Publications:

Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios
J. Staaf, J. Vallon-Christersson, D. Lindgren, G. Juliusson, R. Rosenquist, M. Höglund, Å. Borg, and M. Ringnér
BMC Bioinformatics 9, 409 (2008)
[abstract] [full text at journal]

Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays
J. Staaf, D. Lindgren, J. Vallon-Christersson, A. Isaksson, H. Göransson, G. Juliusson, R. Rosenquist, M. Höglund, Å. Borg, and M. Ringnér
Genome Biology 9, R136 (2008)
[abstract] [full text at journal]

High Myc pathway activity and low stage of neuronal differentiation associate with poor outcome in neuroblastoma
E. Fredlund, M. Ringnér, J.M. Maris, and S. Påhlman
Proceedings of the National Academy of Sciences USA 105, 14094-14099 (2008)
[abstract] [pdf] [full text at journal]

Tiling array-CGH for the assessment of genomic similarities among synchronous unilateral and bilateral invasive breast cancer tumor pairs
S. Brommesson, G. Jönsson, C. Strand, D. Grabau, P. Malmström, M. Ringnér, M. Fernö, and I. Hedenfalk
BMC Clinical Pathology 8, 6 (2008)
[abstract] [pdf] [full text at journal]

• CD44+/CD24- phenotype is enriched in basal-like breast tumors
  G. Honeth, P-O. Bendahl, M. Ringnér, L.H. Saal, S.K. Gruvberger-Saal, K. Lövgren, D. Grabau, M. Fernö, Å. Borg, and C. Hegardt
  Breast Cancer Research 10, R53 (2008)
  [abstract] [pdf] [full text at journal]

What is principal component analysis?
M. Ringnér
Nature Biotechnology 26, 303-304 (2008)
[abstract] [full text at journal]

Normalization of array-CGH data: influence of copy number imbalances
J. Staaf, G. Jönsson, M. Ringnér, and J. Vallon-Christersson
BMC Genomics 8, 382 (2007)
[abstract] [pdf] [full text at journal]

Genomic profiling of malignant melanoma using tiling-resolution arrayCGH
G. Jönsson, C. Dahl, J. Staaf, T. Sandberg, P-O. Bendahl, M. Ringnér, P. Guldberg, and Å. Borg
Oncogene 26, 4738-4748 (2007)
[abstract] [pdf] [full text at journal]

• High-resolution genomic profiles of breast cancer cell lines assessed by tiling BAC array comparative genomic hybridization
  G. Jönsson, J. Staaf, E. Olsson, M. Heidenblad, J. Vallon-Christersson, K. Osoegawa, P. de Jong, S. Oredsson, M. Ringnér, M. Höglund, and Å. Borg
  Genes, Chromosomes and Cancer 46, 543-558 (2007)
  [abstract] [pdf] [full text at journal]

Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis
Y. Liu and M. Ringnér
Genome Biology 8, R77 (2007)
[abstract] [pdf] [full text at journal]

• Poor prognosis in carcinoma is associated with a gene expression signature of aberrant PTEN tumor suppressor pathway activity
  L.H. Saal, P. Johansson, K. Holm, S.K. Gruvberger-Saal, Q.B. She, M. Maurer, S. Koujak, A.A. Ferrando, P. Malmström, L. Memeo, J. Isola, P.O. Bendahl, N. Rosen, H. Hibshoosh, M. Ringnér, Å. Borg, and R. Parsons
  Proceedings of the National Academy of Sciences USA 104, 7564-7569 (2007)
  [abstract] [pdf] [full text at journal]

Classification of genomic and proteomic data using support vector machines
P. Johansson and M. Ringnér
In Fundamentals of Data Mining in Genomics and Proteomics
(eds. D.P. Berrar, W. Dubitzky, and M. Granzow, Springer Verlag), pp. 187-202 (2007)
[pdf]

Osteopontin is a downstream effector of the PI3-kinase pathway in melanomas that is inversely correlated with functional PTEN
L. Packer, S. Pavey, A. Parker, M. Stark, P. Johansson, B. Clarke, P. Pollock, M. Ringnér, and N. Hayward
Carcinogenesis 27, 1778-1786 (2006)
[abstract] [pdf] [full text at journal]

Detection and identification of protein isoforms using cluster analysis of MALDI-MS mass spectra
R. Alm, P. Johansson, K. Hjernø, C. Emanuelsson, M. Ringnér, and J. Häkkinen
Journal of Proteome Research 5, 785-792 (2006)
[abstract] [pdf] [full text at journal] [software]

Folding free energies of 5'-UTRs impact post-transcriptional regulation on a genomic scale in yeast
M. Ringnér and M. Krogh
PLoS Computational Biology 1, e72 (2005)
[abstract] [pdf] [full text at journal] [supplemental data]

Distinct genomic profiles in hereditary breast tumors identified by array-based comparative genomic hybridization G. Jönsson, T.L. Naylor, J. Vallon-Christersson, J. Staaf, J. Huang, M.R. Ward, J.D. Greshock, L. Luts, H. Olsson, N. Rahman, M. Stratton, M. Ringnér, Å. Borg, and B.L. Weber Cancer Research 65, 7612-7621 (2005) [abstract] [pdf] [full text at journal]

Gene expression profiling demonstrates that TGF-β1 signals exclusively through receptor complexes involving Alk5 and identifies targets of TGF-β signaling
G. Karlsson, Y. Liu, J. Larsson, M-J. Goumans, J-S. Lee, S.S. Thorgeirsson, M. Ringnér, and S. Karlsson
Physiological Genomics 21, 396-403 (2005)
[abstract] [pdf] [full text at journal]

Microarray-based analyses of hypoxia-induced transcriptional changes in breast cancer cell lines
I. Hedenfalk, N. Glarner, Å. Kronblad, S. Veerla, M. Ringnér, and G. Landberg
Cancer Genomics and Proteomics 2, 83-96 (2005)
[abstract] [pdf]

ACID: a database for microarray clone information
M. Ringnér, S. Veerla, S. Andersson, J. Staaf, and J. Häkkinen
Bioinformatics 20, 2305-2306 (2004)
[abstract] [pdf] [software]

Multiclass discovery in array data
Y. Liu and M. Ringnér
BMC Bioinformatics 5, 70 (2004)
[abstract] [pdf] [full text at journal] [software]

• Microarray expression profiling in melanoma reveals a BRAF mutation signature
  S. Pavey, P. Johansson, L. Packer, J. Taylor, M. Stark, P.M. Pollock, G.J. Walker, G.M. Boyle, U. Harper, S.J. Cozzi, K. Hansen, L. Yudt, C. Schmidt, P. Hersey, K.A.O. Ellem, M.G.E. O'Rourke, P.G. Parsons, P. Meltzer, M. Ringnér, and N.K. Hayward
  Oncogene 23, 4060-4067 (2004)
  [abstract] [pdf] [full text at journal] [supplement]

A strategy for identifying putative causes of gene expression variation in human cancers
S. Hautaniemi, M. Ringnér, P. Kauraniemi, R. Autio, H. Edgren, O. Yli-Harja, J. Astola, A. Kallioniemi, and O. Kallioniemi
Journal of the Franklin Institute 341, 77-88 (2004)
[abstract] [pdf]

Predicting continuous values of prognostic markers in breast cancer from microarray gene expression profiles
S.K. Gruvberger-Saal, P. Edén, M. Ringnér, B. Baldetorp, G. Chebil, Å. Borg, M. Fernö, C. Peterson, and P.S. Meltzer
Molecular Cancer Therapeutics 3, 161-168 (2004)
[abstract] [pdf] [full text at journal]

• The gene expression response of breast cancer to growth regulators: patterns and correlation with tumor expression profiles
  H.E. Cunliffe, M. Ringnér, S. Bilke, R.L. Walker, J.M. Cheung, Y. Chen, and P.S. Meltzer
  Cancer Research 63, 7158-7166 (2003)
  [abstract] [pdf] [full text at journal] [supplement]

Matching protein structures with fuzzy alignments
R. Blankenbecler, M. Ohlsson, C. Peterson, and M. Ringnér
Proceedings of the National Academy of Sciences USA 100, 11936-11940 (2003)
[abstract] [pdf] [full text at journal] [supplement]

• Gene expression profile in multiple sclerosis patients and healthy controls: identifying pathways relevant to disease
  R. Bomprezzi, M. Ringnér, S. Kim, M.L. Bittner, J. Khan, Y. Chen, A. Elkahloun, A. Yu, B. Bielekova, P.S. Meltzer, R. Martin, H.F. McFarland, and J.M. Trent
  Human Molecular Genetics 12, 2191-2199 (2003)
  [abstract] [pdf] [full text at journal]

Gene expression profiles in a panel of childhood leukemia cell lines mirror critical features of the disease
U.R. Kees, J. Ford, M. Watson, A. Murch, M. Ringnér, R.L. Walker, and P. Meltzer
Molecular Cancer Therapeutics 2, 671-677 (2003)
[abstract] [pdf] [full text at journal]

Analyzing tumor gene expression profiles
C. Peterson and M. Ringnér
Artificial Intelligence in Medicine 28, 59-74 (2003)
[abstract] [pdf] [full text at journal]

Microarray-based cancer diagnosis with artificial neural networks M. Ringnér and C. Peterson Biotechniques 34, S30-S35 (2003) (eds. M.F. Ochs and A.K. Godwin, Eaton Publishing) [abstract] [pdf]

• Molecular classification of familial non-BRCA1/BRCA2 breast cancer
  I. Hedenfalk, M. Ringnér, A. Ben-Dor, Z. Yakhini, Y. Chen, G. Chebil,
  R. Ach, N. Loman, H. Olsson, P. Meltzer, Å. Borg and J. Trent
  Proceedings of the National Academy of Sciences USA 100, 2532-2537 (2003)
  [abstract] [pdf] [full text at journal] [supplement]

• Expression profiling to predict outcome in breast cancer: the influence of sample selection
  S.K. Gruvberger, M. Ringnér, P. Edén, Å. Borg, M. Fernö, C. Peterson, and P.S. Meltzer
  Breast Cancer Research 5, 23-26 (2003)
  [abstract] [pdf] [full text at journal]

Classification of expression patterns using artificial neural networks
M. Ringnér, P. Edén, and P. Johansson
In A Practical Approach to Microarray Data Analysis
(eds. D.P. Berrar, W. Dubitzky, and M. Granzow, Kluwer Academic Publishers), pp. 201-215 (2002)
[abstract] [pdf]

A strategy for identifying putative causes of gene expression variation in human cancer
S. Hautaniemi, M. Ringnér, P. Kauraniemi, A. Kallioniemi, H. Edgren, O. Yli-Harja, J. Astola, and O-P. Kallioniemi
In Proceeding of the Workshop on Genomic Signal Processing and Statistics (GENSIPS) CP1-06 (2002)
[abstract] [pdf]

• Impact of DNA amplification on gene expression patterns in breast cancer
  E. Hyman, P. Kauraniemi, S. Hautaniemi, M. Wolf, S. Mousses, E. Rozenblum, M. Ringnér, G. Sauter, O. Monni, A. Elkahloun, O-P. Kallioniemi, and A. Kallioniemi
  Cancer Research 62, 6240-6245 (2002)
  [abstract] [pdf] [full text at journal] [supplement]

• Analyzing array data using supervised methods
  M. Ringnér, C. Peterson, and J. Khan
  Pharmacogenomics 3, 403-415 (2002)
  [abstract] [pdf]

• Gene expression in inherited breast cancer
  I.A. Hedenfalk, M. Ringnér, J.M. Trent, and Å. Borg
  Advances in Cancer Research 84, 1-34 (2002)
  (eds. G.F. Vande Woude and G. Klein, Academic Press)
  [abstract] [pdf]

Gastrointestinal stromal tumors with KIT mutations exhibit a remarkably homogeneous gene expression profile S.V. Allander, N.N. Nupponen, M. Ringnér, G. Hostetter, G.W. Maher, N. Goldberger, Y. Chen, J. Carpten, A.G. Elkahloun, and P.S. Meltzer Cancer Research 61, 8624-8628 (2001) [abstract][pdf] [full text at journal] [supplemental data] [cover]

• Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns
  S. Gruvberger, M. Ringnér, Y. Chen, S. Panavally, L.H. Saal, Å. Borg, M. Fernö, C. Peterson, and P.S. Meltzer
  Cancer Research 61, 5979-5984 (2001)
  [abstract] [pdf] [full text at journal] [supplemental data]

Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks J. Khan, J.S. Wei, M. Ringnér, L.H. Saal, M. Ladanyi, F. Westermann, F. Berthold, M. Schwab, C.R. Atonescu, C. Peterson, and P.S. Meltzer Nature Medicine 7, 673-679 (2001) [abstract] [pdf] [full text at journal] [supplemental_data] [supplemental_methods] [cover] [reviews]

The Feynman-Wilson gas and the Lund model
B. Andersson, G. Gustafson, M. Ringnér, and P.J. Sutton
European Physical Journal C7, 251-261 (1999)
[abstract] [pdf]

Three-particle Bose-Einstein correlations - a sensitive probe for Lund string fragmentation
M. Ringnér
In Proceedings of Correlations and Fluctuations '98 - From QCD to Particle Interferometry
(eds. T. Csörgö, S. Hegyi, G. Jancsó, and R.C. Hwa, World Scientific, Singapore), pp. 90-97 (1999)
[ps.gz]

Transverse and longitudinal Bose-Einstein correlations in e⁺e^- annihilation
M. Ringnér
In Proceedings of the International Europhysics Conference on High Energy Physics (EPS HEP 97)
(eds. D. Lellouch, G. Mikenberg, and E. Rabinovici, Springer-Verlag, Berlin, Germany), pp. 425-428 (1999)
[abstract] [ps.gz]

Is there screwiness at the end of the QCD cascades?
B. Andersson, G. Gustafson, J. Häkkinen, M. Ringnér, and P.J. Sutton
Journal of High Energy Physics 9809, 014 (1998)
[abstract] [pdf]

Bose-Einstein and colour interference in W-pair decays
J. Häkkinen and M. Ringnér
European Physical Journal C5, 275-281 (1998)
[abstract] [pdf]

1. Transverse and longitudinal Bose-Einstein correlations
   B. Andersson and M. Ringnér
   Physics Letters B421, 283-288 (1998)
   [abstract] [pdf]

• Bose-Einstein correlations in the Lund model
  B. Andersson and M. Ringnér
  Nuclear Physics B513, 627-644 (1998)
  [abstract] [pdf]

Unpublished reports:

SPECLUST: a web tool for clustering of mass spectra
P. Johansson, R. Alm, C. Emanuelsson, J. Häkkinen, and M. Ringnér
LU TP 07-14

A novel approach to structure alignment
M. Ohlsson, C. Peterson, M. Ringnér, and R. Blankenbecler
LU TP 00-07 and SLAC-PUB-8429 (2000)
[abstract] [ps.gz]

An investigation of screwiness in hadronic final states from DELPHI
A. de Angelis, P. Eerola, and M. Ringnér
DELPHI 98-156 PHYS 799 (1998)
[ps.gz]

Monte Carlo simulation of a multiparticle imaging Cherenkov counter
M. Ringnér
NA44-NOTE 142 (1993)
CERN summer student project
[abstract]

Theses:

Correlations in multiparticle production
M. Ringnér
Ph.D. Thesis, Lund University, 1998
ISBN 91-628-3190-9
[abstract] [ps.gz]

Bose-Einstein correlations in e⁺e^- and pBe collisions
M. Ringnér
Masters Thesis, Lund Institute of Technology, 1994
LUNFD6/(NFFL-7086) 1994
[abstract]