Publications - Markus Ringnér

[publications] [unpublished reports] [theses]

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Publications:

Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration
M. Smid, F.G. Rodríguez-González, A.M. Sieuwerts, R. Salgado, W.J. Prager-Van der Smissen, M.V. Vlugt-Daane, A. van Galen, S. Nik-Zainal, J. Staaf, A.B. Brinkman, M.J. van de Vijver, A.L. Richardson, A. Fatima, K. Berentsen, A. Butler, S. Martin, H.R. Davies, S. Debets, M.E. Gelder, C.H. van Deurzen, G. MacGrogan, G.G. Van den Eynden, C. Purdie, A.M. Thompson, C. Caldas, P.N. Span, P.T. Simpson, S.R. Lakhani, S. Van Laere, C. Desmedt, M. Ringnér, S. Tommasi, J. Eyford, A. Broeks, A. Vincent-Salomon, P.A. Futreal, S. Knappskog, T. King, G. Thomas, A. Viari, A. Langerød, A.L. Børresen-Dale, E. Birney, H.G. Stunnenberg, M. Stratton, J.A. Foekens, and J.W. Martens
Nature Communications 7, 12910 (2016)
[full text at journal]

Consensus of gene expression phenotypes and prognostic risk predictors in primary lung adenocarcinoma
M. Ringnér and J. Staaf
Oncotarget 7, 52957-52973 (2016)
[full text at journal]

Landscape of somatic mutations in 560 breast cancer whole-genome sequences
S. Nik-Zainal, H. Davies, J. Staaf, M. Ramakrishna, D. Glodzik, X. Zou, I. Martincorena, L.B. Alexandrov, S. Martin, D.C. Wedge, P. Van Loo, Y.S. Ju, M. Smid, A.B. Brinkman, S. Morganella, M.R. Aure, O.C. Lingjærde, A. Langerød, M. Ringnér, S.M. Ahn, S. Boyault, J.E. Brock, A. Broeks, A. Butler, C. Desmedt, L. Dirix, S. Dronov, A. Fatima, J.A. Foekens, M. Gerstung, G.K. Hooijer, S.J. Jang, D.R. Jones, K.Y. Kim, T.A. King, S. Krishnamurthy, H.J. Lee, J.Y. Lee, Y. Li, S. McLaren, A. Menzies, V. Mustonen, S. O'Meara, I. Pauporté, X. Pivot, C.A. Purdie, K. Raine, K. Ramakrishnan, F.G. Rodríguez-González, G. Romieu, A.M. Sieuwerts, P.T. Simpson, R. Shepherd, L. Stebbings, O.A. Stefansson, J. Teague, S. Tommasi, I. Treilleux, G.G. Van den Eynden, P. Vermeulen, A. Vincent-Salomon, L. Yates, C. Caldas, L. van't Veer, A. Tutt, S. Knappskog, B.K. Tan, J. Jonkers, Å. Borg, N.T. Ueno, C. Sotiriou, A. Viari, P.A. Futreal, P.J. Campbell, P.N. Span, S. Van Laere, S.R. Lakhani, J.E. Eyfjord, A.M. Thompson, E. Birney, H.G. Stunnenberg, M.J. van de Vijver, J.W. Martens, A.L. Børresen-Dale, A.L. Richardson, G. Kong, G. Thomas, and M.R. Stratton
Nature 534, 47-54 (2016)
[full text at journal]

An integrated genomics analysis of epigenetic subtypes in human breast tumors links DNA methylation patterns to chromatin states in normal mammary cells
K. Holm, J. Staaf, M. Lauss, M. Aine, D. Lindgren, P-O. Bendahl, J. Vallon-Christersson, R.B. Barkardottir, M. Höglund, Å. Borg, G. Jönsson, and M. Ringnér
Breast Cancer Research 18, 27 (2016)
[full text at journal]

Prognostic and chemotherapy predictive value of gene expression phenotypes in primary lung adenocarcinoma
M. Ringnér, G. Jönsson, and J. Staaf
Clinical Cancer Research 22, 218-229 (2016)
[full text at journal]

DNA methylation subgroups in melanoma are associated with proliferative and immunological processes
M. Lauss, M. Ringnér, A. Karlsson, K. Harbst, C. Busch, J. Geisler, P.E. Lønning, J. Staaf, and G. Jönsson
BMC Medical Genomics 8, 73 (2015)
[full text at journal]

MicroRNA-200c-141 and ΔNp63 are required for breast epithelial differentiation and branching morphogenesis
B. Hilmarsdóttir, E. Briem, V. Sigurdsson, S.R. Franzdóttir, M. Ringnér, J.A. Arason, J.T. Bergthorsson, M.K. Magnusson, and T. Gudjonsson
Developmental Biology 403, 150-161 (2015)
[full text at journal]

Genome methylation patterns in male breast cancer - identification of an epitype with hypermethylation of polycomb target genes
I. Johansson, M. Lauss, K. Holm, J. Staaf, C. Nilsson, M-L. Fjällskog, M. Ringnér, and I. Hedenfalk
Molecular Oncology 9, 1565-1579 (2015)
[full text at journal]

Molecular stratification of metastatic melanoma using gene expression profiling: prediction of survival outcome and benefit from molecular targeted therapy
H. Cirenajwis, H. Ekedahl, M. Lauss, K. Harbst, A. Carneiro, J. Enoksson, F. Rosengren, L. Werner-Hartman, T. Törngren, A. Kvist, E. Fredlund, P-O. Bendahl, K. Jirström, L. Lundgren, J. Howlin, Å. Borg, S.K. Gruvberger-Saal, L.H. Saal, K. Nielsen, M. Ringnér, H. Tsao, H. Olsson, C. Ingvar, J. Staaf, and G. Jönsson
Oncotarget 6, 12297-12309 (2015)
[full text at journal]

DNA methylation and histone modifications regulate SOX11 expression in lymphoid and solid cancer cells
L. Nordström, E. Andersson, V. Kuci, E. Gustavsson, K. Holm, M. Ringnér, P. Guldberg, and S. Ek
BMC Cancer 15, 273 (2015)
[full text at journal]

Integrative epigenomic analysis of differential DNA methylation in urothelial carcinoma
M. Aine, G. Sjödahl, P. Eriksson, S. Veerla, D. Lindgren, M. Ringnér, and M. Höglund
Genome Medicine 7, 23 (2015)
[full text at journal]

Genome-wide DNA methylation analysis in melanoma reveals the importance of CpG methylation in MITF regulation
M. Lauss, R. Haq, H. Cirenajwis, B. Phung, K. Harbst, J. Staaf, F. Rosengren, K. Holm, M. Aine, K. Jirström, Å. Borg, C. Busch, J. Geisler, P.E. Lønning, M. Ringnér, J. Howlin, D. Fisher, and G. Jönsson
Journal of Investigative Dermatolology 135, 1820-1828 (2015)
[full text at journal]

Making breast cancer molecular subtypes robust?
J. Staaf and M. Ringnér
Journal of the National Cancer Institute 107, 386 (2015)
[full text at journal]

Genome-wide DNA methylation analysis of lung carcinoma reveals one neuroendocrine and four adenocarcinoma epitypes associated with patient outcome
A. Karlsson, M. Jönsson, M. Lauss, H. Brunnström, P. Jönsson, Å. Borg, G. Jönsson, M. Ringnér, M. Planck, and J. Staaf
Clinical Cancer Research, 20, 6127-6140 (2014)
[full text at journal]

Genomic and transcriptional alterations in lung adenocarcinoma in relation to smoking history
A. Karlsson, M. Ringnér, M. Lauss, J. Botling, P. Micke, M. Planck, and J. Staaf
Clinical Cancer Research 20, 4912-4924 (2014)
[full text at journal]

Primary melanoma tumors from CDKN2A mutation carriers do not belong to a distinct molecular subclass
J. Staaf, K. Harbst, M. Lauss, M. Ringnér, A. Måsbäck, J. Howlin, K. Jirström, M. Harland, A. Zebary, J.M. Palmer, C. Ingvar, H. Olsson, J. Newton-Bishop, J. Hansson, N. Hayward, N. Gruis, G. Jönsson, and the Melanoma Genetics Consortium (GenoMEL)
Journal of Investigative Dermatology 134, 3000-3003 (2014)
[full text at journal]

The landscape of candidate driver genes differs between male and female breast cancer
I. Johansson, M. Ringnér, and I. Hedenfalk
PLoS One 8, e78299 (2013)
[full text at journal]

Monitoring of technical variation in quantitative high-throughput datasets
M. Lauss, I. Visne, A. Kriegner, M. Ringnér, G. Jönsson, and M. Höglund
Cancer Informatics 12, 193-201 (2013)
[full text at journal]

High expression of ZNF703 independent of amplification indicates worse prognosis in patients with luminal B breast cancer
I. Reynisdottir, A. Arason, B.O. Einarsdottir, H. Gunnarsson, J. Staaf, J. Vallon-Christersson, G. Jönsson, M. Ringnér, B.A. Agnarsson, K. Olafsdottir, R. Fagerholm, T. Einarsdottir, G. Johannesdottir, O.T. Johannsson, H. Nevanlinna, Å. Borg, and R.B. Barkardottir
Cancer Medicine 2, 437-446 (2013)
[full text at journal]

Exosomes reflect the hypoxic status of glioma cells and mediate hypoxia-dependent activation of vascular cells during tumor development
P. Kucharzewska, H.C. Christianson, J.E. Welch, K.J. Svensson, E. Fredlund, M. Ringnér, M. Mörgelin, E. Bourseau-Guilmain, J. Bengzon, and M. Belting
Proceedings of the National Academy of Sciences USA 110, 7312-7317 (2013)
[full text at journal]

Nonfamilial breast cancer subtypes
M. Ringnér, J. Staaf, and G. Jönsson
Methods in Molecular Biology 973, 279-295 (2013)
[full text at journal]

The gene expression landscape of breast cancer is shaped by tumor protein p53 status and epithelial-mesenchymal transition
E. Fredlund, J. Staaf, J.K. Rantala, O. Kallioniemi, Å. Borg, and M. Ringnér
Breast Cancer Research 14, R113 (2012)
[full text at journal]

Global H3K27 trimethylation and EZH2 abundance in breast tumor subtypes
K. Holm, D. Grabau, K. Lövgren, S. Aradottir, S. Gruvberger-Saal, J. Howlin, L.H. Saal, S.P. Ethier, P-O. Bendahl, O. Stål, P. Malmström, M. Fernö, L. Rydén, C. Hegardt, Å. Borg, and M. Ringnér
Molecular Oncology 6, 494-506 (2012)
[full text at journal]

The retinoblastoma gene undergoes rearrangements in BRCA1-deficient basal-like breast cancer
G. Jönsson, J. Staaf, J. Vallon-Christersson, M. Ringnér, S.K. Gruvberger-Saal, L.H. Saal, K. Holm, C. Hegardt, A. Arason, R. Fagerholm, C. Persson, D. Grabau, E. Johnsson, K. Lövgren, L. Magnusson, P. Heikkilä, B.A. Agnarsson, O.T. Johannsson, P. Malmström, M. Fernö, H. Olsson, N. Loman, H. Nevanlinna, R.B. Barkardottir, and Å. Borg
Cancer Research 72, 4028-4036 (2012)
[full text at journal]

Molecular profiling reveals low- and high-grade forms of primary melanoma
K. Harbst, J. Staaf, M. Lauss, A. Karlsson, A. Måsback, I. Johansson, P-O. Bendahl, J. Vallon-Christersson, T. Törngren, H. Ekedahl, J. Geisler, M. Höglund, M. Ringnér, L. Lundgren, K. Jirström, H. Olsson, C. Ingvar, Å. Borg, H. Tsao, and G. Jönsson
Clinical Cancer Research 18, 4026-4036 (2012)
[full text at journal]

DNA methylation analyses of urothelial carcinoma reveal distinct epigenetic subtypes and an association between gene copy number and methylation status
M. Lauss, M. Aine, G. Sjödahl, S. Veerla, O. Patschan, S. Gudjonsson, G. Chebil, K. Lövgren, M. Fernö, W. Månsson, F. Liedberg, M. Ringnér, D. Lindgren, and M. Höglund
Epigenetics 7, 858-867 (2012)
[full text at journal]

A molecular taxonomy for urothelial carcinoma
G. Sjödahl, M. Lauss, K. Lövgren, G. Chebil, S. Gudjonsson, S. Veerla, O. Patschan, M. Aine, M. Fernö, M. Ringnér, W. Månsson, F. Liedberg, D. Lindgren, and M.  Höglund
Clinical Cancer Research 18, 3377-3386 (2012)
[full text at journal]

Characterisation of amplification patterns and target genes at chromosome 11q13 in CCND1-amplified sporadic and familial breast tumours
K. Holm, J. Staaf, G. Jönsson, J. Vallon-Christersson, H. Gunnarsson, A. Arason, L. Magnusson, R.B. Barkardottir, C. Hegardt, M. Ringnér, and Å. Borg
Breast Cancer Research and Treatment 133, 583-594 (2012)
[full text at journal]

Gene expression profiling of primary male breast cancers reveals two unique subgroups and identifies N-acetyltransferase-1 (NAT1) as a novel prognostic biomarker
I. Johansson, C. Nilsson, P. Berglund, M. Lauss, M. Ringnér, H. Olsson, L. Luts, E. Sim, S. Thorstensson, M-L. Fjällskog, and I. Hedenfalk
Breast Cancer Research 14, R31 (2012)
[full text at journal]

Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer
J. Staaf, G. Jönsson, M. Ringnér, B. Baldetorp, and Å. Borg
Breast Cancer Research 13, R129 (2011)
[full text at journal]

CD44 isoforms are heterogeneously expressed in breast cancer and correlate with tumor subtypes and cancer stem cell markers
E. Olsson, G. Honeth, P-O. Bendahl, L.H. Saal, S. Gruvberger-Saal, M. Ringnér, J. Vallon-Christersson, G. Jönsson, K. Holm, K. Lövgren, M. Fernö, D. Grabau, Å. Borg, and C. Hegardt
BMC Cancer 11, 418 (2011)
[full text at journal]

Endothelial induced EMT in breast epithelial cells with stem cell properties
V. Sigurdsson, B. Hilmarsdottir, H. Sigmundsdottir, A.J.R. Fridriksdottir, M. Ringnér, R. Villadsen, Å. Borg, B.A. Agnarsson, O.W. Petersen, M.K. Magnusson, and T. Gudjonsson
PLoS One 6, e23833 (2011)
[full text at journal]

GOBO: Gene expression-based outcome for breast cancer online
M. Ringnér, E. Fredlund, J. Häkkinen, Å. Borg, and J. Staaf
PLoS One 6, e17911 (2011)
[full text at journal]

High-resolution genomic profiling of male breast cancer reveals differences hidden behind the similarities with female breast cancer
I. Johansson, C. Nilsson, P. Berglund, C. Strand, G. Jönsson, J. Staaf, M. Ringnér, H. Nevanlinna, R.B. Barkardottir, Å. Borg, H. Olsson, L. Luts L, M.L. Fjällskog, and I. Hedenfalk
Breast Cancer Research and Treatment 129, 747-760 (2011)
[abstract] [full text at journal]

Prediction of stage, grade, and survival in bladder cancer using genome wide expression data: a validation study
M. Lauss, M. Ringnér, and M. Höglund
Clinical Cancer Research 16, 4421-4433 (2010)
[abstract] [full text at journal]

Multiple metastases from cutaneous malignant melanoma patients may display heterogeneous genomic and epigenomic patterns
K. Harbst, J. Staaf, A. Måsbäck, H. Olsson, C. Ingvar, J. Vallon-Christersson, M. Ringnér, Å. Borg, and G. Jönsson
Melanoma Research 20, 381-391 (2010)
[abstract]

Genomic subtypes of breast cancer identified by array comparative genomic hybridization display distinct molecular and clinical characteristics
G. Jönsson, J. Staaf, J. Vallon-Christersson, M. Ringnér, K. Holm, C. Hegardt, H. Gunnarsson, R. Fagerholm, C. Strand, B.A. Agnarsson, O. Kilpivaara, L. Luts, P. Heikkila, K. Aittomaki, C. Blomqvist, N. Loman, P. Malmström, H. Olsson, O.T. Johannsson, A. Arason, H. Nevanlinna, R.B. Barkardottir, and Å. Borg
Breast Cancer Research 12, R42 (2010)
[abstract] [full text at journal]

Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns
K. Holm, C. Hegardt, J. Staaf, J. Vallon-Christersson, G. Jönsson, H. Olsson, Å. Borg, and M. Ringnér
Breast Cancer Research 12, R36 (2010)
[abstract] [full text at journal]

Gene expression profiling-based identification of molecular subtypes in stage IV melanomas with different clinical outcome
G.B. Jönsson, C. Busch, S. Knappskog, J.  Geisler, H. Miletic, M. Ringnér, J.R. Lillehaug, Å. Borg, and P.E. Lønning
Clinical Cancer Research 16, 3356-3367 (2010)
[abstract] [full text at journal]

High-resolution genomic and expression analyses of copy number alterations in HER2-amplified breast cancer
J. Staaf, G. Jönsson, M. Ringnér, J. Vallon-Christersson, D. Grabau, A. Arason, H. Gunnarsson, B.A. Agnarsson, P-O. Malmström, O.T. Johannsson, N. Loman, R.B. Barkardottir, and Å. Borg
Breast Cancer Research 12, R25 (2010)
[abstract] [full text at journal] [editorial]

An integrative genomics screen uncovers ncRNA T-UCR functions in neuroblastoma tumours
P. Mestdagh, E. Fredlund, F. Pattyn, A. Rihani, T. Van Maerken, J. Vermeulen, C. Kumps, B. Menten, K. De Preter, A. Schramm, J. Schulte, R. Noguera, G. Schleiermacher, I. Janoueix-Lerosey, G. Laureys, R. Powel, D. Nittner, J-C. Marine, M. Ringnér, F. Speleman, and J. Vandesompele
Oncogene 29, 3583-3592 (2010)
[abstract] [full text at journal]

Identification of subtypes in human epidermal growth factor receptor 2-positive breast cancer reveals a gene signature prognostic of outcome
J. Staaf, M. Ringnér, J. Vallon-Christersson, G. Jönsson, P-O.  Bendahl, K. Holm, A. Arason, H. Gunnarsson, C. Hegardt, B.A. Agnarsson, L. Luts, D. Grabau, M. Fernö, P-O. Malmström, O.T. Johannsson, N. Loman, R.B. Barkardottir, and Å. Borg
Journal of Clinical Oncology 28, 1813-1820 (2010)
[abstract] [full text at journal] [editorial]

Genome-wide transcription factor binding site/promoter databases for the analysis of gene sets and co-occurrence of transcription factor binding motifs
S. Veerla, M. Ringnér, and M. Höglund
BMC Genomics 11, 145 (2010)
[abstract] [full text at journal]

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]

A method for finding putative causes of gene expression variation
R. Autio, S. Hautaniemi, M. Ringnér, P. Kauraniemi, H. Edgren, O. Yli-Harja, J. Astola, A. Kallioniemi, and O-P. Kallioniemi
In Proceedings of the 2nd TICSP Workshop on Computational Systems Biology, WCSB 2004, TICSP Series #24
(eds. T. Aho, H. Lähdesmäki, and O. Yli-Harja, TICSP Publications, Tampere International Center for Signal Processing (TICSP), Institute of Signal Processing, Tampere University of Technology, Tampere, Finland, ISBN 952-15-1204-0), pp. 29-30 (2004)
[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 (2003)
[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 Proceedings 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)
[pdf]

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] [pdf]

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]

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
[pdf] [software]

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] [pdf]

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

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


Theses:

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

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

This page was created in 1998.
Available at http://cbbp.thep.lu.se/~markus/publications/index.html.
Latest update: November 28, 2016.