Decentralization of multimedia content in a heterogeneous environment (2009)
Koskenvaara, Tuomo, Tarhio, Jorma
The aim of this study has been the decentralization of multimedia content in a heterogeneous environment. The environment consisted of the research networks connecting the European Organization for...
Philippe, Nicolas, Boureux, Anthony, Bréhélin, Laurent, Tarhio, Jorma, Commes, Thérèse, Rivals, Eric
Next-generation sequencing technologies, able to yield millions of sequences in a single run, allow to interrogate the transcriptome or to assay protein-DNA interactions (by Chromatin...
Philippe, Nicolas, Boureux, Anthony, Bréhélin, Laurent, Tarhio, Jorma, Commes, Thérèse, Rivals, Eric
Next-generation sequencing technologies, able to yield millions of sequences in a single run, allow to interrogate the transcriptome or to assay protein-DNA interactions (by Chromatin...
String processing and information retrieval (2009)
Karlgren, Jussi, Tarhio, Jorma, Hyyrö, Heikki
Proceedings of the 16th International Symposium on String Processing and Information Retrieval (SPIRE 2009), Saariselkä, Finland, 25-27 August 2009.
Philippe, Nicolas, Boureux, Anthony, Bréhélin, Laurent, Tarhio, Jorma, Commes, Thérèse, Rivals, Éric
Ultra high-throughput sequencing is used to analyse the transcriptome or interactome at unprecedented depth on a genome-wide scale. These techniques yield short sequence reads that are then mapped on...
MPSCAN: Fast Localisation of Multiple Reads in Genomes (2009)
Rivals, Eric, Salmela, Leena, Kalsi, Petri, Kiiskinen, Petteri, Tarhio, Jorma
With Next Generation Sequencers, sequence based transcriptomic or epigenomic assays yield millions of short sequence reads that need to map back on a reference genome. The upcoming versions of these...
MPSCAN: Fast Localisation of Multiple Reads in Genomes (2009)
Rivals, Eric, Salmela, Leena, Kalsi, Petri, Kiiskinen, Petteri, Tarhio, Jorma
With Next Generation Sequencers, sequence based transcriptomic or epigenomic assays yield millions of short sequence reads that need to map back on a reference genome. The upcoming versions of these...
Philippe, Nicolas, Boureux, Anthony, Bréhélin, Laurent, Tarhio, Jorma, Commes, Thérèse, Rivals, Eric
Ultra high-throughput sequencing is used to analyse the transcriptome or interactome at unprecedented depth on a genome-wide scale. These techniques yield short sequence reads that are then mapped on...
Philippe, Nicolas, Boureux, Anthony, Bréhélin, Laurent, Tarhio, Jorma, Commes, Thérèse, Rivals, Eric
Ultra high-throughput sequencing is used to analyse the transcriptome or interactome at unprecedented depth on a genome-wide scale. These techniques yield short sequence reads that are then mapped on...
Searching for long DNA strings is studied. A q-gram variation of the Boyer–Moore algorithm is considered. An alphabet transformation with precomputed tables is utilized to reduce the...
Algorithms for Weighted Matching (2008)
Abstract. We consider the matching of weighted patterns against an unweighted text. We adapt the shift-add algorithm for this problem. We also present an algorithm that enumerates all strings that...
Pasi J. Eronen, Jussi Nuutinen, Erkki Rautama, Erkki Sutinen, Jorma Tarhio
Concept learning belongs to the fundamental challenges of educational technology. Contrary to the current trend of designing and implementing contents for various web–based virtual courses, concept...
Masaru Kitsuregawa, Betty Salzberg, Gonzalo Navarro, Ricardo Baeza-yates, Erkki Sutinen, Jorma Tarhio, ...
IntegratingDiverseInformationManagementSystems:ABriefSurvey..................................
Combining SAGE Tags to Predict Genomic Transcribed Regions (2008)
Rivals, Eric, Boureux, Anthony, Lejeune, Mireille, Ottones, Florence, Pecharromàn Pérez, Oscar, Tarhio, Jorma, ...
Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial Analysis of...
Combining SAGE Tags to Predict Genomic Transcribed Regions (2008)
Rivals, Eric, Boureux, Anthony, Lejeune, Mireille, Ottones, Florence, Pecharromàn Pérez, Oscar, Tarhio, Jorma, ...
Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial Analysis of...
Transcriptome Annotation using Tandem SAGE Tags (2007)
Rivals, Eric, Boureux, Anthony, Lejeune, Mireille, Ottones, Florence, Pecharromàn Pérez, Oscar, Tarhio, Jorma, ...
Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial analysis of...
Gonzalo Navarro, Jani Tanninen, Jorma Tarhio
Abstract. We present a new index for approximate string matching. The index collects text q-samples, i.e. disjoint text substrings of length q, at fixed intervals and stores their positions. At...
Report of the ITiCSE’97 Working Group on Visualization (2007)
Joseph Bergin, Ricardo Jiménez-peris, Myles F. Mcnally, Viera K. Proulx, Jorma Tarhio
Using the WWW as the delivery mechanism for interactive, visualization-based
Kimmo Fredriksson, Jorma Tarhio
Abstract. We present an ecient algorithm for scanning Human compressed texts. The algorithm parses the compressed text in O(n log 2 b) time, where n is the size of the compressed text in bytes, is...
Transcriptome annotation using tandem SAGE tags (2007)
Rivals, Eric, Boureux, Anthony, Lejeune, Mireille, Ottones, Florence, Pecharromàn Pérez, Oscar, Tarhio, Jorma, ...
Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial analysis of...
Transcriptome Annotation using Tandem SAGE Tags (2007)
Rivals, Eric, Boureux, Anthony, Lejeune, Mireille, Ottones, Florence, Pecharromàn Pérez, Oscar, Tarhio, Jorma, ...
Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial analysis of...
Transcriptome annotation using tandem SAGE tags (2007)
Rivals, Eric, Boureux, Anthony, Lejeune, Mireille, Ottones, Florence, Pecharromàn Pérez, Oscar, Tarhio, Jorma, ...
Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial Analysis of...
Transcriptome annotation using tandem SAGE tags (2007)
Rivals, Eric, Boureux, Anthony, Lejeune, Mireille, Ottones, Florence, Pecharromàn Pérez, Oscar, Tarhio, Jorma, ...
Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial Analysis of...
Transcriptome Annotation using Tandem SAGE Tags (2007)
Rivals, Eric, Boureux, Anthony, Lejeune, Mireille, Ottones, Florence, Pecharromàn Pérez, Oscar, Tarhio, Jorma, ...
Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial analysis of...
doi:10.1093/nar/gkm495 Transcriptome annotation using tandem SAGE tags (2007)
Eric Rivals, Anthony Boureux, Mireille Lejeune, Florence Ottones, Oscar Pecharromàn Pérez, Jorma Tarhio, ...
Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial analysis of...
doi:10.1093/nar/gkm495 Transcriptome (2007)
Eric Rivals, Anthony Boureux, Mireille Lejeune, Florence Ottones, Oscar Pecharromàn Pérez, Jorma Tarhio, ...
Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial analysis of...
Human Transcriptome Annotation using Tandem SAGE Tags (2006)
Rivals, Eric, Boureux, Anthony, Lejeune, Mireille, Ottones, Florence, Pecharromàn Pérez, Oscar, Tarhio, Jorma, ...
Recently, experiments based on tiling arrays have revealed the huge difference between number of active transcripts and the number of annotated genes. This discrepancy is not only due to...
Multi-pattern string matching with q-grams (2006)
We present three algorithms for exact string matching of multiple patterns. Our algorithms are filtering methods, which apply q-grams and bit parallelism. We ran extensive experiments with them and...
Supervisor Prof, Jorma Tarhio, Instructor Antti Huima, M. Sc
Model transformation is used in a wide range of applications including program synthesis, refactoring, and reverse engineering. A model transformation is a mapping of a set of source models onto a...
Oskar Ojala, Tekijä Oskar Ojala, Osasto Tietotekniikka, Pääaine Ohjelmistojärjestelmät, Sivumäärä X, ...
Palvelusuuntautunut arkkitehtuuri (SOA) edustaa uutta tapaa rakentaa väljästi keskenään sidonnaisia hajautettuja järjestelmiä. Siinä korostuvat hyvin määritellyt palvelurajapinnat ja...
LZgrep: A Boyer-Moore String Matching Tool for Ziv-Lempel Compressed Text (2005)
We present a Boyer-Moore approach to string matching over LZ78 and LZW compressed text. The idea is to search the text directly in compressed form instead of decompressing and then searching it. We...
LZgrep: A Boyer-Moore String Matching Tool for Ziv-Lempel Compressed Text (2005)
We present a Boyer-Moore approach to string matching over LZ78 and LZW compressed text. The idea is to search the text directly in compressed form instead of decompressing and then searching it. We...
We present a Boyer-Moore approach to string matching over LZ78 and LZW compressed text. The idea is to search the text directly in compressed form instead of decompressing and then searching it. We...
Tuomas Korpilahti, Supervisor Prof, Jorma Tarhio, Instructor Prof, Eero Hyvönen, Tuomas Korpilahti, ...
This thesis analyses a set of ontology change operations that break ontology dependencies, and describes a client-server based ontology library architecture capable of identifying those changes and...
Understanding Algorithms by Means of Visualized Path Testing (2002)
Ari Korhonen, Erkki Sutinen, Jorma Tarhio
Visualization of an algorithm offers only a rough picture of operations. Explanations are crucial for deeper understanding, because they help the viewer to associate the visualization with the...
Indexing Methods for Approximate String Matching (2001)
Gonzalo Navarro, Ricardo Baeza-yates, Erkki Sutinen, Jorma Tarhio
Indexing for approximate text searching is a novel problem receiving much attention because of its applications in signal processing, computational biology and text retrieval, to name a few. We...
Searching monophonic patterns within polyphonic sources (2000)
The string matching problem for strings in which one should find the occurrences of a pattern string within a text, is well-studied in the past literature. The problem can be solved efficiently,...
How a visualization tool can be used: Evaluating a tool in a research and development project (2000)
Keywords: POP-III.B. java; POP-III.B. visualisation; POP-V.B. case studies Veijo Meisalo (1 This paper outlines a part of a larger qualitative evaluation study where Jeliot, a tool designed to aid...
Searching monophonic patterns within polyphonic sources (2000)
The string matching problem for strings in which one should find the occurrences of a pattern string within a text, is well-studied in the past literature. The problem can be solved efficiently,...
Indexing Text with Approximate q-grams (2000)
Gonzalo Navarro, Erkki Sutinen, Jorma Tarhio
We present a new index for approximate string matching. The index collects text q-samples, that is, disjoint text substrings of length q, at fixed intervals and stores their positions. At search...
Eliot - an Algorithm Animation Environment (1997)
Erkki Sutinen, Erkki Sutinen, Jorma Tarhio, Jorma Tarhio, Simo-pekka Lahtinen, ...
Eliot is an interactive animation environment, for visualizing algorithms written in the C programming language. Eliot provides a library of visual data types which are ordinary data types with a set...
Indexing Methods for Approximate Text Retrieval (Extended Abstract) (1997)
Ricardo Baeza-yates, Gonzalo Navarro, Erkki Sutinen, Jorma Tarhio
While the problem of on-line approximate string matching is well studied, only recently the first off-line indexing techniques have emerged. We study the different indexing mechanisms for this...
Color dithering with n-best algorithm (1996)
Kjell Lemstrom, Jorma Tarhio, Tapio Takala
One of the interesting problems of digital image processing is how much the color table can be reduced without any detectable difference in the quality of an image. The process of reducing the color...
Transcriptome annotation using tandem SAGE tags
Rivals, Eric, Boureux, Anthony, Lejeune, Mireille, Ottones, Florence, Pecharromàn Pérez, Oscar, Tarhio, Jorma, ...
Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial analysis of...
Philippe, Nicolas, Boureux, Anthony, Bréhélin, Laurent, Tarhio, Jorma, Commes, Thérèse, Rivals, Éric
Ultra high-throughput sequencing is used to analyse the transcriptome or interactome at unprecedented depth on a genome-wide scale. These techniques yield short sequence reads that are then mapped on...