SVERIGES LANTBRUKSUNIVERSITET Sweden

SLU (Sveriges lantbruksuniversitet – Swedish University of Agricultural Sciences) is a university with a clearly defined role in society: to take responsibility for the development of learning and expertise in areas concerning biological resources and biological production. This responsibility stretches over the wide-ranging fields of agriculture, forestry and food industry to environmental questions, veterinary medicine and biotechnology. A comprehensive viewpoint, inter-disciplinary approach and applicability are keywords in SLU's research and teaching and in the contacts with industry and society.

University activities are spread between several departments in four faculties: the Faculty of Landscape Planning, Horticulture and Agricultural Science, the Faculty of Natural Resources and Agriculture Sciences, the Faculty of Veterinary Medicine and Animal Science and the Faculty of Forest Sciences. A total of 3 200 people are employed at the University.

SLU offers a broad spectrum of educational programmes and single subjects courses. About 3 300 undergraduates and 800 postgraduate students are enrolled at SLU.

Main campuses are located at Alnarp, Skara, Ultuna and Umeå. Research and teaching activities are carried out throughout the country.

http://www.slu.se/en/

Prof. Erik Bongcam­‐Rudloff

Associate Professor Erik Bongcam-Rudloff, is a doctor in medical sciences and a computer scientist. http://www.rudloff.se

COMMISSIONS: ONGOING

  • Coordinator of the FP7 project ALLBIO: “Broadening the Bioinformatics Infrastructure to unicellular, animal, and plant sciences” (http://www.allbioinformatics.eu ). 2011-2014.
  • Coordinator COST Action: Next Generation Sequencing Data Analysis Network” SeqAhead, www.nextgensequencing.org 2011-2015
  • Board Member of the International Society for computational Biology (ISCB www.iscb.org ), 2012-2015.
  • Executive board member of EMBnet, 2010-2013.
  • Coordinator WP7 in the EU FP7 Affinomics project, www.affinomics.org, 2010-2014
  • Board member of UPPMAX, Uppsala Multidisciplinary Center for Advanced Computational Sciences www.uppmax.uu.se.
  • Board member of the National Supercomputer Centre in Sweden (NSC). Linköping, Sweden. www.nsc.liu.se
  • Editor in Chief for EMBnet.Journal since 2000. http://journal.embnet.org/
  • Director of eBioinformatics.org creators of eBiotools and BioX. www.ebioinformatics.org.

PAST

  • Chairman of EMBnet, a science-based group of collaborating bioinformatics nodes
  • throughout Europe and a number of nodes outside Europe. www.embnet.org. 2003-2009.
  • Executive board member of EMBRACE, a FP6 funded Network of Excellence, which encompasses computational biologists from 17 institutes in 11 European countries. www.embracegrid.info. 2005-2010. WP4 Coordinator.
  • Member of the WP4 in the ESFRI BBMRI project. www.bbmri.org
  • Member of the WP10 in the ESFRI ELIXIR project http://www.elixir-europe.org/
  • Coordinator WP4 Eurokup, EU COST action. www.eurokup.org

SOFTWARE DEVELOPMENT: The Bongcam-Rudloff group has developed web-based bioinformatics analysis systems and desktop applications.

Desktop applications:

  • eBioTools: is a collection of more than 300 open source bioinformatics programs, www.ebioinformatics.org.
  • eBioX: A highly popular graphic user interface for the eBiotools programmes. eBioX brings easy-to-use sequence analysis to Mac-using biologists. www.ebioinformatics.org

WEB-BASED ANALYSIS SYSTEMS:

Publications 2012

1. Klingström T, Soldatova L, Stevens R, et. al. - “Workshop on laboratory protocol standards for the molecular methods database” N Biotechnol. 2012 Jun 2. [Epub ahead of print]

2. Biao Wang, Robert Ekblom, Todd A. Castoe, et. al. - “Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development” 10.1098/rsob.120054 Open Biol April 2012

3. Anne Fischer, Beth Shapiro, Cecilia Muriuki, et. al. - “The origin of the 'Mycoplasma mycoides cluster' coincides with domestication of ruminants” 2012. PLoS ONE 7(4): e36150. doi:10.1371/journal.pone.0036150

4. Harald Mischak, John P.A., Ioannidis Angel Argiles, et. al. - “Implementation of proteomic biomarkers: making it work. European Journal of Clinical Investigation” Article first published online: 21 APR 2012. DOI: 10.1111/j.1365-2362.2012.02674.x

Publications 2011

1. SEQscoring: a tool to facilitate the interpretation of data generated with next generation sequencing technologies. Katarina Truvé, Oscar Eriksson, Martin Norling, Maria Wilbe, Evan Mauceli, Kerstin Lindblad-Toh, Erik Bongcam-Rudloff. EMBnet.journal. 2011, Vol 17, no 1, pp 38-45

2. SEQAHEAD - COST Action BM1006: Next Generation Sequencing Data Analysis Network , EMBnet.journal, 2011, Vol 17, no1, pp 7-9

3. The first sequenced carnivore genome shows complex host-endogenous retrovirus relationships. Martínez Barrio A, Ekerljung M, Jern P, Benachenhou F, Sperber GO, Bongcam-Rudloff E, Blomberg J, Andersson G. PLoS One. 2011 May 12;6(5):e19832.

4. A novel unstable duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs. Olsson M, Meadows JR, Truvé K, Rosengren Pielberg G, Puppo F, Mauceli E, Quilez J, Tonomura N, Zanna G, Docampo MJ, Bassols A, Avery AC, Karlsson EK, Thomas A, Kastner DL, Bongcam-Rudloff E, Webster MT, Sanchez A, Hedhammar A, Remmers EF, Andersson L, Ferrer L, Tintle L, Lindblad-Toh K. PLoS Genet. 2011 Mar;7(3):e1001332. Epub 2011 Mar 17.

5. Contributions of the EMERALD project to assessing and improving microarray data quality. Beisvåg V, Kauffmann A, Malone J, Foy C, Salit M, Schimmel H, Bongcam-Rudloff E, Landegren U, Parkinson H, Huber W, Brazma A, Sandvik AK, Kuiper M. Biotechniques. 2011 Jan;50(1):27-31.

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