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

Viser treff 21-36 av 36

    • Novel loci for childhood body mass index and shared heritability with adult cardiometabolic traits 

      Vogelezang, Suzanne; Bradfield, Jonathan P.; Ahluwalia, Tarunveer S.; Curtin, John A.; Lakka, Timo A.; Grarup, Niels; Scholz, Markus; van der Most, Peter J.; Monnereau, Claire; Stergiakouli, Evie; Heiskala, Anni; Horikoshi, Momoko; Fedko, Iryna O.; Vilor-Tejedor, Natalia; Cousminer, Diana L.; Standl, Marie; Wang, Carol A.; Viikari, Jorma; Geller, Frank; Íñiguez, Carmen; Pitkänen, Niina; Chesi, Alessandra; Bacelis, Jonas; Yengo, Loic; Torrent, Maties; Ntalla, Ioanna; Helgeland, Øyvind; Selzam, Saskia; Vonk, Judith M.; Zafarmand, Mohammed H.; Heude, Barbara; Farooqi, Ismaa Sadaf; Alyass, Akram; Beaumont, Robin N.; Have, Christian T.; Rzehak, Peter; Bilbao, Jose Ramon; Schnurr, Theresia M.; Barroso, Inês; Bønnelykke, Klaus; Beilin, Lawrence J.; Carstensen, Lisbeth; Charles, Marie-Aline; Chawes, Bo; Clément, Karine; Closa-Monasterolo, Ricardo; Custovic, Adnan; Eriksson, Johan G.; Vaudel, Marc; Njølstad, Pål Rasmus (Journal article; Peer reviewed, 2020)
      The genetic background of childhood body mass index (BMI), and the extent to which the well-known associations of childhood BMI with adult diseases are explained by shared genetic factors, are largely unknown. We performed ...

    • PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping 

      Hernández Sánchez, Luis Francisco; Burger, Bram; Horro Marcos, Carlos; Fabregat, Antonio; Johansson, Stefan; Njølstad, Pål Rasmus; Barsnes, Harald; Hermjakob, Henning; Vaudel, Marc (Peer reviewed; Journal article, 2019-07-30)
      Background Mapping biomedical data to functional knowledge is an essential task in bioinformatics and can be achieved by querying identifiers (e.g., gene sets) in pathway knowledge bases. However, the isoform and ...

    • PeptideShaker Online: A User-Friendly Web-Based Framework for the Identification of Mass Spectrometry-Based Proteomics Data 

      Farag, Yehia Mokhtar; Horro Marcos, Carlos; Vaudel, Marc; Barsnes, Harald (Journal article; Peer reviewed, 2021)
      Mass spectrometry-based proteomics is a high-throughput technology generating ever-larger amounts of data per project. However, storing, processing, and interpreting these data can be a challenge. A key element in simplifying ...

    • Placental weight centiles adjusted for age, parity and fetal sex 

      Flatley, Christopher; Sole-Navais, Pol; Vaudel, Marc; Helgeland, Øyvind; Modzelewska, Dominika; Johansson, Stefan; Jacobsson, Bo; Njølstad, Pål Rasmus (Journal article; Peer reviewed, 2022)
      Introduction The weight of the placenta can be indicative of efficacy in nutrient and oxygen supply. Furthermore, it has been suggested that a measure of the placenta's ability to adequately supply nutrients to the fetus ...

    • Population prevalence and inheritance pattern of recurrent CNVs associated with neurodevelopmental disorders in 12,252 newborns and their parents 

      Smajlagic, Dinka; Lavrichenko, Ksenia; Berland, Siren; Helgeland, Øyvind; Knudsen, Gun Peggy Strømstad; Vaudel, Marc; Haavik, Jan; Knappskog, Per; Njølstad, Pål Rasmus; Houge, Gunnar; Johansson, Stefan (Journal article; Peer reviewed, 2020)
      Recurrent copy number variations (CNVs) are common causes of neurodevelopmental disorders (NDDs) and associated with a range of psychiatric traits. These CNVs occur at defined genomic regions that are particularly prone ...

    • A Potential Golden Age to Come-Current Tools, Recent Use Cases, and Future Avenues for De Novo Sequencing in Proteomics 

      Muth, Thilo; Hartkopf, Felix; Vaudel, Marc; Renard, Bernhard Y (Peer reviewed; Journal article, 2018-07-02)
      In shotgun proteomics, peptide and protein identification is most commonly conducted using database search engines, the method of choice when reference protein sequences are available. Despite its widespread use the ...

    • Practical considerations for omics experiments in biomedical sciences 

      Vaudel, Marc; Barsnes, Harald; Bjerkvig, Rolf; Bikfalvi, Andreas; Selheim, Frode; Berven, Frode; Daubon, Thomas (Peer reviewed; Journal article, 2016)
      Modern analytical techniques provide an unprecedented insight to biomedical samples, allowing an in depth characterization of cells or body fluids, to the level of genes, transcripts, peptides, proteins, metabolites, or ...

    • Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia 

      Aasebø, Elise; Berven, Frode; Bartaula-Brevik, Sushma; Stokowy, Tomasz; Hovland, Randi; Vaudel, Marc; Døskeland, Stein Ove; Mc Cormack, Emmet; Batth, Tanveer S; Olsen, Jesper V; Bruserud, Øystein; Selheim, Frode; Hernandez-Valladares, Maria (Journal article; Peer reviewed, 2020)
      Acute myeloid leukemia (AML) is a hematological cancer that mainly affects the elderly. Although complete remission (CR) is achieved for the majority of the patients after induction and consolidation therapies, nearly ...

    • A proteomics sample metadata representation for multiomics integration and big data analysis 

      Dai, Chengxin; Füllgrabe, Anja; Pfeuffer, Julianus; Solovyeva, Elizaveta M.; Deng, Jingwen; Moreno, Pablo; Kamatchinathan, Selvakumar; Kundu, Deepti Jaiswal; George, Nancy; Fexova, Silvie; Grüning, Björn A.; Föll, Melanie Christine; Griss, Johannes; Vaudel, Marc; Audain, Enrique; Locard-Paulet, Marie; Turewicz, Michael; Eisenacher, Martin; Uszkoreit, Julian; Van Den Bossche, Tim; Schwämmle, Veit; Webel, Henry; Schulze, Stefan; Bouyssié, David; Jayaram, Savita; Duggineni, Vinay Kumar; Samaras, Patroklos; Wilhelm, Mathias; Choi, Meena; Wang, Mingxun; Kohlbacher, Oliver; Brazma, Alvis; Papatheodorou, Irene; Bandeira, Nuno; Deutsch, Eric W.; Vizcaíno, Juan Antonio; Bai, Mingze; Sachsenberg, Timo; Levitsky, Lev I.; Perez-Riverol, Yasset (Journal article; Peer reviewed, 2021)
      The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding ...

    • Reliable FASP-based procedures for optimal quantitative proteomic and phosphoproteomic analysis on samples from acute myeloid leukemia patients 

      Hernandez-Valladares, Maria; Aasebø, Elise; Mjaavatten, Olav; Vaudel, Marc; Bruserud, Øystein; Berven, Frode; Selheim, Frode (Peer reviewed; Journal article, 2016-06-21)
      Background Satisfactory sample preparation for mass spectrometry-based analysis is a critical step in the proteomics workflow. The quality and reproducibility of sample preparation can determine the coverage and confidence ...

    • Reprogrammed Cells Display Distinct Proteomic SignaturesAssociated with Colony Morphology Variability 

      Bjørlykke, Yngvild; Søviknes, Anne Mette; Hoareau, Laurence; Vethe, Heidrun; Mathisen, Andreas; Chera, Simona; Vaudel, Marc; Ghila, Luiza; Ræder, Helge (Peer reviewed; Journal article, 2019-11-18)
      Human induced pluripotent stem cells (hiPSCs) are of high interest because they can be differentiated into a vast range of different cell types. Ideally, reprogrammed cells should sustain long-term culturing in an ...

    • Retention Time and Fragmentation Predictors Increase Confidence in Identification of Common Variant Peptides 

      Skiadopoulou, Dafni; Vasicek, Jakub; Kuznetsova, Ksenia; Bouyssié, David; Käll, Lukas; Vaudel, Marc (Journal article; Peer reviewed, 2023)
      Precision medicine focuses on adapting care to the individual profile of patients, for example, accounting for their unique genetic makeup. Being able to account for the effect of genetic variation on the proteome holds ...

    • SearchGUI: a highly adaptable common interface for proteomics search and de novo engines 

      Barsnes, Harald; Vaudel, Marc (Peer reviewed; Journal article, 2018)
      Mass-spectrometry-based proteomics has become the standard approach for identifying and quantifying proteins. A vital step consists of analyzing experimentally generated mass spectra to identify the underlying peptide ...

    • Shedding light on black boxes in protein identification 

      Vaudel, Marc; Venne, A. Saskia; Berven, Frode; Zahedi, René P.; Martens, Lennart; Barsnes, Harald (Peer reviewed; Journal article, 2014-05)
      Performing a well thought-out proteomics data analysis can be a daunting task, especially for newcomers to the field. Even researchers experienced in the proteomics field can find it challenging to follow existing publication ...

    • thermo-msf-parser: An Open Source Java Library to Parse and Visualize Thermo Proteome Discoverer msf Files 

      Colaert, Niklaas; Barsnes, Harald; Vaudel, Marc; Helsens, Kenny; Timmerman, Evy; Sickmann, Albert; Gevaert, Kris; Martens, Lennart (Peer reviewed; Journal article, 2011)
      The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with Thermo mass spectrometers has ...

    • A trans-ancestral meta-analysis of genome-wide association studies reveals loci associated with childhood obesity 

      Bradfield, Jonathan P.; Vogelezang, Suzanne; Felix, Janine F.; Chesi, Alessandra; Helgeland, Øyvind; Horikoshi, Momoko; Karhunen, Ville; Lowry, Estelle; Cousminer, Diana L.; Ahluwalia, Tarunveer S.; Thiering, Elisabeth; Boh, Eileen Tai-Hui; Zafarmand, Mohammad H.; Vilor-Tejedor, Natalia; Wang, Carol A.; Joro, Raimo; Chen, Zhanghua; Gauderman, William J.; Pitkänen, Niina; Parra, Esteban J.; Fernandez-Rhodes, Lindsay; Alyass, Akram; Monnereau, Claire; Curtin, John A.; Have, Christian T.; McCormack, Shana E.; Hollensted, Mette; Frithioff-Bøjsøe, Christine; Valladares-Salgado, Adan; Peralta-Romero, Jesus; Teo, Yik-Ying; Standl, Marie; Leinonen, Jaakko T.; Holm, Jens-Christian; Peters, Triinu; Vioque, Jesus; Vrijheid, Martine; Simpson, Angela; Custovic, Adnan; Vaudel, Marc; Canouil, Mickaël; Lindi, Virpi; Atalay, Mustafa; Kahonen, Mika; Raitakari, Olli T.; van Schaik, Barbera D.C.; Berkowitz, Robert I.; Cole, Shelley A.; Voruganti, V. Saroja; Wang, Yujie; Highland, Heather M.; Comuzzie, Anthony G.; Butte, Nancy F.; Justice, Anne E.; Gahagan, Sheila; Blanco, Estela; Lehtimäki, Terho; Lakka, Timo A.; Hebebrand, Johannes; Bonnefond, Amélie; Grarup, Niels; Froguel, Philippe; Lyytikäinen, Leo-Pekka; Cruz, Miguel; Kobes, Sayuko; Hanson, Robert L.; Zemel, Babette S.; Hinney, Anke; Teo, Koon K.; Meyre, David; North, Kari E.; Gilliland, Frank D.; Bisgaard, Hans; Bustamante, Mariona; Bønnelykke, Klaus; Pennell, Craig E.; Rivadeneira, Fernando; Uitterlinden, André G.; Baier, Leslie J.; Vrijkotte, Tanja G.M.; Heinrich, Joachim; Sørensen, Thorkild I.A.; Saw, Seang-Mei; Pedersen, Oluf; Hansen, Torben; Eriksson, Johan; Widén, Elisabeth; McCarthy, Mark I.; Njølstad, Pål Rasmus; Power, Christine; Hyppönen, Elina; Sebert, Sylvain; Brown, Christopher D.; Järvelin, Marjo-Riitta; Timpson, Nicholas J.; Johansson, Stefan; Hakonarson, Hakon; Jaddoe, Vincent W.V. (Peer reviewed; Journal article, 2019)
      Although hundreds of genome-wide association studies-implicated loci have been reported for adult obesity-related traits, less is known about the genetics specific for early-onset obesity and with only a few studies conducted ...