Staaf, Johan, Vallon-Christersson, Johan, Lindgren, David, Juliusson, Gunnar, Rosenquist, Richard, Höglund, Mattias, ...
Abstract Background Illumina Infinium whole genome genotyping (WGG) arrays are increasingly being applied in cancer genomics to study gene copy number alterations and allele-specific aberrations such...
Staaf, Johan, Lindgren, David, Vallon-Christersson, Johan, Isaksson, Anders, Göransson, Hanna, Juliusson, Gunnar, ...
Abstract We present a strategy for detection of loss-of-heterozygosity and allelic imbalance in cancer cells from whole genome single nucleotide polymorphism genotyping data. Using a dilution series...
Brommesson, Sara, Jönsson, Göran, Strand, Carina, Grabau, Dorthe, Malmström, Per, Ringnér, Markus, ...
Abstract Background Today, no objective criteria exist to differentiate between individual primary tumors and intra- or intermammary dissemination respectively, in patients diagnosed with two or more...
The CD44+/CD24-phenotype is enriched in basal-like breast tumors (2008)
Honeth, Gabriella, Bendahl, Pär-Ola, Ringnér, Markus, Saal, Lao H, Gruvberger-Saal, Sofia K, Lövgren, Kristina, ...
Abstract Introduction Human breast tumors are heterogeneous and consist of phenotypically diverse cells. Breast cancer cells with a CD44 + /CD24 - phenotype have been suggested to have...
Patrik Edén, Markus Ringnér, Bo Baldetorp, Gunilla Chebil, A Ke Borg, ...
continuous values of prognostic markers in breast
receptor complexes involving Alk5 and identifies targets of TGF-β signaling. (2008)
Göran Karlsson, Yingchun Liu, Jonas Larsson, Marie-josé Goumans, Snorri S Thorgeirsson, Markus Ringnér, ...
expression profiling demonstrates that TGF-β1 signals exclusively through
Göran Jönsson, Tara L. Naylor, Johan Vallon-christersson, Johan Staaf, Jia Huang, M. Renee Ward, ...
Mutations in BRCA1 and BRCA2 account for a significant proportion of hereditary breast cancers. Earlier studies have shown that inherited and sporadic tumors progress along different somatic genetic...
[Abstract] [Full Text] [PDF] Smad3 Signaling Involved in Pulmonary Fibrosis and Emphysema (2008)
Göran Karlsson, Yingchun Liu, Jonas Larsson, Marie-josé Goumans, Snorri S. Thorgeirsson, Markus Ringnér, ...
doi:10.1152/physiolgenomics.00303.2004 You might find this additional information useful... Supplemental material for this article can be found at:
Correlations in Multiparticle Production (2007)
Markus Ringnér, Markus Ringn Er
Key words Classification system and/or index terms (if any) Supplementary bibliographical information Language ISSN and key title ISBN Recipient's notes Number of pages Price Security...
Ashley Publications Ltd www.ashley-pub.com TECHNOLOGY REPORT (2007)
Markus Ringnér, Carsten Peterson, Javed Khan, Cancer Genetics Branch, National Human Genome, Grovemont Circle
Analyzing array data using supervised methods
Classification Of Expression, Markus Ringnér, Patrik Edén, Peter Johansson
Introduction Artificial neural networks in the form of feed-forward networks (ANNs) have emerged as a practical technology for classification with applications in many fields. ANNs have in particular...
Sofia K Gruvberger, Markus Ringnér, Patrik Edén, Åke Borg, Mårten Fernö, Carsten Peterson, ...
Breast Cancer Research Vol 5 No 1 Gruvberger et al.
Normalization of array-CGH data: influence of copy number imbalances (2007)
Staaf, Johan, Jönsson, Göran, Ringnér, Markus, Vallon-Christersson, Johan
Abstract Background High-resolution microarray-based comparative genomic hybridization (CGH) techniques have successfully been applied to study copy number imbalances in a number of settings such as...
Liu, Yingchun, Ringnér, Markus
Abstract Gene expression signatures consisting of tens to hundreds of genes have been found to be informative for different biological states. Recently, many computational methods have been proposed...
Jonsson, Goran, Staaf, Johan, Olsson, Eleonor, Heidenblad, Markus, Vallon-Christersson, Johan, Osoegawa, Kazutoyo, ...
Abstract is not available
2007 Liu Volume and Ringnér 8, Issue 5, Article R77 Open Access Method (2007)
Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis
Using high-throughput technologies, abundances and other features of genes and proteins have been measured on a genome-wide scale in Saccharomyces cerevisiae. In contrast, secondary structure in...
Jönsson, Göran, Naylor, Tara L, Vallon-Christersson, Johan, Staaf, Johan, Huang, Jia, Ward, M Renee, ...
Abstract is not available
Multiclass discovery in array data (2004)
Liu, Yingchun, Ringnér, Markus
Abstract Background A routine goal in the analysis of microarray data is to identify genes with expression levels that correlate with known classes of experiments. In a growing number of array data...
Gruvberger-Saal, Sofia K, Edén, Patrik, Ringnér, Markus, Baldetorp, Bo, Chebil, Gunilla, Borg, Ake, ...
Abstract is not available
Microarray expression profiling in melanoma reveals a BRAF mutation signature (2004)
Pavey, Sandra, Johansson, Peter, Packer, Leisl, Taylor, Jennifer, Stark, Mitchell, Pollock, Pamela M., ...
We have used microarray gene expression pro. ling and machine learning to predict the presence of BRAF mutations in a panel of 61 melanoma cell lines. The BRAF gene was found to be mutated in 42...
ACID: a database for microarray clone information (2004)
Ringnér, Markus, Veerla, Srinivas, Andersson, Samuel, Staaf, Johan, Häkkinen, Jari
Summary: ACID is an online database for information about microarray cDNA clones. For each clone, the database contents include assigned UniGene cluster(s), location in the full-length transcript,...
ACID: a database for microarray clone information (2004)
Ringnér, Markus, Veerla, Srinivas, Andersson, Samuel, Staaf, Johan, Häkkinen, Jari
Summary: Array Close Information Database is an online database for information about microarray cDNA clones. For each clone, the database contents include assigned UniGene cluster(s), location in...
ACID: a database for microarray clone information (2004)
Ringnér, Markus, Veerla, Srinivas, Andersson, Samuel, Staaf, Johan, Häkkinen, Jari
Summary: ACID is an online database for information about microarray cDNA clones. For each clone, the database contents include assigned UniGene cluster(s), location in the full-length transcript,...
Expression profiling to predict outcome in breast cancer: the influence of sample selection (2003)
Gruvberger, Sofia K, Ringnér, Markus, Edén, Patrik, Borg, Åke, Fernö, Mårten, Peterson, Carsten, ...
Gene expression profiling of tumors using DNA microarrays is a promising method for predicting prognosis and treatment response in cancer patients. It was recently reported that expression profiles...
Heather E. Cunliffe, Markus Ringnér, Sven Bilke, Robert L. Walker, Jennifer M. Cheung, Yidong Chen, ...
The effects of hormone and growth factor signaling on gene expression contribute significantly to breast tumorigenesis and disease progression; however, the targets of signaling networks associated...
Roberto Bomprezzi, Markus Ringnér, Seungchan Kim, Michael L. Bittner, Javed Khan, Yidong Chen, ...
Gene expression profile in multiple sclerosis
Microarray-Based Cancer Diagnosis with Artificial Neural Networks (2003)
Markus Ringnér, Carsten Peterson
In recent years, the advent of experimental methods to probe gene expression profiles of cancer on a genome-wide scale has led to widespread use of supervised machine learning algorithms to...
Bomprezzi, Roberto, Ringnér, Markus, Kim, Seungchan, Bittner, Michael L., Khan, Javed, Chen, Yidong, ...
Multiple sclerosis (MS) and other T cell-mediated autoimmune diseases develop in individuals carrying a complex susceptibility trait, probably following exposure to various environmental triggers....
Bomprezzi, Roberto, Ringnér, Markus, Kim, Seungchan, Bittner, Michael L., Khan, Javed, Chen, Yidong, ...
Multiple sclerosis (MS) and other T cell-mediated autoimmune diseases develop in individuals carrying a complex susceptibility trait, probably following exposure to various environmental triggers....
Bomprezzi, Roberto, Ringnér, Markus, Kim, Seungchan, Bittner, Michael L., Khan, Javed, Chen, Yidong, ...
Multiple sclerosis (MS) and other T cell-mediated autoimmune diseases develop in individuals carrying a complex susceptibility trait, probably following exposure to various environmental triggers....
Expression profiling to predict outcome in breast cancer: the influence of sample selection (2002)
Gruvberger, Sofia K, Ringnér, Markus, Edén, Patrik, Borg, Åke, Fernö, Mårten, Peterson, Carsten, ...
Abstract Gene expression profiling of tumors using DNA microarrays is a promising method for predicting prognosis and treatment response in cancer patients. It was recently reported that expression...
A strategy for identifying putative causes of gene expression variation in human cancer (2002)
Sampsa Hautaniemi, Markus Ringnér, Päivikki Kauraniemi, Anne Kallioniemi, Henrik Edgren, Olli Yli-harja, ...
There is often a need to predict the impact of alterations in one variable on another variable. This is especially the case in cancer research, where much effort has been made to carry out...
Impact of DNA amplification on gene expression patterns in breast cancer (2002)
Elizabeth Hyman, Päivikki Kauraniemi, Sampsa Hautaniemi, Maija Wolf, Spyro Mousses, Ester Rozenblum, ...
Genetic changes underlie tumor progression and may lead to cancerspecific expression of critical genes. Over 1100 publications have described the use of comparative genomic hybridization (CGH) to...
Analyzing Tumor Gene Expression Profiles (2002)
Carsten Peterson, Markus Ringnér
A brief introduction to high throughput technologies for measuring and analyzing gene expression is given. Various supervised and unsupervised data mining methods for analyzing the produced...
Sofia Gruvberger, Markus Ringnér, Yidong Chen, Sujatha Panavally, Lao H. Saal, Åke Borg, ...
To investigate the phenotype associated with estrogen receptor � (ER) expression in breast carcinoma, gene expression profiles of 58 nodenegative breast carcinomas discordant for ER status were...
A Novel Approach to Structure Alignment (2000)
Mattias Ohlsson, Carsten Peterson, Markus Ringnér, Richard Blankenbecler
Motivation: Aligning protein structures is a highly relevant task. It enables the study of functional and ancestry relationships between proteins and is very important for homology and threading...
A Novel Approach to Structure Alignment (2000)
Mattias Ohlsson, Carsten Peterson, Markus Ringnér, Richard Blankenbecler
Motivation: Aligning protein structures is a highly relevant task. It enables the study of functional and ancestry relationships between proteins and is very important for homology and threading...
Correlations in multiparticle production (1998)
Different aspects of the strong interaction in particle collisions are studied. Most of the work is based on the Lund string fragmentation model for hadron production. A model which incorporates...
Is there screwiness at the end of the QCD cascades? (1998)
Bo Andersson, Gösta Gustafson, Jari Hakkinen, Markus Ringnér, Peter Sutton
this paper we examine what happens at the end of this cascade. We find that the conditions are favourable for the field to utilize the azimuthal degree of freedom and wind itself into the form of a...
Transverse and Longitudinal Bose-Einstein Correlations (1997)
: We show how a difference in the correlation length longitudinally and transversely, with respect to the jet axis in e + e \Gamma annihilation, arises naturally in a model for Bose-Einstein...
Transverse and Longitudinal Bose-Einstein Correlations in ... Annihilation (1997)
: We show how a difference in the correlation length longitudinally and transversely, with respect to the jet axis in e + e \Gamma annihilation, arises naturally in a model for Bose-Einstein...
Bose-Einstein Correlations in the Lund Model (1997)
: By providing the Lund Model fragmentation process with a quantum-mechanical framework we extend the results of [6] to situations where there are very many identical bosons. We investigate the...
Bose-Einstein and Colour Interference in W-pair Decays (1997)
We study effects on the W mass measurements at LEP2 from non-perturbative interference effects in the fully hadronic decay channel. Based on a model for Bose-Einstein interference, which is in...
Molecular classification of familial non-BRCA1/BRCA2 breast cancer
Hedenfalk, Ingrid, Ringnér, Markus, Ben-Dor, Amir, Yakhini, Zohar, Chen, Yidong, Chebil, Gunilla, ...
In the decade since their discovery, the two major breast cancer susceptibility genes BRCA1 and BRCA2, have been shown conclusively to be involved in a significant fraction of families segregating...
Expression profiling to predict outcome in breast cancer: the influence of sample selection
Gruvberger, Sofia K, Ringnér, Markus, Edén, Patrik, Borg, Åke, Fernö, Mårten, Peterson, Carsten, ...
Gene expression profiling of tumors using DNA microarrays is a promising method for predicting prognosis and treatment response in cancer patients. It was recently reported that expression profiles...
Matching protein structures with fuzzy alignments
Blankenbecler, Richard, Ohlsson, Mattias, Peterson, Carsten, Ringnér, Markus
Unraveling functional and ancestral relationships between proteins as well as structure-prediction procedures require powerful protein-alignment methods. A structure-alignment method is presented...
Khan, Javed, Wei, Jun S., Ringnér, Markus, Saal, Lao H., Ladanyi, Marc, Westermann, Frank, ...
The purpose of this study was to develop a method of classifying cancers to specific diagnostic categories based on their gene expression signatures using artificial neural networks (ANNs). We...
Folding Free Energies of 5′-UTRs Impact Post-Transcriptional Regulation on a Genomic Scale in Yeast
Ringnér, Markus, Krogh, Morten
Using high-throughput technologies, abundances and other features of genes and proteins have been measured on a genome-wide scale in Saccharomyces cerevisiae. In contrast, secondary structure in...
Molecular classification of familial non-BRCA1/BRCA2 breast cancer
Hedenfalk, Ingrid, Ringnér, Markus, Ben-Dor, Amir, Yakhini, Zohar, Chen, Yidong, Chebil, Gunilla, ...
In the decade since their discovery, the two major breast cancer susceptibility genes BRCA1 and BRCA2, have been shown conclusively to be involved in a significant fraction of families segregating...
Expression profiling to predict outcome in breast cancer: the influence of sample selection
Gruvberger, Sofia K, Ringnér, Markus, Edén, Patrik, Borg, Åke, Fernö, Mårten, Peterson, Carsten, ...
Gene expression profiling of tumors using DNA microarrays is a promising method for predicting prognosis and treatment response in cancer patients. It was recently reported that expression profiles...
Matching protein structures with fuzzy alignments
Blankenbecler, Richard, Ohlsson, Mattias, Peterson, Carsten, Ringnér, Markus
Unraveling functional and ancestral relationships between proteins as well as structure-prediction procedures require powerful protein-alignment methods. A structure-alignment method is presented...
Folding Free Energies of 5′-UTRs Impact Post-Transcriptional Regulation on a Genomic Scale in Yeast
Ringnér, Markus, Krogh, Morten
Using high-throughput technologies, abundances and other features of genes and proteins have been measured on a genome-wide scale in Saccharomyces cerevisiae. In contrast, secondary structure in...
Liu, Yingchun, Ringnér, Markus
A strategy for identifying cell signaling pathways whose deregulation result in an observed expression signature is presented.
Saal, Lao H., Johansson, Peter, Holm, Karolina, Gruvberger-Saal, Sofia K., She, Qing-Bai, Maurer, Matthew, ...
Pathway-specific therapy is the future of cancer management. The oncogenic phosphatidylinositol 3-kinase (PI3K) pathway is frequently activated in solid tumors; however, currently, no reliable test...
Normalization of array-CGH data: influence of copy number imbalances
Staaf, Johan, Jönsson, Göran, Ringnér, Markus, Vallon-Christersson, Johan
Brommesson, Sara, Jönsson, Göran, Strand, Carina, Grabau, Dorthe, Malmström, Per, Ringnér, Markus, ...
The CD44+/CD24- phenotype is enriched in basal-like breast tumors
Honeth, Gabriella, Bendahl, Pär-Ola, Ringnér, Markus, Saal, Lao H, Gruvberger-Saal, Sofia K, Lövgren, Kristina, ...
Staaf, Johan, Vallon-Christersson, Johan, Lindgren, David, Juliusson, Gunnar, Rosenquist, Richard, Höglund, Mattias, ...
Staaf, Johan, Lindgren, David, Vallon-Christersson, Johan, Isaksson, Anders, Göransson, Hanna, Juliusson, Gunnar, ...
A strategy is presented for detection of loss-of-heterozygosity and allelic imbalance in cancer cells from whole genome SNP genotyping data.
Fredlund, Erik, Ringnér, Markus, Maris, John M., Påhlman, Sven
The childhood cancer neuroblastoma arises in the developing sympathetic nervous system and is a genotypically and phenotypically heterogeneous disease. Prognostic markers of poor survival probability...