CV

Date of birth:     (yymmdd) 750601
Nationality:       Swedish
Titles:    Doctor of Philosophy in Functional Genomics, Master of Science in Molecular Biology  [Swedish: Filosofie Doktor i funktionsgenomik, Filosofie Magister i molekylärbiologi]

Acadmic position/degrees 
Dec 2007-present
Assistant Professor  at the Bioinformatics Centre, Copenhagen University

Oct 2006- Dec 2007
Assistant Professor (externally funded) at the Bioinformatics Centre, Copenhagen University

Jan 2006 – Dec 2006
Adjunct Associate Professor at Tokyo Medical and Dental University, Japan

Feb 2005 – Oct 2006
Researcher at the Genome Sciences Center, RIKEN Yokohama Institute, Japan. Chief scientist: Dr. Yoshihide Hayashizaki.

May 2004 – Jan 2005
Postdoctoral position at Center for Genomics and Bioinformatics, Karolinska Institute, Sweden. Supervisor: Dr. Boris Lenhard

May 2004
Awarded PhD in Functional Genomics. Center for Genomics and Bioinformatics, Karolinska Institute, Sweden. The main text of the doctoral thesis, entitled “In silico prediction of cis-regulatory elements”, is available at http://diss.kib.ki.se/2004/91-7349-879-3/

September 2000 – May 2004
PhD period at Center for Genomics and Bioinformatics, Karolinska Institute, Sweden (part time at CMMT, University of British Columbia, Canada), supervised by Dr. Wyeth Wasserman, focused on the computational biology of transcriptional regulation.

June 2000
Awarded Master of Science in Molecular Biology, Stockholm University, Sweden. Rotation periods at Dep. of Biochemistry at Stockholm University, Biomedicum at Uppsala University and Center for Genomics and Bioinformatics, Karolinska Institute.

Pedagogic experience
Course leader and lecturer
Introduction for Bioinformatics (1-week course for Stockholm Biomedical Graduate School, Karolinska), 2002, 2003, 2004, 2005
Beginning Perl Programming for Biologists (4 credit Graduate level course, Karolinska Institute) 2004, 2005
Applied Bioinformatics  (Graduate level course, Copenhagen University) 2007

Lecturer
Molecular Techniques in Biology, Karolinska Institute, Novum 2002, 2004
Bioinformatics, KTH 2002
    
Project/PhD students
Sara Bruce    SVM classification of Ultra-Conserved Regions in neural development
[10 week rotation project, Stockholm Biomedical School, co-supervised by dr Boris Lenhard, CGB, Karolinska Institute]
Ilka Hof    Correlation between Ultra-conserved regions and chromosomal breakpoints
[2 month project student, co-supervised by dr Boris Lenhard, CGB, Karolinska Institute]
Jasmina Ponjavic    Correlation between TATA-TSS spacing and transcriptional specificity; Evolution of macrophage-specific gene promoters, Transcription start site turnover
[10 month project student, GSC, RIKEN Yokohama Institute]
Eivind Valen        Present PhD student: mainly focused on hippocampus-specific promoters                 and promoter predictions
Eric Man-Hung        Present PhD student: mainly focused on pattern finding and TATA-less                 promoters
Troels Marstrand    Present PhD student: mainly focused on TSS-TFBS distances




Education and coursework:
( where 1p=1 credit= 1 week of study, G= passed, VG=passed with distinction)
 

2000-2003 Advanced Graduate Courses
Statistics for Scientists 5p    (Stockholm University)  VG
Algorithms, data structures and  complexity 5p   (Royal Institute of Technology)    VG
Algorithmic bioinformatics 4p   (Stockholm Bioinformatics Center, Royal Institute of Technology)   G
Object-oriented C++  4p    (Royal Institute of Technology)  G
Statistical Genomics  5p    (Stockholm University ) G
Classical Papers in Bioinformatics 3p   (Stockholm Bioinformatics Center)G
 
2000
Master of Science in Molecular Biology, Stockholm University. Master student year at Stockholm Graduate School of Molecular Life sciences (Stockholm University, Karolinska Institute and Royal Institute of Technology)
 
Stockholm Graduate School of Molecular Life sciences 40p
 
- Introduction 4p   G
- Human genetics 4p  G
- Drug Discovery and Innovation 4p  G
- Structural Problems in Cell Biology 4p G
 

 
- Master thesis 1 (12p):  
Critical Residues in Proton Transfer  in Cytochrome c Oxidase : Crystallization and Kinetic Measurements
Supervisor: Peter Brezezinki, Department of Biochemistry, Stockholm University and BMC,  Uppsala university  VG
 
 - Master thesis 2 (12p)  
Clustering Transcription Factors by Similarities in DNA-binding Specificity
Supervisor Wyeth Wasserman, Bioinformatics unit, Center for Genomics and Bioinformatics, Karolinska Institutet VG                                        
 

 
Advanced Graduate Courses
Biochemistry  10p  VG
Struktural biochemistry and Bioinformatics 10p VG
Neurochemistry 10p  G
Micro biology 10p   G
 
Undergraduate Courses
General Chemistry 10p  G
Inorganic Chemistry 5p  VG
Organic Chemistry 10p  VG
Biochemistry 10p   G
Separation techniques 6p  G  
Cellular biology 5p  G
Micro biology 9p   G
Physiologi 5p   VG
Ecology and Evolution 4p  VG
Immunology 1p   VG
Molecular biology 5p  VG
Eukaryotic molecular genetics 5p  VG
Physical chemistry 5p  VG
 
Additional university-level courses
Commercial Law 10p  VG
Astronomy 5p   G
Popular Music and Jazz 5p  G
English  20p   G
 

Primary fields of research

• Gene regulation bioinformatics
• Tag-based expression and promoter analysis