Dynamical systems analysis of stack filters (2009)
Nykter, Matti, Kesseli, Juha, Shmulevich, Ilya
We study classes of dynamical systems that can be obtained by constructing recursive networks with monotone Boolean functions. Stack filters in nonlinear signal processing are special cases of such...
Adaptable data management for systems biology investigations (2009)
Boyle, John, Rovira, Hector, Cavnor, Chris, Burdick, David, Killcoyne, Sarah, Shmulevich, Ilya
Abstract Background Within research each experiment is different, the focus changes and the data is generated from a continually evolving barrage of technologies. There is a continual introduction of...
Huang, Albert C, Hu, Limei, Kauffman, Stuart A, Zhang, Wei, Shmulevich, Ilya
Abstract Background The process of cellular differentiation is governed by complex dynamical biomolecular networks consisting of a multitude of genes and their products acting in concert to determine...
Fewer permutations, more accurate P-values (2009)
Knijnenburg, Theo A., Wessels, Lodewyk F. A., Reinders, Marcel J. T., Shmulevich, Ilya
Motivation: Permutation tests have become a standard tool to assess the statistical significance of an event under investigation. The statistical significance, as expressed in a P-value, is...
REDUCTION FACTORS IN FINITE AUTOMATA WITH APPLICATION TO NONLINEAR FILTERS (2008)
Antti Niemistö, Olli Yli-harja, Antti Valmari, Pertti Koivisto, Ilya Shmulevich
We examine the reduction factors achieved in finite automata describing several important classes of stack filters. It has been shown that finite automata and Markov Chain theory can be used to...
Systems biology driven software design for the research enterprise (2008)
Boyle, John, Cavnor, Christopher, Killcoyne, Sarah, Shmulevich, Ilya
Abstract Background In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to...
Running head: RHYTHM COMPLEXITY Mailing address of corresponding author: (2008)
Ilya Shmulevich, Dirk-jan Povel, Ilya Shmulevich
In this study, three measures of temporal pattern complexity were compared as regards their perceptual validity. The first measure, based on the work of Tanguiane (1993), uses the idea that a...
1. Representation and analysis of DNA sequences, (2008)
Edited Edward, R. Dougherty, Ilya Shmulevich, Jie Chen, Z. Jane Wang, Editorial Board, ...
c ○ 2005 Hindawi Publishing Corporation All rights reserved. No part of the material protected by this copyright notice may be reproduced or utilized in any form or by any means, electronic or...
COMPLEXITY MEASURES OF MUSICAL RHYTHMS 1 Complexity measures of musical (2008)
Ilya Shmulevich, Dirk-jan Povel
rhythms
1. Representation and analysis of DNA sequences, (2008)
Edited Edward, R. Dougherty, Ilya Shmulevich, Jie Chen, Z. Jane Wang, Editorial Board, ...
c ○ 2005 Hindawi Publishing Corporation All rights reserved. No part of the material protected by this copyright notice may be reproduced or utilized in any form or by any means, electronic or...
The Innate Immune Database (IIDB) (2008)
Korb, Martin, Rust, Alistair G, Thorsson, Vesteinn, Battail, Christophe, Li, Bin, Hwang, Daehee, ...
Abstract Background As part of a National Institute of Allergy and Infectious Diseases funded collaborative project, we have performed over 150 microarray experiments measuring the response of...
Quantification of in Vitro Cell Invasion through Image Analysis (2008)
Antti Niemistö, Limei Hu, Olli Yli-harja, Wei Zhang, Ilya Shmulevich
An image analysis method for quantification of in vitro cell invasion is presented. The method is designed for in vitro assays that are based on invasion of cells through a porous membrane. The...
Set-based complexity and biological information (2008)
Galas, David J., Nykter, Matti, Carter, Gregory W., Price, Nathan D., Shmulevich, Ilya
It is not obvious what fraction of all the potential information residing in the molecules and structures of living systems is significant or meaningful to the system. Sets of random sequences or...
Critical Networks Exhibit Maximal Information Diversity in Structure-Dynamics Relationships (2008)
Nykter, Matti, Price, Nathan D., Larjo, Antti, Aho, Tommi, Kauffman, Stuart A., Yli-Harja, Olli, ...
Network structure strongly constrains the range of dynamic behaviors available to a complex system. These system dynamics can be classified based on their response to perturbations over time into two...
Inference of Boolean Networks Using Sensitivity Regularization (2008)
Wenbin Liu, Harri Lähdesmäki, Edward R. Dougherty, Ilya Shmulevich
The inference of genetic regulatory networks from global measurements of gene expressions is an important problem in computational biology. Recent studies suggest that such dynamical molecular...
Inference of Boolean Networks Using Sensitivity Regularization (2008)
Wenbin Liu, Harri Lähdesmäki, Edward R. Dougherty, Ilya Shmulevich
The inference of genetic regulatory networks from global measurements of gene expressions is an important problem in computational biology. Recent studies suggest that such dynamical molecular...
Fast communication Breakdown probabilities of recursive stack "lters (2007)
Pertti Koivisto, Olli Yli-harja, Antti Niemistok, Ilya Shmulevich
A method for calculating breakdown probabilities of recursive stack "lters is presented. The method is based on Markov chain models and on an interpretation of a noisy signal as a binary...
Measures of Temporal Pattern Complexity (2007)
Dirk-Jan Povel, Ilya Shmulevich, Ilya Shmulevich
In this study, three measures of temporal pattern complexity were compared as regards their perceptual validity. The first measure, based on the work of Tanguiane (1993), uses the idea that a...
Asymptotic Analysis Of Expected Run-Lengths Of Recursive Median Filters (2007)
Olli Yli-harja, Ilya Shmulevich
In this paper we perform asymptotic analysis of run-length distributions of the Recursive Median (RM) filter, for which we rely on Finite State Machine (FSM) representation. We observe radical...
CLUSTERING GENES AND SAMPLES FROM GLIOMA MICROARRAY DATA (2007)
Ciprian Doru Giurcsneanu, Ioan Tsbus, Ilya Shmulevich, Wei Zhang
Abstract: In this paper we perform a twofold analysis of a microarray dataset containing gene expressions from patients with various types of glioma, with the goal of finding regular structures along...
Ilya Shmulevich, Harri Lähdesmäki F, Karen Egiazarian F
Abstract – Forcing functions represent an important class of Boolean functions that have been extensively studied in the analysis of the dynamics of random Boolean networks as models of genetic...
A Note on the Pitch Contour Similarity Index (2007)
incorporates relations between adjacent as well as non-adjacent notes. Having a formal mathematical representation of contour structure, this model allows for quantification of similarity between...
Chapter 11 INFERENCE OF GENETIC REGULATORY NETWORKS VIA BEST-FIT EXTENSIONS (2007)
Ilya Shmulevich, Antti Saarinen, Jaakko Astola
One of the most important breakthroughs in recent years in molecular biology is microarray technology, which allows monitoring of gene expression at the transcript level for thousands of genes in...
normalization of gene expression data (2007)
Motivation: Most approaches to gene expression analysis use real-valued expression data, produced by highthroughput screening technologies, such as microarrays. Often, some measure of similarity must...
Output Distributions of Stack Filters Based on Mirrored Threshold Decomposition (2007)
Ilya Shmulevich, José Luis Paredes, Gonzalo R. Arce
Abstract—The output distribution formula for stack filters based on mirrored threshold decomposition is derived. This formula allows one to compute the cumulative distribution function of the...
ADAPTIVE VARYING WINDOW SIZE SELECTION BASED ON INTERSECTION OF CONFIDENCE INTERVALS RULE (2007)
Vladimir Katkovnik, Karen Egiazarian, Ilya Shmulevich
We propose an approach to resolve the problem of varying window size selection for a wide class of linear and nonlinear lters. A window size of a ¡ lter is considered as a parameter of estimation...
Fast communication Breakdown probabilities of recursive stack "lters (2007)
Pertti Koivisto, Olli Yli-harja, Antti Niemistok, Ilya Shmulevich
A method for calculating breakdown probabilities of recursive stack "lters is presented. The method is based on Markov chain models and on an interpretation of a noisy signal as a binary...
GENERALIZED MALLOWS ’ OPTIMIZATION FOR WEIGHTED MEDIAN FILTERS ADMITTING NEGATIVE WEIGHTS (2007)
A closed-form spectral optimization method for the design of weighted median ¡ lters admitting negative weights is presented. The algorithm is a generalization of Mallows ’ theory for nonlinear...
Antti Niemistö, Ilya Shmulevich, Vladimir V. Lukin, Alexander N. Dolia, Olli Yli-harja
An estimation method for correcting misclassifications in signal and image processing is presented. The method is based on the use of context-based (temporal or spatial) information in a...
Edward R. Dougherty, Ilya Shmulevich, Michael L. Bittner
This paper considers key issues in the emerging field of genomic signal processing and its relationship to functional genomics. It focuses on some of the biological mechanisms driving the development...
Tohru Kobayashi, Motoko Yamaguchi, Seungchan Kim, Jun Morikawa, Shoko Ogawa, Satoshi Ueno, ...
Malignant lymphoma is a heterogeneous disease with different clinical features. Among diffuse large B-cell lymphomas (DLBCLs), a unique subtype has been identified recently based on cell surface...
Ilya Shmulevich, Edward R. Dougherty, Seungchan Kim, Wei Zhang
Motivation: Our goal is to construct a model for genetic regulatory networks such that the model class: (i) incorporates rule-based dependencies between genes; (ii) allows the systematic study of...
Ilya Shmulevich, Ilya Gluhovsky, Ronaldo F. Hashimoto, Edward R. Dougherty, Wei Zhang, Ilya Shmulevich Cancer
Steady-state analysis of genetic regulatory networks modelled by probabilistic Boolean networks
ProbCD: enrichment analysis accounting for categorization uncertainty (2007)
Vêncio, Ricardo ZN, Shmulevich, Ilya
Abstract Background As in many other areas of science, systems biology makes extensive use of statistical association and significance estimates in contingency tables, a type of categorical data...
Simcluster: clustering enumeration gene expression data on the simplex space (2007)
Vêncio, Ricardo ZN, Varuzza, Leonardo, De B Pereira, Carlos A, Brentani, Helena, Shmulevich, Ilya
Abstract Background Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST "digital northern", are important high-throughput techniques for digital gene expression...
ProbCD: enrichment analysis accounting for categorization uncertainty (2007)
Vêncio, Ricardo, Shmulevich, Ilya
As in many other areas of science, systems biology makes extensive use of statistical association and significance estimates in contingency tables, a type of categorical data analysis known in this...
ProbCD: enrichment analysis accounting for categorization uncertainty (2007)
Ricardo Vêncio, Ilya Shmulevich
As in many other areas of science, systems biology makes extensive use of statistical association and significance estimates in contingency tables, a type of categorical data analysis known in this...
Simcluster: clustering enumeration gene expression data on the simplex space (2007)
Carlos Pereira, Helena Brentani, Ilya Shmulevich
Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST "digital northern", are important high-throughput techniques for digital gene expression measurement. As...
Simcluster: clustering enumeration gene expression data on the simplex space (2007)
Vêncio, Ricardo ZN, Varuzza, Leonardo, Pereira, Carlos AB, Brentani, Helena, Shmulevich, Ilya
Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST ``digital northern'', are important high-throughput techniques for digital gene expression measurement. As other...
Basin Entropy in Boolean Network Ensembles (2007)
Krawitz, Peter, Shmulevich, Ilya
The information processing capacity of a complex dynamical system is reflected in the partitioning of its state space into disjoint basins of attraction, with state trajectories in each basin flowing...
Simcluster: clustering enumeration gene expression data on the simplex space (2007)
Leonardo Varuzza, Helena Brentani, Ilya Shmulevich
Transcript enumeration methods such as SAGE, MPSS, and sequencingby-synthesis EST “digital northern”, are important high-throughput techniques for digital gene expression measurement. As other...
Bmc Bioinformatics, Ricardo Zn Vêncio, Ilya Shmulevich
Software ProbCD: enrichment analysis accounting for categorization uncertainty
Ilya Shmulevich, Ilya Gluhovsky, Ronaldo F. Hashimoto, Edward R. Dougherty, Wei Zhang
Probabilistic Boolean networks (PBNs) have recently been introduced as a promising class of models of genetic regulatory networks. The dynamic behaviour of PBNs can be analysed in the context of...
The Role of Redundancy in the Robustness of Random Boolean Networks (2005)
Gershenson, Carlos, Kauffman, Stuart A., Shmulevich, Ilya
Evolution depends on the possibility of successfully exploring fitness landscapes via mutation and recombination. With these search procedures, exploration is difficult in "rugged" fitness...
Average Sensitivity of Typical Monotone Boolean Functions (2005)
We derive asymptotic formulas for the expected average sensitivity of a typical monotone Boolean function. The formulas, given in Theorems 4 and 5, are different depending on whether n, the number of...
Insulin-like growth factor binding protein 2 promotes ovarian cancer cell invasion (2005)
Lee, Eun-Ju, Mircean, Cristian, Shmulevich, Ilya, Wang, Huamin, Liu, Jinsong, Niemistö, Antti, ...
Abstract Background Insulin-like growth factor binding protein 2 (IGFBP2) is overexpressed in ovarian malignant tissues and in the serum and cystic fluid of ovarian cancer patients, suggesting an...
I.: Normalized compression distance for gene expression analysis (2005)
Matti Nykter, Olli Yli-harja, Ilya Shmulevich
Abstract — In this paper we show that the normalized compression distance can be applied to gene expression data analysis. Typically, microarray-based classification involves using a feature subset...
Robust estimation of protein expression ratios with lysate microarray technology (2005)
Mircean, Cristian, Shmulevich, Ilya, Cogdell, David, Choi, Woonyoung, Jia, Yu, Tabus, Ioan, ...
Motivation: The protein lysate microarray is a developing proteomic technology for measuring protein expression levels in a large number of biological samples simultaneously. A challenge for accurate...
Robust estimation of protein expression ratios with lysate microarray technology (2005)
Mircean, Cristian, Shmulevich, Ilya, Cogdell, David, Choi, Woonyoung, Jia, Yu, Tabus, Ioan, ...
Motivation: The protein lysate microarray is a developing proteomic technology for simultaneously measuring protein expression levels in a large number of biological samples. A challenge for accurate...
Correction of Misclassifications Using a Proximity-Based Estimation Method (2004)
Antti Niemistö, Ilya Shmulevich, Vladimir V. Lukin, Alexander N. Dolia, Olli Yli-Harja
An estimation method for correcting misclassifications in signal and image processing is presented. The method is based on the use of context-based (temporal or spatial) information in a...
Genomic Signal Processing: The Salient Issues (2004)
Edward R. Dougherty, Ilya Shmulevich, Michael L. Bittner
This paper considers key issues in the emerging field of genomic signal processing and its relationship to functional genomics. It focuses on some of the biological mechanisms driving the development...
Correction of Misclassifications Using a Proximity-Based Estimation Method (2004)
Olli Yli-Harja, Alexander N. Dolia, Vladimir V. Lukin, Ilya Shmulevich, Antti Niemistö
An estimation method for correcting misclassifications in signal and image processing is presented. The method is based on the use of context-based (temporal or spatial) information in a...
Genomic Signal Processing: The Salient Issues (2004)
Michael L. Bittner, Ilya Shmulevich, Edward R. Dougherty
This paper considers key issues in the emerging field of genomic signal processing and its relationship to functional genomics. It focuses on some of the biological mechanisms driving the development...
Genomic Signal Processing: The Salient Issues (2004)
Edward R. Dougherty, Ilya Shmulevich, Michael L. Bittner
This paper considers key issues in the emerging field of genomic signal processing and its relationship to functional genomics. It focuses on some of the biological mechanisms driving the development...
Correction of Misclassifications Using a Proximity-Based Estimation Method (2004)
Antti Niemistö, Ilya Shmulevich, Vladimir V. Lukin, Alexander N. Dolia, Olli Yli-Harja
An estimation method for correcting misclassifications in signal and image processing is presented. The method is based on the use of context-based (temporal or spatial) information in a...
Growing genetic regulatory networks from seed genes (2004)
Hashimoto, Ronaldo F., Kim, Seungchan, Shmulevich, Ilya, Zhang, Wei, Bittner, Michael L., Dougherty, Edward R.
Motivation: A number of models have been proposed for genetic regulatory networks. In principle, a network may contain any number of genes, so long as data are available to make inferences about...
The number and probability of canalizing functions (2003)
Just, Winfried, Shmulevich, Ilya, Konvalina, John
Canalizing functions have important applications in physics and biology. For example, they represent a mechanism capable of stabilizing chaotic behavior in Boolean network models of discrete...
On learning gene regulatory networks under the Boolean network model (2003)
Harri Lähdesmäki, Ilya Shmulevich, Olli Yli-Harja
Boolean networks are a popular model class for capturing the interactions of genes and global dynamical behavior of genetic regulatory networks. Recently, a significant amount of attention has been...
Ilya Shmulevich, Ilya Gluhovsky, Ronaldo F. Hashimoto, Edward R. Dougherty, Wei Zhang
Probabilistic Boolean networks (PBNs) have recently been introduced as a promising class of models of genetic regulatory networks. The dynamic behaviour of PBNs can be analysed in the context of...
Data extraction from composite oligonucleotide microarrays (2003)
Shmulevich, Ilya, Astola, Jaakko, Cogdell, David, Hamilton, Stanley R., Zhang, Wei
Microarray or DNA chip technology is revolutionizing biology by empowering researchers in the collection of broad‐scope gene information. It is well known that microarray‐based measurements...
Gene perturbation and intervention in probabilistic Boolean networks (2002)
Ilya Shmulevich, Edward R. Dougherty
Motivation: A major objective of gene regulatory network modeling, in addition to gaining a deeper understanding of genetic regulation and control, is the development of computational tools for the...
Nonparametric Density Estimation with Adaptive Varying Window Size (2002)
Vladimir Katkovnik, Ilya Shmulevich
We propose a new method of kernel density estimation with a varying adaptive window width. This method is different from traditional ones in two aspects. First, we use symmetric as well as...
Ilya Shmulevich, Edward R. Dougherty
Probabilistic Boolean Networks (PBNs) were recently introduced as models of gene regulatory networks. The dynamical behavior of PBNs, which are probabilistic generalizations of Boolean networks, can...
From Boolean to probabilistic Boolean networks as models of genetic regulatory networks (2002)
Ilya Shmulevich, Edward R. Dougherty
Mathematical and computational modeling of genetic regulatory networks promises to uncover the fundamental principles governing biological systems in an integrative and holistic manner. It also paves...
From Boolean to probabilistic Boolean networks as models of genetic regulatory networks (2002)
Ilya Shmulevich, Edward R. Dougherty, Wei Zhang
Mathematical and computational modeling of genetic regulatory networks promises to uncover the fundamental principles governing biological systems in an integrative and holistic manner. It also paves...
Identification of combination gene sets for glioma classification (2002)
Seungchan Kim, Edward R. Dougherty, Ilya Shmulevich, Kenneth R. Hess, Stanley R. Hamilton, Jeffrey M. Trent, ...
One goal for the gene expression profiling of cancer tissues is to identify signature genes that robustly distinguish different types or grades of tumors. Such signature genes would ideally provide a...
Gene perturbation and intervention in probabilistic Boolean networks (2002)
Shmulevich, Ilya, Dougherty, Edward R., Zhang, Wei
Motivation: A major objective of gene regulatory network modeling, in addition to gaining a deeper understanding of genetic regulation and control, is the development of computational tools for the...
Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks (2002)
Shmulevich, Ilya, Dougherty, Edward R., Kim, Seungchan, Zhang, Wei
Motivation: Our goal is to construct a model for genetic regulatory networks such that the model class: (i) incorporates rule-based dependencies between genes; (ii) allows the systematic study of...
Binary analysis and optimization-based normalization of gene expression data (2002)
Motivation: Most approaches to gene expression analysis use real-valued expression data, produced by high-throughput screening technologies, such as microarrays. Often, some measure of similarity...
Inference of genetic regulatory networks under the best-fit extension paradigm (2001)
Ilya Shmulevich, Cancer Genomics Core
We address the problem of inferring the structure of genetic regulatory networks using the Boolean network model system. In realistic situations, gene expression measurements are noisy and lead to...
Block-median pyramidal transform: Analysis and denoising applications (2001)
Vladimir P. Melnik, Ilya Shmulevich, Karen Egiazarian, Senior Member, Jaakko Astola
Abstract—A nonlinear multiscale pyramidal transform based on nonoverlapping block decompositions using the median operation and a polynomial approximation is considered. It is shown that this...
Complexity of the consistency problem for certain post classes (2001)
Ilya Shmulevich, Moncef Gabbouj, Jaakko Astola
Abstract—The complexity of the consistency problem for several important classes of Boolean functions is analyzed. The classes of functions under investigation are those which are closed under...
Reduction Factors In Finite Automata With Application To Nonlinear Filters (2000)
Antti Niemistö, Olli Yli-harja, Antti Valmari, Pertti Koivisto, Ilya Shmulevich
We examine the reduction factors achieved in finite automata describing several important classes of stack filters. It has been shown that finite automata and Markov Chain theory can be used to...
Vladimir V. Lukin, Ilya Shmulevich, Alexander N. Dolia
A description of an approach to primary local image recognition is given. The motivation for its application and its characteristics are discussed. Then a method for correction of misclassifications...
The Use of Sample Selection Probabilities for Stack Filter Design (2000)
Ilya Shmulevich, Vladimir Melnik, Karen Egiazarian, Senior Member
We propose a procedure for stack filter design that takes into consideration the filter's sample selection probabilitites. A statistical optimization of stack filters can result in a class of...
Pertti Koivisto, Olli Yli-harja, Antti Niemistö, Ilya Shmulevich
Abstract — A novel method for calculating breakdown probabilities of recursive stack filters is presented. The method is based on Markov chain models and on an interpretation of a noisy signal as a...
Perceptual issues in music pattern recognition - complexity of rhythm and key finding (1999)
Ilya Shmulevich, Olli Yli-harja, Edward Coyle
Abstract. We consider several perceptual issues in the context of machine recognition of music patterns. It is argued that a successful implementation of a music recognition system must incorporate...
Output Distributions of Recursive Stack Filters (1999)
Ilya Shmulevich, Olli Yli-harja, Karen Egiazarian, Jaakko Astola, Senior Member, Senior Member
In this letter, we provide a method for deriving the output distribution function of any recursive stack filter. In particular, we give the output distribution of the recursive median filter. The...
Olli Yli-harja, Ilya Shmulevich
The simplified implementation of Recursive Median (RM) filters is discussed. It is shown that every RM filter has an alternative implementation that implies a fast algorithm, (O(1) per pixel on...
Properties and applications of monotone Boolean functions and stack filters (1997)
We examine various structural properties of idempotent monotone Boolean functions. The free distributive lattice (FDL) provides a useful framework for studying this class of functions. Algorithms for...
The Use Of Recursive Median Filters For Establishing The Tonal Context In Music (1997)
Ilya Shmulevich, Edward J. Coyle
The recursive median filter is used to improve the structure of the output of the key finding algorithm for establishing tonal contexts of musical patterns in a musical composition. This is...
Data extraction from composite oligonucleotide microarrays
Shmulevich, Ilya, Astola, Jaakko, Cogdell, David, Hamilton, Stanley R., Zhang, Wei
Microarray or DNA chip technology is revolutionizing biology by empowering researchers in the collection of broad-scope gene information. It is well known that microarray-based measurements exhibit a...
The role of certain Post classes in Boolean network models of genetic networks
Shmulevich, Ilya, Lähdesmäki, Harri, Dougherty, Edward R., Astola, Jaakko, Zhang, Wei
A topic of great interest and debate concerns the source of order and remarkable robustness observed in genetic regulatory networks. The study of the generic properties of Boolean networks has proven...
Insulin-like growth factor binding protein 2 promotes ovarian cancer cell invasion
Lee, Eun-Ju, Mircean, Cristian, Shmulevich, Ilya, Wang, Huamin, Liu, Jinsong, Niemistö, Antti, ...
Eukaryotic cells are dynamically ordered or critical but not chaotic
Shmulevich, Ilya, Kauffman, Stuart A., Aldana, Maximino
Two important theoretical approaches have been developed to generically characterize the relationship between the structure and function of large genetic networks: The continuous approach, based on...
Activities and Sensitivities in Boolean Network Models
Shmulevich, Ilya, Kauffman, Stuart A.
We study how the notions of importance of variables in Boolean functions as well as the sensitivities of the functions to changes in these variables impact the dynamical behavior of Boolean networks....
Noise in a Small Genetic Circuit that Undergoes Bifurcation
TOULOUSE, TRENT, AO, PING, SHMULEVICH, ILYA, KAUFFMAN, STUART
Based on the consideration of Boolean dynamics, it has been hypothesized that cell types may correspond to alternative attractors of a gene regulatory network. Recent stochastic Boolean network...
Data extraction from composite oligonucleotide microarrays
Shmulevich, Ilya, Astola, Jaakko, Cogdell, David, Hamilton, Stanley R., Zhang, Wei
Microarray or DNA chip technology is revolutionizing biology by empowering researchers in the collection of broad-scope gene information. It is well known that microarray-based measurements exhibit a...
The role of certain Post classes in Boolean network models of genetic networks
Shmulevich, Ilya, Lähdesmäki, Harri, Dougherty, Edward R., Astola, Jaakko, Zhang, Wei
A topic of great interest and debate concerns the source of order and remarkable robustness observed in genetic regulatory networks. The study of the generic properties of Boolean networks has proven...
Insulin-like growth factor binding protein 2 promotes ovarian cancer cell invasion
Lee, Eun-Ju, Mircean, Cristian, Shmulevich, Ilya, Wang, Huamin, Liu, Jinsong, Niemistö, Antti, ...
Eukaryotic cells are dynamically ordered or critical but not chaotic
Shmulevich, Ilya, Kauffman, Stuart A., Aldana, Maximino
Two important theoretical approaches have been developed to generically characterize the relationship between the structure and function of large genetic networks: The continuous approach, based on...
Price, Nathan D., Trent, Jonathan, El-Naggar, Adel K., Cogdell, David, Taylor, Ellen, Hunt, Kelly K., ...
Gastrointestinal stromal tumor (GIST) has emerged as a clinically distinct type of sarcoma with frequent overexpression and mutation of the c-Kit oncogene and a favorable response to imatinib...
Simcluster: clustering enumeration gene expression data on the simplex space
Vêncio, Ricardo ZN, Varuzza, Leonardo, De B Pereira, Carlos A, Brentani, Helena, Shmulevich, Ilya
Ramsey, Stephen A., Klemm, Sandy L., Zak, Daniel E., Kennedy, Kathleen A., Thorsson, Vesteinn, Li, Bin, ...
Macrophages are versatile immune cells that can detect a variety of pathogen-associated molecular patterns through their Toll-like receptors (TLRs). In response to microbial challenge, the...
The Innate Immune Database (IIDB)
Korb, Martin, Rust, Aistair G, Thorsson, Vesteinn, Battail, Christophe, Li, Bin, Hwang, Daehee, ...
Probabilistic Inference of Transcription Factor Binding from Multiple Data Sources
Lähdesmäki, Harri, Rust, Alistair G., Shmulevich, Ilya
An important problem in molecular biology is to build a complete understanding of transcriptional regulatory processes in the cell. We have developed a flexible, probabilistic framework to predict TF...
Critical Dynamics in Genetic Regulatory Networks: Examples from Four Kingdoms
Balleza, Enrique, Alvarez-Buylla, Elena R., Chaos, Alvaro, Kauffman, Stuart, Shmulevich, Ilya, Aldana, Maximino
The coordinated expression of the different genes in an organism is essential to sustain functionality under the random external perturbations to which the organism might be subjected. To cope with...
Inference of Boolean Networks Using Sensitivity Regularization
Liu, Wenbin, Lähdesmäki, Harri, Dougherty, Edward R., Shmulevich, Ilya
The inference of genetic regulatory networks from global measurements of gene expressions is an important problem in computational biology. Recent studies suggest that such dynamical molecular...
Steady-State Analysis of Genetic Regulatory Networks Modelled by Probabilistic Boolean Networks
Shmulevich, Ilya, Gluhovsky, Ilya, Hashimoto, Ronaldo F., Dougherty, Edward R., Zhang, Wei
Probabilistic Boolean networks (PBNs) have recently been introduced as a promising class of models of genetic regulatory networks. The dynamic behaviour of PBNs can be analysed in the context of...
Systems biology driven software design for the research enterprise
Boyle, John, Cavnor, Christopher, Killcoyne, Sarah, Shmulevich, Ilya
Gene expression dynamics in the macrophage exhibit criticality
Nykter, Matti, Price, Nathan D., Aldana, Maximino, Ramsey, Stephen A., Kauffman, Stuart A., Hood, Leroy E., ...
Cells are dynamical systems of biomolecular interactions that process information from their environment to mount diverse yet specific responses. A key property of many self-organized systems is that...
Ramsey, Stephen A., Klemm, Sandy L., Zak, Daniel E., Kennedy, Kathleen A., Thorsson, Vesteinn, Li, Bin, ...
Ramsey, Stephen A., Klemm, Sandy L., Zak, Daniel E., Kennedy, Kathleen A., Thorsson, Vesteinn, Li, Bin, ...
Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation
Huang, Albert C, Hu, Limei, Kauffman, Stuart A, Zhang, Wei, Shmulevich, Ilya
Cristian Mircean, Ioan Tabus, Jaakko Astola, Tohru Kobayashi, Hiroshi Shiku, Motoko Yamaguchi, ...
Molecular classification of tumors holds great potential for cancer research, diagnosis, and treatment. In this study, we apply a novel classification technique to cDNA microarray data for...
Adaptable data management for systems biology investigations
Boyle, John, Rovira, Hector, Cavnor, Chris, Burdick, David, Killcoyne, Sarah, Shmulevich, Ilya
Fewer permutations, more accurate P-values
Knijnenburg, Theo A., Wessels, Lodewyk F. A., Reinders, Marcel J. T., Shmulevich, Ilya
Motivation: Permutation tests have become a standard tool to assess the statistical significance of an event under investigation. The statistical significance, as expressed in a P-value, is...