Microsoft word - cv jan 2008 jo english litteratur utan födelsedat.doc

CV Jacob Odeberg
Title: MD PhD, Associate Professor in Molecular Biotechnology
Present affiliation:
- Karolinska Institutet, Karolinska University Hospital: 1Dept of Medicine, Atherosclerosis Research unit (CMM) 2Centre for Haematology, 3Karolinska Biomics Centre. - Dept of Proteomics, School of Biotechnology, Royal Institute Education:
University
Degree
date
Discipline
Professional experience:
2005-
Resident physician (ST läk) Clinical Haematology, Karolinska University Hospital, Research Associate, Karolinska Biomics Centre, Karolinska University Hospital Senior Scientist, Dept of Medicine, Atherosclerosis Research Unit, Karolinska. 2002 - 2005 Internship (Forskar AT), Karolinska University Hospital
1999 -
Senior Scientist, School of Biotechnology, KTH Post doc in Dept of Biotechnology, KTH, under Prof. Mathias Uhlén. PhD student at Dept of Biochemistry, KTH. . Research and Development Engineer, Vattenfall Utveckling AB, Stockholm Boards and assignments:
Deputy board member of the JC and Seth M. Kempe foundations (2005-) Member of the steering board of “Stockholm graduate school of molecular life sciences” (2000-2003). Board member of CytaCoat AB (2005-) and HeliCure AB (2007-) Teaching:
Course organizer and examination responsible for the undergraduate course ”Cell Biology with Immunology” (2001-2007) in the core curriculum for the Biotechnology engineering program, KTH, and for the postgraduate course “Current topics in Molecular Biotechnology”, KTH (2004-2007). Co-organizer of the postgraduate course “Applied Bioinformatics and Methodologies in SNP Lecturer on the courses; "Cell Biology with Immunology", KTH, (2001-2007), “Introductory Biotechnology”, KTH, (2001); “From Genomics to Proteomics”, KTH, (2001); ”Molecular Biotechnology”, KTH, (2002). Supervision of PhD students
Main supervisor for Malin Andersen and Jorge Andrade, Dept of Biotechnology, KTH. Co-supervisor for Anna Lindström, (Karolinska, dissert. March 2005), Nina Ståhlberg, (Karolinska, Dec 2003), Stina Boräng (KTH, Jan 2004), and Tove Andersen (KTH, Sept 2002) Reviewer of scientific work
Reviewer of grant applications to the Kempe foundations (2005 - ) Reviewer for Human Mutation, Nucleic Acid Research, Circulation, ATVB. Committee member at the halftime seminars of Louisa Cheung (Karolinska March 2006), Zheng Ge (Karolinska March 2007) and Hanna Agardh (Karolinska, Dec 2007), at the dissertation of Hagit Katzov (Karolinska Jun 2006), and at the licentiate thesis seminar of Annika Ahlford (Uppsala University May 2007).
Original publications 2002-
Lisa Berglund, Jorge Andrade, Jacob Odeberg and Mathias Uhlen. The linear epitope space of the human
proteome Protein Science, (2008) Accepted

Andersen M, Engström PG, Lithwick S, Arenillas D, Eriksson P, Lenhard B, Wassermann WW, Odeberg
J. In Silico detection of sequence variations modifying transcriptional regulation. PLoS Computational
Biology, (2008) Accepted

Marianne van Rooijen, Angela Silveira, Stella Thomassen, Jacob Odeberg, Anders Hamsten, Jan Rosing,
Katarina Bremm1. APC resistance during the normal menstrual cycle. Thromb Haemost. 2007
Dec;98(6):1246-51.
Anna Sillén, Jorge Andrade, Lena Lilius, Charlotte Forsell, Karin Axelman, Jacob Odeberg,
Bengt Winblad, and Caroline Graff. Expanded high-resolution genetic study of 109 Swedish families with
Alzheimer's disease. Eur J Hum Genet. 2007 Oct 24
Louisa Cheung, Malin Andersen, , Carolina Gustavsson Jacob Odeberg Leandro Fernández-Pérez
Gunnar Norstedt and Petra Tollet-Egnell. Hormonal and nutritional regulation of alternative CD36
transcripts in rat liver--a role for growth hormone in alternative exon usage.BMC Mol Biol. 2007 Jul 17
Andrade J, Andersen M, Sillén A, Graff C, Odeberg J. The use of Grid computing to facilitate data
intensive genetic research. European Journal of Human Genetics 2007, Jun;15(6):694-702

Andrade J, Andersen M, Berglund L, Odeberg J. Applications of Grid computing in genetics and
proteomics. Proceedings of PARA06 workshop on state-of-the-art in scientific and parallel computing
Springer series Lecture Notes in Computer Science (LNCS) 2007.
Kaller M, Hultin E, Holmberg H, Persson ML, Odeberg J, Lundeberg J, Ahmadian A. Comparison of PrASE
and Pyrosequencing for SNP Genotyping. BMC Genomics 2006 2006 Nov 16;7:29
Andrade J, Berglund L, Uhlén M, Odeberg J. Using Grid technology for computationally intensive
applied bioinformatics analyses. In Silico Biology 2006; vol 6, 495-504
Mercke Odeberg J, Andrade J, Holmberg K, Hoglund P, Malmqvist U, Odeberg J. UGT1A
polymorphisms in a Swedish cohort and a human diversity panel, and the relation to bilirubin plasma
levels in males and females. European Journal of Clinical Pharmacology. 2006 Aug 15
Chaoyong Z, Odeberg J, Hamsten A, Eriksson P. Allele-specific MMP-3 transcription under in vivo
conditions. Biochemical and Biophysical Research Communications, 2006 Aug 4
Lahermo P, Liljedahl U, Alnaes G, Axelsson T, Brookes AJ, Ellonen P, Groop PH, Hallden C, Holmberg
D, Holmberg K, Keinanen M, Kepp K, Kere J, Kiviluoma P, Kristensen V, Lindgren C, Odeberg J,
Osterman P, Parkkonen M, Saarela J, Sterner M, Stromqvist L, Talas U, Wessman M, Palotie A, Syvanen
AC. A quality assessment survey of SNP genotyping laboratories.
Hum Mutat. 2006 Jul;27(7):711-4.
Sandholm T., Andrade, J., Odeberg J., Lai K. Market-Based Resource Allocation using Price Prediction
in a High Performance Computing Grid for Scientific Applications. HPDC '06: IEEE Computer Society
Press HPDC '06: Proceedings of the 15th IEEE International Symposium on High Performance
Distributed Computing 2006

Andersen M., Lenhard B., Whatling C., Eriksson P., Odeberg J. Alternative promoter usage of the
glycoprotein CD36. BMC Molecular Biology 2006 Mar 3;7(1):8
Odeberg, J., Freitag, M., Odeberg, H., Andrade J., Råstam L. Lindblad U. Severity of the acute coronary
syndrome is predicted by interactions between fibrinogen concentrations and polymorphisms in the
GpIIIa and FXIII genes. J Thromb Haemostasis, April 2006.
Ågren A, Wiman B, Stiller V, Lindmarker P, Sten-Linder M, Carlsson A, Holmström M, Odeberg J,
Schulman S. Evaluation of low PAI-1 activity as a risk factor for hemorrhagic diatesis. J Thromb
Haemostasis, 2006 Jan;4(1):201-8
Velázquez-Fernández D, Laurell C, Geli J, Höög A, Odeberg J, Kjellman M, Lundeberg J, Hamberger
B, Nilsson P, Bäckdahl M. Expression profiling of adrenocortical tumors suggests a molecular signature
of malignancy. Surgery 2005, Dec;138(6):1087-94.
Samnegard A, Silveira A, Lundman P, Boquist S, Odeberg J, Hulthe J, McPheat W, Tornvall P,
Bergstrand L, Ericsson CG, Hamsten A, Eriksson P. Metalloproteinase-3 concentration is influenced by
MMP-3 -1612 5A/6A promoter genotype and associated with myocardial infarction. J Intern Med. 2005
Nov;258(5):411-9.
Holmberg K, Persson ML, Uhlen M, Odeberg J. Pyrosequencing-analysis of thrombosis-associated risk
markers. Clinical Chemistry 2005;51(8):1549-52.
Sandalova T, Michaelsson J, Harris RA, Odeberg J, Schneider G, Kärre K, Achour A. A structural basis
for CD8+ T cell-dependent recognition of non-homologous peptide ligands: implications for molecular
mimicry in autoreactivity. J Biol Chem. 2005 Jul 22;280(29):27069-75.
Lindström A, Odeberg J, Albert J. Pyrosequencing for detection of Lamivudine-resistant hepatitis B
virus. J Clin Microbiol. 2004 Oct;42(10):4788-95.
Magnusson V, Zunec R, Odeberg J, Sturfelt G, Truedsson L, Gunnarsson I, Alarcon-Riquelme ME .
Polymorphisms of the Fc gamma receptor type IIB gene are not associated with systemic lupus
erythematosus in the Swedish population. Arthritis Rheum. 2004 Apr;50(4):1348-50. *
Magnusson V, Johanneson B, Lima G, Odeberg J, Alarcon-Segovia D, Alarcon-Riquelme ME. Both risk
alleles for FcgammaRIIA and FcgammaRIIIA are susceptibility factors for SLE: a unifying hypothesis.
Genes Immun. 2004 Jan 22.


Boräng S, Andersson A, Thelin A, Odeberg J, Lundeberg J. Vascular Gene Expression in
Atherosclerotic Plaque-Prone Regions Analyzed by Representational Difference Analysis. Pathobiology
2003, 71(2): 107-14.
Andersson T, Boräng S, Unneberg P, Wirta V, Thelin A, Lundeberg J, Odeberg J.. Shotgun sequencing
and microarray analysis of RDA Transcripts. Gene. 2003. May 22;310:39-47

Achour A, Michaelsson J, Harris RA, Odeberg J, Grufman P, Sandberg JK, Levitsky V, Kärre K,
Sandalova T, Schneider G. A structural basis for LCMV immune evasion: subversion of H-2D(b) and H-
2K(b) presentation of gp33 revealed by comparative crystal structure analyses. Immunity. 2002
Dec;17(6):757-68.

Odeberg, J; Holmberg, K; Eriksson, P; Uhlén, M. Molecular Haplotyping by Pyrosequencing,
Biotechniques. 2002 Nov;33(5):1104, 1106, 1108.
Andersson, T; Boräng, S; Larsson, M; Wirta, V.; Wennborg, A.; Lundeberg, J. and Odeberg, J.: Novel
candidate genes for atherosclerosis are identified by RDA-based transcript profiling of cholesterol loaded
macrophages. Pathobiology. 2002;69(6):304-14.
Andersson, T; Unneberg, P; Nilsson, P; Quackenbush, J; Odeberg, J; Lundeberg, J. Monitoring
of representational difference analysis subtraction procedures by global microarrays. Biotechniques. 2002
Jun;32(6):1348-50, 1352, 1354-6, 1358.
Agaton, C.; Sievertzon, M.; Holmberg, A.; Larsson, M.; Unnerberg, P.; Odeberg, J.; Uhlén, M. and
Lundeberg, J.; Gene Expression Analysis by Signature Pyrosequencing. Gene 2002 May, 289(1-2):31-9
O’Meara, D; Ahmadian, A; Odeberg, J; Lundeberg, J. SNP typing by apyrase-mediated allele-specific
primer extension on DNA microarrays. Nucleic Acids Res. 2002 Aug 1;30(15):e75.

Ahmadian, A.; Gharizadeh, B.; O’Meara, D.; Odeberg, J.; and Lundeberg, J. Genotyping by
apyrase-mediated allele-specific extension. Nucleic Acids Res. 2001 Dec 15;29(24)
Boräng, S; Andersson, T; Thelin, A.; Larsson, M.; Odeberg, J. and Lundeberg, J.
Monitoring of the subtraction process in solid phase representational difference analysis -
Characterisation of a candidate drug.Gene. 2001 Jun 27;271(2):183-92
Odeberg, J; Wood, T; Blucher, Å; Rafter, J; Norstedt, G; Lundeberg, J. A cDNA RDA protocol
using solid phase technology for analysis of small tissue samples. 17, 1-9. (2000) Genet Anal:
Biomolecular engineering
Tollet-Egnell P., Flores-Morales A., Odeberg J., Lundeberg J., Norstedt G.: Differential cloning
of growth hormone-regulated hepatic transcripts in the aged rat. Endocrinology. 141 (2000) 910-
21.
Røsok, O., Pedeutour F., Odeberg J., Lundeberg J., Aasheim HC.: The c1orf9 gene encodes a
putative transmembrane member of a novel protein family. Biochem Biophys Res Commun. 267
(2000) 855-62.
Odeberg, J., Ahmadian, A., Williams, C., Uhlen, M., Ponten, F. and Lundeberg, J.: Context-
dependent Taq-polymerase-mediated nucleotide alterations, as revealed by direct sequencing of
the ZNF189 gene: implications for mutation detection. Gene 235 (1999) 103-9.
Odeberg, J., Røsok, O., Gudmundsson, G.H., Ahmadian, A., Roshani, L., Williams, C., Larsson,
C., Pontén, F., Uhlén, M., Asheim, H.C. and Lundeberg, J.: Cloning and characterization of
ZNF189, a novel human Krüppel-like zinc finger gene localized to chromosome 9q22-q31.
Genomics 50 (1998) 213-21.
Odeberg, J., Yun, Z., Sönnerborg, A., Weiland, O. and Lundeberg, J.: Variation in the hepatitis
C virus NS5a region in relation to hypervariable region 1 heterogeneity during interferon
treatment. J Med Virol 56 (1998) 33-8.
Ahmadian, A., Ren, Z.P., Williams, C., Pontén, F., Odeberg, J., Pontén, J., Uhlén, M. and
Lundeberg, J.: Genetic instability in the 9q22.3 region is a late event in the development of
squamous cell carcinoma. Oncogene 17 (1998) 1837-43.
Odeberg, J., Yun, Z., Sönnerborg, A., Bjøro, K., Uhlén, M. and Lundeberg, J.: Variation of
hepatitis C virus hypervariable region 1 in immunocompromised patients. J Infect Dis 175 (1997)
938-43.
Røsok, Ø., Odeberg, J., Rode, M., Stokke, T., Funderud, S., Smeland, E. and Lundeberg, J.:
Solid-phase method for differential display of genes expressed in haematopoietic stem cells.
BioTechniques 21 (1996) 114-121.
Yun, Z.B., Odeberg, J., Lundeberg, J., Weiland, O., Uhlén, M. and Sönnerborg, A.: Restriction
of hepatitis C virus heterogeneity during prolonged interferon-alpha therapy in relation to
changes in virus load. J Infect Dis 173 (1996) 992-6
Odeberg, J., Yun, Z., Sönnerborg, A., Uhlén, M. and Lundeberg, J. Dynamic analysis of
heterogeneous hepatitis C virus populations by direct solid-phase sequencing.
J Clin Microbiol. 1995 Jul;33(7):1870-4.
Gudmundsson, G.H., Agerberth, B., Odeberg, J., Bergman, T., Olsson, B. and Salcedo, R.: The
human gene FALL39 and processing of the cathelin precursor to the antibacterial peptide LL-37
in granulocytes. Eur J Biochem 238 (1996) 325.*
Agerberth, B., Gunne, H., Odeberg, J., Kogner, P., Boman, H.G. and Gudmundsson, G.H.:
FALL-39, a putative human peptide antibiotic, is cysteine-free and expressed in bone marrow and
testis. Proc Natl Acad Sci U S A 92 (1995).


3. Översiktsartiklar
Odeberg, J. and Uhlén, M. New techniques in SNP typing. Medizinische Genetik 2002.
Ståhl, S., Odeberg, J., Larsson, M., Rosok, O., Ree, A.H. and Lundeberg, J.: Solid-phase
differential display and bacterial expression systems in selection and functional analysis of
cDNAs. Methods Enzymol 303 (1999) 495-511.
Lundeberg, J., Røsok, Ø., Hansen Ree, A. and Odeberg, J.: Solid-phase differential display. In:
Siebert, P.D. and Larick, J.W. (Eds.), Gene cloning and analysis by RT-PCR. Eaton Publishing,
Palo Alto, 1998.
Lundeberg, J., Odeberg, J. and Uhlén, M.: Dynamic analysis of viral populations by direct DNA
sequencing and Solid-phase Technology. In: Stephenson, J.R. and Warnes, A. (Eds.), Diagnostic
Virology Protocols. Humana Press, Totowa, New Jersey, 1998, pp. 277-286.
4. Patent:
WO 2006/101438 A1
“An antimicrobial agent comprising a cysteine compound covalently bound to a susbtrate, in
particular by binding through an S-S bridge via a spacer molecule”
PCT application. Lindberg, Odeberg, Gudmundsson, Agerberth, Wirsén.

5. Egenutvecklade datorprogram/datorresurser:

RAVEN – a web based resource for analysing genetic variation in regulatory regions
http://www.cisreg.ca/cgi-bin/RAVEN/a
Grid-allegro- a grid based tool for genetic analysis using the Allegro program
http://kthgridproxy.biotech.kth.se/grid-allegro/index.html.
Gridblast – a tool for protein sequence similarity analysis with a sliding window http://kthgridproxy.biotech.kth.se/grid_blast/index.html

Source: http://www.cytacoat.se/doc/CV_Jacob_Odeberg.pdf