Laajala, Essi, Aittokallio, Tero, Lahesmaa, Riitta, Elo, Laura L
Abstract The recent advent of exon microarrays has made it possible to reveal differences in alternative splicing events on a global scale. We introduce a novel statistical procedure that takes full...
Statistical Methods for Identifying Conserved Residues in Multiple Sequence Alignment (2009)
Ahola, Virpi, Aittokallio, Tero, Uusipaikka, Esa, Vihinen, Mauno
Geometrical Distortions in Two-Dimensional Gels: Applicable Correction Methods (2009)
Aittokallio, Tero, Salmi, Jussi, Nyman, Tuula A., Nevalainen, Olli S.
Two-dimensional electrophoresis (2-DE) provides a rapid means for separating thousands of proteins from cell and tissue samples in one run. Although this powerful research tool has been...
Elo, Laura L., Hiissa, Jukka, Tuimala, Jarno, Kallio, Aleksi, Korpelainen, Eija, Aittokallio, Tero
Identification of reliable molecular markers that show differential expression between distinct groups of samples has remained a fundamental research problem in many large-scale profiling studies,...
Clément-Ziza, Mathieu, Malabat, Christophe, Weber, Christian, Moszer, Ivan, Aittokallio, Tero, Letondal, Catherine, ...
Summary: Genoscape is an open-source Cytoscape plug-in that visually integrates gene expression data sets from GenoScript, a transcriptomic database, and KEGG pathways into Cytoscape networks. The...
Identification of Novel IL-4/Stat6-Regulated Genes in T (2008)
Zhi Chen, Riikka Lund, Tero Aittokallio, Minna Kosonen, Olli Nevalainen, Riitta Lahesmaa
IL-4, primarily produced by T cells, mast cells, and basophiles, is a cytokine which has pleiotropic effects on the immune system. IL-4 induces T cells to differentiate to Th2 cells and activated B...
Filtering strategies for improving protein identification in high-throughput MS/MS studies (2008)
Salmi, Jussi, Nyman, Tuula A., Nevalainen, Olli S., Aittokallio, Tero
Despite the recent advances in streamlining high-throughput proteomic pipelines using tandem mass spectrometry (MS/MS), reliable identification of peptides and proteins on a larger scale has remained...
Tuikkala, Johannes, Elo, Laura L, Nevalainen, Olli S, Aittokallio, Tero
Abstract Background Missing values frequently pose problems in gene expression microarray experiments as they can hinder downstream analysis of the datasets. While several missing value imputation...
Olivier Garcia, Cosmin Saveanu, Melissa Cline, Micheline Fromont-racine, Alain Jacquier, Benno Schwikowski, ...
Summary: We have implemented a graph layout algorithm that exposes Gene Ontology (GO) class structure on the network nodes. It can be used in conjunction with BiNGO plug-in to Cytoscape, which finds...
BIOINFORMATICS ORIGINAL PAPER (2008)
Genome Analysis, Jussi Salmi, Robert Moulder, Jan-jonas Filén, Olli S. Nevalainen, Tuula A. Nyman, ...
doi:10.1093/bioinformatics/bti829
BIOINFORMATICS Quality classification of tandem mass spectrometry data (2008)
Jussi Salmi, Robert Moulder, Jan-jonas Filén, Olli S. Nevalainen, Tuula A. Nyman, Riitta Lahesmaa, ...
Motivation: Peptide identification by tandem mass spectrometry is an important tool in proteomic research. Powerful identification programs exist, such as SEQUEST, ProICAT and Mascot, which can...
A Multilevel Graph Layout Algorithm for Cytoscape Bioinformatics Software Platform (2008)
Salmela, Pekka, Nevalainen, Olli S., Aittokallio, Tero
We have implemented a graph layout algorithm of C. Walshaw as a plug-in in the Cytoscape bioinformatics software platform. The algorithm combines traditional forcedirected placement of graphs with an...
Model-based prediction of sequence alignment quality (2008)
Ahola, Virpi, Aittokallio, Tero, Vihinen, Mauno, Uusipaikka, Esa
Motivation: Multiple sequence alignment (MSA) is an essential prerequisite for many sequence analysis methods and valuable tool itself for describing relationships between protein sequences. Since...
Bmc Bioinformatics, Johannes Tuikkala, Laura L Elo, Olli S Nevalainen, Tero Aittokallio
Research article Missing value imputation improves clustering and interpretation of gene expression microarray data
In snorers, the physiologic decrease of postural muscle tone during sleep results in increased collapsibility of the upper airway. This paper presents a mathematical model for the collapsible upper...
Automated Detection of Dioeerentially Expressed Fragments in mRNA Dioeerential Display (2007)
Tero Aittokallio, Olli Nevalainen, Pekka Ojala, Timo J. Nevalainen
We present a novel method for the automated detection of fragments showing dissimilar expression in mRNA dioeerential display. The analysis is based on aligning the numerical electrophoretic lane...
Tero Aittokallio, Mats Gyllenberg, Olli Nevalainen
A simple method for detecting periodic components of unknown periodicity in a signal is presented. The method is based on spectral decomposition of signal using orthonormal functions. Traditionally,...
Computation of Standard Errors for Maximum-likelihood Estimates in Hidden Markov Models (2007)
Tero Aittokallio, Esa Uusipaikka
Explicit computation of the score vector and the observed information matrix in hidden Markov models is described. With the help of the information matrix Wald's condence intervals can be formed...
Computation of Restricted Maximum-penalized-likelihood Estimates in Hidden Markov Models (2007)
Tero Aittokallio, Olli Nevalainen, Jussi Tolvi, Kalle Lertola, Esa Uusipaikka
The maximum-penalized-likelihood estimation for hidden Markov models with general observation densities is described. All statistical inference, including the model estimation, testing, and...
Tero Aittokallio, Mats Gyllenberg
A cardiorespiratory model incorporating control of the human upper airway during sleep is described. Most previous models have not considered the possibility that the upper airway could be a limiting...
Elo, Laura L., Järvenpää, Henna, Oresic, Matej, Lahesmaa, Riitta, Aittokallio, Tero
Motivation: Coexpression networks have recently emerged as a novel holistic approach to microarray data analysis and interpretation. Choosing an appropriate cutoff threshold, above which a...
Elo, Laura L., Tuikkala, Johannes, Nevalainen, Olli S., Aittokallio, Tero
Gene expression microarrays have become a popular high-throughput technique in functional genomics. By enabling the monitoring of thousands of genes simultaneously, this technique holds enormous...
Vähämaa, Heidi, Ojala, Pekka, Pahikkala, Tapio, Nevalainen, Olli S., Lahesmaa, Riitta, Aittokallio, Tero
Available by Journal
Biochemical and Clinical Approaches in Evaluating the Prognosis of Colonic Cancer (2007)
Talvinen, Kati, Tuikkala, Johannes, Grönroos, Juha, Huhtinen, Heikki, Kronqvist, Pauliina, Aittokallio, Tero, ...
Background: Colorectal adenocarcinoma is a common malignant neoplasm in the western world. To achieve optimal treatment results, the estimation of risk of recurrence should be as accurate as...
Aittokallio, Tero, Malminen, Jani S., Pahikkala, Tapio, Polo, Olli, Nevalainen, Olli S.
We describe an automated method for monitoring airflow dynamics in the upper airway of a sleeping subject. Its main task is to determine a set of inspiratory flow shape representatives...
Elo, Laura L., Järvenpää, Henna, Oresic, Matej, Lahesmaa, Riitta, Aittokallio, Tero
Bioinformatics Vol.23 Nr.26, 2096 - 2103
Garcia, Olivier, Saveanu, Cosmin, Cline, Melissa, Fromont-Racine, Micheline, Jacquier, Alain, Schwikowski, Benno, ...
Summary: We have implemented a graph layout algorithm that exposes Gene Ontology (GO) class structure on the network nodes. It can be used in conjunction with BiNGO plug-in to Cytoscape, which finds...
A statistical score for assessing the quality of multiple sequence alignments (2006)
Ahola, Virpi, Aittokallio, Tero, Vihinen, Mauno, Uusipaikka, Esa
Abstract Background Multiple sequence alignment is the foundation of many important applications in bioinformatics that aim at detecting functionally important regions, predicting protein structures,...
Th1 Response and Cytotoxicity Genes Are Down-Regulated in Cutaneous T-Cell Lymphoma (2006)
Hahtola, Sonja, Tuomela, Soile, Elo, Laura, Häkkinen, Tiina, Karenko, Leena, Nedoszytko, Boguslaw, ...
Filtering Bad Quality Tandem Mass Spectra Prior to Protein Identification (2006)
Salmi, Jussi, Moulder, Robert, Filén, Jan-Jonas, Nevalainen, Olli S., Lahesmaa, Riitta, Nyman, Tuula A., ...
The identification of proteins is an important task in proteomics. Protein or peptide identification from mass spectrometry data is usually accomplished by using database search programs which match...
Improving Missing Value Estimation in Microarray Data with Gene Ontology (2006)
Tuikkala, Johannes, Elo, Laura, Nevalainen, Olli S., Aittokallio, Tero
Model-Based Analysis of Mechanisms Responsible for Sleep-Induced Carbon Dioxide Differences (2006)
Aittokallio, Tero, Gyllenberg, Mats, Polo, Olli, Toivonen, Jenni, Virkki, Arho
This work describes a comprehensive mathematical model of the human respiratory control system which incorporates the central mechanisms for predicting sleep-induced changes in chemical regulation of...
Quality Classification of Tandem Mass Spectrometry Data (2006)
Salmi, Jussi, Moulder, Robert, Filén, Jan-Jonas, Nevalainen, Olli S., Nyman, Tuula A., Lahesmaa, Riitta, ...
Motivation: Peptide identification by tandem mass spectrometry is an important tool in proteomic research. Powerful identification programs exist, such as SEQUEST, ProICATand Mascot, which can relate...
Aittokallio, Jenni, Virkki, Arho, Aittokallio, Tero, Saaresranta, Tarja, Polo-Kantola, Päivi, Polo, Olli
Menopause and aging cause hormonal changes with respiratory consequences. The aim of the present study was to investigate the physiological changes in respiration during wakefulness and sleep across...
Elo, Laura L., Katajamaa, Mikko, Lund, Riikka, Oresic, Matej, Lahesmaa, Riitta, Aittokallio, Tero
OMICS: A Journal of Integrative Biology Vol.10 Nr.3, 369 - 380
Inference of Gene Coexpression Networks by Integrative Analysis across Microarray Experiments (2006)
Elo, Laura L., Lahesmaa, Riitta, Aittokallio, Tero
We improve the reliability of detecting coexpressed gene pairs from microarray data by introducing a novel probe-level quality-weighted similarity measure for combining data across different...
Gene Ontology-based layout and coloring (2006)
Olivier Garcia, Cosmin Saveanu, Melissa Cline, Micheline Fromont-racine, Alain Jacquier, Benno Schwikowski, ...
doi:10.1093/bioinformatics/btl605 GOlorize: a Cytoscape plug-in for network visualization with
Improving missing value estimation in microarray data with gene ontology (2006)
Tuikkala, Johannes, Elo, Laura, Nevalainen, Olli S., Aittokallio, Tero
Motivation: Gene expression microarray experiments produce datasets with frequent missing expression values. Accurate estimation of missing values is an important prerequisite for efficient data...
Graph-based methods for analysing networks in cell biology (2006)
Aittokallio, Tero, Schwikowski, Benno
Availability of large-scale experimental data for cell biology is enabling computational methods to systematically model the behaviour of cellular networks. This review surveys the recent advances in...
Integrating Probe-Level Expression Changes Across Generations of Affymetrix Arrays (2005)
Elo, Laura, Lahti, Leo, Skottman, Heli, Kyläniemi, Minna, Lahesmaa, Riitta, Aittokallio, Tero
Filtering Bad Quality Tandem Mass Spectra Prior to Protein Identification (2005)
Salmi, Jussi, Moulder, Robert, Filén, Jan-Jonas, Nevalainen, Olli S., Lahesmaa, Riitta, Nyman, Tuula A., ...
An important task in proteomics is the identification of peptides from tandem mass spectrometry data. Peptide identification is usually accomplished by using database search programs which match the...
Considerations when Using Gene Expression Microarray Data to Diagnostic Classification (2005)
Pahikkala, Tapio, Nikula, Tuomas, Mykkänen, Juha, Näntö-Salonen, Kirsti, Simell, Olli, Lahesmaa, Riitta, ...
Gene expression microarrays provide a powerful tool for biomedical research. However, there are a number of challenging problems that need to be considered before applying microarray data in...
Automated Pattern Rranking in Differential Display Data Analysis (2005)
Aittokallio, Tero, Ojala, Pekka, Nevalainen, Timo J., Nevalainen, Olli S.
Improving Missing Value Estimation in Microarray Data with Gene Ontology (2005)
Tuikkala, Johannes, Nevalainen, Olli S., Aittokallio, Tero
Gene expression microarray experiments produce data sets with frequent missing expression values. Accurate estimation of missing values is an important prerequisite for efficient data analysis as...
A Human ImmunoChip cDNA Microarray Provides a Comprehensive Tool to Study Immune Responses (2005)
Nikula, Tuomas, West, Anne, Katajamaa, Mikko, Lönnberg, Tapio, Sara, Rolf, Aittokallio, Tero, ...
DNA microarray technology has developed rapidly in recent years and has become an essential tool, providing novel approaches to biomedical research. In this paper, we describe a self-designed...
Moulder, Robert, Filen, Jan-Jonas, Salmi, Jussi, Katajamaa, Mikko, Nevalainen, Olli, Oresic, Matej, ...
The options available for processing quantitative data from isotope coded affinity tag (ICAT) experiments have mostly been confined to software specific to the instrument of acquisition. However,...
Saaresranta, Tarja, Aittokallio, Tero, Utriainen, Karri, Polo, Olli
Abstract Background Progestins as respiratory stimulants in chronic obstructive pulmonary disease (COPD) have been investigated in males and during wakefulness. However, sleep and gender may...
On the Robustness of Fluorescence Fingerprinting of Plants (2005)
Codrea, Marius C., Aittokallio, Tero, Keränen, Mika, Tyystjärvi, Esa, Nevalainen, Olli S.
In the present work, we study the effect of temporal changes on the identification accuracy in fluorescence fingerprinting of plants. Here, the time series comprises consecutive datasets (chlorophyll...
Laura L. Elo, Leo Lahti, Heli Skottman, Minna Kyläniemi, Riitta Lahesmaa, Tero Aittokallio
studies are of practical interest for minimizing the number There is an urgent need for bioinformatic methods that allow integrative analysis of multiple microarray datasets.While...
Johannes Tuikkala, Laura Elo, Olli S. Nevalainen, Tero Aittokallio
Improving missing value estimation in microarray data with gene ontology
Integrating probe-level expression changes across generations of Affymetrix arrays (2005)
Elo, Laura L., Lahti, Leo, Skottman, Heli, Kyläniemi, Minna, Lahesmaa, Riitta, Aittokallio, Tero
There is an urgent need for bioinformatic methods that allow integrative analysis of multiple microarray data sets. While previous studies have mainly concentrated on reproducibility of gene...
Quality classification of tandem mass spectrometry data (2005)
Salmi, Jussi, Moulder, Robert, Filén, Jan-Jonas, Nevalainen, Olli S., Nyman, Tuula A., Lahesmaa, Riitta, ...
Motivation: Peptide identification by tandem mass spectrometry is an important tool in proteomic research. Powerful identification programs exist, such as SEQUEST, ProICAT and Mascot, which can...
Improving missing value estimation in microarray data with gene ontology (2005)
Tuikkala, Johannes, Elo, Laura, Nevalainen, Olli S., Aittokallio, Tero
Motivation: Gene expression microarray experiments produce data sets with frequent missing expression values. Accurate estimation of missing values is an important prerequisite for efficient data...
Correcting Distortions in 2D Gels - A Survey (2004)
Salmi, Jussi, Aittokallio, Tero, Nyman, Tuula A., Nevalainen, Olli S.
Two-dimensional electrophoresis (2-DE) provides a rapid means for separating thousands of proteins from cell and tissue samples in one run. Although this powerful research tool has been...
Statistical Methods for Identifying Conserved Residues in Multiple Sequence Alignment (2004)
Ahola, Virpi, Aittokallio, Tero, Uusipaikka, Esa, Vihinen, Mauno
The assessment of residue conservation in a multiple sequence alignment is a central issue in bioinformatics. Conserved residues and regions are used to determine structural and functional motifs or...
Statistical Methods for Identifying Conserved Residues in Multiple Sequence Alignment (2004)
Ahola, Virpi, Aittokallio, Tero, Uusipaikka, Esa, Vihinen, Mauno
The assessment of residue conservation in a multiple sequence alignment is a central issue in bioinformatics. Conserved residues and regions are used to determine structural and functional motifs or...
Statistical Methods for Identifying Conserved Residues in Multiple Sequence Alignment (2004)
Ahola, Virpi, Aittokallio, Tero, Uusipaikka, Esa, Vihinen, Mauno
The assessment of residue conservation in a multiple sequence alignment is a central issue in bioinformatics. Conserved residues and regions are used to determine structural and functional motifs or...
Statistical Methods for Identifying Conserved Residues in Multiple Sequence Alignment (2004)
Ahola, Virpi, Aittokallio, Tero, Uusipaikka, Esa, Vihinen, Mauno
The assessment of residue conservation in a multiple sequence alignment is a central issue in bioinformatics. Conserved residues and regions are used to determine structural and functional motifs or...
Genetic Feature Learning Algorithm for Fluorescence Fingerprinting of Plants (2004)
Codrea, Marius C., Aittokallio, Tero, Keränen, Mika, Tyystjärvi, Esa, Nevalainen, Olli S.
Aittokallio, Tero, Malminen, Jani S., Pahikkala, Tapio, Polo, Olli, Nevalainen, Olli S.
An automated method for monitoring the performance of upper airway during sleep is described. The method assesses the upper airway airflow dynamics based on the clusters of inspiratory flow shapes...
Efficient Estimation of Emission Probabilities in Profile Hidden Markov Models (2003)
Ahola, Virpi, Aittokallio, Tero, Uusipaikka, Esa, Vihinen, Mauno
Feature Learning with a Genetic Algorithm for Fluorescence Fingerprinting of Plant Species (2003)
Codrea, Marius Cosmin, Aittokallio, Tero, Keränen, Mika, Tyystjärvi, Esa, Nevalainen, Olli S.
Proper feature analysis facilitates recognition by focusing the process to those characteristics of observed data that carry the most significant information for the given classification task. In...
Rosengren, Arsi, Salmi, Jussi, Aittokallio, Tero, Westerholm, Jan, Lahesmaa, Riitta, Nyman, Tuula, ...
Computational Strategies for Analyzing Data in Gene Expression Microarray Experiments (2003)
Aittokallio, Tero, Kurki, Markus, Nikula, Tuomas, West, Anne, Lahesmaa, Riitta, Nevalainen, Olli
Virtanen, Irina, Aittokallio, Tero, Tähtinen, Jarno, Salmi, Jussi, Järvi, Jaakko, Polo-Kantola, Päivi, ...
Identification of Novel IL-4/Stat6-Regulated Genes in T Lymphocytes (2003)
Chen, Zhi, Lund, Riikka, Aittokallio, Tero, Kosonen, Minna, Nevalainen, Olli, Lahesmaa, Riitta
Effect of Medroxyprogesterone on Inspiratory Flow Shapes During Sleep in Postmenopausal Women (2003)
Saaresranta, Tarja, Aittokallio, Tero, Polo-Kantola, Päivi, Helenius, Hans, Polo, Olli
Electrophoretic Signal Comparison Applied to mRNA Differential Display Analysis (2003)
Aittokallio, Tero, Pahikkala, Tapio, Ojala, Pekka, Nevalainen, Timo J., Nevalainen, Olli
On the Computational Analysis of Gene Expression Microarray Data (2003)
Aittokallio, Tero, Kurki, Markus, Nikula, Tuomas, West, Anne, Lahesmaa, Riitta, Nevalainen, Olli
Microarray analysis has become a widely used method for generating gene expression data on a genomic scale. DNA microarrays have been enthusiastically applied in many fields of biological research,...
Efficient estimation of emission probabilities in profile hidden Markov models (2003)
Ahola, Virpi, Aittokallio, Tero, Uusipaikka, Esa, Vihinen, Mauno
Motivation: Profile hidden Markov models provide a sensitive method for performing sequence database search and aligning multiple sequences. One of the drawbacks of the hidden Markov model is that...
Salmi, Jussi, Aittokallio, Tero, Westerholm, Jan, Griese, Matias, Rosengren, Arsi, Nyman, Tuula, ...
Feature Learning with a Genetic Algorithm for Fluorescence Fingerprinting of Plant Species (2002)
Codrea, Marius, Aittokallio, Tero, Keränen, Mika, Tyystjärvi, Esa, Nevalainen, Olli
It is known that proper feature analysis facilitates the recognition process by including only those characteristics of observed data that carry the most significant information for the given...
Automated detection of differentially expressed fragments in mRNA differential display (2001)
Aittokallio, Tero, Ojala, Pekka, Nevalainen, Timo J., Nevalainen, Olli
Characterization and Modelling of the Cardiorespiratory System in Sleep-disordered Breathing (2001)
http://www.tucs.fi/Publications/phdthesis/phdAittokallioa.php
Adjustment of the Human Respiratory System to Increased Upper Airway Resistance During Sleep (2001)
Aittokallio, Tero, Gyllenberg, Mats, Polo, Olli
http://www.tucs.fi/Publications/techreports/TR404.php
Automated Detection of Differentially Expressed Fragments in mRNA Differential Display (2000)
Aittokallio, Tero, Nevalainen, Olli, Ojala, Pekka, Nevalainen, Timo J.
We present a novel method for the automated detection of fragments showing dissimilar expression in mRNA differential display. The analysis is based on aligning the numerical electrophoretic lane...
Aittokallio, Tero, Gyllenberg, Mats, Nevalainen, Olli, Polo, Olli
A simple method for detecting periodic components of unknown periodicity in a signal is presented. The method is based on spectral decomposition of signal using orthonormal functions. Traditionally,...
Computation of Standard Errors for Maximum-likelihood Estimates in Hidden Markov Models (2000)
Aittokallio, Tero, Uusipaikka, Esa
http://www.tucs.fi/Publications/techreports/TR379.php
Computation of Restricted Maximum-penalized-likelihood Estimates in Hidden Markov Models (2000)
Aittokallio, Tero, Nevalainen, Olli, Tolvi, Jussi, Lertola, Kalle, Uusipaikka, Esa
The maximum-penalized-likelihood estimation for hidden Markov models with general observation densities is described. All statistical inference, including the model estimation, testing, and...
Analysis of similarity of electrophoretic patterns in mRNA differential display (2000)
Aittokallio, Tero, Ojala, Pekka, Nevalainen, Timo J., Nevalainen, Olli
Detection of high-frequency respiratory movements during sleep (2000)
Aittokallio, Tero, Gyllenberg, Mats, Järvi, Jaakko, Nevalainen, Olli
http://www.tucs.fi/Publications/journals/jAiGyJaNe99a.php
Improving the False Nearest Neighbors Method with Graphical Analysis (1999)
Aittokallio, Tero, Gyllenberg, Mats, Hietarinta, Jarmo, Kuusela, Tom, Multamäki, Tuomas
http://www.tucs.fi/Publications/journals/jAiGyHiKuMu99a.php
Likelihood Based Statistical Inference in Hidden Markov Models (1999)
Aittokallio, Tero, Ahola, Virpi, Uusipaikka, Esa
http://www.tucs.fi/Publications/techreports/TR260.php
Detection of High-frequency Respiratory Movements During Sleep (1999)
Aittokallio, Tero, Gyllenberg, Mats, Järvi, Jaakko, Polo, Olli, Nevalainen, Olli
Sleep-related breathing disorders are common in adults and they have a significant impact on health and safety. In previous sleep studies it has come evident that many important breathing disorders...
A Model of a Snorer's Upper Airway (1999)
Aittokallio, Tero, Gyllenberg, Mats, Polo, Olli
http://www.tucs.fi/Publications/techreports/TR266.php
Classification of Nasal Inspiratory Flow Shapes by Attributed Finite Automata (1999)
Aittokallio, Tero, Nevalainen, Olli, Pursiheimo, Ulla, Saaresranta, Tarja, Polo, Olli
Likelihood based statistical inference in hidden markov models (1999)
Tero Aittokallio, Virpi Ahola, Esa Uusipaikka
The hidden Markov model (HMM) is one type of stochastic signal model which is widely used in modeling and classication problems. Yet the more advanced statistical inference in this model has been...
Integrating probe-level expression changes across generations of Affymetrix arrays
Elo, Laura L., Lahti, Leo, Skottman, Heli, Kyläniemi, Minna, Lahesmaa, Riitta, Aittokallio, Tero
There is an urgent need for bioinformatic methods that allow integrative analysis of multiple microarray data sets. While previous studies have mainly concentrated on reproducibility of gene...
A statistical score for assessing the quality of multiple sequence alignments
Ahola, Virpi, Aittokallio, Tero, Vihinen, Mauno, Uusipaikka, Esa
Integrating probe-level expression changes across generations of Affymetrix arrays
Elo, Laura L., Lahti, Leo, Skottman, Heli, Kyläniemi, Minna, Lahesmaa, Riitta, Aittokallio, Tero
There is an urgent need for bioinformatic methods that allow integrative analysis of multiple microarray data sets. While previous studies have mainly concentrated on reproducibility of gene...
A statistical score for assessing the quality of multiple sequence alignments
Ahola, Virpi, Aittokallio, Tero, Vihinen, Mauno, Uusipaikka, Esa
Statistical Methods for Identifying Conserved Residues in Multiple Sequence Alignment
Virpi Ahola, Tero Aittokallio, Esa Uusipaikka, Mauno Vihinen
The assessment of residue conservation in a multiple sequence alignment is a central issue in bioinformatics. Conserved residues and regions are used to determine structural and functional motifs or...
Missing value imputation improves clustering and interpretation of gene expression microarray data
Tuikkala, Johannes, Elo, Laura L, Nevalainen, Olli S, Aittokallio, Tero
Predicting Quantitative Genetic Interactions by Means of Sequential Matrix Approximation
Järvinen, Aki P., Hiissa, Jukka, Elo, Laura L., Aittokallio, Tero
Despite the emerging experimental techniques for perturbing multiple genes and measuring their quantitative phenotypic effects, genetic interactions have remained extremely difficult to predict on a...
Laajala, Essi, Aittokallio, Tero, Lahesmaa, Riitta, Elo, Laura L
A novel statistical procedure is presented that uses probe-level information on Affymetrix exon arrays to detect differential splicing.
Clément-Ziza, Mathieu, Malabat, Christophe, Weber, Christian, Moszer, Ivan, Aittokallio, Tero, Letondal, Catherine, ...
Summary: Genoscape is an open-source Cytoscape plug-in that visually integrates gene expression data sets from GenoScript, a transcriptomic database, and KEGG pathways into Cytoscape networks. The...