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Bioinformatics Short-term Support and Infrastructure (BILS)

National facility

Bioinformatics short-term support

Bioinformatics short-term support and infrastructure is a facility at SciLifeLab that provides expertise in multiple bioinformatics areas (please see our services and equipments below). Several of the facility personnel are also members of BILS (Bioinformatics Infrastructure for Life Sciences). BILS is a distributed national research infrastructure supported by the Swedish Research Council providing bioinformatics support to life science researchers in Sweden. BILS is also the Swedish contact point to the European infrastructure for biological information ELIXIR. The facility has BILS-associated personnel in both Uppsala and Stockholm. In addition, the facility offers access to Uppsala-based application experts within imaging and evolutionary biology.

SERVICES

  • We can help with infrastructure related to bioinformatics. data storage, data publishing, access to computing and access to bioinformatics tools
  • We provide expertise in multiple bioinformatics areas. Biostatistics, phylogenomics, metabolomics, systems biology, protein bioinformatics, mass-spectrometry proteomics, genome annotation and large scale sequencing (NGS) including metagenomics

EQUIPMENT

Our main resource is our staff. For compute and storage, we rely on the SNIC centres, where BILS has access to dedicated partitions of the systems. BILS has cluster for genome annotation.

APPLICATIONS

  • RNA seq analysis
  • Genome annotation
  • Multivariate analysis
  • Evolutionary analysis of proteins
  • Ancestral state reconstructions
  • Disorder and indel analysis
  • Analysis platform for mass-spectrometry data
  • Tools for phenomics analysis
  • Cancer data analysis
  • Mass spectrometry data storage
  • Bioinformatics training, workshops
  • Information about our BILS staff expertise is available via this link
  • More details about projects are available in our BILS Annual Report 2013

RECENT PROJECTS

Arabi, A., Ullah, K., Branca, R.M., Johansson, J., Bandarra, D., Haneklaus, M., Fu, J., Aries, I., Nilsson, P., Den Boer, M.L., Pokrovskaja, K., Grander, D., Xiao, G., Rocha, S., Lehtio, J. and Sangfelt, O. (2012) Proteomic screen reveals Fbw7 as a modulator of the NF-κB pathway. Nat Commun, 3, 976.

 

Carlsson, F., Trilling, M., Perez, F. and Ohlin, M. (2012) A dimerized single-chain variable

fragment system for the assessment of neutralizing activity of phage display-selected antibody

fragments specific for cytomegalovirus. J. Immunol. Methods, 376, 69–78.

 

Kallberg, Y., Segerstolpe, A., Lackmann, F., Persson, B. and Wieslander, L. (2012) Evolutionary conservation of the ribosomal biogenesis factor Rbm19/Mrd1: implications for function. PLoS ONE, 7, e43786.

 

Kirik, U., Cifani, P., Albrekt, A.S., Lindstedt, M., Heyden, A. and Levander, F. (2012) Multimodel pathway enrichment methods for functional evaluation of expression regulation. J. Proteome Res., 11, 2955–2967.

 

Light, S., Sagit, R., Ithychanda, S.S., Qin, J. and Elofsson, A. (2012) The evolution of filamin – a protein domain repeat perspective. J. Struct. Biol., 179, 289–298.

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Olsson, N., James, P., Borrebaeck, C.A. and Wingren, C. (2012) Quantitative proteomics

targeting classes of motif-containing peptides using immunoaffinity-based mass spectrometry. Mol. Cell Proteomics, 11, 342–354.

 

Pinto, R.C., Gerber, L., Eliasson, M., Sundberg, B. and Trygg, J. (2012) Strategy for minimizing between-study variation of large-scale phenotypic experiments using multivariate analysis. Anal. Chem., 84, 8675–8681.