, Mortensen, Martin Steen, additional, Brejnrod, Asker Daniel, additional, Fleming, Louise J, additional, Murray, Clare S, additional, Fowler, Stephen J, additional, Frey, Urs, additional, Bush, Andrew, additional, Singer, Florian, additional, Hedlin, Gunilla, additional, Nordlund, Björn, additional, Shaw, Dominick E, additional, Chung, Kian Fan, additional, Adcock, Ian M, additional, Djukanovic, Ratko, additional, Auffray, Charles, additional, Bansal, Aruna T, additional, Sousa, Ana R, additional, Wagers, Scott S, additional, Chawes, Bo Lund, additional, Bønnelykke, Klaus, additional, Sørensen, Søren Johannes, additional, Kraneveld, Aletta D., additional, Sterk, Peter J, additional, Roberts, Graham, additional, Bisgaard, Hans, additional, and Maitland-van der Zee, Anke H., additional

Published
2023
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32. Haemophilus influenzae and Moraxella catarrhalis in sputum of severe asthma with inflammasome and neutrophil activation.

Author

Versi, Ali, Ivan, Fransiskus Xaverius, Abdel‐Aziz, Mahmoud I., Bates, Stewart, Riley, John, Baribaud, Frederic, Kermani, Nazanin Zounemat, Montuschi, Paolo, Dahlen, Sven‐Erik, Djukanovic, Ratko, Sterk, Peter, Maitland‐Van Der Zee, Anke H., Chotirmall, Sanjay H., Howarth, Peter, Adcock, Ian M., Chung, Kian Fan, Andersson, LI, Auffray, C, Badi, YE, and Bakke, P

Subjects
HAEMOPHILUS influenzae, MORAXELLA catarrhalis, SPUTUM, ASTHMA, ASTHMATICS, HAEMOPHILUS diseases
Abstract

Background: Because of altered airway microbiome in asthma, we analysed the bacterial species in sputum of patients with severe asthma. Methods: Whole genome sequencing was performed on induced sputum from non‐smoking (SAn) and current or ex‐smoker (SAs/ex) severe asthma patients, mild/moderate asthma (MMA) and healthy controls (HC). Data were analysed by asthma severity, inflammatory status and transcriptome‐associated clusters (TACs). Results: α‐diversity at the species level was lower in SAn and SAs/ex, with an increase in Haemophilus influenzae and Moraxella catarrhalis, and Haemophilus influenzae and Tropheryma whipplei, respectively, compared to HC. In neutrophilic asthma, there was greater abundance of Haemophilus influenzae and Moraxella catarrhalis and in eosinophilic asthma, Tropheryma whipplei was increased. There was a reduction in α‐diversity in TAC1 and TAC2 that expressed high levels of Haemophilus influenzae and Tropheryma whipplei, and Haemophilus influenzae and Moraxella catarrhalis, respectively, compared to HC. Sputum neutrophils correlated positively with Moraxella catarrhalis and negatively with Prevotella, Neisseria and Veillonella species and Haemophilus parainfluenzae. Sputum eosinophils correlated positively with Tropheryma whipplei which correlated with pack‐years of smoking. α‐ and β‐diversities were stable at one year. Conclusions: Haemophilus influenzae and Moraxella catarrhalis were more abundant in severe neutrophilic asthma and TAC2 linked to inflammasome and neutrophil activation, while Haemophilus influenzae and Tropheryma whipplei were highest in SAs/ex and in TAC1 associated with highest expression of IL‐13 type 2 and ILC2 signatures with the abundance of Tropheryma whipplei correlating positively with sputum eosinophils. Whether these bacterial species drive the inflammatory response in asthma needs evaluation. [ABSTRACT FROM AUTHOR]

Published
2023
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35. Macrophage migration inhibitory factor promotes glucocorticoid resistance of neutrophilic inflammation in a murine model of severe asthma.

Author

Rama Raju Allam, Venkata Sita, Pavlidis, Stelios, Gang Liu, Kermani, Nazanin Zounemat, Simpson, Jennifer, To, Joyce, Donnelly, Sheila, Yi-Ke Guo, Hansbro, Philip M., Phipps, Simon, Morand, Eric F., Djukanovic, Ratko, Sterk, Peter, Kian Fan Chung, Adcock, Ian, Harris, James, Sukkar, Maria B., Allam, Venkata Sita Rama Raju, Liu, Gang, and Guo, Yi-Ke

Subjects
MACROPHAGE migration inhibitory factor, ASTHMA, WHEEZE, ECZEMA, GLUCOCORTICOIDS, NLRP3 protein, CHRONIC obstructive pulmonary disease
Abstract

Background: Severe neutrophilic asthma is resistant to treatment with glucocorticoids. The immunomodulatory protein macrophage migration inhibitory factor (MIF) promotes neutrophil recruitment to the lung and antagonises responses to glucocorticoids. We hypothesised that MIF promotes glucocorticoid resistance of neutrophilic inflammation in severe asthma.Methods: We examined whether sputum MIF protein correlated with clinical and molecular characteristics of severe neutrophilic asthma in the Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes (U-BIOPRED) cohort. We also investigated whether MIF regulates neutrophilic inflammation and glucocorticoid responsiveness in a murine model of severe asthma in vivo.Results: MIF protein levels positively correlated with the number of exacerbations in the previous year, sputum neutrophils and oral corticosteroid use across all U-BIOPRED subjects. Further analysis of MIF protein expression according to U-BIOPRED-defined transcriptomic-associated clusters (TACs) revealed increased MIF protein and a corresponding decrease in annexin-A1 protein in TAC2, which is most closely associated with airway neutrophilia and NLRP3 inflammasome activation. In a murine model of severe asthma, treatment with the MIF antagonist ISO-1 significantly inhibited neutrophilic inflammation and increased glucocorticoid responsiveness. Coimmunoprecipitation studies using lung tissue lysates demonstrated that MIF directly interacts with and cleaves annexin-A1, potentially reducing its biological activity.Conclusion: Our data suggest that MIF promotes glucocorticoid-resistance of neutrophilic inflammation by reducing the biological activity of annexin-A1, a potent glucocorticoid-regulated protein that inhibits neutrophil accumulation at sites of inflammation. This represents a previously unrecognised role for MIF in the regulation of inflammation and points to MIF as a potential therapeutic target for the management of severe neutrophilic asthma. [ABSTRACT FROM AUTHOR]

Published
2023
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37. H influenzae & M catarrhalis in sputum of severe asthma with inflammasome and neutrophil activation

Author

Chung, Kian Fan, primary, Versi, Ali, additional, Ivan, Fransiskus Xaverius, additional, Ibrahim, Mahmoud, additional, Bates, Stewart, additional, Riley, John, additional, Baribaud, Frederic, additional, Kermani, Nazanin Zounemat, additional, Montuschi, Paolo, additional, Dahlén, Sven-Erik, additional, Djukanovic, Ratko, additional, Sterk, Peter, additional, Zee, Anke-Hilse Maitland-van der, additional, Chotirmall, Sanjay Haresh, additional, Howarth, Peter, additional, and Adcock, Ian, additional

Published
2022
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38. Th2 high and mast cell gene signatures are associated with corticosteroid sensitivity in COPD

Author

Faiz, Alen, primary, Pavlidis, Stelios, additional, Kuo, Chih-Hsi, additional, Rowe, Anthony, additional, Hiemstra, Pieter S, additional, Timens, Wim, additional, Berg, Marijn, additional, Wisman, Marissa, additional, Guo, Yi-Ke, additional, Djukanović, Ratko, additional, Sterk, Peter, additional, Meyer, Kerstin B, additional, Nawijn, Martijn C, additional, Adcock, Ian, additional, Chung, Kian Fan, additional, and van den Berge, Maarten, additional

Published
2022
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39. Asthma and Wheeze Severity and the Oropharyngeal Microbiota in Children and Adolescents

Author

Thorsen, Jonathan, primary, Stokholm, Jakob, additional, Rasmussen, Morten Arendt, additional, Roggenbuck-Wedemeyer, Michael, additional, Vissing, Nadja H., additional, Mortensen, Martin S., additional, Brejnrod, Asker D., additional, Fleming, Louise, additional, Bush, Andrew, additional, Roberts, Graham, additional, Singer, Florian, additional, Frey, Urs, additional, Hedlin, Gunilla, additional, Nordlund, Björn, additional, Murray, Clare S., additional, Abdel-Aziz, Mahmoud I., additional, Hashimoto, Simone, additional, van Aalderen, Wim, additional, Maitland-van der Zee, Anke H., additional, Shaw, Dominick, additional, Fowler, Stephen J., additional, Sousa, Ana, additional, Sterk, Peter J., additional, Chung, Kian Fan, additional, Adcock, Ian M., additional, Djukanovic, Ratko, additional, Auffray, Charles, additional, Bansal, Aruna T., additional, Wagers, Scott, additional, Chawes, Bo, additional, Bønnelykke, Klaus, additional, Sørensen, Søren Johannes, additional, and Bisgaard, Hans, additional

Published
2022
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40. Macrophage migration inhibitory factor promotes glucocorticoid resistance of neutrophilic inflammation in a murine model of severe asthma

Author

Allam, Venkata Sita Rama Raju, primary, Pavlidis, Stelios, additional, Liu, Gang, additional, Kermani, Nazanin Zounemat, additional, Simpson, Jennifer, additional, To, Joyce, additional, Donnelly, Sheila, additional, Guo, Yi-Ke, additional, Hansbro, Philip M, additional, Phipps, Simon, additional, Morand, Eric F, additional, Djukanovic, Ratko, additional, Sterk, Peter, additional, Chung, Kian Fan, additional, Adcock, Ian, additional, Harris, James, additional, and Sukkar, Maria B, additional

Published
2022
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43. Sputum transcriptomics reveal upregulation of IL-1 receptor family members in patients with severe asthma

Author

Rossios, Christos, Pavlidis, Stelios, Hoda, Uruj, Kuo, Chih-Hsi, Wiegman, Coen, Russell, Kirsty, Sun, Kai, Loza, Matthew J., Baribaud, Frederic, Durham, Andrew L., Ojo, Oluwaseun, Lutter, Rene, Rowe, Anthony, Bansal, Aruna, Auffray, Charles, Sousa, Ana, Corfield, Julie, Djukanovic, Ratko, Guo, Yike, Sterk, Peter J., Chung, Kian Fan, and Adcock, Ian M.

Published
2018
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45. Th2 high and mast cell gene signatures are associated with corticosteroid sensitivity in COPD.

Author

Faiz, Alen, Pavlidis, Stelios, Chih-Hsi Kuo, Rowe, Anthony, Hiemstra, Pieter S., Timens, Wim, Berg, Marijn, Wisman, Marissa, Yi-Ke Guo, Djukanović, Ratko, Sterk, Peter, Meyer, Kerstin B., Nawijn, Martijn C., Adcock, Ian, Kian Fan Chung, and van den Berge, Maarten

Subjects
MAST cells, WHEEZE, MAST cell disease, CHRONIC obstructive pulmonary disease, MOLECULAR biology, OBSTRUCTIVE lung diseases, CONNECTIVE tissue cells
Published
2023
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46. Lipid phenotyping of lung epithelial lining fluid in healthy human volunteers

Author

Brandsma, Joost, Goss, Victoria M., Yang, Xian, Bakke, Per S., Caruso, Massimo, Chanez, Pascal, Dahlén, Sven-Erik, Fowler, Stephen J., Horvath, Ildiko, Krug, Norbert, Montuschi, Paolo, Sanak, Marek, Sandström, Thomas, Shaw, Dominick E., Chung, Kian Fan, Singer, Florian, Fleming, Louise J., Sousa, Ana R., Pandis, Ioannis, Bansal, Aruna T., Sterk, Peter J., Djukanović, Ratko, Postle, Anthony D., and The U-BIOPRED Study Group

Published
2018
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47. A computational framework for complex disease stratification from multiple large-scale datasets

Author

De Meulder, Bertrand, Lefaudeux, Diane, Bansal, Aruna T., Mazein, Alexander, Chaiboonchoe, Amphun, Ahmed, Hassan, Balaur, Irina, Saqi, Mansoor, Pellet, Johann, Ballereau, Stéphane, Lemonnier, Nathanaël, Sun, Kai, Pandis, Ioannis, Yang, Xian, Batuwitage, Manohara, Kretsos, Kosmas, van Eyll, Jonathan, Bedding, Alun, Davison, Timothy, Dodson, Paul, Larminie, Christopher, Postle, Anthony, Corfield, Julie, Djukanovic, Ratko, Chung, Kian Fan, Adcock, Ian M., Guo, Yi-Ke, Sterk, Peter J., Manta, Alexander, Rowe, Anthony, Baribaud, Frédéric, Auffray, Charles, and the U-BIOPRED Study Group and the eTRIKS Consortium

Published
2018
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