Metagenomic analysis of phosphorus removing sludge communities (2008)
Garcia Martin, Hector, Ivanova, Natalia, Kunin, Victor, Warnecke, Falk, Barry, Kerrie, McHardy, Alice C., ...
Enhanced Biological Phosphorus Removal (EBPR) is not well understood at the metabolic level despite being one of the best-studied microbially-mediated industrial processes due to its ecological and...
Report on BIOKDD04: Workshop on Data Mining in (2008)
Mohammed J. Zaki, Shinichi Morishita, Isidore Rigoutsos
are numerous sources of biological data that provides challenging opportunities for data mining. For example, the structural genomics initiative aims to catalog the structurefunction information for...
Ioannis Iliopoulos, Sophia Tsoka, Miguel A. Andrade, Anton J. Enright, Mark Carroll, Patrick Poullet, ...
BIOINFORMATICS Motivation: Genome-wide functional annotation either by manual or automatic means has raised considerable concerns regarding the accuracy of assignments and the reproducibility of...
BIOINFORMATICS ORIGINAL PAPER Sequence analysis (2008)
Kyle L. Jensen, Mark P. Styczynski, Isidore Rigoutsos, Gregory N. Stephanopoulos
A generic motif discovery algorithm for sequential data
Spring Semester 2003 10.555 Bioinformatics: Principles, Methods and Applications Instructors (2008)
Gregory Stephanopoulos, Isidore Rigoutsos
This course provides an introduction to Bioinformatics. We define this field as the principles and computational methods aiming at the upgrade of the information content of the large volume of...
Tsirigos, Aristotelis, Rigoutsos, Isidore
We identified the most frequent, variable-length DNA sequence motifs in the human and mouse genomes and sub-selected those with multiple recurrences in the intergenic and intronic regions and at...
The amphioxus genome illuminates vertebrate origins and cephalochordate biology (2008)
Holland, Linda Z., Albalat, Ricard, Azumi, Kaoru, Benito-Gutiérrez, Èlia, Blow, Matthew J., Bronner-Fraser, Marianne, ...
Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we...
Use of simulated data sets to evaluate the fidelity of Metagenomic processing methods (2006)
Mavromatis, Konstantinos, Ivanova, Natalia, Barry, Kerri, Shapiro, Harris, Goltsman, Eugene, McHardy, Alice C., ...
Accurate phylogenetic classification of DNA fragments based on sequence composition (2006)
McHardy, Alice C., Garcia Martin, Hector, Tsirigos, Aristotelis, Hugenholtz, Philip, Rigoutsos, Isidore
Metagenome studies have retrieved vast amounts of sequence out of a variety of environments, leading to novel discoveries and great insights into the uncultured microbial world. Except for very...
Pattern-based phylogenetic distance estimation and tree reconstruction (2006)
Höhl, Michael, Rigoutsos, Isidore, Ragan, Mark A.
We have developed an alignment-free method that calculates phylogenetic distances using a maximum likelihood approach for a model of sequence change on patterns that are discovered in unaligned...
Pattern-Based Phylogenetic Distance Estimation and Tree Reconstruction (2006)
Michael Höhl, Isidore Rigoutsos, Mark A. Ragan
We have developed an alignment-free method that calculates phylogenetic distances using a maximum-likelihood approach for a model of sequence change on patterns that are discovered in unaligned...
Kevin C. Mir, Tien Huynh, Yvonne Tay, Yen-sin Ang, Wai-leong Tam, Andrew M. Thomson, ...
These authors contributed equally to this work.
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities (2006)
Martín, Hector Garcia, Ivanova, Natalia, Kunin, Victor, Warnecke, Falk, Barry, Kerrie W., McHardy, Alice C., ...
Enhanced biological phosphorus removal (EBPR) is one of the best-studied microbially mediated industrial processes because of its ecological and economic relevance. Despite this, it is not well...
A generic motif discovery algorithm for sequential data (2006)
Jensen, Kyle L., Styczynski, Mark P., Rigoutsos, Isidore, Stephanopoulos, Gregory N.
Motivation: Motif discovery in sequential data is a problem of great interest and with many applications. However, previous methods have been unable to combine exhaustive search with complex motif...
Rigoutsos, Isidore, Brown, Christopher M.
Given an image that has been scaled both horizontally and vertically (possibly with different scale factors in the two directions), we determine the camera position and orientation, as well as the...
Evolution of distinct EGF domains with specific functions (2005)
Wouters, Merridee A., Rigoutsos, Isidore, Chu, Carmen K., Feng, Lina L., Sparrow, Duncan B., Dunwoodie, Sally L.
EGF domains are extracellular protein modules cross-linked by three intradomain disulfides. Past studies suggest the existence of two types of EGF domain with three-disulfides, human EGF-like (hEGF)...
A generic motif discovery algorithm for sequential data (2005)
Jensen, Kyle L., Styczynski, Mark P., Rigoutsos, Isidore, Stephanopoulos, Gregory N.
Motivation: Motif discovery in sequential data is a problem of great interest and with many applications. However, previous methods have been unable to combine exhaustive search with complex motif...
A new computational method for the detection of horizontal gene transfer events (2005)
Tsirigos, Aristotelis, Rigoutsos, Isidore
In recent years, the increase in the amounts of available genomic data has made it easier to appreciate the extent by which organisms increase their genetic diversity through horizontally transferred...
An Extension and Novel Solution to the (l,d)-Motif Challenge Problem (2004)
Mark P Styczynski, Kyle L Jensen, Isidore Rigoutsos, Gregory N Stephanopoulos
The (l,d )--motif challenge problem, as introduced by Pevzner and Sze [12], is a mathematical abstraction of the DNA functional site discovery task. Here we expand the (l,d )--motif problem to more...
In this paper, we present Chung-Kwei , a system for the analysis of electronic messages and the automatic identification of unsolicited email messages (=SPAM). The method uses pattern-discovery as...
The web server of IBM’s Bioinformatics and Pattern Discovery group: 2004 update (2004)
In this report, we provide an update on the services and content which are available on the web server of IBM’s Bioinformatics and Pattern Discovery group. The server, which is operational around...
The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update (2004)
Huynh, Tien, Rigoutsos, Isidore
In this report, we provide an update on the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server, which is operational around the...
Transcriptional organization of the Clostridium acetobutylicum genome (2004)
Paredes, Carlos J., Rigoutsos, Isidore, Papoutsakis, E. Terry
Prokaryotic genes are frequently organized in multicistronic operons (or transcriptional units, TUs), and usually the regulatory motifs for the whole TU are located upstream of the first TU gene....
The web server of IBM's Bioinformatics and Pattern Discovery group (2003)
Huynh, Tien, Rigoutsos, Isidore, Parida, Laxmi, Platt, Daniel, Shibuya, Tetsuo
We herein present and discuss the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server is operational around the clock and...
Rigoutsos, Isidore, Riek, Peter, Graham, Robert M., Novotny, Jiri
One of the promising methods of protein structure prediction involves the use of amino acid sequence‐derived patterns. Here we report on the creation of non‐degenerate motif descriptors...
Aloimonos,John Y., Rigoutsos,Isidore
A method is presented for the recovery of the 3D motion parameters of a rigidly moving textured surface. The novelty of the method is based on the following two facts: 1) no point-to-point...
Xiong Wang, Dennis Shasha, Bruce A. Shapiro, Isidore Rigoutsos, Kaizhong Zhang
This paper presents a method for finding patterns in three dimensional (3D) graphs. Each node in a graph is an undecomposable or atomic unit and has a label. Edges are links between the atomic units....
Cytomegalovirus Genome, Isidore Rigoutsos, Jiri Novotny, Tien Huynh, Laxmi Parida, ...
More than 200 open reading frames (ORFs) from the human cytomegalovirus genome have been reported as potentially coding for proteins. We have used two pattern-based in silico approaches to analyze...
Dictionary-driven prokaryotic gene finding (2002)
Shibuya, Tetsuo, Rigoutsos, Isidore
Gene identification, also known as gene finding or gene recognition, is among the important problems of molecular biology that have been receiving increasing attention with the advent of large scale...
Dictionary-driven protein annotation (2002)
Rigoutsos, Isidore, Huynh, Tien, Floratos, Aris, Parida, Laxmi, Platt, Daniel
Computational methods seeking to automatically determine the properties (functional, structural, physicochemical, etc.) of a protein directly from the sequence have long been the focus of numerous...
The emergence of pattern discovery techniques in computational biology (2000)
Isidore Rigoutsos, Aris Floratos, Laxmi Parida, Yuan Gao, Daniel Platt
In the past few years, pattern discovery has been emerging as a generic tool of choice for tackling problems from the computational biology domain. In this presentation, and after defining the...
The emergence of pattern discovery techniques in computational biology (2000)
Isidore Rigoutsos, Aris Floratos, Laxmi Parida, Yuan Gao, Daniel Platt
In the last few years, pattern discovery has been emerging as a generic tool of choice for tackling problems from the computational biology domain. In this presentation, and after defining the...
Aloimonos,John Y., Rigoutsos,Isidore
A method is presented for the recovery of the three dimensional motion parameters of a rigidly moving textured surface. The novelty of the method is based on the following two facts: no point to...
Homotopies: A Panacea or Just Another Method? (1998)
A general framework is presented for the solving of non-linear equations. Also, a discussion about its potential applications in the field of computer vision is made and illustrated by an example...
Musca: An algorithm for constrained alignment of multiple data sequences (1998)
Laxmi Parida, Aris Floratos, Isidore Rigoutsos
Given a set of N sequences, the Multiple Sequence Alignment problem is to align these N sequences, possibly with gaps, that brings out the best commonality of the N sequences. MUSCA 1 is a two-stage...
Musca: An algorithm for constrained alignment of multiple data sequences (1998)
Laxmi Parida, Aris Floratos, Isidore Rigoutsos
Given a set of N sequences, the Multiple Sequence Alignment problem is to align these N sequences, possibly with gaps, that brings out the best commonality of the N sequences. MUSCA 1 isatwo-stage...
Automated Discovery of Active Motifs in Three Dimensional Molecules (1997)
Xiong Wang, Dennis Shasha, Sitaram Dikshitulu, Isidore Rigoutsos, Kaizhong Zhang
In this paper we present a method for discovering approximately common motifs (also known as active motifs) in three dimensional (3D) molecules. Each node in a molecule is represented by a 3D point...
Isidore Rigoutsos, Haim Wolfson
In this paper we describe the Geometric Hashing paradigm for matching of a set of geometric features against a database of such feature sets. Specific examples are model based object recognition in...
Homotopies: A Panacea or Just Another Method? (1986)
A general framework is presented for the solving of non-linear equations. Also, a discussion about its potential applications in the field of computer vision is made and illustrated by an example...
Rigoutsos, Isidore, Brown, Christopher M.
Given an image that has been scaled both horizontally and vertically (possibly with different scale factors in the two directions), we determine the camera position and orientation, as well as the...
Aloimonos, John (Yiannis), Rigoutsos, Isidore
A method is presented for the recovery of the 3-D motion parameters of a rigidly moving textured surface. The novelty of the method is based on the following two facts: 1) no point-to-point...
Dictionary-driven prokaryotic gene finding
Shibuya, Tetsuo, Rigoutsos, Isidore
Gene identification, also known as gene finding or gene recognition, is among the important problems of molecular biology that have been receiving increasing attention with the advent of large scale...
Dictionary-driven protein annotation
Rigoutsos, Isidore, Huynh, Tien, Floratos, Aris, Parida, Laxmi, Platt, Daniel
Computational methods seeking to automatically determine the properties (functional, structural, physicochemical, etc.) of a protein directly from the sequence have long been the focus of numerous...
In Silico Pattern-Based Analysis of the Human Cytomegalovirus Genome
Rigoutsos, Isidore, Novotny, Jiri, Huynh, Tien, Chin-Bow, Stephen T., Parida, Laxmi, Platt, Daniel, ...
More than 200 open reading frames (ORFs) from the human cytomegalovirus genome have been reported as potentially coding for proteins. We have used two pattern-based in silico approaches to analyze...
The web server of IBM's Bioinformatics and Pattern Discovery group
Huynh, Tien, Rigoutsos, Isidore, Parida, Laxmi, Platt, Daniel, Shibuya, Tetsuo
We herein present and discuss the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server is operational around the clock and...
Rigoutsos, Isidore, Riek, Peter, Graham, Robert M., Novotny, Jiri
One of the promising methods of protein structure prediction involves the use of amino acid sequence-derived patterns. Here we report on the creation of non-degenerate motif descriptors derived...
Reevaluation of human cytomegalovirus coding potential
Murphy, Eain, Rigoutsos, Isidore, Shibuya, Tetsuo, Shenk, Thomas E.
The Bio-Dictionary-based Gene Finder was used to reassess the coding potential of the AD169 laboratory strain of human cytomegalovirus and sequences in the Toledo strain that are missing in the...
Transcriptional organization of the Clostridium acetobutylicum genome
Paredes, Carlos J., Rigoutsos, Isidore, Papoutsakis, E. Terry
Prokaryotic genes are frequently organized in multicistronic operons (or transcriptional units, TUs), and usually the regulatory motifs for the whole TU are located upstream of the first TU gene....
The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update
Huynh, Tien, Rigoutsos, Isidore
In this report, we provide an update on the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server, which is operational around the...
A new computational method for the detection of horizontal gene transfer events
Tsirigos, Aristotelis, Rigoutsos, Isidore
In recent years, the increase in the amounts of available genomic data has made it easier to appreciate the extent by which organisms increase their genetic diversity through horizontally transferred...
Tsirigos, Aristotelis, Rigoutsos, Isidore
In earlier work, we introduced and discussed a generalized computational framework for identifying horizontal transfers. This framework relied on a gene's nucleotide composition, obviated the need...
Rigoutsos, Isidore, Huynh, Tien, Miranda, Kevin, Tsirigos, Aristotelis, McHardy, Alice, Platt, Daniel
Using an unsupervised pattern-discovery method, we processed the human intergenic and intronic regions and catalogued all variable-length patterns with identically conserved copies and multiplicities...
Dictionary-driven prokaryotic gene finding
Shibuya, Tetsuo, Rigoutsos, Isidore
Gene identification, also known as gene finding or gene recognition, is among the important problems of molecular biology that have been receiving increasing attention with the advent of large scale...
Dictionary-driven protein annotation
Rigoutsos, Isidore, Huynh, Tien, Floratos, Aris, Parida, Laxmi, Platt, Daniel
Computational methods seeking to automatically determine the properties (functional, structural, physicochemical, etc.) of a protein directly from the sequence have long been the focus of numerous...
In Silico Pattern-Based Analysis of the Human Cytomegalovirus Genome
Rigoutsos, Isidore, Novotny, Jiri, Huynh, Tien, Chin-Bow, Stephen T., Parida, Laxmi, Platt, Daniel, ...
More than 200 open reading frames (ORFs) from the human cytomegalovirus genome have been reported as potentially coding for proteins. We have used two pattern-based in silico approaches to analyze...
The web server of IBM's Bioinformatics and Pattern Discovery group
Huynh, Tien, Rigoutsos, Isidore, Parida, Laxmi, Platt, Daniel, Shibuya, Tetsuo
We herein present and discuss the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server is operational around the clock and...
Rigoutsos, Isidore, Riek, Peter, Graham, Robert M., Novotny, Jiri
One of the promising methods of protein structure prediction involves the use of amino acid sequence-derived patterns. Here we report on the creation of non-degenerate motif descriptors derived...
Reevaluation of human cytomegalovirus coding potential
Murphy, Eain, Rigoutsos, Isidore, Shibuya, Tetsuo, Shenk, Thomas E.
The Bio-Dictionary-based Gene Finder was used to reassess the coding potential of the AD169 laboratory strain of human cytomegalovirus and sequences in the Toledo strain that are missing in the...
Transcriptional organization of the Clostridium acetobutylicum genome
Paredes, Carlos J., Rigoutsos, Isidore, Papoutsakis, E. Terry
Prokaryotic genes are frequently organized in multicistronic operons (or transcriptional units, TUs), and usually the regulatory motifs for the whole TU are located upstream of the first TU gene....
The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update
Huynh, Tien, Rigoutsos, Isidore
In this report, we provide an update on the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server, which is operational around the...
A new computational method for the detection of horizontal gene transfer events
Tsirigos, Aristotelis, Rigoutsos, Isidore
In recent years, the increase in the amounts of available genomic data has made it easier to appreciate the extent by which organisms increase their genetic diversity through horizontally transferred...
Tsirigos, Aristotelis, Rigoutsos, Isidore
In earlier work, we introduced and discussed a generalized computational framework for identifying horizontal transfers. This framework relied on a gene's nucleotide composition, obviated the need...
Rigoutsos, Isidore, Huynh, Tien, Miranda, Kevin, Tsirigos, Aristotelis, McHardy, Alice, Platt, Daniel
Using an unsupervised pattern-discovery method, we processed the human intergenic and intronic regions and catalogued all variable-length patterns with identically conserved copies and multiplicities...
Evolution of distinct EGF domains with specific functions
Wouters, Merridee A., Rigoutsos, Isidore, Chu, Carmen K., Feng, Lina L., Sparrow, Duncan B., Dunwoodie, Sally L.
EGF domains are extracellular protein modules cross-linked by three intradomain disulfides. Past studies suggest the existence of two types of EGF domain with three-disulfides, human EGF-like (hEGF)...
Tsirigos, Aristotelis, Rigoutsos, Isidore
We identified the most frequent, variable-length DNA sequence motifs in the human and mouse genomes and sub-selected those with multiple recurrences in the intergenic and intronic regions and at...
The amphioxus genome illuminates vertebrate origins and cephalochordate biology
Holland, Linda Z., Albalat, Ricard, Azumi, Kaoru, Benito-Gutiérrez, Èlia, Blow, Matthew J., Bronner-Fraser, Marianne, ...
Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we...
Pattern-Based Phylogenetic Distance Estimation and Tree Reconstruction
Höhl, Michael, Rigoutsos, Isidore, Ragan, Mark A.
We have developed an alignment-free method that calculates phylogenetic distances using a maximum-likelihood approach for a model of sequence change on patterns that are discovered in unaligned...