Blar i Bergen Open Research Archive på forfatter "Brazma, Alvis"

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    • An integrated landscape of protein expression in human cancer 

      Jarnuczak, Andrew F.; Najgebauer, Hanna; Barzine, Mitra; Kundu, Deepti J.; Zamanzad Ghavidel, Fatemeh; Perez-Riverol, Yasset; Papatheodorou, Irene; Brazma, Alvis; Vizcaíno, Juan Antonio (Journal article; Peer reviewed, 2021)
      Using 11 proteomics datasets, mostly available through the PRIDE database, we assembled a reference expression map for 191 cancer cell lines and 246 clinical tumour samples, across 13 lineages. We found unique peptides ...

    • Predicting Gene Regulatory Elements in Silico on a Genomic Scale 

      Brazma, Alvis; Jonassen, Inge; Vilo, Jaak; Ukkonen, Esko (Journal article, 1998-05-18)
      We performed a systematic analysis of gene upstream regions in the yeast genome for occurrences of regular expression-type patterns with the goal of identifying potential regulatory elements. To achieve this goal, we have ...

    • 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 ...

    • A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB 

      Rayner, Tim F.; Rocca-Serra, Philippe; Spellman, Paul T.; Causton, Helen C.; Farne, Anna; Holloway, Ele; Irizarry, Rafael A.; Liu, Junmin; Maier, Donald S.; Miller, Michael; Petersen, Kjell; Quackenbush, John; Sherlock, Gavin; Stoeckert, Christian J. Jr; White, Joseph; Whetzel, Patricia L.; Wymore, Farrell; Parkinson, Helen; Sarkans, Ugis; Ball, Catherine A.; Brazma, Alvis (Peer reviewed; Journal article, 2006-11-06)
      Background: Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGEML by the MGED Society. However, the complexity ...