Author: "Debyser, Griet" - Searchworks@Jio Institute Digital Library Search Results

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31 results on '"Debyser, Griet"'

1. Diving into the Structural Details of In Vitro Transcribed mRNA Using Liquid Chromatography-Mass Spectrometry-Based Oligonucleotide Profiling

Author: Morreel, Kris, t'Kindt, Ruben, Debyser, Griet, Jonckheere, Stefanie, Sandra, Pat, and Sandra, Koen
Subjects: Genetic translation, Messenger RNA, Mass spectrometry, Nucleotides, Liquid chromatography, Vaccines, Chemistry, Science and technology
Abstract: The production process of in vitro transcribed messenger RNA (IVT-mRNA)-based vaccines has matured in recent years, partly due to the fight against infectious diseases such as COVID-19. One key to success has been the use of modified, next to canonical, nucleotides and the efficient addition of a Cap-structure and poly A tail to the 5' and 3' end, respectively, of this massive biomolecule. These important features affect mRNA stability and impact translation efficiency, consequently boosting the optimization and implementation of liquid chromatography-mass spectrometry (LC-MS)-based oligonucleotide profiling methods for their characterization. This article will provide an overview of these LC-MS methods at a fundamental and application level. It will be shown how LC-MS is implemented in mRNA-based vaccine analysis to determine the capping efficiency and the poly A tail length, and how it allows, via RNA mapping, (i) to determine the mRNA sequence, (ii) to screen the fidelity of the manufactured modifications, and (iii) to identify and quantify unwanted modifications resulting from manufacturing or storage, and sequence variants resulting from mutation or transcription errors., When dealing with the coronavirus pandemic, academia and pharmaceutical companies have been investing greatly in vaccine development and production during the last two years (1,2). Noticeably for the first time, [...]
Published: 2022

2. A Method for Comprehensive Proteomic Analysis of Human Faecal Samples to Investigate Gut Dysbiosis in Patients with Cystic Fibrosis

Author: Debyser, Griet, Aerts, Maarten, Van Hecke, Pieter, Mesuere, Bart, Duytschaever, Gwen, Dawyndt, Peter, De Boeck, Kris, Vandamme, Peter, Devreese, Bart, COHEN, IRUN R., Editorial Board Member, LAJTHA, ABEL, Editorial Board Member, LAMBRIS, JOHN D., Editorial Board Member, PAOLETTI, RODOLFO, Editorial Board Member, REZAEI, NIMA, Editorial Board Member, and Capelo-Martínez, José-Luis, editor
Published: 2019
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3. Faecal proteomics: A tool to investigate dysbiosis and inflammation in patients with cystic fibrosis

Author: Debyser, Griet, Mesuere, Bart, Clement, Lieven, Van de Weygaert, Jens, Van Hecke, Pieter, Duytschaever, Gwen, Aerts, Maarten, Dawyndt, Peter, De Boeck, Kris, Vandamme, Peter, and Devreese, Bart
Published: 2016
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4. Unraveling the venom proteome of the bumblebee (Bombus terrestris) by integrating a combinatorial peptide ligand library approach with FT-ICR MS

Author: Van Vaerenbergh, Matthias, Debyser, Griet, Smagghe, Guy, Devreese, Bart, and de Graaf, Dirk C.
Published: 2015
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5. Exploring the hidden honeybee (Apis mellifera) venom proteome by integrating a combinatorial peptide ligand library approach with FTMS

Author: Van Vaerenbergh, Matthias, Debyser, Griet, Devreese, Bart, and de Graaf, Dirk C.
Published: 2014
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6. Elevated faecal ovotransferrin concentrations are indicative for intestinal barrier failure in broiler chickens

Author: Goossens, Evy, Debyser, Griet, Callens, Chana, De Gussem, Maarten, Dedeurwaerder, Annelike, Devreese, Bart, Haesebrouck, Freddy, Flügel, Monika, Pelzer, Stefan, Thiemann, Frank, Ducatelle, Richard, and Van Immerseel, Filip
Published: 2018
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7. Milk fat globule membrane glycoproteins prevent adhesion of the colonic microbiota and result in increased bacterial butyrate production

Author: Struijs, Karin, Van de Wiele, Tom, Le, Thien Trung, Debyser, Griet, Dewettinck, Koen, Devreese, Bart, and Van Camp, John
Published: 2013
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8. Distribution and isolation of milk fat globule membrane proteins during dairy processing as revealed by proteomic analysis

Author: Le, Thien Trung, Debyser, Griet, Gilbert, William, Struijs, Karin, Van Camp, John, Van de Wiele, Tom, Devreese, Bart, and Dewettinck, Koen
Published: 2013
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9. Multiplicity of aspartic proteinases from Cynara cardunculus L.

Author: Sergeant, Kuell, Sarmento, Ana Cristina, Lopes, Henrique, Oliveira, Cláudia S., Vitorino, Rui, Samyn, Bart, Sergeant, Kjell, Debyser, Griet, Van Beeumen, Jozef, Domingues, Pedro, Amado, Francisco, Pires, Euclides, Domingues, M. Rosário M., and Barros, Marlene T.
Published: 2009

10. Resistance of the dopamine D4 receptor to agonist-induced internalization and degradation

Author: Spooren, Anneleen, Rondou, Pieter, Debowska, Katarzyna, Lintermans, Béatrice, Vermeulen, Linda, Samyn, Bart, Skieterska, Kamila, Debyser, Griet, Devreese, Bart, Vanhoenacker, Peter, Wojda, Urszula, Haegeman, Guy, and Van Craenenbroeck, Kathleen
Published: 2010
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11. Multiplicity of aspartic proteinases from Cynara cardunculus L.

Author: Sarmento, Ana Cristina, Lopes, Henrique, Oliveira, Cláudia S., Vitorino, Rui, Samyn, Bart, Sergeant, Kjell, Debyser, Griet, Van Beeumen, Jozef, Domingues, Pedro, Amado, Francisco, Pires, Euclides, Domingues, M. Rosário M., and Barros, Marlene T.
Published: 2009
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12. Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients

Author: Van Puyvelde, Bart, primary, Van Uytfanghe, Katleen, additional, Tytgat, Olivier, additional, Van Oudenhove, Laurence, additional, Gabriels, Ralf, additional, Bouwmeester, Robbin, additional, Daled, Simon, additional, Van Den Bossche, Tim, additional, Ramasamy, Pathmanaban, additional, Verhelst, Sigrid, additional, De Clerck, Laura, additional, Corveleyn, Laura, additional, Willems, Sander, additional, Debunne, Nathan, additional, Wynendaele, Evelien, additional, De Spiegeleer, Bart, additional, Judak, Peter, additional, Roels, Kris, additional, De Wilde, Laurie, additional, Van Eenoo, Peter, additional, Reyns, Tim, additional, Cherlet, Marc, additional, Dumont, Emmie, additional, Debyser, Griet, additional, t’Kindt, Ruben, additional, Sandra, Koen, additional, Gupta, Surya, additional, Drouin, Nicolas, additional, Harms, Amy, additional, Hankemeier, Thomas, additional, Jones, Donald J. L., additional, Gupta, Pankaj, additional, Lane, Dan, additional, Lane, Catherine S., additional, El Ouadi, Said, additional, Vincendet, Jean-Baptiste, additional, Morrice, Nick, additional, Oehrle, Stuart, additional, Tanna, Nikunj, additional, Silvester, Steve, additional, Hannam, Sally, additional, Sigloch, Florian C., additional, Bhangu-Uhlmann, Andrea, additional, Claereboudt, Jan, additional, Anderson, N. Leigh, additional, Razavi, Morteza, additional, Degroeve, Sven, additional, Cuypers, Lize, additional, Stove, Christophe, additional, Lagrou, Katrien, additional, Martens, Geert A., additional, Deforce, Dieter, additional, Martens, Lennart, additional, Vissers, Johannes P. C., additional, and Dhaenens, Maarten, additional
Published: 2021
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13. A case study of de novo sequence analysis of N-sulfonated peptides by MALDI TOF/TOF mass spectrometry

Author: Samyn, Bart, Debyser, Griet, Sergeant, Kjell, Devreese, Bart, and Van Beeumen, Jozef
Published: 2004
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14. Finding the Missing Honey Bee Genes: Lessons Learned From a Genome Upgrade

Author: Elsik, Christine G, Worley, Kim C, Bennett, Anna K, Beye, Martin, Camara, Francisco, Childers, Christopher P, de Graaf, Dirk C, Debyser, Griet, Deng, Jixin, Devreese, Bart, Elhaik, Eran, Evans, Jay D, Foster, Leonard J, Graur, Dan, Guigo, Roderic, HGSC production teams, Hoff, Katharina Jasmin, Holder, Michael E, Hudson, Matthew E, Hunt, Greg, Jiang, Huaiyang, Joshi, Vandita, Khetani, Radhika S, Kosarev, Peter, Kovar, Christie L, Ma, Jian, Maleszka, Ryszard, Moritz, Robin FA, Munoz-Torres, Monica C, Murphy, Terence D, Muzny, Donna M, Newsham, Irene F, Reese, Justin T, Robertson, Hugh M, Robinson, Gene E, Rueppell, Olav, Solovyev, Victor, Stanke, Mario, Stolle, Eckart, Tsuruda, Jennifer M, Van Vaerenbergh, Matthias, Waterhouse, Robert M, Weaver, Daniel B, Whitfield, Charles W, Wu, Yuanqing, Zdobnov, Evgeny M, Zhang, Lan, Zhu, Dianhui, and Gibbs, Richard A
Subjects: Apis mellifera, GC content, Gene annotation, Gene prediction, Genome assembly, Genome improvement, Genome sequencing, Repetitive DNA, Transcriptome, fungi
Abstract: Background The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. Results Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. Conclusions Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.
Published: 2014

15. A shotgun metaproteomics approach to study the microbiome of cystic fibrosis (CF) patients

Author: Debyser, Griet, Mesuere, Bart, Dawyndt, Peter, Vandamme, Peter, and Devreese, Bart
Subjects: Medicine and Health Sciences
Published: 2012

16. The genomes of two key bumblebee species with primitive eusocial organization

Author: Sadd, Ben M., Barribeau, Seth M., Bloch, Guy, de Graaf, Dirk C., Dearden, Peter, Elsik, Christine G., Gadau, Jürgen, Grimmelikhuijzen, Cornelis J. P., Hasselmann, Martin, Lozier, Jeffrey D., Robertson, Hugh M., Smagghe, Guy, Stolle, Eckart, Van Vaerenbergh, Matthias, Waterhouse, Robert M., Bornberg-Bauer, Erich, Klasberg, Steffen, Bennett, Anna K., Câmara, Francisco, Guigó, Roderic, Hoff, Katharina, Mariotti, Marco, Munoz-Torres, Monica, Murphy, Terence, Santesmasses, Didac, Amdam, Gro V., Beckers, Matthew, Beye, Martin, Biewer, Matthias, Bitondi, Márcia M. G., Blaxter, Mark L., Bourke, Andrew F. G., Brown, Mark J. F., Buechel, Severine D., Cameron, Rossanah, Cappelle, Kaat, Carolan, James C., Christiaens, Olivier, Ciborowski, Kate L., Clarke, David F., Colgan, Thomas J., Collins, David H., Cridge, Andrew G., Dalmay, Tamas, Dreier, Stephanie, du Plessis, Louis, Duncan, Elizabeth, Erler, Silvio, Evans, Jay, Falcon, Tiago, Flores, Kevin, Freitas, Flávia C. P., Fuchikawa, Taro, Gempe, Tanja, Hartfelder, Klaus, Hauser, Frank, Helbing, Sophie, Humann, Fernanda C., Irvine, Frano, Jermiin, Lars S., Johnson, Claire E., Johnson, Reed M., Jones, Andrew K., Kadowaki, Tatsuhiko, Kidner, Jonathan H., Koch, Vasco, Köhler, Arian, Kraus, F. Bernhard, Lattorff, H. Michael G., Leask, Megan, Lockett, Gabrielle A., Mallon, Eamonn B., Antonio, David S. Marco, Marxer, Monika, Meeus, Ivan, Moritz, Robin F. A., Nair, Ajay, Näpflin, Kathrin, Nissen, Inga, Niu, Jinzhi, Nunes, Francis M. F., Oakeshott, John G., Osborne, Amy, Otte, Marianne, Pinheiro, Daniel G., Rossié, Nina, Rueppell, Olav, Santos, Carolina G., Schmid-Hempel, Regula, Schmitt, Björn D., Schulte, Christina, Simões, Zilá L. P., Soares, Michelle P. M., Swevers, Luc, Winnebeck, Eva C., Wolschin, Florian, Yu, Na, Zdobnov, Evgeny M., Aqrawi, Peshtewani K., Blankenburg, Kerstin P., Coyle, Marcus, Francisco, Liezl, Hernandez, Alvaro G., Holder, Michael, Hudson, Matthew E., Jackson, LaRonda, Jayaseelan, Joy, Joshi, Vandita, Kovar, Christie, Lee, Sandra L., Mata, Robert, Mathew, Tittu, Newsham, Irene F., Ngo, Robin, Okwuonu, Geoffrey, Pham, Christopher, Pu, Ling-Ling, Saada, Nehad, Santibanez, Jireh, Simmons, DeNard, Thornton, Rebecca, Venkat, Aarti, Walden, Kimberly Ko, Wu, Yuan-Qing, Debyser, Griet, Devreese, Bart, Asher, Claire, Blommaert, Julie, Chipman, Ariel D., Chittka, Lars, Fouks, Bertrand, Liu, Jisheng, O'Neill, Meaghan P., Sumner, Seirian, Puiu, Daniela, Qu, Jiaxin, Salzberg, Steven L., Scherer, Steven E., Muzny, Donna M., Richards, Stephen, Robinson, Gene E., Gibbs, Richard A., Schmid-Hempel, Paul, Worley, Kim C., Sadd, Ben M., Barribeau, Seth M., Bloch, Guy, de Graaf, Dirk C., Dearden, Peter, Elsik, Christine G., Gadau, Jürgen, Grimmelikhuijzen, Cornelis J. P., Hasselmann, Martin, Lozier, Jeffrey D., Robertson, Hugh M., Smagghe, Guy, Stolle, Eckart, Van Vaerenbergh, Matthias, Waterhouse, Robert M., Bornberg-Bauer, Erich, Klasberg, Steffen, Bennett, Anna K., Câmara, Francisco, Guigó, Roderic, Hoff, Katharina, Mariotti, Marco, Munoz-Torres, Monica, Murphy, Terence, Santesmasses, Didac, Amdam, Gro V., Beckers, Matthew, Beye, Martin, Biewer, Matthias, Bitondi, Márcia M. G., Blaxter, Mark L., Bourke, Andrew F. G., Brown, Mark J. F., Buechel, Severine D., Cameron, Rossanah, Cappelle, Kaat, Carolan, James C., Christiaens, Olivier, Ciborowski, Kate L., Clarke, David F., Colgan, Thomas J., Collins, David H., Cridge, Andrew G., Dalmay, Tamas, Dreier, Stephanie, du Plessis, Louis, Duncan, Elizabeth, Erler, Silvio, Evans, Jay, Falcon, Tiago, Flores, Kevin, Freitas, Flávia C. P., Fuchikawa, Taro, Gempe, Tanja, Hartfelder, Klaus, Hauser, Frank, Helbing, Sophie, Humann, Fernanda C., Irvine, Frano, Jermiin, Lars S., Johnson, Claire E., Johnson, Reed M., Jones, Andrew K., Kadowaki, Tatsuhiko, Kidner, Jonathan H., Koch, Vasco, Köhler, Arian, Kraus, F. Bernhard, Lattorff, H. Michael G., Leask, Megan, Lockett, Gabrielle A., Mallon, Eamonn B., Antonio, David S. Marco, Marxer, Monika, Meeus, Ivan, Moritz, Robin F. A., Nair, Ajay, Näpflin, Kathrin, Nissen, Inga, Niu, Jinzhi, Nunes, Francis M. F., Oakeshott, John G., Osborne, Amy, Otte, Marianne, Pinheiro, Daniel G., Rossié, Nina, Rueppell, Olav, Santos, Carolina G., Schmid-Hempel, Regula, Schmitt, Björn D., Schulte, Christina, Simões, Zilá L. P., Soares, Michelle P. M., Swevers, Luc, Winnebeck, Eva C., Wolschin, Florian, Yu, Na, Zdobnov, Evgeny M., Aqrawi, Peshtewani K., Blankenburg, Kerstin P., Coyle, Marcus, Francisco, Liezl, Hernandez, Alvaro G., Holder, Michael, Hudson, Matthew E., Jackson, LaRonda, Jayaseelan, Joy, Joshi, Vandita, Kovar, Christie, Lee, Sandra L., Mata, Robert, Mathew, Tittu, Newsham, Irene F., Ngo, Robin, Okwuonu, Geoffrey, Pham, Christopher, Pu, Ling-Ling, Saada, Nehad, Santibanez, Jireh, Simmons, DeNard, Thornton, Rebecca, Venkat, Aarti, Walden, Kimberly Ko, Wu, Yuan-Qing, Debyser, Griet, Devreese, Bart, Asher, Claire, Blommaert, Julie, Chipman, Ariel D., Chittka, Lars, Fouks, Bertrand, Liu, Jisheng, O'Neill, Meaghan P., Sumner, Seirian, Puiu, Daniela, Qu, Jiaxin, Salzberg, Steven L., Scherer, Steven E., Muzny, Donna M., Richards, Stephen, Robinson, Gene E., Gibbs, Richard A., Schmid-Hempel, Paul, and Worley, Kim C.
Abstract: BACKGROUND: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. RESULTS: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. CONCLUSIONS: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.
Published: 2015
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17. Honeybee Venom Proteome Profile of Queens and Winter Bees as Determined by a Mass Spectrometric Approach

Author: Danneels, Ellen, primary, Van Vaerenbergh, Matthias, additional, Debyser, Griet, additional, Devreese, Bart, additional, and de Graaf, Dirk, additional
Published: 2015
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18. The genomes of two key bumblebee species with primitive eusocial organization

Author: Sadd, Ben M, primary, Barribeau, Seth M, additional, Bloch, Guy, additional, de Graaf, Dirk C, additional, Dearden, Peter, additional, Elsik, Christine G, additional, Gadau, Jürgen, additional, Grimmelikhuijzen, Cornelis JP, additional, Hasselmann, Martin, additional, Lozier, Jeffrey D, additional, Robertson, Hugh M, additional, Smagghe, Guy, additional, Stolle, Eckart, additional, Van Vaerenbergh, Matthias, additional, Waterhouse, Robert M, additional, Bornberg-Bauer, Erich, additional, Klasberg, Steffen, additional, Bennett, Anna K, additional, Câmara, Francisco, additional, Guigó, Roderic, additional, Hoff, Katharina, additional, Mariotti, Marco, additional, Munoz-Torres, Monica, additional, Murphy, Terence, additional, Santesmasses, Didac, additional, Amdam, Gro V, additional, Beckers, Matthew, additional, Beye, Martin, additional, Biewer, Matthias, additional, Bitondi, Márcia MG, additional, Blaxter, Mark L, additional, Bourke, Andrew FG, additional, Brown, Mark JF, additional, Buechel, Severine D, additional, Cameron, Rossanah, additional, Cappelle, Kaat, additional, Carolan, James C, additional, Christiaens, Olivier, additional, Ciborowski, Kate L, additional, Clarke, David F, additional, Colgan, Thomas J, additional, Collins, David H, additional, Cridge, Andrew G, additional, Dalmay, Tamas, additional, Dreier, Stephanie, additional, du Plessis, Louis, additional, Duncan, Elizabeth, additional, Erler, Silvio, additional, Evans, Jay, additional, Falcon, Tiago, additional, Flores, Kevin, additional, Freitas, Flávia CP, additional, Fuchikawa, Taro, additional, Gempe, Tanja, additional, Hartfelder, Klaus, additional, Hauser, Frank, additional, Helbing, Sophie, additional, Humann, Fernanda C, additional, Irvine, Frano, additional, Jermiin, Lars S, additional, Johnson, Claire E, additional, Johnson, Reed M, additional, Jones, Andrew K, additional, Kadowaki, Tatsuhiko, additional, Kidner, Jonathan H, additional, Koch, Vasco, additional, Köhler, Arian, additional, Kraus, F Bernhard, additional, Lattorff, H Michael G, additional, Leask, Megan, additional, Lockett, Gabrielle A, additional, Mallon, Eamonn B, additional, Antonio, David S Marco, additional, Marxer, Monika, additional, Meeus, Ivan, additional, Moritz, Robin FA, additional, Nair, Ajay, additional, Näpflin, Kathrin, additional, Nissen, Inga, additional, Niu, Jinzhi, additional, Nunes, Francis MF, additional, Oakeshott, John G, additional, Osborne, Amy, additional, Otte, Marianne, additional, Pinheiro, Daniel G, additional, Rossié, Nina, additional, Rueppell, Olav, additional, Santos, Carolina G, additional, Schmid-Hempel, Regula, additional, Schmitt, Björn D, additional, Schulte, Christina, additional, Simões, Zilá LP, additional, Soares, Michelle PM, additional, Swevers, Luc, additional, Winnebeck, Eva C, additional, Wolschin, Florian, additional, Yu, Na, additional, Zdobnov, Evgeny M, additional, Aqrawi, Peshtewani K, additional, Blankenburg, Kerstin P, additional, Coyle, Marcus, additional, Francisco, Liezl, additional, Hernandez, Alvaro G, additional, Holder, Michael, additional, Hudson, Matthew E, additional, Jackson, LaRonda, additional, Jayaseelan, Joy, additional, Joshi, Vandita, additional, Kovar, Christie, additional, Lee, Sandra L, additional, Mata, Robert, additional, Mathew, Tittu, additional, Newsham, Irene F, additional, Ngo, Robin, additional, Okwuonu, Geoffrey, additional, Pham, Christopher, additional, Pu, Ling-Ling, additional, Saada, Nehad, additional, Santibanez, Jireh, additional, Simmons, DeNard, additional, Thornton, Rebecca, additional, Venkat, Aarti, additional, Walden, Kimberly KO, additional, Wu, Yuan-Qing, additional, Debyser, Griet, additional, Devreese, Bart, additional, Asher, Claire, additional, Blommaert, Julie, additional, Chipman, Ariel D, additional, Chittka, Lars, additional, Fouks, Bertrand, additional, Liu, Jisheng, additional, O’Neill, Meaghan P, additional, Sumner, Seirian, additional, Puiu, Daniela, additional, Qu, Jiaxin, additional, Salzberg, Steven L, additional, Scherer, Steven E, additional, Muzny, Donna M, additional, Richards, Stephen, additional, Robinson, Gene E, additional, Gibbs, Richard A, additional, Schmid-Hempel, Paul, additional, and Worley, Kim C, additional
Published: 2015
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19. MALDI-TOF/TOF de novo sequence analysis of 2-D PAGE-separated proteins from Halorhodospira halophila, a bacterium with unsequenced genome

Author: Samyn, Bart, Sergeant, Kjell, Memmi, Samy, Debyser, Griet, Devreese, Bart, and Van Beeumen, Jozef
Subjects: Science General
Published: 2006

20. The Unipept metaproteomics analysis pipeline

Author: Mesuere, Bart, primary, Debyser, Griet, additional, Aerts, Maarten, additional, Devreese, Bart, additional, Vandamme, Peter, additional, and Dawyndt, Peter, additional
Published: 2015
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21. Finding the missing honey bee genes: lessons learned from a genome upgrade

Author: Elsik, Christine G., Worley, Kim C., Bennett, Anna K., Beye, Martin, Camara, Francisco, Childers, Christopher P., de Graaf, Dirk C., Debyser, Griet, Deng, Jixin, Devreese, Bart, Elhaik, Eran, Evans, Jay D., Foster, Leonard J., Graur, Dan, Guigo, Roderic, Hoff, Katharina J., Holder, Michael E., Hudson, Matthew E., Hunt, Greg J., Jiang, Huaiyang, Joshi, Vandita, Khetani, Radhika S, Kosarev, Peter, Kovar, Christie L., Ma, Jian, Maleszka, Ryszard, Moritz, Robin F. A., Munoz-Torres, Monica C., Murphy, Terence D., Muzny, Donna M., Newsham, Irene F., Reese, Justin T., Robertson, Hugh M., Robinson, Gene E, Rueppell, Olav, Solovyev, Victor, Stanke, Mario, Stolle, Eckart, Tsuruda, Jennifer M., Vaerenbergh, Matthias V., Waterhouse, Robert M., Weaver, Daniel B., Whitfield, Charles W., Wu, Yuanqing, Zdobnov, Evgeny M., Zhang, Lan, Zhu, Dianhui, Gibbs, Richard A., Elsik, Christine G., Worley, Kim C., Bennett, Anna K., Beye, Martin, Camara, Francisco, Childers, Christopher P., de Graaf, Dirk C., Debyser, Griet, Deng, Jixin, Devreese, Bart, Elhaik, Eran, Evans, Jay D., Foster, Leonard J., Graur, Dan, Guigo, Roderic, Hoff, Katharina J., Holder, Michael E., Hudson, Matthew E., Hunt, Greg J., Jiang, Huaiyang, Joshi, Vandita, Khetani, Radhika S, Kosarev, Peter, Kovar, Christie L., Ma, Jian, Maleszka, Ryszard, Moritz, Robin F. A., Munoz-Torres, Monica C., Murphy, Terence D., Muzny, Donna M., Newsham, Irene F., Reese, Justin T., Robertson, Hugh M., Robinson, Gene E, Rueppell, Olav, Solovyev, Victor, Stanke, Mario, Stolle, Eckart, Tsuruda, Jennifer M., Vaerenbergh, Matthias V., Waterhouse, Robert M., Weaver, Daniel B., Whitfield, Charles W., Wu, Yuanqing, Zdobnov, Evgeny M., Zhang, Lan, Zhu, Dianhui, and Gibbs, Richard A.
Abstract: BACKGROUND: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. RESULTS: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. CONCLUSIONS: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.
Published: 2014

22. Unipept: Tryptic Peptide-Based Biodiversity Analysis of Metaproteome Samples

Author: Mesuere, Bart, primary, Devreese, Bart, additional, Debyser, Griet, additional, Aerts, Maarten, additional, Vandamme, Peter, additional, and Dawyndt, Peter, additional
Published: 2012
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23. The cDNA sequence of three hemocyanin subunits from the garden snail Helix lucorum

Author: De Smet, Lina, primary, Dimitrov, Ivan, additional, Debyser, Griet, additional, Dolashka-Angelova, Pavlina, additional, Dolashki, Aleksandar, additional, Van Beeumen, Jozef, additional, and Devreese, Bart, additional
Published: 2011
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24. PTPBR7 Binding Proteins in Myelinating Neurons of the Mouse Brain

Author: Chesini, Irene M., primary, Debyser, Griet, additional, Croes, Huib, additional, ten Dam, Gerdy B., additional, Devreese, Bart, additional, Stoker, Andrew W., additional, and Hendriks, Wiljan J.A.J., additional
Published: 2011
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25. A proteome map of the pituitary melanotrope cell activated by black‐background adaptation of Xenopus laevis

Author: Devreese, Bart, primary, Sergeant, Kjell, additional, Van Bakel, Nick H. M., additional, Debyser, Griet, additional, Van Beeumen, Jozef, additional, Martens, Gerard J. M., additional, and Van Herp, François, additional
Published: 2010
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26. Variability of polymorphic families of three types of xylanase inhibitors in the wheat grain proteome

Author: Croes, Evi, primary, Gebruers, Kurt, additional, Robben, Johan, additional, Noben, Jean-Paul, additional, Samyn, Bart, additional, Debyser, Griet, additional, Van Beeumen, Jozef, additional, Delcour, Jan A., additional, and Courtin, Christophe M., additional
Published: 2008
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27. Functional Proteome Analysis of the Banana Plant (Musa spp.) Using de Novo Sequence Analysis of Derivatized Peptides

Author: Samyn, Bart, primary, Sergeant, Kjell, additional, Carpentier, Sebastien, additional, Debyser, Griet, additional, Panis, Bart, additional, Swennen, Rony, additional, and Van Beeumen, Jozef, additional
Published: 2006
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28. De novo sequence analysis of N‐terminal sulfonated peptides after in‐gel guanidination

Author: Sergeant, Kjell, primary, Samyn, Bart, additional, Debyser, Griet, additional, and Van Beeumen, Jozef, additional
Published: 2005
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29. Unipept: Tryptic Peptide-Based Biodiversity Analysisof Metaproteome Samples.

Author: Mesuere, Bart, Devreese, Bart, Debyser, Griet, Aerts, Maarten, Vandamme, Peter, and Dawyndt, Peter
Published: 2012
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30. Functional proteome analysis of the banana plant (Musa spp.) using de novo sequence analysis of derivatized peptides.

Author: Samyn B, Sergeant K, Carpentier S, Debyser G, Panis B, Swennen R, and Van Beeumen J
Subjects: Algorithms, Amino Acid Sequence, Electrophoresis, Gel, Two-Dimensional, Genome, Plant, Genotype, Molecular Sequence Data, Plant Proteins chemistry, Proteome, Sequence Analysis, Protein, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Trypsin pharmacology, Mass Spectrometry methods, Musa metabolism, Peptides chemistry, Proteomics methods
Abstract: We report the use of chemical derivatization with MALDI-MS/MS analysis for de novo sequence analysis. Using three frequently used homology-based search algorithms, we were able to identify more than 40 proteins from banana, a nonmodel plant with unsequenced genome. Furthermore, this approach allowed the identification of different isoforms. We also observed that the identification score obtained varied according to the position of the peptide sequences in the query using the MS-Blast algorithm.
Published: 2007
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31. MALDI-TOF/TOF de novo sequence analysis of 2-D PAGE-separated proteins from Halorhodospira halophila, a bacterium with unsequenced genome.

Author: Samyn B, Sergeant K, Memmi S, Debyser G, Devreese B, and Van Beeumen J
Subjects: Amino Acid Sequence, Genome, Bacterial genetics, Halorhodospira halophila genetics, Molecular Sequence Data, Sequence Analysis, DNA, Bacterial Proteins analysis, Electrophoresis, Gel, Two-Dimensional, Halorhodospira halophila chemistry, Sequence Analysis, Protein methods, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization methods
Abstract: Because protein identifications rely on matches with sequence databases, high-throughput proteomics is currently largely restricted to those species for which comprehensive sequence databases are available. The identification of proteins derived from organisms with unsequenced genomes mainly depends on homology searching. Here, we report the use of a simplified, gel-based, chemical derivatization strategy for de novo sequence analysis using a MALDI-TOF/TOF mass spectrometer. This approach allows the determination of de novo peptide sequences of up to 20 amino acid residues in length. The protocol was applied on a proteomic study of 2-D PAGE-separated proteins from Halorhodospira halophila, an extremophilic eubacterium with yet unsequenced genome. Using three different homology-based search algorithms, we were able to identify more than 30 proteins from this organism using subpicomole quantities of protein.
Published: 2006
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31 results on '"Debyser, Griet"'

1. Diving into the Structural Details of In Vitro Transcribed mRNA Using Liquid Chromatography-Mass Spectrometry-Based Oligonucleotide Profiling

2. A Method for Comprehensive Proteomic Analysis of Human Faecal Samples to Investigate Gut Dysbiosis in Patients with Cystic Fibrosis

3. Faecal proteomics: A tool to investigate dysbiosis and inflammation in patients with cystic fibrosis

4. Unraveling the venom proteome of the bumblebee (Bombus terrestris) by integrating a combinatorial peptide ligand library approach with FT-ICR MS

5. Exploring the hidden honeybee (Apis mellifera) venom proteome by integrating a combinatorial peptide ligand library approach with FTMS

6. Elevated faecal ovotransferrin concentrations are indicative for intestinal barrier failure in broiler chickens

7. Milk fat globule membrane glycoproteins prevent adhesion of the colonic microbiota and result in increased bacterial butyrate production

8. Distribution and isolation of milk fat globule membrane proteins during dairy processing as revealed by proteomic analysis

9. Multiplicity of aspartic proteinases from Cynara cardunculus L.

10. Resistance of the dopamine D4 receptor to agonist-induced internalization and degradation

11. Multiplicity of aspartic proteinases from Cynara cardunculus L.

12. Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients

13. A case study of de novo sequence analysis of N-sulfonated peptides by MALDI TOF/TOF mass spectrometry

14. Finding the Missing Honey Bee Genes: Lessons Learned From a Genome Upgrade

15. A shotgun metaproteomics approach to study the microbiome of cystic fibrosis (CF) patients

16. The genomes of two key bumblebee species with primitive eusocial organization

17. Honeybee Venom Proteome Profile of Queens and Winter Bees as Determined by a Mass Spectrometric Approach

18. The genomes of two key bumblebee species with primitive eusocial organization

19. MALDI-TOF/TOF de novo sequence analysis of 2-D PAGE-separated proteins from Halorhodospira halophila, a bacterium with unsequenced genome

20. The Unipept metaproteomics analysis pipeline

21. Finding the missing honey bee genes: lessons learned from a genome upgrade

22. Unipept: Tryptic Peptide-Based Biodiversity Analysis of Metaproteome Samples

23. The cDNA sequence of three hemocyanin subunits from the garden snail Helix lucorum

24. PTPBR7 Binding Proteins in Myelinating Neurons of the Mouse Brain

25. A proteome map of the pituitary melanotrope cell activated by black‐background adaptation of Xenopus laevis

26. Variability of polymorphic families of three types of xylanase inhibitors in the wheat grain proteome

27. Functional Proteome Analysis of the Banana Plant (Musa spp.) Using de Novo Sequence Analysis of Derivatized Peptides

28. De novo sequence analysis of N‐terminal sulfonated peptides after in‐gel guanidination

29. Unipept: Tryptic Peptide-Based Biodiversity Analysisof Metaproteome Samples.

30. Functional proteome analysis of the banana plant (Musa spp.) using de novo sequence analysis of derivatized peptides.

31. MALDI-TOF/TOF de novo sequence analysis of 2-D PAGE-separated proteins from Halorhodospira halophila, a bacterium with unsequenced genome.

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31 results on '"Debyser, Griet"'

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