Blar i Bergen Open Research Archive på forfatter "Vaudel, Marc"

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    • An accessible proteogenomics informatics resource for cancer researchers 

      Chambers, Matthew C.; Jagtap, Pratik D.; Johnson, James E.; McGowan, Thomas; Kumar, Praveen; Onsongo, Getiria; Guerrero, Candace R.; Barsnes, Harald; Vaudel, Marc; Martens, Lennart; Grüning, Björn; Cooke, Ira R.; Heydarian, Mohammad; Reddy, Karen L.; Griffin, Timothy J. (Peer reviewed; Journal article, 2017)
      Proteogenomics has emerged as a valuable approach in cancer research, which integrates genomic and transcriptomic data with mass spectrometry–based proteomics data to directly identify expressed, variant protein sequences ...

    • Analyzing the Structure of Pathways and Its Influence on the Interpretation of Biomedical Proteomics Data Sets 

      Burger, Bram; Hernández Sánchez, Luis Francisco; Lereim, Ragnhild Reehorst; Barsnes, Harald; Vaudel, Marc (Peer reviewed; Journal article, 2018)
      Biochemical pathways are commonly used as a reference to conduct functional analysis on biomedical omics data sets, where experimental results are mapped to knowledgebases comprising known molecular interactions collected ...

    • Anatomy and evolution of database search engines — a central component of mass spectrometry based proteomic workflows 

      Verheggen, Kenneth; Ræder, Helge; Berven, Frode; Martens, Lennart Martens; Barsnes, Harald; Vaudel, Marc (Peer reviewed; Journal article, 2017-09-13)
      Sequence database search engines are bioinformatics algorithms that identify peptides from tandem mass spectra using a reference protein sequence database. Two decades of development, notably driven by advances in mass ...

    • Automated splitting into batches for observational biomedical studies with sequential processing 

      Burger, Bram; Vaudel, Marc; Barsnes, Harald (Journal article; Peer reviewed, 2022)
      Experimental design usually focuses on the setting where treatments and/or other aspects of interest can be manipulated. However, in observational biomedical studies with sequential processing, the set of available samples ...

    • Autozygosity mapping and time-to-spontaneous delivery in Norwegian parent-offspring trios 

      Solé-Navais, Pol; Bacelis, Jonas; Helgeland, Øyvind; Modzelewska, Dominika; Vaudel, Marc; Flatley, Christopher; Andreassen, Ole; Njølstad, Pål Rasmus; Muglia, Louis J.; Johansson, Stefan; Zhang, Ge; Jacobsson, Bo (Journal article; Peer reviewed, 2020)
      Parental genetic relatedness may lead to adverse health and fitness outcomes in the offspring. However, the degree to which it affects human delivery timing is unknown. We use genotype data from ≃25 000 parent-offspring ...

    • BioContainers: An open-source and community-driven framework for software standardization 

      Leprevost, Felipe da Veiga; Grüning, Björn A.; Alves Aflitos, Saulo; Röst, Hannes L.; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; Bai, Mingze; Jimenez, Rafael C.; Sachsenberg, Timo; Pfeuffer, Julianus; Vera Alvarez, Roberto; Griss, Johannes; Nesvizhskii, Alexey I.; Perez-Riverol, Yasset (Peer reviewed; Journal article, 2017-03-30)
      Motivation BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes ...

    • Characterization of the genetic architecture of infant and early childhood body mass index 

      Helgeland, Øyvind; Vaudel, Marc; Sole-Navais, Pol; Flatley, Christopher; Juodakis, Julius; Bacelis, Jonas; Koløen, Ingvild; Knudsen, Gun Peggy Strømstad; Johansson, Bente Berg; Magnus, Per Minor; Reichborn-Kjennerud, Ted; Juliusson, Pétur Benedikt; Stoltenberg, Camilla; Holmen, Oddgeir Lingaas; Andreassen, Ole; Jacobsson, Bo; Njølstad, Pål Rasmus; Johansson, Stefan (Journal article; Peer reviewed, 2022)
      Early childhood obesity is a growing global concern; however, the role of common genetic variation on infant and child weight development is unclear. Here, we identify 46 loci associated with early childhood body mass index ...

    • Compomics-utilities: an open-source Java library for computational proteomics 

      Barsnes, Harald; Vaudel, Marc; Colaert, Niklaas; Helsens, Kenny; Sickmann, Albert; Berven, Frode S.; Martens, Lennart (Peer reviewed; Journal article, 2011-03-08)
      Background The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary ...

    • DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra 

      Muth, Thilo; Weilnböck, Lisa; Rapp, Erdmann; Huber, Christian G.; Martens, Lennart; Vaudel, Marc; Barsnes, Harald (Peer reviewed; Journal article, 2014)
      De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, ...

    • Exploring the human plasma proteome for humoral mediators of remote ischemic preconditioning - A word of caution 

      Helgeland, Erik; Breivik, Lars Ertesvåg; Vaudel, Marc; Svendsen, Øyvind Sverre; Garberg, Hilde Kristin; Nordrehaug, Jan Erik; Berven, Frode S.; Jonassen, Anne Kristin (Peer reviewed; Journal article, 2014-10-15)
      Despite major advances in early revascularization techniques, cardiovascular diseases are still the leading cause of death worldwide, and myocardial infarctions contribute heavily to this. Over the past decades, it has ...

    • Exploring the potential of public proteomics data 

      Vaudel, Marc; Verheggen, Kenneth; Csordas, Attila; Ræder, Helge; Berven, Frode; Martens, Lennart; Vizcaíno, Juan Antonio; Barsnes, Harald (Peer reviewed; Journal article, 2016)
      In a global effort for scientific transparency, it has become feasible and good practice to share experimental data supporting novel findings. Consequently, the amount of publicly available MS‐based proteomics data has ...

    • Finding haplotypic signatures in proteins 

      Vasicek, Jakub; Skiadopoulou, Dafni; Kuznetsova, Ksenia; Wen, Bo; Johansson, Stefan; Njølstad, Pål Rasmus; Bruckner, Stefan; Käll, Lukas; Vaudel, Marc (Journal article; Peer reviewed, 2023)
      Background The nonrandom distribution of alleles of common genomic variants produces haplotypes, which are fundamental in medical and population genetic studies. Consequently, protein-coding genes with different ...

    • Genetic effects on the timing of parturition and links to fetal birth weight 

      Solé-Navais, Pol; Flatley, Christopher; Steinthorsdottir, Valgerdur; Vaudel, Marc; Juodakis, Julius; Chen, Jing; Laisk, Triin; LaBella, Abigail L.; Westergaard, David; Bacelis, Jonas; Brumpton, Ben Michael; Skotte, Line; Borges, Maria C.; Helgeland, Øyvind; Mahajan, Anubha; Wielscher, Matthias; Lin, Frederick; Briggs, Catherine; Wang, Carol A.; Moen, Gunn-Helen Øiseth; Beaumont, Robin N.; Bradfield, Jonathan P.; Abraham, Abin; Thorleifsson, Gudmar; Gabrielsen, Maiken Elvestad; Ostrowski, Sisse R.; Modzelewska, Dominika; Nøhr, Ellen Aagaard; Hypponen, Elina; Srivastava, Amit; Talbot, Octavious; Allard, Catherine; Williams, Scott M.; Menon, Ramkumar; Shields, Beverley M.; Sveinbjornsson, Gardar; Xu, Huan; Melbye, Mads; Lowe, William; Bouchard, Luigi; Oken, Emily; Pedersen, Ole B.; Gudbjartsson, Daniel F.; Erikstrup, Christian; Sørensen, Erik; Lie, Rolv T.; Teramo, Kari; Hallman, Mikko; Juliusdottir, Thorhildur; Hakonarson, Hakon; Ullum, Henrik; Hattersley, Andrew T.; Sletner, Line; Merialdi, Mario; Rifas-Shiman, Sheryl L.; Steingrimsdottir, Thora; Scholtens, Denise; Power, Christine; West, Jane; Nyegaard, Mette; Capra, John A.; Skogholt, Anne Heidi; Magnus, Per Minor; Andreassen, Ole; Thorsteinsdottir, Unnur; Grant, Struan F. A.; Qvigstad, Elisabeth; Pennell, Craig E.; Hivert, Marie-France; Hayes, Geoffrey M.; Jarvelin, Marjo-Riitta; McCarthy, Mark I.; Lawlor, Deborah A.; Nielsen, Henriette S.; Mägi, Reedik; Rokas, Antonis; Hveem, Kristian; Stefansson, Kari; Feenstra, Bjarke; Njølstad, Pål Rasmus; Muglia, Louis J.; Freathy, Rachel M.; Johansson, Stefan; Zhang, Ge; Jacobsson, Bo (Journal article; Peer reviewed, 2023)
      The timing of parturition is crucial for neonatal survival and infant health. Yet, its genetic basis remains largely unresolved. We present a maternal genome-wide meta-analysis of gestational duration (n = 195,555), ...

    • Genome-wide association study of offspring birth weight in 86 577 women identifies five novel loci and highlights maternal genetic effects that are independent of fetal genetics 

      Beaumont, Robin N.; Warrington, Nicole M.; Cavadino, Alana; Tyrrell, Jessica; Nodzenski, Michael; Horikoshi, Momoko; Geller, Frank; Myhre, Ronny; Richmond, Rebecca C.; Paternoster, Lavinia; Bradfield, Jonathan P.; Kreiner-Møller, Eskil; Huikari, Ville; Metrustry, Sarah; Lunetta, Kathryn L.; Painter, Jodie N.; Hottenga, Jouke-Jan; Allard, Catherine; Barton, Sheila J.; Espinosa, Ana; Marsh, Julie A.; Potter, Catherine; Zhang, Ge; Ang, Wei; Berry, Diane J.; Bouchard, Luigi; Das, Shikta; Hakonarson, Hakon; Heikkinen, Jani; Helgeland, Øyvind; Hocher, Berthold; Hofman, Albert; Inskip, Hazel M.; Jones, Samuel E.; Kogevinas, Manolis; Lind, Penelope A.; Marullo, Letizia; Medland, Sarah E.; Murray, Anna; Murray, Jeffrey C.; Njølstad, Pål Rasmus; Nohr, Ellen A.; Reichetzeder, Christoph; Ring, Susan M.; Ruth, Katherine S.; Santa-Marina, Loreto; Scholtens, Denise M.; Sebert, Sylvain; Sengpiel, Verena; Tuke, Marcus A.; Vaudel, Marc; Weedon, Michael N.; Willemsen, Gonneke; Wood, Andrew R.; Yaghootkar, Hanieh; Muglia, Louis J.; Bartels, Meike; Relton, Caroline L.; Pennell, Craig E.; Chatzi, Leda; Estivill, Xavier; Holloway, John W.; Boomsma, Dorret I.; Montgomery, Grant W.; Murabito, Joanne M.; Spector, Tim D.; Power, Christine; Järvelin, Marjo-Riitta; Bisgaard, Hans; Grant, Struan F.A.; Sørensen, Thorkild I.A.; Jaddoe, Vincent W.; Jacobsson, Bo; Melbye, Mads; McCarthy, Mark I.; Hattersley, Andrew T.; Hayes, M. Geoffrey; Hivert, Marie-France; Frayling, Timothy M.; Felix, Janine F.; Hyppönen, Elina; Lowe, William L.; Evans, David M.; Lawlor, Debbie A.; Feenstra, Bjarke; Freathy, Rachel M. (Peer reviewed; Journal article, 2018-02)
      Genome-wide association studies of birth weight have focused on fetal genetics, whereas relatively little is known about the role of maternal genetic variation. We aimed to identify maternal genetic variants associated ...

    • Genome-wide association study reveals dynamic role of genetic variation in infant and early childhood growth 

      Helgeland, Øyvind; Vaudel, Marc; Juliusson, Petur Benedikt; Holmen, Oddgeir Lingaas; Juodakis, Julius; Bacelis, Jonas; Jacobsson, Bo; Lindekleiv, Haakon; Hveem, Kristian; Lie, Rolv T.; Knudsen, Gun Peggy Strømstad; Stoltenberg, Camilla; Magnus, Per; Sagen, Jørn V.; Molven, Anders; Johansson, Stefan; Njølstad, Pål Rasmus (Peer reviewed; Journal article, 2019-10-01)
      Infant and childhood growth are dynamic processes with large changes in BMI during development. By performing genome-wide association studies of BMI at 12 time points from birth to eight years (9286 children, 74,105 ...

    • GWAS for autoimmune Addison's disease identifies multiple risk loci and highlights AIRE in disease susceptibility 

      Eriksson, Daniel; Røyrvik, Ellen Christine; Aranda-Guillen, Maribel; Berger, Amund Holte; Landegren, Nils; Artaza, Haydee; Hallgren, Åsa; Grytaas, Marianne; Strøm, Sara; Bratland, Eirik; Botusan, Ileana; Oftedal, Bergithe Eikeland; Breivik, Lars Ertesvåg; Vaudel, Marc; Helgeland, Øyvind; Falorni, Alberto; Jørgensen, Anders Palmstrøm; Hulting, Anna-Lena; Svartberg, Johan; Ekwall, Olov; Fougner, Kristian J; Wahlberg, Jeanette; Nedrebø, Bjørn Gunnar; Dahlqvist, Per; Study group, Norwegian Addison Registry; Study Group, Swedish Addison Registry; Knappskog, Per Morten; Wolff, Anette Susanne Bøe; Bensing, Sophie; Johansson, Stefan; Kämpe, Olof; Husebye, Eystein Sverre (Journal article; Peer reviewed, 2021)
      Autoimmune Addison’s disease (AAD) is characterized by the autoimmune destruction of the adrenal cortex. Low prevalence and complex inheritance have long hindered successful genetic studies. We here report the first ...

    • In-depth cerebrospinal fluid quantitative proteome and deglycoproteome analysis: presenting a comprehensive picture of pathways and processes affected by multiple sclerosis 

      Kroksveen, Ann Cathrine; Guldbrandsen, Astrid; Vaudel, Marc; Lereim, Ragnhild Reehorst; Barsnes, Harald; Myhr, Kjell-Morten; Torkildsen, Øivind; Berven, Frode (Peer reviewed; Journal article, 2017)
      In the current study, we conducted a quantitative in-depth proteome and deglycoproteome analysis of cerebrospinal fluid (CSF) from relapsing-remitting multiple sclerosis (RRMS) and neurological controls using mass spectrometry ...

    • Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics 

      Vaudel, Marc; Sickmann, Albert; Martens, Lennart (Peer reviewed; Journal article, 2014-01)
      With the advent of mass spectrometry based proteomics, the identification of thousands of proteins has become commonplace in biology nowadays. Increasingly, efforts have also been invested toward the detection and localization ...

    • Leptin receptor signaling regulates protein synthesis pathways and neuronal differentiation in pluripotent stem cells 

      Gupta, Manoj K.; Vethe, Heidrun; Softic, Samir; Rao, Tata Nageswara; Wagh, Vilas; Shirakawa, Jun; Barsnes, Harald; Vaudel, Marc; Takatani, Tomozumi; Kahraman, Sevim; Sakaguchi, Masaji; Martinez, Rachael; Hu, Jiang; Bjørlykke, Yngvild; Ræder, Helge; Kulkarni, Rohit N. (Journal article; Peer reviewed, 2020)
      The role of leptin receptor (OB-R) signaling in linking pluripotency with growth and development and the consequences of dysfunctional leptin signaling on progression of metabolic disease is poorly understood. Using a ...

    • The mzIdentML data standard version 1.2, supporting advances in proteome informatics 

      Vizcaíno, Juan Antonio; Mayer, Gerhard; Perkins, Simon; Barsnes, Harald; Vaudel, Marc; Perez-Riverol, Yasset; Ternent, Tobias; Uszkoreit, Julian; Eisenacher, Martin; Fischer, Lutz; Rappsilber, Juri; Netza, Eugen; Walzer, Mathias; Kohlbacher, Oliver; Leitner, Alexander; Chalkley, Robert J.; Ghali, Fawaz; Martínez-Bartolomé, Salvador; Deutsch, Eric W.; Jones, Andrew R. (Peer reviewed; Journal article, 2017-07-01)
      The first stable version of the Proteomics Standards Initiative mzIdentML open data standard (version 1.1) was published in 2012—capturing the outputs of peptide and protein identification software. In the intervening ...