for Rikard Erlandsson
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Content Neuronova 2001 - 2008 ..................................................... 3 Research ........................................................................... 4 Published papers ............................................................... 6 Teaching experience .......................................................... 8 Other employments ........................................................... 9 Education ....................................................................... 10 Shorter courses ............................................................ 10 Other experiences............................................................ 11
Rikard Erlandsson b. 1958-10-09 Råstensgatan 12 S-172 70 Sundbyberg + 46 8 733 2569 + 4670 698 8534 mail: [email protected]
www: www.rikarderlandsson.se - 2 -
Neuronova 2001 - 2008 When I joined (June 2001) the company, it had been operational for about a year and had no bioinformatics activity. I was employed to handle cDNA expression data from brain stem cells. In the process I built a DNA sequence database using MySQL with a web interface in Perl. This was done the first year on a Linux Mandriva computer using an Apache webserver. Since then, I have been expanding and revising the initial database and included functions to handle all data produced in the Target Discovery process. I have supervised three Master Thesis students in building the Cell database part, Sequence database and Business information database. Today these databases (together with Firewall logging DB, Lead compound DB, Target DB) are integrated parts of our DiscoverySuite that handles all data produced at the company. Raw data is downloaded from special equipment. It is also used to analyze and extract information from the databases. In the system we are using a centralized Active Directory for user administration. The system is built in Perl using CVS to handle multiple developer cooperation. It is using the modular build up using objects to access the underlying data. Every night an automatic download of relevant data from public sources is done and integrated into the system using e-mail alerts to report from the monitoring process. The system is run on a Red Hat Linux server and developed on two Linux workstations. Today I am responsible for the bioinformatics system handling all our research data but also for the entire IT infrastructure, making sure we have the correct hardware at every level, handling contacts with consultants regarding special implementations, etc. I have good knowledge of Perl (object oriented), MySQL, Apache, Windows server, Firewall and Network administration. I also have some experience of PHP, java,C++ and Joomla.
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Research 1999 – 2001, Scientist, Biotechnology, KTH, Stockholm, Sweden. Projects: Gene identification in Populus Tremula by EST sequencing. Clones from different tissues were sequenced and analyzed. Quality control, contaminating sequences clustering. The work was presented at several conferences. Techniques: Automated DNA sequencing. Large scale DNA sequencing. Cycle sequencing of PCR and plasmid templates. Automation in 96-well format. Linux computers. Equipment: ABI 377, MegBACE 1000 DNA sequenators, 9600 PCR machines. Beckman Biomek 1000 robot. Software: Windows/Solaris/Linux/Mac computers Sequencher, Phred/Phrap for sequence analysis. Wrote programs using C and Perl. Did gene identification through EST sequencing. Clones were picked from cDNA libraries from different tissues, sequenced and analyzed, including quality control, removal of contaminating sequences and cluster analysis. The work was presented at different conferences. I planned and reported from the all different steps. 1997 – 1999, PostDoc, Zoology, University of Munich, Munich, Germany. Projects: Study of evolution by DNA sequence comparison. The genomic region of the human ZFY gene was sequenced, analysed and compared with the Xlinked homologue, ZFX. Techniques: Automated DNA sequencing. Large scale DNA sequencing by shotgun techniques. Cycle sequencing of PCR and plasmid templates. Equipment: Autogen740 (plasmid prep machine), Arakis (EMBL dual-lasersequencer), LiCor sequencers, Pharmacia A.L.F. and ALFexpress. MJ and Perkin-Elmer 9600 thermocyclers. Beckman Biomek 2000 robot. Software: Windows/Solaris/Mac computers with DNAstar, sequencher, Phred/Phrap for sequence analysis. Wrote programs using PASCAL. Studied evolution using DNA sequence comparisons. The genome region around the human ZFY gene were sequenced, analyzed and compared with the homolog, ZFX, on the X chromosome. I planed the project, bought the equippement decided what methods to use. I taught the group members the techniques and organized the work.
1996 - 1997, PostDoc, Medical Genetics, University of Uppsala, Sweden. Projects: Research focused on cloning of MHC-DRB in seals and MHC from other species. In a second project I studied the HFE mutation in hereditary hemochromatosis patients in Jämtland using PCR and sequencing. Techniques: PCR on genomic and plasmid DNA also long-range PCR. DNA cycle sequencing. Equipment: Perkin-Elmer 9600 and 2400. ABI 373 and 377. Software: Dos, MS-Access, Windows/Mac with Sequencher. Constructed databases for cervical tissue collection. Organized the the collection of samples identifed in the Swedish cancer registry. Collected and analyzed samples from hemochromatosis patients in Jämtland using PCR and sequencing. Cloned and sequensed MHC from different animals.
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1986 - 1996, PhD student, Tumor Biology, Karolinska Institute, Stockholm, Sweden. (part of Microbiology and Tumor Biology Center, Karolinska Institute from 1994). Project: Research on renal cell cancer and mapping of human chromosome 3. Techniques: DNA/RNA isolation from frozen tissue and tissue culture. Jumping/linking library construction. Cloning of PCR products. Manual and automated DNA sequencing. T7 and Cycle sequencing of PCR products and plasmids. Solid phase sequencing etc. Equipment: Pharmacia A.L.F., Perkin-Elmer 2400, Techne thermal cyclers. Software: CP/M, PC, Dos Windows with DNASIS. Wrote some programs using Turbo PASCAL (object oriented pascal), C. Used VMS. Cloning and isolation of DNA from tissue and culture. Construction of DNA/cDNA libraries, jumping/linking-libraries in plasmids and phages.
1980 - 1981, Student and Civil, Virology, Karolinska Institutet, Stockholm, Sweden. Project: Research on Vaccina virus and glucoproteins. Techniques: Tissue culture. Cell fractionation. Protein purification mainly from Vaccinia infected cells. Equipment: SDS-PAGE gels, ultra-centrifuges etc. No computers. Master Thesis work. Tissue culture, protein purification and characterization.
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Published papers 22. Sievertzon M, Wirta V, Mercer A, Meletis K, Erlandsson R, Wikstrom L, Frisen J, Lundeberg J (2005): Transcriptome analysis in primary neural stem cells using a tag cDNA amplification method. BMC Neurosci. 6:28. 21. Johansson T, Le Quere A, Ahren D, Soderstrom B, Erlandsson R, Lundeberg J, Uhlen M, Tunlid A (2004): Transcriptional responses of Paxillus involutus and Betula pendula during formation of ectomycorrhizal root tissue. Mol Plant Microbe Interact 17:202-215. 20. Amarger V, Erlandsson R, Pielberg G, Jeon JT, Andersson L (2003): Comparative sequence analysis of the PRKAG3 region between human and pig: evolution of repetitive sequences and potential new exons. Cytogenet Genome Res 102:163-172. 19. Bhalerao R, Keskitalo J, Sterky F, Erlandsson R, Bjorkbacka H, Birve SJ, Karlsson J, Gardestrom P, Gustafsson P, Lundeberg J, Jansson S: Gene expression in autumn leaves. Plant Physiol. (2003) Feb;131(2):430-42. 18. Hertzberg M, Aspeborg H, Schrader J, Andersson A, Erlandsson R, Blomqvist K, Bhalerao R, Uhlen M, Teeri TT, Lundeberg J, Sundberg B, Nilsson P and Sandberg G (2001): A transcriptional roadmap to wood formation. Procc Natl Acad Sci U S A 98:14732-14737 17. Erlandsson R, Wilson JF and Pääbo S (2000): Sex chromosomal transposable element accumulation and male-driven substitutional evolution in humans. Mol Biol Evol 17:804-812. 16. Bergström TF, Engkvist H, Erlandsson R, Josefsson A, Mack SJ, Erlich HA, Gyllensten U (1999): Tracing the origin of HLA-DRB1 alleles by microsatellite polymorphism. Am J Hum Genet 64:1709-1718. 15. Bergström TF, Erlandsson R, Engkvist H, Josefsson A, Erlich HA, Gyllensten U (1999): Phylogenetic history of hominoid DRB loci and alleles inferred from intron sequences. Immunol Rev 167:351-65. 14. Wilson JF, Erlandsson R (1998): Sexing of human and other primate DNA. Biol Chem. 379:1287-1288. 13. Erlandsson R (1998): Molecular genetics of renal cell carcinoma [REVIEW]. Cancer Genet Cytogenet 104:1-18. 12. Zabarovsky ER, Kashuba VI, Gizatullin RZ, Winberg G, Zabarovska VI, Erlandsson R, Domninsky DA, Bannikov VM, Pokrovskaja E, Kholodnyuk I, Petrov N, Zakharyev VM, Kisselev LL, Klein G (1996): NotI jumping and linking clones as a tool for genome mapping and analysis of chromosome rearrangements in different tumors [REVIEW]. Cancer Detect Prevent, 20:1-11. 11. Zabarovsky ER, Kashuba VI, Pettersson B, Petrov N, Zachariev V, Gizatullin R, Lebedeva T, Bannikov V, Pokrovskaja E, Zabarovska V, Allikmets R, Erlandsson R, Domninsky D, Sumegi J, Stanbridge EJ, Winberg G, Uhlén M, Kisselev LL, Klein G (1994): Shot-gun sequencing strategy for long-range genome mapping: a pilot study. Genonics, 21:495-500. 10. Zabarovsky ER, Kashuba VI, Marcsek Z, Pokrovskaja ES, Zabarovska V, Kholodnyuk I, Erlandsson R, Sümegi J, Winberg G, Kisselev LL, Klein G: Molecular mapping of the human 3p region. In Contemporary research on renal cell carcinoma. Basic and clinical developments. Ed(s): Staehler G, Pomer S. (1994) pp 69-79. Springer-Verlag, Heidelberg. 9. Boldog F, Arheden K, Imreh S, Strömbeck B, Szekely L, Erlandsson R, Marcsek Z, Sümegi J, Mitelman F, Klein G (1991): Involvement of 3p deletions
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in sporadic and hereditary forms of renal cell carcinoma. Genes Chromosom Cancer 3:403-406. 8. Zabarovsky ER, Boldog F, Erlandsson R, Kashuba VI, Allikmets RL, Marcsek Z, Stanbridge E, Sümegi G, Klein G, Winberg G (1991): New strategy for mapping of the human genome based on a novel procedure for constructing jumping libraries. Genomics 11:1030-1039. 7. Erlandsson R, Szpirer J, Islam MQ, Boldog F, Klein G, Ingvarsson S (1991): The most frequently lost allelic site in human renal cell carcinoma (D3F15S2) on the short arm chromosome 3 has homologous sequences on rat chromosome 8. Cytogenet Cell Genet 57:149-150. 6. Erlandsson R, Boldog F, Persson B, Zabarovsky ER, Allikmets RL, Sümegi J, Klein G, Jörnvall H (1991): The gene from the short arm of chromosome 3, at D3F15S2, frequently deleted in renal cell carcinoma, encodes acylpeptide hydrolase. Oncogene 6:1293-1295. 5. Zabarovsky ER, Boldog F, Thompson T, Scanlon D, Winberg G, Marcsek Z, Erlandsson R, Stanbridge EJ, Klein G, Sümegi J (1990): Construction of a human chromosome 3 specific NotI linking library using a novel cloning procedure. Nucleic Acids Res 18:6319-6324. 4. Erlandsson R, Bergerheim US, Boldog F, Marcsek Z, Kunimi K, Lin BY, Ingvarsson S, Castresana JS, Lee WH, Lee E, Klein G, Sümegi J (1990): A gene near the D3F15S2 site on 3p is expressed in normal human kidney but not or only at a severely reduced level in 11 of 15 primary renal cell carcinomas (RCC). Oncogene 5:1207-1211. 3. Boldog F, Erlandsson R, Klein G, Sümegi J (1989): Long-range restriction enzyme maps of DNF15S2, D3S2, and c-raf1 loci on the short arm of human chromosome 3. Cancer Genet Cytogenet 15:295-306. 2. Erlandsson R, Boldog F, Sümegi J, Klein G (1988): Do human renal cell carcinoma arise by a double loss mechanism? Cancer Genet Cytogenet 36:197202. 1. Kovacs G, Erlandsson R, Boldog F, Ingvarsson S, Müller-Breclin R, Klein G, Sümegi J (1988): Consistent chromosome 3p deletion and loss of heterozygosity in renal cell carcinoma. Proc Natl Acad Sci USA 85:1571-1575.
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Teaching experience Time
Supervisor for Master Thesis at Computer science, Uppsala university. Supervisor for Master Thesis at Skövde University. ”Data modelling and implementation of a chemical compounds database”, Computer science, Bioinformatics program. Supervisor for Master Thesis at Molecular Biotechnics at Uppsala University. ”Study of gene expression in mouse brain by analysis of EST sequences.” Course responsible at Biotechnology/KTH "Linux for bioinformatics and DNA sequence analysis" 3p. Lessons in "From Genomics to Proteomics" about EST sequencing and DNA sequence analysis. Lessons in Biochemistry on nucleic acids, protein synthesis involved techniques. Lessons in "Computerized reference handling", part of research education at K.I./M.I.C. Lessons on "DNA, chromosomes and laboratory methods", for technicians. Supervisor for Master Thesis at Karolinska Institute, Stockholm: "No mutations found in the 3' region of the suggested tumor suppressor gene, acylpeptide hydrolase, in four sequenced renal cell carcinoma cell lines."
May 2000 1991-1995 1994 1993
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Other employments Time Company Work/ Comments 1988-2000 Datagen Erlandsson HB My own company, selling computer hard- and software, especially for medical research. Including customer support and education. 1983-1986 Sundbybers kommun /Patient care Vårdbiträde /Förste vårdbiträde, Helping elderly people, Planned the work for 15 people. 1980-1981 AMS Civil service (VTPag). 1982-1983 Pkfinans /Stockholm Internal service. Key and mail responsibility, Telephone switch board. 1973-1978 Hasselblads foto /Östersund Affärsbiträde. Extra- and summer work. During 1987 until 2001 I worked with academic research (for details, see Research page 4). I have always enjoyed working togeher with people and have a highly developed social competence.
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Education PhD defended, march 15, 1996 (MTC, Karolinska Insitutet): Molecular genetics of kidney cancer: Chromosomal regions of importance in the development of renal cell carcinoma. Immunology, Stockholm university. 1983, 0.25 år 10 p Fil Kand 1982, 3 years 120 p Matematics, Uppsala university 1977 0,5 yr 20 p Chemistry, Stockholm universty 1979 1 yr 40 p Microbiology, Stockholm university 1980-1982 1,5 yr 60 p Wargentinskolan Östersund, Natural science program 1977
Shorter courses Time Mar 2004
Duration 5 weeks
Course/City Administration of relational databases (Oracle) KTH, Stockholm Project leadership Projektstyrning AB, Stockholm Drug development Läkemedelsakademin, Stockholm, Sverige Linux – system administration Raditex AB, Nacka, Sverige Avancerad course forrest biotechnology and enzymologi (6p), Biotechnology, KTH, Sigtuna, Sverige Protein and DNA sequence analysis CMB, Karolinska Institutet, Stockholm Proteinexpression från klonad cDNA i mammalie och bakteriesystem, Molecular biology, KI Epidemiology och biostatistics II Environmental medicin, KI Epidemiology och biostatistics I Environmental medicin, KI The molecular biology of the tumor cell Tumor biology, Karolinska Institutet Library techniques and reference handling M.I.C., Karolinska Institutet
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Other experiences I have a driver’s license for car. Languages Swedish English German French
Born Fluent Fluent Some knowledge
I have studied Litterature for three semesters at Mittuniversitetet in Härnösand Have two adult daughters born 1985 och 1988.
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