PUBLICATIONS FROM STUDENTS IN THE RESEARCH SCHOOL

 

Licentiate theses

2007

Karlsson S, Holmberg E, Askerlund A, Levan KK (2007)
Altered transforming growth factor-beta pathway expression pattern in rat endometrial cancer.
Cancer Genet Cytogenet 177(1):43-50

E. Larsson, X. Zhou and L. M. Akyurek (2007)
RhoA-dependent vascular smooth muscle cell-specific transcription: adding diaphanous formins to the puzzle
Arterioscler Thromb Vasc Biol 27, 448-9.

Nordlander C, Karlsson S, Karlsson A, Sjoling A, Winnes M, Klinga-Levan K, Behboudi A. (2007 )
Analysis of chromosome 10 aberrations in rat endometrial cancer-evidence for a tumor suppressor locus distal to Tp53.
Int J Cancer. Apr 1;120(7):1472-81.

 

2006

R. Alm, P. Johansson, K. Hjerno, C. Emanuelsson, M. Ringner and J. Hakkinen (2006)
Detection and identification of protein isoforms using cluster analysis of MALDI-MS mass spectra
J Proteome Res 5, 785-92.


M. X. Andersson, M. Hamberg, O. Kourtchenko, A. Brunnstrom, K. L. McPhail, W. H. Gerwick, C. Gobel, I. Feussner and M. Ellerstrom (2006)
Oxylipin profiling of the hypersensitive response in Arabidopsis thaliana. Formation of a novel oxo-phytodienoic acid-containing galactolipid, arabidopside E
J Biol Chem 281, 31528-37.
 

M. X. Andersson, O. Kourtchenko, J. L. Dangl, D. Mackey and M. Ellerstrom (2006)
Phospholipase-dependent signalling during the AvrRpm1- and AvrRpt2-induced disease resistance responses in Arabidopsis thaliana
Plant J 47, 947-59.


D. Dalevi, D. Dubhashi and M. Hermansson (2006)
Bayesian classifiers for detecting HGT using fixed and variable order Markov models of genomic signatures
Bioinformatics.


D. Dalevi, D. Dubhashi and M. Hermansson (2006)
A new order estimator for fixed and variable length Markov models with applications to DNA sequence similarity
Stat Appl Genet Mol Biol 5, Article8.


T. Z. DeSantis, P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu and G. L. Andersen (2006)
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
Appl Environ Microbiol 72, 5069-72.


K. Hjerno, R. Alm, B. Canback, R. Matthiesen, K. Trajkovski, L. Bjork, P. Roepstorff and C. Emanuelsson (2006)
Down-regulation of the strawberry Bet v 1-homologous allergen in concert with the flavonoid biosynthesis pathway in colorless strawberry mutant
Proteomics 6, 1574-87.


E. Kristiansson, A. Sjogren, M. Rudemo and O. Nerman (2006)
Quality optimised analysis of general paired microarray experiments
Stat Appl Genet Mol Biol 5, Article10.


A. Kurbasic and O. Hössjer (2006)
Relative risk and effective number of mesioses: A unified approach for general genetic models and phenotypes
Ann Hum Genet 70(Pt 6):907-22


A. Le Quere, K. A. Eriksen, B. Rajashekar, A. Schutzendubel, B. Canback, T. Johansson and A. Tunlid (2006)
Screening for rapidly evolving genes in the ectomycorrhizal fungus Paxillus involutus using cDNA microarrays
Mol Ecol 15, 535-50.


H. Lindskog, E. Athley, E. Larsson, S. Lundin, M. Hellstrom and P. Lindahl (2006)
New insights to vascular smooth muscle cell and pericyte differentiation of mouse embryonic stem cells in vitro
Arterioscler Thromb Vasc Biol 26, 1457-64.


M. Moller and L. Hederstedt (2006)
Role of membrane-bound thiol-disulfide oxidoreductases in endospore-forming bacteria
Antioxid Redox Signal 8, 823-33.

 
R. H. Nilsson, M. Ryberg, E. Kristiansson, K. Abarenkov, K. H. Larsson and U. Koljalg (2006)
Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective
PLoS ONE 1, e59.

R. H. Nilsson, K. H. Larsson, E. Larsson and U. Koljalg (2006)
Fruiting body-guided molecular identification of root-tip mantle mycelia provides strong indications of ectomycorrhizal associations in two species of Sistotrema (Basidiomycota)
Mycol Res 110, 1426-32.


2005


E. Alexandersson, L. Fraysse, S. Sjovall-Larsen, S. Gustavsson, M. Fellert, M. Karlsson, U. Johanson and P. Kjellbom (2005)
Whole gene family expression and drought stress regulation of aquaporins
Plant Mol Biol 59, 469-84.


J. Almqvist, J. Zou, Y. Linderson, C. Borestrom, E. Altiok, H. Zetterberg, L. Rymo, S. Pettersson and I. Ernberg (2005)
Functional interaction of Oct transcription factors with the family of repeats in Epstein-Barr virus oriP
J Gen Virol 86, 1261-7.


D. Ahren, M. Tholander, C. Fekete, B. Rajashekar, E. Friman, T. Johansson and A. Tunlid (2005)
Comparison of gene expression in trap cells and vegetative hyphae of the nematophagous fungus Monacrosporium haptotylum
Microbiology 151, 789-803.


M. Brautigam, A. Lindlof, S. Zakhrabekova, G. Gharti-Chhetri, B. Olsson and O. Olsson (2005)
Generation and analysis of 9792 EST sequences from cold acclimated oat, Avena sativa
BMC Plant Biol 5, 18.


T. Breslin, M. Krogh, C. Peterson and C. Troein (2005)
Signal transduction pathway profiling of individual tumor samples
BMC Bioinformatics 6, 163.


H. Caren, K. Ejeskar, S. Fransson, L. Hesson, F. Latif, R. M. Sjoberg, C. Krona and T. Martinsson (2005)
A cluster of genes located in 1p36 are down-regulated in neuroblastomas with poor prognosis, but not due to CpG island methylation
Mol Cancer 4, 10.


D. Dalevi and D. Dubhashi (2005)
The Peres-Shields Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity
Lecture Notes in Bioinformatics (LNBI/LNCS).


J. Holmkvist, P. Almgren, H. Parikh, M. Zucchelli, J. Kere, L. Groop and C. M. Lindgren (2005)
Haplotype construction of the FRDA gene and evaluation of its role in type II diabetes
Eur J Hum Genet 13, 849-55.


K. Ejeskar, C. Krona, H. Caren, F. Zaibak, L. Li, T. Martinsson and P. A. Ioannou (2005)
Introduction of in vitro transcribed ENO1 mRNA into neuroblastoma cells induces cell death
BMC Cancer 5, 161.


M. G. Fagerlind, P. Nilsson, M. Harlen, S. Karlsson, S. A. Rice and S. Kjelleberg (2005)
Modeling the effect of acylated homoserine lactone antagonists in Pseudomonas aeruginosa
Biosystems 80, 201-13.


L. Fernandez-Ricaud, J. Warringer, E. Ericson, I. Pylvanainen, G. J. Kemp, O. Nerman and A. Blomberg (2005)
PROPHECY--a database for high-resolution phenomics
Nucleic Acids Res 33, D369-73.


B. G. Gabrielsson, L. E. Olofsson, A. Sjogren, M. Jernas, A. Elander, M. Lonn, M. Rudemo and L. M. Carlsson (2005)
Evaluation of reference genes for studies of gene expression in human adipose tissue
Obes Res 13, 649-52.


P. Garden, R. Alm and J. Hakkinen (2005)
PROTEIOS: an open source proteomics initiative
Bioinformatics 21, 2085-7.


C. Hagman, M. Ramstrom, M. Jansson, P. James, P. Hakansson and J. Bergquist (2005)
Reproducibility of tryptic digestion investigated by quantitative fourier transform ion cyclotron resonance mass spectrometry
J Proteome Res 4, 394-9.


D. S. Hibbett, R. H. Nilsson, M. Snyder, M. Fonseca, J. Costanzo and M. Shonfeld (2005)
Automated phylogenetic taxonomy: an example in the homobasidiomycetes (mushroom-forming fungi)
Syst Biol 54, 660-8.


M. Johannesson, L. M. Olsson, A. K. Lindqvist, S. Moller, D. Koczan, L. Wester-Rosenlof, H. J. Thiesen, S. Ibrahim and R. Holmdahl (2005)
Gene expression profiling of arthritis using a QTL chip reveals a complex gene regulation of the Cia5 region in mice
Genes Immun 6, 575-83.


G. Jonsson, P. O. Bendahl, T. Sandberg, A. Kurbasic, J. Staaf, L. Sunde, D. G. Cruger, C. Ingvar, H. Olsson and A. Borg (2005)
Mapping of a novel ocular and cutaneous malignant melanoma susceptibility locus to chromosome 9q21.32
J Natl Cancer Inst 97, 1377-82


G. Karlsson, Y. Liu, J. Larsson, M. J. Goumans, J. S. Lee, S. S. Thorgeirsson, M. Ringner and S. Karlsson (2005)
Gene expression profiling demonstrates that TGF-beta1 signals exclusively through receptor complexes involving Alk5 and identifies targets of TGF-beta signaling
Physiol Genomics 21, 396-403.


U. Koljalg, K. H. Larsson, K. Abarenkov, R. H. Nilsson, I. J. Alexander, U. Eberhardt, S. Erland, K. Hoiland, R. Kjoller, E. Larsson, T. Pennanen, R. Sen, A. F. Taylor, L. Tedersoo, T. Vralstad and B. M. Ursing (2005)
UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi
New Phytol 166, 1063-8.


E. Kristiansson, A. Sjögren, M. Rudemo and O. Nerman (2005)
Weighted Analysis of Paired Microarray Experiments
Statistical Applications in Genetics and Molecular Biology 4, 30.


A. Lindlof and Z. Lubovac (2005)
Simulations of simple artificial genetic networks reveal features in the use of Relevance Networks
In Silico Biol 5, 239-49.


M. Lantz, T. Vondrichova, H. Parikh, C. Frenander, M. Ridderstrale, P. Asman, M. Aberg, L. Groop and B. Hallengren (2005)
Overexpression of immediate early genes in active Graves' ophthalmopathy
J Clin Endocrinol Metab 90, 4784-91.


S. Nelander, E. Larsson, E. Kristiansson, R. Mansson, O. Nerman, M. Sigvardsson, P. Mostad and P. Lindahl (2005)
Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals
BMC Genomics 6, 68.


R. H. Nilsson, E. Kristiansson, M. Ryberg and K. H. Larsson (2005)
Approaching the taxonomic affiliation of unidentified sequences in public databases--an example from the mycorrhizal fungi
BMC Bioinformatics 6, 178.


M. Persson and J. Bigun (2005)
Detection of Spots in 2-D Electrophoresis Gels by Symmetry Features
Lecture Notes in Computer ScienceJ


P. Piccinelli, M. A. Rosenblad and T. Samuelsson (2005)
Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes
Nucleic Acids Res 33, 4485-95.


M. Ridderstrale, H. Parikh and L. Groop (2005)
Calpain 10 and type 2 diabetes: are we getting closer to an explanation?
Curr Opin Clin Nutr Metab Care 8, 361-6.


B. Samuelsson and C. Troein (2005)
Random maps and attractors in random Boolean networks
Phys Rev E Stat Nonlin Soft Matter Phys 72, 046112.


K. Sjoholm, J. Palming, L. E. Olofsson, A. Gummesson, P. A. Svensson, T. C. Lystig, E. Jennische, J. Brandberg, J. S. Torgerson, B. Carlsson and L. M. Carlsson (2005)
A microarray search for genes predominantly expressed in human omental adipocytes: adipose tissue as a major production site of serum amyloid A
J Clin Endocrinol Metab 90, 2233-9.


S. Swaminathan, T. Masek, C. Molin, M. Pospisek and P. Sunnerhagen (2005)
Rck2 Is Required for Reprogramming of Ribosomes during Oxidative Stress
Mol Biol Cell.


L. You, D. Garwicz and T. Rognvaldsson (2005)
Comprehensive bioinformatic analysis of the specificity of human immunodeficiency virus type 1 protease
J Virol 79, 12477-86.

 

2004

 

D. Ahren, M. Faedo, B. Rajashekar and A. Tunlid (2004)
Low genetic diversity among isolates of the nematode-trapping fungus Duddingtonia flagrans: evidence for recent worldwide dispersion from a single common ancestor
Mycol Res 108, 1205-14.


D. Ahren, C. Troein, T. Johansson and A. Tunlid (2004)
phorest: a web-based tool for comparative analyses of expressed sequence tag data
Molecular Ecology Notes 4, 311-314.


E. Alexandersson, G. Saalbach, C. Larsson and P. Kjellbom (2004)
Arabidopsis plasma membrane proteomics identifies components of transport, signal transduction and membrane trafficking
Plant Cell Physiol 45, 1543-56.


M. Benson, L. Carlsson, M. Adner, M. Jernas, M. Rudemo, A. Sjogren, P. A. Svensson, R. Uddman and L. O. Cardell (2004)
Gene profiling reveals increased expression of uteroglobin and other anti-inflammatory genes in glucocorticoid-treated nasal polyps
J Allergy Clin Immunol 113, 1137-43.


M. Benson, M. Olsson, M. Rudemo, G. Wennergren and L. O. Cardell (2004)
Pros and cons of microarray technology in allergy research
Clin Exp Allergy 34, 1001-6.


E. Bilsland, C. Molin, S. Swaminathan, A. Ramne and P. Sunnerhagen (2004)
Rck1 and Rck2 MAPKAP kinases and the HOG pathway are required for oxidative stress resistance
Mol Microbiol 53, 1743-56.


E. Parmasto, H. Nilsson and K.-H. Larsson (2004)
Cortbase version 2. Extensive updates of a nomenclatural database for corticioid fungi (Hymenomycetes)
Phyloinformatics 1.


L. S. Erlendsson, M. Moller and L. Hederstedt (2004)
Bacillus subtilis StoA Is a thiol-disulfide oxidoreductase important for spore cortex synthesis
J Bacteriol 186, 6230-8.


B. G. Gabrielsson, A. C. Karlsson, M. Lonn, L. E. Olofsson, J. M. Johansson, J. S. Torgerson, L. Sjostrom, B. Carlsson, S. Eden and L. M. Carlsson (2004)
Molecular characterization of a local sulfonylurea system in human adipose tissue
Mol Cell Biochem 258, 65-71.


A. L. Karlsson, R. Alm, B. Ekstrand, S. Fjelkner-Modig, A. Schiott, U. Bengtsson, L. Bjork, K. Hjerno, P. Roepstorff and C. S. Emanuelsson (2004)
Bet v 1 homologues in strawberry identified as IgE-binding proteins and presumptive allergens
Allergy 59, 1277-84.


S. Kauffman, C. Peterson, B. Samuelsson and C. Troein (2004)
Genetic networks with canalyzing Boolean rules are always stable
Proc Natl Acad Sci U S A 101, 17102-7.


M. Krantz, B. Nordlander, H. Valadi, M. Johansson, L. Gustafsson and S. Hohmann (2004)
Anaerobicity prepares Saccharomyces cerevisiae cells for faster adaptation to osmotic shock
Eukaryot Cell 3, 1381-90.


C. Krona, K. Ejeskar, H. Caren, F. Abel, R. M. Sjoberg and T. Martinsson (2004)
A novel 1p36.2 located gene, APITD1, with tumour-suppressive properties and a putative p53-binding domain, shows low expression in neuroblastoma tumours
Br J Cancer 91, 1119-30.


A. Kurbasic and O. Hossjer (2004)
On computation of p-values in parametric linkage analysis
Hum Hered 57, 207-19.


A. Le Quere, A. Schutzendubel, B. Rajashekar, B. Canback, J. Hedh, S. Erland, T. Johansson and A. Tunlid (2004)
Divergence in gene expression related to variation in host specificity of an ectomycorrhizal fungus
Mol Ecol 13, 3809-19.


Y. Liu and M. Ringner (2004)
Multiclass discovery in array data
BMC Bioinformatics 5, 70.


R. H. Nilsson, K. H. Larsson and B. M. Ursing (2004)
galaxie--CGI scripts for sequence identification through automated phylogenetic analysis
Bioinformatics 20, 1447-52.


R. H. Nilsson, B. Rajashekar, K. H. Larsson and B. M. Ursing (2004)
galaxieEST: addressing EST identity through automated phylogenetic analysis
BMC Bioinformatics 5, 87.


H. Parikh and L. Groop (2004)
Candidate genes for type 2 diabetes
Rev Endocr Metab Disord 5, 151-76.


T. Rognvaldsson and L. You (2004)
Why neural networks should not be used for HIV-1 protease cleavage site prediction
Bioinformatics 20, 1702-9.


R. Wysocki, P. K. Fortier, E. Maciaszczyk, M. Thorsen, A. Leduc, A. Odhagen, G. Owsianik, S. Ulaszewski, D. Ramotar and M. J. Tamas (2004)
Transcriptional activation of metalloid tolerance genes in Saccharomyces cerevisiae requires the AP-1-like proteins Yap1p and Yap8p
Mol Biol Cell 15, 2049-60.


H. Zetterberg, C. Borestrom, T. Nilsson and L. Rymo (2004)
Multiple EBNA1-binding sites within oriPI are required for EBNA1-dependent transactivation of the Epstein-Barr virus C promoter
Int J Oncol 25, 693-6.

 

2003


C. Borestrom, H. Zetterberg, K. Liff and L. Rymo (2003)
Functional interaction of nuclear factor y and sp1 is required for activation of the epstein-barr virus C promoter
J Virol 77, 821-9.


B. G. Gabrielsson, J. M. Johansson, M. Lonn, M. Jernas, T. Olbers, M. Peltonen, I. Larsson, L. Lonn, L. Sjostrom, B. Carlsson and L. M. Carlsson (2003)
High expression of complement components in omental adipose tissue in obese men
Obes Res 11, 699-708.


M. S. Johnson, J. M. Johansson, P. A. Svensson, M. A. Aberg, P. S. Eriksson, L. M. Carlsson and B. Carlsson (2003)
Interaction of scavenger receptor class B type I with peroxisomal targeting receptor Pex5p
Biochem Biophys Res Commun 312, 1325-34.


S. Kauffman, C. Peterson, B. Samuelsson and C. Troein (2003)
Random Boolean network models and the yeast transcriptional network
Proc Natl Acad Sci U S A 100, 14796-9.


A. Lindlof (2003)
Gene identification through large-scale EST sequence processing
Appl Bioinformatics 2, 123-9.


A. Lindlof and B. Olsson (2003)
Genetic network inference: the effects of preprocessing
Biosystems 72, 229-39.


R. H. Nilsson and N. Hallenberg (2003)
Phylogeny of the Hypochnicium punctulatum complex as inferred from ITS sequence data
Mycologia 95, 54.


R. H. Nilsson, N. Hallenberg, B. Norden, N. Maekawa and S. H. Wu (2003)
Phylogeography of Hyphoderma setigerum (Basidiomycota) in the Northern Hemisphere
Mycol Res 107, 645-52.


M. Persson and J. Bigun (2003)
Protein Spot Detection by Symmetry Derivatives of Gaussians
Lecture Notes in Computer Science


B. Samuelsson and C. Troein (2003)
Superpolynomial growth in the number of attractors in Kauffman networks
Phys Rev Lett 90, 098701.


J. Warringer, E. Ericson, L. Fernandez, O. Nerman and A. Blomberg (2003)
High-resolution yeast phenomics resolves different physiological features in the saline response
Proc Natl Acad Sci U S A 100, 15724-9.

 

2002

 

B. G. Gabrielsson, J. M. Johansson, E. Jennische, M. Jernas, Y. Itoh, M. Peltonen, T. Olbers, L. Lonn, H. Lonroth, L. Sjostrom, B. Carlsson, L. M. Carlsson and M. Lonn (2002)
Depot-specific expression of fibroblast growth factors in human adipose tissue
Obes Res 10, 608-16.


A. Irbäck and C. Troein (2002)
Enumerating Designing Sequences in the HP Model
Journal of Biological Physics 28, 1.


L. H. Saal, C. Troein, J. Vallon-Christersson, S. Gruvberger, A. Borg and C. Peterson (2002)
BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data
Genome Biol 3, SOFTWARE0003.